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\n@article{AHMADPOUR2024109326,\ntitle = {Deep learning-augmented T-junction droplet generation},\njournal = {iScience},\nvolume = {27},\nnumber = {4},\npages = {109326},\nyear = {2024},\nissn = {2589-0042},\ndoi = {https://doi.org/10.1016/j.isci.2024.109326},\nurl = {https://www.sciencedirect.com/science/article/pii/S2589004224005479},\nauthor = {Abdollah Ahmadpour and Mostafa Shojaeian and Savas Tasoglu},\nkeywords = {Fluidics, Physics, Computer science},\nabstract = {Droplet generation technology has become increasingly important in a wide range of applications, including biotechnology and chemical synthesis. T-junction channels are commonly used for droplet generation due to their integration capability of a larger number of droplet generators in a compact space. In this study, a finite element analysis (FEA) approach is employed to simulate droplet production and its dynamic regimes in a T-junction configuration and collect data for post-processing analysis. Next, image analysis was performed to calculate the droplet length and determine the droplet generation regime. Furthermore, machine learning (ML) and deep learning (DL) algorithms were applied to estimate outputs through examination of input parameters within the simulation range. At the end, a graphical user interface (GUI) was developed for estimation of the droplet characteristics based on inputs, enabling the users to preselect their designs with comparable microfluidic configurations within the studied range.}\n}\n\n
@article{https://doi.org/10.1002/adem.202301217,\nauthor = {Shojaeian, Mostafa and Yetisen, Ali K. and Tasoglu, Savas},\ntitle = {Anisotropic Wettability Induced by Femtosecond Laser Ablation},\njournal = {Advanced Engineering Materials},\nvolume = {26},\nnumber = {2},\npages = {2301217},\nkeywords = {anisotropic wettability, femtosecond lasers, laser ablation, surface functionalization},\ndoi = {https://doi.org/10.1002/adem.202301217},\nurl = {https://onlinelibrary.wiley.com/doi/abs/10.1002/adem.202301217},\neprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/adem.202301217},\nabstract = {Laser ablation has been utilized for locally and selectively modifying the surface wettability of materials in situ and enabling on-demand microfabrication. The anisotropic wettability has been observed on chemical and/or topographical patterns, such as an array of laser-inscribed strips with spacings, created on surfaces during the fabrication process. Herein, the effectiveness of the femtosecond laser ablation is evaluated in selectively modifying surface wettability. The areas processed by laser ablation exhibit anisotropic wetting behavior, even after the laser strips are overlapped. The laser-induced anisotropic surface wettability is present in space governed by laser scanning speed, scan/strip overlap, laser fluence, scan repetition, and bidirectional scanning angle. Moreover, the femtosecond laser ablation process is optimized to enhance the conventional laser inscription, leading to a modified and consistent methodology to achieve cost-effective fabrication.},\nyear = {2024}\n}\n\n
@article{ONURUYGUN2024109190,\ntitle = {Impedimetric Antimicrobial Peptide Biosensor for the Detection of HIV envelope protein gp120},\njournal = {iScience},\npages = {109190},\nyear = {2024},\nissn = {2589-0042},\ndoi = {https://doi.org/10.1016/j.isci.2024.109190},\nurl = {https://www.sciencedirect.com/science/article/pii/S2589004224004115},\nauthor = {Zihni {Onur UYGUN} and Savas TASOGLU},\nkeywords = {Biosensors, Electrochemical impedance spectroscopy, HIV, AIDS, MXene},\nabstract = {Summary\nThis study presents the design and implementation of an antimicrobial peptide-based electrochemical impedance spectroscopy (EIS) based biosensor system. The biosensor consists of gold coated carbon electrode with MXene and silver nanoparticles (AgNPs) for the label-free detection of the Human Immunodeficiency Virus (HIV) envelope protein gp120. Scanning electron microscopy was used to confirm the presence and distribution of MXene and AgNPs on the biosensor surface. The employment of the antimicrobial peptide on the electrode surface minimized the denaturation of biorecognition receptor to ensure reliable and stable performance. The biosensor exhibited a linear range of 10-4000 pg mL-1 for gp120 detection, demonstrating good repeatability in real samples. Limit of detection (LOD) and limit of quantification (LOQ) were also calculated as 0.05 pg mL-1 and 0.14 pg mL-1, respectively. This biosensing platform has promising applications in the detection of HIV in clinical and point-of-care settings.}\n}\n\n
@article{abdullah_machine_2024,\n\ttitle = {Machine learning‐enabled optimization of melt electro‐writing three‐dimensional printing},\n\tissn = {2692-4560, 2692-4560},\n\turl = {https://onlinelibrary.wiley.com/doi/10.1002/agt2.495},\n\tdoi = {10.1002/agt2.495},\n\tabstract = {Abstract\n Melt electrowriting (MEW) is a solvent‐free (i.e., no volatile chemicals), a high‐resolution three‐dimensional (3D) printing method that enables the fabrication of semi‐flexible structures with rigid polymers. Despite its advantages, the MEW process is sensitive to changes in printing parameters (e.g., voltage, printing pressure, and temperature), which can cause fluid column breakage, jet lag, and/or fiber pulsing, ultimately deteriorating the resolution and printing quality. In spite of the commonly used error‐and‐trial method to determine the most suitable parameters, here, we present a machine learning (ML)‐enabled image analysis‐based method for determining the optimum MEW printing parameters through an easy‐to‐use graphical user interface (GUI). We trained five different ML algorithms using 168 MEW 3D print samples, among which the Gaussian process regression ML model yielded 93\\% accuracy of the variability in the dependent variable, 0.12329 on root mean square error for the validation set and 0.015201 mean square error in predicting line thickness. Integration of ML with a control feedback loop and MEW can reduce the error‐and‐trial steps prior to the 3D printing process, decreasing the printing time (i.e., increasing the overall throughput of MEW) and material waste (i.e., improving the cost‐effectiveness of MEW). Moreover, embedding a trained ML model with the feedback control system in a GUI facilitates a more straightforward use of ML‐based optimization techniques in the industrial section (i.e., for users with no ML skills).},\n\tlanguage = {en},\n\turldate = {2024-01-25},\n\tjournal = {Aggregate},\n\tauthor = {Abdullah, Ahmed Choukri and Ozarslan, Olgac and Farshi, Sara Soltanabadi and Dabbagh, Sajjad Rahmani and Tasoglu, Savas},\n\tmonth = jan,\n\tyear = {2024},\n\tpages = {e495},\n\tfile = {Full Text:files/441/Abdullah et al. - 2024 - Machine learning‐enabled optimization of melt elec.pdf:application/pdf},\n}\n\n
@article{yigci_loop-mediated_2023,\n\ttitle = {Loop-{Mediated} {Isothermal} {Amplification}-{Integrated} {CRISPR} {Methods} for {Infectious} {Disease} {Diagnosis} at {Point} of {Care}},\n\tvolume = {8},\n\tissn = {2470-1343, 2470-1343},\n\turl = {https://pubs.acs.org/doi/10.1021/acsomega.3c04422},\n\tdoi = {10.1021/acsomega.3c04422},\n\tabstract = {Infectious diseases continue to pose an imminent threat to global public health, leading to high numbers of deaths every year and disproportionately impacting developing countries where access to healthcare is limited. Biological, environmental, and social phenomena, including climate change, globalization, increased population density, and social inequity, contribute to the emergence of novel communicable diseases. Rapid and accurate diagnoses of infectious diseases are essential to preventing the transmission of infectious diseases. Although some commonly used diagnostic technologies provide highly sensitive and specific measurements, limitations including the requirement for complex equipment/infrastructure and refrigeration, the need for trained personnel, long sample processing times, and high cost remain unresolved. To ensure global access to affordable diagnostic methods, loop-mediated isothermal amplification (LAMP) integrated clustered regularly interspaced short palindromic repeat (CRISPR) based pathogen detection has emerged as a promising technology. Here, LAMP-integrated CRISPR-based nucleic acid detection methods are discussed in point-of-care (PoC) pathogen detection platforms, and current limitations and future directions are also identified.},\n\tlanguage = {en},\n\tnumber = {46},\n\turldate = {2024-01-25},\n\tjournal = {ACS Omega},\n\tauthor = {Yigci, Defne and Atçeken, Nazente and Yetisen, Ali K. and Tasoglu, Savas},\n\tmonth = nov,\n\tyear = {2023},\n\tpages = {43357--43373},\n\tfile = {Full Text:files/443/Yigci et al. - 2023 - Loop-Mediated Isothermal Amplification-Integrated .pdf:application/pdf},\n}\n\n\n
@article{yigci_aibased_2023,\n\ttitle = {{AI}‐{Based} {Metamaterial} {Design} for {Wearables}},\n\tissn = {2751-1219, 2751-1219},\n\turl = {https://onlinelibrary.wiley.com/doi/10.1002/adsr.202300109},\n\tdoi = {10.1002/adsr.202300109},\n\tabstract = {Abstract\n Continuous monitoring of physiological parameters has remained an essential component of patient care. With an increased level of consciousness regarding personal health and wellbeing, the scope of physiological monitoring has extended beyond the hospital. From implanted rhythm devices to non‐contact video monitoring for critically ill patients and at‐home health monitors during Covid‐19, many applications have enabled continuous health monitorization. Wearable health sensors have allowed chronic patients as well as seemingly healthy individuals to track a wide range of physiological and pharmacological parameters including movement, heart rate, blood glucose, and sleep patterns using smart watches or textiles, bracelets, and other accessories. The use of metamaterials in wearable sensor design has offered unique control over electromagnetic, mechanical, acoustic, optical, or thermal properties of matter, enabling the development of highly sensitive, user‐friendly, and lightweight wearables. However, metamaterial design for wearables has relied heavily on manual design processes including human‐intuition‐based and bio‐inspired design. Artificial intelligence (AI)‐based metamaterial design can support faster exploration of design parameters, allow efficient analysis of large data‐sets, and reduce reliance on manual interventions, facilitating the development of optimal metamaterials for wearable health sensors. Here, AI‐based metamaterial design for wearable healthcare is reviewed. Current challenges and future directions are discussed.},\n\tlanguage = {en},\n\turldate = {2024-01-25},\n\tjournal = {Advanced Sensor Research},\n\tauthor = {Yigci, Defne and Ahmadpour, Abdollah and Tasoglu, Savas},\n\tmonth = oct,\n\tyear = {2023},\n\tpages = {2300109},\n\tfile = {Full Text:files/445/Yigci et al. - 2023 - AI‐Based Metamaterial Design for Wearables.pdf:application/pdf},\n}\n\n
@article{akbari_nakhjavani_electrochemiluminescent_2023,\n\ttitle = {Electrochemiluminescent immunosensor for detection of carcinoembryonic antigen using luminol-coated silver nanoparticles},\n\tvolume = {190},\n\tissn = {0026-3672},\n\turl = {http://dx.doi.org/10.1007/s00604-023-05656-8},\n\tdoi = {10.1007/s00604-023-05656-8},\n\tabstract = {Recently, electrochemiluminescent (ECL) immunosensors have received much\nattention in the field of biomarker detection. Here, a highly enhanced ECL\nimmunosensing platform was designed for ultrasensitive detection of\ncarcinoembryonic antigen (CEA). The surface of the glassy carbon electrode\nwas enhanced by applying functional nanostructures such as thiolated\ngraphene oxide (S-GO) and streptavidin-coated gold nanoparticles\n(SA-AuNPs). The selectivity and sensitivity of the designed immunosensor\nwere improved by entrapping CEA biomolecules using a sandwich approach.\nLuminol/silver nanoparticles (Lu-SNPs) were applied as the main core of\nthe signaling probe, which were then coated with streptavidin to provide\noverloading of the secondary antibody. The highly ECL signal enhancement\nwas obtained due to the presence of horseradish peroxidase (HRP) in the\nsignaling probe, in which the presence of H2O2 further amplified the\nintensity of the signals. The engineered immunosensor presented excellent\nsensitivity for CEA detection, with limit of detection (LOD) and linear\ndetection range (LDR) values of 58 fg mL-1 and 0.1 pg mL-1 to 5 pg mL-1\n(R2 = 0.9944), respectively. Besides its sensitivity, the fabricated ECL\nimmunosensor presented outstanding selectivity for the detection of CEA in\nthe presence of various similar agents. Additionally, the developed\nimmunosensor showed an appropriate repeatability (RSD 3.8\\%) and proper\nstability (2 weeks). Having indicated a robust performance in the real\nhuman serum with stated LOD and LDR, the engineered immunosensor can be\nconsidered for the detection and monitoring of CEA in the clinic.},\n\tnumber = {2},\n\tjournal = {Mikrochim. Acta},\n\tauthor = {Akbari Nakhjavani, Sattar and Khalilzadeh, Balal and Afsharan, Hadi and Hosseini, Nashmin and Ghahremani, Mohammad Hossein and Carrara, Sandro and Tasoglu, Savas and Omidi, Yadollah},\n\tmonth = jan,\n\tyear = {2023},\n\tkeywords = {Bio-nanocomposite, Biosensor, Breast cancer, Electrochemiluminescence, Immunosensor, Savas Scholar},\n\tpages = {77},\n}\n\n\n
@article{torun_microfluidic_2023,\n\ttitle = {Microfluidic contact lenses for ocular diagnostics and drug delivery},\n\tvolume = {4},\n\tissn = {2688-4011},\n\turl = {https://onlinelibrary.wiley.com/doi/10.1002/nano.202200202},\n\tdoi = {10.1002/nano.202200202},\n\tnumber = {1},\n\tabstract = {The human eye and tear provide essential physiological information for the detection of ocular dysfunctions and therapy monitoring. The measurements of biomarkers in tear composition are critical for disease diagnosis and early interventions. Hence, significant efforts are dedicated to the development of functional contact lenses that can quantify tear analytes and ocular physiological condition. The combination of microfluidics and contact lens technologies offer real-time monitoring of ocular physiology and timely detection of eye disorders through wireless components. This review discusses the fundamentals of microfluidic contact lenses and their diverse applications in ophthalmic diagnostics and drug delivery. It also elucidates the strategies for the commercialization of microfluidic contact lenses to create clinical and point-of-care products.},\n\tjournal = {Nano Sel.},\n\tauthor = {Torun, Hulya and Fazla, Bartu and Arman, Samaneh and Ozdalgic, Berin and Yetisen, Ali K and Tasoglu, Savas},\n\tmonth = jan,\n\tyear = {2023},\n\tnote = {Publisher: Wiley},\n\tkeywords = {Savas Scholar},\n\tpages = {79--89},\n}\n\n\n
@article{dam_wound_2023,\n\ttitle = {Wound healing strategies based on nanoparticles incorporated in hydrogel wound patches},\n\tvolume = {13},\n\tissn = {2046-2069},\n\turl = {http://dx.doi.org/10.1039/d3ra03477a},\n\tdoi = {10.1039/d3ra03477a},\n\tabstract = {The intricate, tightly controlled mechanism of wound healing that is a\nvital physiological mechanism is essential to maintaining the skin's\nnatural barrier function. Numerous studies have focused on wound healing\nas it is a massive burden on the healthcare system. Wound repair is a\ncomplicated process with various cell types and microenvironment\nconditions. In wound healing studies, novel therapeutic approaches have\nbeen proposed to deliver an effective treatment. Nanoparticle-based\nmaterials are preferred due to their antibacterial activity,\nbiocompatibility, and increased mechanical strength in wound healing. They\ncan be divided into six main groups: metal NPs, ceramic NPs, polymer NPs,\nself-assembled NPs, composite NPs, and nanoparticle-loaded hydrogels. Each\ngroup shows several advantages and disadvantages, and which material will\nbe used depends on the type, depth, and area of the wound. Better wound\ncare/healing techniques are now possible, thanks to the development of\nwound healing strategies based on these materials, which mimic the\nextracellular matrix (ECM) microenvironment of the wound. Bearing this in\nmind, here we reviewed current studies on which NPs have been used in\nwound healing and how this strategy has become a key biotechnological\nprocedure to treat skin infections and wounds.},\n\tnumber = {31},\n\tjournal = {RSC Adv.},\n\tauthor = {Dam, Paulami and Celik, Merve and Ustun, Merve and Saha, Sayantan and Saha, Chirantan and Kacar, Elif Ayse and Kugu, Senanur and Karagulle, Elif Naz and Tasoglu, Savaş and Buyukserin, Fatih and Mondal, Rittick and Roy, Priya and Macedo, Maria L R and Franco, Octávio L and Cardoso, Marlon H and Altuntas, Sevde and Mandal, Amit Kumar},\n\tmonth = jul,\n\tyear = {2023},\n\tkeywords = {Savas Scholar},\n\tpages = {21345--21364},\n}\n\n\n
@article{rezapour_sarabi_bioprinting_2023,\n\ttitle = {Bioprinting in {Microgravity}},\n\tvolume = {9},\n\tissn = {2373-9878},\n\turl = {http://dx.doi.org/10.1021/acsbiomaterials.3c00195},\n\tdoi = {10.1021/acsbiomaterials.3c00195},\n\tabstract = {Bioprinting as an extension of 3D printing offers capabilities for\nprinting tissues and organs for application in biomedical engineering.\nConducting bioprinting in space, where the gravity is zero, can enable new\nfrontiers in tissue engineering. Fabrication of soft tissues, which\nusually collapse under their own weight, can be accelerated in\nmicrogravity conditions as the external forces are eliminated.\nFurthermore, human colonization in space can be supported by providing\ncritical needs of life and ecosystems by 3D bioprinting without relying on\ncargos from Earth, e.g., by development and long-term employment of living\nengineered filters (such as sea sponges-known as critical for initiating\nand maintaining an ecosystem). This review covers bioprinting methods in\nmicrogravity along with providing an analysis on the process of shipping\nbioprinters to space and presenting a perspective on the prospects of\nzero-gravity bioprinting.},\n\tnumber = {6},\n\tjournal = {ACS Biomater Sci Eng},\n\tauthor = {Rezapour Sarabi, Misagh and Yetisen, Ali K and Tasoglu, Savas},\n\tmonth = jun,\n\tyear = {2023},\n\tkeywords = {3D bioprinting, microgravity, regenerative medicine, Savas Scholar, space exploration, tissue engineering},\n\tpages = {3074--3083},\n}\n\n\n
@article{tarar_bayesian_2023,\n\ttitle = {Bayesian machine learning optimization of microneedle design for biological fluid sampling},\n\tvolume = {2},\n\tissn = {2635-0998},\n\turl = {http://xlink.rsc.org/?DOI=D3SD00103B},\n\tdoi = {10.1039/d3sd00103b},\n\tabstract = {The deployment of microneedles in biological fluid sampling and drug\ndelivery is an emerging field in biotechnology, which contributes greatly\nto minimally-invasive methods in medicine.},\n\tnumber = {4},\n\tjournal = {Sens. Diagn.},\n\tauthor = {Tarar, Ceren and Aydın, Erdal and Yetisen, Ali K and Tasoglu, Savas},\n\tyear = {2023},\n\tnote = {Publisher: Royal Society of Chemistry (RSC)},\n\tkeywords = {Savas Scholar},\n\tpages = {858--866},\n}\n\n\n
@article{yasli_additive_2023,\n\ttitle = {Additive manufacturing and three-dimensional printing in obstetrics and gynecology: a comprehensive review},\n\tissn = {0932-0067},\n\turl = {http://dx.doi.org/10.1007/s00404-023-06912-1},\n\tdoi = {10.1007/s00404-023-06912-1},\n\tabstract = {Three-dimensional (3D) printing, also known as additive manufacturing, is\na technology used to create complex 3D structures out of a digital model\nthat can be almost any shape. Additive manufacturing allows the creation\nof customized, finely detailed constructs. Improvements in 3D printing,\nincreased 3D printer availability, decreasing costs, development of\nbiomaterials, and improved cell culture techniques have enabled complex,\nnovel, and customized medical applications to develop. There have been\nrapid development and utilization of 3D printing technologies in\northopedics, dentistry, urology, reconstructive surgery, and other health\ncare areas. Obstetrics and Gynecology (OBGYN) is an emerging application\nfield for 3D printing. This technology can be utilized in OBGYN for\npreventive medicine, early diagnosis, and timely treatment of\nwomen-and-fetus-specific health issues. Moreover, 3D printed simulations\nof surgical procedures enable the training of physicians according to the\nneeds of any given procedure. Herein, we summarize the technology and\nmaterials behind additive manufacturing and review the most recent\nadvancements in the application of 3D printing in OBGYN studies, such as\ndiagnosis, surgical planning, training, simulation, and customized\nprosthesis. Furthermore, we aim to give a future perspective on the\nintegration of 3D printing and OBGYN applications and to provide insight\ninto the potential applications.},\n\tjournal = {Arch. Gynecol. Obstet.},\n\tauthor = {Yasli, Mert and Dabbagh, Sajjad Rahmani and Tasoglu, Savas and Aydin, Serdar},\n\tmonth = jan,\n\tyear = {2023},\n\tkeywords = {3D printing, Additive manufacturing, Bioprinting, Customized devices, Gynecology, Savas Scholar},\n}\n\n\n
