@article{van_dung_large-scale_2016,
	title = {Large-scale screening and characterization of enteroviruses and kobuviruses infecting pigs in {Vietnam}.},
	volume = {97},
	issn = {1465-2099 0022-1317},
	doi = {10.1099/jgv.0.000366},
	abstract = {A recent survey of pigs in Dong Thap province, Vietnam identified a high frequency of enterovirus species G (EV-G) infection (144/198; 72.7\%). Amongst these was a plethora of EV-G types (EV-G1, EV-G6 and four new types},
	language = {eng},
	number = {2},
	journal = {The Journal of general virology},
	author = {Van Dung, Nguyen and Anh, Pham Hong and Van Cuong, Nguyen and Hoa, Ngo Thi and Carrique-Mas, Juan and Hien, Vo Be and Sharp, C. and Rabaa, M. and Berto, A. and Campbell, James and Baker, Stephen and Farrar, Jeremy and Woolhouse, Mark E. and Bryant, Juliet E. and Simmonds, Peter},
	month = feb,
	year = {2016},
	pmid = {26653281},
	pmcid = {PMC5115164},
	keywords = {Animals, Diarrhea/epidemiology/veterinary/virology, Enterovirus Infections/epidemiology/*veterinary/virology, Enterovirus/classification/genetics/*isolation \& purification, Feces/*virology, Genetic Variation, Kobuvirus/classification/genetics/*isolation \& purification, Mass Screening, Picornaviridae Infections/epidemiology/*veterinary/virology, Prevalence, Sus scrofa, Swine, Swine Diseases/*epidemiology/*virology, Vietnam/epidemiology, Viral Load},
	pages = {378--388},
}

@article{li_comparison_2016,
	title = {Comparison of liver {microRNA} transcriptomes of {Tibetan} and {Yorkshire} pigs by deep sequencing},
	volume = {577},
	issn = {1879-0038},
	doi = {10.1016/j.gene.2015.12.003},
	abstract = {MicroRNAs (miRNAs) play an important role in the modulation of various metabolic processes in the liver, yet little is known about the liver microRNAome (miRNAome) of the Tibetan pig. Here we used the Yorkshire pig as a control to analyze the Tibetan pig-specific liver miRNAome, and for preliminary investigation of differentially expressed miRNAs participating in metabolism. A comprehensive analysis of Tibetan and Yorkshire pig liver miRNAomes by small RNA sequencing identified 362 unique miRNAs. Among these, 304 were co-expressed in both libraries, and 10 and 48 miRNAs were specifically expressed. Differential expression analysis of miRNAs, miRNA target prediction and KEGG analysis revealed that differentially expressed miRNAs were associated mainly with the metabolism of glucose, lipid and protein. Six differentially expressed miRNAs (miR-34a, miR-326, miR-1, miR-335, miR-185 and miR-378) participating in the metabolism of glucose and lipid were identified. Additionally, qPCR results revealed that a lower expression of miR-34a in Tibetan pig liver may promote gluconeogenesis by increasing the expression of Sirtuin type 1 (Sirt1); a lower expression of miR-1 in Tibetan pig liver may promote the synthesis and accumulation of lipid by increasing the expression of Liver X receptor α (LXRα); and a lower expression of miR-185 in Tibetan pig liver may promote the uptake of cholesterol from blood and secretion of bile by increasing the expression of the scavenger receptor class B type I (SR-BI). Our results provide new information and understanding of porcine miRNA profiles, which may help explain the regulatory mechanisms of miRNAs in the metabolic functions of Tibetan pig liver, and provide new biomarkers to assist in the development of Tibetan pig breeding characteristics.},
	language = {eng},
	number = {2},
	journal = {Gene},
	author = {Li, Yanyue and Li, Xiaocheng and Sun, Wen-Kui and Cheng, Chi and Chen, Yi-Hui and Zeng, Kai and Chen, Xiaohui and Gu, Yiren and Gao, Rong and Liu, Rui and Lv, Xuebin},
	month = feb,
	year = {2016},
	pmid = {26656174},
	keywords = {Animals, Base Sequence, Liver, MiRNAome, MiRNAs, MicroRNAs, Molecular Sequence Data, Sequence Alignment, Sus scrofa, Tibetan pig, Transcriptome, Yorkshire pig},
	pages = {244--250},
}

@article{brandl_planmine--mineable_2016,
	title = {{PlanMine}--a mineable resource of planarian biology and biodiversity},
	volume = {44},
	issn = {1362-4962},
	doi = {10.1093/nar/gkv1148},
	abstract = {Planarian flatworms are in the midst of a renaissance as a model system for regeneration and stem cells. Besides two well-studied model species, hundreds of species exist worldwide that present a fascinating diversity of regenerative abilities, tissue turnover rates, reproductive strategies and other life history traits. PlanMine (http://planmine.mpi-cbg.de/) aims to accomplish two primary missions: First, to provide an easily accessible platform for sharing, comparing and value-added mining of planarian sequence data. Second, to catalyze the comparative analysis of the phenotypic diversity amongst planarian species. Currently, PlanMine houses transcriptomes independently assembled by our lab and community contributors. Detailed assembly/annotation statistics, a custom-developed BLAST viewer and easy export options enable comparisons at the contig and assembly level. Consistent annotation of all transcriptomes by an automated pipeline, the integration of published gene expression information and inter-relational query tools provide opportunities for mining planarian gene sequences and functions. For inter-species comparisons, we include transcriptomes of, so far, six planarian species, along with images, expert-curated information on their biology and pre-calculated cross-species sequence homologies. PlanMine is based on the popular InterMine system in order to make the rich biology of planarians accessible to the general life sciences research community.},
	language = {eng},
	number = {D1},
	journal = {Nucleic Acids Research},
	author = {Brandl, Holger and Moon, HongKee and Vila-Farré, Miquel and Liu, Shang-Yun and Henry, Ian and Rink, Jochen C.},
	month = jan,
	year = {2016},
	pmid = {26578570},
	pmcid = {PMC4702831},
	keywords = {Animals, Data Mining, Databases, Genetic, Gene Expression Profiling, Genes, Helminth, Phenotype, Planarians, Sequence Analysis},
	pages = {D764--773}
}

Paper  doi  abstract   bibtex   

@article{devaux_proteomic_2016,
	title = {Proteomic {Analysis} of the {Spatio}-temporal {Based} {Molecular} {Kinetics} of {Acute} {Spinal} {Cord} {Injury} {Identifies} a {Time}- and {Segment}-specific {Window} for {Effective} {Tissue} {Repair}},
	volume = {15},
	issn = {1535-9484 (Electronic) 1535-9476 (Linking)},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/27250205},
	doi = {10.1074/mcp.M115.057794},
	abstract = {Spinal cord injury (SCI) represents a major debilitating health issue with a direct socioeconomic burden on the public and private sectors worldwide. Although several studies have been conducted to identify the molecular progression of injury sequel due from the lesion site, still the exact underlying mechanisms and pathways of injury development have not been fully elucidated. In this work, based on OMICs, 3D matrix-assisted laser desorption ionization (MALDI) imaging, cytokines arrays, confocal imaging we established for the first time that molecular and cellular processes occurring after SCI are altered between the lesion proximity, i.e. rostral and caudal segments nearby the lesion (R1-C1) whereas segments distant from R1-C1, i.e. R2-C2 and R3-C3 levels coexpressed factors implicated in neurogenesis. Delay in T regulators recruitment between R1 and C1 favor discrepancies between the two segments. This is also reinforced by presence of neurites outgrowth inhibitors in C1, absent in R1. Moreover, the presence of immunoglobulins (IgGs) in neurons at the lesion site at 3 days, validated by mass spectrometry, may present additional factor that contributes to limited regeneration. Treatment in vivo with anti-CD20 one hour after SCI did not improve locomotor function and decrease IgG expression. These results open the door of a novel view of the SCI treatment by considering the C1 as the therapeutic target.},
	number = {8},
	journal = {Mol Cell Proteomics},
	author = {Devaux, S. and Cizkova, D. and Quanico, J. and Franck, J. and Nataf, S. and Pays, L. and Hauberg-Lotte, L. and Maass, P. and Kobarg, J. H. and Kobeissy, F. and Meriaux, C. and Wisztorski, M. and Slovinska, L. and Blasko, J. and Cigankova, V. and Fournier, I. and Salzet, M.},
	year = {2016},
	keywords = {Animal, Animals, Biomarkers/*metabolism, Cytokines/*metabolism, Disease Models, Humans, Mass, Matrix-Assisted Laser Desorption-Ionization/methods, Protein Array Analysis, Protein Interaction Maps, Proteomics/*methods, Rats, Spectrometry, Spinal Cord Injuries/*metabolism, Time Factors},
	pages = {2641--70},
}

@article{motenko_mousemine:_2015,
	title = {{MouseMine}: a new data warehouse for {MGI}},
	volume = {26},
	issn = {1432-1777},
	shorttitle = {{MouseMine}},
	doi = {10.1007/s00335-015-9573-z},
	abstract = {MouseMine (www.mousemine.org) is a new data warehouse for accessing mouse data from Mouse Genome Informatics (MGI). Based on the InterMine software framework, MouseMine supports powerful query, reporting, and analysis capabilities, the ability to save and combine results from different queries, easy integration into larger workflows, and a comprehensive Web Services layer. Through MouseMine, users can access a significant portion of MGI data in new and useful ways. Importantly, MouseMine is also a member of a growing community of online data resources based on InterMine, including those established by other model organism databases. Adopting common interfaces and collaborating on data representation standards are critical to fostering cross-species data analysis. This paper presents a general introduction to MouseMine, presents examples of its use, and discusses the potential for further integration into the MGI interface.},
	language = {eng},
	number = {7-8},
	journal = {Mammalian Genome: Official Journal of the International Mammalian Genome Society},
	author = {Motenko, H. and Neuhauser, S. B. and O'Keefe, M. and Richardson, J. E.},
	month = aug,
	year = {2015},
	pmid = {26092688},
	pmcid = {PMC4534495},
	keywords = {Animals, Data Mining, Databases, Genetic, Genomics, Internet, Mice, Software},
	pages = {325--330}
}

@article{lyne_cross-organism_2015,
	title = {Cross-organism analysis using {InterMine}},
	volume = {53},
	issn = {1526-968X},
	doi = {10.1002/dvg.22869},
	abstract = {InterMine is a data integration warehouse and analysis software system developed for large and complex biological data sets. Designed for integrative analysis, it can be accessed through a user-friendly web interface. For bioinformaticians, extensive web services as well as programming interfaces for most common scripting languages support access to all features. The web interface includes a useful identifier look-up system, and both simple and sophisticated search options. Interactive results tables enable exploration, and data can be filtered, summarized, and browsed. A set of graphical analysis tools provide a rich environment for data exploration including statistical enrichment of sets of genes or other entities. InterMine databases have been developed for the major model organisms, budding yeast, nematode worm, fruit fly, zebrafish, mouse, and rat together with a newly developed human database. Here, we describe how this has facilitated interoperation and development of cross-organism analysis tools and reports. InterMine as a data exploration and analysis tool is also described. All the InterMine-based systems described in this article are resources freely available to the scientific community.},
	language = {eng},
	number = {8},
	journal = {Genesis (New York, N.Y.: 2000)},
	author = {Lyne, Rachel and Sullivan, Julie and Butano, Daniela and Contrino, Sergio and Heimbach, Joshua and Hu, Fengyuan and Kalderimis, Alex and Lyne, Mike and Smith, Richard N. and Štěpán, Radek and Balakrishnan, Rama and Binkley, Gail and Harris, Todd and Karra, Kalpana and Moxon, Sierra A. T. and Motenko, Howie and Neuhauser, Steven and Ruzicka, Leyla and Cherry, Mike and Richardson, Joel and Stein, Lincoln and Westerfield, Monte and Worthey, Elizabeth and Micklem, Gos},
	month = aug,
	year = {2015},
	pmid = {26097192},
	pmcid = {PMC4545681},
	keywords = {Animals, Computational Biology, Databases, Factual, Databases, Genetic, Genomics, Humans, Internet, Software, Systems Integration, User-Computer Interface, comparative analysis, cross-organism analysis, data analysis, data integration, genomics, integrative analysis, proteomics},
	pages = {547--560}
}

Paper  doi  abstract   bibtex   

@article{chu_thermal_2014,
	title = {Thermal ablation of tumours: biological mechanisms and advances in therapy},
	volume = {14},
	copyright = {2014 Nature Publishing Group},
	issn = {1474-1768},
	shorttitle = {Thermal ablation of tumours},
	url = {https://www.nature.com/articles/nrc3672},
	doi = {10.1038/nrc3672},
	abstract = {Minimally invasive thermal ablation of tumours has become common since the advent of modern imaging. From the ablation of small, unresectable tumours to experimental therapies, percutaneous radiofrequency ablation, microwave ablation, cryoablation and irreversible electroporation have an increasing role in the treatment of solid neoplasms. This Opinion article examines the mechanisms of tumour cell death that are induced by the most common thermoablative techniques and discusses the rapidly developing areas of research in the field, including combinatorial ablation and immunotherapy, synergy with conventional chemotherapy and radiation, and the development of a new ablation modality in irreversible electroporation.},
	language = {en},
	number = {3},
	urldate = {2018-09-22},
	journal = {Nature Reviews Cancer},
	author = {Chu, Katrina F. and Dupuy, Damian E.},
	month = mar,
	year = {2014},
	note = {00506},
	keywords = {Ablation Techniques, Animals, Apoptosis, History, 19th Century, History, 20th Century, History, 21st Century, Humans, Neoplasms, Surgery, Computer-Assisted},
	pages = {199--208},
}

@article{ kidd_influenza_2014,
  title = {Influenza viruses: update on epidemiology, clinical features, treatment and vaccination},
  volume = {20},
  issn = {1531-6971},
  shorttitle = {Influenza viruses},
  doi = {10.1097/MCP.0000000000000049},
  abstract = {PURPOSE OF REVIEW: In the last decade, sporadic and lethal human disease caused by zoonotic avian influenza viruses, and the seasonal activity of human H1N1 2009 pandemic type have driven intense epidemiological and laboratory studies into the virus life cycle. This article highlights major developments from mid-2012 to early 2014.
RECENT FINDINGS: Advances in molecular techniques and efficient rollout of diagnostic tests have enabled the rapid identification of clinical cases and detailed genetic sequencing of viral genomes. Studies have contributed widely to the understanding of how and when influenza viruses circulate, what determines their innate pathogenicity in particular hosts and whether host cofactors influence disease severity. Other imperatives include investigations into how influenza can be better prevented by vaccination, or treated with antiviral drugs.
SUMMARY: Avian influenza viruses present a continuous threat to human populations. There is a need for sustained surveillance and downstream research to evaluate the potential for future pandemics.},
  language = {eng},
  number = {3},
  journal = {Current Opinion in Pulmonary Medicine},
  author = {Kidd, Mike},
  month = {May},
  year = {2014},
  pmid = {24637227},
  keywords = {Animals, Antiviral Agents, DNA, Viral, Drug Resistance, Viral, Female, Humans, Influenza A Virus, H1N1 Subtype, Influenza A Virus, H5N1 Subtype, Influenza A Virus, H7N9 Subtype, Influenza A virus, Influenza in Birds, Influenza, Human, Male, Pandemics, Poultry, Seasons, Sentinel Surveillance, Sequence Analysis, DNA, Viral Vaccines, Zanamivir},
  pages = {242--246}
}

Website  abstract   bibtex   

@article{
 title = {A review of signals used in sleep analysis.},
 type = {article},
 year = {2014},
 identifiers = {[object Object]},
 keywords = {Animals,Humans,Monitoring, Physiologic,Monitoring, Physiologic: methods,Signal Processing, Computer-Assisted,Sleep,Sleep: physiology},
 pages = {R1-57},
 volume = {35},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/24346125},
 month = {1},
 id = {3fe40fe0-6165-3e94-add9-153b51b31675},
 created = {2016-03-29T18:26:49.000Z},
 accessed = {2014-10-12},
 file_attached = {false},
 profile_id = {304786e8-5116-360a-80be-e62833097578},
 group_id = {d7b44578-07c1-3210-ae74-3bcd7f980767},
 last_modified = {2017-03-14T15:45:25.917Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Roebuck2014},
 private_publication = {false},
 abstract = {This article presents a review of signals used for measuring physiology and activity during sleep and techniques for extracting information from these signals. We examine both clinical needs and biomedical signal processing approaches across a range of sensor types. Issues with recording and analysing the signals are discussed, together with their applicability to various clinical disorders. Both univariate and data fusion (exploiting the diverse characteristics of the primary recorded signals) approaches are discussed, together with a comparison of automated methods for analysing sleep.},
 bibtype = {article},
 author = {Roebuck, a and Monasterio, V and Gederi, E and Osipov, M and Behar, J and Malhotra, a and Penzel, T and Clifford, G D},
 journal = {Physiological measurement},
 number = {1}
}

@article{jang_rutin_2014,
	title = {Rutin improves functional outcome via reducing the elevated matrix metalloproteinase-9 level in a photothrombotic focal ischemic model of rats},
	volume = {339},
	issn = {1878-5883},
	doi = {10.1016/j.jns.2014.01.024},
	abstract = {BACKGROUND: Blood-brain barrier (BBB) disruption mediated by proteases plays a pivotal role in neural tissue damage after acute ischemic stroke. In an animal stroke model, the activation of matrix metalloproteinases (MMPs), especially MMP-9, was significantly increased and it showed potential association with blood-brain barrier (BBB) disruption and cerebral edema. Theoretically, it is expected that early blockade of expression and activation of MMP-9 after ischemic stroke provides neuroprotective effects from secondary neural tissue damage. This study was aimed to determine the ability of rutin to influence MMP-9 expression, activity and BBB disruption using a photothrombotic focal ischemic model in rats.
METHODS: Adult male Sprague-Dawley rats, weighing between 250 and 300 g (aged 8 weeks) received focal cerebral ischemia by photothrombosis using Rose Bengal (RB) and cold light. Injured animals were divided into two groups; one group received 50mg/kg of rutin intraperitoneally, starting 1h after injury and at 12h intervals for 3 days, while animals in the control group received weight-adjusted doses of saline vehicle over the same period. In each group, the expressions and activities of MMP-9 were assessed by Western blot and gelatin zymography at 6, 24, 48, and 72 h after photothrombotic insult. The effects of rutin on BBB disruption and functional outcomes were also determined.
RESULTS: Western blot and zymographic analysis showed up-regulated MMP-9 expression and activity in the ischemic cortex. The expression and activity of MMP-9 were significantly elevated at 6h after photothrombotic insult, which remained up-regulated for at least until 72 h after injury. In the rutin-treated group, MMP-9 expression and activity were significantly attenuated at 6, 24, and 48 h compared to the control group. Relative to the control group, BBB permeability was significantly reduced in the rutin-treated group. The results of the rotarod test revealed that rutin treatment significantly improved functional outcomes.
CONCLUSIONS: Rutin treatment starting 1h after injury attenuated BBB disruption during photothrombotic focal ischemia, which was partly, at least, achieved through inhibitory effects on MMP-9 expression and activity. The results of this study suggest that rutin might be useful in clinical trials aimed to improve the outcome of patients suffering from acute ischemic stroke.},
	language = {eng},
	number = {1-2},
	journal = {Journal of the Neurological Sciences},
	author = {Jang, Jae-Won and Lee, Jung-Kil and Hur, Hyuk and Kim, Tae-Wan and Joo, Sung-Pil and Piao, Min-Sheng},
	month = apr,
	year = {2014},
	pmid = {24507948},
	note = {00016 },
	keywords = {Animals, Blood-Brain Barrier, Brain Ischemia, Cerebral ischemia, Disease Models, Animal, Enzyme Inhibitors, Funcional outcome, Intracranial Thrombosis, Male, Matrix Metalloproteinase 9, Matrix metalloproteinases, Photic Stimulation, Photothrombosis, Rat, Rats, Rats, Sprague-Dawley, Recovery of Function, Rose Bengal, Rutin, Treatment Outcome},
	pages = {75--80}
}

@article{brown_evaluation_2014,
	title = {Evaluation of varying morphological parameters on the biomechanics of a cranial cruciate ligament-deficient or intact canine stifle joint with a computer simulation model},
	volume = {75},
	issn = {1943-5681},
	doi = {10.2460/ajvr.75.1.26},
	abstract = {OBJECTIVE: To investigate the influence of varying morphological parameters on canine stifle joint biomechanics by use of a 3-D rigid-body canine pelvic limb computer model that simulated an intact and cranial cruciate ligament (CrCL)-deficient stifle joint across the stance phase of gait at a walk.
SAMPLE: Data from computer simulations.
PROCEDURES: Computer model morphological parameters, including patellar ligament insertion location, tibial plateau angle (TPA), and femoral condyle diameter (FCD), were incrementally altered to determine their influence on outcome measures (ligament loads, relative tibial translation, and relative tibial rotation) during simulation of the stance phase of gait at a walk. Outcome measures were assessed for each scenario and compared between an intact and CrCL-deficient stifle joint with the sensitivity index (the percentage change in outcome measure divided by the percentage change in input parameter).
RESULTS: In a CrCL-intact stifle joint, ligament loads were most sensitive to TPA. In a CrCL-deficient stifle joint, outcome measures were most sensitive to TPA with the exception of caudal cruciate ligament and lateral collateral ligament loads, which were sensitive to FCD and TPA. Relative tibial translation was sensitive to TPA and patellar ligament insertion location, whereas relative tibial rotation was most sensitive to TPA.
CONCLUSIONS AND CLINICAL RELEVANCE: The computer model sensitivity analyses predicted that individual parameters, particularly TPA and FCD, influence stifle joint biomechanics. Therefore, tibial and femoral morphological parameters may affect the likelihood, prevention, and management of CrCL deficiency.},
	language = {eng},
	number = {1},
	journal = {American Journal of Veterinary Research},
	author = {Brown, Nathan P. and Bertocci, Gina E. and Marcellin-Little, Denis J.},
	month = jan,
	year = {2014},
	pmid = {24370242},
	keywords = {Animals, Anterior Cruciate Ligament, Biomechanical Phenomena, Computer Simulation, Dogs, Femur, Gait, Male, Patellar Ligament, Rotation, Stifle, Tibia, Walking},
	pages = {26--33}
}

@article{kalff_lateral_2014,
	title = {Lateral patellar luxation in dogs: a retrospective study of 65 dogs},
	volume = {27},
	issn = {0932-0814},
	shorttitle = {Lateral patellar luxation in dogs},
	doi = {10.3415/VCOT-13-05-0064},
	abstract = {OBJECTIVE: To report the signalment and clinical features of dogs with non-traumatic lateral patellar luxation and to report the complications and outcomes following surgery.
METHODS: A multicentre retrospective study was performed. Medical records were reviewed and the signalment, clinical features, and treatment of dogs presenting with lateral patellar luxation were recorded. In dogs treated surgically, the outcome and complications were investigated.
RESULTS: Sixty-five dogs (95 stifles) were included; 39 were male and median age at presentation was 10 months. Breeds were classified as small (n = 6), medium (n = 23), large (n = 27), and giant (n = 9). Lateral patellar luxation was classified as grade I (n = 14), II (n = 41), III (n = 29), and IV (n = 11). Conformational abnormalities were noted in 34 stifles; genu valgum was the most common (n = 28). Higher-grade luxation was associated with a younger age at presentation (p = 0.032) and genu valgum (p = 0.01). Surgery was performed on 58 stifles, 22 of which sustained one or more complications; 16 complications were managed conservatively, four with implant removal and six with revision surgery. Surgeon-assessed outcome was good or excellent in 47 of the 51 dogs available for review.
CONCLUSIONS: Non-traumatic lateral patellar luxation is a disease of predominantly medium and large breed dogs. It has several similar clinical features and can be surgically treated in a similar manner to medial patellar luxation with similar types of complications and outcomes expected.},
	language = {eng},
	number = {2},
	journal = {Veterinary and Comparative Orthopaedics and Traumatology: V.C.O.T},
	author = {Kalff, S. and Butterworth, S. J. and Miller, A. and Keeley, B. and Baines, S. and McKee, W. M.},
	year = {2014},
	pmid = {24441512},
	keywords = {Animals, Dislocations, Dogs, Female, Male, Patella, Retrospective Studies, Stifle, Treatment Outcome},
	pages = {130--134}
}

@article{tan_identification_2013,
	title = {Identification of a new cyclovirus in cerebrospinal fluid of patients with acute  central nervous system infections.},
	volume = {4},
	issn = {2150-7511},
	doi = {10.1128/mBio.00231-13},
	abstract = {Acute central nervous system (CNS) infections cause substantial morbidity and mortality, but the etiology remains unknown in a large proportion of cases. We identified and characterized the full genome of a novel cyclovirus (tentatively named cyclovirus-Vietnam [CyCV-VN]) in cerebrospinal fluid (CSF) specimens of two Vietnamese patients with CNS infections of unknown etiology. CyCV-VN was subsequently detected in 4\% of 642 CSF specimens from Vietnamese patients with suspected CNS infections and none of 122 CSFs from patients with noninfectious neurological disorders. Detection rates were similar in patients with CNS infections of unknown etiology and those in whom other pathogens were detected. A similar detection rate in feces from healthy children suggested food-borne or orofecal transmission routes, while high detection rates in feces from pigs and poultry (average, 58\%) suggested the existence of animal reservoirs for such transmission. Further research is needed to address the epidemiology and pathogenicity of this novel, potentially zoonotic virus.},
	language = {eng},
	number = {3},
	journal = {mBio},
	author = {Tan, Le Van and van Doorn, H. Rogier and Nghia, Ho Dang Trung and Chau, Tran Thi Hong and Tu, Le Thi Phuong and de Vries, Michel and Canuti, Marta and Deijs, Martin and Jebbink, Maarten F. and Baker, Stephen and Bryant, Juliet E. and Tham, Nguyen Thi and BKrong, Nguyen Thi Thuy Chinh and Boni, Maciej F. and Loi, Tran Quoc and Phuong, Le Thi and Verhoeven, Joost T. P. and Crusat, Martin and Jeeninga, Rienk E. and Schultsz, Constance and Chau, Nguyen Van Vinh and Hien, Tran Tinh and van der Hoek, Lia and Farrar, Jeremy and de Jong, Menno D.},
	month = jun,
	year = {2013},
	pmid = {23781068},
	pmcid = {PMC3684831},
	keywords = {Adolescent, Adult, Aged, Animals, Central Nervous System Infections/epidemiology/*virology, Child, Child, Preschool, Circoviridae Infections/epidemiology/*virology, Circoviridae/*classification/genetics/*isolation \& purification, Cluster Analysis, DNA, Viral/chemistry/genetics, Female, Genome, Viral, Humans, Infant, Male, Middle Aged, Molecular Sequence Data, Phylogeny, Prevalence, Prospective Studies, Sequence Analysis, DNA, Vietnam, Young Adult},
	pages = {e00231--00213},
}