@article{ozdalgic_smartphone_2023,\n\ttitle = {Smartphone and wearable diagnostics},\n\tvolume = {23},\n\tissn = {1473-7159},\n\turl = {http://dx.doi.org/10.1080/14737159.2023.2203817},\n\tdoi = {10.1080/14737159.2023.2203817},\n\tnumber = {5},\n\tjournal = {Expert Rev. Mol. Diagn.},\n\tauthor = {Ozdalgic, Berin and Yetisen, Ali K and Tasoglu, Savas},\n\tmonth = may,\n\tyear = {2023},\n\tkeywords = {Artificial Intelligence, Diagnostics, Health care, Savas Scholar, Smartphones, Wearable biosensors},\n\tpages = {357--359},\n}\n\n\n
@article{ahmadpour_microneedle_2023,\n\ttitle = {Microneedle arrays integrated with microfluidic systems: {Emerging} applications and fluid flow modeling},\n\tvolume = {17},\n\tissn = {1932-1058},\n\turl = {http://dx.doi.org/10.1063/5.0121578},\n\tdoi = {10.1063/5.0121578},\n\tabstract = {Microneedle arrays are patches of needles at micro- and nano-scale, which\nare competent and versatile technologies that have been merged with\nmicrofluidic systems to construct more capable devices for biomedical\napplications, such as drug delivery, wound healing, biosensing, and\nsampling body fluids. In this paper, several designs and applications are\nreviewed. In addition, modeling approaches used in microneedle designs for\nfluid flow and mass transfer are discussed, and the challenges are\nhighlighted.},\n\tnumber = {2},\n\tjournal = {Biomicrofluidics},\n\tauthor = {Ahmadpour, Abdollah and Isgor, Pelin Kubra and Ural, Berk and Eren, Busra Nimet and Sarabi, Misagh Rezapour and Muradoglu, Metin and Tasoglu, Savas},\n\tmonth = mar,\n\tyear = {2023},\n\tkeywords = {Savas Scholar},\n\tpages = {021501},\n}\n\n\n
@article{derakhshankhah_electro-conductive_2023,\n\ttitle = {Electro-conductive silica nanoparticles-incorporated hydrogel based on alginate as a biomimetic scaffold for bone tissue engineering application},\n\tissn = {0091-4037},\n\turl = {https://www.tandfonline.com/doi/abs/10.1080/00914037.2022.2155159},\n\tabstract = {An innovative electrically conductive hydrogel was fabricated through the\nincorporation of silica nanoparticles (SiO2 NPs) and poly\n(aniline-co-dopamine)(PANI-co-PDA) into oxidized …},\n\tjournal = {Int. J. Polym. Mater.},\n\tauthor = {Derakhshankhah, H and Eskandani, M and {others}},\n\tyear = {2023},\n\tnote = {Publisher: Taylor \\& Francis},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{akbari_nakhjavani_biosensors_2023,\n\ttitle = {Biosensors for prostate cancer detection},\n\tvolume = {41},\n\tissn = {0167-7799},\n\turl = {http://dx.doi.org/10.1016/j.tibtech.2023.04.001},\n\tdoi = {10.1016/j.tibtech.2023.04.001},\n\tabstract = {Prostate cancer (PC) is one of the most common tumors and a leading cause\nof mortality among men, resulting in {\\textasciitilde}375 000 deaths annually worldwide.\nVarious analytical methods have been designed for quantitative and rapid\ndetection of PC biomarkers. Electrochemical (EC), optical, and magnetic\nbiosensors have been developed to detect tumor biomarkers in clinical and\npoint-of-care (POC) settings. Although POC biosensors have shown potential\nfor detection of PC biomarkers, some limitations, such as the sample\npreparation, should be considered. To tackle such shortcomings, new\ntechnologies have been utilized for development of more practical\nbiosensors. Here, biosensing platforms for the detection of PC biomarkers\nsuch as immunosensors, aptasensors, genosensors, paper-based devices,\nmicrofluidic systems, and multiplex high-throughput platforms, are\ndiscussed.},\n\tnumber = {10},\n\tjournal = {Trends Biotechnol.},\n\tauthor = {Akbari Nakhjavani, Sattar and Tokyay, Begum K and Soylemez, Cansu and Sarabi, Misagh R and Yetisen, Ali K and Tasoglu, Savas},\n\tmonth = oct,\n\tyear = {2023},\n\tkeywords = {biomarkers, biosensors, healthcare, point of care, prostate cancer, Savas Scholar},\n\tpages = {1248--1267},\n}\n\n\n
@article{atceken_pointcare_2023,\n\ttitle = {Point‐of‐{Care} {Diagnostic} {Platforms} for {Loop}‐{Mediated} {Isothermal} {Amplification}},\n\turl = {https://onlinelibrary.wiley.com/doi/abs/10.1002/adem.202201174},\n\tabstract = {The loop‐mediated isothermal amplification (LAMP) method is one of the\nNucleic acid amplification tests (NAATs) that allows for the amplification\nof target regions without using a …},\n\tjournal = {Advanced},\n\tauthor = {Atceken, N and Munzer Alseed, M and {others}},\n\tyear = {2023},\n\tnote = {Publisher: Wiley Online Library},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{nasrollahpour_nanotechnologybased_2023,\n\ttitle = {Nanotechnology‐based electrochemical biosensors for monitoring breast cancer biomarkers},\n\tissn = {0198-6325},\n\turl = {https://onlinelibrary.wiley.com/doi/abs/10.1002/med.21931},\n\tabstract = {Breast cancer is categorized as the most widespread cancer type among\nwomen globally. On‐time diagnosis can decrease the mortality rate by\nmaking the right decision in the …},\n\tjournal = {Med. Res. Rev.},\n\tauthor = {Nasrollahpour, H and Khalilzadeh, B and {others}},\n\tyear = {2023},\n\tnote = {Publisher: Wiley Online Library},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{sarabi_3d-printed_2023,\n\ttitle = {{3D}-{Printed} {Microrobots}: {Translational} {Challenges}},\n\tvolume = {14},\n\tissn = {2072-666X},\n\turl = {http://dx.doi.org/10.3390/mi14061099},\n\tdoi = {10.3390/mi14061099},\n\tabstract = {The science of microrobots is accelerating towards the creation of new\nfunctionalities for biomedical applications such as targeted delivery of\nagents, surgical procedures, tracking and imaging, and sensing. Using\nmagnetic properties to control the motion of microrobots for these\napplications is emerging. Here, 3D printing methods are introduced for the\nfabrication of microrobots and their future perspectives are discussed to\nelucidate the path for enabling their clinical translation.},\n\tnumber = {6},\n\tjournal = {Micromachines (Basel)},\n\tauthor = {Sarabi, Misagh Rezapour and Karagoz, Ahmet Agah and Yetisen, Ali K and Tasoglu, Savas},\n\tmonth = may,\n\tyear = {2023},\n\tkeywords = {3D printing, biomaterials, clinical translation, microrobots, Savas Scholar},\n}\n\n\n
@article{ahmadpour_piezoelectric_2023,\n\ttitle = {Piezoelectric metamaterial blood pressure sensor},\n\tvolume = {5},\n\tissn = {2637-6113},\n\turl = {https://pubs.acs.org/doi/10.1021/acsaelm.3c00344},\n\tdoi = {10.1021/acsaelm.3c00344},\n\tnumber = {6},\n\tabstract = {Continuous blood pressure monitoring allows for detecting the\nearly onset of cardiovascular disease and assessing personal health status.\nConventional piezoelectric blood pressure monitoring techniques have the\nability to sense biosignals due to their good dynamic responses but have\nsignificant drawbacks in terms of power consumption, which limits the operation\nof blood pressure sensors. Although piezoelectric materials can be used to\nenhance the self-powered blood pressure sensor responses, the structure of the\npiezoelectric element can be modified to achieve a higher output voltage. Here, a\nstructural study on piezoelectric metamaterials in blood pressure sensors is\ndemonstrated, and output voltages are computed and compared to other\narchitectures. Next, a Bayesian optimization framework is defined to get the\noptimal design according to the metamaterial design space. Machine learning\nalgorithms were used for applying regression models to a simulated dataset, and\na 2D map was visualized for key parameters. Finally, a time-dependent blood pressure was applied to the inner surface of an artery\nvessel inside a 3D tissue skin model to compare the output voltage for different metamaterials. Results revealed that all types of\nmetamaterials can generate a higher electric potential in comparison to normal square-shaped piezoelectric elements. Bayesian\noptimization showed that honeycomb metamaterials had the optimal performance in generating output voltage, which was validated\naccording to regression model analysis resulting from machine learning algorithms. The simulation of time-dependent blood\npressure in a 3D skin tissue model revealed that the design suggested by the Bayesian optimization process can generate an electric\npotential more than two times greater than that of a conventional square-shaped piezoelectric element.},\n\tjournal = {ACS Appl. Electron. Mater.},\n\tauthor = {Ahmadpour, Abdollah and Yetisen, Ali K and Tasoglu, Savas},\n\tmonth = jun,\n\tyear = {2023},\n\tnote = {Publisher: American Chemical Society (ACS)},\n\tkeywords = {Savas Scholar},\n\tpages = {3280--3290},\n}\n\n\n
@article{tarar_machine_2023,\n\ttitle = {Machine {Learning}-{Enabled} {Optimization} of {Interstitial} {Fluid} {Collection} via a {Sweeping} {Microneedle} {Design}},\n\tvolume = {8},\n\tissn = {2470-1343},\n\turl = {http://dx.doi.org/10.1021/acsomega.3c01744},\n\tdoi = {10.1021/acsomega.3c01744},\n\tabstract = {Microneedles (MNs) allow for biological fluid sampling and drug delivery\ntoward the development of minimally invasive diagnostics and treatment in\nmedicine. MNs have been fabricated based on empirical data such as\nmechanical testing, and their physical parameters have been optimized\nthrough the trial-and-error method. While these methods showed adequate\nresults, the performance of MNs can be enhanced by analyzing a large data\nset of parameters and their respective performance using artificial\nintelligence. In this study, finite element methods (FEMs) and machine\nlearning (ML) models were integrated to determine the optimal physical\nparameters for a MN design in order to maximize the amount of collected\nfluid. The fluid behavior in a MN patch is simulated with several\ndifferent physical and geometrical parameters using FEM, and the resulting\ndata set is used as the input for ML algorithms including multiple linear\nregression, random forest regression, support vector regression, and\nneural networks. Decision tree regression (DTR) yielded the best\nprediction of optimal parameters. ML modeling methods can be utilized to\noptimize the geometrical design parameters of MNs in wearable devices for\napplication in point-of-care diagnostics and targeted drug delivery.},\n\tnumber = {23},\n\tjournal = {ACS Omega},\n\tauthor = {Tarar, Ceren and Aydın, Erdal and Yetisen, Ali K and Tasoglu, Savas},\n\tmonth = jun,\n\tyear = {2023},\n\tkeywords = {Savas Scholar},\n\tpages = {20968--20978},\n}\n\n\n
@article{birtek_machine_2023,\n\ttitle = {Machine learning-augmented fluid dynamics simulations for micromixer educational module},\n\tvolume = {17},\n\tissn = {1932-1058},\n\turl = {http://dx.doi.org/10.1063/5.0146375},\n\tdoi = {10.1063/5.0146375},\n\tabstract = {Micromixers play an imperative role in chemical and biomedical systems.\nDesigning compact micromixers for laminar flows owning a low Reynolds\nnumber is more challenging than flows with higher turbulence. Machine\nlearning models can enable the optimization of the designs and\ncapabilities of microfluidic systems by receiving input from a training\nlibrary and producing algorithms that can predict the outcomes prior to\nthe fabrication process to minimize development cost and time. Here, an\neducational interactive microfluidic module is developed to enable the\ndesign of compact and efficient micromixers at low Reynolds regimes for\nNewtonian and non-Newtonian fluids. The optimization of Newtonian fluids\ndesigns was based on a machine learning model, which was trained by\nsimulating and calculating the mixing index of 1890 different micromixer\ndesigns. This approach utilized a combination of six design parameters and\nthe results as an input data set to a two-layer deep neural network with\n100 nodes in each hidden layer. A trained model was achieved with R2 =\n0.9543 that can be used to predict the mixing index and find the optimal\nparameters needed to design micromixers. Non-Newtonian fluid cases were\nalso optimized using 56700 simulated designs with eight varying input\nparameters, reduced to 1890 designs, and then trained using the same deep\nneural network used for Newtonian fluids to obtain R2 = 0.9063. The\nframework was subsequently used as an interactive educational module,\ndemonstrating a well-structured integration of technology-based modules\nsuch as using artificial intelligence in the engineering curriculum, which\ncan highly contribute to engineering education.},\n\tnumber = {4},\n\tjournal = {Biomicrofluidics},\n\tauthor = {Birtek, Mehmet Tugrul and Alseed, M Munzer and Sarabi, Misagh Rezapour and Ahmadpour, Abdollah and Yetisen, Ali K and Tasoglu, Savas},\n\tmonth = jul,\n\tyear = {2023},\n\tkeywords = {Savas Scholar},\n\tpages = {044101},\n}\n\n\n
@article{dabbagh_biomedical_2022,\n\ttitle = {Biomedical applications of magnetic levitation},\n\tvolume = {2},\n\tissn = {2699-9307},\n\turl = {https://scholar.google.ca/scholar?cluster=12639602581380268001&hl=en&as_sdt=0,5&sciodt=0,5},\n\tdoi = {10.1002/anbr.202100103},\n\tnumber = {3},\n\tjournal = {Adv. Nanobiomed Res.},\n\tabstract = {Magnetic levitation (MagLev) is a user-friendly, electricity-free, accurate, affordable, and label-free platform for chemical and biological applications owing to its ability to suspend and separate a wide range of diamagnetic materials (e.g., plastics, polymers, cells, and proteins) based on their density. Various MagLev designs (e.g., standard, single and double ring, titled, and rotational MagLev setups) are presented in the literature with a trade-off between sensitivity and detection range. Herein, various MagLev designs, the advantages and pitfalls of each method, and current challenges encountered by MagLev platforms are reviewed. Moreover, end applications of MagLev are presented in single-cell and protein analysis, diseases diagnosis (e.g., cancer and hepatitis C), tissue engineering, 3D self-assembly, and forensic case studies to provide an insight regarding the potentials of MagLev.},\n\tauthor = {Dabbagh, Sajjad Rahmani and Alseed, M Munzer and Saadat, Milad and Sitti, Metin and Tasoglu, Savas},\n\tmonth = mar,\n\tyear = {2022},\n\tnote = {Publisher: Wiley},\n\tkeywords = {Savas Scholar},\n\tpages = {2100103},\n}\n\n\n
@article{dabbagh_three-dimensional-bioprinted_2022,\n\ttitle = {Three-dimensional-bioprinted liver chips and challenges},\n\tvolume = {12},\n\tissn = {1454-5101},\n\turl = {https://scholar.google.ca/scholar?cluster=12897305411556603285&hl=en&as_sdt=0,5&sciodt=0,5},\n\tdoi = {10.3390/app12105029},\n\tabstract = {Drug testing, either on animals or on 2D cell cultures, has its\nlimitations due to inaccurate mimicking of human pathophysiology. The\nliver, as one of the key organs that filters and detoxifies the blood, is\nsusceptible to drug-induced injuries. Integrating 3D bioprinting with\nmicrofluidic chips to fabricate organ-on-chip platforms for 3D liver cell\ncultures with continuous perfusion can offer a more physiologically\nrelevant liver-mimetic platform for screening drugs and studying liver\nfunction. The development of organ-on-chip platforms may ultimately\ncontribute to personalized medicine as well as body-on-chip technology\nthat can test drug responses and organ–organ interactions on a single or\nlinked chip model.},\n\tnumber = {10},\n\tjournal = {Appl. Sci.},\n\tauthor = {Dabbagh, Sajjad Rahmani and Ozdalgic, Berin and Mustafaoglu, Nur and Tasoglu, Savas},\n\tmonth = may,\n\tyear = {2022},\n\tnote = {Publisher: MDPI AG},\n\tkeywords = {Savas Scholar},\n\tpages = {5029},\n}\n\n\n
@article{rahmani_dabbagh_3d_2022,\n\ttitle = {{3D} bioprinted organ‐on‐chips},\n\tissn = {2766-8541},\n\turl = {https://scholar.google.ca/scholar?cluster=11803033441446105706&hl=en&as_sdt=0,5&sciodt=0,5},\n\tdoi = {10.1002/agt2.197},\n\tabstract ={Organ-on-a-chip (OOC) platforms recapitulate human in vivo-like conditions more realistically compared to many animal models and conventional two-dimensional cell cultures. OOC setups benefit from continuous perfusion of cell cultures through microfluidic channels, which promotes cell viability and activities. Moreover, microfluidic chips allow the integration of biosensors for real-time monitoring and analysis of cell interactions and responses to administered drugs. Three-dimensional (3D) bioprinting enables the fabrication of multicell OOC platforms with sophisticated 3D structures that more closely mimic human tissues. 3D-bioprinted OOC platforms are promising tools for understanding the functions of organs, disruptive influences of diseases on organ functionality, and screening the efficacy as well as toxicity of drugs on organs. Here, common 3D bioprinting techniques, advantages, and limitations of each method are reviewed. Additionally, recent advances, applications, and potentials of 3D-bioprinted OOC platforms for emulating various human organs are presented. Last, current challenges and future perspectives of OOC platforms are discussed.},\n\tjournal = {Aggregate (Hoboken)},\n\tauthor = {Rahmani Dabbagh, Sajjad and Rezapour Sarabi, Misagh and Birtek, Mehmet Tugrul and Mustafaoglu, Nur and Zhang, Yu Shrike and Tasoglu, Savas},\n\tmonth = may,\n\tyear = {2022},\n\tnote = {Publisher: Wiley},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{rabbi_deep_2022,\n\ttitle = {Deep {Learning}-{Enabled} {Technologies} for {Bioimage} {Analysis}},\n\tvolume = {13},\n\tissn = {2072-666X},\n\turl = {http://dx.doi.org/10.3390/mi13020260},\n\tdoi = {10.3390/mi13020260},\n\tabstract = {Deep learning (DL) is a subfield of machine learning (ML), which has\nrecently demonstrated its potency to significantly improve the\nquantification and classification workflows in biomedical and clinical\napplications. Among the end applications profoundly benefitting from DL,\ncellular morphology quantification is one of the pioneers. Here, we first\nbriefly explain fundamental concepts in DL and then we review some of the\nemerging DL-enabled applications in cell morphology quantification in the\nfields of embryology, point-of-care ovulation testing, as a predictive\ntool for fetal heart pregnancy, cancer diagnostics via classification of\ncancer histology images, autosomal polycystic kidney disease, and chronic\nkidney diseases.},\n\tnumber = {2},\n\tjournal = {Micromachines (Basel)},\n\tauthor = {Rabbi, Fazle and Dabbagh, Sajjad Rahmani and Angin, Pelin and Yetisen, Ali Kemal and Tasoglu, Savas},\n\tmonth = feb,\n\tyear = {2022},\n\tkeywords = {bioimage quantification, cancer diagnosis, cell morphology classification, deep learning, machine learning, Savas Scholar},\n}\n\n\n
@article{tasoglu_toilet-based_2022,\n\ttitle = {Toilet-based continuous health monitoring using urine},\n\tvolume = {19},\n\tissn = {1759-4812},\n\turl = {http://dx.doi.org/10.1038/s41585-021-00558-x},\n\tdoi = {10.1038/s41585-021-00558-x},\n\tabstract = {Regular health monitoring can result in early detection of disease,\naccelerate the delivery of medical care and, therefore, considerably\nimprove patient outcomes for countless medical conditions that affect\npublic health. A substantial unmet need remains for technologies that can\ntransform the status quo of reactive health care to preventive,\nevidence-based, person-centred care. With this goal in mind, platforms\nthat can be easily integrated into people's daily lives and identify a\nrange of biomarkers for health and disease are desirable. However, urine -\na biological fluid that is produced in large volumes every day and can be\nobtained with zero pain, without affecting the daily routine of\nindividuals, and has the most biologically rich content - is discarded\ninto sewers on a regular basis without being processed or monitored.\nToilet-based health-monitoring tools in the form of smart toilets could\noffer preventive home-based continuous health monitoring for early\ndiagnosis of diseases while being connected to data servers (using the\nInternet of Things) to enable collection of the health status of users. In\naddition, machine learning methods can assist clinicians to classify,\nquantify and interpret collected data more rapidly and accurately than\nthey were able to previously. Meanwhile, challenges associated with user\nacceptance, privacy and test frequency optimization should be considered\nto facilitate the acceptance of smart toilets in society.},\n\tnumber = {4},\n\tjournal = {Nat. Rev. Urol.},\n\tauthor = {Tasoglu, Savas},\n\tmonth = apr,\n\tyear = {2022},\n\tkeywords = {Savas Scholar},\n\tpages = {219--230},\n}\n\n\n
@article{yigci_3d_2022,\n\ttitle = {{3D} bioprinted glioma models},\n\turl = {https://iopscience.iop.org/article/10.1088/2516-1091/ac7833/meta},\n\tdoi ={10.1088/2516-1091/ac7833},\n\tabstract = {Glioma is one of the most malignant types of cancer and most gliomas remain incurable. One of the hallmarks of glioma is its invasiveness. Furthermore, glioma cells tend to readily detach from the primary tumor and travel through the brain tissue, making complete tumor resection impossible in many cases. To expand the knowledge regarding the invasive behavior of glioma, evaluate drug resistance, and recapitulate the tumor microenvironment, various modeling strategies were proposed in the last decade, including three-dimensional (3D) biomimetic scaffold-free cultures, organ-on-chip microfluidics chips, and 3D bioprinting platforms, which allow for the investigation on patient-specific treatments. The emerging method of 3D bioprinting technology has introduced a time- and cost-efficient approach to create in vitro models that possess the structural and functional characteristics of human organs and tissues by spatially positioning cells and bioink. Here, we review emerging 3D bioprinted models developed for recapitulating the brain environment and glioma tumors, with the purpose of probing glioma cell invasion and gliomagenesis and discuss the potential use of 4D printing and machine learning applications in glioma modelling.},\n\tjournal = {Progress in},\n\tauthor = {Yigci, D and Sarabi, M R and Ustun, M and Atceken, N and {others}},\n\tyear = {2022},\n\tnote = {Publisher: iopscience.iop.org},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{sokullu_three-dimensional_2022,\n\ttitle = {{THREE}-{DIMENSIONAL} {NEUROVASCULAR} {CO}-{CULTURE} {INSIDE} {A} {MICROFLUIDIC} {INVASION} {CHEMOTAXIS} {CHIP}},\n\turl = {https://scholar.google.ca/scholar?cluster=9917949269638580982&hl=en&as_sdt=0,5&sciodt=0,5},\n\tjournal = {TISSUE},\n\tauthor = {Sokullu, E and Cucuk, L and Polat, I and {others}},\n\tyear = {2022},\n\tnote = {Publisher: MARY ANN LIEBERT, INC 140 …},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{sarabi_magnetic_2022,\n\ttitle = {Magnetic levitation for space exploration},\n\tvolume = {40},\n\tissn = {0167-7799},\n\turl = {http://dx.doi.org/10.1016/j.tibtech.2022.03.010},\n\tdoi = {10.1016/j.tibtech.2022.03.010},\n\tabstract = {Magnetic levitation allows for simulating the microgravity conditions to\nadvance bottom-up tissue engineering, forging regenerative medicine ahead\nto enable space exploration. Here, magnetic levitation methods for\nmicrogravity studies and the biofabrication of 3D cellular structures are\ndiscussed.},\n\tnumber = {8},\n\tjournal = {Trends Biotechnol.},\n\tauthor = {Sarabi, Misagh Rezapour and Yetisen, Ali K and Tasoglu, Savas},\n\tmonth = aug,\n\tyear = {2022},\n\tkeywords = {3D bioprinting, magnetic levitation, microgravity, Savas Scholar, space exploration},\n\tpages = {915--917},\n}\n\n\n
@article{rezapour_sarabi_machine_2022,\n\ttitle = {Machine {Learning}-{Enabled} {Prediction} of {3D}-{Printed} {Microneedle} {Features}},\n\tvolume = {12},\n\tissn = {0265-928X},\n\turl = {http://dx.doi.org/10.3390/bios12070491},\n\tdoi = {10.3390/bios12070491},\n\tabstract = {Microneedles (MNs) introduced a novel injection alternative to\nconventional needles, offering a decreased administration pain and phobia\nalong with more efficient transdermal and intradermal drug delivery/sample\ncollecting. 3D printing methods have emerged in the field of MNs for their\ntime- and cost-efficient manufacturing. Tuning 3D printing parameters with\nartificial intelligence (AI), including machine learning (ML) and deep\nlearning (DL), is an emerging multidisciplinary field for optimization of\nmanufacturing biomedical devices. Herein, we presented an AI framework to\nassess and predict 3D-printed MN features. Biodegradable MNs were\nfabricated using fused deposition modeling (FDM) 3D printing technology\nfollowed by chemical etching to enhance their geometrical precision. DL\nwas used for quality control and anomaly detection in the fabricated MNAs.\nTen different MN designs and various etching exposure doses were used\ncreate a data library to train ML models for extraction of similarity\nmetrics in order to predict new fabrication outcomes when the mentioned\nparameters were adjusted. The integration of AI-enabled prediction with 3D\nprinted MNs will facilitate the development of new healthcare systems and\nadvancement of MNs' biomedical applications.},\n\tnumber = {7},\n\tjournal = {Biosensors},\n\tauthor = {Rezapour Sarabi, Misagh and Alseed, M Munzer and Karagoz, Ahmet Agah and Tasoglu, Savas},\n\tmonth = jul,\n\tyear = {2022},\n\tkeywords = {3D printing, artificial intelligence, deep learning, image processing, machine learning, microneedles, Savas Scholar},\n}\n\n\n
@article{rezapour_sarabi_3d-printed_2022,\n\ttitle = {{3D}-{Printed} {Microneedles} for {Point}-of-{Care} {Biosensing} {Applications}},\n\tvolume = {13},\n\tissn = {2072-666X},\n\turl = {http://dx.doi.org/10.3390/mi13071099},\n\tdoi = {10.3390/mi13071099},\n\tabstract = {Microneedles (MNs) are an emerging technology for user-friendly and\nminimally invasive injection, offering less pain and lower tissue damage\nin comparison to conventional needles. With their ability to extract body\nfluids, MNs are among the convenient candidates for developing biosensing\nsetups, where target molecules/biomarkers are detected by the biosensor\nusing the sample collected with the MNs. Herein, we discuss the 3D\nprinting of microneedle arrays (MNAs) toward enabling point-of-care (POC)\nbiosensing applications.},\n\tnumber = {7},\n\tjournal = {Micromachines (Basel)},\n\tauthor = {Rezapour Sarabi, Misagh and Nakhjavani, Sattar Akbari and Tasoglu, Savas},\n\tmonth = jul,\n\tyear = {2022},\n\tkeywords = {3D printing, biosensing, microneedles, point-of-care, Savas Scholar},\n}\n\n\n
@article{sarabi_disposable_2022,\n\ttitle = {Disposable paper-based microfluidics for fertility testing},\n\tvolume = {25},\n\tissn = {2589-0042},\n\turl = {http://dx.doi.org/10.1016/j.isci.2022.104986},\n\tdoi = {10.1016/j.isci.2022.104986},\n\tabstract = {Fifteen percent of couples of reproductive age suffer from infertility\nglobally and the burden of infertility disproportionately impacts\nresidents of developing countries. Assisted reproductive technologies\n(ARTs), including in vitro fertilization (IVF) and intracytoplasmic sperm\ninjection (ICSI), have been successful in overcoming various reasons for\ninfertility including borderline and severe male factor infertility which\nconsists of 20\\%-30\\% of all infertile cases. Approximately half of male\ninfertility cases stem from suboptimal sperm parameters. Therefore,\nhealthy/normal sperm enrichment and sorting remains crucial in advancing\nreproductive medicine. Microfluidic technologies have emerged as promising\ntools to develop in-home rapid fertility tests and point-of-care (POC)\ndiagnostic tools. Here, we review advancements in fabrication methods for\npaper-based microfluidic devices and their emerging fertility testing\napplications assessing sperm concentration, sperm motility, sperm DNA\nanalysis, and other sperm functionalities, and provide a glimpse into\nfuture directions for paper-based fertility microfluidic systems.},\n\tnumber = {9},\n\tjournal = {iScience},\n\tauthor = {Sarabi, Misagh Rezapour and Yigci, Defne and Alseed, M Munzer and Mathyk, Begum Aydogan and Ata, Baris and Halicigil, Cihan and Tasoglu, Savas},\n\tmonth = sep,\n\tyear = {2022},\n\tkeywords = {Biodevices, Biotechnology, Medical device in health technology, Savas Scholar},\n\tpages = {104986},\n}\n\n\n
@article{sokullu_3d_2022,\n\ttitle = {{3D} engineered neural co-culture model and neurovascular effects of marine fungi-derived citreohybridonol},\n\turl = {https://pubs.aip.org/aip/adv/article/12/9/095102/2819749},\n\tdoi = {10.1063/5.0100452},\n\tabstract = {Marine-based biomolecules are emerging metabolites that have gained attention for developing novel biomaterials, drugs, and pharmaceutical in vitro platforms. Here, we developed a 3D engineered neural co-culture model via a 3D prototyped sliding frame-platform for multi-step UV lithography and investigated the neurovascular potential of citreohybridonol in neuroblastoma treatment. Citreohybridonol was isolated from a sponge-derived fungus Penicillium atrovenetum. The model was characterized by Fourier-transform infrared spectroscopy and scanning electron microscopy analysis. Human umbilical cord vein endothelial cells (HUVECs) and neuroblastoma (SH-SY5Y) cell lines were encapsulated in gelatin methacrylate (GelMA) with and without citreohybridonol. The effect of citreohybridonol on the proliferation capacity of cells was assessed via cell viability and immunostaining assays. GelMA and 3D culture characterization indicated that the cells were successfully encapsulated as axenic and mixed with/without citreohybridonol. The cytotoxic test confirmed that the 3D microenvironment was non-toxic for cultural experiments, and it showed the inhibitory effects of citreohybridonol on SH-SY5Y cells and induced the proliferation of HUVECs. Finally, immunohistochemical staining demonstrated that citreohybridonol suppressed SH-SY5Y cells and induced vascularization of HUVECs in mixed 3D cell culture.},\n\tjournal = {AIP Adv.},\n\tauthor = {Sokullu, E and Polat, İ and Özkaya, F C and El-Neketi, M and Ebrahim, W and {others}},\n\tyear = {2022},\n\tnote = {Publisher: pubs.aip.org},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{ozdalgic_emerging_2022,\n\ttitle = {Emerging {Applications} of {Electrochemical} {Impedance} {Spectroscopy} in {Tear} {Film} {Analysis}},\n\tissn = {0265-928X},\n\turl = {https://www.mdpi.com/2079-6374/12/10/827},\n\tdoi = {10.3390/bios12100827},\n\tabstract = {Human tear film, with a flow rate of 1–3 µL/min, is a rich bodily fluid that transmits a variety of metabolites and hormones containing proteins, lipids and electrolytes that provide clues about ocular and systemic diseases. Analysis of disease biomarkers such as proteins, mRNA, enzymes and cytokines in the tear film, collected by noninvasive methods, can provide significant results for sustaining a predictive, preventive and personalized medicine regarding various diseases such as glaucoma, diabetic retinopathy, keratoconus, dry eye, cancer, Alzheimer’s disease, Parkinson’s disease and COVID-19. Electrochemical impedance spectroscopy (EIS) offers a powerful technique for analyzing these biomarkers. EIS detects electrical equivalent circuit parameters related to biorecognition of receptor–analyte interactions on the electrode surface. This method is advantageous as it performs a label-free detection and allows the detection of non-electroactive compounds that cannot be detected by direct electron transfer, such as hormones and some proteins. Here, we review the opportunities regarding the integration of EIS into tear fluid sampling approaches.},\n\tjournal = {Biosensors},\n\tauthor = {Ozdalgic, B and Gul, M and Uygun, Z O and Atçeken, N and Tasoglu, S},\n\tyear = {2022},\n\tnote = {Publisher: mdpi.com},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{sokullu_microfluidic_2022,\n\ttitle = {Microfluidic invasion chemotaxis platform for {3D} neurovascular {Co}-culture},\n\turl = {https://www.mdpi.com/2311-5521/7/7/238},\n\tdoi = {10.3390/fluids7070238},\n\tabstract = {Abstract\nAdvances in microfabrication and biomaterials have enabled the development of microfluidic chips for studying tissue and organ models. While these platforms have been developed primarily for modeling human diseases, they are also used to uncover cellular and molecular mechanisms through in vitro studies, especially in the neurovascular system, where physiological mechanisms and three-dimensional (3D) architecture are difficult to reconstruct via conventional assays. An extracellular matrix (ECM) model with a stable structure possessing the ability to mimic the natural extracellular environment of the cell efficiently is useful for tissue engineering applications. Conventionally used techniques for this purpose, for example, Matrigels, have drawbacks of owning complex fabrication procedures, in some cases not efficient enough in terms of functionality and expenses. Here, we proposed a fabrication protocol for a GelMA hydrogel, which has shown structural stability and the ability to imitate the natural environment of the cell accurately, inside a microfluidic chip utilizing co-culturing of two human cell lines. The chemical composition of the synthesized GelMA was identified by Fourier transform infrared spectrophotometry (FTIR), its surface morphology was observed by field emission electron microscopy (FESEM), and the structural properties were analyzed by atomic force microscopy (AFM). The swelling behavior of the hydrogel in the microfluidic chip was imaged, and its porosity was examined for 72 h by tracking cell localization using immunofluorescence. GelMA exhibited the desired biomechanical properties, and the viability of cells in both platforms was more than 80% for seven days. Furthermore, GelMA was a viable platform for 3D cell culture studies and was structurally stable over long periods, even when prepared by photopolymerization in a microfluidic platform. This work demonstrated a viable strategy to conduct co-culturing experiments as well as modeling invasion and migration events. This microfluidic assay may have application in drug delivery and dosage optimization studies.},\n\tjournal = {Fluids Barriers CNS},\n\tauthor = {Sokullu, E and Cücük, Z L and Sarabi, M R and Birtek, M T and Bagheri, H S and {others}},\n\tyear = {2022},\n\tnote = {Publisher: mdpi.com},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{ozdalgic_3d-printed_2022,\n\ttitle = {{3D}-printed contact lenses: challenges towards translation and commercialization},\n\turl = {https://www.futuremedicine.com/doi/full/10.2217/3dp-2022-0010},\n\tdoi = {10.2217/3dp-2022-0010},\n\tabstract = {Smart contact lenses are promising platforms for ocular diagnosis and\ntreatment. Developments in microfabrication techniques and miniaturization\nmethods played a …},\n\tjournal = {Journal of 3D printing in},\n\tauthor = {Ozdalgic, B and Yetisen, A K and Tasoglu, S},\n\tyear = {2022},\n\tnote = {Publisher: Future Medicine},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{atceken_crispr-cas-integrated_2022,\n\ttitle = {{CRISPR}-{Cas}-{Integrated} {LAMP}},\n\tvolume = {12},\n\tissn = {0265-928X},\n\turl = {http://dx.doi.org/10.3390/bios12111035},\n\tdoi = {10.3390/bios12111035},\n\tabstract = {Pathogen-specific point-of-care (PoC) diagnostic tests have become an\nimportant need in the fight against infectious diseases and epidemics in\nrecent years. PoC diagnostic tests are designed with the following\nparameters in mind: rapidity, accuracy, sensitivity, specificity, and ease\nof use. Molecular techniques are the gold standard for pathogen detection\ndue to their accuracy and specificity. There are various limitations in\nadapting molecular diagnostic methods to PoC diagnostic tests. Efforts to\novercome limitations are focused on the development of integrated\nmolecular diagnostics by utilizing the latest technologies available to\ncreate the most successful PoC diagnostic platforms. With this point of\nview, a new generation technology was developed by combining loop-mediated\nisothermal amplification (LAMP) technology with clustered regularly\ninterspaced short palindromic repeat (CRISPR)-associated (CRISPR-Cas)\ntechnology. This integrated approach benefits from the properties of LAMP\ntechnology, namely its high efficiency, short turnaround time, and the\nlack of need for a complex device. It also makes use of the programmable\nfunction of CRISPR-Cas technology and the collateral cleavage activity of\ncertain Cas proteins that allow for convenient reporter detection. Thus,\nthis combined technology enables the development of PoC diagnostic tests\nwith high sensitivity, specificity, and ease of use without the need for\ncomplicated devices. In this review, we discuss the advantages and\nlimitations of the CRISPR/Cas combined LAMP technology. We review current\nlimitations to convert CRISPR combined LAMP into pathogen-specific PoC\nplatforms. Furthermore, we point out the need to design more useful PoC\nplatforms using microfabrication technologies by developing strategies\nthat overcome the limitations of this new technology, reduce its\ncomplexity, and reduce the risk of contamination.},\n\tnumber = {11},\n\tjournal = {Biosensors},\n\tauthor = {Atçeken, Nazente and Yigci, Defne and Ozdalgic, Berin and Tasoglu, Savas},\n\tmonth = nov,\n\tyear = {2022},\n\tkeywords = {clustered regularly interspaced short palindromic repeat (CRISPR)-associated (CRISPR-Cas), CRISPR/Cas combined LAMP technology, loop-mediated isothermal amplification (LAMP), point-of-care (PoC) platform, Savas Scholar},\n}\n\n\n
@article{rahmani_dabbagh_machine_2022,\n\ttitle = {Machine learning-enabled optimization of extrusion-based {3D} printing},\n\tvolume = {206},\n\tissn = {1046-2023},\n\turl = {http://dx.doi.org/10.1016/j.ymeth.2022.08.002},\n\tdoi = {10.1016/j.ymeth.2022.08.002},\n\tabstract = {Machine learning (ML) and three-dimensional (3D) printing are among the\nfastest-growing branches of science. While ML can enable computers to\nindependently learn from available data to make decisions with minimal\nhuman intervention, 3D printing has opened up an avenue for modern,\nmulti-material, manufacture of complex 3D structures with a rapid\nturn-around ability for users with limited manufacturing experience.\nHowever, the determination of optimum printing parameters is still a\nchallenge, increasing pre-printing process time and material wastage.\nHere, we present the first integration of ML and 3D printing through an\neasy-to-use graphical user interface (GUI) for printing parameter\noptimization. Unlike the widely held orthogonal design used in most of the\n3D printing research, we, for the first time, used nine different\ncomputer-aided design (CAD) images and in order to enable ML algorithms to\ndistinguish the difference between designs, we devised a self-designed\nmethod to calculate the "complexity index" of CAD designs. In addition,\nfor the first time, the similarity of the print outcomes and CAD images\nare measured using four different self-designed labeling methods (both\nmanually and automatically) to figure out the best labeling method for ML\npurposes. Subsequently, we trained eight ML algorithms on 224 datapoints\nto identify the best ML model for 3D printing applications. The "gradient\nboosting regression" model yields the best prediction performance with an\nR-2 score of 0.954. The ML-embedded GUI developed in this study enables\nusers (either skilled or unskilled in 3D printing and/or ML) to simply\nupload a design (desired to print) to the GUI along with desired printing\ntemperature and pressure to obtain the approximate similarity in the case\nof actual 3D printing of the uploaded design. This ultimately can prevent\nerror-and-trial steps prior to printing which in return can speed up\noverall design-to-end-product time with less material waste and more\ncost-efficiency.},\n\tjournal = {Methods},\n\tauthor = {Rahmani Dabbagh, Sajjad and Ozcan, Oguzhan and Tasoglu, Savas},\n\tmonth = oct,\n\tyear = {2022},\n\tkeywords = {3D Printing, Artificial Intelligence, Graphical User Interface, Image Analysis, Machine Learning, Optimization, Savas Scholar},\n\tpages = {27--40},\n}\n\n\n