@article{murhekar_avian_2013,
	title = {Avian influenza {A}({H7N9}) and the closure of live bird markets.},
	volume = {4},
	issn = {2094-7313 2094-7321},
	doi = {10.5365/WPSAR.2013.4.2.008},
	language = {eng},
	number = {2},
	journal = {Western Pacific surveillance and response journal : WPSAR},
	author = {Murhekar, Manoj and Arima, Yuzo and Horby, Peter and Vandemaele, Katelijn A. H. and Vong, Sirenda and Zijian, Feng and Lee, Chin-Kei and Li, Ailan},
	month = jun,
	year = {2013},
	pmid = {24015364},
	pmcid = {PMC3762972},
	keywords = {*Marketing, Agriculture, Animals, China, Disease Reservoirs/*statistics \& numerical data/virology, Humans, Influenza A Virus, H7N9 Subtype/*isolation \& purification, Influenza in Birds/*diagnosis/epidemiology/virology, Influenza, Human/*diagnosis/epidemiology/virology, Poultry/*virology},
	pages = {4--7},
}

Paper  Website  abstract   bibtex   

@article{
 title = {Reference-free population genomics from next-generation transcriptome data and the vertebrate-invertebrate gap.},
 type = {article},
 year = {2013},
 identifiers = {[object Object]},
 keywords = {Animals,Base Sequence,Drosophila,Drosophila: genetics,Genome,Genotype,Hares,Hares: genetics,High-Throughput Nucleotide Sequencing,Human,Humans,Invertebrates,Invertebrates: genetics,Isoptera,Isoptera: genetics,Metagenomics,Ostreidae,Ostreidae: genetics,Polymorphism,Single Nucleotide,Transcriptome,Transcriptome: genetics,Turtles,Turtles: genetics,Urochordata,Urochordata: genetics,Vertebrates,Vertebrates: genetics},
 pages = {e1003457},
 volume = {9},
 websites = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3623758&tool=pmcentrez&rendertype=abstract},
 month = {4},
 id = {3639b6ed-7592-301f-8fc7-56d3d09c7c76},
 created = {2017-09-18T09:15:16.356Z},
 accessed = {2013-08-21},
 file_attached = {true},
 profile_id = {1c95d708-d42d-399e-b365-9d34fead1a19},
 last_modified = {2017-09-18T09:21:29.525Z},
 read = {true},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Gayral2013},
 source_type = {article},
 notes = {
        <m:bold>From Duplicate 2 ( </m:bold>
        <m:bold>
          <m:italic>Reference-free population genomics from next-generation transcriptome data and the vertebrate-invertebrate gap.</m:italic>
        </m:bold>
        <m:bold> - Gayral, Philippe; Melo-Ferreira, José; Glémin, Sylvain; Bierne, Nicolas; Carneiro, Miguel; Nabholz, Benoit; Lourenco, Joao M; Alves, Paulo C; Ballenghien, Marion; Faivre, Nicolas; Belkhir, Khalid; Cahais, Vincent; Loire, Etienne; Bernard, Aurélien; Galtier, Nicolas )<m:linebreak></m:linebreak>
        </m:bold>
        <m:linebreak></m:linebreak>
        <m:linebreak></m:linebreak>
        <m:linebreak></m:linebreak>
      },
 abstract = {In animals, the population genomic literature is dominated by two taxa, namely mammals and drosophilids, in which fully sequenced, well-annotated genomes have been available for years. Data from other metazoan phyla are scarce, probably because the vast majority of living species still lack a closely related reference genome. Here we achieve de novo, reference-free population genomic analysis from wild samples in five non-model animal species, based on next-generation sequencing transcriptome data. We introduce a pipe-line for cDNA assembly, read mapping, SNP/genotype calling, and data cleaning, with specific focus on the issue of hidden paralogy detection. In two species for which a reference genome is available, similar results were obtained whether the reference was used or not, demonstrating the robustness of our de novo inferences. The population genomic profile of a hare, a turtle, an oyster, a tunicate, and a termite were found to be intermediate between those of human and Drosophila, indicating that the discordant genomic diversity patterns that have been reported between these two species do not reflect a generalized vertebrate versus invertebrate gap. The genomic average diversity was generally higher in invertebrates than in vertebrates (with the notable exception of termite), in agreement with the notion that population size tends to be larger in the former than in the latter. The non-synonymous to synonymous ratio, however, did not differ significantly between vertebrates and invertebrates, even though it was negatively correlated with genetic diversity within each of the two groups. This study opens promising perspective regarding genome-wide population analyses of non-model organisms and the influence of population size on non-synonymous versus synonymous diversity.},
 bibtype = {article},
 author = {Gayral, Philippe and Melo-Ferreira, José and Glémin, Sylvain and Bierne, Nicolas and Carneiro, Miguel and Nabholz, Benoit and Lourenco, Joao M and Alves, Paulo C and Ballenghien, Marion and Faivre, Nicolas and Belkhir, Khalid and Cahais, Vincent and Loire, Etienne and Bernard, Aurélien and Galtier, Nicolas},
 journal = {PLoS genetics},
 number = {4}
}

@article{volkova_electrophysiological_2013,
	title = {Electrophysiological correlations of morphological restructuring in experimental local ischemia of different severity in the rat sensorimotor cortex},
	volume = {155},
	issn = {1573-8221},
	abstract = {Local cerebrovascular disorders were modeled by reversible photochemical clotting of hemispheric cortical vessels. Mild ischemia led to reversible edema in the surface layers of the cortex: cytotoxic edema of the neuropile, primarily of the distal dendrites. This status led to an increase in the lower delta rhythm frequency band power. After administration of systemic anesthetic, delta rhythm appeared sooner in the ischemic foci than in intact cortical areas. More severe ischemia led to the appearance of dark and pyknotic neurons and reduction of oscillation power in all EEG spectrum bands. Restructuring of primarily dendrites caused by local moderate ischemia of the surface cortical layers at the early stage of neurodegenerative processes stimulated the inhibitory recovery processes.},
	language = {eng},
	number = {2},
	journal = {Bulletin of Experimental Biology and Medicine},
	author = {Volkova, D. A. and Kositzyn, N. S. and Goloborodko, E. V. and Loginova, N. A. and Svinov, M. M.},
	month = jun,
	year = {2013},
	pmid = {24131005},
	note = {00000 },
	keywords = {Anesthetics, Animals, Brain, Cerebral Cortex, Cerebral Infarction, Delta Rhythm, Dendrites, Electroencephalography, Hypoxia-Ischemia, Brain, Male, Neuropil, Rats, Rats, Wistar, Rose Bengal},
	pages = {264--267}
}

Paper  doi  abstract   bibtex   

@article{chan_disruption_2012,
	title = {Disruption of the hypothalamic-pituitary-thyroid axis in zebrafish embryo-larvae following waterborne exposure to {BDE}-47, {TBBPA} and {BPA}.},
	volume = {108},
	issn = {1879-1514},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/22100034},
	doi = {10.1016/j.aquatox.2011.10.013},
	abstract = {We performed waterborne exposures of 2,2',4,4'-tetrabromodiphenyl ether (BDE-47), tetrabromobisphenol A (TBBPA) or bisphenol A (BPA) on zebrafish (Danio rerio) embryo-larvae and quantitatively measured the expression of genes belonging to the hypothalamic-pituitary-thyroid (HPT) axis to assess for adverse thyroid function. For analysis on the effects of BDE-47, TBBPA and BPA on the hypothalamic-pituitary-thyroid genes, zebrafish embryo-larvae were acutely exposed to lethal concentrations of the chemical agents in order to determine the 96 h-LC50 (96 h lethal median concentration) and 96 h-EC50 (96 h effective median concentration) values. Further exposures at sub-lethal concentrations were then carried out and total RNA samples were extracted to quantify the mRNA expression levels of the genes of interest. In larvae, BDE-47 was found to have significantly induced many genes of interest, namely thyroglobulin, thyroid peroxidase, thyroid receptors α and β, thyroid stimulating hormone, and transthyretin. TBBPA only significantly induced three genes of interest (thyroid receptor α, thyroid stimulating hormone, and transthyretin) while BPA only induced thyroid stimulating hormone. In embryos, BDE-47 significantly induced the sodium iodide symporter and thyroid stimulating hormone. TBBPA significantly induced thyroid receptor α and thyroid stimulating hormone, while BPA did not significantly induce any of the genes. Most genes were only induced at the 75\% 96 h-LC50 or 96 h-EC50 value; however, thyroid peroxidase and thyroid stimulating hormone demonstrated upregulation in a level as little as the 10\% 96 h-LC50 value. The present study provides a new set of data on zebrafish mRNA induction of hypothalamic-pituitary-thyroid genes from exposure to BDE-47, TBBPA, or BPA. This information would serve useful for elucidating the toxicological mechanism of brominated flame retardants, assessing appropriate safety levels in the environment for these compounds, as well as serve as a reference for other man-made contaminants.},
	journal = {Aquatic toxicology (Amsterdam, Netherlands)},
	author = {Chan, Winson K and Chan, King Ming},
	month = feb,
	year = {2012},
	pmid = {22100034},
	keywords = {Acute, Animals, Chemical, Chemical: toxicity, Developmental, Developmental: drug ef, Embryo, Flame Retardants: toxicity, Flame retardants, Gene Expression Profiling, Gene Expression Regulation, Hypothalamus, Hypothalamus: drug effects, Lethal Dose 50, Nonmammalian, Nonmammalian: drug effects, Phenols, Phenols: toxicity, Pituitary Gland, Pituitary Gland: drug effects, Polybrominated Biphenyls, Polybrominated Biphenyls: toxicity, Thyroid Gland, Thyroid Gland: drug effects, Thyroid Hormones, Thyroid Hormones: metabolism, Toxicity Tests, Water Pollutants, Zebrafish, Zebrafish: embryology, Zebrafish: physiology, unsure},
	pages = {106--11}
}

Website  abstract   bibtex   

@article{
 title = {Host-gut microbiota metabolic interactions.},
 type = {article},
 year = {2012},
 identifiers = {[object Object]},
 keywords = {Aging,Animals,Bacteria,Bacteria: metabolism,Diet,Gastrointestinal Tract,Gastrointestinal Tract: metabolism,Gastrointestinal Tract: microbiology,Health,Humans,Immune System,Immune System: physiology,Inflammation,Liver,Liver: metabolism,Metabolic Diseases,Metabolic Diseases: metabolism,Metabolic Diseases: microbiology,Metabolic Networks and Pathways,Metagenome,Signal Transduction},
 pages = {1262-7},
 volume = {336},
 websites = {http://www.sciencemag.org.ezproxy.library.wisc.edu/content/336/6086/1262.long},
 month = {6},
 day = {8},
 id = {bd6afe2b-28a5-318b-84ed-c145f06e6ed2},
 created = {2016-06-24T20:49:29.000Z},
 accessed = {2014-07-10},
 file_attached = {false},
 profile_id = {954a987f-819f-3985-95a4-2991e0cf0552},
 group_id = {8440dcff-74cc-3783-aef7-fe2749cfc7ef},
 last_modified = {2016-06-24T20:49:29.000Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {Nicholson2012},
 abstract = {The composition and activity of the gut microbiota codevelop with the host from birth and is subject to a complex interplay that depends on the host genome, nutrition, and life-style. The gut microbiota is involved in the regulation of multiple host metabolic pathways, giving rise to interactive host-microbiota metabolic, signaling, and immune-inflammatory axes that physiologically connect the gut, liver, muscle, and brain. A deeper understanding of these axes is a prerequisite for optimizing therapeutic strategies to manipulate the gut microbiota to combat disease and improve health.},
 bibtype = {article},
 author = {Nicholson, Jeremy K and Holmes, Elaine and Kinross, James and Burcelin, Remy and Gibson, Glenn and Jia, Wei and Pettersson, Sven},
 journal = {Science (New York, N.Y.)},
 number = {6086}
}

Website  abstract   bibtex   

@article{
 title = {Syndecan-1 promotes the angiogenic phenotype of multiple myeloma endothelial cells.},
 type = {article},
 year = {2012},
 identifiers = {[object Object]},
 keywords = {Animals,Cells, Cultured,Cultured,Endothelium,Endothelium: pathology,Flow Cytometry,Gene Silencing,Humans,Immunoprecipitation,Mice,Multiple Myeloma,Multiple Myeloma: blood supply,Multiple Myeloma: pathology,Neovascularization, Pathologic,Pathologic,Real-Time Polymerase Chain Reaction,Signal Transduction,Syndecan-1,Syndecan-1: genetics,Syndecan-1: physiology,Tumor Cells, Cultured,Vascular Endothelial Growth Factor A,Vascular Endothelial Growth Factor A: metabolism,Vascular Endothelial Growth Factor Receptor-2,Vascular Endothelial Growth Factor Receptor-2: met},
 pages = {1081-90},
 volume = {26},
 websites = {http://dx.doi.org/10.1038/leu.2011.290},
 month = {5},
 publisher = {Macmillan Publishers Limited},
 id = {0dc3a323-ae53-325a-9f8b-74d28f5e217a},
 created = {2016-06-24T20:50:03.000Z},
 accessed = {2014-12-01},
 file_attached = {false},
 profile_id = {954a987f-819f-3985-95a4-2991e0cf0552},
 group_id = {8440dcff-74cc-3783-aef7-fe2749cfc7ef},
 last_modified = {2016-06-24T20:50:03.000Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {Lamorte2012},
 short_title = {Leukemia},
 abstract = {Angiogenesis is considered a hallmark of multiple myeloma (MM) progression. In the present study, we evaluated the morphological and functional features of endothelial cells (ECs) derived from bone marrow (BM) of patients affected by MM (MMECs). We found that MMECs compared with normal BM ECs (BMECs) showed increased expression of syndecan-1. Silencing of syndecan-1 expression by RNA interference technique decreased in vitro EC survival, proliferation and organization in capillary-like structures. In vivo, in severe combined immunodeficient mice, syndecan-1 silencing inhibited MMEC organization into patent vessels. When overexpressed in human umbilical vein ECs and BMECs, syndecan-1 induced in vitro and in vivo angiogenic effects. Flow-cytometric analysis of MMECs silenced for syndecan-1 expression indicated a decreased membrane expression of vascular endothelial growth factor (VEGF) receptor-2 (VEGFR-2). Immunoprecipitation and confocal analysis showed colocalization of VEGFR-2 with syndecan-1. Absence of nuclear translocation of VEGFR-2 in syndecan-1-knockdown cells together with the shift from perinuclear localization to recycling compartments suggest a role of syndecan-1 in modulation of VEGFR-2 localization. This correlated with an in vitro decreased VEGF-induced invasion and motility. These results suggest that syndecan-1 may contribute to the highly angiogenic phenotype of MMECs by promoting EC proliferation, survival and modulating VEGF-VEGFR-2 signalling.},
 bibtype = {article},
 author = {Lamorte, S and Ferrero, S and Aschero, S and Monitillo, L and Bussolati, B and Omedè, P and Ladetto, M and Camussi, G},
 journal = {Leukemia},
 number = {5}
}

@article{hori_use_2012,
	title = {Use of traditional environmental knowledge to assess the impact of climate change on subsistence fishing in the {James} {Bay} {Region} of {Northern} {Ontario}, {Canada}},
	volume = {12},
	issn = {1445-6354},
	abstract = {INTRODUCTION: In Canada, unique food security challenges are being faced by Aboriginal people living in remote-northern communities due to the impacts of climate change on subsistence harvesting. This study used traditional environmental knowledge (TEK) to investigate whether there was a temporal relationship between extreme climatic events in the summer of 2005, and fish die-offs in the Albany River, northern Ontario, Canada. Also, TEK was utilized to examine a potential shift in subsistence fish species distribution due to climate change.
METHODS: To investigate whether there was a temporal relationship between the fish die-offs of July 2005 (as identified by TEK) and an extreme climatic event, temperature and daily precipitation data for Moosonee weather station were utilized. To determine if there was an increasing trend in mean maximal summer temperatures with year, temperature data were examined, using regression analysis. Present-day fish distributions were determined using unpublished TEK data collated from previous studies and purposive, semi-directive interviews with elders and experienced bushman.
RESULTS: Fish die-offs in 2005 occurred during the time period 11-18 July, as reported by participants. Recorded air-temperature maxima of the two July 2005 heat waves delineate exactly the time period of fish die-offs. Two heat waves occurring during the same summer season and so close together has never before been recorded for this region. A highly significant (p {\textless} 0.0009) positive relationship between mean maximal summer temperatures and year was evident. Regionally novel fish species were not apparent, utilizing TEK.
CONCLUSIONS: Traditional environmental knowledge coupled with climate data revealed temporal relationships between extreme climatic events in 2005, and fish die-offs in the Albany River. Thus, climate change can directly impact food security by decreasing the number of fish through mortality - and indirectly through population dynamics - by impacting the yield of fish subsistence harvests in the future. By contrast, TEK did not reveal northward expansion of novel fish species in the Albany River or fish distributional contraction in the western James Bay region.},
	language = {eng},
	journal = {Rural and Remote Health},
	author = {Hori, Yukari and Tam, Benita and Gough, William A. and Ho-Foong, Elise and Karagatzides, Jim D. and Liberda, Eric N. and Tsuji, Leonard J. S.},
	year = {2012},
	pmid = {22471525},
	keywords = {Animals, Climate Change, Culture, Ecosystem, Environmental Health, Fishes, Food Supply, Humans, Indians, North American, Interviews as Topic, Knowledge, Male, Ontario, Temperature},
	pages = {1878},
}

Paper  abstract   bibtex   

@article{
 id = {c833f827-d0f9-33bf-86c2-b8903285f617},
 title = {Structural features of aquaporin 4 supporting the formation of arrays and junctions in biomembranes.},
 type = {article},
 year = {2012},
 identifiers = {[object Object]},
 keywords = {Animals,Aquaporin 4,Aquaporin 4: chemistry,Biophysics,Biophysics: methods,Cattle,Cell Membrane,Cell Membrane: metabolism,Lipids,Lipids: chemistry,Models, Molecular,Molecular Conformation,Molecular Dynamics Simulation,Protein Binding,Protein Interaction Mapping,Protein Interaction Mapping: methods,Protein Structure, Tertiary,Proteins,Proteins: chemistry,Rats,Thermodynamics,Water,Water: chemistry},
 created = {2014-12-10T04:09:01.000Z},
 pages = {2234-43},
 volume = {1818},
 websites = {http://www.sciencedirect.com/science/article/pii/S0005273612001319},
 month = {9},
 accessed = {2014-06-23},
 file_attached = {true},
 profile_id = {6708b05a-e661-38c6-9bb8-cf4f304b6385},
 group_id = {424eb3e1-9b50-35ed-91d3-65c78c3164d7},
 last_modified = {2014-12-10T09:11:31.000Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {Hofinger2012a},
 abstract = {A limited class of aquaporins has been described to form regular arrays and junctions in membranes. The biological significance of these structures, however, remains uncertain. Here we analyze the underlying physical principles with the help of a computational procedure that takes into account protein-protein as well as protein-membrane interactions. Experimentally observed array/junction structures are systematically (dis)assembled and major driving forces identified. Aquaporin 4 was found to be markedly different from the non-junction forming aquaporin 1. The environmental stabilization resulting from embedding into the biomembrane was identified as the main driving force. This highlights the role of protein-membrane interactions in aquaporin 4. Analysis of the type presented here can help to decipher the biological role of membrane arrays and junctions formed by aquaporin.},
 bibtype = {article},
 author = {Höfinger, Siegfried and Yamamoto, Eiji and Hirano, Yoshinori and Zerbetto, Francesco and Narumi, Tetsu and Yasuoka, Kenji and Yasui, Masato},
 journal = {Biochim. Biophys. Acta},
 number = {9}
}

Paper  Website  abstract   bibtex   

@article{
 title = {Growth of Western Australian corals in the anthropocene.},
 type = {article},
 year = {2012},
 identifiers = {[object Object]},
 keywords = {Animals,Anthozoa,Anthozoa: growth & development,Calcification, Physiologic,Calcium Carbonate,Calcium Carbonate: analysis,Coral Reefs,Geologic Sediments,Hydrogen-Ion Concentration,Indian Ocean,Linear Models,Regression Analysis,Seawater,Seawater: chemistry,Temperature,Western Australia},
 pages = {593-6},
 volume = {335},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/22301320},
 month = {2},
 day = {3},
 id = {1c6121a6-bb4d-3dfa-98ae-b5d477834165},
 created = {2012-12-06T09:09:03.000Z},
 accessed = {2012-11-07},
 file_attached = {true},
 profile_id = {0b777e31-8c9d-39dd-97a3-3e054bd99cfe},
 group_id = {764582e8-5773-3a66-8d6b-9b40e4fb5a88},
 last_modified = {2017-03-14T17:27:14.020Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {Cooper2012},
 abstract = {Anthropogenic increases of atmospheric carbon dioxide lead to warmer sea surface temperatures and altered ocean chemistry. Experimental evidence suggests that coral calcification decreases as aragonite saturation drops but increases as temperatures rise toward thresholds optimal for coral growth. In situ studies have documented alarming recent declines in calcification rates on several tropical coral reef ecosystems. We show there is no widespread pattern of consistent decline in calcification rates of massive Porites during the 20th century on reefs spanning an 11° latitudinal range in the southeast Indian Ocean off Western Australia. Increasing calcification rates on the high-latitude reefs contrast with the downward trajectory reported for corals on Australia's Great Barrier Reef and provide additional evidence that recent changes in coral calcification are responses to temperature rather than ocean acidification.},
 bibtype = {article},
 author = {Cooper, Timothy F and O'Leary, Rebecca a and Lough, Janice M},
 journal = {Science (New York, N.Y.)},
 number = {6068}
}

@article{ slupianek_bcr/abl_2011,
  title = {{}/{ABL} stimulates {WRN} to promote survival and genomic instability},
  volume = {71},
  issn = {1538-7445},
  doi = {10.1158/0008-5472.CAN-10-1066},
  abstract = {BCR/ABL-transformed chronic myeloid leukemia (CML) cells accumulate numerous DNA double-strand breaks (DSB) induced by reactive oxygen species (ROS) and genotoxic agents. To repair these lesions BCR/ABL stimulate unfaithful DSB repair pathways, homologous recombination repair (HRR), nonhomologous end-joining (NHEJ), and single-strand annealing (SSA). Here, we show that BCR/ABL enhances the expression and increase nuclear localization of WRN (mutated in Werner syndrome), which is required for processing DSB ends during the repair. Other fusion tyrosine kinases (FTK), such as TEL/ABL, TEL/JAK2, TEL/PDGFβR, and NPM/ALK also elevate WRN. BCR/ABL induces WRN mRNA and protein expression in part by c-MYC-mediated activation of transcription and Bcl-xL-dependent inhibition of caspase-dependent cleavage, respectively. WRN is in complex with BCR/ABL resulting in WRN tyrosine phosphorylation and stimulation of its helicase and exonuclease activities. Activated WRN protects BCR/ABL-positive cells from the lethal effect of oxidative and genotoxic stresses, which causes DSBs. In addition, WRN promotes unfaithful recombination-dependent repair mechanisms HRR and SSA, and enhances the loss of DNA bases during NHEJ in leukemia cells. In summary, we postulate that BCR/ABL-mediated stimulation of WRN modulates the efficiency and fidelity of major DSB repair mechanisms to protect leukemia cells from apoptosis and to facilitate genomic instability.},
  language = {eng},
  number = {3},
  journal = {Cancer Research},
  author = {Slupianek, Artur and Poplawski, Tomasz and Jozwiakowski, Stanislaw K. and Cramer, Kimberly and Pytel, Dariusz and Stoczynska, Ewelina and Nowicki, Michal O. and Blasiak, Janusz and Skorski, Tomasz},
  month = {February},
  year = {2011},
  pmid = {21123451},
  pmcid = {PMC3032814},
  keywords = {Animals, Cell Line, Tumor, Chromosome Aberrations, DNA Breaks, Double-Stranded, DNA Repair, DNA, Neoplasm, Disease Progression, Exodeoxyribonucleases, Fusion Proteins, bcr-abl, Genomic Instability, Humans, Leukemia, Myelogenous, Chronic, BCR-ABL Positive, Mice, Oxidative Stress, Phosphorylation, Protein-Tyrosine Kinases, RecQ Helicases, Recombinant Fusion Proteins},
  pages = {842--851}
}

Paper  doi  abstract   bibtex   

@article{kim_para-_2011,
	title = {Para- and ortho-substitutions are key determinants of polybrominated diphenyl ether activity toward ryanodine receptors and neurotoxicity.},
	volume = {119},
	issn = {1552-9924},
	url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3080935&tool=pmcentrez&rendertype=abstract},
	doi = {10.1289/ehp.1002728},
	abstract = {Polybrominated diphenyl ethers (PBDEs) are widely used flame retardants that bioaccumulate in human tissues. Their neurotoxicity involves dysregulation of calcium ion (Ca(2+))signaling; however, specific mechanisms have yet to be defined.},
	number = {4},
	journal = {Environmental health perspectives},
	author = {Kim, Kyung Ho and Bose, Diptiman D and Ghogha, Atefeh and Riehl, Joyce and Zhang, Rui and Barnhart, Christopher D and Lein, Pamela J and Pessah, Isaac N},
	month = apr,
	year = {2011},
	pmid = {21106467},
	keywords = {Animals, Calcium, Calcium Signaling, Calcium Signaling: drug effects, Calcium: metabolism, Environmental Pollutants, Environmental Pollutants: chemistry, Environmental Pollutants: metabolism, Environmental Pollutants: toxicity, Flame retardants, Halogenated Diphenyl Ethers, Halogenated Diphenyl Ethers: chemistry, Halogenated Diphenyl Ethers: metabolism, Halogenated Diphenyl Ethers: toxicity, Humans, Nervous System, Nervous System: drug effects, Nervous System: metabolism, Rats, Ryanodine Receptor Calcium Release Channel, Ryanodine Receptor Calcium Release Channel: metabo, Sprague-Dawley, Structure-Activity Relationship, cell line},
	pages = {519--26}
}