@article{alseed_machine_2022,\n\ttitle = {Machine learning-enabled classification of forearm {sEMG} signals to control robotic hands prostheses},\n\turl = {https://ieeexplore.ieee.org/abstract/document/9925273/},\n\tdoi = {10.1109/ASYU56188.2022.9925273},\n\tabstract = {In this paper, we aim to use and compare different machine learning algorithms, including k-nearest neighbors (k-NN) and support vector machines (SVM), to classify surface electromyography (sEMG) signals that correspond to the flexing of the 4 hand fingers, and recorded through 8 sensor channels. k-NN algorithm was optimized to find the values of k and the best type of distance, while four different kernels were used for SVM to find the optimal one. Moreover, linear discriminant analysis (LDA) was used to reduce the number of dimensions and investigate the effect of reducing the features on classification accuracy. Finally, the best performing ML algorithm was used to classify again using all possible combinations of 2 channels to assess LDA results. Training the algorithms shows that SVM with a Radial basis function (RBF) kernel outperforms k-NN and other SVM kernels, with 100% classification accuracy. Moreover, dimensionality reduction with LDA shows that using only 3 features keeps the accuracy at 100%, suggesting that using less sEMG sensors may not affect the quality of classification, which was confirmed by the result that using only channels 6 and 7 yielded 100% accuracy. Our results can pave the way for implementing strategies to decrease the cost of manufacturing prostheses and accelerate the execution of the classification algorithm since it should be performed in real-time.},\n\tjournal = {2022 Innovations in Intelligent},\n\tauthor = {Alseed, M M and Tasoglu, S},\n\tyear = {2022},\n\tnote = {Publisher: ieeexplore.ieee.org},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{dabbagh_3d-printed_2022,\n\ttitle = {{3D}-printed microrobots from design to translation},\n\tvolume = {13},\n\tissn = {2041-1723},\n\turl = {http://dx.doi.org/10.1038/s41467-022-33409-3},\n\tdoi = {10.1038/s41467-022-33409-3},\n\tabstract = {Microrobots have attracted the attention of scientists owing to their\nunique features to accomplish tasks in hard-to-reach sites in the human\nbody. Microrobots can be precisely actuated and maneuvered individually or\nin a swarm for cargo delivery, sampling, surgery, and imaging\napplications. In addition, microrobots have found applications in the\nenvironmental sector (e.g., water treatment). Besides, recent advancements\nof three-dimensional (3D) printers have enabled the high-resolution\nfabrication of microrobots with a faster design-production turnaround time\nfor users with limited micromanufacturing skills. Here, the latest end\napplications of 3D printed microrobots are reviewed (ranging from\nenvironmental to biomedical applications) along with a brief discussion\nover the feasible actuation methods (e.g., on- and off-board), and\npractical 3D printing technologies for microrobot fabrication. In\naddition, as a future perspective, we discussed the potential advantages\nof integration of microrobots with smart materials, and conceivable\nbenefits of implementation of artificial intelligence (AI), as well as\nphysical intelligence (PI). Moreover, in order to facilitate\nbench-to-bedside translation of microrobots, current challenges impeding\nclinical translation of microrobots are elaborated, including entry\nobstacles (e.g., immune system attacks) and cumbersome standard test\nprocedures to ensure biocompatibility.},\n\tnumber = {1},\n\tjournal = {Nat. Commun.},\n\tauthor = {Dabbagh, Sajjad Rahmani and Sarabi, Misagh Rezapour and Birtek, Mehmet Tugrul and Seyfi, Siamak and Sitti, Metin and Tasoglu, Savas},\n\tmonth = oct,\n\tyear = {2022},\n\tkeywords = {Savas Scholar},\n\tpages = {5875},\n}\n\n\n
@article{temirel_shape_2022,\n\ttitle = {Shape {Fidelity} {Evaluation} of {Alginate}-{Based} {Hydrogels} through {Extrusion}-{Based} {Bioprinting}},\n\tvolume = {13},\n\tissn = {2079-4983},\n\turl = {http://dx.doi.org/10.3390/jfb13040225},\n\tdoi = {10.3390/jfb13040225},\n\tabstract = {Extrusion-based 3D bioprinting is a promising technique for fabricating\nmulti-layered, complex biostructures, as it enables multi-material\ndispersion of bioinks with a straightforward procedure (particularly for\nusers with limited additive manufacturing skills). Nonetheless, this\nmethod faces challenges in retaining the shape fidelity of the\n3D-bioprinted structure, i.e., the collapse of filament (bioink) due to\ngravity and/or spreading of the bioink owing to the low viscosity,\nultimately complicating the fabrication of multi-layered designs that can\nmaintain the desired pore structure. While low viscosity is required to\nensure a continuous flow of material (without clogging), a bioink should\nbe viscous enough to retain its shape post-printing, highlighting the\nimportance of bioink properties optimization. Here, two quantitative\nanalyses are performed to evaluate shape fidelity. First, the filament\ncollapse deformation is evaluated by printing different concentrations of\nalginate and its crosslinker (calcium chloride) by a co-axial nozzle over\na platform to observe the overhanging deformation over time at two\ndifferent ambient temperatures. In addition, a mathematical model is\ndeveloped to estimate Young’s modulus and filament collapse over time.\nSecond, the printability of alginate is improved by optimizing gelatin\nconcentrations and analyzing the pore size area. In addition, the\nbiocompatibility of proposed bioinks is evaluated with a cell viability\ntest. The proposed bioink (3\\% w/v gelatin in 4\\% alginate) yielded a 98\\%\nnormalized pore number (high shape fidelity) while maintaining {\\textgreater}90\\% cell\nviability five days after being bioprinted. Integration of quantitative\nanalysis/simulations and 3D printing facilitate the determination of the\noptimum composition and concentration of different elements of a bioink to\nprevent filament collapse or bioink spreading (post-printing), ultimately\nresulting in high shape fidelity (i.e., retaining the shape) and printing\nquality.},\n\tnumber = {4},\n\tjournal = {J. Funct. Biomater.},\n\tauthor = {Temirel, Mikail and Dabbagh, Sajjad Rahmani and Tasoglu, Savas},\n\tmonth = nov,\n\tyear = {2022},\n\tkeywords = {alginate, bioink, bioprinter, extrusion, gelatin, Savas Scholar, shape fidelity},\n}\n\n\n
@article{dabbagh_increasing_2021,\n\ttitle = {Increasing the packing density of assays in paper-based microfluidic devices},\n\tvolume = {15},\n\tissn = {1932-1058},\n\turl = {http://dx.doi.org/10.1063/5.0042816},\n\tdoi = {10.1063/5.0042816},\n\tabstract = {Paper-based devices have a wide range of applications in point-of-care\ndiagnostics, environmental analysis, and food monitoring. Paper-based\ndevices can be deployed to resource-limited countries and remote settings\nin developed countries. Paper-based point-of-care devices can provide\naccess to diagnostic assays without significant user training to perform\nthe tests accurately and timely. The market penetration of paper-based\nassays requires decreased device fabrication costs, including larger\npacking density of assays (i.e., closely packed features) and minimization\nof assay reagents. In this review, we discuss fabrication methods that\nallow for increasing packing density and generating closely packed\nfeatures in paper-based devices. To ensure that the paper-based device is\nlow-cost, advanced fabrication methods have been developed for the mass\nproduction of closely packed assays. These emerging methods will enable\nminimizing the volume of required samples (e.g., liquid biopsies) and\nreagents in paper-based microfluidic devices.},\n\tnumber = {1},\n\tjournal = {Biomicrofluidics},\n\tauthor = {Dabbagh, Sajjad Rahmani and Becher, Elaina and Ghaderinezhad, Fariba and Havlucu, Hayati and Ozcan, Oguzhan and Ozkan, Mehmed and Yetisen, Ali Kemal and Tasoglu, Savas},\n\tmonth = jan,\n\tyear = {2021},\n\tkeywords = {Savas Scholar},\n\tpages = {011502},\n}\n\n\n
@article{balbach_smartphone-based_2021,\n\ttitle = {Smartphone-based colorimetric detection system for portable health tracking},\n\tvolume = {13},\n\tissn = {1759-9679},\n\turl = {http://dx.doi.org/10.1039/d1ay01209f},\n\tdoi = {10.1039/d1ay01209f},\n\tabstract = {Colorimetric tests for at-home health monitoring became popular 50 years\nago with the advent of the urinalysis test strips, due to their reduced\ncosts, practicality, and ease of operation. However, developing digital\nsystems that can interface these sensors in an efficient manner remains a\nchallenge. Efforts have been put towards the development of portable\noptical readout systems, such as smartphones. However, their use in daily\nsettings is still limited by their error-prone nature associated to\noptical noise from the ambient lighting, and their low sensitivity. Here,\na smartphone application (Colourine) to readout colorimetric signals was\ndeveloped on Android OS and tested on commercial urinalysis test strips\nfor pH, proteins, and glucose detection. The novelty of this approach\nincludes two features: a pre-calibration step where the user is asked to\ntake a photo of the commercial reference chart, and a CIE-RGB-to-HSV color\nspace transformation of the acquired data. These two elements allow the\nbackground noise given by environmental lighting to be minimized. The\nsensors were characterized in the ambient light range 100-400 lx, yielding\na reliable output. Readouts were taken from urine strips in buffer\nsolutions of pH (5.0-9.0 units), proteins (0-500 mg dL-1) and glucose\n(0-1000 mg dL-1), yielding a limit of detection (LOD) of 0.13 units (pH),\n7.5 mg dL-1 (proteins) and 22 mg dL-1 (glucose), resulting in an average\nLOD decrease by about 2.8 fold compared to the visual method.},\n\tnumber = {38},\n\tjournal = {Anal. Methods},\n\tauthor = {Balbach, Samira and Jiang, Nan and Moreddu, Rosalia and Dong, Xingchen and Kurz, Wolfgang and Wang, Congyan and Dong, Jie and Yin, Yixia and Butt, Haider and Brischwein, Martin and Hayden, Oliver and Jakobi, Martin and Tasoglu, Savas and Koch, Alexander W and Yetisen, Ali K},\n\tmonth = oct,\n\tyear = {2021},\n\tkeywords = {Savas Scholar},\n\tpages = {4361--4369},\n}\n\n\n
@article{jiang_low-cost_2021,\n\ttitle = {Low-{Cost} {Optical} {Assays} for {Point}-of-{Care} {Diagnosis} in {Resource}-{Limited} {Settings}},\n\tvolume = {6},\n\tissn = {2379-3694},\n\turl = {http://dx.doi.org/10.1021/acssensors.1c00669},\n\tdoi = {10.1021/acssensors.1c00669},\n\tabstract = {Readily deployable, low-cost point-of-care medical devices such as lateral\nflow assays (LFAs), microfluidic paper-based analytical devices (μPADs),\nand microfluidic thread-based analytical devices (μTADs) are urgently\nneeded in resource-poor settings. Governed by the ASSURED criteria\n(affordable, sensitive, specific, user-friendly, rapid and robust,\nequipment-free, and deliverability) set by the World Health Organization,\nthese reliable platforms can screen a myriad of chemical and biological\nanalytes including viruses, bacteria, proteins, electrolytes, and\nnarcotics. The Ebola epidemic in 2014 and the ongoing pandemic of\nSARS-CoV-2 have exemplified the ever-increasing importance of timely\ndiagnostics to limit the spread of diseases. This review provides a\ncomprehensive survey of LFAs, μPADs, and μTADs that can be deployed in\nresource-limited settings. The subsequent commercialization of these\ntechnologies will benefit the public health, especially in areas where\naccess to healthcare is limited.},\n\tnumber = {6},\n\tjournal = {ACS Sens},\n\tauthor = {Jiang, Nan and Tansukawat, Natha Dean and Gonzalez-Macia, Laura and Ates, H Ceren and Dincer, Can and Güder, Firat and Tasoglu, Savas and Yetisen, Ali K},\n\tmonth = jun,\n\tyear = {2021},\n\tkeywords = {lateral flow assays, low-cost, on-site testing, paper-based analytical devices, paper-based sensors, point-of-care medical devices, resource-limited settings, SARS-CoV-2, Savas Scholar, thread-based sensors},\n\tpages = {2108--2124},\n}\n\n\n
@article{alseed_design_2021,\n\ttitle = {Design and {Adoption} of {Low}-{Cost} {Point}-of-{Care} {Diagnostic} {Devices}: {Syrian} {Case}},\n\tvolume = {12},\n\tissn = {2072-666X},\n\turl = {http://dx.doi.org/10.3390/mi12080882},\n\tdoi = {10.3390/mi12080882},\n\tabstract = {Civil wars produce immense humanitarian crises, causing millions of\nindividuals to seek refuge in other countries. The rate of disease\nprevalence has inclined among the refugees, increasing the cost of\nhealthcare. Complex medical conditions and high numbers of patients at\nhealthcare centers overwhelm the healthcare system and delay diagnosis and\ntreatment. Point-of-care (PoC) testing can provide efficient solutions to\nhigh equipment cost, late diagnosis, and low accessibility of healthcare\nservices. However, the development of PoC devices in developing countries\nis challenged by several barriers. Such PoC devices may not be adopted due\nto prejudices about new technologies and the need for special training to\nuse some of these devices. Here, we investigated the concerns of end users\nregarding PoC devices by surveying healthcare workers and doctors. The\ntendency to adopt PoC device changes is based on demographic factors such\nas work sector, education, and technology experience. The most apparent\nconcern about PoC devices was issues regarding low accuracy, according to\nthe surveyed clinicians.},\n\tnumber = {8},\n\tjournal = {Micromachines (Basel)},\n\tauthor = {Alseed, M Munzer and Syed, Hamzah and Onbasli, Mehmet Cengiz and Yetisen, Ali K and Tasoglu, Savas},\n\tmonth = jul,\n\tyear = {2021},\n\tkeywords = {adoption, diagnostics, point-of-care devices, Savas Scholar, Syrian refugees, Syrian war},\n}\n\n\n
@article{sarabi_finger-actuated_2021,\n\ttitle = {Finger-actuated microneedle array for sampling body fluids},\n\tvolume = {11},\n\tissn = {1454-5101},\n\turl = {https://scholar.google.ca/scholar?cluster=4247798112456879405&hl=en&as_sdt=0,5&sciodt=0,5},\n\tdoi = {10.3390/app11125329},\n\tabstract = {The application of microneedles (MNs) for minimally invasive biological\nfluid sampling is rapidly emerging, offering a user-friendly approach with\ndecreased insertion pain and less harm to the tissues compared to\nconventional needles. Here, a finger-powered microneedle array (MNA)\nintegrated with a microfluidic chip was conceptualized to extract body\nfluid samples. Actuated by finger pressure, the microfluidic device\nenables an efficient approach for the user to collect their own body\nfluids in a simple and fast manner without the requirement for a\nhealthcare worker. The processes for extracting human blood and\ninterstitial fluid (ISF) from the body and the flow across the device,\nestimating the amount of the extracted fluid, were simulated. The design\nin this work can be utilized for the minimally invasive personalized\nmedical equipment offering a simple usage procedure.},\n\tnumber = {12},\n\tjournal = {Appl. Sci.},\n\tauthor = {Sarabi, Misagh Rezapour and Ahmadpour, Abdollah and Yetisen, Ali K and Tasoglu, Savas},\n\tmonth = jun,\n\tyear = {2021},\n\tnote = {Publisher: MDPI AG},\n\tkeywords = {Savas Scholar},\n\tpages = {5329},\n}\n\n\n
@article{jiang_intracranial_2021,\n\ttitle = {Intracranial sensors for continuous monitoring of neurophysiology},\n\tvolume = {6},\n\tissn = {2365-709X},\n\turl = {https://scholar.google.ca/scholar?cluster=8607581069563155938&hl=en&as_sdt=0,5&sciodt=0,5},\n\tdoi = {10.1002/admt.202100339},\n\tnumber = {12},\n\tjournal = {Adv. Mater. Technol.},\n\tauthor = {Jiang, Nan and Flyax, Sergey and Kurz, Wolfgang and Jakobi, Martin and Tasoglu, Savas and Koch, Alexander W and Yetisen, Ali K},\n\tmonth = dec,\n\tyear = {2021},\n\tnote = {Publisher: Wiley},\n\tkeywords = {Savas Scholar},\n\tpages = {2100339},\n}\n\n\n
@article{temirel_long-term_2021,\n\ttitle = {Long-term cyclic use of a sample collector for toilet-based urine analysis},\n\turl = {https://www.nature.com/articles/s41598-021-81842-z},\n\tdoi ={10.1038/s41598-021-81842-z},\n\tabstract = {Urine analysis via a toilet-based device can enable continuous health monitoring, a transformation away from hospital-based care towards more proactive medicine. To enable reliable sample collection for a toilet-attached analyzer, here a novel sample collector is proposed. The applicability of the proposed sample collector is validated for long-term use. Geometric parameters of the 3D-printed sample collector are optimized. The collected and leftover volumes are quantified for a range of urination speeds and design parameters. For long-term cyclic use, the protein concentrations of samples are quantified and the effectiveness of washing the sample collector is assessed.},\n\tjournal = {Sci. Rep.},\n\tauthor = {Temirel, M and Yenilmez, B and Tasoglu, S},\n\tyear = {2021},\n\tnote = {Publisher: nature.com},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{temirel_hemp-based_2021,\n\ttitle = {Hemp-based microfluidics},\n\turl = {https://www.mdpi.com/2072-666X/12/2/182},\n\tdoi = {10.3390/mi12020182},\n\tabstract = {Hemp is a sustainable, recyclable, and high-yield annual crop that can be used to produce textiles, plastics, composites, concrete, fibers, biofuels, bionutrients, and paper. The integration of microfluidic paper-based analytical devices (µPADs) with hemp paper can improve the environmental friendliness and high-throughputness of µPADs. However, there is a lack of sufficient scientific studies exploring the functionality, pros, and cons of hemp as a substrate for µPADs. Herein, we used a desktop pen plotter and commercial markers to pattern hydrophobic barriers on hemp paper, in a single step, in order to characterize the ability of markers to form water-resistant patterns on hemp. In addition, since a higher resolution results in densely packed, cost-effective devices with a minimized need for costly reagents, we examined the smallest and thinnest water-resistant patterns plottable on hemp-based papers. Furthermore, the wicking speed and distance of fluids with different viscosities on Whatman No. 1 and hemp papers were compared. Additionally, the wettability of hemp and Whatman grade 1 paper was compared by measuring their contact angles. Besides, the effects of various channel sizes, as well as the number of branches, on the wicking distance of the channeled hemp paper was studied. The governing equations for the wicking distance on channels with laser-cut and hydrophobic side boundaries are presented and were evaluated with our experimental data, elucidating the applicability of the modified Washburn equation for modeling the wicking distance of fluids on hemp paper-based microfluidic devices. Finally, we validated hemp paper as a substrate for the detection and analysis of the potassium concentration in artificial urine.},\n\tjournal = {Micromachines},\n\tauthor = {Temirel, M and Dabbagh, S R and Tasoglu, S},\n\tyear = {2021},\n\tnote = {Publisher: mdpi.com},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{temirel_shape_2021,\n\ttitle = {Shape fidelity of {3D}-bioprinted biodegradable patches},\n\tdoi = {10.3390/mi12020195},\n\turl = {https://www.mdpi.com/2072-666X/12/2/195},\n\tabstract = {There is high demand in the medical field for rapid fabrication of biodegradable patches at low cost and high throughput for various instant applications, such as wound healing. Bioprinting is a promising technology, which makes it possible to fabricate custom biodegradable patches. However, several challenges with the physical and chemical fidelity of bioprinted patches must be solved to increase the performance of patches. Here, we presented two hybrid hydrogels made of alginate-cellulose nanocrystal (CNC) (2% w/v alginate and 4% w/v CNC) and alginate-TEMPO oxidized cellulose nanofibril (T-CNF) (4% w/v alginate and 1% w/v T-CNC) via ionic crosslinking using calcium chloride (2% w/v). These hydrogels were rheologically characterized, and printing parameters were tuned for improved shape fidelity for use with an extrusion printing head. Young’s modulus of 3D printed patches was found to be 0.2–0.45 MPa, which was between the physiological ranges of human skin. Mechanical fidelity of patches was assessed through cycling loading experiments that emulate human tissue motion. 3D bioprinted patches were exposed to a solution mimicking the body fluid to characterize the biodegradability of patches at body temperature. The biodegradation of alginate-CNC and alginate-CNF was around 90% and 50% at the end of the 30-day in vitro degradation trial, which might be sufficient time for wound healing. Finally, the biocompatibility of the hydrogels was tested by cell viability analysis using NIH/3T3 mouse fibroblast cells. This study may pave the way toward improving the performance of patches and developing new patch material with high physical and chemical fidelity for instant application.},\n\tjournal = {Micromachines},\n\tauthor = {Temirel, M and Hawxhurst, C and Tasoglu, S},\n\tyear = {2021},\n\tnote = {Publisher: mdpi.com},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{bilirgen_plant-based_2021,\n\ttitle = {Plant-based scaffolds in tissue engineering},\n\turl = {https://pubs.acs.org/doi/abs/10.1021/acsbiomaterials.0c01527},\n\tdoi = {10.1021/acsbiomaterials.0c01527},\n\tabstract = {A wide range of platforms has been developed for 3D culture of cells in vitro to aggregate and align cells to resemble in vivo conditions in order to enhance communication between cells and promote differentiation. The cellulose skeleton of plant tissue can serve as an attainable scaffold for mammalian cells after decellularization, which is advantageous when compared to synthetic polymers or animal-derived scaffolds. Adjustable variables to modify the physical and biochemical properties of the resulting scaffolds include the protocol for the sodium dodecyl sulfate (SDS)-based decellularization procedure, surface coatings for cell attachment, plant type for decellularization, differentiation media, and integrity and shape of the substrate. These tunable cellulose platforms can host a wide range of mammalian cell types from muscle to bone cells, as well as malignancies. Here, fundamentals and applications of decellularized plant-based scaffolds are discussed. These biocompatible, naturally perfused, tunable, and easily prepared decellularized scaffolds may allow eco-friendly manufacturing frameworks for application in tissue engineering and organs-on-a-chip.},\n\tjournal = {ACS Biomaterials},\n\tauthor = {Bilirgen, A C and Toker, M and Odabas, S and {others}},\n\tyear = {2021},\n\tnote = {Publisher: ACS Publications},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{yu_optical_2021,\n\ttitle = {Optical sensors for continuous glucose monitoring},\n\turl = {https://iopscience.iop.org/article/10.1088/2516-1091/abe6f8/meta},\n\tdoi = {10.1088/2516-1091/abe6f8},\n\tabstract = {For decades, diabetes mellitus has been of wide concern with its high global prevalence, resulting in increasing social and financial burdens for individuals, clinical systems and governments. Continuous glucose monitoring (CGM) has become a popular alternative to the portable finger-prick glucometers available in the market for the convenience of diabetic patients. Hence, it has attracted much interest in various glucose sensing technologies to develop novel glucose sensors with better performance and longer lifetime, especially non-invasive or minimally invasive glucose sensing. Effort has also been put into finding biocompatible materials for implantable applications to achieve effective in vivo CGM. Here, we review the state-of-the-art researches in the field of CGM. The currently commercially available CGM technologies have been analyzed and a summary is provided of the potential types of recently researched non-invasive glucose monitors. Furthermore, the challenges and advances towards implantable applications have also been introduced and discussed, especially the novel biocompatible hydrogel aimed at minimizing the adverse impact from foreign-body response. In addition, a large variety of promising glucose-sensing technologies under research have been reviewed, from traditional electrochemical-based glucose sensors to novel optical and other electrical glucose sensors. The recent development and achievement of the reviewed glucose sensing technologies are discussed, together with the market analysis in terms of the statistical data for the newly published patents in the related field. Thus, the promising direction for future work in this field could be concluded.},\n\tjournal = {Progress in},\n\tauthor = {Ziyi Yu and Nan Jiang and Sergei G Kazarian and Savas Tasoglu and Ali K Yetisen},\n\tyear = {2021},\n\tnote = {Publisher: iopscience.iop.org},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@patent{demirci_system_2021,\n\ttitle = {System and method for cell levitation and monitoring},\n\turl = {https://patents.google.com/patent/US10928404B2/en},\n\tabstract = {Magnetic cell levitation and cell monitoring systems and methods are\ndisclosed. A method for separating a heteroge neous population of cells is\nperformed by placing a micro capillary …},\n\tauthor = {Demirci, U and Ghiran, I and Tasoglu, S and Davis, R W and {others}},\n\tyear = {2021},\n\tnote = {Publication Title: US Patent},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{ozdalgic_microfluidics_2021,\n\ttitle = {Microfluidics for microalgal biotechnology},\n\turl = {https://onlinelibrary.wiley.com/doi/abs/10.1002/bit.27669},\n\tdoi ={10.1002/bit.27669},\n\tabstract = {Microalgae have expanded their roles as renewable and sustainable feedstocks for biofuel, smart nutrition, biopharmaceutical, cosmeceutical, biosensing, and space technologies. They accumulate valuable biochemical compounds from protein, carbohydrate, and lipid groups, including pigments and carotenoids. Microalgal biomass, which can be adopted for multivalorization under biorefinery settings, allows not only the production of various biofuels but also other value-added biotechnological products. However, state-of-the-art technologies are required to optimize yield, quality, and the economical aspects of both upstream and downstream processes. As such, the need to use microfluidic-based devices for both fundamental research and industrial applications of microalgae, arises due to their microscale sizes and dilute cultures. Microfluidics-based devices are superior to their competitors through their ability to perform multiple functions such as sorting and analyzing small amounts of samples (nanoliter to picoliter) with higher sensitivities. Here, we review emerging applications of microfluidic technologies on microalgal processes in cell sorting, cultivation, harvesting, and applications in biofuels, biosensing, drug delivery, and nutrition.},\n\tjournal = {BioTechnology},\n\tauthor = {Ozdalgic, Berin and Ustun, Merve and Dabbagh, Sajjad Rahmani and Haznedaroglu, Berat Z. and Kiraz, Alper and Tasoglu, Savas},\n\tyear = {2021},\n\tnote = {Publisher: Wiley Online Library},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{alseed_portable_2021,\n\ttitle = {Portable magnetic levitation technologies},\n\turl = {https://www.degruyter.com/document/doi/10.1515/aot-2021-0010/html},\n\tdoi = {10.1515/aot-2021-0010},\n\tabstract = {Magnetic levitation (MagLev) is a density-based method which uses magnets and a paramagnetic medium to suspend multiple objects simultaneously as a result of an equilibrium between gravitational, buoyancy, and magnetic forces acting on the particle. Early MagLev setups were bulky with a need for optical or fluorescence microscopes for imaging, confining portability, and accessibility. Here, we review design criteria and the most recent end-applications of portable smartphone-based and self-contained MagLev setups for density-based sorting and analysis of microparticles. Additionally, we review the most recent end applications of those setups, including disease diagnosis, cell sorting and characterization, protein detection, and point-of-care testing.},\n\tjournal = {Advanced Optical Technologies},\n\tauthor = {M. Munzer Alseed and Sajjad Rahmani Dabbagh and Peng Zhao and Oguzhan Ozcan and Savas Tasoglu},\n\tyear = {2021},\n\tnote = {Publisher: degruyter.com},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{sarabi_3d_2021,\n\ttitle = {{3D} printing of microneedle arrays: {Challenges} towards clinical translation},\n\turl = {https://www.futuremedicine.com/doi/abs/10.2217/3dp-2021-0010},\n\tdoi ={10.2217/3dp-2021-0010},\n\tabstract = {Microneedles (MNs) are a rapidly emerging technology for user-friendly and\nminimally invasive drug delivery and biological fluid sampling\napplications [1]. Simple, low-cost and …},\n\tjournal = {Journal of 3D printing},\n\tauthor = {Sarabi, M R and Bediz, B and Falo, L D and Korkmaz, E and {others}},\n\tyear = {2021},\n\tnote = {Publisher: Future Medicine},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{deshmukh_recent_2021,\n\ttitle = {Recent technological developments in the diagnosis and treatment of cerebral edema},\n\turl = {https://onlinelibrary.wiley.com/doi/abs/10.1002/anbr.202100001},\n\tdoi ={10.1002/anbr.202100001},\n\tabstract = {Latest technological advancements in neurocritical care have translated to improved clinical outcomes and have paved the way for the effective diagnosis and treatment of cerebral edema. Effective management of cerebral edema has the potential to provide a personalized treatment by obtaining the complete pathophysiological information of the patient. The aims of this review are to inform the reader about the research and development in this field in the past decade as well as the materialization of scientific literature through patents. There is a growing interest in multimodal monitoring of the diseased brain as it provides a necessary means to implement effective intervention strategies. Although there is a gradual shift toward the adoption of noninvasive devices for research purposes, their clinical applications are hindered by their inaccuracies. However, the inherent risk of complication and high costs of implementation challenge the status quo. The role of neuroprotectants is explored and the combination of neurodiagnostic and neuroprotective approaches is proposed. Finally, the impacts of the current state of global affairs are discussed and it is predicted that the rising number of traumatic brain injury patents will inevitably translate to improvements in technologies to effectively address cerebral edema.},\n\tjournal = {Advanced},\n\tauthor = {Deshmukh, Karthikeya P. and Rahmani Dabbagh, Sajjad and Jiang, Nan and Tasoglu, Savas and Yetisen, Ali K.},\n\tyear = {2021},\n\tnote = {Publisher: Wiley Online Library},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{li_3dprinted_2020,\n\ttitle = {{3D}‐printed microfluidics: {Formation} of polarized, functional artificial cells from compartmentalized droplet networks and nanomaterials, using one‐step, dual‐material {3D}‐printed microfluidics (adv. {Sci}. 1/2020)},\n\tvolume = {7},\n\tissn = {0001-866X},\n\turl = {https://scholar.google.ca/scholar?cluster=6139431045256285288&hl=en&as_sdt=0,5&sciodt=0,5},\n\tdoi = {10.1002/advs.202070005},\n\tnumber = {1},\n\tjournal = {Adv. Sci.},\n\tauthor = {Li, Jin and Baxani, Divesh Kamal and Jamieson, William David and Xu, Wen and Rocha, Victoria Garcia and Barrow, David Anthony and Castell, Oliver Kieran},\n\tmonth = jan,\n\tyear = {2020},\n\tnote = {Publisher: Wiley},\n\tkeywords = {Savas Scholar},\n\tpages = {2070005},\n}\n\n\n
@article{dabbagh_machine_2020,\n\ttitle = {Machine learning-enabled multiplexed microfluidic sensors},\n\tvolume = {14},\n\tissn = {1932-1058},\n\turl = {http://dx.doi.org/10.1063/5.0025462},\n\tdoi = {10.1063/5.0025462},\n\tabstract = {High-throughput, cost-effective, and portable devices can enhance the\nperformance of point-of-care tests. Such devices are able to acquire\nimages from samples at a high rate in combination with microfluidic chips\nin point-of-care applications. However, interpreting and analyzing the\nlarge amount of acquired data is not only a labor-intensive and\ntime-consuming process, but also prone to the bias of the user and low\naccuracy. Integrating machine learning (ML) with the image acquisition\ncapability of smartphones as well as increasing computing power could\naddress the need for high-throughput, accurate, and automatized detection,\ndata processing, and quantification of results. Here, ML-supported\ndiagnostic technologies are presented. These technologies include\nquantification of colorimetric tests, classification of biological samples\n(cells and sperms), soft sensors, assay type detection, and recognition of\nthe fluid properties. Challenges regarding the implementation of ML\nmethods, including the required number of data points, image acquisition\nprerequisites, and execution of data-limited experiments are also\ndiscussed.},\n\tnumber = {6},\n\tjournal = {Biomicrofluidics},\n\tauthor = {Dabbagh, Sajjad Rahmani and Rabbi, Fazle and Doğan, Zafer and Yetisen, Ali Kemal and Tasoglu, Savas},\n\tmonth = nov,\n\tyear = {2020},\n\tkeywords = {Savas Scholar},\n\tpages = {061506},\n}\n\n\n
@article{ghaderinezhad_sensing_2020,\n\ttitle = {Sensing of electrolytes in urine using a miniaturized paper-based device},\n\tvolume = {10},\n\tissn = {2045-2322},\n\turl = {http://dx.doi.org/10.1038/s41598-020-70456-6},\n\tdoi = {10.1038/s41598-020-70456-6},\n\tabstract = {Analyzing electrolytes in urine, such as sodium, potassium, calcium,\nchloride, and nitrite, has significant diagnostic value in detecting\nvarious conditions, such as kidney disorder, urinary stone disease,\nurinary tract infection, and cystic fibrosis. Ideally, by regularly\nmonitoring these ions with the convenience of dipsticks and portable\ntools, such as cellphones, informed decision making is possible to control\nthe consumption of these ions. Here, we report a paper-based sensor for\nmeasuring the concentration of sodium, potassium, calcium, chloride, and\nnitrite in urine, accurately quantified using a smartphone-enabled\nplatform. By testing the device with both Tris buffer and artificial urine\ncontaining a wide range of electrolyte concentrations, we demonstrate that\nthe proposed device can be used for detecting potassium, calcium,\nchloride, and nitrite within the whole physiological range of\nconcentrations, and for binary quantification of sodium concentration.},\n\tnumber = {1},\n\tjournal = {Sci. Rep.},\n\tauthor = {Ghaderinezhad, Fariba and Ceylan Koydemir, Hatice and Tseng, Derek and Karinca, Doruk and Liang, Kyle and Ozcan, Aydogan and Tasoglu, Savas},\n\tmonth = aug,\n\tyear = {2020},\n\tkeywords = {Savas Scholar},\n\tpages = {13620},\n}\n\n\n
@article{bagheri_mitochondrial_2020,\n\ttitle = {Mitochondrial donation in translational medicine; from imagination to reality},\n\tvolume = {18},\n\tissn = {1479-5876},\n\turl = {http://dx.doi.org/10.1186/s12967-020-02529-z},\n\tdoi = {10.1186/s12967-020-02529-z},\n\tabstract = {The existence of active crosstalk between cells in a paracrine and\njuxtacrine manner dictates specific activity under physiological and\npathological conditions. Upon juxtacrine interaction between the cells,\nvarious types of signaling molecules and organelles are regularly\ntransmitted in response to changes in the microenvironment. To date, it\nhas been well-established that numerous parallel cellular mechanisms\nparticipate in the mitochondrial transfer to modulate metabolic needs in\nthe target cells. Since the conception of stem cells activity in the\nrestoration of tissues' function, it has been elucidated that these cells\npossess a unique capacity to deliver the mitochondrial package to the\njuxtaposed cells. The existence of mitochondrial donation potentiates the\ncapacity of modulation in the distinct cells to achieve better therapeutic\neffects. This review article aims to scrutinize the current knowledge\nregarding the stem cell's mitochondrial transfer capacity and their\nregenerative potential.},\n\tnumber = {1},\n\tjournal = {J. Transl. Med.},\n\tauthor = {Bagheri, Hesam Saghaei and Bani, Farhad and Tasoglu, Savas and Zarebkohan, Amir and Rahbarghazi, Reza and Sokullu, Emel},\n\tmonth = sep,\n\tyear = {2020},\n\tkeywords = {Cellular mechanisms, Mitochondrial transfer, Regenerative potential, Savas Scholar, Stem cells},\n\tpages = {367},\n}\n\n\n
@article{amin_pushing_2020,\n\ttitle = {Pushing the {Limits} of {Spatial} {Assay} {Resolution} for {Paper}-{Based} {Microfluidics} {Using} {Low}-{Cost} and {High}-{Throughput} {Pen} {Plotter} {Approach}},\n\tvolume = {11},\n\tissn = {2072-666X},\n\turl = {https://www.mdpi.com/2072-666X/11/6/611},\n\tdoi = {10.3390/mi11060611},\n\tabstract = {To transform from reactive to proactive healthcare, there is an increasing need for low-cost and portable assays to continuously perform health measurements. The paper-based analytical devices could be a potential fit for this need. To miniaturize the multiplex paper-based microfluidic analytical devices and minimize reagent use, a fabrication method with high resolution along with low fabrication cost should be developed. Here, we present an approach that uses a desktop pen plotter and a high-resolution technical pen for plotting high-resolution patterns to fabricate miniaturized paper-based microfluidic devices with hundreds of detection zones to conduct different assays. In order to create a functional multiplex paper-based analytical device, the hydrophobic solution is patterned on the cellulose paper and the reagents are deposited in the patterned detection zones using the technical pens. We demonstrated the effect of paper substrate thickness on the resolution of patterns by investigating the resolution of patterns on a chromatography paper with altered effective thickness. As the characteristics of the cellulose paper substrate such as thickness, resolution, and homogeneity of pore structure affect the obtained patterning resolution, we used regenerated cellulose paper to fabricate detection zones with a diameter as small as 0.8 mm. Moreover, in order to fabricate a miniaturized multiplex paper-based device, we optimized packing of the detection zones. We also showed the capability of the presented method for fabrication of 3D paper-based microfluidic devices with hundreds of detection zones for conducting colorimetric assays.},\n\tlanguage = {en},\n\tnumber = {6},\n\turldate = {2023-09-29},\n\tjournal = {Micromachines},\n\tauthor = {Amin, Reza and Ghaderinezhad, Fariba and Bridge, Caleb and Temirel, Mikail and Jones, Scott and Toloueinia, Panteha and Tasoglu, Savas},\n\tmonth = jun,\n\tyear = {2020},\n\tpages = {611},\n\tfile = {Full Text:files/425/Amin et al. - 2020 - Pushing the Limits of Spatial Assay Resolution for.pdf:application/pdf},\n}\n\n\n
@article{nooranidoost_computational_2019,\n\ttitle = {A computational study of droplet-based bioprinting: {Effects} of viscoelasticity},\n\tvolume = {31},\n\tissn = {1070-6631},\n\turl = {https://scholar.google.ca/scholar?cluster=14945434612832273647&hl=en&as_sdt=0,5&sciodt=0,5},\n\tdoi = {10.1063/1.5108824},\n\tabstract = {Despite significant progress, cell viability continues to be a central\nissue in droplet-based bioprinting applications. Common bioinks exhibit\nviscoelastic behavior owing to the presence of long-chain molecules in\ntheir mixture. We computationally study effects of viscoelasticity of\nbioinks on cell viability during deposition of cell-loaded droplets on a\nsubstrate using a compound droplet model. The inner droplet, which\nrepresents the cell, and the encapsulating droplet are modeled as\nviscoelastic liquids with different material properties, while the ambient\nfluid is Newtonian. The model proposed by Takamatsu and Rubinsky\n[“Viability of deformed cells,” Cryobiology 39(3), 243–251 (1999)] is used\nto relate cell deformation to cell viability. We demonstrate that adding\nviscoelasticity to the encapsulating droplet fluid can significantly\nenhance the cell viability, suggesting that viscoelastic properties of\nbioinks can be tailored to achieve high cell viability in droplet-based\nbioprinting systems. The effects of the cell viscoelasticity are also\nexamined, and it is shown that the Newtonian cell models may significantly\noverpredict the cell viability.},\n\tnumber = {8},\n\tjournal = {Phys. Fluids},\n\tauthor = {Nooranidoost, M and Izbassarov, D and Tasoglu, S and Muradoglu, M},\n\tmonth = aug,\n\tyear = {2019},\n\tnote = {Publisher: AIP Publishing},\n\tkeywords = {Savas Scholar},\n\tpages = {081901},\n}\n\n\n
@article{ghaderinezhad_hybrid_2019,\n\ttitle = {A hybrid approach for large-scale fabrication of paper-based electrochemical assays for biomedical diagnosis},\n\tissn = {1305-130X},\n\turl = {http://dergipark.org.tr/en/doi/10.18466/cbayarfbe.542120},\n\tdoi = {10.18466/cbayarfbe.542120},\n\tjournal = {Celal Bayar Üniv. fen bilim. derg.},\n\tauthor = {Ghaderinezhad, Fariba and Tasoglu, Savas},\n\tmonth = sep,\n\tyear = {2019},\n\tnote = {Publisher: Celal Bayar University Journal of Science},\n\tkeywords = {Savas Scholar},\n\tpages = {271--277},\n}\n\n\n
@article{tasoglu_density-based_2019,\n\ttitle = {Density-based food analysis using a smartphone},\n\tvolume = {15},\n\tissn = {1305-130X},\n\turl = {http://dergipark.org.tr/en/doi/10.18466/cbayarfbe.496371},\n\tdoi = {10.18466/cbayarfbe.496371},\n\tabstract = {Density is a crucial factor of interest in the food industry because it\ncan reveal valuable information about the content and quality of food\nproducts. Traditionally, this physical property is quantified using a\nhydrometer or a pyncometer. However, the accuracy of analog instruments is\nlimited by human error and more modern digital adaptations of such methods\ncome with high monetary costs. Here, we present a low-cost, portable, and\nuser-friendly platform for density-based analysis of liquid food samples\nof very small volumes ({\\textless}10 µL) via magnetic levitation. The platform is\nfully compatible with an Android smartphone which collects magnified\nimages and conducts automated density-based metric determination using a\ncustom-designed Android application. Validity of the device was shown by\nmeasuring the density of oils (indicating fat content) and ethanol\nsolutions (indicating alcohol content). This technique offers an accurate\nand low-cost alternative to current density measurement techniques for\nanalysis of food quality for broad use in-home or in the food industry},\n\tnumber = {2},\n\tjournal = {Celal Bayar Üniv. fen bilim. derg.},\n\tauthor = {Tasoglu, Savas and Knowlton, Stephanie},\n\tmonth = jun,\n\tyear = {2019},\n\tnote = {Publisher: Celal Bayar University Journal of Science},\n\tkeywords = {Savas Scholar},\n\tpages = {181--186},\n}\n\n\n