Paper  doi  abstract   bibtex   

@article{pena-abaurrea_comprehensive_2011,
	title = {Comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry for the identification of organobrominated compounds in bluefin tuna.},
	volume = {1218},
	issn = {1873-3778},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/21872866},
	doi = {10.1016/j.chroma.2011.08.031},
	abstract = {This study evaluates comprehensive two-dimensional gas chromatography (GC×GC) coupled to time-of-flight mass spectrometry (GC×GC-ToF MS) for the simultaneous analysis of several classes of organobromines (OBs), including polybrominated diphenyl ethers (PBDEs), polybrominated biphenyls (PBBs), methoxylated PBDEs (MeO-PBDEs), several halogenated naturally produced compounds (HNPs) and eight novel brominated flame retardants (NBFRs), polybrominated hexahydroxanthene derivates (PBHDs), 2,4,6-tribromoanisole and a mixed halogenated compound (MHC-1), in bluefin tuna muscles. The proposed methodology maximised separation of both within and among OB families, and among these and other halogenated micropollutants detected in these samples and co-extracted matrix components. Special attention has been paid to solve co-elution problems observed during the analysis of OBs with one-dimensional GC-based techniques. Satisfactory separation among several relevant PBDEs and MeO-PBDEs has been obtained allowing their unambiguous determination in a single run. Additional studies were conducted to identify selected NBFRs and HNPs. 2,4-Dibromoanisole, a dibromophenol isomer and hexabromobenzene were identified in the investigated samples. Several new tri- and tetra-BHD derivates were also identified, indicating that these compounds could apparently exist as structured families in nature. In addition, a tetrabrominated diMeO-biphenyl and two tetrabrominated diMeO-BDEs were also tentatively identified.},
	number = {39},
	journal = {Journal of chromatography. A},
	author = {Pena-Abaurrea, Miren and Covaci, Adrian and Ramos, Lourdes},
	month = sep,
	year = {2011},
	pmid = {21872866},
	keywords = {Animals, Brominated, Brominated: analysis, Environmental Monitoring, Environmental Monitoring: methods, Female, Flame Retardants: analysis, Flame retardants, Gas Chromatography-Mass Spectrometry, Gas Chromatography-Mass Spectrometry: methods, Halogenated Diphenyl Ethers, Halogenated Diphenyl Ethers: analysis, Hydrocarbons, Male, Muscles, Muscles: chemistry, Tuna, unsure},
	pages = {6995--7002}
}

Paper  doi  abstract   bibtex   

@article{johansson_temporal_2011,
	title = {Temporal trends of polybrominated diphenyl ethers and hexabromocyclododecane in {Swedish} {Peregrine} {Falcon} ({Falco} peregrinus peregrinus) eggs.},
	volume = {37},
	issn = {1873-6750},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/21396716},
	doi = {10.1016/j.envint.2011.01.010},
	abstract = {A temporal trend study of brominated flame retardants in eggs from peregrine falcon (Falco peregrinus peregrinus), a terrestrial bird of prey, is presented. Eggs collected between 1974 and 2007 were analyzed for the major constituents of the Penta-, Octa- and Decabromodiphenyl ether technical products (BDE-47, -99, -100, -153, -183 and -209), and hexabromocyclododecane (HBCD). Concentrations of BDE-99, -100, -153, -183, -209 and HBCD increased from 1974 to 2000. After the early 2000s, BDE-99, -100, -153 and -183 concentrations decreased, whereas BDE-209 and HBCD concentrations continued to increase. No temporal trend was detected for BDE-47. Rates of increase also differed, with BDE-99 and -100 increasing 3-fold between the 1980s and mid-1990s, and BDE-153 and -183 increasing approximately 10-fold during the same period. The average yearly increase was 15\% and 11\% for BDE-209 and HBCD, respectively, based on log-linear regression trends. There is a change in BDE congener patterns over time, with a shift from the predominance of BDE-99 and -47 until the late 1980s, to BDE-153 becoming the predominant congener later on. BFR temporal trends in Swedish peregrine falcon eggs reflect European BFR usage patterns.},
	number = {4},
	journal = {Environment international},
	author = {Johansson, Anna-Karin and Sellström, Ulla and Lindberg, Peter and Bignert, Anders and de Wit, Cynthia A},
	month = may,
	year = {2011},
	pmid = {21396716},
	keywords = {Animals, Brominated, Brominated: metabolism, Environmental Monitoring, Environmental Pollutants, Environmental Pollutants: metabolism, Environmental Pollution, Environmental Pollution: statistics \& numerical da, Falconiformes, Falconiformes: metabolism, Flame Retardants: metabolism, Flame retardants, Halogenated Diphenyl Ethers, Halogenated Diphenyl Ethers: metabolism, Hydrocarbons, Ovum, Ovum: metabolism, Sweden},
	pages = {678--86}
}

Paper  Website  abstract   bibtex   

@article{
 title = {Ocean acidification affects prey detection by a predatory reef fish.},
 type = {article},
 year = {2011},
 identifiers = {[object Object]},
 keywords = {Acids,Acids: toxicity,Animals,Carbon Dioxide,Carbon Dioxide: pharmacology,Climate Change,Environmental Exposure,Fishes,Fishes: physiology,Food Chain,Larva,Larva: drug effects,Oceans and Seas,Perciformes,Perciformes: physiology,Population Dynamics,Predatory Behavior,Seawater,Seawater: chemistry,Skin,Skin: drug effects},
 pages = {e22736},
 volume = {6},
 websites = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3145675&tool=pmcentrez&rendertype=abstract},
 month = {1},
 id = {c52bd206-ec67-3f12-b972-c26d99be5327},
 created = {2012-12-06T09:09:03.000Z},
 accessed = {2012-11-03},
 file_attached = {true},
 profile_id = {0b777e31-8c9d-39dd-97a3-3e054bd99cfe},
 group_id = {764582e8-5773-3a66-8d6b-9b40e4fb5a88},
 last_modified = {2017-03-14T17:27:14.020Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {Cripps2011},
 abstract = {Changes in olfactory-mediated behaviour caused by elevated CO(2) levels in the ocean could affect recruitment to reef fish populations because larval fish become more vulnerable to predation. However, it is currently unclear how elevated CO(2) will impact the other key part of the predator-prey interaction--the predators. We investigated the effects of elevated CO(2) and reduced pH on olfactory preferences, activity levels and feeding behaviour of a common coral reef meso-predator, the brown dottyback (Pseudochromis fuscus). Predators were exposed to either current-day CO(2) levels or one of two elevated CO(2) levels (∼600 µatm or ∼950 µatm) that may occur by 2100 according to climate change predictions. Exposure to elevated CO(2) and reduced pH caused a shift from preference to avoidance of the smell of injured prey, with CO(2) treated predators spending approximately 20% less time in a water stream containing prey odour compared with controls. Furthermore, activity levels of fish was higher in the high CO(2) treatment and feeding activity was lower for fish in the mid CO(2) treatment; indicating that future conditions may potentially reduce the ability of the fish to respond rapidly to fluctuations in food availability. Elevated activity levels of predators in the high CO(2) treatment, however, may compensate for reduced olfactory ability, as greater movement facilitated visual detection of food. Our findings show that, at least for the species tested to date, both parties in the predator-prey relationship may be affected by ocean acidification. Although impairment of olfactory-mediated behaviour of predators might reduce the risk of predation for larval fishes, the magnitude of the observed effects of elevated CO(2) acidification appear to be more dramatic for prey compared to predators. Thus, it is unlikely that the altered behaviour of predators is sufficient to fully compensate for the effects of ocean acidification on prey mortality.},
 bibtype = {article},
 author = {Cripps, Ingrid L and Munday, Philip L and McCormick, Mark I},
 journal = {PloS one},
 number = {7}
}

Paper  doi  abstract   bibtex   

@article{villanger_disruptive_2011,
	title = {Disruptive effects of persistent organohalogen contaminants on thyroid function in white whales ({Delphinapterus} leucas) from {Svalbard}.},
	volume = {409},
	issn = {1879-1026},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/21497377},
	doi = {10.1016/j.scitotenv.2011.03.014},
	abstract = {We analysed levels of 56 organohalogen contaminants (OHCs) including brominated flame retardants, polychlorinated biphenyls (PCBs), and organochlorine pesticides in the blubber of white (beluga) whales (Delphinapterus leucas) from Svalbard, Norway (N=12; 6 adults [5 males and 1 female] and 6 subadults [4 males and 2 females]) collected in 1996-2001. We also measured circulating levels of thyroid hormones (THs) and thyroid stimulating hormone (TSH) in the whales. The results confirm that OHC levels in these white whales are among the highest levels recorded in wildlife from Svalbard, and at the high end of the range when compared to white whales from the North American Arctic. A projection to latent structure (PLS) model (subadults and adult males grouped together) revealed that known or suspected thyroid disruptive contaminants (polybrominated diphenylether [PBDE]-28, -47, -99, -100, and -154, hexachlorobenzene [HCB], and PCB-105) were negatively correlated with circulating levels of total thyroxin (TT4), free T4 (FT4) and free triiodothyronine (FT3). Most of these negative relationships were also confirmed using partial correlations controlling for length (and thus age) of the whales. The positive correlations of TT4, FT4 and FT3 with hexabromocyclododecane (HBCD), α-hexachlorocyclohexane (α-HCH), chlorinated bornanes CHB-40 and CHB-62 revealed by the PLS model were not confirmed by partial correlations. TH levels in the present study appeared to be somewhat lower than levels measured in beluga whales from the Canadian Arctic. However, we were not able to determine if this was caused by different levels of OHCs, or differences in biological factors (e.g. age, sex, moulting status, and season) and analytical methods between the studies. Although the sample sizes were low and statistical models cannot depict the biological cause-effect relationships, this study suggests negative influences of specific OHCs, particularly PBDEs, on thyroid hormone levels in white whales. The impact this might have on individual and population health is unknown.},
	number = {13},
	journal = {The Science of the total environment},
	author = {Villanger, G D and Lydersen, C and Kovacs, K M and Lie, E and Skaare, J U and Jenssen, B M},
	month = jun,
	year = {2011},
	pmid = {21497377},
	keywords = {Animals, Beluga Whale, Beluga Whale: metabolism, Chemical, Chemical: metabolism, Chemical: toxicity, Endocrine Disruptors, Endocrine Disruptors: metabolism, Endocrine Disruptors: toxicity, Environmental Monitoring, Female, Flame Retardants: metabolism, Flame Retardants: toxicity, Flame retardants, Halogenated, Halogenated: metabolism, Halogenated: toxicity, Hydrocarbons, Male, Pesticides, Pesticides: metabolism, Pesticides: toxicity, Polychlorinated Biphenyls, Polychlorinated Biphenyls: metabolism, Polychlorinated Biphenyls: toxicity, Svalbard, Thyroid Gland, Thyroid Gland: drug effects, Thyroid Gland: metabolism, Thyroid Hormones, Thyroid Hormones: metabolism, Water Pollutants},
	pages = {2511--24}
}

Paper  doi  abstract   bibtex   

@article{ibhazehiebo_suppression_2011,
	title = {Suppression of thyroid hormone receptor-mediated transcription and disruption of thyroid hormone-induced cerebellar morphogenesis by the polybrominated biphenyl mixture, {BP}-6.},
	volume = {32},
	issn = {1872-9711},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/21396401},
	doi = {10.1016/j.neuro.2011.02.008},
	abstract = {Polybrominated biphenyls (PBBs) are polyhalogenated, bioaccumulative flame retardant chemicals, which have been used in a variety of consumer and household products. They were accidentally introduced into the food chain in Michigan in 1973 and have remained a source of health concern. Studies have shown that exposure to PBB may cause adverse neurotoxic effects. We therefore examined the effects of BP-6, a PBB mixture, on thyroid hormone (TH) receptor (TR)-mediated transcription, on TH-induced Purkinje cell dendritogenesis, and on TH-induced cerebellar granule cell neurite extension. Our study shows that BP-6 suppressed TR-mediated transcription in CV-1 cells. Mammalian two-hybrid studies revealed that BP-6 did not inhibit coactivator binding to TR nor did it recruit corepressors to TR. Further examination using the liquid chemiluminescent DNA pull down assay revealed partial dissociation of TR from TH response element (TRE). In primary rat cerebellar culture, BP-6 significantly suppressed TH-induced dendrite arborization of Purkinje cells, and in reaggregate rat granule cell culture, impaired TH-induced neurite extension of granule cells. Taken together, our results indicate that BP-6 may disrupt TH homeostasis and consequently impair normal neuronal development.},
	number = {4},
	journal = {Neurotoxicology},
	author = {Ibhazehiebo, Kingsley and Iwasaki, Toshiharu and Okano-Uchida, Takayuki and Shimokawa, Noriaki and Ishizaki, Yasuki and Koibuchi, Noriyuki},
	month = aug,
	year = {2011},
	pmid = {21396401},
	keywords = {Animals, Binding Sites, Cercopithecus aethiops, Cerebellum, Cerebellum: drug effects, Cerebellum: growth \& development, Cerebellum: metabolism, Cerebellum: pathology, Dendrites, Dendrites: drug effects, Dendrites: metabolism, Dendrites: pathology, Dose-Response Relationship, Down-Regulation, Drug, Flame Retardants: toxicity, Flame retardants, Genetic, Genetic: drug effects, Glucocorticoid, Glucocorticoid: drug effects, Glucocorticoid: metabolism, Neurites, Neurites: drug effects, Neurites: metabolism, Neurites: pathology, Neurogenesis, Neurogenesis: drug effects, Newborn, Polybrominated Biphenyls, Polybrominated Biphenyls: toxicity, Purkinje Cells, Purkinje Cells: drug effects, Purkinje Cells: metabolism, Purkinje Cells: pathology, Rats, Receptors, Response Elements, Response Elements: drug effects, Thyroid Hormone Receptors beta, Thyroid Hormone Receptors beta: drug effects, Thyroid Hormone Receptors beta: genetics, Thyroid Hormone Receptors beta: metabolism, Thyroxine, Thyroxine: metabolism, Transcription, Transfection, Triiodothyronine, Triiodothyronine: metabolism, Wistar, cell line},
	pages = {400--9}
}

Paper  doi  abstract   bibtex   

@article{roberts_identification_2011,
	title = {Identification of novel transcripts in annotated genomes using {RNA}-{Seq}.},
	volume = {27},
	issn = {1367-4811},
	url = {http://bioinformatics.oxfordjournals.org/content/27/17/2325},
	doi = {10.1093/bioinformatics/btr355},
	abstract = {SUMMARY: We describe a new 'reference annotation based transcript assembly' problem for RNA-Seq data that involves assembling novel transcripts in the context of an existing annotation. This problem arises in the analysis of expression in model organisms, where it is desirable to leverage existing annotations for discovering novel transcripts. We present an algorithm for reference annotation-based transcript assembly and show how it can be used to rapidly investigate novel transcripts revealed by RNA-Seq in comparison with a reference annotation. AVAILABILITY: The methods described in this article are implemented in the Cufflinks suite of software for RNA-Seq, freely available from http://bio.math.berkeley.edu/cufflinks. The software is released under the BOOST license. CONTACT: cole@broadinstitute.org; lpachter@math.berkeley.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
	number = {17},
	journal = {Bioinformatics (Oxford, England)},
	author = {Roberts, Adam and Pimentel, Harold and Trapnell, Cole and Pachter, Lior},
	month = sep,
	year = {2011},
	pmid = {21697122},
	keywords = {Algorithms, Animals, Gene Expression Profiling, Genome, Humans, Messenger, Messenger: chemistry, Messenger: metabolism, Molecular Sequence Annotation, RNA, Sequence Analysis, Software},
	pages = {2325--9}
}

Paper  Website  abstract   bibtex   

@article{
 title = {Immune suppression of the echinoderm Asterias rubens (L.) following long-term ocean acidification.},
 type = {article},
 year = {2011},
 identifiers = {[object Object]},
 keywords = {Animals,Asterias,Asterias: drug effects,Asterias: immunology,Asterias: metabolism,Carbon Dioxide,Carbon Dioxide: toxicity,Global Warming,HSP70 Heat-Shock Proteins,HSP70 Heat-Shock Proteins: metabolism,Hydrogen-Ion Concentration,Immunosuppressive Agents,Immunosuppressive Agents: toxicity,Seawater,Seawater: chemistry,Water Pollutants, Chemical,Water Pollutants, Chemical: toxicity},
 pages = {222-4},
 volume = {103},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/21473849},
 month = {6},
 publisher = {Elsevier B.V.},
 id = {48128cdb-e815-3c77-8f8d-0db9dc7c4c69},
 created = {2014-09-03T13:23:08.000Z},
 accessed = {2014-08-22},
 file_attached = {true},
 profile_id = {8f50d4f9-2497-37bc-bdbb-bc94be0e6cfa},
 group_id = {764582e8-5773-3a66-8d6b-9b40e4fb5a88},
 last_modified = {2017-03-14T17:27:14.020Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 abstract = {We compared effects of exposure to predict near-future (2100) ocean acidification (OA; pH 7.7) and normal seawater (Control; pH 8.1) on immune and stress responses in the adult sea star Asterias rubens. Analyses were made after one week and after six months of continuous exposure. Following one week exposure to acidified water, the pH of coelomic fluid was significantly reduced. Levels of the chaperon Hsp70 were elevated while key cellular players in immunity, coelomocytes, were reduced by approximately 50%. Following long-term exposure (six months) levels of Hsp70 returned to control values, whereas immunity was further impaired, evidenced by the reduced phagocytic capacity of coelomocytes and inhibited activation of p38 MAP-kinase. Such impacts of reduced seawater pH may have serious consequences for resistance to pathogens in a future acidified ocean.},
 bibtype = {article},
 author = {Hernroth, Bodil and Baden, Susanne and Thorndyke, Mike and Dupont, Sam},
 journal = {Aquatic toxicology (Amsterdam, Netherlands)},
 number = {3-4}
}

Paper  Website  abstract   bibtex   

@article{
 title = {iqr: A Tool for the Construction of Multi-level Simulations of Brain and Behaviour.},
 type = {article},
 year = {2010},
 identifiers = {[object Object]},
 keywords = {Access to Information,Animal,Animals,Behavior,Behavior: physiology,Brain,Brain: physiology,Computer Simulation,Humans,Insects,Internet,Memory,Memory: physiology,Models,Neurological,Neurons,Neurons: physiology,Robotics,Software,Synapses,Synapses: physiology,Time Factors,User-Computer Interface},
 pages = {113-34},
 volume = {8},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/20502987},
 publisher = {Humana Press Inc.},
 id = {59515ef3-1a82-3d32-b933-751e65c1b13e},
 created = {2016-02-18T20:36:44.000Z},
 file_attached = {true},
 profile_id = {666a093a-6015-3506-8b43-c65cadb20ea2},
 last_modified = {2017-03-09T23:31:28.082Z},
 read = {true},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Bernardet2010},
 source_type = {article},
 folder_uuids = {2e9f9bfc-4801-4871-9757-39a0ad79563e,79387ff2-9353-4bd0-8477-6c81b81f953f},
 abstract = {The brain is the most complex system we know of. Despite the wealth of data available in neuroscience, our understanding of this system is still very limited. Here we argue that an essential component in our arsenal of methods to advance our understanding of the brain is the construction of artificial brain-like systems. In this way we can encompass the multi-level organisation of the brain and its role in the context of the complete embodied real-world and real-time perceiving and behaving system. Hence, on the one hand, we must be able to develop and validate theories of brains as closing the loop between perception and action, and on the other hand as interacting with the real world. Evidence is growing that one of the sources of the computational power of neuronal systems lies in the massive and specific connectivity, rather than the complexity of single elements. To meet these challenges-multiple levels of organisation, sophisticated connectivity, and the interaction of neuronal models with the real-world-we have developed a multi-level neuronal simulation environment, iqr. This framework deals with these requirements by directly transforming them into the core elements of the simulation environment itself. iqr provides a means to design complex neuronal models graphically, and to visualise and analyse their properties on-line. In iqr connectivity is defined in a flexible, yet compact way, and simulations run at a high speed, which allows the control of real-world devices-robots in the broader sense-in real-time. The architecture of iqr is modular, providing the possibility to write new neuron, and synapse types, and custom interfaces to other hardware systems. The code of iqr is publicly accessible under the GNU General Public License (GPL). iqr has been in use since 1996 and has been the core tool for a large number of studies ranging from detailed models of neuronal systems like the cerebral cortex, and the cerebellum, to robot based models of perception, cognition and action to large-scale real-world systems. In addition, iqr has been widely used over many years to introduce students to neuronal simulation and neuromorphic control. In this paper we outline the conceptual and methodological background of iqr and its design philosophy. Thereafter we present iqr's main features and computational properties. Finally, we describe a number of projects using iqr, singling out how iqr is used for building a "synthetic insect".},
 bibtype = {article},
 author = {Bernardet, Ulysses and Verschure, Paul F.M.J.},
 journal = {Neuroinformatics},
 number = {2}
}

@article{bessell_estimating_2010,
	title = {Estimating risk factors for farm-level transmission of disease: foot and mouth disease during the 2001 epidemic in {Great} {Britain}.},
	volume = {2},
	copyright = {Copyright (c) 2010 Elsevier B.V. All rights reserved.},
	issn = {1878-0067 1878-0067},
	doi = {10.1016/j.epidem.2010.06.002},
	abstract = {Controlling an epidemic would be aided by establishing whether particular individuals in infected populations are more likely to transmit infection. However, few analyses have characterised such individuals. Such analyses require  both data on who infected whom and on the likely determinants of transmission; data that are available at the farm level for the 2001 Foot and Mouth Disease epidemic in Great Britain. Using these data a putative number of daughter infected premises (IPs) resulting from each IP was calculated where these daughters were within 3km of the IP. A set of possible epidemiological, demographic, spatial and temporal risk factors were analysed, with the final multivariate generalised linear model (Poisson error term) having 6 statistically significant (p{\textless}0.05) main effects including geographic area, local cattle and sheep densities, and the number of non-IP culls. This model demonstrates that farms are heterogeneous in their propensity to transmit infection to other farms  and, importantly, that it may be possible to identify holdings that are at high risk of spreading disease a priori. Such information could be used to help prioritise the response to an epidemic.},
	language = {eng},
	number = {3},
	journal = {Epidemics},
	author = {Bessell, Paul R. and Shaw, Darren J. and Savill, Nicholas J. and Woolhouse, Mark E. J.},
	month = sep,
	year = {2010},
	pmid = {21352781},
	keywords = {Animal Husbandry, Animals, Cattle, Epidemics/prevention \& control/statistics \& numerical data/*veterinary, Foot-and-Mouth Disease Virus/physiology, Foot-and-Mouth Disease/epidemiology/*transmission, Models, Biological, Multivariate Analysis, Poisson Distribution, Risk Factors, Sheep, United Kingdom/epidemiology},
	pages = {109--115}
}

@article{hofmann_living_2010,
	title = {Living in the now: {Physiological} mechanisms to tolerate a rapidly changing environment.},
	volume = {72},
	journal = {Annual Review of Physiology},
	author = {Hofmann, G. E. and Todgham, A. E.},
	year = {2010},
	keywords = {disturbance, MCR, populations}
}

Paper  doi  abstract   bibtex   

@article{nishijima_association_2010,
	title = {Association of thioautotrophic bacteria with deep-sea sponges.},
	volume = {12},
	issn = {1436-2236},
	url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2891489&tool=pmcentrez&rendertype=abstract},
	doi = {10.1007/s10126-009-9253-7},
	abstract = {We investigated microorganisms associated with a deep-sea sponge, Characella sp. (Pachastrellidae) collected at a hydrothermal vent site (686 m depth) in the Sumisu Caldera, Ogasawara Island chain, Japan, and with two sponges, Pachastrella sp. (Pachastrellidae) and an unidentified Poecilosclerida sponge, collected at an oil seep (572 m depth) in the Gulf of Mexico, using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) directed at bacterial 16S rRNA gene sequences. In the PCR-DGGE profiles, we detected a single clearly dominant band in each of the Characella sp. and the unidentified Poecilosclerida sponge. BLAST search of their sequences showed that they were most similar ({\textgreater}99\% identity) to those of the gammaproteobacterial thioautotrophic symbionts of deep-sea bivalves from hydrothermal vents, Bathymodiolus spp. Phylogenetic analysis of the near-full length sequences of the 16S rRNA genes cloned from the unidentified Poecilosclerida sponge and Characella sp. confirmed that they were closely related to thioautotrophic symbionts. Although associations between sponges and methanotrophic bacteria have been reported previously, this is the first report of a possible stable association between sponges and thioautotrophic bacteria.},
	number = {3},
	journal = {Marine biotechnology (New York, N.Y.)},
	author = {Nishijima, Miyuki and Lindsay, Dhugal J and Hata, Junko and Nakamura, Aoi and Kasai, Hiroaki and Ise, Yuji and Fisher, Charles R and Fujiwara, Yoshihiro and Kawato, Masaru and Maruyama, Tadashi},
	month = jun,
	year = {2010},
	keywords = {16S, 16S: genetics, Animals, Bacteria, Bacteria: classification, Bacteria: genetics, Bacteria: isolation \& purification, Bacterial, Bacterial: genetics, Ecosystem, Electrophoresis, Gel, Geological Phenomena, Nucleic Acid Denaturation, Oceans and Seas, Phylogeny, Polymerase Chain Reaction, Porifera, Porifera: microbiology, RNA, Ribosomal, Symbiosis, Two-Dimensional, misaki},
	pages = {253--60}
}