@article{amin_assessing_2019,\n\ttitle = {Assessing reusability of microfluidic devices: {Urinary} protein uptake by {PDMS}-based channels after long-term cyclic use},\n\tvolume = {192},\n\tissn = {0039-9140},\n\turl = {http://dx.doi.org/10.1016/j.talanta.2018.08.053},\n\tdoi = {10.1016/j.talanta.2018.08.053},\n\tabstract = {In the search for transformative technologies for person-centered health\nmonitoring, reusability of microfluidic chips would be a critical design\nconsideration in many biomedical applications. With this unmet need in\nmind, in this study, we develop and validate a novel microfluidic platform\nfor automated sample pumping with an integrated channel-cleaning\nprocedure. The proposed system leverages micropumps and on-chip solenoid\nvalves to dynamically control fluid flow. We provide a thorough\ncharacterization of the custom-designed chip, including quantitative\nmeasures of the protein uptake by the chip, as well as cross-contamination\nusing both simulated samples and human urine samples. The effectiveness of\nthe cleaning procedure is assessed by testing the samples collected from\nthe cleaning chip with commercially available urine dipstick protein\ntests. The results of the longitudinal protein level measurement of the\nurine samples after the cleaning cycles show high accuracy of protein\nmeasurement and negligible protein cross-contamination. Additionally, the\ncleaning procedure after pumping each sample results in a very low protein\nuptake (150 ng/cm2). We have also demonstrated that the efficiency of the\nautomated cleaning microfluidic device can be further improved by an\nanti-fouling coating via PLL-g-PEG pretreatment and a posttreatment via\nTrypsin. The developed platform could potentially be further miniaturized\nand integrated into point-of-care devices to provide an effective cleaning\nprocess and to enable the reusability of microfluidic devices.},\n\tjournal = {Talanta},\n\tauthor = {Amin, Reza and Li, Lu and Tasoglu, Savas},\n\tmonth = jan,\n\tyear = {2019},\n\tkeywords = {PDMS, Protein uptake, Reusability, Savas Scholar, Urine analysis},\n\tpages = {455--462},\n}\n\n\n
@article{tasoglu_3d_2019,\n\ttitle = {{3D} printed microfluidic devices},\n\turl = {https://books.google.ca/books?hl=en&lr=&id=UAGDDwAAQBAJ&oi=fnd&pg=PA202&ots=7POAtILl_s&sig=ovYR1ZCcq9ORRepG4ScuZiixXcs},\n\tabstract = {3D printed microfluidic devices Page 1 3D Printed Microfluidic Devices\nSavas Tasoglu and Albert Folch Edited by Printed Edition of the Special\nIssue Published in Micromachines www. mdpi …},\n\tauthor = {Tasoglu, S and Folch, A},\n\tyear = {2019},\n\tnote = {Publisher: books.google.com},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{yenilmez_development_2019,\n\ttitle = {Development and characterization of a low-cost {3D} bioprinter},\n\turl = {https://www.sciencedirect.com/science/article/pii/S2405886618300265},\n\tabstract = {Bioprinting complex three-dimensional architectures of cell-laden\nhydrogels is a promising approach for creating custom living tissues.\nHowever, it is challenging to fabricate hydrogel …},\n\tjournal = {Bioprinting},\n\tauthor = {Yenilmez, B and Temirel, M and Knowlton, S and Lepowsky, E and {others}},\n\tyear = {2019},\n\tnote = {Publisher: Elsevier},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{thomason_structured_2018,\n\ttitle = {Structured {Spontaneity}: {Building} {Circuits} in the {Human} {Prenatal} {Brain}},\n\tvolume = {41},\n\tissn = {0166-2236},\n\turl = {http://dx.doi.org/10.1016/j.tins.2017.11.004},\n\tdoi = {10.1016/j.tins.2017.11.004},\n\tabstract = {Early brain activity is crucial for neurogenesis and the development of brain networks. However, it has been challenging to localize regions in the developing human brain that contribute to spontaneous waves of neuronal activity. Recently, Arichi and colleagues reported that the temporal and heteromodal insular cortices have a central role in propagating these neural instructional signals.},\n\tnumber = {1},\n\tjournal = {Trends Neurosci.},\n\tauthor = {Thomason, Moriah E},\n\tmonth = jan,\n\tyear = {2018},\n\tkeywords = {Savas Scholar},\n\tpages = {1--3},\n}\n\n\n
@article{lepowsky_3d_2018,\n\ttitle = {{3D} printing for drug manufacturing: {A} perspective on the future of pharmaceuticals},\n\tvolume = {4},\n\tissn = {2424-8002},\n\turl = {http://dx.doi.org/10.18063/IJB.v4i1.119},\n\tdoi = {10.18063/IJB.v4i1.119},\n\tabstract = {Since a three-dimensional (3D) printed drug was first approved by the Food\nand Drug Administration in 2015, there has been a growing interest in 3D\nprinting for drug manufacturing. There are multiple 3D printing methods -\nincluding selective laser sintering, binder deposition, stereolithography,\ninkjet printing, extrusion-based printing, and fused deposition modeling -\nwhich are compatible with printing drug products, in addition to both\npolymer filaments and hydrogels as materials for drug carriers. We see the\nadaptability of 3D printing as a revolutionary force in the pharmaceutical\nindustry. Release characteristics of drugs may be controlled by complex 3D\nprinted geometries and architectures. Precise and unique doses can be\nengineered and fabricated via 3D printing according to individual\nprescriptions. On-demand printing of drug products can be implemented for\ndrugs with limited shelf life or for patient-specific medications,\noffering an alternative to traditional compounding pharmacies. For these\nreasons, 3D printing for drug manufacturing is the future of\npharmaceuticals, making personalized medicine possible while also\ntransforming pharmacies.},\n\tnumber = {1},\n\tjournal = {Int J Bioprint},\n\tauthor = {Lepowsky, Eric and Tasoglu, Savas},\n\tyear = {2018},\n\tkeywords = {drug dosing and delivery, drug release characteristics, hydrogels, personalized medicine, Savas Scholar, three-dimensional (3D) printing},\n\tpages = {119},\n}\n\n\n
@article{gu_engineering_2018,\n\ttitle = {Engineering {Human} {Neural} {Tissue} by {3D} {Bioprinting}},\n\tvolume = {1758},\n\tissn = {1064-3745},\n\turl = {http://dx.doi.org/10.1007/978-1-4939-7741-3_10},\n\tdoi = {10.1007/978-1-4939-7741-3_10},\n\tabstract = {Bioprinting provides an opportunity to produce three-dimensional (3D)\ntissues for biomedical research and translational drug discovery,\ntoxicology, and tissue replacement. Here we describe a method for\nfabricating human neural tissue by 3D printing human neural stem cells\nwith a bioink, and subsequent gelation of the bioink for cell\nencapsulation, support, and differentiation to functional neurons and\nsupporting neuroglia. The bioink uniquely comprises the polysaccharides\nalginate, water-soluble carboxymethyl-chitosan, and agarose. Importantly,\nthe method could be adapted to fabricate neural and nonneural tissues from\nother cell types, with the potential to be applied for both research and\nclinical product development.},\n\tjournal = {Methods Mol. Biol.},\n\tauthor = {Gu, Qi and Tomaskovic-Crook, Eva and Wallace, Gordon G and Crook, Jeremy M},\n\tyear = {2018},\n\tkeywords = {3D bioprinting, Bioink, Cell encapsulation, Gel, Human neural tissue, Savas Scholar, Stem cells},\n\tpages = {129--138},\n}\n\n\n
@article{lepowsky_emerging_2018,\n\ttitle = {Emerging {Anti}-{Fouling} {Methods}: {Towards} {Reusability} of {3D}-{Printed} {Devices} for {Biomedical} {Applications}},\n\tvolume = {9},\n\tissn = {2072-666X},\n\turl = {http://dx.doi.org/10.3390/mi9040196},\n\tdoi = {10.3390/mi9040196},\n\tabstract = {Microfluidic devices are used in a myriad of biomedical applications such\nas cancer screening, drug testing, and point-of-care diagnostics.\nThree-dimensional (3D) printing offers a low-cost, rapid prototyping,\nefficient fabrication method, as compared to the costly-in terms of time,\nlabor, and resources-traditional fabrication method of soft lithography of\npoly(dimethylsiloxane) (PDMS). Various 3D printing methods are applicable,\nincluding fused deposition modeling, stereolithography, and photopolymer\ninkjet printing. Additionally, several materials are available that have\nlow-viscosity in their raw form and, after printing and curing, exhibit\nhigh material strength, optical transparency, and biocompatibility. These\nfeatures make 3D-printed microfluidic chips ideal for biomedical\napplications. However, for developing devices capable of long-term use,\nfouling-by nonspecific protein absorption and bacterial adhesion due to\nthe intrinsic hydrophobicity of most 3D-printed materials-presents a\nbarrier to reusability. For this reason, there is a growing interest in\nanti-fouling methods and materials. Traditional and emerging approaches to\nanti-fouling are presented in regard to their applicability to\nmicrofluidic chips, with a particular interest in approaches compatible\nwith 3D-printed chips.},\n\tnumber = {4},\n\tjournal = {Micromachines (Basel)},\n\tauthor = {Lepowsky, Eric and Tasoglu, Savas},\n\tmonth = apr,\n\tyear = {2018},\n\tkeywords = {3D printing, anti-fouling, microfluidic chips, Savas Scholar, surface coatings},\n}\n\n\n
@article{lepowsky_assessing_2018,\n\ttitle = {Assessing the {Reusability} of {3D}-{Printed} {Photopolymer} {Microfluidic} {Chips} for {Urine} {Processing}},\n\tvolume = {9},\n\tissn = {2072-666X},\n\turl = {http://dx.doi.org/10.3390/mi9100520},\n\tdoi = {10.3390/mi9100520},\n\tabstract = {Three-dimensional (3D) printing is emerging as a method for microfluidic\ndevice fabrication boasting facile and low-cost fabrication, as compared\nto conventional fabrication approaches, such as photolithography, for\npoly(dimethylsiloxane) (PDMS) counterparts. Additionally, there is an\nincreasing trend in the development and implementation of miniaturized and\nautomatized devices for health monitoring. While nonspecific protein\nadsorption by PDMS has been studied as a limitation for reusability, the\nprotein adsorption characteristics of 3D-printed materials have not been\nwell-studied or characterized. With these rationales in mind, we study the\nreusability of 3D-printed microfluidics chips. Herein, a 3D-printed\ncleaning chip, consisting of inlets for the sample, cleaning solution, and\nair, and a universal outlet, is presented to assess the reusability of a\n3D-printed microfluidic device. Bovine serum albumin (BSA) was used a\nrepresentative urinary protein and phosphate-buffered solution (PBS) was\nchosen as the cleaning agent. Using the\n3-(4-carboxybenzoyl)quinoline-2-carboxaldehyde (CBQCA) fluorescence\ndetection method, the protein cross-contamination between samples and the\nprotein uptake of the cleaning chip were assessed, demonstrating a\nfeasible 3D-printed chip design and cleaning procedure to enable reusable\nmicrofluidic devices. The performance of the 3D-printed cleaning chip for\nreal urine sample handling was then validated using a commercial dipstick\nassay.},\n\tnumber = {10},\n\tjournal = {Micromachines (Basel)},\n\tauthor = {Lepowsky, Eric and Amin, Reza and Tasoglu, Savas},\n\tmonth = oct,\n\tyear = {2018},\n\tkeywords = {3D printing, biofouling, microfluidics, reusability, Savas Scholar},\n}\n\n\n
@article{lepowsky_towards_2018,\n\ttitle = {Towards preserving post-printing cell viability and improving the resolution: {Past}, present, and future of {3D} bioprinting theory},\n\turl = {https://www.sciencedirect.com/science/article/pii/S2405886618300204},\n\tabstract = {Three-dimensional bioprinting as an additive manufacturing technology for\nconstructing biomimetic tissues by the deposition of individual layers is\nan ever growing and evolving …},\n\tjournal = {Bioprinting},\n\tauthor = {Lepowsky, E and Muradoglu, M and Tasoglu, S},\n\tyear = {2018},\n\tnote = {Publisher: Elsevier},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{tasoglu_editorial_2018,\n\ttitle = {Editorial for the {Special} {Issue} on {3D} {Printed} {Microfluidic} {Devices}},\n\tvolume = {9},\n\tissn = {2072-666X},\n\turl = {http://dx.doi.org/10.3390/mi9110609},\n\tdoi = {10.3390/mi9110609},\n\tabstract = {Three-dimensional (3D) printing has revolutionized the microfabrication\nprototyping workflow over the past few years. [...].},\n\tnumber = {11},\n\tjournal = {Micromachines (Basel)},\n\tauthor = {Tasoglu, Savas and Folch, Albert},\n\tmonth = nov,\n\tyear = {2018},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{lepowsky_paper-based_2017,\n\ttitle = {Paper-based assays for urine analysis},\n\tvolume = {11},\n\tissn = {1932-1058},\n\turl = {http://dx.doi.org/10.1063/1.4996768},\n\tdoi = {10.1063/1.4996768},\n\tabstract = {A transformation of the healthcare industry is necessary and imminent:\nhospital-centered, reactive care will soon give way to proactive,\nperson-centered care which focuses on individuals' well-being. However,\nthis transition will only be made possible through scientific innovation.\nNext-generation technologies will be the key to developing affordable and\naccessible care, while also lowering the costs of healthcare. A promising\nsolution to this challenge is low-cost continuous health monitoring; this\napproach allows for effective screening, analysis, and diagnosis and\nfacilitates proactive medical intervention. Urine has great promise for\nbeing a key resource for health monitoring; unlike blood, it can be\ncollected effortlessly on a daily basis without pain or the need for\nspecial equipment. Unfortunately, the commercial rapid urine analysis\ntests that exist today can only go so far-this is where the promise of\nmicrofluidic devices lies. Microfluidic devices have a proven record of\nbeing effective analytical devices, capable of controlling the flow of\nfluid samples, containing reaction and detection zones, and displaying\nresults, all within a compact footprint. Moving past traditional glass-\nand polymer-based microfluidics, paper-based microfluidic devices possess\nthe same diagnostic ability, with the added benefits of facile\nmanufacturing, low-cost implementation, and disposability. Hence, we\nreview the recent progress in the application of paper-based microfluidics\nto urine analysis as a solution to providing continuous health monitoring\nfor proactive care. First, we present important considerations for\npoint-of-care diagnostic devices. We then discuss what urine is and how\npaper functions as the substrate for urine analysis. Next, we cover the\ncurrent commercial rapid tests that exist and thereby demonstrate where\npaper-based microfluidic urine analysis devices may fit into the\ncommercial market in the future. Afterward, we discuss various fabrication\ntechniques that have been recently developed for paper-based microfluidic\ndevices. Transitioning from fabrication to implementation, we present some\nof the clinically implemented urine assays and their importance in\nhealthcare and clinical diagnosis, with a focus on paper-based\nmicrofluidic assays. We then conclude by providing an overview of select\nbiomarker research tailored towards urine diagnostics. This review will\ndemonstrate the applicability of paper-based assays for urine analysis and\nwhere they may fit into the commercial healthcare market.},\n\tnumber = {5},\n\tjournal = {Biomicrofluidics},\n\tauthor = {Lepowsky, Eric and Ghaderinezhad, Fariba and Knowlton, Stephanie and Tasoglu, Savas},\n\tmonth = sep,\n\tyear = {2017},\n\tkeywords = {Savas Scholar},\n\tpages = {051501},\n}\n\n\n
@article{amin_commercialization_2017,\n\ttitle = {Commercialization of {3D}-printed microfluidic devices},\n\tvolume = {1},\n\tissn = {2059-4755},\n\turl = {https://scholar.google.ca/scholar?cluster=14027030843883857860&hl=en&as_sdt=0,5&sciodt=0,5},\n\tdoi = {10.2217/3dp-2016-0010},\n\tnumber = {2},\n\tjournal = {J. 3D Print. Med.},\n\tauthor = {Amin, Reza and Joshi, Ashwini and Tasoglu, Savas},\n\tmonth = apr,\n\tyear = {2017},\n\tnote = {Publisher: Future Medicine Ltd},\n\tkeywords = {Savas Scholar},\n\tpages = {85--89},\n}\n\n\n
@article{knowlton_3d-printed_2017,\n\ttitle = {{3D}-printed smartphone-based point of care tool for fluorescence- and magnetophoresis-based cytometry},\n\tvolume = {17},\n\tissn = {1473-0197},\n\turl = {http://dx.doi.org/10.1039/c7lc00706j},\n\tdoi = {10.1039/c7lc00706j},\n\tabstract = {In developing countries, there are often limited resources available to\nprovide important medical diagnostics, which severely limits our ability\nto diagnose conditions and administer proper treatment, leading to high\nmortality rates for treatable conditions. Here, we propose a multiplex\ntool capable of density-based cell sorting via magnetic focusing in\nparallel with fluorescence imaging to provide highly specific clinical\nassays. While many cell sorting techniques and fluorescence microscopes\ngenerally are costly and require extensive user training, limiting\naccessibility and usability in developing countries, this device is\ncompact, low-cost, and portable. The device can separate cells on the\nbasis of density, which can be used to identify cell type and cell\nactivity, and image the cells in either brightfield, darkfield, or\nfluorescent imaging modes using the built-in smartphone camera. The\ncombination of these two powerful and versatile techniques - magnetic\nfocusing and fluorescence imaging - will make this platform broadly\napplicable to a range of biomedical assays. Clinical applications include\ncell cytometry and immunocytochemistry-based assays in limited-resource\nsettings, which can ultimately help to improve worldwide accessibility to\nmedical diagnostics.},\n\tnumber = {16},\n\tjournal = {Lab Chip},\n\tauthor = {Knowlton, Stephanie and Joshi, Ashwini and Syrrist, Philip and Coskun, Ahmet F and Tasoglu, Savas},\n\tmonth = aug,\n\tyear = {2017},\n\tkeywords = {Savas Scholar},\n\tpages = {2839--2851},\n}\n\n\n
@article{knowlton_photocrosslinking-based_2017,\n\ttitle = {Photocrosslinking-based bioprinting: {Examining} crosslinking schemes},\n\turl = {https://www.sciencedirect.com/science/article/pii/S2405886616300136},\n\tabstract = {Bioprinting has been widely used for rapid fabrication of biomimetic\ntissues and organs with the goal of closely mimicking biological\nstructures and their functionalities. Photocrosslinking …},\n\tjournal = {Bioprinting},\n\tauthor = {Knowlton, S and Yenilmez, B and Anand, S and Tasoglu, S},\n\tyear = {2017},\n\tnote = {Publisher: Elsevier},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{knowlton_magnetic_2017,\n\ttitle = {Magnetic {Levitation} {Coupled} with {Portable} {Imaging} and {Analysis} for {Disease} {Diagnostics}},\n\tissn = {1940-087X},\n\turl = {http://dx.doi.org/10.3791/55012},\n\tdoi = {10.3791/55012},\n\tabstract = {Currently, many clinical diagnostic procedures are complex, costly,\ninefficient, and inaccessible to a large population in the world. The\nrequirements for specialized equipment and trained personnel require that\nmany diagnostic tests be performed at remote, centralized clinical\nlaboratories. Magnetic levitation is a simple yet powerful technique and\ncan be applied to levitate cells, which are suspended in a paramagnetic\nsolution and placed in a magnetic field, at a position determined by\nequilibrium between a magnetic force and a buoyancy force. Here, we\npresent a versatile platform technology designed for point-of-care\ndiagnostics which uses magnetic levitation coupled to microscopic imaging\nand automated analysis to determine the density distribution of a\npatient's cells as a useful diagnostic indicator. We present two platforms\noperating on this principle: (i) a smartphone-compatible version of the\ntechnology, where the built-in smartphone camera is used to image cells in\nthe magnetic field and a smartphone application processes the images and\nto measures the density distribution of the cells and (ii) a\nself-contained version where a camera board is used to capture images and\nan embedded processing unit with attached thin-film-transistor (TFT)\nscreen measures and displays the results. Demonstrated applications\ninclude: (i) measuring the altered distribution of a cell population with\na disease phenotype compared to a healthy phenotype, which is applied to\nsickle cell disease diagnosis, and (ii) separation of different cell types\nbased on their characteristic densities, which is applied to separate\nwhite blood cells from red blood cells for white blood cell cytometry.\nThese applications, as well as future extensions of the essential\ndensity-based measurements enabled by this portable, user-friendly\nplatform technology, will significantly enhance disease diagnostic\ncapabilities at the point of care.},\n\tnumber = {120},\n\tjournal = {J. Vis. Exp.},\n\tauthor = {Knowlton, Stephanie M and Yenilmez, Bekir and Amin, Reza and Tasoglu, Savas},\n\tmonth = feb,\n\tyear = {2017},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{ghaderinezhad_high-throughput_2017,\n\ttitle = {High-throughput rapid-prototyping of low-cost paper-based microfluidics},\n\turl = {https://www.nature.com/articles/s41598-017-02931-6},\n\tabstract = {Paper-based micro analytical devices offer significant advantages compared\nto the conventional microfluidic chips including cost-effectiveness, ease\nof fabrication, and ease of …},\n\tjournal = {Sci. Rep.},\n\tauthor = {Ghaderinezhad, F and Amin, R and Temirel, M and Yenilmez, B and {others}},\n\tyear = {2017},\n\tnote = {Publisher: nature.com},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{amin_continuous-ink_2017,\n\ttitle = {Continuous-{Ink}, {Multiplexed} {Pen}-{Plotter} {Approach} for {Low}-{Cost}, {High}-{Throughput} {Fabrication} of {Paper}-{Based} {Microfluidics}},\n\tvolume = {89},\n\tissn = {0003-2700},\n\turl = {http://dx.doi.org/10.1021/acs.analchem.7b01418},\n\tdoi = {10.1021/acs.analchem.7b01418},\n\tabstract = {There is an unmet need for high-throughput fabrication techniques for\npaper-based microanalytical devices, especially in limited resource areas.\nFabrication of these devices requires precise and repeatable deposition of\nhydrophobic materials in a defined pattern to delineate the hydrophilic\nreaction zones. In this study, we demonstrated a cost- and time-effective\nmethod for high-throughput, easily accessible fabrication of paper-based\nmicrofluidics using a desktop pen plotter integrated with a\ncustom-designed multipen holder. This approach enabled simultaneous\nprinting with multiple printing heads and, thus, multiplexed fabrication.\nMoreover, we proposed an ink supply system connected to commercial\ntechnical pens to allow continuous flow of the ink, thereby increasing the\nprinting capacity of the system. We tested the use of either hot- or\ncold-laminating layers to improve (i) the durability, stability, and\nmechanical strength of the paper-based devices and (ii) the seal on the\nback face of the chromatography paper to prevent wetting of the sample\nbeyond the hydrophilic testing region. To demonstrate a potential\napplication of the paper-based microfluidic devices fabricated by the\nproposed method, colorimetric urine assays were implemented and tested:\nnitrite, urobilinogen, protein, blood, and pH.},\n\tnumber = {12},\n\tjournal = {Anal. Chem.},\n\tauthor = {Amin, Reza and Ghaderinezhad, Fariba and Li, Lu and Lepowsky, Eric and Yenilmez, Bekir and Knowlton, Stephanie and Tasoglu, Savas},\n\tmonth = jun,\n\tyear = {2017},\n\tkeywords = {Savas Scholar},\n\tpages = {6351--6357},\n}\n\n\n