Paper  doi  abstract   bibtex   

@article{lotufo_benthic_2010,
	title = {Benthic bioaccumulation and bioavailability of polybrominated diphenyl ethers from surficial {Lake} {Ontario} sediments near {Rochester}, {New} {York}, {USA}.},
	volume = {85},
	issn = {1432-0800},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/20658224},
	doi = {10.1007/s00128-010-0088-8},
	abstract = {Polybrominated diphenyl ethers in Lake Ontario watershed sediments were assessed for benthic bioavailability through the use of biota-sediment accumulation factors. Sediments from lake and Rochester Harbor (lower Genesee River) areas were investigated. Congeners 47, 66, 85, 99 and 100 were detected in tissues of the oligochaete Lumbriculus variegatus. Biota-sediment accumulation factors ranged from 3.95 (congener 154) to 19.5 (congener 28) and were higher at the Lake Ontario area. The lower biota-sediment accumulation factors for the Rochester Harbor sediment may result from a higher fraction of black carbon generally expected in highly urbanized rivers. Degree of bromination may reduce bioavailability.},
	number = {3},
	journal = {Bulletin of environmental contamination and toxicology},
	author = {Lotufo, G R and Pickard, S W},
	month = sep,
	year = {2010},
	pmid = {20658224},
	keywords = {Animals, Chemical, Chemical: analysis, Chemical: metabolism, Environmental Monitoring, Flame Retardants: analysis, Flame Retardants: metabolism, Flame retardants, Fresh Water, Fresh Water: chemistry, Geologic Sediments, Geologic Sediments: chemistry, Halogenated Diphenyl Ethers, Halogenated Diphenyl Ethers: analysis, Halogenated Diphenyl Ethers: metabolism, New York, Oligochaeta, Oligochaeta: metabolism, Water Pollutants},
	pages = {348--51}
}

Paper  doi  abstract   bibtex   

@article{schecter_polybrominated_2010-1,
	title = {Polybrominated diphenyl ethers ({PBDEs}) and hexabromocyclodecane ({HBCD}) in composite {U}.{S}. food samples.},
	volume = {118},
	issn = {1552-9924},
	url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2854763&tool=pmcentrez&rendertype=abstract},
	doi = {10.1289/ehp.0901345},
	abstract = {This study was designed to update previous U.S. market basket surveys of levels and polybrominated diphenyl ether (PBDE) dietary intake calculations. This study also quantifies hexabromocyclododecane (HBCD) levels in U.S.-purchased foods for the first time and estimates U.S. dietary intake of HBCD. This is part of a larger market basket study reported in two companion articles, of current levels of certain persistent organic pollutants (POPs) PBDEs, HBCD, perfluorinated compounds, polychlorinated biphenyls, and pesticides in composite food samples collected in 2008-2009.},
	number = {3},
	journal = {Environmental health perspectives},
	author = {Schecter, Arnold and Haffner, Darrah and Colacino, Justin and Patel, Keyur and Päpke, Olaf and Opel, Matthias and Birnbaum, Linda},
	month = mar,
	year = {2010},
	pmid = {20064778},
	keywords = {Animals, Brominated, Brominated: analysis, Dairy Products, Dairy Products: analysis, Data Collection, Diet, Diet: classification, Fish Products, Fish Products: analysis, Flame Retardants: analysis, Flame retardants, Food Analysis, Food Contamination, Food Contamination: analysis, Halogenated Diphenyl Ethers, Halogenated Diphenyl Ethers: analysis, Hydrocarbons, Meat Products, Meat Products: analysis, United States},
	pages = {357--62}
}

Website  abstract   bibtex   

@article{
 title = {Conservation and divergence of methylation patterning in plants and animals.},
 type = {article},
 year = {2010},
 identifiers = {[object Object]},
 keywords = {Animals,Arabidopsis,Arabidopsis: genetics,DNA Methylation,DNA Methylation: genetics,Evolution,Exons,Exons: genetics,Introns,Introns: genetics,Molecular,Mutation,Mutation: genetics,Nucleic Acid,Nucleic Acid: genetics,Oligonucleotide Array Sequence Analysis,Open Reading Frames,Open Reading Frames: genetics,Phylogeny,Plants,Plants: genetics,Repetitive Sequences,Trans-Activators,Trans-Activators: genetics,Zebrafish,Zebrafish Proteins,Zebrafish Proteins: genetics,Zebrafish: genetics},
 pages = {8689-94},
 volume = {107},
 websites = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2889301&tool=pmcentrez&rendertype=abstract},
 month = {5},
 id = {547cadeb-6193-3fc8-9ebd-cf6d888d2748},
 created = {2017-10-14T10:53:29.339Z},
 file_attached = {false},
 profile_id = {57cbaa4c-3609-3597-b91c-bd12e56638fb},
 group_id = {b97159aa-8fdc-3227-aa16-9de80bf090dd},
 last_modified = {2017-10-14T10:53:29.339Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {Feng2010},
 source_type = {article},
 private_publication = {false},
 abstract = {Cytosine DNA methylation is a heritable epigenetic mark present in many eukaryotic organisms. Although DNA methylation likely has a conserved role in gene silencing, the levels and patterns of DNA methylation appear to vary drastically among different organisms. Here we used shotgun genomic bisulfite sequencing (BS-Seq) to compare DNA methylation in eight diverse plant and animal genomes. We found that patterns of methylation are very similar in flowering plants with methylated cytosines detected in all sequence contexts, whereas CG methylation predominates in animals. Vertebrates have methylation throughout the genome except for CpG islands. Gene body methylation is conserved with clear preference for exons in most organisms. Furthermore, genes appear to be the major target of methylation in Ciona and honey bee. Among the eight organisms, the green alga Chlamydomonas has the most unusual pattern of methylation, having non-CG methylation enriched in exons of genes rather than in repeats and transposons. In addition, the Dnmt1 cofactor Uhrf1 has a conserved function in maintaining CG methylation in both transposons and gene bodies in the mouse, Arabidopsis, and zebrafish genomes.},
 bibtype = {article},
 author = {Feng, Suhua and Cokus, Shawn J and Zhang, Xiaoyu and Chen, Pao-Yang and Bostick, Magnolia and Goll, Mary G and Hetzel, Jonathan and Jain, Jayati and Strauss, Steven H and Halpern, Marnie E and Ukomadu, Chinweike and Sadler, Kirsten C and Pradhan, Sriharsa and Pellegrini, Matteo and Jacobsen, Steven E},
 journal = {Proceedings of the National Academy of Sciences of the United States of America},
 number = {19}
}

Paper  Website  abstract   bibtex   

@article{
 title = {Perspectives on carbonic anhydrase.},
 type = {article},
 year = {2010},
 identifiers = {[object Object]},
 keywords = {Animals,Carbonic Anhydrase Inhibitors,Carbonic Anhydrase Inhibitors: pharmacology,Carbonic Anhydrase Inhibitors: therapeutic use,Carbonic Anhydrases,Carbonic Anhydrases: blood,Carbonic Anhydrases: physiology,Humans,Isoenzymes,Isoenzymes: physiology,Species Specificity},
 pages = {193-7},
 volume = {157},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/20541618},
 month = {11},
 publisher = {Elsevier Inc.},
 id = {11e52690-fbac-3475-a0e4-050cbfda485f},
 created = {2012-12-06T09:11:04.000Z},
 accessed = {2012-11-07},
 file_attached = {true},
 profile_id = {0b777e31-8c9d-39dd-97a3-3e054bd99cfe},
 group_id = {764582e8-5773-3a66-8d6b-9b40e4fb5a88},
 last_modified = {2017-03-14T17:27:14.020Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {Gilmour2010a},
 abstract = {In the years since Larimer and Schmidt-Nielsen published their examination of red blood cell (RBC) carbonic anhydrase (CA) activities as a function of body mass in mammals, our knowledge of CA has expanded dramatically. We are now aware of the diversity of CA isoforms and their implication in a wide array of physiological processes. The catalytic mechanism of CA has been described, and numerous compounds that function as activators or inhibitors of CA activity have been identified. CA is investigated as a diagnostic tumor marker, and CA inhibitors are used or emerging as clinical treatments for diseases as diverse as glaucoma, cancer and obesity. Yet despite the intensity of research effort over the last 50years and the wealth of information that has accumulated, the questions asked by Larimer and Schmidt-Nielsen remain relevant today - we still have much to learn about the patterns and physiological significance of interspecific differences in CA expression and activity.},
 bibtype = {article},
 author = {Gilmour, K M},
 journal = {Comparative biochemistry and physiology. Part A, Molecular & integrative physiology},
 number = {3}
}

Paper  Website  abstract   bibtex   

@article{
 title = {Structure, composition and mechanical relations to function in sea urchin spine.},
 type = {article},
 year = {2010},
 identifiers = {[object Object]},
 keywords = {Analysis of Variance,Animal Structures,Animal Structures: anatomy & histology,Animal Structures: metabolism,Animals,Anisotropy,Biomechanics,Magnesium,Magnesium: metabolism,Microscopy, Electron, Transmission,Sea Urchins,Sea Urchins: anatomy & histology,Sea Urchins: physiology,Spectrometry, X-Ray Emission,Spectrophotometry, Atomic},
 pages = {41-9},
 volume = {170},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/20064619},
 month = {4},
 publisher = {Elsevier Inc.},
 id = {c16e4f04-a7b7-3242-ab56-5bea7db2b124},
 created = {2014-11-18T15:01:22.000Z},
 accessed = {2012-10-04},
 file_attached = {true},
 profile_id = {c6c6f844-18d2-32db-a619-2e915134a952},
 group_id = {764582e8-5773-3a66-8d6b-9b40e4fb5a88},
 last_modified = {2017-03-14T17:27:14.020Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {Moureaux2010a},
 folder_uuids = {090e2126-2ea2-4873-99f4-533b24d0906f},
 abstract = {Sea urchins have characteristic spines that fulfil critical functions. Several studies revealed marked spine internal heterogeneities at different structural levels despite the single-crystal character of the spines. Most of these studies did not speculate about the functional meaning of these heterogeneities. Spine heterogeneities were investigated in the sea urchin Paracentrotuslividus and their possible functional implications discussed. Spines mainly show two morphological parts: the base, made of a meshwork stereom, and the shaft, with longitudinal plain septa and a central core of meshwork stereom. Electron Backscatter Diffraction showed no difference in crystallite orientation between the two structures. Atomic Absorption Spectrometry and Energy dispersive X-ray analysis revealed that Mg was not uniformly distributed in the spine. Mg concentration is higher in the inner part of the septa than in the septum outer part. Furthermore, a cyclic pattern of Mg concentration in septa was observed. This is suggested to be linked to the spine ontogeny. Nano- and microindentation analyses revealed that the septa have higher stiffness and hardness than the meshwork stereom and that septum stiffness and hardness present different trends in longitudinal and transverse section. These mechanical heterogeneities may have an adaptive functional value.},
 bibtype = {article},
 author = {Moureaux, C and Pérez-Huerta, a and Compère, P and Zhu, W and Leloup, T and Cusack, M and Dubois, P},
 journal = {Journal of structural biology},
 number = {1}
}

@article{ dufour-rainfray_behavior_2010,
  title = {Behavior and serotonergic disorders in rats exposed prenatally to valproate: a model for autism},
  volume = {470},
  issn = {1872-7972},
  shorttitle = {Behavior and serotonergic disorders in rats exposed prenatally to valproate},
  doi = {10.1016/j.neulet.2009.12.054},
  abstract = {In order to explore whether some aspects of the autistic phenotype could be related to impairment of the serotonergic system, we chose an animal model which mimics a potential cause of autism, i.e. rats exposed to valproate ({VPA}) on the 9th embryonic day (E9). Previous studies have suggested that {VPA} exposure in rats at E9 caused a dramatic shift in the distribution of serotonergic neurons on postnatal day 50 ({PND}50). Behavioral studies have also been performed but on rats that were exposed to {VPA} later (E12.5). Our aim was to test whether {VPA} exposure at E9 induces comparable behavioral impairments than at E12.5 and causes serotonergic impairments which could be related to behavioral modifications. The results showed significant behavioral impairments such as a lower tendency to initiate social interactions and hyperlocomotor activity in juvenile male rats. The serotonin levels of these animals at {PND}50 were decreased (-46%) in the hippocampus, a structure involved in social behavior. This study suggests that {VPA} could have a direct or indirect action on the serotonergic system as early as the progenitor cell stage. Early embryonic exposure to {VPA} in rats provides a good model for several specific aspects of autism and should help to continue to explore pathophysiological hypotheses.},
  language = {eng},
  number = {1},
  journal = {Neuroscience Letters},
  author = {Dufour-Rainfray, Diane and Vourc'h, Patrick and Le Guisquet, Anne-Marie and Garreau, Lucette and Ternant, David and Bodard, Sylvie and Jaumain, Emilie and Gulhan, Zuhal and Belzung, Catherine and Andres, Christian R. and Chalon, Sylvie and Guilloteau, Denis},
  month = {February},
  year = {2010},
  pmid = {20036713},
  keywords = {Animals, Autistic Disorder, Behavior, Animal, Brain, Disease Models, Animal, Female, {GABA} Agents, Hippocampus, Hydroxyindoleacetic Acid, Male, Motor Activity, Pregnancy, Prenatal Exposure Delayed Effects, {RNA}-Binding Proteins, Rats, Rats, Wistar, Serotonin, Social Behavior, Time Factors, Valproic Acid},
  pages = {55--59}
}

Paper  abstract   bibtex   

@article{
 title = {Impact of Bt -corn MON88017 in comparison to three conventional lines on Trigonotylus caelestialium (Kirkaldy) (Heteroptera: Miridae) field densities},
 type = {article},
 year = {2009},
 identifiers = {[object Object]},
 keywords = {Cyperales,Field Crops (FF005) (New March 2000),GMOs,Gene Transfer and Transgenics,Genetic Engineering,Hemiptera,Heteroptera,Hexapoda,Miridae,Plant Breeding and Genetics (FF020),Plant Pests (FF620) (New March 2000),Poaceae,Spermatophyta,Trigonotylus,Trigonotylus coelestialium,Zea,Zea mays,angiosperms,animals,arthropods,corn,eukaryotes,genetically engineered plants,genetically modified plants,insect pests,insects,invertebrates,maize,monocotyledons,nontarget effects,nontarget organisms,plant pests,plants,risk assessment,transgenic plants},
 pages = {203-214},
 volume = {18},
 websites = {http://www.lib.ncsu.edu/cgi-bin/proxy.pl?server=http://search.ebscohost.com/login.aspx?direct=true&db=lah&AN=20093111513&site=ehost-live&scope=site,http://springerlink.metapress.com/link.asp?id=100225,email: Rauschen@Bio5.RWTH-Aachen.de,http://dx.doi.org/10.1007/s11248-008-9207-2},
 publisher = {Springer},
 city = {Dordrecht; Netherlands},
 id = {2bf1f556-5022-3a78-85be-1603b6126276},
 created = {2012-01-05T13:08:45.000Z},
 file_attached = {true},
 profile_id = {1a467167-0a41-3583-a6a3-034c31031332},
 group_id = {0e532975-1a47-38a4-ace8-4fe5968bcd72},
 last_modified = {2015-03-05T16:02:07.000Z},
 tags = {Bt corn,Europe,Germany,environmental,habitat,non-target},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 abstract = {In Europe, Bt-corn resistant against the European Corn Borer has until now been the only genetically modified plant to be grown commercially. With the advent of the Western Corn Rootworm Bt-corn varieties with resistance against Coleoptera will become important. The cultivation of Bt-plants may have negative impacts on non-target organisms, i.e. all species not explicitly targeted by a given Bt-crop. One prominent non-target group in corn are the herbivorous plant bugs (Heteroptera: Miridae). They are common, abundant and exposed to the Cry-protein. We therefore assessed the potential impact of the cultivation of the Cry3Bb1-expressing Bt-corn variety MON88017 and three conventional varieties on this group. Trigonotylus caelestialium (Kirkaldy) was the most abundant plant bug at the experimental field. There was no evidence for a negative impact of MON88017 on this species, despite its considerable exposure to Cry3Bb1 demonstrated with ELISA. The conventional corn varieties, however, had a consistent and significant influence on the field densities of this species over all three growing seasons.},
 bibtype = {article},
 author = {Rauschen, Stefan and Schultheis, Eva and Pagel-Wieder, Sibylle and Schuphan, Ingolf and Eber, Sabine},
 journal = {Transgenic Research},
 number = {2}
}

Paper  Website  abstract   bibtex   

@article{
 title = {The effect of CO2 acidified sea water and reduced salinity on aspects of the embryonic development of the amphipod Echinogammarus marinus (Leach).},
 type = {article},
 year = {2009},
 identifiers = {[object Object]},
 keywords = {Amphipoda,Amphipoda: growth & development,Animals,Carbon Dioxide,Carbon Dioxide: chemistry,Female,Hydrogen-Ion Concentration,Salinity,Seawater,Seawater: chemistry},
 pages = {1187-91},
 volume = {58},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/19541328},
 month = {8},
 publisher = {Elsevier Ltd},
 id = {0111b01d-a0b1-333f-b64e-06e303ba9515},
 created = {2012-12-06T09:10:32.000Z},
 accessed = {2010-07-14},
 file_attached = {true},
 profile_id = {0b777e31-8c9d-39dd-97a3-3e054bd99cfe},
 group_id = {764582e8-5773-3a66-8d6b-9b40e4fb5a88},
 last_modified = {2017-03-14T17:27:14.020Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {Egilsdottir2009b},
 abstract = {We investigated the effect of CO(2) acidified sea water (S=35, 22 and 10(PSU)) on embryonic development of the intertidal amphipod Echinogammarus marinus (Leach). Low pH, but not low salinity (22(PSU)), resulted in a more protracted embryonic development in situ although the effect was only evident at low salinity. However reduced salinity, not pH, exerted a strong significant effect, on numbers and calcium content of hatchlings. Females exposed to low salinity (10(PSU)) did not carry eggs through to hatching. There was no significant difference in the number of viable hatchlings between females cultured in 22 and 35(PSU) but the exoskeleton of the juveniles at 22(PSU) contained significantly less calcium. Ocean acidification may affect aspects of E. marinus development but exposure to realistic low salinities appear, in the short term, to be more important in impacting development than exposure to CO(2) acidified sea water at levels predicted for 300 years time.},
 bibtype = {article},
 author = {Egilsdottir, Hronn and Spicer, John I and Rundle, Simon D},
 journal = {Marine pollution bulletin},
 number = {8}
}

Paper  abstract   bibtex   

@article{Esposito2009,
  abstract = {Fluorescence microscopy is a non-invasive technique that allows high
	resolution imaging of cytoskeletal structures. Advances in the field
	of fluorescent labelling (e.g., fluorescent proteins, quantum dots,
	tetracystein domains) and optics (e.g., super-resolution techniques
	and quantitative methods) not only provide better images of the cytoskeleton,
	but also offer an opportunity to quantify the complex of molecular
	events that populate this highly organised, yet dynamic, structure.For
	instance, fluorescence lifetime imaging microscopy and Forster resonance
	energy transfer imaging allow mapping of protein-protein interactions;
	furthermore, techniques based on the measurement of photobleaching
	kinetics (e.g., fluorescence recovery after photobleaching, fluorescence
	loss in photobleaching, and fluorescence localisation after photobleaching)
	permit the characterisation of axonal transport and, more generally,
	diffusion of relevant biomolecules.Quantitative fluorescence microscopy
	techniques offer powerful tools for understanding the physiological
	and pathological roles of molecular machineries in the living cell.},
  added-at = {2010-12-14T18:12:02.000+0100},
  author = {Esposito, A. and Schlachter, S. and Schierle, G. S. and Elder, A. D. and Diaspro, A. and Wouters, F. S. and Kaminski, C. F. and Iliev, A. I.},
  biburl = {http://www.bibsonomy.org/bibtex/2e233c6531b3b38c0e14016d30b887410/pharmawuerz},
  endnotereftype = {Journal Article},
  interhash = {f0c57923ba9d698668d19dcc5a81ab70},
  intrahash = {e233c6531b3b38c0e14016d30b887410},
  issn = {1940-6029 (Electronic) 1940-6029 (Linking)},
  journal = {Methods Mol Biol},
  keywords = {imported},
  note = {Esposito, Alessandro Schlachter, Simon Schierle, Gabriele S Kaminski
	Elder, Alan D Diaspro, Alberto Wouters, Fred S Kaminski, Clemens
	F Iliev, Asparouh I Biotechnology and Biological Sciences Research
	Council/United Kingdom Research Support, Non-U.S. Gov't United States
	Methods in molecular biology (Clifton, N.J.) Methods Mol Biol. 2009;586:117-42.},
  pages = {117-42},
  shorttitle = {Quantitative fluorescence microscopy techniques},
  timestamp = {2010-12-14T18:12:10.000+0100},
  title = {Quantitative fluorescence microscopy techniques},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19768427},
  volume = 586,
  year = 2009
}

Paper  doi  bibtex   

@article{sims_processing_2009,
	title = {Processing the {H}3K36me3 signature.},
	volume = {41},
	issn = {1546-1718},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/19240748},
	doi = {10.1038/ng0309-270},
	number = {3},
	journal = {Nature genetics},
	author = {Sims, Robert J and Reinberg, Danny},
	month = mar,
	year = {2009},
	pmid = {19240748},
	keywords = {Animals, Biological, Caenorhabditis elegans, Caenorhabditis elegans: metabolism, Gene Expression Profiling, Gene Expression Regulation, Histone-Lysine N-Methyltransferase, Histones, Histones: chemistry, Histones: metabolism, Histones: physiology, Humans, Lysine, Lysine: metabolism, Metabolic Networks and Pathways, Metabolic Networks and Pathways: physiology, Methylation, Models, Post-Translational, Post-Translational: physiology, Protein Methyltransferases, Protein Methyltransferases: metabolism, Protein Processing},
	pages = {270--1}
}

Paper  Website  abstract   bibtex   

@article{
 title = {Scaling rules for the final decline to extinction.},
 type = {article},
 year = {2009},
 identifiers = {[object Object]},
 keywords = {Animals,Biological,Daphnia,Extinction,Models,Population Dynamics},
 pages = {1361-1367},
 volume = {276},
 websites = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2660959&tool=pmcentrez&rendertype=abstract},
 month = {4},
 day = {7},
 id = {194e4705-4398-3e27-b8ac-d3d2484ae811},
 created = {2012-03-21T15:22:14.000Z},
 accessed = {2012-03-03},
 file_attached = {true},
 profile_id = {8988cb35-8a91-3e80-98d8-a7359f954673},
 last_modified = {2016-09-02T19:26:59.000Z},
 tags = {drake-lab,nsf-nipt},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Griffen2009},
 abstract = {Space-time scaling rules are ubiquitous in ecological phenomena. Current theory postulates three scaling rules that describe the duration of a population's final decline to extinction, although these predictions have not previously been empirically confirmed. We examine these scaling rules across a broader set of conditions, including a wide range of density-dependent patterns in the underlying population dynamics. We then report on tests of these predictions from experiments using the cladoceran Daphnia magna as a model. Our results support two predictions that: (i) the duration of population persistence is much greater than the duration of the final decline to extinction and (ii) the duration of the final decline to extinction increases with the logarithm of the population's estimated carrying capacity. However, our results do not support a third prediction that the duration of the final decline scales inversely with population growth rate. These findings not only support the current standard theory of population extinction but also introduce new empirical anomalies awaiting a theoretical explanation.},
 bibtype = {article},
 author = {Griffen, Blaine D and Drake, John M},
 journal = {Proceedings of the Royal Society, Series B},
 number = {1660}
}

Paper  Website  abstract   bibtex   

@article{
 title = {Retinoic acid promotes limb induction through effects on body axis extension but is unnecessary for limb patterning.},
 type = {article},
 year = {2009},
 identifiers = {[object Object]},
 keywords = {Aldehyde Oxidoreductases,Aldehyde Oxidoreductases: genetics,Aldehyde Oxidoreductases: metabolism,Animals,Body Patterning,Body Patterning: physiology,Embryo, Mammalian,Embryo, Mammalian: anatomy & histology,Embryo, Mammalian: drug effects,Embryo, Mammalian: physiology,Embryonic Induction,Extremities,Extremities: anatomy & histology,Extremities: embryology,Fibroblast Growth Factor 8,Fibroblast Growth Factor 8: genetics,Fibroblast Growth Factor 8: metabolism,Limb Buds,Limb Buds: physiology,Mice,Mice, Knockout,Retinal Dehydrogenase,Signal Transduction,Signal Transduction: physiology,Tretinoin,Tretinoin: pharmacology},
 pages = {1050-7},
 volume = {19},
 websites = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2701469&tool=pmcentrez&rendertype=abstract},
 month = {7},
 publisher = {Elsevier Ltd},
 day = {23},
 id = {515e0bca-299c-394e-b95d-ed7a2b842bc8},
 created = {2016-04-08T12:19:45.000Z},
 accessed = {2014-03-31},
 file_attached = {true},
 profile_id = {994bc413-6766-31df-917a-32165aa30f6c},
 group_id = {cec5aa9e-65e1-3c21-bc44-78fa6504020e},
 last_modified = {2017-03-14T10:42:46.538Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {Zhao2009},
 folder_uuids = {37786225-e8d4-483b-be04-dfc97f200748},
 private_publication = {false},
 abstract = {Retinoic acid (RA) is thought to be a key signaling molecule involved in limb bud patterning along the proximodistal or anteroposterior axes functioning through induction of Meis2 and Shh, respectively. Here, we utilize Raldh2-/- and Raldh3-/- mouse embryos lacking RA synthesis to demonstrate that RA signaling is not required for limb expression of Shh and Meis2. We demonstrate that RA action is required outside of the limb field in the body axis during forelimb induction but that RA is unnecessary at later stages when hindlimb budding and patterning occur. We provide evidence for a model of trunk mesodermal RA action in which forelimb induction requires RA repression of Fgf8 in the developing trunk similar to how RA controls somitogenesis and heart development. We demonstrate that pectoral fin development in RA-deficient zebrafish embryos can be rescued by an FGF receptor antagonist SU5402. In addition, embryo ChIP assays demonstrate that RA receptors bind the Fgf8 promoter in vivo. Our findings suggest that RA signaling is not required for limb proximodistal or anteroposterior patterning but that RA inhibition of FGF8 signaling during the early stages of body axis extension provides an environment permissive for induction of forelimb buds.},
 bibtype = {article},
 author = {Zhao, Xianling and Sirbu, Ioan Ovidiu and Mic, Felix a and Molotkova, Natalia and Molotkov, Andrei and Kumar, Sandeep and Duester, Gregg},
 journal = {Current biology : CB},
 number = {12}
}