@article{amin_3d-printed_2017,\n\ttitle = {{3D}-printed smartphone-based device for label-free cell separation},\n\turl = {https://www.futuremedicine.com/doi/abs/10.2217/3dp-2016-0007},\n\tabstract = {Aim: To assess several fabrication metrics of a 3D-printed\nsmartphone-attachable continuous-flow magnetic focusing device for\nreal-time separation and detection of different …},\n\tjournal = {Journal of 3D printing},\n\tauthor = {Amin, R and Knowlton, S and Dupont, J and {others}},\n\tyear = {2017},\n\tnote = {Publisher: Future Medicine},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{knowlton_3d-printed_2016,\n\ttitle = {{3D}-printed microfluidic chips with patterned, cell-laden hydrogel constructs},\n\tvolume = {8},\n\tissn = {1758-5082},\n\turl = {http://dx.doi.org/10.1088/1758-5090/8/2/025019},\n\tdoi = {10.1088/1758-5090/8/2/025019},\n\tabstract = {Three-dimensional (3D) printing offers potential to fabricate\nhigh-throughput and low-cost fabrication of microfluidic devices as a\npromising alternative to traditional techniques which enables efficient\ndesign iterations in the development stage. In this study, we demonstrate\na single-step fabrication of a 3D transparent microfluidic chip using two\nalternative techniques: a stereolithography-based desktop 3D printer and a\ntwo-step fabrication using an industrial 3D printer based on polyjet\ntechnology. This method, compared to conventional fabrication using\nrelatively expensive materials and labor-intensive processes, presents a\nlow-cost, rapid prototyping technique to print functional 3D microfluidic\nchips. We enhance the capabilities of 3D-printed microfluidic devices by\ncoupling 3D cell encapsulation and spatial patterning within\nphotocrosslinkable gelatin methacryloyl (GelMA). The platform presented\nhere serves as a 3D culture environment for long-term cell culture and\ngrowth. Furthermore, we have demonstrated the ability to print complex 3D\nmicrofluidic channels to create predictable and controllable fluid flow\nregimes. Here, we demonstrate the novel use of 3D-printed microfluidic\nchips as controllable 3D cell culture environments, advancing the\napplicability of 3D printing to engineering physiological systems for\nfuture applications in bioengineering.},\n\tnumber = {2},\n\tjournal = {Biofabrication},\n\tauthor = {Knowlton, Stephanie and Yu, Chu Hsiang and Ersoy, Fulya and Emadi, Sharareh and Khademhosseini, Ali and Tasoglu, Savas},\n\tmonth = jun,\n\tyear = {2016},\n\tkeywords = {Savas Scholar},\n\tpages = {025019},\n}\n\n\n
@article{knowlton_bioprinted_2016,\n\ttitle = {A {Bioprinted} {Liver}-on-a-{Chip} for {Drug} {Screening} {Applications}},\n\tvolume = {34},\n\tissn = {0167-7799},\n\turl = {http://dx.doi.org/10.1016/j.tibtech.2016.05.014},\n\tdoi = {10.1016/j.tibtech.2016.05.014},\n\tabstract = {The need for a liver-on-a-chip tissue model for drug screening is\nparticularly important in tissue engineering because of the high frequency\nof drug-induced liver injury. Recently, a liver tissue model conducive to\nhepatotoxicity testing was developed by bioprinting hepatic spheroids\nencapsulated in a hydrogel scaffold into a microfluidic device.},\n\tnumber = {9},\n\tjournal = {Trends Biotechnol.},\n\tauthor = {Knowlton, Stephanie and Tasoglu, Savas},\n\tmonth = sep,\n\tyear = {2016},\n\tkeywords = {3D cell cultures, bioprinting, liver tissue engineering, microfluidics, organ-on-a-chip, Savas Scholar, tissue engineering},\n\tpages = {681--682},\n}\n\n\n
@article{knowlton_utilizing_2016,\n\ttitle = {Utilizing stem cells for three-dimensional neural tissue engineering},\n\tissn = {0142-9612},\n\turl = {https://pubs.rsc.org/en/content/articlehtml/2016/bm/c5bm00324e},\n\tabstract = {Three-dimensional neural tissue engineering has made great strides in\ndeveloping neural disease models and replacement tissues for patients.\nHowever, the need for biomimetic …},\n\tjournal = {Biomaterials},\n\tauthor = {Knowlton, S and Cho, Y and Li, X J and Khademhosseini, A and {others}},\n\tyear = {2016},\n\tnote = {Publisher: pubs.rsc.org},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{amin_smart-phone_2016,\n\ttitle = {Smart-phone attachable, flow-assisted magnetic focusing device},\n\turl = {https://pubs.rsc.org/en/content/articlehtml/2016/ra/c6ra19483d},\n\tabstract = {Detection and sorting of particles and cells in a continuous flow stream\nis of great importance to downstream biological studies and\nhigh-throughput screening. Many particle …},\n\tjournal = {RSC Adv.},\n\tauthor = {Amin, R and Knowlton, S and Yenilmez, B and Hart, A and Joshi, A and {others}},\n\tyear = {2016},\n\tnote = {Publisher: pubs.rsc.org},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{amin_3d-printed_2016,\n\ttitle = {{3D}-printed microfluidic devices},\n\turl = {https://iopscience.iop.org/article/10.1088/1758-5090/8/2/022001/meta},\n\tabstract = {Microfluidics is a flourishing field, enabling a wide range of biochemical\nand clinical applications such as cancer screening, micro-physiological\nsystem engineering, high …},\n\tauthor = {Amin, R and Knowlton, S and Hart, A and Yenilmez, B and {others}},\n\tyear = {2016},\n\tnote = {Publisher: iopscience.iop.org},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{chen_cell-encapsulating_2016,\n\ttitle = {Cell-encapsulating hydrogels for biosensing},\n\turl = {https://www.worldscientific.com/doi/abs/10.1142/9789813140417_0012},\n\tabstract = {Cell-based biosensors (CBBs) are emerging as a sensing platform in which\nlive cells are utilized to sense external stimuli including physical,\nchemical, and biological changes. Till …},\n\tjournal = {Volume 3: Application …},\n\tauthor = {Chen, P and Wang, S and Inci, F and Güven, S and {others}},\n\tyear = {2016},\n\tnote = {Publisher: World Scientific},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{knowlton_building_2016,\n\ttitle = {Building blocks for bottom-up neural tissue engineering: tools for in vitro assembly and interrogation of neural circuits},\n\turl = {https://link.springer.com/chapter/10.1007/978-3-319-31433-4_4},\n\tabstract = {Bottom-up tissue engineering approaches provide unique opportunities to\ninvestigate the formation and dynamics of neural circuits. Given the fact\nthat spatial organization of cells …},\n\tjournal = {Neural Engineering: From},\n\tauthor = {Knowlton, S and Li, D and Ersoy, F and Cho, Y K and {others}},\n\tyear = {2016},\n\tnote = {Publisher: Springer},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{knowlton_advancing_2016,\n\ttitle = {Advancing cancer research using bioprinting for tumor-on-a-chip platforms},\n\turl = {http://ijb.whioce.com/index.php/int-j-bioprinting/article/view/77},\n\tabstract = {There is an urgent for a novel approach to cancer research with 1.7\nmillion new cases of cancer occurring every year in the United States of\nAmerica. Tumor models offer promise as …},\n\tjournal = {Journal of Bioprinting},\n\tauthor = {Knowlton, S and Joshi, A and Yenilmez, B and Ozbolat, I T and {others}},\n\tyear = {2016},\n\tnote = {Publisher: ijb.whioce.com},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{yenilmez_selfcontained_2016,\n\ttitle = {Self‐contained handheld magnetic platform for point of care cytometry in biological samples},\n\tissn = {0935-9648},\n\turl = {https://onlinelibrary.wiley.com/doi/abs/10.1002/admt.201600144},\n\tabstract = {Magnetic levitation is a powerful tool capable of distinguishing\nmicrometer‐scale particles based on their densities. When a particle is\nsuspended in a paramagnetic medium and …},\n\tjournal = {Adv. Mater.},\n\tauthor = {Yenilmez, B and Knowlton, S and {others}},\n\tyear = {2016},\n\tnote = {Publisher: Wiley Online Library},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{knowlton_towards_2016,\n\ttitle = {Towards {Single}-{Step} {Biofabrication} of {Organs} on a {Chip} via {3D} {Printing}},\n\tvolume = {34},\n\tissn = {0167-7799},\n\turl = {http://dx.doi.org/10.1016/j.tibtech.2016.06.005},\n\tdoi = {10.1016/j.tibtech.2016.06.005},\n\tabstract = {Organ-on-a-chip engineering employs microfabrication of living tissues\nwithin microscale fluid channels to create constructs that closely mimic\nhuman organs. With the advent of 3D printing, we predict that single-step\nfabrication of these devices will enable rapid design and cost-effective\niterations in the development stage, facilitating rapid innovation in this\nfield.},\n\tnumber = {9},\n\tjournal = {Trends Biotechnol.},\n\tauthor = {Knowlton, Stephanie and Yenilmez, Bekir and Tasoglu, Savas},\n\tmonth = sep,\n\tyear = {2016},\n\tkeywords = {3D printing, biofabrication, bioprinting, microfluidics., organ-on-a-chip, Savas Scholar, tissue engineering},\n\tpages = {685--688},\n}\n\n\n
@article{temirel_three-dimensional-printed_2016,\n\ttitle = {Three-dimensional-printed carnivorous plant with snap trap},\n\turl = {https://www.liebertpub.com/doi/abs/10.1089/3dp.2016.0036},\n\tabstract = {Abstract Three-dimensional (3D) printing has a variety of applications,\nfrom efficient iterations of engineering designs to fabrication of tissues\nfor regenerative medicine. In soft …},\n\tjournal = {3D Printing and},\n\tauthor = {Temirel, M and Yenilmez, B and Knowlton, S and {others}},\n\tyear = {2016},\n\tnote = {Publisher: liebertpub.com},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{yenilmez_labelfree_2016,\n\ttitle = {Label‐free sickle cell disease diagnosis using a low‐cost, handheld platform},\n\tissn = {0935-9648},\n\turl = {https://onlinelibrary.wiley.com/doi/abs/10.1002/admt.201600100},\n\tabstract = {Recent technological advancements have made strides in shifting clinical\ndiagnostics from large centralized laboratories to the point of care, thus\nwidely increasing the accessibility to …},\n\tjournal = {Adv. Mater.},\n\tauthor = {Yenilmez, B and Knowlton, S and Yu, C H and {others}},\n\tyear = {2016},\n\tnote = {Publisher: Wiley Online Library},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{domalapally_computational_2015,\n\ttitle = {Computational thermal fluid dynamic analysis of {Hypervapotron} heat sink for high heat flux devices application},\n\tvolume = {98-99},\n\tissn = {0920-3796},\n\turl = {https://linkinghub.elsevier.com/retrieve/pii/S0920379615001003},\n\tdoi = {10.1016/j.fusengdes.2015.02.017},\n\tabstract = {In fusion devices, plasma is the environment in which light elements fuse producing energy. More than 20\\% of this power reaches the surface of plasma facing components (e.g. the divertor targets, first wall), where the heat flux local value can be several MW/m2. In order to handle such heat fluxes several coolants are proposed such as water, helium and liquid metals along with different heat sink devices, such as Swirl tubes, Hypervapotrons, Jet cooling, Pin-fins, etc. Among these, Hypervapotron concept, operating in highly subcooled boiling regime with water as a coolant is considered as one of the potential candidates. In this paper, a Computational Fluid Dynamic (CFD) approach is used to analyze the boiling flow inside Hypervapotron channel using two different boiling models: Rohsenow boiling model and Transition boiling model, these models are available in the commercial CFD code STARCCM+, and uses Volume of Fluid approach for the multiphase flow analysis. They are benchmarked using experimental data obtained from experiments conducted at Joint European Torus, UK. The simulated results are then compared with each other and also with other simulated data available to test the quantitative, qualitative features of boiling models in modeling nucleate as well as hard boiling regimes.},\n\tjournal = {Fusion Eng. Des.},\n\tauthor = {Domalapally, Phani and Subba, Fabio},\n\tmonth = oct,\n\tyear = {2015},\n\tnote = {Publisher: Elsevier BV},\n\tkeywords = {Savas Scholar},\n\tpages = {1267--1270},\n}\n\n\n
@article{tasoglu_advances_2015,\n\ttitle = {Advances in nanotechnology and microfluidics for human papillomavirus diagnostics},\n\turl = {https://ieeexplore.ieee.org/abstract/document/7067030/},\n\tabstract = {Human papillomavirus (HPV) has been shown in many studies as a\nprerequisite for the development of cervical cancer, which is the second\nmost common and predominant form of …},\n\tjournal = {Proceedings of the},\n\tauthor = {Tasoglu, S and Tekin, H C and Inci, F and Knowlton, S and {others}},\n\tyear = {2015},\n\tnote = {Publisher: ieeexplore.ieee.org},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{knowlton_microfluidics_2015,\n\ttitle = {Microfluidics for sperm research},\n\tissn = {0167-7799},\n\turl = {https://www.cell.com/trends/biotechnology/fulltext/S0167-7799(15)00021-9},\n\tabstract = {One in six couples of reproductive age worldwide are affected at least\nonce by some form of infertility. In vitro fertilization (IVF) and\nintracytoplasmic sperm injection (ICSI) are widely …},\n\tjournal = {Trends Biotechnol.},\n\tauthor = {Knowlton, S M and Sadasivam, M and Tasoglu, S},\n\tyear = {2015},\n\tnote = {Publisher: cell.com},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{guven_multiscale_2015,\n\ttitle = {Multiscale assembly for tissue engineering and regenerative medicine},\n\turl = {https://www.cell.com/trends/biotechnology/fulltext/S0167-7799(15)00026-8?mobileUi\\u003d0\\u0026code\\u003dcell-site=},\n\tabstract = {Our understanding of cell biology and its integration with materials\nscience has led to technological innovations in the bioengineering of\ntissue-mimicking grafts that can be …},\n\tjournal = {Trends in},\n\tauthor = {Guven, S and Chen, P and Inci, F and Tasoglu, S and Erkmen, B and {others}},\n\tyear = {2015},\n\tnote = {Publisher: cell.com},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{tasoglu_cytometry_2015,\n\ttitle = {Cytometry: {Levitational} {Image} {Cytometry} with {Temporal} {Resolution} ({Adv}. {Mater}. 26/2015)},\n\turl = {https://onlinelibrary.wiley.com/doi/abs/10.1002/adma.201570175},\n\tabstract = {Abstract On page 3901, IC Ghiran, U. Demirci, and co-workers design a\nmagnetic-levitation- based device that allows both label-free separation\nand high-resolution real-time monitoring …},\n\tjournal = {Advanced},\n\tauthor = {Tasoglu, S and Khoory, J A and Tekin, H C and Thomas, C and {others}},\n\tyear = {2015},\n\tnote = {Publisher: Wiley Online Library},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{tasoglu_levitational_2015,\n\ttitle = {Levitational image cytometry with temporal resolution},\n\turl = {https://onlinelibrary.wiley.com/doi/abs/10.1002/adma.201405660},\n\tabstract = {A simple, yet powerful magnetic-levitation-based device is reported for\nreal-time, label-free separation, as well as high-resolution monitoring of\ncell populations based on their unique …},\n\tjournal = {Advanced},\n\tauthor = {Tasoglu, S and Khoory, J A and Tekin, H C and Thomas, C and {others}},\n\tyear = {2015},\n\tnote = {Publisher: Wiley Online Library},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{knowlton_smart-phone_2015,\n\ttitle = {Smart-phone based magnetic levitation for measuring densities},\n\turl = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0134400},\n\tabstract = {Magnetic levitation, which uses a magnetic field to suspend objects in a\nfluid, is a powerful and versatile technology. We develop a compact\nmagnetic levitation platform compatible …},\n\tjournal = {PLoS One},\n\tauthor = {Knowlton, S and Yu, C H and Jain, N and Ghiran, I C and Tasoglu, S},\n\tyear = {2015},\n\tnote = {Publisher: journals.plos.org},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{tasoglu_magnetic_2015,\n\ttitle = {Magnetic levitational assembly for living material fabrication},\n\tissn = {2192-2640},\n\turl = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4504784/},\n\tabstract = {Assembly with guidance of field forces or without guidance is a promising\nand noninvasive strategy for aligning and biomanufacturing soft biological\nsystems made of numerous …},\n\tjournal = {Adv. Healthc. Mater.},\n\tauthor = {Tasoglu, S and Yu, C H and Liaudanskaya, V and {others}},\n\tyear = {2015},\n\tnote = {Publisher: ncbi.nlm.nih.gov},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{knowlton_bioprinting_2015,\n\ttitle = {Bioprinting for cancer research},\n\tissn = {0167-7799},\n\turl = {https://www.cell.com/trends/biotechnology/fulltext/S0167-7799(15)00135-3?elsca1=etoc&elsca2=email&elsca3=0167-7799_201509_33_9_&elsca4=Cell+Press},\n\tabstract = {Bioprinting offers the ability to create highly complex 3D architectures\nwith living cells. This cutting-edge technique has significantly gained\npopularity and applicability in several fields …},\n\tjournal = {Trends Biotechnol.},\n\tauthor = {Knowlton, S and Onal, S and Yu, C H and Zhao, J J and Tasoglu, S},\n\tyear = {2015},\n\tnote = {Publisher: cell.com},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{luo_deformation_2015,\n\ttitle = {Deformation of a single mouse oocyte in a constricted microfluidic channel},\n\tissn = {1613-4982},\n\turl = {https://link.springer.com/article/10.1007/s10404-015-1614-0},\n\tabstract = {Single oocyte manipulation in microfluidic channels via precisely\ncontrolled flow is critical in microfluidics-based in vitro fertilization.\nSuch systems can potentially minimize the number of …},\n\tjournal = {Microfluid. Nanofluidics},\n\tauthor = {Luo, Z Y and Güven, S and Gozen, I and Chen, P and Tasoglu, S and {others}},\n\tyear = {2015},\n\tnote = {Publisher: Springer},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{knowlton_sickle_2015,\n\ttitle = {Sickle cell detection using a smartphone},\n\turl = {https://www.nature.com/articles/srep15022},\n\tabstract = {Sickle cell disease affects 25\\% of people living in Central and West\nAfrica and, if left undiagnosed, can cause life threatening “silent”\nstrokes and lifelong damage. However …},\n\tjournal = {Sci. Rep.},\n\tauthor = {Knowlton, S M and Sencan, I and Aytar, Y and Khoory, J and {others}},\n\tyear = {2015},\n\tnote = {Publisher: nature.com},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@inproceedings{clement_engineering_2015,\n\taddress = {Troy, NY, USA},\n\ttitle = {Engineering a microfluidic organ model using 3-dimensional micropatterned cellular constructs},\n\tisbn = {978-1-4799-8360-5},\n\turl = {http://ieeexplore.ieee.org/document/7117104/},\n\tdoi = {10.1109/NEBEC.2015.7117104},\n\turldate = {2023-09-29},\n\tbooktitle = {2015 41st {Annual} {Northeast} {Biomedical} {Engineering} {Conference} ({NEBEC})},\n\tpublisher = {IEEE},\n\tauthor = {Clement, E. and Knowlton, S. and Mandelkern, T. and Tasoglu, S.},\n\tmonth = apr,\n\tyear = {2015},\n\tpages = {1--2},\n}\n\n\n