Paper  doi  abstract   bibtex   

@article{szabo_effects_2009,
	title = {Effects of perinatal {PBDE} exposure on hepatic phase {I}, phase {II}, phase {III}, and deiodinase 1 gene expression involved in thyroid hormone metabolism in male rat pups.},
	volume = {107},
	issn = {1096-0929},
	url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2638650&tool=pmcentrez&rendertype=abstract},
	doi = {10.1093/toxsci/kfn230},
	abstract = {Previous studies demonstrated that perinatal exposure to polybrominated diphenyl ethers (PBDEs), a major class of brominated flame retardants, may affect thyroid hormone (TH) concentrations by inducing hepatic uridinediphosphate-glucoronosyltransferases (UGTs). This study further examines effects of the commercial penta mixture, DE-71, on genes related to TH metabolism at different developmental time points in male rats. DE-71 is predominately composed of PBDE congeners 47, 99, 100, 153, 154 with low levels of brominated dioxin and dibenzofuran contaminants. Pregnant Long-Evans rats were orally administered 1.7 (low), 10.2 (mid), or 30.6 (high) mg/kg/day of DE-71 in corn oil from gestational day (GD) 6 to postnatal day (PND) 21. Serum and liver were collected from male pups at PND 4, 21, and 60. Total serum thyroxine (T(4)) decreased to 57\% (mid) and 51\% (high) on PND 4, and 46\% (mid) dose and 25\% (high) on PND 21. Cyp1a1, Cyp2b1/2, and Cyp3a1 enzyme and mRNA expression, regulated by aryl hydrocarbon receptor, constitutive androstane receptor, and pregnane xenobiotic receptor, respectively, increased in a dose-dependent manner. UGT-T(4) enzymatic activity significantly increased, whereas age and dose-dependent effects were observed for Ugt1a6, 1a7, and 2b mRNA. Sult1b1 mRNA expression increased, whereas that of transthyretin (Ttr) decreased as did both the deiodinase I (D1) enzyme activity and mRNA expression. Hepatic efflux transporters Mdr1 (multidrug resistance), Mrp2 (multidrug resistance-associated protein), and Mrp3 and influx transporter Oatp1a4 mRNA expression increased. In this study the most sensitive responses to PBDEs following DE-71 exposure were CYP2B and D1 activities and Cyb2b1/2, d1, Mdr1, Mrp2, and Mrp3 gene expression. All responses were reversible by PND 60. In conclusion, deiodination, active transport, and sulfation, in addition to glucuronidation, may be involved in disruption of TH homeostasis due to perinatal exposure to DE-71 in male rat offspring.},
	number = {1},
	journal = {Toxicological sciences},
	author = {Szabo, David T and Richardson, Vicki M and Ross, David G and Diliberto, Janet J and Kodavanti, Prasada R S and Birnbaum, Linda S},
	month = jan,
	year = {2009},
	pmid = {18978342},
	keywords = {Analysis of Variance, Animals, Aryl Hydrocarbon Hydroxylases, Aryl Hydrocarbon Hydroxylases: genetics, Aryl Hydrocarbon Hydroxylases: metabolism, Developmental, Developmental: drug ef, Female, Flame Retardants: administration \& dosage, Flame Retardants: toxicity, Flame retardants, Gene Expression Regulation, Gene Expression Regulation: drug effects, Glucuronosyltransferase, Glucuronosyltransferase: genetics, Glucuronosyltransferase: metabolism, Halogenated Diphenyl Ethers, Halogenated Diphenyl Ethers: administration \& dosa, Halogenated Diphenyl Ethers: toxicity, Liver, Liver: chemistry, Long-Evans, Male, Microsomes, Newborn, Pregnancy, Rats, Sulfotransferases, Sulfotransferases: genetics, Sulfotransferases: metabolism, Thyroxine, Thyroxine: analysis, Thyroxine: blood, Triiodothyronine, Triiodothyronine: analysis, Triiodothyronine: blood, ffr, tox},
	pages = {27--39}
}

Website  abstract   bibtex   

@article{
 title = {Clonogenic multiple myeloma progenitors, stem cell properties, and drug resistance.},
 type = {article},
 year = {2008},
 identifiers = {[object Object]},
 keywords = {Animals,Antigens,Antineoplastic Agents,Antineoplastic Agents: pharmacology,B-Lymphocytes,B-Lymphocytes: pathology,Boronic Acids,Boronic Acids: pharmacology,CD20,CD20: analysis,CD27,CD27: analysis,Clone Cells,Clone Cells: drug effects,Clone Cells: pathology,Cyclophosphamide,Cyclophosphamide: analogs & derivatives,Cyclophosphamide: pharmacology,Dexamethasone,Dexamethasone: pharmacology,Drug Resistance,Humans,Inbred Strains,Mice,Multiple Myeloma,Multiple Myeloma: pathology,Neoplasm,Neoplastic Stem Cells,Neoplastic Stem Cells: drug effects,Neoplastic Stem Cells: pathology,Plasma Cells,Plasma Cells: drug effects,Plasma Cells: pathology,Pyrazines,Pyrazines: pharmacology,Syndecan-1,Syndecan-1: analysis,Thalidomide,Thalidomide: analogs & derivatives,Thalidomide: pharmacology,Tumor Stem Cell Assay},
 pages = {190-7},
 volume = {68},
 websites = {http://cancerres.aacrjournals.org/content/68/1/190.full},
 month = {1},
 day = {1},
 id = {494ed8c9-5c08-3403-8b42-0d004f92312a},
 created = {2016-06-24T20:49:19.000Z},
 accessed = {2014-11-18},
 file_attached = {false},
 profile_id = {954a987f-819f-3985-95a4-2991e0cf0552},
 group_id = {8440dcff-74cc-3783-aef7-fe2749cfc7ef},
 last_modified = {2016-06-24T20:49:19.000Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {Matsui2008},
 abstract = {Many agents are active in multiple myeloma, but the majority of patients relapse. This clinical pattern suggests most cancer cells are eliminated, but cells with the clonogenic potential to mediate tumor regrowth are relatively chemoresistant. Our previous data suggested that CD138(+) multiple myeloma plasma cells cannot undergo long-term proliferation but rather arise from clonogenic CD138(neg) B cells. We compared the relative sensitivity of these distinct cell types to clinical antimyeloma agents and found that dexamethasone, lenadilomide, bortezomib, and 4-hydroxycyclophosphamide inhibited CD138(+) multiple myeloma plasma cells but had little effect on CD138(neg) precursors in vitro. We further characterized clonogenic multiple myeloma cells and stained cell lines using the Hoechst side population and Aldefluor assays. Each assay identified CD138(neg) cells suggesting that they possess high drug efflux capacity and intracellular drug detoxification activity. We also found that multiple myeloma cells expressing the memory B-cell markers CD20 and CD27 could give rise to clonogenic multiple myeloma growth in vitro and engraft immunodeficient nonobese diabetes/severe combined immunodeficient mice during both primary and secondary transplantation. Furthermore, both the side population and Aldefluor assays were capable of identifying circulating clonotypic memory B-cell populations within the peripheral blood of multiple myeloma patients. Our results suggest that circulating clonotypic B-cell populations represent multiple myeloma stem cells, and the relative drug resistance of these cells is mediated by processes that protect normal stem cells from toxic injury.},
 bibtype = {article},
 author = {Matsui, William and Wang, Qiuju and Barber, James P and Brennan, Sarah and Smith, B Douglas and Borrello, Ivan and McNiece, Ian and Lin, Lan and Ambinder, Richard F and Peacock, Craig and Watkins, D Neil and Huff, Carol Ann and Jones, Richard J},
 journal = {Cancer research},
 number = {1}
}

Paper  Website  bibtex   

@article{
 title = {Molecular aspects of biomineralization of the echinoderm endoskeleton.},
 type = {article},
 year = {2008},
 identifiers = {[object Object]},
 keywords = {Animals,Echinodermata,Echinodermata: anatomy & histology,Echinodermata: embryology,Echinodermata: genetics,Echinodermata: metabolism,Evolution, Molecular,Humans,Minerals,Minerals: chemistry,Minerals: metabolism,Proteins,Proteins: genetics,Proteins: metabolism,Skeleton},
 pages = {4463-74},
 volume = {108},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/18821807},
 month = {11},
 id = {c18795b2-be8e-3cb2-bc9c-c4c8a26f9cca},
 created = {2012-12-06T09:12:59.000Z},
 file_attached = {true},
 profile_id = {0b777e31-8c9d-39dd-97a3-3e054bd99cfe},
 group_id = {764582e8-5773-3a66-8d6b-9b40e4fb5a88},
 last_modified = {2017-03-14T17:27:14.020Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {Killian2008b},
 bibtype = {article},
 author = {Killian, Christopher E and Wilt, Fred H},
 journal = {Chemical reviews},
 number = {11}
}

Website  abstract   bibtex   

@article{
 title = {Visualizing cold spots: TRPM8-expressing sensory neurons and their projections.},
 type = {article},
 year = {2008},
 identifiers = {[object Object]},
 keywords = {Afferent Pathways,Afferent Pathways: metabolism,Animals,Antipruritics,Antipruritics: pharmacology,Blood Vessels,Blood Vessels: innervation,Blood Vessels: metabolism,Calcitonin Gene-Related Peptide,Calcitonin Gene-Related Peptide: metabolism,Capsaicin,Capsaicin: pharmacology,Cells, Cultured,Cold Temperature,Ganglia, Spinal,Ganglia, Spinal: cytology,Gene Expression Regulation,Gene Expression Regulation: drug effects,Gene Expression Regulation: physiology,Green Fluorescent Proteins,Green Fluorescent Proteins: genetics,Green Fluorescent Proteins: metabolism,Menthol,Menthol: pharmacology,Mice,Mice, Inbred C57BL,Mice, Transgenic,Neurons, Afferent,Neurons, Afferent: cytology,Neurons, Afferent: drug effects,Neurons, Afferent: physiology,Spinal Cord,Spinal Cord: cytology,Spinal Cord: physiology,TRPM Cation Channels,TRPM Cation Channels: deficiency,TRPM Cation Channels: metabolism,TRPV Cation Channels,TRPV Cation Channels: metabolism},
 pages = {566-75},
 volume = {28},
 websites = {http://www.jneurosci.org/content/28/3/566.long},
 month = {1},
 day = {16},
 id = {4d21c71d-9f99-3b94-b72a-2b06dbb03877},
 created = {2016-02-10T11:58:54.000Z},
 accessed = {2016-02-10},
 file_attached = {false},
 profile_id = {3e449d8a-90c5-35f9-aaa3-cdbb3ca120e9},
 group_id = {2ad31c26-29a3-3f9c-b495-1b90dc1c4bb6},
 last_modified = {2016-02-10T11:58:54.000Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 abstract = {Environmental stimuli such as temperature and pressure are sensed by dorsal root ganglion (DRG) neurons. DRG neurons are heterogeneous, but molecular markers that identify unique functional subpopulations are mainly lacking. ThermoTRPs are members of the transient receptor potential family of ion channels and are gated by shifts in temperature. TRPM8 is activated by cooling, and TRPM8-deficient mice have severe deficits in cool thermosensation. The anatomical and functional properties of TRPM8-expressing fibers have not been not comprehensively investigated. We use mice engineered to express the farnesylated enhanced green fluorescent protein (EGFPf) from the TRPM8 locus (TRPM8(EGFPf)) to explore this issue. Virtually all EGFPf-positive cultured DRG neurons from hemizygous mice (TRPM8(EGFPf/+)) responded to cold and menthol. In contrast, EGFPf-positive DRGs from homozygous mice (TRPM8(EGFPf/EGFPf)) had drastically reduced cold responses and no menthol responses. In vivo, EGFPf-positive neurons marked a unique population of DRG neurons, a majority of which do not coexpress nociceptive markers. The fraction of DRG neurons expressing EGFPf was not altered under an inflammatory condition, although an increase in TRPV1-coexpressing neurons was observed. TRPM8(EGFPf) neurons project to the superficial layer I of the spinal cord, making distinct contacts when compared with peptidergic projections. At the periphery, TRPM8(EGFPf) projections mark unique endings in the most superficial layers of epidermis, including bush/cluster endings of the mystacial pads. We show that TRPM8 expression functionally associates with cold sensitivity in cultured DRGs, and provide the first glimpses of the unique anatomical architecture of cold fibers in vivo.},
 bibtype = {article},
 author = {Dhaka, Ajay and Earley, Taryn J and Watson, James and Patapoutian, Ardem},
 journal = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
 number = {3}
}

Paper  Website  abstract   bibtex   

@article{
 title = {Effects of anthropogenic seawater acidification on acid-base balance in the sea urchin Psammechinus miliaris.},
 type = {article},
 year = {2007},
 identifiers = {[object Object]},
 keywords = {Acid-Base Equilibrium,Acid-Base Equilibrium: physiology,Animals,Bicarbonates,Bicarbonates: analysis,Carbon Dioxide,Carbon Dioxide: analysis,Carbon Dioxide: physiology,Hydrogen-Ion Concentration,Magnesium,Magnesium: analysis,Sea Urchins,Sea Urchins: metabolism,Seawater,Seawater: chemistry},
 pages = {89-96},
 volume = {54},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/17083950},
 month = {1},
 id = {630102e9-9501-3c53-bf49-3f49073c5f86},
 created = {2012-12-06T09:13:40.000Z},
 accessed = {2012-10-30},
 file_attached = {true},
 profile_id = {0b777e31-8c9d-39dd-97a3-3e054bd99cfe},
 group_id = {764582e8-5773-3a66-8d6b-9b40e4fb5a88},
 last_modified = {2017-03-14T17:27:14.020Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {Miles2007},
 abstract = {The purple-tipped sea urchin, Psammechinus miliaris, was exposed to artificially acidified seawater treatments (pH(w) 6.16, 6.63 or 7.44) over a period of 8 days. Urchin mortality of 100% was observed at pH(w) 6.16 after 7 days and coincided with a pronounced hypercapnia in the coelomic fluid producing an irrecoverable acidosis. Coelomic fluid acid-base measures showed that an accumulation of CO(2) and a significant reduction in pH occurred in all treatments compared with controls. Bicarbonate buffering was employed in each case, reducing the resultant acidosis, but compensation was incomplete even under moderate environmental hypercapnia. Significant test dissolution was inferred from observable increases in the Mg(2+) concentration of the coelomic fluid under all pH treatments. We show that a chronic reduction of surface water pH to below 7.5 would be severely detrimental to the acid-base balance of this predominantly intertidal species; despite its ability to tolerate fluctuations in pCO(2) and pH in the rock pool environment. The absence of respiratory pigment (or any substantial protein in the coelomic fluid), a poor capacity for ionic regulation and dependency on a magnesium calcite test, make echinoids particularly vulnerable to anthropogenic acidification. Geological sequestration leaks may result in dramatic localised pH reductions, e.g. pH 5.8. P. miliaris is intolerant of pH 6.16 seawater and significant mortality is seen at pH 6.63.},
 bibtype = {article},
 author = {Miles, Hayley and Widdicombe, Stephen and Spicer, John I and Hall-Spencer, Jason},
 journal = {Marine pollution bulletin},
 number = {1}
}

@article{kiani_object_2007,
	title = {Object category structure in response patterns of neuronal population in monkey inferior temporal cortex},
	volume = {97},
	issn = {0022-3077},
	doi = {10.1152/jn.00024.2007},
	abstract = {Our mental representation of object categories is hierarchically organized, and our rapid and seemingly effortless categorization ability is crucial for our daily behavior. Here, we examine responses of a large number ({\textgreater}600) of neurons in monkey inferior temporal (IT) cortex with a large number ({\textgreater}1,000) of natural and artificial object images. During the recordings, the monkeys performed a passive fixation task. We found that the categorical structure of objects is represented by the pattern of activity distributed over the cell population. Animate and inanimate objects created distinguishable clusters in the population code. The global category of animate objects was divided into bodies, hands, and faces. Faces were divided into primate and nonprimate faces, and the primate-face group was divided into human and monkey faces. Bodies of human, birds, and four-limb animals clustered together, whereas lower animals such as fish, reptile, and insects made another cluster. Thus the cluster analysis showed that IT population responses reconstruct a large part of our intuitive category structure, including the global division into animate and inanimate objects, and further hierarchical subdivisions of animate objects. The representation of categories was distributed in several respects, e.g., the similarity of response patterns to stimuli within a category was maintained by both the cells that maximally responded to the category and the cells that responded weakly to the category. These results advance our understanding of the nature of the IT neural code, suggesting an inherently categorical representation that comprises a range of categories including the amply investigated face category.},
	language = {eng},
	number = {6},
	journal = {Journal of neurophysiology},
	author = {Kiani, Roozbeh and Esteky, Hossein and Mirpour, Koorosh and Tanaka, Keiji},
	month = jun,
	year = {2007},
	pmid = {17428910},
	keywords = {Action Potentials, Animals, Behavior, Animal, Brain Mapping, Cluster Analysis, Humans, Macaca mulatta, Neurons, Pattern Recognition, Visual, Photic Stimulation, Probability, Reaction Time, Temporal Lobe, Visual Pathways},
	pages = {4296--4309}
}

@article{keightley_joint_2007,
	title = {Joint inference of the distribution of fitness effects of deleterious mutations and population demography based on nucleotide polymorphism frequencies},
	volume = {177},
	issn = {0016-6731},
	doi = {10.1534/genetics.107.080663},
	abstract = {The distribution of fitness effects of new mutations (DFE) is important for addressing several questions in genetics, including the nature of quantitative variation and the evolutionary fate of small populations. Properties of the DFE can be inferred by comparing the distributions of the frequencies of segregating nucleotide polymorphisms at selected and neutral sites in a population sample, but demographic changes alter the spectrum of allele frequencies at both neutral and selected sites, so can bias estimates of the DFE if not accounted for. We have developed a maximum-likelihood approach, based on the expected allele-frequency distribution generated by transition matrix methods, to estimate parameters of the DFE while simultaneously estimating parameters of a demographic model that allows a population size change at some time in the past. We tested the method using simulations and found that it accurately recovers simulated parameter values, even if the simulated demography differs substantially from that assumed in our analysis. We use our method to estimate parameters of the DFE for amino acid-changing mutations in humans and Drosophila melanogaster. For a model of unconditionally deleterious mutations, with effects sampled from a gamma distribution, the mean estimate for the distribution shape parameter is approximately 0.2 for human populations, which implies that the DFE is strongly leptokurtic. For Drosophila populations, we estimate that the shape parameter is approximately 0.35. Differences in the shape of the distribution and the mean selection coefficient between humans and Drosophila result in significantly more strongly deleterious mutations in Drosophila than in humans, and, conversely, nearly neutral mutations are significantly less frequent.},
	language = {eng},
	number = {4},
	journal = {Genetics},
	author = {Keightley, Peter D. and Eyre-Walker, Adam},
	month = dec,
	year = {2007},
	pmid = {18073430},
	pmcid = {PMC2219502},
	keywords = {Amino Acid Substitution, Animals, Demography, Drosophila, Gene Frequency, Genetic, Humans, Likelihood Functions, Missense, Mutation, Polymorphism, Selection},
	pages = {2251--2261},
}

@article{ sibille_lack_2007,
  title = {Lack of serotonin1B receptor expression leads to age-related motor dysfunction, early onset of brain molecular aging and reduced longevity},
  volume = {12},
  issn = {1359-4184},
  doi = {10.1038/sj.mp.4001990},
  abstract = {Normal aging of the brain differs from pathological conditions and is associated with increased risk for psychiatric and neurological disorders. In addition to its role in the etiology and treatment of mood disorders, altered serotonin (5-{HT}) signaling is considered a contributing factor to aging; however, no causative role has been identified in aging. We hypothesized that a deregulation of the 5-{HT} system would reveal its contribution to age-related processes and investigated behavioral and molecular changes throughout adult life in mice lacking the regulatory presynaptic 5-{HT}(1B) receptor (5-{HT}(1B)R), a candidate gene for 5-{HT}-mediated age-related functions. We show that the lack of 5-{HT}(1B)R (Htr1b({KO}) mice) induced an early age-related motor decline and resulted in decreased longevity. Analysis of life-long transcriptome changes revealed an early and global shift of the gene expression signature of aging in the brain of Htr1b({KO}) mice. Moreover, molecular changes reached an apparent maximum effect at 18-months in Htr1b({KO}) mice, corresponding to the onset of early death in that group. A comparative analysis with our previous characterization of aging in the human brain revealed a phylogenetic conservation of age-effect from mice to humans, and confirmed the early onset of molecular aging in Htr1b({KO}) mice. Potential mechanisms appear independent of known central mechanisms (Bdnf, inflammation), but may include interactions with previously identified age-related systems ({IGF}-1, sirtuins). In summary, our findings suggest that the onset of age-related events can be influenced by altered 5-{HT} function, thus identifying 5-{HT} as a modulator of brain aging, and suggesting age-related consequences to chronic manipulation of 5-{HT}.},
  language = {eng},
  number = {11},
  journal = {Molecular Psychiatry},
  author = {Sibille, E. and Su, J. and Leman, S. and Le Guisquet, A. M. and Ibarguen-Vargas, Y. and Joeyen-Waldorf, J. and Glorioso, C. and Tseng, G. C. and Pezzone, M. and Hen, R. and Belzung, C.},
  month = {November},
  year = {2007},
  pmid = {17420766},
  pmcid = {PMC2515886},
  keywords = {Age Factors, Aging, Analysis of Variance, Animals, Animals, Newborn, Behavior, Animal, Dopamine Plasma Membrane Transport Proteins, Enzyme-Linked Immunosorbent Assay, Gene Expression, Gene Expression Regulation, Hand Strength, In Situ Hybridization, Maze Learning, Mice, Mice, Knockout, Microarray Analysis, Motor Activity, Reaction Time, Receptor, Serotonin, 5-{HT}1B, Survival Analysis},
  pages = {1042--1056, 975}
}

@Article{VonWegner_2007_5301,
  author = {Von Wegner, F. and Both, M. and Fink, R. H. and Friedrich, O.},
 journal = {IEEE Transactions on Medical Imaging},
 number = {7},
 pages = {925-34},
 title = {Fast XYT imaging of elementary calcium release events in muscle with multifocal multiphoton microscopy and wavelet denoising and detection},
 volume = {26},
 year = {2007},
 keywords = {Algorithms, Animals, Calcium/*metabolism, Calcium, Signaling/physiology, Cells, Cultured, Image, Enhancement/methods, Image, Interpretation, Computer-Assisted/*methods, Imaging, Three-Dimensional/methods, Metabolic, Clearance, Rate, Mice, Microscopy, Fluorescence, Multiphoton/*methods, Muscle, Fibers/*cytology/*metabolism, Muscle, Skeletal/*cytology/*metabolism, Reproducibility, of, Results, Sensitivity, and, Specificity},
 title_with_no_special_chars = {Fast XYT imaging of elementary calcium release events in muscle with multifocal multiphoton microscopy and wavelet denoising and detection}
}

Paper  doi  abstract   bibtex   

@article{viberg_neonatal_2006,
	title = {Neonatal exposure to higher brominated diphenyl ethers, hepta-, octa-, or nonabromodiphenyl ether, impairs spontaneous behavior and learning and memory functions of adult mice.},
	volume = {92},
	issn = {1096-6080},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/16611620},
	doi = {10.1093/toxsci/kfj196},
	abstract = {Polybrominated diphenyl ethers (PBDEs), used as flame retardants, have been shown to be increasing in the environment and in human mother's milk. We have earlier reported that lower brominated PBDEs, such as tetra-, penta-, and hexa-brominated diphenyl ethers, can cause developmental neurotoxic effects in mice. Recently, this was also observed with the full-brominated PBDE, deca-brominated diphenyl ether (PBDE 209), although it was suggested that the effects were caused by a (possibly debrominated) metabolite thereof. The present study revealed that 2,2',3,3',4,4',5,5',6-nonabromodiphenyl ether (PBDE 206), 2,2',3,4,4',5,5',6-octabromodiphenyl ether (PBDE 203), and to a minor extent also 2,2',3,4,4',5',6'-heptabromodiphenyl ether (PBDE 183) can induce developmental neurotoxic effects. Neonatal Naval Medical Research Institute male mice were exposed on postnatal day 3 or 10 to PBDE 206, PBDE 203, or PBDE 183, given as a single oral dose of 21 mumol/kg body weight. At the adult age of 2-3 months, the mice were observed for performance in a spontaneous behavior test and the Morris water maze test. PBDE 203 and PBDE 206, when administered on neonatal day 10, caused disturbances in spontaneous behavior, leading to disrupted habituation and a hyperactive condition in adults at the age of 2 months. These behavioral changes were also seen in 2-month-old mice exposed to PBDE 203 on neonatal day 3. Furthermore, exposure to PBDE 203 on neonatal day 10 affected learning and memory functions in adult mice. The developmental neurotoxic effects were most pronounced in mice exposed to PBDE 203. These developmental neurobehavioral defects were in agreement with those we observed previously with lower brominated PBDEs and with PBDE 209. It is important to consider the fact that different PBDE congeners can have differing degrees of potency, when comparing levels of PBDEs in the environment and in mother's milk.},
	number = {1},
	journal = {Toxicological sciences},
	author = {Viberg, Henrik and Johansson, Niclas and Fredriksson, Anders and Eriksson, Johan and Marsh, Göran and Eriksson, Per},
	month = jul,
	year = {2006},
	pmid = {16611620},
	keywords = {Animal, Animal: drug effects, Animals, Behavior, Ethers, Flame retardants, Learning, Learning: drug effects, Male, Memory, Memory: drug effects, Mice, Newborn, Polybrominated Biphenyls, Polybrominated Biphenyls: toxicity, frelec, tox},
	pages = {211--8}
}

Paper  Website  abstract   bibtex   

@article{
 title = {Maternal transfer of organohalogen contaminants and metabolites to eggs of Arctic-breeding glaucous gulls.},
 type = {article},
 year = {2006},
 identifiers = {[object Object]},
 keywords = {Animals,Arctic Regions,Biological Transport,Charadriiformes,Charadriiformes: metabolism,Eggs,Eggs: analysis,Environmental Monitoring,Environmental Monitoring: methods,Environmental Pollutants,Environmental Pollutants: analysis,Environmental Pollutants: blood,Environmental Pollutants: metabolism,Female,Gas Chromatography-Mass Spectrometry,Mothers,Norway,Pesticide Residues,Pesticide Residues: analysis,Pesticide Residues: blood,Pesticide Residues: metabolism,Polychlorinated Biphenyls,Polychlorinated Biphenyls: analysis,Polychlorinated Biphenyls: blood,Polychlorinated Biphenyls: metabolism},
 pages = {1053-60},
 volume = {144},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/16563578},
 month = {12},
 id = {740e5ba5-c77d-366e-a109-7383cb39d7ff},
 created = {2012-10-26T12:49:03.000Z},
 accessed = {2012-10-26},
 file_attached = {true},
 profile_id = {c6c6f844-18d2-32db-a619-2e915134a952},
 group_id = {764582e8-5773-3a66-8d6b-9b40e4fb5a88},
 last_modified = {2017-03-14T17:27:14.020Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {Verreault2006},
 abstract = {Eggs of seabirds have routinely been used as indicators of environmental pollution in the Arctic. However, the variability in organohalogen concentration and composition associated with the laying sequence, have not been defined. We examined a suite of PCBs, organochlorine (OC) pesticides and by-products, polybrominated diphenyl ethers (PBDEs), polybrominated biphenyls (PBBs) and methylsulfonyl- (MeSO2) PCBs in complete 3-egg clutches of glaucous gulls (Larus hyperboreus), and plasma samples of the laying females collected from the Norwegian Arctic. SigmaPCB, SigmaOC and SigmaPBDE, but not SigmaMeSO2-PCB, concentrations in eggs were positively associated, with increasing magnitude and significance from the first through the last-laid egg, with concentrations in female plasma. However, the concentrations of these organohalogen classes fluctuated irrespective of the laying order in the clutch. In general, maternal transfer favored low K(ow) and/or less persistent compounds, whereas the recalcitrant and/or higher-halogenated compounds were less readily transferred, and consequently more selectively retained in the mother.},
 bibtype = {article},
 author = {Verreault, Jonathan and Villa, Rosa a and Gabrielsen, Geir W and Skaare, Janneche U and Letcher, Robert J},
 journal = {Environmental pollution (Barking, Essex : 1987)},
 number = {3}
}

Paper  doi  abstract   bibtex   

@article{bayen_chlorinated_2006,
	title = {Chlorinated paraffins: a review of analysis and environmental occurrence.},
	volume = {32},
	issn = {0160-4120},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/16814386},
	doi = {10.1016/j.envint.2006.05.009},
	abstract = {Chlorinated paraffins (CPs), as technical mixtures of polychlorinated alkanes (PCAs), are ubiquitous in the environment. CPs tend to behave in a similar way to persistent organic pollutants (POPs), leading several countries to impose regulations on the use of CPs. In this article, we review the literature on the properties of CPs, the current analytical tools available to determine CPs in various types of environmental matrices, and concentrations found in the environment. In particular, concentrations of CPs in environmental compartments including air, water, sediments, biota, human food products and human tissues are summarized. Priorities for future research are: improvements in analytical methodologies (reducing the complexity of the analysis, producing reference materials and performing interlaboratory studies); determining background levels of chlorinated paraffins in the environment and human populations (this question should be answered using quality assured analytical tools allowing the intercomparison of data); and investigating the sources of CPs to the environment and to humans.},
	number = {7},
	journal = {Environment international},
	author = {Bayen, Stéphane and Obbard, Jeffrey Philip and Thomas, Gareth O},
	month = sep,
	year = {2006},
	pmid = {16814386},
	keywords = {Animals, Biodiversity, Chlorinated, Chlorinated: analysis, Chlorinated: chemistry, Environmental Monitoring, Environmental Monitoring: methods, Environmental Pollutants, Environmental Pollutants: analysis, Environmental Pollutants: chemistry, Flame retardants, Food, Humans, Hydrocarbons, Paraffin, Paraffin: analysis, Paraffin: chemistry, Principal Component Analysis, Principal Component Analysis: methods, Quality Control, Tissue Distribution},
	pages = {915--29}
}

Paper  Website  abstract   bibtex   

@article{
 title = {Bioaccumulation of PCBs in the cuttlefish Sepia officinalis from seawater, sediment and food pathways.},
 type = {article},
 year = {2005},
 identifiers = {[object Object]},
 keywords = {Animals,Environmental Monitoring,Environmental Monitoring: methods,Environmental Pollutants,Environmental Pollutants: analysis,Environmental Pollutants: pharmacokinetics,Food Chain,Geologic Sediments,Mollusca,Mollusca: chemistry,Mollusca: metabolism,Polychlorinated Biphenyls,Polychlorinated Biphenyls: analysis,Polychlorinated Biphenyls: pharmacokinetics,Seawater},
 pages = {113-22},
 volume = {134},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/15572229},
 month = {3},
 id = {9bd781c2-cfe1-3349-a68b-f151c790002a},
 created = {2010-09-15T14:45:54.000Z},
 accessed = {2010-09-15},
 file_attached = {true},
 profile_id = {c6c6f844-18d2-32db-a619-2e915134a952},
 last_modified = {2017-03-31T08:28:21.048Z},
 read = {true},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Danis2005a},
 folder_uuids = {b555a2ae-97cc-4492-ae3a-910c81afb80f,a6bf1321-9beb-4f7c-9715-6ab10e069d78},
 abstract = {The cuttlefish Sepia officinalis was selected as a model cephalopod to study PCB bioaccumulation via seawater, sediments and food. Newly hatched, juvenile cuttlefish were exposed for 17 days to environmentally realistic concentrations of (14)C-labeled 2,2',4,4',5,5'-hexachlorobiphenyl (PCB#153) (18 ng PCB l(-1) seawater; 30 ng PCB g(-1) dry wt sediments; Artemia salina exposed to 18 ng PCB l(-1) seawater). Accumulation of PCB#153 was followed in three body compartments: digestive gland, cuttlebone and the combined remaining tissues. Results showed that (1) uptake kinetics were source- and body compartment-dependent, (2) for each body compartment, the accumulation was far greater when S. officinalis was exposed via seawater, (3) the cuttlebone accumulated little of the contaminant regardless of the source, and (4) the PCB congener showed a similar distribution pattern among the different body compartments following exposure to contaminated seawater, sediment or food with the lowest concentrations in the cuttlebone and the highest in the remaining tissues. The use of radiotracer techniques allowed delineating PCB kinetics in small whole organisms as well as in their separate tissues. The results underscore the enhanced ability of cephalopods to concentrate organic pollutants such as PCBs, and raise the question of potential risk to their predators in contaminated areas.},
 bibtype = {article},
 author = {Danis, B and Bustamante, P and Cotret, O and Teyssié, J L and Fowler, S W and Warnau, M},
 journal = {Environmental pollution (Barking, Essex : 1987)},
 number = {1}
}

@Article{Granada_2005_989,
  author = {Granada, J.F. and Moreno, P.R. and Burke, A.P. and Schulz, D.G. and Raizner, A.E. and Kaluza, G.L.},
 journal = {Coronary Artery Dispatch},
 note = {DA - 20050525 NOT IN FILE},
 number = {4},
 pages = {217-224},
 title = {Endovascular needle injection of cholesteryl linoleate into the arterial wall produces complex vascular lesions identifiable by intravascular ultrasound: {E}arly development in a porcine model of vulnerable plaque},
 volume = {16},
 year = {2005},
 keywords = {analysis, Animals, Arteriosclerosis, Biopsy, Needle, Cholesterol, Esters, Comparative, Study, Coronary, Vessels, Disease, Models, Animal, Iliac, Artery, Immunohistochemistry, Injections, Intra-Arterial, methods, pathology, Probability, Research, Support, Non-U.S.Gov't, Sensitivity, and, Specificity, Sus, scrofa, Tunica, Intima, ultrasonography, Ultrasonography, Interventional},
 title_with_no_special_chars = {Endovascular needle injection of cholesteryl linoleate into the arterial wall produces complex vascular lesions identifiable by intravascular ultrasound Early development in a porcine model of vulnerable plaque}
}

@Article{Hartung_2005_994,
  author = {Hartung, D. and Sarai, M. and Petrov, A. and Kolodgie, F. and Narula, N. and Verjans, J. and Virmani, R. and Reutelingsperger, C. and Hofstra, L. and Narula, J.},
 journal = {J.Nucl.Med.},
 note = {DA - 20051206 NOT IN FILE},
 number = {12},
 pages = {2051-2056},
 title = {Resolution of apoptosis in atherosclerotic plaque by dietary modification and statin therapy},
 volume = {46},
 year = {2005},
 keywords = {Animal, Feed, Animals, Annexin, A5, Aorta, Apoptosis, Atherosclerosis, chemistry, Cholesterol, Coronary, Disease, drug, therapy, Female, Hydroxymethylglutaryl, CoA, Reductases, Hydroxymethylglutaryl-CoA, Reductase, Inhibitors, Immunohistochemistry, Incidence, Macrophages, Male, metabolism, methods, Mutation, pathology, pharmacokinetics, pharmacology, Rabbits, radionuclide, imaging, Recombinant, Proteins, Research, Support, N.I.H., Extramural, therapy},
 title_with_no_special_chars = {Resolution of apoptosis in atherosclerotic plaque by dietary modification and statin therapy}
}

@article{ matarazzo_functional_2005,
  title = {Functional characterization of two human olfactory receptors expressed in the baculovirus Sf9 insect cell system},
  volume = {30},
  issn = {0379-864X},
  doi = {10.1093/chemse/bji015},
  abstract = {Olfactory receptors ({ORs}) are the largest member of the G-protein-coupled receptors which mediate early olfactory perception in discriminating among thousands of odorant molecules. Assigning odorous ligands to {ORs} is a prerequisite to gaining an understanding of the mechanisms of odorant recognition. The functional expression of {ORs} represents a critical step in addressing this issue. Due to limitations in heterologous expression, very few mammal {ORs} have been characterized, and so far only one is from human origin. Consequently, {OR} function still remains poorly understood, especially in humans, whose genome encodes a restricted chemosensory repertoire compared with most mammal species. In this study, we have designed cassette baculovirus vectors to coexpress human {OR} 17-209 or {OR} 17-210 with either G(alpha olf) or G(alpha16) proteins in Sf9 cells. Each {OR} was found to be expressed at the cell surface and colocalized with both G(alpha) proteins. Using Ca2+ imaging, we showed that {OR} 17-209 and {OR} 17-210 proteins are activated by esters and ketones respectively. Odorant-induced calcium response was increased when {ORs} were coexpressed with G(alpha16) protein, whereas coexpression with G(alpha olf) abolished calcium signaling. This strategy has been found to overcome most of the limitations encountered when expressing an {OR} protein and has permitted odorant screening of functional {ORs}. Our approach could thus be of interest for further expression and ligand assignment of other orphan receptor proteins.},
  language = {eng},
  number = {3},
  journal = {Chemical Senses},
  author = {Matarazzo, Valéry and Clot-Faybesse, Olivier and Marcet, Brice and Guiraudie-Capraz, Gaëlle and Atanasova, Boriana and Devauchelle, Gérard and Cerutti, Martine and Etiévant, Patrick and Ronin, Catherine},
  month = {March},
  year = {2005},
  pmid = {15741602},
  keywords = {Animals, Baculoviridae, Calcium, Cell Line, {GTP}-Binding Protein alpha Subunits, Genomics, Humans, Insects, Microscopy, Confocal, Odors, Olfactory Receptor Neurons, Receptors, G-Protein-Coupled},
  pages = {195--207}
}

@article{sincich_circuitry_2005,
	title = {The circuitry of {V}1 and {V}2: integration of color, form, and motion},
	volume = {28},
	issn = {0147-006X},
	shorttitle = {The circuitry of {V}1 and {V}2},
	doi = {10.1146/annurev.neuro.28.061604.135731},
	abstract = {Primary and secondary visual cortex (V1 and V2) form the foundation of the cortical visual system. V1 transforms information received from the lateral geniculate nucleus (LGN) and distributes it to separate domains in V2 for transmission to higher visual areas. During the past 20 years, schemes for the functional organization of V1 and V2 have been based on a tripartite framework developed by Livingstone \& Hubel (1988) . Since then, new anatomical data have accumulated concerning V1's input, its internal circuitry, and its output to V2. These new data, along with physiological and imaging studies, now make it likely that the visual attributes of color, form, and motion are not neatly segregated by V1 into different stripe compartments in V2. Instead, there are just two main streams, originating from cytochrome oxidase patches and interpatches, that project to V2. Each stream is composed of a mixture of magno, parvo, and konio geniculate signals. Further studies are required to elucidate how the patches and interpatches differ in the output they convey to extrastriate cortex.},
	language = {eng},
	journal = {Annual review of neuroscience},
	author = {Sincich, Lawrence C and Horton, Jonathan C},
	year = {2005},
	pmid = {16022598},
	keywords = {Animals, Color Perception, Feedback, Form Perception, Humans, Motion, Neural Networks (Computer), Visual Cortex, Visual Pathways},
	pages = {303--326}
}

Paper  Website  abstract   bibtex   

@article{
 title = {Polar ocean ecosystems in a changing world.},
 type = {article},
 year = {2005},
 identifiers = {[object Object]},
 keywords = {Animals,Antarctic Regions,Arctic Regions,Ecosystem,Food Chain,Greenhouse Effect,Ice Cover},
 pages = {362-8},
 volume = {437},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/16163347},
 month = {9},
 id = {e02d41b8-5bb6-330b-8cef-61a45ff42b97},
 created = {2012-12-06T10:07:57.000Z},
 file_attached = {true},
 profile_id = {0b777e31-8c9d-39dd-97a3-3e054bd99cfe},
 group_id = {764582e8-5773-3a66-8d6b-9b40e4fb5a88},
 last_modified = {2017-03-14T17:27:14.020Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {Smetacek2005},
 abstract = {Polar organisms have adapted their seasonal cycles to the dynamic interface between ice and water. This interface ranges from the micrometre-sized brine channels within sea ice to the planetary-scale advance and retreat of sea ice. Polar marine ecosystems are particularly sensitive to climate change because small temperature differences can have large effects on the extent and thickness of sea ice. Little is known about the interactions between large, long-lived organisms and their planktonic food supply. Disentangling the effects of human exploitation of upper trophic levels from basin-wide, decade-scale climate cycles to identify long-term, global trends is a daunting challenge facing polar bio-oceanography.},
 bibtype = {article},
 author = {Smetacek, Victor and Nicol, Stephen},
 journal = {Nature},
 number = {7057}
}

Paper  Website  abstract   bibtex   

@article{
 title = {Global sulfur emissions from 1850 to 2000.},
 type = {article},
 year = {2005},
 identifiers = {[object Object]},
 keywords = {Acid Rain,Aerosols,Animals,Asia,Climate,Environmental Exposure,Environmental Exposure: history,Environmental Pollutants,Environmental Pollutants: history,Europe,History, 19th Century,History, 20th Century,Humans,Predictive Value of Tests,Sulfur Compounds,Sulfur Compounds: economics,Sulfur Compounds: metabolism,World Health},
 pages = {163-75},
 volume = {58},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/15571748},
 month = {1},
 id = {201f641a-5b38-3b69-b69f-82d15752aced},
 created = {2014-05-31T04:14:04.000Z},
 accessed = {2013-05-26},
 file_attached = {true},
 profile_id = {9edae5ec-3a23-3830-8934-2c27bef6ccbe},
 group_id = {63e349d6-2c70-3938-9e67-2f6483f6cbab},
 last_modified = {2014-11-19T06:02:42.000Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 abstract = {The ASL database provides continuous time-series of sulfur emissions for most countries in the World from 1850 to 1990, but academic and official estimates for the 1990s either do not cover all years or countries. This paper develops continuous time series of sulfur emissions by country for the period 1850-2000 with a particular focus on developments in the 1990s. Global estimates for 1996-2000 are the first that are based on actual observed data. Raw estimates are obtained in two ways. For countries and years with existing published data I compile and integrate that data. Previously published data covers the majority of emissions and almost all countries have published emissions for at least 1995. For the remaining countries and for missing years for countries with some published data, I interpolate or extrapolate estimates using either an econometric emissions frontier model, an environmental Kuznets curve model, or a simple extrapolation, depending on the availability of data. Finally, I discuss the main movements in global and regional emissions in the 1990s and earlier decades and compare the results to other studies. Global emissions peaked in 1989 and declined rapidly thereafter. The locus of emissions shifted towards East and South Asia, but even this region peaked in 1996. My estimates for the 1990s show a much more rapid decline than other global studies, reflecting the view that technological progress in reducing sulfur based pollution has been rapid and is beginning to diffuse worldwide.},
 bibtype = {article},
 author = {Stern, David I},
 journal = {Chemosphere},
 number = {2}
}

Paper  Website  abstract   bibtex   

@article{
 title = {Contaminant levels in sediments and asteroids (Asterias rubens L., Echinodermata) from the Belgian coast and Scheldt estuary: polychlorinated biphenyls and heavy metals.},
 type = {article},
 year = {2004},
 identifiers = {[object Object]},
 keywords = {Animals,Environmental Monitoring,Environmental Pollutants,Environmental Pollutants: analysis,Environmental Pollutants: pharmacokinetics,Geologic Sediments,Geologic Sediments: chemistry,Metals, Heavy,Metals, Heavy: analysis,Metals, Heavy: pharmacokinetics,North Sea,Polychlorinated Biphenyls,Polychlorinated Biphenyls: analysis,Polychlorinated Biphenyls: pharmacokinetics,Starfish,Starfish: chemistry,Tissue Distribution},
 pages = {149-65},
 volume = {333},
 websites = {http://dx.doi.org/10.1016/j.scitotenv.2004.05.002},
 month = {10},
 id = {3e9d21fe-f6d2-3a7e-81ca-379c5d431faa},
 created = {2010-09-15T11:24:56.000Z},
 accessed = {2010-09-15},
 file_attached = {true},
 profile_id = {c6c6f844-18d2-32db-a619-2e915134a952},
 last_modified = {2017-03-31T08:27:57.360Z},
 read = {true},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Danis2004},
 folder_uuids = {a6bf1321-9beb-4f7c-9715-6ab10e069d78,25cad246-e846-4c62-92bf-3da69f6f5c57},
 abstract = {The Southern Bight of the North Sea is particularly exposed to anthropogenic contamination, due to heavy urbanisation and industrialisation of its catchment area. The present work focuses on polychlorinated biphenyl (PCB) and metal contamination of the marine environment along and off the Belgian coast. Its objectives were to compare the concentrations of seven PCB congeners and four heavy metals in the sediments (a repository for anthropogenic contaminants) and in the asteroid Asterias rubens (a recognized bioindicator species). Nineteen sampling stations were considered between the mouth of the Scheldt Estuary and the southern limit of the Belgian coast (asteroids were found in 10 out of the 19 stations). PCB and metal concentrations measured in sediments and asteroids were in the range of values reported in previous studies. Stations under direct influence of the Scheldt were the most impacted by the considered contaminants. Metal concentrations varied according to the grain-size fraction considered. In asteroids, PCBs and metals were found to be selectively distributed among body compartments, and pyloric caeca were found to most efficiently discriminate between sampling stations contamination levels. PCB and metal analysis of sediments provided a physicochemical evaluation of the contamination, whereas analysis of asteroids introduced a biological dimension to the approach by taking into account bioavailability of the contaminants.},
 bibtype = {article},
 author = {Danis, B and Wantier, P and Dutrieux, S and Flammang, R and Dubois, Ph and Warnau, M},
 journal = {The Science of the total environment},
 number = {1-3}
}

@Article{Feinstein_2004_1104,
  author = {Feinstein, S.B.},
 journal = {American Journal of Physiology - Heart and Circulatory Physiology},
 note = {0363-6135 (Print) Historical Article Journal Article Review},
 number = {2},
 pages = {H450-457},
 title = {The powerful microbubble: {F}rom bench to bedside, from intravascular indicator to therapeutic delivery system, and beyond},
 volume = {287},
 year = {2004},
 keywords = {Animals, Arteriosclerosis/*therapy/*ultrasonography, Blood, Vessels/*ultrasonography, Carotid, Stenosis/complications/ultrasonography, Decompression, Sickness/ultrasonography, *Diffusion, of, Innovation, Echocardiography, History, 20th, Century, Humans, *Microbubbles, Neovascularization, Pathologic/etiology/ultrasonography, Ultrasonography/history},
 title_with_no_special_chars = {The powerful microbubble From bench to bedside from intravascular indicator to therapeutic delivery system and beyond}
}

Paper  doi  abstract   bibtex   

@article{ Barb_2004_277,
  abstract = {Neural spike train decoding algorithms and techniques to compute Shannon
	mutual information are important methods for analyzing how neural
	systems represent biological signals. Decoding algorithms are also
	one of several strategies being used to design controls for brain-machine
	interfaces. Developing optimal strategies to design decoding algorithms
	and compute mutual information are therefore important problems in
	computational neuroscience. We present a general recursive filter
	decoding algorithm based on a point process model of individual neuron
	spiking activity and a linear stochastic state-space model of the
	biological signal. We derive from the algorithm new instantaneous
	estimates of the entropy, entropy rate, and the mutual information
	between the signal and the ensemble spiking activity. We assess the
	accuracy of the algorithm by computing, along with the decoding error,
	the true coverage probability of the approximate 0.95 confidence
	regions for the individual signal estimates. We illustrate the new
	algorithm by reanalyzing the position and ensemble neural spiking
	activity of CA1 hippocampal neurons from two rats foraging in an
	open circular environment. We compare the performance of this algorithm
	with a linear filter constructed by the widely used reverse correlation
	method. The median decoding error for Animal 1 (2) during 10 minutes
	of open foraging was 5.9 (5.5) cm, the median entropy was 6.9 (7.0)
	bits, the median information was 9.4 (9.4) bits, and the true coverage
	probability for 0.95 confidence regions was 0.67 (0.75) using 34
	(32) neurons. These findings improve significantly on our previous
	results and suggest an integrated approach to dynamically reading
	neural codes, measuring their properties, and quantifying the accuracy
	with which encoded information is extracted.},
  added-at = {2009-06-03T11:20:58.000+0200},
  author = {Barbieri, Riccardo and Frank, Loren M and Nguyen, David P and Quirk, Michael C and Solo, Victor and Wilson, Matthew A and Brown, Emery N},
  biburl = {http://www.bibsonomy.org/bibtex/255b36022e10a07e42f0339963a3ba074/hake},
  description = {The whole bibliography file I use.},
  doi = {10.1162/089976604322742038},
  file = {Barb_2004_277.pdf:Barb_2004_277.pdf:PDF},
  interhash = {068c5ef6cfc1453132764740b244f6a5},
  intrahash = {55b36022e10a07e42f0339963a3ba074},
  journal = {Neural Comput.},
  keywords = {(Computer), 15006097 Action Algorithms, Animals, Behavior, Comparative Computer-Assisted, Exploratory Gov't, Hippocampus, Long-Evans, Nerve Net, Networks Neural Neurons, Non-P.H.S., Non-U.S. P.H.S., Potentials, Processes, Processing, Rats, Reaction Reproducibility Research Results, Signal Stochastic Study, Support, Synaptic Time, Transmission, U.S. of},
  month = {February},
  number = {2},
  pages = {277--307},
  pmid = {15006097},
  timestamp = {2006.07.05},
  title = {Dynamic analyses of information encoding in neural ensembles.},
  url = {http://dx.doi.org/10.1162/089976604322742038},
  volume = {16},
  year = {2004}
}

@article{ jukes_replacement_2004,
  title = {Replacement of harmful animal use in life science education: the approach and activities of {InterNICHE}},
  volume = {32 Suppl 1B},
  issn = {0261-1929},
  shorttitle = {Replacement of harmful animal use in life science education},
  abstract = {Harmful animal use in undergraduate education is increasingly being replaced by alternatives, such as computer software, manikins and simulators, ethically sourced animal cadavers, apprentice work with animal patients, and student self-experimentation. Combinations of such alternatives can better meet teaching objectives, reduce costs and avoid the negative pedagogical and social impact of animal experimentation. Since 1988, the International Network for Humane Education ({InterNICHE}, formerly {EuroNICHE}) has been working with teachers to replace harmful animal use and has been supporting students' right to conscientious objection. This paper presents the approach, history and current activities of {InterNICHE}. With a vision of 100% replacement, the network aims for empowerment by networking information and providing support. It works with the belief that most teachers want investment in the best quality and most humane education possible. The forthcoming second edition of the {InterNICHE} book, from Guinea Pig to Computer Mouse,1 includes practical details of progressive teaching aids and approaches, as well as case studies from teachers who employ such alternatives. In 1999, {InterNICHE} produced the film Alternatives in Education, now available in 20 languages. Such resources are complemented by outreach trips and conferences and an Alternatives Loan System, which offers products for familiarisation and assessment. The {InterNICHE} website (www.interniche.org) was launched in 2001.},
  language = {eng},
  journal = {Alternatives to laboratory animals: {ATLA}},
  author = {Jukes, Nick},
  month = {June},
  year = {2004},
  pmid = {23581127},
  keywords = {Animals, Animal Testing Alternatives, Biological Science Disciplines, computer simulation},
  pages = {511--515}
}

@article{den_brok_situ_2004,
	title = {In situ tumor ablation creates an antigen source for the generation of antitumor immunity},
	volume = {64},
	issn = {0008-5472},
	doi = {10.1158/0008-5472.CAN-03-3949},
	abstract = {Tumor-destructing techniques, like radiofrequency ablation (RFA), allow eradication of large tumors. Potentially, in situ tumor destruction also can provide the immune system with an antigen source for the induction of antitumor immunity. Antigen-presenting cells could take up antigens in the periphery after which they induce specific immune responses. Recent data show that especially antigen-presenting dendritic cells are crucial for the induction of potent immune responses. However, virtually nothing is known regarding the induction of immune responses after in situ tumor destruction in mice or humans. We used the well-defined murine B16-OVA melanoma cell line to develop a novel tumor model to explore: (a). the immunologic consequences of in situ tumor destruction; and (b). the efficacy of a combination approach of tumor destruction and immunostimulation. Applying this model system we demonstrate that following RFA, a weak but detectable immune response develops, directed against OVA, but also against a broader range of B16 antigens. Adoptive transfer experiments further indicate that antitumor reactivity can be transferred to naïve mice by splenocytes. To augment the response observed, we administered a blocking monoclonal antibody against cytotoxic T-lymphocyte-associated antigen 4 at the time of tumor destruction. Interestingly, this strongly enhanced antitumor immunity, resulting in long-lasting tumor protection. These results illustrate that in situ tumor destruction can provide a useful antigen source for the induction of antitumor immunity, provided that additional immunostimulatory signals are coadministered.},
	language = {eng},
	number = {11},
	journal = {Cancer Research},
	author = {den Brok, Martijn H. M. G. M. and Sutmuller, Roger P. M. and van der Voort, Robbert and Bennink, Erik J. and Figdor, Carl G. and Ruers, Theo J. M. and Adema, Gosse J.},
	month = jun,
	year = {2004},
	pmid = {15173017},
	keywords = {Animals, Antibodies, Monoclonal, Antigens, CD, Antigens, Differentiation, Antigens, Neoplasm, CTLA-4 Antigen, Catheter Ablation, Cricetinae, Female, Immunotherapy, Adoptive, Interferon-gamma, Lymphocyte Activation, Male, Melanoma, Experimental, Mice, Mice, Inbred C57BL, T-Lymphocytes},
	pages = {4024--4029},
}

@article{ santarelli_requirement_2003,
  title = {Requirement of hippocampal neurogenesis for the behavioral effects of antidepressants},
  volume = {301},
  issn = {1095-9203},
  doi = {10.1126/science.1083328},
  abstract = {Various chronic antidepressant treatments increase adult hippocampal neurogenesis, but the functional importance of this phenomenon remains unclear. Here, using genetic and radiological methods, we show that disrupting antidepressant-induced neurogenesis blocks behavioral responses to antidepressants. Serotonin 1A receptor null mice were insensitive to the neurogenic and behavioral effects of fluoxetine, a serotonin selective reuptake inhibitor. X-irradiation of a restricted region of mouse brain containing the hippocampus prevented the neurogenic and behavioral effects of two classes of antidepressants. These findings suggest that the behavioral effects of chronic antidepressants may be mediated by the stimulation of neurogenesis in the hippocampus.},
  language = {eng},
  number = {5634},
  journal = {Science (New York, N.Y.)},
  author = {Santarelli, Luca and Saxe, Michael and Gross, Cornelius and Surget, Alexandre and Battaglia, Fortunato and Dulawa, Stephanie and Weisstaub, Noelia and Lee, James and Duman, Ronald and Arancio, Ottavio and Belzung, Catherine and Hen, René},
  month = {August},
  year = {2003},
  pmid = {12907793},
  keywords = {8-Hydroxy-2-(di-n-propylamino)tetralin, Animals, Antidepressive Agents, Antidepressive Agents, Second-Generation, Antidepressive Agents, Tricyclic, Behavior, Animal, Cell Division, Conditioning (Psychology), Dentate Gyrus, Fear, Feeding Behavior, Fluoxetine, Grooming, Hippocampus, Long-Term Potentiation, Male, Mice, Mice, Knockout, Neurons, Receptors, Serotonin, Receptors, Serotonin, 5-{HT}1, Stress, Physiological, Synaptic Transmission},
  pages = {805--809}
}

Paper  Website  abstract   bibtex   

@article{
 title = {Grandmothers and the Evolution of Human Longevity},
 type = {article},
 year = {2003},
 identifiers = {[object Object]},
 keywords = {*Evolution,*Family,*Longevity,Aging,Animals,Biological,Humans,Models,Pan troglodytes},
 pages = {380-400},
 volume = {15},
 websites = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12704714},
 edition = {2003/04/22},
 id = {48b60b26-ce0d-3210-90d4-f3cd1e798e69},
 created = {2017-06-19T13:41:50.765Z},
 file_attached = {true},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:41:50.891Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 language = {eng},
 notes = {<m:note>        <m:bold>From Duplicate 1 ( </m:bold>        <m:bold>          </m:bold><m:bold><m:italic>Grandmothers and the evolution of human longevity</m:italic></m:bold><m:bold>        </m:bold>        <m:bold> - Hawkes, K )<m:linebreak/>        </m:bold>        <m:linebreak/>Hawkes, Kristen<m:linebreak/>Review<m:linebreak/>United States<m:linebreak/>American journal of human biology : the official journal of the Human Biology Council<m:linebreak/>Am J Hum Biol. 2003 May-Jun;15(3):380-400.<m:linebreak/>        <m:linebreak/>      </m:note>},
 abstract = {ABSTRACT Great apes, our closest living relatives, live longer and mature later than most other mammals and modern humans are even later-maturing and potentially longer-lived. Evolutionary life-history theory seeks to explain cross-species differences in these variables and the covariation between them. That provides the foundation for a hypothesis that a novel role for grandmothers underlies the shift from an ape-like ancestral pattern to one more like our own in the first widely successful members of genus Homo. This hypothesis links four distinctive features of human life histories: 1) our potential longevity, 2) our late maturity, 3) our midlife menopause, and 4) our early weaning with next offspring produced before the previous infant can feed itself. I discuss the problem, then, using modern humans and chimpanzees to represent, respectively, genus Homo and australopithecines, I focus on two corollaries of this grandmother hypothesis: 1) that ancestral age-specific fertility declines persisted in our genus, while 2) senescence in other aspects of physiological performance slowed down. The data are scanty but they illustrate similarities in age-specific fertility decline and differences in somatic durability that are consist- ent with the hypothesis that increased longevity in our genus is a legacy of the ‘‘reproductive’’ role of ancestral grandmothers},
 bibtype = {article},
 author = {Hawkes, Kristen},
 journal = {American journal of human biology},
 number = {3}
}

@article{taylor_theileria_2002,
	title = {Theileria annulata: virulence and transmission from single and mixed clone infections in cattle.},
	volume = {100},
	issn = {0014-4894 0014-4894},
	abstract = {Theoretically, parasite virulence should be higher for faster growing parasites,  and higher in mixed infections compared to single-clone infections. Virulence should also be positively correlated to transmission rates. Theileria annulata provides a good model system for studying such hypotheses, as parasite replication causes harm to the host, and there is evidence suggesting that the genetic complexity of an infection might affect its virulence. Two clones of T. annulata were chosen, one fast growing and one slow growing in vitro and these were used to establish cattle infections, either alone, or in a mixed infection.  Virulence was measured using lymph node expansion, temperature, and blood parameters as correlates. As predicted, the faster growing clone was found to produce higher virulence. Mixed infections did not show higher virulence than single-clone infections, but interactions within mixed infections resulted in more transmission stage production than seen in either of the single-clone infections. Index Descriptors and Abbreviations. Theileria annulata, Apicomplexa, mixed infections, virulence, growth rates, red blood cell, RBC; packed cell volume, PCV.},
	language = {eng},
	number = {3},
	journal = {Experimental parasitology},
	author = {Taylor, Louise H. and Welburn, Sue C. and Woolhouse, Mark E. J.},
	month = mar,
	year = {2002},
	pmid = {12173404},
	keywords = {Animals, Cattle, Erythrocyte Count, Genotype, Host-Parasite Interactions, Leukocyte Count, Male, Parasitemia/parasitology, Theileria annulata/classification/genetics/growth \& development/*pathogenicity, Theileriasis/*parasitology/*transmission, Virulence},
	pages = {186--195}
}

@Article{Fayad_2002_1428,
  author = {Fayad, Z. A.},
 journal = {Neuroimaging Clin.N.Am.},
 note = {DA - 20021218 NOT IN FILE},
 number = {3},
 pages = {461-471},
 title = {Noncoronary and coronary atherothrombotic plaque imaging and monitoring of therapy by MRI},
 volume = {12},
 year = {2002},
 keywords = {Animals, Arteries, Arteriosclerosis, Atherosclerosis, Contrast, Media, Coronary, Arteriosclerosis, Coronary, Vessels, diagnosis, Disease, Progression, Humans, Magnetic, Resonance, Angiography, Magnetic, Resonance, Imaging, methods, pathology, Research, Support, Non-U.S.Gov't, Research, Support, U.S.Gov't, P.H.S., Rupture, therapy},
 title_with_no_special_chars = {Noncoronary and coronary atherothrombotic plaque imaging and monitoring of therapy by MRI}
}

@Article{Sparre_2002_1402,
  author = {Sparre, T. and Christensen, U. B. and Mose Larsen, P. and Fey, S. J. and Wrzesinski, K. and Roepstorff, P. and Mandrup-Poulsen, T. and Pociot, F. and Karlsen, A. E. and Nerup, J.},
 journal = {Diabetologia},
 note = {Comparative Study Journal Article Research Support, Non-U.S. Gov't Germany},
 number = {11},
 pages = {1550-61},
 title = {Il-1beta induced protein changes in diabetes prone BB rat islets of langerhans identified by proteome analysis},
 volume = {45},
 year = {2002},
 keywords = {Animals, Animals, Newborn, Cells, Cultured, Diabetes, Mellitus, Type, 1/*genetics, Electrophoresis, Gel, Two-Dimensional, Enzymes/genetics, Interleukin-1/*pharmacology, Islets, of, Langerhans/cytology/drug, effects/*physiology, Proteins/*genetics/isolation, &, purification, *Proteome, Rats, Rats, Inbred, BB, Rats, Inbred, WF},
 title_with_no_special_chars = {IL1beta induced protein changes in diabetes prone BB rat islets of Langerhans identified by proteome analysis}
}

Paper  abstract   bibtex   

@article{
 title = {Middle temporal visual area microstimulation influences veridical judgments of motion direction},
 type = {article},
 year = {2002},
 keywords = {Algorithms,Animals,Brain Mapping,Electric Stimulation/methods,Fixation, Ocular/physiology,Judgment/physiology,Macaca mulatta,Microelectrodes,Models, Neurological,Motion Perception/physiology,Neurons/physiology,Photic Stimulation/methods,Reproducibility of Results,Saccades/physiology,Temporal Lobe/physiology,Visual Cortex/physiology},
 pages = {9530-9540},
 volume = {22},
 id = {997a2ff5-1369-36ff-8481-66f744bb339a},
 created = {2017-09-01T15:54:30.239Z},
 file_attached = {true},
 profile_id = {80da7853-f7b7-36a9-8e4c-d7ddb2d9e538},
 group_id = {a2333ea3-15a4-3d40-8d36-f0d9590ca926},
 last_modified = {2017-09-01T15:54:30.352Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {false},
 hidden = {false},
 language = {eng},
 abstract = {Microstimulation of direction columns in the middle temporal visual area (MT, or V5) provides a powerful tool for probing the relationship between cortical physiology and visual motion perception. In the current study we obtained "veridical" reports of perceived motion from rhesus monkeys by permitting a continuous range of possible responses that mapped isomorphically onto a continuous range of possible motion directions. In contrast to previous studies, therefore, the animals were freed from experimenter-imposed "categories" that typify forced choice tasks. We report three new findings: (1) MT neurons with widely disparate preferred directions can cooperate to shape direction estimates, inconsistent with a pure "winner-take-all" read-out algorithm and consistent with a distributed coding scheme like vector averaging, whereas neurons with nearly opposite preferred directions seem to compete in a manner consistent with the winner-take-all hypothesis, (2) microstimulation can influence direction estimates even when paired with the most powerful motion stimuli available, and (3) microstimulation effects can be elicited when a manual response (instead of our standard oculomotor response) is used to communicate the perceptual report.},
 bibtype = {article},
 author = {Nichols, M. and Newsome, William},
 number = {21}
}

@article{ clement_genetic_2002,
  title = {Genetic basis of anxiety-like behaviour: a critical review},
  volume = {57},
  issn = {0361-9230},
  shorttitle = {Genetic basis of anxiety-like behaviour},
  abstract = {The way genetic and/or environmental factors influence psychiatric disorders is an enduring question in the field of human psychiatric diseases. Anxiety-related disorders provide a relevant example of how such an interaction is involved in the aetiology of a psychiatric disease. In this paper we review the literature on that subject, reporting data derived from human and rodent studies. We present in a critical way the animal models used in the studies aimed at investigating the genetic basis of anxiety, including inbred mice, selected lines, multiple marker strains, or knockout mice and review data reporting environmental components influencing anxiety-related behaviours. We conclude that anxiety is a complex behaviour, underlined not only by genetic or environmental factors but also by multiple interactions between these two factors.},
  language = {eng},
  number = {1},
  journal = {Brain Research Bulletin},
  author = {Clément, Yan and Calatayud, François and Belzung, Catherine},
  month = {January},
  year = {2002},
  pmid = {11827738},
  keywords = {Animals, Anxiety, Chromosome Mapping, Disease Models, Animal, Environment, Gene Targeting, Genetic Predisposition to Disease, Humans, Mice, Mice, Inbred Strains, Neurotransmitter Agents, Rats},
  pages = {57--71}
}

Paper  abstract   bibtex   

@article{picciotto_neuronal_2002,
	title = {Neuronal systems underlying behaviors related to nicotine addiction: neural circuits and molecular genetics.},
	volume = {22},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/11978809},
	abstract = {Nicotine addiction is a complex behavioral phenomenon comprising effects on several neural systems. Recent studies have expanded initial observations that the actions of nicotine on dopaminergic systems increase dopaminergic activity and release, leading to nicotine-induced reinforcement. Indeed, the actions of nicotine on many systems, including brainstem cholinergic, GABAergic, noradrenergic, and serotonergic nuclei, may help to mediate nicotine effects related to addiction. Furthermore, studies of mice lacking nicotinic acetylcholine receptor subunits or expressing supersensitive forms of these subunits have begun to tie together the molecular, neurochemical, and behavioral effects of nicotine. The use of multiple techniques by many laboratories provides optimism that the field is advancing toward elucidating the basic mechanisms of nicotine dependence.},
	number = {9},
	journal = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	author = {Picciotto, Marina R and Corrigall, William a},
	month = may,
	year = {2002},
	keywords = {Animals, Behavior, Addictive, Behavior, Addictive: etiology, Brain Stem, Brain Stem: drug effects, Brain Stem: physiopathology, Disease Models, Animal, Humans, Nerve Net, Nerve Net: drug effects, Nerve Net: physiopathology, Nervous System, Nervous System: drug effects, Nervous System: physiopathology, Nicotine, Nicotine: pharmacology, Nucleus Accumbens, Nucleus Accumbens: drug effects, Nucleus Accumbens: physiopathology, Receptors, Nicotinic, Receptors, Nicotinic: drug effects, Receptors, Nicotinic: physiology, Tobacco Use Disorder, Tobacco Use Disorder: etiology, Tobacco Use Disorder: genetics, Tobacco Use Disorder: physiopathology, Ventral Tegmental Area, Ventral Tegmental Area: drug effects, Ventral Tegmental Area: physiopathology},
	pages = {3338--41}
}

@Article{Rekhter_2002_1390,
  author = {Rekhter, M.},
 journal = {Curr.Opin.Cardiol.},
 note = {DA - 20021205 NOT IN FILE},
 number = {6},
 pages = {626-632},
 title = {Vulnerable atherosclerotic plaque: {E}merging challenge for animal models},
 volume = {17},
 year = {2002},
 keywords = {Animals, Collagen, Coronary, Arteriosclerosis, Coronary, Thrombosis, Disease, Models, Animal, etiology, Models, Cardiovascular, pathology, therapy, Thrombosis},
 title_with_no_special_chars = {Vulnerable atherosclerotic plaque Emerging challenge for animal models}
}

Paper  Website  abstract   bibtex   

@article{
 title = {Activity-dependent regulation of HCN pacemaker channels by cyclic AMP: signaling through dynamic allosteric coupling.},
 type = {article},
 year = {2002},
 identifiers = {[object Object]},
 keywords = {Action Potentials,Action Potentials: drug effects,Action Potentials: physiology,Allosteric Regulation,Allosteric Regulation: drug effects,Allosteric Regulation: physiology,Animals,Central Nervous System,Central Nervous System: metabolism,Cerebral Cortex,Cerebral Cortex: metabolism,Cyclic AMP,Cyclic AMP: metabolism,Cyclic AMP: pharmacology,Dose-Response Relationship,Drug,Electric Stimulation,Female,Ion Channels,Ion Channels: drug effects,Ion Channels: metabolism,Kinetics,Models,Muscle Proteins,Muscle Proteins: drug effects,Muscle Proteins: metabolism,Neural Pathways,Neural Pathways: metabolism,Neurological,Neurons,Neurons: drug effects,Neurons: metabolism,Oocytes,Reaction Time,Reaction Time: drug effects,Reaction Time: physiology,Signal Transduction,Signal Transduction: drug effects,Signal Transduction: physiology,Synaptic Transmission,Synaptic Transmission: drug effects,Synaptic Transmission: physiology,Thalamus,Thalamus: metabolism,Xenopus laevis},
 pages = {451-61},
 volume = {36},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/12408847},
 month = {10},
 day = {24},
 id = {4ef89909-f8bc-37f5-ace7-73124dabac80},
 created = {2012-06-14T17:02:50.000Z},
 file_attached = {true},
 profile_id = {b662c5f6-8d1c-39ee-8a62-3ff04dae55cf},
 last_modified = {2017-03-09T18:36:24.602Z},
 read = {true},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 folder_uuids = {65a9638b-8c1a-4479-b941-46ea2e673403},
 private_publication = {false},
 abstract = {Signal transduction in neurons is a dynamic process, generally thought to be driven by transient changes in the concentration of second messengers. Here we describe a novel regulatory mechanism in which the dynamics of signaling through cyclic AMP are mediated by activity-dependent changes in the affinity of the hyperpolarization-activated, cation nonselective (HCN) channels for cAMP, rather than by changes in cAMP concentration. Due to the allosteric coupling of channel opening and ligand binding, changes in cellular electrical activity that alter the opening of the HCN channels modify the binding of static, basal levels of cAMP. These changes in ligand binding produce long-lasting changes in channel function which can contribute to the regulation of rhythmic firing patterns.},
 bibtype = {article},
 author = {Wang, Jing and Chen, Shan and Nolan, Matthew F and Siegelbaum, Steven a},
 journal = {Neuron},
 number = {3}
}

@Article{Libby_2002_1361,
  author = {Libby, P. and Aikawa, M.},
 journal = {Nat.Med.},
 note = {DA - 20021104 NOT IN FILE},
 number = {11},
 pages = {1257-1262},
 title = {Stabilization of atherosclerotic plaques: {N}ew mechanisms and clinical targets},
 volume = {8},
 year = {2002},
 keywords = {Animals, Antilipemic, Agents, Arteriosclerosis, drug, therapy, Humans, Hydroxymethylglutaryl-CoA, Reductase, Inhibitors, pathology, Research, Support, Non-U.S.Gov't, Research, Support, U.S.Gov't, P.H.S., therapeutic, use, Thrombosis},
 title_with_no_special_chars = {Stabilization of atherosclerotic plaques New mechanisms and clinical targets}
}

@article{coleman_endemic_2001,
	title = {Endemic stability--a veterinary idea applied to human public health.},
	volume = {357},
	issn = {0140-6736 0140-6736},
	abstract = {Endemic stability is an epidemiological state of a population, in which clinical  disease is scarce despite high level of infection. The notion was developed to describe patterns of tick-borne disease in cattle. However, we propose a general  model of endemic stability that is applicable to a broader range of diseases that are important in public health, including malaria, rubella, and mumps. We postulate that endemic stability requires only that (1) the probability, or severity, of clinical disease after infection increases with age, and (2) after one infection, the probability that subsequent infections result in disease is reduced. We present these criteria in simple mathematical terms. Our hypothesis predicts that partial disease control activities might, under certain circumstances, lead to an increase in disease incidence. We discuss the implications for public health interventions.},
	language = {eng},
	number = {9264},
	journal = {Lancet (London, England)},
	author = {Coleman, P. G. and Perry, B. D. and Woolhouse, M. E.},
	month = apr,
	year = {2001},
	pmid = {11418173},
	keywords = {*Endemic Diseases, *Epidemiologic Methods, *Models, Theoretical, *Public Health, Age Distribution, Animals, Child, Preschool, Communicable Diseases/*epidemiology/etiology, Humans, Incidence, Infant, Infant, Newborn},
	pages = {1284--1286}
}

@article{ziprin_role_2001,
	title = {Role of {Campylobacter} jejuni potential virulence genes in cecal colonization},
	volume = {45},
	issn = {0005-2086},
	abstract = {Campylobacter jejuni, a common commensal in chickens, is one of the leading causes of bacterial gastroenteritis in humans worldwide. The aims of this investigation were twofold. First, we sought to determine whether mutations in the C. jejuni ciaB and pldA virulence-associated genes impaired the organism's ability to colonize chickens. Second, we sought to determine if inoculation of chicks with C. jejuni mutants could confer protection from subsequent challenge with the C. jejuni wild-type strain. The C. jejuni ciaB gene encodes a secreted protein necessary for the maximal invasion of C. jejuni into cultured epithelial cells, and the pldA gene encodes a protein with phospholipase activity. Also included in this study were two additional C. jejuni mutants, one harboring a mutation in cadF and the other in dnaJ, with which we have previously performed colonization studies. In contrast to results with the parental C. jejuni strain, viable organisms were not recovered from any of the chicks inoculated with the C. jejuni mutants. To determine if chicks inoculated with the C. jejuni mutants become resistant to colonization by the C. jejuni parental strain upon subsequent challenge, chicks were inoculated either intraperitoneally (i.p.) or both orally and i.p. with the C. jejuni mutants. Inoculated birds were then orally challenged with the parental strain. Inoculation with the C. jejuni mutants did not provide protection from subsequent challenge with the wild-type strain. In addition, neither the C. jejuni parental nor the mutant strains caused any apparent morbidity or mortality of the chicks. We conclude that mutations in genes cadF, dnaJ, pldA, and ciaB impair the ability of C. jejuni to colonize the cecum, that chicks tolerate massive inoculation with these mutant strains, and that such inoculations do not provide biologically significant protection against colonization by the parental strain.},
	language = {eng},
	number = {3},
	journal = {Avian Diseases},
	author = {Ziprin, R. L. and Young, C. R. and Byrd, J. A. and Stanker, L. H. and Hume, M. E. and Gray, S. A. and Kim, B. J. and Konkel, M. E.},
	month = sep,
	year = {2001},
	pmid = {11569726},
	keywords = {Administration, Oral, Animals, Antigens, Bacterial, Bacterial Outer Membrane Proteins, Campylobacter Infections, Campylobacter jejuni, Cecum, Chickens, Colony Count, Microbial, Genes, Bacterial, Injections, Intraperitoneal, Mutation, Phospholipases A, Phospholipases A1, Poultry Diseases, Virulence},
	pages = {549--557}
}

Paper  abstract   bibtex   

@article{jones_control_2001,
	title = {Control of cell shape in bacteria: helical, actin-like filaments in {Bacillus} subtilis},
	volume = {104},
	issn = {0092-8674},
	shorttitle = {Control of cell shape in bacteria},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/11290328},
	abstract = {In the absence of an overt cytoskeleton, the external cell wall of bacteria has traditionally been assumed to be the primary determinant of cell shape. In the Gram-positive bacterium Bacillus subtilis, two related genes, mreB and mbl, were shown to be required for different aspects of cell morphogenesis. Subcellular localization of the MreB and Mbl proteins revealed that each forms a distinct kind of filamentous helical structure lying close to the cell surface. The distribution of the proteins in different species of bacteria, and the similarity of their sequence to eukaryotic actins, suggest that the MreB-like proteins have a cytoskeletal, actin-like role in bacterial cell morphogenesis.},
	number = {6},
	urldate = {2009-05-04TZ},
	journal = {Cell},
	author = {Jones, L J and Carballido-López, R and Errington, J},
	month = mar,
	year = {2001},
	pmid = {11290328},
	keywords = {Actins, Amino Acid Sequence, Animals, Bacillus subtilis, Bacteria, Bacterial Proteins, Cytoskeletal Proteins, Escherichia coli Proteins, Genes, Bacterial, Humans, Molecular Sequence Data, Morphogenesis, Sequence Alignment, Sequence Homology, Amino Acid},
	pages = {913--922}
}

Paper  Website  abstract   bibtex   

@article{
 title = {Determination of dioxins/furans and PCBs by quadrupole ion-trap gas chromatography-mass spectrometry.},
 type = {article},
 year = {2000},
 identifiers = {[object Object]},
 keywords = {Animals,Furans,Furans: analysis,Furans: toxicity,Gas Chromatography-Mass Spectrometry,Gas Chromatography-Mass Spectrometry: instrumentat,Gas Chromatography-Mass Spectrometry: methods,Humans,Polychlorinated Biphenyls,Polychlorinated Biphenyls: analysis,Polychlorinated Biphenyls: toxicity,Tetrachlorodibenzodioxin,Tetrachlorodibenzodioxin: analogs & derivatives,Tetrachlorodibenzodioxin: analysis,Tetrachlorodibenzodioxin: toxicity},
 pages = {305-65},
 volume = {19},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/11079247},
 id = {99906347-4120-3a61-9bc4-5bb2ae3a2e80},
 created = {2014-05-31T04:14:15.000Z},
 file_attached = {true},
 profile_id = {9edae5ec-3a23-3830-8934-2c27bef6ccbe},
 group_id = {63e349d6-2c70-3938-9e67-2f6483f6cbab},
 last_modified = {2014-11-19T06:02:42.000Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 abstract = {The versatility and sensitivity of the quadrupole ion trap tandem mass spectrometer has been applied to the determination of polychlorodibenzo-p-dioxins (PCDDs) and polychlorodibenzofurans (PCDFs), and of polychlorinated biphenyls (PCBs). A brief introduction to the theory of ion confinement in a quadrupole ion trap permits discussion of ion trajectory stability, mass-selective ion ejection, the frequencies of ion motion, and the role of resonant excitation of ion motion. The tandem mass spectrometric examination of PCDDs and PCDFs eluting and co-eluting from a gas chromatographic column is described. Illustrative examples are given of the analysis of field samples containing PCDDs and PCDFs. A comparison is presented of the performance of each of a quadrupole ion trap tandem mass spectrometer, a triple stage quadrupole mass spectrometer, and a sector instrument of relatively high mass resolution for the determination of PCDDs and PCDFs. This comparison is made with respect to instrument tuning, calibration plots, detection limits, ion signals at low concentration, relative response factors, ionization cross-sections, and the examination of field samples. The application of quadrupole ion trap tandem mass spectrometry to the examination of PCBs is focused upon those PCB congeners that have the greatest toxicity. 39 congeners of the total of 209 PCB congeners have been identified as having the greatest toxicities. Chemical ionization has been used for the determination of co-eluting congeners #77 and #110 where the toxicity of the former is much greater than that of the latter. An analytical protocol, based on the variation of molecular ion fragmentation according to the degree (or absence) of chlorine ortho-substitution, has been proposed for distinguishing between toxic and nontoxic PCB congeners.},
 bibtype = {article},
 author = {Plomley, J B and Lausevic, M and March, R E},
 journal = {Mass spectrometry reviews},
 number = {5}
}

@article{
 title = {In vivo penetration of experimentally produced clots by monoclonal antibodies},
 type = {article},
 year = {2000},
 identifiers = {[object Object]},
 keywords = {Animals,Antibodies, Monoclonal/metabolism,Antibody Specificity,Autoradiography,Blood Coagulation/immunology,Disease Models, Animal,Fibrin/immunology,Fluorescent Antibody Technique,Humans,Immunoglobulin G/metabolism,Iodine Radioisotopes/diagnostic use,Jugular Veins/pathology,Phlebography,Protein Binding,Rabbits,Saphenous Vein/pathology,Sheep,Thrombosis/immunology/radiography,Time Factors},
 pages = {882-886},
 volume = {83},
 month = {6},
 city = {Royal Veterinary College, Hatfield, UK. f.mcevoy@swipnet.se},
 id = {e17cc696-c7cd-3a2f-822a-fbb9eea6c336},
 created = {2016-09-06T13:34:39.000Z},
 file_attached = {false},
 profile_id = {cacab941-be62-3845-982b-a7700857a11d},
 last_modified = {2016-09-07T14:54:39.000Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 source_type = {JOUR},
 notes = {LR: 20041117; PUBM: Print; JID: 7608063; 0 (Antibodies, Monoclonal); 0 (Immunoglobulin G); 0 (Iodine Radioisotopes); 9001-31-4 (Fibrin); ppublish},
 abstract = {Antifibrin monoclonal antibodies show potential as clot targeting agents for diagnosis and possibly therapy in thrombotic disease. To be effective the antibody must bind to the fibrin component of the clot. The ability of two antifibrin mabs (NIB 1H10 and NIB 12B3) to penetrate occlusive clots in vivo was investigated. Both mabs react with human fibrin but not with human fibrinogen nor with the fibrin or fibrinogen from the species used in this study. Two heterologous animal (sheep and rabbit) thrombus models were used. Clots in both cases were made within isolated vein segments using a mixture of human and native fibrinogen. The clots in sheep veins were observed radiographically and found to be occlusive for a mean of 4.2 +/- 2.2 days and thereafter appeared only partially occlusive. When targeted in their occlusive phase (131)I labelled mab accumulated in the clot reaching a maximum ratio of 1.82 +/- 0.42 when compared to counts in homologous sheep clots in the contralateral limb. It was confirmed in the rabbit jugular vein model that total occlusivity did not prevent antibody accumulation in the heterologous clot by injecting the fibrin specific mab 1H10 and examining the clot excised after 1, 6 and 24 h using immunofluorescence. In a further series of similar experiments (125)I labelled mab 1H10 was used and detected using autoradiography. Both sets of experiments indicated that penetration of occlusive clots by the antibody occurred and that considerable accumulation was present at 6 and 24 h. The results indicate that a circulating antibody can readily gain access to experimentally produced clots in occluded veins.},
 bibtype = {article},
 author = {McEvoy, F J and Edgell, T A and Webbon, P M and Gaffney, P J},
 journal = {Thrombosis and haemostasis},
 number = {6}
}

Paper  Website  bibtex   

@article{
 title = {Single-particle electron cryo-microscopy: towards atomic resolution.},
 type = {article},
 year = {2000},
 identifiers = {[object Object]},
 keywords = {Animals,Computers,Cryoelectron Microscopy,Cryoelectron Microscopy: instrumentation,Cryoelectron Microscopy: methods,Escherichia coli,Escherichia coli: chemistry,Hemoglobins,Hemoglobins: chemistry,Image Processing, Computer-Assisted,Models, Theoretical,Software},
 pages = {307-69},
 volume = {33},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/11233408},
 month = {11},
 id = {1ea4b56b-251a-34f0-92ba-2542e4d21394},
 created = {2011-07-28T18:39:52.000Z},
 file_attached = {true},
 profile_id = {219e8e76-b8c8-3aa5-898d-2153cb61efd4},
 group_id = {cd79d359-3d3b-38cd-822c-b775fd5f31ce},
 last_modified = {2017-03-14T11:02:08.776Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {VanHeel2000},
 private_publication = {false},
 bibtype = {article},
 author = {van Heel, M and Gowen, B and Matadeen, R and Orlova, E V and Finn, R and Pape, T and Cohen, D and Stark, H and Schmidt, R and Schatz, M and Patwardhan, a},
 journal = {Quarterly reviews of biophysics},
 number = {4}
}

Website  abstract   bibtex   

@article{
 title = {Dynamic seeding and in vitro culture of hepatocytes in a flow perfusion system.},
 type = {article},
 year = {2000},
 identifiers = {[object Object]},
 keywords = {Albumins,Albumins: secretion,Animals,Biocompatible Materials,Biomedical Engineering,Cell Culture Techniques,Cell Culture Techniques: methods,Cell Survival,Cell Transplantation,Electron,Liver,Liver Transplantation,Liver: cytology,Liver: physiology,Microscopy,Perfusion,Polyglycolic Acid,Rats,Scanning},
 pages = {39-44},
 volume = {6},
 websites = {http://online.liebertpub.com/doi/abs/10.1089/107632700320874},
 month = {2},
 publisher = {Mary Ann Liebert, Inc.},
 day = {9},
 id = {db57a436-04ea-3e50-83e2-1cad83b9dd51},
 created = {2016-06-24T20:49:55.000Z},
 accessed = {2015-12-07},
 file_attached = {false},
 profile_id = {954a987f-819f-3985-95a4-2991e0cf0552},
 group_id = {8440dcff-74cc-3783-aef7-fe2749cfc7ef},
 last_modified = {2016-06-24T20:49:55.000Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {Kim2000},
 language = {en},
 abstract = {Our laboratory has investigated hepatocyte transplantation using biodegradable polymer matrices as an alternative treatment to end-stage liver disease. One of the major limitations has been the insufficient survival of an adequate mass of transplanted cells. This study investigates a novel method of dynamic seeding and culture of hepatocytes in a flow perfusion system. In experiment I, hepatocytes were flow-seeded onto PGA scaffolds and cultured in a flow perfusion system for 24 h. Overall metabolic activity and distribution of cells were assessed by their ability to reduce MTT. DNA quantification was used to determine the number of cells attached. Culture medium was analyzed for albumin content. In Experiment II, hepatocyte/polymer constructs were cultured in a perfusion system for 2 and 7 days. The constructs were examined by SEM and histology. Culture medium was analyzed for albumin. In experiment I, an average of 4.4 X 10(6) cells attached to the scaffolds by DNA quantification. Cells maintained a high metabolic activity and secreted albumin at a rate of 13 pg/cell/day. In experiment II, SEM demonstrated successful attachment of hepatocytes on the scaffolds after 2 and 7 days. Cells appeared healthy on histology and maintained a high rate of albumin secretion through day 7. Hepatocytes can be dynamically seeded onto biodegradable polymers and survive with a high rate of albumin synthesis in the flow perfusion culture system.},
 bibtype = {article},
 author = {Kim, S S and Sundback, C A and Kaihara, S and Benvenuto, M S and Kim, B S and Mooney, D J and Vacanti, J P},
 journal = {Tissue engineering},
 number = {1}
}

Paper  Website  abstract   bibtex   

@article{
 title = {Analysis of Hox gene expression in the chick limb bud.},
 type = {article},
 year = {1996},
 identifiers = {[object Object]},
 keywords = {Amino Acid Sequence,Animals,Base Sequence,Cell Movement,Chick Embryo,Extremities,Extremities: embryology,Gene Expression Regulation, Developmental,Gene Library,Genes, Homeobox,Hedgehog Proteins,Immunohistochemistry,In Situ Hybridization,Models, Genetic,Molecular Sequence Data,Morphogenesis,Muscles,Muscles: cytology,Muscles: embryology,Polymerase Chain Reaction,Proteins,Proteins: metabolism,Time Factors,Tissue Distribution,Trans-Activators,Transcription, Genetic},
 pages = {1449-66},
 volume = {122},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/8625833},
 month = {5},
 id = {9e81f849-717e-3abe-be53-e44f82a2f3f6},
 created = {2016-04-08T12:19:40.000Z},
 file_attached = {true},
 profile_id = {994bc413-6766-31df-917a-32165aa30f6c},
 group_id = {cec5aa9e-65e1-3c21-bc44-78fa6504020e},
 last_modified = {2017-03-14T10:42:46.538Z},
 read = {true},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {Nelson1996},
 folder_uuids = {37786225-e8d4-483b-be04-dfc97f200748},
 private_publication = {false},
 abstract = {The vertebrate Hox genes have been shown to be important for patterning the primary and secondary axes of the developing vertebrate embryo. The function of these genes along the primary axis of the embryo has been generally interpreted in the context of positional specification and homeotic transformation of axial structures. The way in which these genes are expressed and function during the development of the secondary axes, particularly the limb, is less clear. In order to provide a reference for understanding the role of the Hox genes in limb patterning, we isolated clones of 23 Hox genes expressed during limb development, characterized their expression patterns and analyzed their regulation by the signalling centers which pattern the limb. The expression patterns of the Abd-B-related Hoxa and Hoxd genes have previously been partially characterized; however, our study reveals that these genes are expressed in patterns more dynamic and complex than generally appreciated, only transiently approximating simple, concentric, nested domains. Detailed analysis of these patterns suggests that the expression of each of the Hoxa and Hoxd genes is regulated in up to three independent phases. Each of these phases appears to be associated with the specification and patterning of one of the proximodistal segments of the limb (upper arm, lower arm and hand). Interestingly, in the last of these phases, the expression of the Hoxd genes violates the general rule of spatial and temporal colinearity of Hox gene expression with gene order along the chromosome. In contrast to the Abd-B-related Hoxa and Hoxd genes, which are expressed in both the fore and hind limbs, different sets of Hoxc genes are expressed in the two limbs. There is a correlation between the relative position of these genes along the chromosome and the axial level of the limb bud in which they are expressed. The more 3' genes are expressed in the fore limb bud while the 5' genes are expressed in the hind limb bud; intermediate genes are transcribed in both limbs. However, there is no clear correlation between the relative position of the genes along the chromosome and their expression domains within the limb. With the exception of Hoxc-11, which is transcribed in a posterior portion of the hind limb, Hoxc gene expression is restricted to the anterior/proximal portion of the limb bud. Importantly, comparison of the distributions of Hoxc-6 RNA and protein products reveals posttranscriptional regulation of this gene, suggesting that caution must be exercised in interpreting the functional significance of the RNA distribution of any of the vertebrate Hox genes. To understand the genesis of the complex patterns of Hox gene expression in the limb bud, we examined the propagation of Hox gene expression relative to cell proliferation. We find that shifts in Hox gene expression cannot be attributed to passive expansion due to cell proliferation. Rather, phase-specific Hox gene expression patterns appear to result from a context-dependent response of the limb mesoderm to Sonic hedgehog. Sonic hedgehog (the patterning signal from the Zone of Polarizing Activity) is known to be able to activate Hoxd gene expression in the limb. Although we find that Sonic hedgehog is capable of initiating and polarizing Hoxd gene expression during both of the latter two phases of Hox gene expression, the specific patterns induced are not determined by the signal, but depend upon the temporal context of the mesoderm receiving the signal. Misexpression of Sonic hedgehog also reveals that Hoxb-9, which is normally excluded from the posterior mesenchyme of the leg, is negatively regulated by Sonic hedgehog and that Hoxc-11, which is expressed in the posterior portion of the leg, is not affected by Sonic hedgehog and hence is not required to pattern the skeletal elements of the lower leg.},
 bibtype = {article},
 author = {Nelson, C E and Morgan, B a and Burke, a C and Laufer, E and DiMambro, E and Murtaugh, L C and Gonzales, E and Tessarollo, L and Parada, L F and Tabin, C},
 journal = {Development (Cambridge, England)},
 number = {5}
}

@Article{Nakashima_1994_1801,
  author = {Nakashima, Y. and Plump, A. S. and Raines, E. W. and Breslow, J. L. and Ross, R.},
 journal = {Arterioscler.Thromb.},
 note = {DA - 19940204 NOT IN FILE},
 number = {1},
 pages = {133-140},
 title = {Apoe-deficient mice develop lesions of all phases of atherosclerosis throughout the arterial tree},
 volume = {14},
 year = {1994},
 keywords = {Animals, Aorta, Aorta, Thoracic, Apolipoproteins, E, Arteries, Arteriosclerosis, Atherosclerosis, Carotid, Arteries, Connective, Tissue, Coronary, Vessels, deficiency, Diet, Endothelium, Vascular, etiology, Humans, Hypercholesterolemia, Leukocytes, Mononuclear, Macrophages, Mice, Mice, Inbred, BALB, C, Mice, Inbred, C57BL, Mice, Transgenic, Microscopy, Electron, pathology, Pulmonary, Artery, Research, Support, Non-U.S.Gov't, Research, Support, U.S.Gov't, P.H.S., therapy},
 title_with_no_special_chars = {ApoEdeficient mice develop lesions of all phases of atherosclerosis throughout the arterial tree}
}

Paper  Website  bibtex   

@article{
 title = {Physiological and metabolic responses to hypoxia in invertebrates.},
 type = {article},
 year = {1994},
 identifiers = {[object Object]},
 keywords = {Anaerobiosis,Anaerobiosis: physiology,Animals,Anoxia,Anoxia: metabolism,Anoxia: physiopathology,Energy Metabolism,Energy Metabolism: physiology,Environmental Exposure,Invertebrates,Invertebrates: metabolism,Oxygen,Oxygen: physiology},
 pages = {43-147},
 volume = {125},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/7984874},
 month = {1},
 id = {75b0419c-af14-3ba4-9795-dd12b07b15c3},
 created = {2012-12-06T09:11:04.000Z},
 file_attached = {true},
 profile_id = {0b777e31-8c9d-39dd-97a3-3e054bd99cfe},
 group_id = {764582e8-5773-3a66-8d6b-9b40e4fb5a88},
 last_modified = {2017-03-14T17:27:14.020Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {Grieshaber1994},
 bibtype = {article},
 author = {Grieshaber, M K and Hardewig, I and Kreutzer, U and Pörtner, H O},
 journal = {Reviews of physiology, biochemistry and pharmacology}
}

@Article{Zhang_1994_1781,
  author = {Zhang, S. H. and Reddick, R. L. and Burkey, B. and Maeda, N.},
 journal = {J.Clin.Invest},
 note = {DA - 19941013 NOT IN FILE},
 number = {3},
 pages = {937-945},
 title = {Diet-induced atherosclerosis in mice heterozygous and homozygous for apolipoprotein E gene disruption},
 volume = {94},
 year = {1994},
 keywords = {Animals, Aorta, Apolipoproteins, E, Arteries, Arteriosclerosis, Atherosclerosis, blood, Cholesterol, Comparative, Study, Diet, Diet, Atherogenic, Female, genetics, Heterozygote, Homozygote, Humans, Lipoproteins, Lipoproteins, HDL, Cholesterol, Liver, Macrophages, Male, metabolism, Mice, Mice, Inbred, C57BL, Mice, Inbred, Strains, Mice, Mutant, Strains, Muscle, Smooth, Vascular, pathology, Reference, Values, Research, Support, Non-U.S.Gov't, Research, Support, U.S.Gov't, P.H.S., Triglycerides, ultrastructure},
 title_with_no_special_chars = {Dietinduced atherosclerosis in mice heterozygous and homozygous for apolipoprotein E gene disruption}
}

@Article{Ge_1992_1834,
  author = {Ge, J. and Erbel, R. and Gorge, G. and Gerber, T. and Brennecke, R. and Seidel, I. and Reichert, T. and Meyer, J.},
 journal = {Echocardiography.},
 note = {DA - 19930225 NOT IN FILE},
 number = {5},
 pages = {475-483},
 title = {Intravascular ultrasound imaging of arterial wall architecture},
 volume = {9},
 year = {1992},
 keywords = {anatomy, &, histology, Animals, Aorta, Aortic, Diseases, Arteries, blood, Blood, Vessels, Connective, Tissue, Femoral, Artery, Humans, IVUS, pathology, Swine, ultrasonography},
 title_with_no_special_chars = {Intravascular ultrasound imaging of arterial wall architecture}
}

Paper  abstract   bibtex   

@article{lincoln_serum_1990,
	title = {Serum ionized calcium concentration in clinically normal dairy cattle, and changes associated with calcium abnormalities.},
	volume = {197},
	issn = {0003-1488},
	url = {http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&DbFrom=pubmed&Cmd=Link&LinkName=pubmed_pubmed&LinkReadableName=Related%20Articles&IdsFromResult=2272878&ordinalpos=3&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum},
	abstract = {Serum ionized calcium (ICa) concentration was determined in 141 clinically normal dairy cattle by use of a direct-measuring calcium ion-selective electrode instrument. Mean serum ICa concentration 2 hours after blood withdrawal was 4.59 mg/dl; range varied from 3.79 to 5.25 mg/dl. Regression analysis indicated a high degree of correlation between ICa and serum total calcium concentrations if serum stored at 23 C was analyzed within 12 hours after blood withdrawal. Abnormal ICa concentration was detected in 19 of 85 dairy cows that were affected with various pathologic conditions. All 19 cows had hypocalcemia (n = 13 with parturient hypocalcemia, 4 with hypomagnesemic tetany, and 2 with renal disease). In all cases, the ICa concentration clearly related to the clinical manifestation of disease and the functional status of the cow's calcium metabolism.},
	number = {11},
	journal = {Journal of the American Veterinary Medical Association},
	author = {Lincoln, S D and Lane, V M},
	month = dec,
	year = {1990},
	keywords = {Animals, Calcium, Cattle, Cattle Diseases, Female, Hydrogen-Ion Concentration, Hypocalcemia, Lactation, Potentiometry, Reference Values, Regression Analysis},
	pages = {1471--4}
}

Website  bibtex   

@article{
 title = {DNA binding study of isophorone in rats and mice},
 type = {article},
 year = {1990},
 identifiers = {[object Object]},
 keywords = {Animals,Cyclohexanones/*metabolism,DNA/*metabolism,Female,Male,Mice,Rats,Rats, Inbred F344},
 pages = {684-685},
 volume = {64},
 websites = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=2090039},
 edition = {1990/01/01},
 id = {be1a97a7-cc9c-3bef-a0c9-625b8898ee26},
 created = {2017-06-19T13:43:15.318Z},
 file_attached = {false},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:43:15.427Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 language = {eng},
 notes = {<m:note>Thier, R<m:linebreak/>Peter, H<m:linebreak/>Wiegand, H J<m:linebreak/>Bolt, H M<m:linebreak/>Letter<m:linebreak/>Germany<m:linebreak/>Archives of toxicology<m:linebreak/>Arch Toxicol. 1990;64(8):684-5.</m:note>},
 bibtype = {article},
 author = {Thier, R and Peter, H and Wiegand, H J and Bolt, H M},
 journal = {Arch Toxicol},
 number = {8}
}

Paper  abstract   bibtex   

@article{
 title = {Primate motor cortex and free arm movements to visual targets in three-dimensional space. I. Relations between single cell discharge and direction of movement},
 type = {article},
 year = {1988},
 keywords = {Animals,Arm,Carpus, Animal,Electromyography,Macaca mulatta/physiology,Macaca/physiology,Male,Models, Neurological,Motor Cortex/cytology/physiology,Movement,Neurons/physiology,Psychomotor Performance/physiology,Reaction Time,Regression Analysis},
 pages = {2913-2927},
 volume = {8},
 id = {4a8e9b14-6f4d-34a2-a9f8-cb190a906c6c},
 created = {2017-09-01T15:54:32.099Z},
 file_attached = {true},
 profile_id = {80da7853-f7b7-36a9-8e4c-d7ddb2d9e538},
 group_id = {a2333ea3-15a4-3d40-8d36-f0d9590ca926},
 last_modified = {2017-09-01T15:54:32.217Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {false},
 hidden = {false},
 language = {eng},
 abstract = {We describe the relations between the neuronal activity in primate motor cortex and the direction of arm movement in three-dimensional (3-D) space. The electrical signs of discharge of 568 cells were recorded while monkeys made movements of equal amplitude from the same starting position to 8 visual targets in a reaction time task. The layout of the targets in 3-D space was such that the direction of the movement ranged over the whole 3-D directional continuum in approximately equal angular intervals. We found that the discharge rate of 475/568 (83.6%) cells varied in an orderly fashion with the direction of movement: discharge rate was highest with movements in a certain direction (the cell's "preferred direction") and decreased progressively with movements in other directions, as a function of the cosine of the angle formed by the direction of the movement and the cell's preferred direction. The preferred directions of different cells were distributed throughout 3-D space. These findings generalize to 3-D space previous results obtained in 2-D space (Georgopoulos et al., 1982) and suggest that the motor cortex is a nodal point in the construction of patterns of output signals specifying the direction of arm movement in extrapersonal space.},
 bibtype = {article},
 author = {Schwartz, A. and Kettner, R. and Georgopoulos, A.},
 number = {8}
}

@article{
 title = {Frequency and intensity discrimination in humans and monkeys},
 type = {article},
 year = {1985},
 keywords = {Acoustic Stimulation,Adult,Animals,Auditory Perception/physiology,Cercopithecus aethiops/physiology,Female,Humans,Macaca/physiology,Male,Species Specificity,Speech Acoustics,Speech Perception/physiology,Vestibulocochlear Nerve/physiology},
 pages = {1977-1985},
 volume = {78},
 id = {163a1c5d-06e6-3686-9f07-6e1f76a6fc88},
 created = {2017-09-01T15:54:31.569Z},
 file_attached = {false},
 profile_id = {80da7853-f7b7-36a9-8e4c-d7ddb2d9e538},
 group_id = {a2333ea3-15a4-3d40-8d36-f0d9590ca926},
 last_modified = {2017-09-01T15:54:31.713Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {false},
 hidden = {false},
 language = {eng},
 abstract = {Frequency and intensity DLs were compared in humans and monkeys using a repeating standard "yes-no" procedure in which subjects reported frequency increments, frequency decrements, intensity increments, or intensity decrements in an ongoing train of 1.0-kHz tone bursts. There was only one experimental condition (intensity increments) in which monkey DLs (1.5-2.0 dB) overlapped those of humans (1.0-1.8 dB). For discrimination of both increments and decrements in frequency, monkey DLs (16-33 Hz) were approximately seven times larger than those of humans (2.4-4.8 Hz), and for discrimination of intensity decrements, monkey DLs (4.4-7.0 dB) were very unstable and larger than those of humans (1.0-1.8 dB). For intensity increment discrimination, humans and monkeys also exhibited similar DLs as SL was varied. However, for frequency increment discrimination, best DLs for humans occurred at a high (50 dB) SL, whereas best DLs for monkeys occurred at a moderate (30 dB) SL. Results are discussed in terms of various neural mechanisms that might be differentially engaged by humans and monkeys in performing these tasks; for example, different amounts of temporal versus rate coding in frequency discrimination, and different mechanisms for monitoring rate decreases in intensity discrimination. The implications of these data for using monkeys as models of human speech sound discrimination are also discussed.},
 bibtype = {article},
 author = {Sinnott, J. and Petersen, M. and Hopp, S.},
 number = {6}
}

Paper  doi  abstract   bibtex   

@article{kerker_is_1982,
	title = {Is the central dogma of flow cytometry true: {That} fluorescence intensity is proportional to cellular dye content?},
	volume = {3},
	issn = {0196-4763},
	url = {http://doi.wiley.com/10.1002/cyto.990030202},
	doi = {10.1002/cyto.990030202},
	abstract = {Measurements and theoretical calculations of fluorescent emission from four samples of polystyrene microspheres (diameter 0.92, 1.63, 1.90 and 4.18 microns) containing the same fluorescent dye show a general dependence upon particle size, emission angle, and polarization conditions. However, for the excitation and detection conditions used in flow cytometry, the relative fluorescent intensities measured for the four particle sizes are proportional to the dye content to +10\% accuracy, independent of particle size. Accordingly, the central dogma of flow cytometry 'that fluorescence is proportional to cellular dye content' is valid to this accuracy for these solid, highly refractive polymer particles. Most mammalian cells are much less refractive, therefore, should conform more closely to the central dogma.},
	number = {2},
	journal = {Cytometry},
	author = {Kerker, M and Van Dilla, M a and Brunsting, A and Kratohvil, J P and Hsu, P and Wang, D S and Gray, J W and Langlois, R G},
	year = {1982},
	pmid = {7140481},
	keywords = {Animals, Biophysical Phenomena, Biophysics, Cells, Flow cytometry, Fluorescent Dyes, microspheres, Particle Size},
	pages = {71--78},
	file = {Kerker et al_1982_Is the central dogma of flow cytometry true.pdf:/Users/baptiste/Library/Application Support/Zotero/Profiles/d9rq1atq.default/zotero/storage/8QGMSGE9/Kerker et al_1982_Is the central dogma of flow cytometry true.pdf:application/pdf}
}

Paper  bibtex   

@article{
 title = {Uniformity of monkey striate cortex: a parallel relationship between field size, scatter, and magnification factor},
 type = {article},
 year = {1974},
 keywords = {Animals,Brain Mapping,Dominance, Cerebral,Functional Laterality,Macaca mulatta/anatomy & histology,Macaca/anatomy & histology,Mathematics,Orientation,Visual Cortex/anatomy & histology/physiology,Visual Fields,Visual Perception/physiology},
 pages = {295-305},
 volume = {158},
 id = {2cd9ec9a-0494-33f9-b6b3-b4160dd7dbd2},
 created = {2017-09-01T15:54:30.493Z},
 file_attached = {true},
 profile_id = {80da7853-f7b7-36a9-8e4c-d7ddb2d9e538},
 group_id = {a2333ea3-15a4-3d40-8d36-f0d9590ca926},
 last_modified = {2017-09-01T15:54:30.610Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {false},
 hidden = {false},
 language = {eng},
 bibtype = {article},
 author = {Hubel, D. and Wiesel, T.},
 number = {3}
}