@article{keiser_review_2014,\n\ttitle = {Review of diverse optical fibers used in biomedical research and clinical practice},\n\tvolume = {19},\n\tissn = {1083-3668},\n\turl = {https://scholar.google.ca/scholar?cluster=6998380133619793197&hl=en&as_sdt=0,5&sciodt=0,5},\n\tdoi = {10.1117/1.JBO.19.8.080902},\n\tabstract = {Optical fiber technology has significantly bolstered the growth of\nphotonics applications in basic life sciences research and in biomedical\ndiagnosis, therapy, monitoring, and surgery. The unique operational\ncharacteristics of diverse fibers have been exploited to realize advanced\nbiomedical functions in areas such as illumination, imaging, minimally\ninvasive surgery, tissue ablation, biological sensing, and tissue\ndiagnosis. This review paper provides the necessary background to\nunderstand how optical fibers function, to describe the various categories\nof available fibers, and to illustrate how specific fibers are used for\nselected biomedical photonics applications. Research articles and vendor\ndata sheets were consulted to describe the operational characteristics of\nconventional and specialty multimode and single-mode solid-core fibers,\ndouble-clad fibers, hard-clad silica fibers, conventional hollow-core\nfibers, photonic crystal fibers, polymer optical fibers, side-emitting and\nside-firing fibers, middle-infrared fibers, and optical fiber bundles.\nRepresentative applications from the recent literature illustrate how\nvarious fibers can be utilized in a wide range of biomedical disciplines.\nIn addition to helping researchers refine current experimental setups, the\nmaterial in this review paper will help conceptualize and develop emerging\noptical fiber-based diagnostic and analysis tools.},\n\tnumber = {8},\n\tjournal = {J. Biomed. Opt.},\n\tauthor = {Keiser, Gerd and Xiong, Fei and Cui, Ying and Shum, Perry Ping},\n\tmonth = aug,\n\tyear = {2014},\n\tnote = {Publisher: SPIE-Intl Soc Optical Eng},\n\tkeywords = {Savas Scholar},\n\tpages = {080902},\n}\n\n\n
@article{wang_micro--fluidics_2014,\n\ttitle = {Micro-a-fluidics {ELISA} for rapid {CD4} cell count at the point-of-care},\n\turl = {https://www.nature.com/articles/srep03796},\n\tabstract = {HIV has become one of the most devastating pathogens in human history.\nDespite fast progress in HIV-related basic research, antiretroviral\ntherapy (ART) remains the most …},\n\tjournal = {Sci. Rep.},\n\tauthor = {Wang, S Q and Tasoglu, S and Chen, P Z and Chen, M and Akbas, R and {others}},\n\tyear = {2014},\n\tnote = {Publisher: nature.com},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{diller_untethered_2014,\n\ttitle = {Untethered micro-robotic coding of three-dimensional material composition},\n\turl = {https://www.nature.com/articles/ncomms4124},\n\tabstract = {Complex functional materials with three-dimensional micro-or nano-scale\ndynamic compositional features are prevalent in nature. However, the\ngeneration of three …},\n\tjournal = {Nat. Commun.},\n\tauthor = {Diller, E and Guven, S and Sitti, M and Demirci, U},\n\tyear = {2014},\n\tnote = {Publisher: nature.com},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{tasoglu_organ_2014,\n\ttitle = {Organ printing and cell encapsulation},\n\turl = {https://www.researchgate.net/profile/Sinan-Guven/publication/300375783_Organ_Printing_and_Cell_Encapsulation/links/5767fbc208ae1658e2f8c0dd/Organ-Printing-and-Cell-Encapsulation.pdf},\n\tabstract = {transport through scaffold porosity mimicking vascular network in vivo.\nBioprinting is an emerging bottom-up approach to provide spatial\nmicrocontrol over placement of living cells …},\n\tauthor = {Tasoglu, S and Guven, S},\n\tyear = {2014},\n\tnote = {Publisher: researchgate.net},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{chen_microscale_2014,\n\ttitle = {Microscale assembly: {Microscale} assembly directed by liquid-based template (adv. {Mater}. 34/2014)},\n\tvolume = {26},\n\tissn = {0935-9648},\n\turl = {https://onlinelibrary.wiley.com/doi/10.1002/adma.201470236},\n\tdoi = {10.1002/adma.201470236},\n\tnumber = {34},\n\tjournal = {Adv. Mater.},\n\tauthor = {Chen, Pu and Luo, Zhengyuan and Güven, Sinan and Tasoglu, Savas and Ganesan, Adarsh Venkataraman and Weng, Andrew and Demirci, Utkan},\n\tmonth = sep,\n\tyear = {2014},\n\tnote = {Publisher: Wiley},\n\tkeywords = {Savas Scholar},\n\tpages = {6044--6044},\n}\n\n\n
@article{tasoglu_guided_2014,\n\ttitle = {Guided and magnetic self-assembly of tunable magnetoceptive gels},\n\tissn = {0028-0836},\n\turl = {https://www.nature.com/articles/ncomms5702},\n\tabstract = {Self-assembly of components into complex functional patterns at microscale\nis common in nature, and used increasingly in numerous disciplines such as\noptoelectronics …},\n\tjournal = {Nature},\n\tauthor = {Tasoglu, S and Yu, C H and Gungordu, H I and Guven, S and {others}},\n\tyear = {2014},\n\tnote = {Publisher: nature.com},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{chen_microscale_2014-1,\n\ttitle = {Microscale assembly directed by liquid‐based template},\n\turl = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ADMA.201402079},\n\tabstract = {A liquid surface established by standing waves is used as a dynamically\nreconfigurable template to assemble microscale materials into ordered,\nsymmetric structures in a scalable …},\n\tjournal = {Advanced},\n\tauthor = {Chen, P and Luo, Z and Güven, S and Tasoglu, S and {others}},\n\tyear = {2014},\n\tnote = {Publisher: Wiley Online Library},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@patent{demirci_analysis_2014,\n\ttitle = {Analysis and sorting of motile cells},\n\turl = {https://patents.google.com/patent/US20140248656A1/en},\n\tabstract = {A method for sorting motile cells includes introducing an initial\npopulation of motile cells into an inlet port of a microfluidic channel,\nthe initial population of motile cells having a first …},\n\tauthor = {Demirci, U and Zhang, X and Kayaalp, E and Safaee, H and {others}},\n\tyear = {2014},\n\tnote = {Publication Title: US Patent App. 14},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{luo_two-dimensional_2014,\n\ttitle = {Two-dimensional numerical study of flow dynamics of a nucleated cell tethered under shear flow},\n\tissn = {1005-9954},\n\turl = {https://www.sciencedirect.com/science/article/pii/S0009250914003935},\n\tabstract = {When blood components (eg., leukocytes and platelets) adhere to a surface\n(eg., blood vessel wall), shear flow causes the elongation of the\nnon-adherent part of the cell membrane …},\n\tjournal = {Chem. Eng.},\n\tauthor = {Luo, Z Y and He, L and Wang, S Q and Tasoglu, S and Xu, F and {others}},\n\tyear = {2014},\n\tnote = {Publisher: Elsevier},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@inproceedings{tasoglu_robotic_2014,\n\taddress = {WILEY-BLACKWELL 111 RIVER ST, HOBOKEN 07030-5774, NJ USA},\n\ttitle = {Robotic assembly of hydrogels for tissue engineering and regenerative medicine},\n\tvolume = {8},\n\tlanguage = {en},\n\tpublisher = {WILEY-BLACKWELL},\n\tauthor = {Tasoglu, Savas and Sitti, Metin and Diller, E and Guven, S and Demirci, Utkan},\n\tyear = {2014},\n\tpages = {181--182},\n}\n\n
@article{tasoglu_cheminform_2013,\n\ttitle = {{ChemInform} abstract: {Manipulating} biological agents and cells in micro-scale volumes for applications in medicine},\n\tvolume = {44},\n\tissn = {0931-7597},\n\turl = {https://scholar.google.ca/scholar?cluster=13096907130619381893&hl=en&as_sdt=0,5&sciodt=0,5},\n\tdoi = {10.1002/chin.201335240},\n\tnumber = {35},\n\tjournal = {ChemInform},\n\tauthor = {Tasoglu, Savas and Gurkan, Umut Atakan and Wang, Shiqi and Demirci, Utkan},\n\tmonth = aug,\n\tyear = {2013},\n\tnote = {Publisher: Wiley},\n\tkeywords = {Savas Scholar},\n\tpages = {no--no},\n}\n\n\n
@article{tasoglu_microfluidic_2013,\n\ttitle = {Microfluidic sorting: {Exhaustion} of racing sperm in nature-mimicking microfluidic channels during sorting (small 20/2013)},\n\tvolume = {9},\n\tissn = {1613-6810},\n\turl = {https://scholar.google.ca/scholar?cluster=715259596550991944&hl=en&as_sdt=0,5&sciodt=0,5},\n\tdoi = {10.1002/smll.201370121},\n\tnumber = {20},\n\tjournal = {Small},\n\tauthor = {Tasoglu, Savas and Safaee, Hooman and Zhang, Xiaohui and Kingsley, James L and Catalano, Paolo N and Gurkan, Umut Atakan and Nureddin, Aida and Kayaalp, Emre and Anchan, Raymond M and Maas, Richard L and Tüzel, Erkan and Demirci, Utkan},\n\tmonth = oct,\n\tyear = {2013},\n\tnote = {Publisher: Wiley},\n\tkeywords = {Savas Scholar},\n\tpages = {3366--3366},\n}\n\n\n
@article{asghar_vitro_2013,\n\ttitle = {In vitro three-dimensional cancer culture models},\n\turl = {https://link.springer.com/chapter/10.1007/978-1-4614-7876-8_24},\n\tabstract = {The efficacy of chemotherapy drug candidates is conventionally\ninvestigated using 2D cancer cell cultures and in vivo animal models. It\nis crucial to determine signaling pathways …},\n\tjournal = {Cancer Targeted Drug},\n\tauthor = {Asghar, W and Shafiee, H and Chen, P and Tasoglu, S and {others}},\n\tyear = {2013},\n\tnote = {Publisher: Springer},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{tasoglu_bioprinting_2013,\n\ttitle = {Bioprinting for stem cell research},\n\tissn = {0167-7799},\n\turl = {https://www.cell.com/trends/biotechnology/fulltext/S0167-7799(12)00185-0?cc=y},\n\tabstract = {Recently, there has been growing interest in applying bioprinting\ntechniques to stem cell research. Several bioprinting methods have been\ndeveloped utilizing acoustics …},\n\tjournal = {Trends Biotechnol.},\n\tauthor = {Tasoglu, S and Demirci, U},\n\tyear = {2013},\n\tnote = {Publisher: cell.com},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{tasoglu_paramagnetic_2013,\n\ttitle = {Paramagnetic levitational assembly of hydrogels},\n\turl = {https://onlinelibrary.wiley.com/doi/abs/10.1002/adma.201200285},\n\tabstract = {We have presented, for the first time, hydrogels that can be directed and\nassembled into 3D constructs by exploiting their magnetic properties\nwithout using magnetic particles. We have …},\n\tjournal = {Advanced},\n\tauthor = {Tasoglu, S and Kavaz, D and Gurkan, U A and Guven, S and {others}},\n\tyear = {2013},\n\tnote = {Publisher: Wiley Online Library},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{tasoglu_transient_2013,\n\ttitle = {Transient swelling, spreading, and drug delivery by a dissolved anti-{HIV} microbicide-bearing film},\n\tissn = {1070-6631},\n\turl = {https://pubs.aip.org/aip/pof/article/25/3/031901/257885},\n\tabstract = {There is a widespread agreement that more effective drug delivery vehicles\nwith more alternatives, as well as better active pharmaceutical\ningredients (APIs), must be developed …},\n\tjournal = {Phys. Fluids},\n\tauthor = {Tasoglu, S and Rohan, L C and Katz, D F and Szeri, A J},\n\tyear = {2013},\n\tnote = {Publisher: pubs.aip.org},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{rizvi_flow_2013,\n\ttitle = {Flow induces epithelial-mesenchymal transition, cellular heterogeneity and biomarker modulation in {3D} ovarian cancer nodules},\n\turl = {https://www.pnas.org/doi/abs/10.1073/pnas.1216989110},\n\tabstract = {Seventy-five percent of patients with epithelial ovarian cancer present\nwith advanced-stage disease that is extensively disseminated\nintraperitoneally and prognosticates the poorest …},\n\tjournal = {Proceedings of the},\n\tauthor = {Rizvi, I and Gurkan, U A and Tasoglu, S and {others}},\n\tyear = {2013},\n\tnote = {Publisher: National Acad Sciences},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{tasoglu_hydrogels_2013,\n\ttitle = {Hydrogels: {Paramagnetic} {Levitational} {Assembly} of {Hydrogels} ({Adv}. {Mater}. 8/2013)},\n\turl = {https://onlinelibrary.wiley.com/doi/abs/10.1002/adma.201370046},\n\tabstract = {Manipulation and assembly of cell‐encapsulating hydrogels offer unique\nopportunities for regenerative medicine, microphysiological system\nengineering, pharmaceutical research …},\n\tjournal = {Advanced},\n\tauthor = {Tasoglu, S and Kavaz, D and Gurkan, U A and Guven, S and {others}},\n\tyear = {2013},\n\tnote = {Publisher: Wiley Online Library},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{inci_nanoplasmonic_2013,\n\ttitle = {Nanoplasmonic quantitative detection of intact viruses from unprocessed whole blood},\n\turl = {https://pubs.acs.org/doi/abs/10.1021/nn3036232},\n\tabstract = {Infectious diseases such as HIV and hepatitis B pose an omnipresent threat\nto global health. Reliable, fast, accurate, and sensitive platforms that\ncan be deployed at the point-of-care …},\n\tjournal = {ACS},\n\tauthor = {Inci, F and Tokel, O and Wang, S Q and Gurkan, U A and Tasoglu, S and {others}},\n\tyear = {2013},\n\tnote = {Publisher: ACS Publications},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{gurkan_smart_2012,\n\ttitle = {Smart interface materials integrated with microfluidics for on-demand local capture and release of cells},\n\tvolume = {1},\n\tissn = {2192-2640},\n\turl = {https://scholar.google.ca/scholar?cluster=7209687675203628004&hl=en&as_sdt=0,5&sciodt=0,5},\n\tdoi = {10.1002/adhm.201200009},\n\tabstract = {Stimuli responsive, smart interface materials are integrated with\nmicrofluidic technologies creating new functions for a broad range of\nbiological and clinical applications by controlling the material and cell\ninteractions. Local capture and on-demand local release of cells are\ndemonstrated with spatial and temporal control in a microfluidic system.},\n\tnumber = {5},\n\tjournal = {Adv. Healthc. Mater.},\n\tauthor = {Gurkan, Umut Atakan and Tasoglu, Savas and Akkaynak, Derya and Avci, Oguzhan and Unluisler, Sebnem and Canikyan, Serli and Maccallum, Noah and Demirci, Utkan},\n\tmonth = sep,\n\tyear = {2012},\n\tnote = {Publisher: Wiley},\n\tkeywords = {Savas Scholar},\n\tpages = {661--668},\n}\n\n\n
@article{gurkan_emerging_2012,\n\ttitle = {Emerging technologies for assembly of microscale hydrogels},\n\tvolume = {1},\n\tissn = {2192-2640},\n\turl = {http://dx.doi.org/10.1002/adhm.201200011},\n\tdoi = {10.1002/adhm.201200011},\n\tabstract = {Assembly of cell encapsulating building blocks (i.e., microscale\nhydrogels) has significant applications in areas including regenerative\nmedicine, tissue engineering, and cell-based in vitro assays for\npharmaceutical research and drug discovery. Inspired by the repeating\nfunctional units observed in native tissues and biological systems (e.g.,\nthe lobule in liver, the nephron in kidney), assembly technologies aim to\ngenerate complex tissue structures by organizing microscale building\nblocks. Novel assembly technologies enable fabrication of engineered\ntissue constructs with controlled properties including tunable\nmicroarchitectural and predefined compositional features. Recent advances\nin micro- and nano-scale technologies have enabled engineering of microgel\nbased three dimensional (3D) constructs. There is a need for\nhigh-throughput and scalable methods to assemble microscale units with a\ncomplex 3D micro-architecture. Emerging assembly methods include novel\ntechnologies based on microfluidics, acoustic and magnetic fields,\nnanotextured surfaces, and surface tension. In this review, we survey\nemerging microscale hydrogel assembly methods offering rapid, scalable\nmicrogel assembly in 3D, and provide future perspectives and discuss\npotential applications.},\n\tnumber = {2},\n\tjournal = {Adv. Healthc. Mater.},\n\tauthor = {Gurkan, Umut Atakan and Tasoglu, Savas and Kavaz, Doga and Demirel, Melik C and Demirci, Utkan},\n\tmonth = mar,\n\tyear = {2012},\n\tkeywords = {Savas Scholar},\n\tpages = {149--158},\n}\n\n\n
@article{tasoglu_magnetic_2012,\n\ttitle = {Magnetic {3D} assembly of microgels for tissue engineering and regenerative medicine},\n\turl = {https://scholar.google.ca/scholar?cluster=6003201647578917350&hl=en&as_sdt=0,5&sciodt=0,5},\n\tjournal = {JOURNAL OF},\n\tauthor = {Tasoglu, S and Kavaz, D and Gurkan, U A and {others}},\n\tyear = {2012},\n\tnote = {Publisher: … ST, HOBOKEN 07030-5774, NJ USA},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{tasoglu_transient_2012,\n\ttitle = {Transient spreading and swelling behavior of a gel deploying an anti-{HIV} topical microbicide},\n\turl = {https://www.sciencedirect.com/science/article/pii/S0377025712001772},\n\tabstract = {Drug delivery of topical microbicidal molecules against HIV offers promise\nas a modality to prevent sexual transmission of the virus. Success of any\nmicrobicide product depends, in an …},\n\tjournal = {J. Non-Newtonian Fluid Mech.},\n\tauthor = {Tasoglu, S and Katz, D F and Szeri, A J},\n\tyear = {2012},\n\tnote = {Publisher: Elsevier},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{tasoglu_effects_2011,\n\ttitle = {The effects of inhomogeneous boundary dilution on the coating flow of an anti-{HIV} microbicide vehicle},\n\tvolume = {23},\n\tissn = {1070-6631},\n\turl = {https://scholar.google.ca/scholar?cluster=342392562646688721&hl=en&as_sdt=0,5&sciodt=0,5},\n\tdoi = {10.1063/1.3633337},\n\tabstract = {A recent study in South Africa has confirmed, for the first time, that a\nvaginal gel formulation of the antiretroviral drug Tenofovir, when\ntopically applied, significantly inhibits sexual HIV transmission to women\n[Karim et al., Science 329, 1168 (2010)]. However, the gel for this drug\nand anti-HIV microbicide gels in general have not been designed using an\nunderstanding of how gel spreading and retention in the vagina govern\nsuccessful drug delivery. Elastohydrodynamic lubrication theory can be\napplied to model spreading of microbicide gels [Szeri et al., Phys. Fluids\n20, 083101 (2008)]. This should incorporate the full rheological behavior\nof a gel, including how rheological properties change due to contact with,\nand dilution by, ambient vaginal fluids. Here, we extend our initial\nanalysis, incorporating the effects of gel dilution due to contact with\nvaginal fluid produced at the gel-tissue interface. Our original model is\nsupplemented with a convective-diffusive transport equation to\ncharacterize water transport into the gel and, thus, local gel dilution.\nThe problem is solved using a multi-step scheme in a moving domain. The\nassociation between local dilution of gel and rheological properties is\nobtained experimentally, delineating the way constitutive parameters of a\nshear-thinning gel are modified by dilution. Results show that dilution\naccelerates the coating flow by creating a slippery region near the\nvaginal wall akin to a dilution boundary layer, especially if the boundary\nflux exceeds a certain value. On the other hand, if the diffusion\ncoefficient of boundary fluid is increased, the slippery region diminishes\nin extent and the overall rate of gel spreading decreases.},\n\tnumber = {9},\n\tjournal = {Phys. Fluids},\n\tauthor = {Tasoglu, Savas and Peters, Jennifer J and Park, Su Chan and Verguet, Stéphane and Katz, David F and Szeri, Andrew J},\n\tmonth = sep,\n\tyear = {2011},\n\tnote = {Publisher: AIP Publishing},\n\tkeywords = {Savas Scholar},\n\tpages = {93101--931019},\n}\n\n\n
@article{lopour_continuous_2011,\n\ttitle = {A continuous mapping of sleep states through association of {EEG} with a mesoscale cortical model},\n\tvolume = {30},\n\tissn = {0929-5313},\n\turl = {https://scholar.google.ca/scholar?cluster=2736796018824873675&hl=en&as_sdt=0,5&sciodt=0,5},\n\tdoi = {10.1007/s10827-010-0272-1},\n\tabstract = {Here we show that a mathematical model of the human sleep cycle can be\nused to obtain a detailed description of electroencephalogram (EEG) sleep\nstages, and we discuss how this analysis may aid in the prediction and\nprevention of seizures during sleep. The association between EEG data and\nthe cortical model is found via locally linear embedding (LLE), a method\nof dimensionality reduction. We first show that LLE can distinguish\nbetween traditional sleep stages when applied to EEG data. It reliably\nseparates REM and non-REM sleep and maps the EEG data to a low-dimensional\noutput space where the sleep state changes smoothly over time. We also\nincorporate the concept of strongly connected components and use this as a\nmethod of automatic outlier rejection for EEG data. Then, by using LLE on\na hybrid data set containing both sleep EEG and signals generated from the\nmesoscale cortical model, we quantify the relationship between the data\nand the mathematical model. This enables us to take any sample of sleep\nEEG data and associate it with a position among the continuous range of\nsleep states provided by the model; we can thus infer a trajectory of\nstates as the subject sleeps. Lastly, we show that this method gives\nconsistent results for various subjects over a full night of sleep and can\nbe done in real time.},\n\tnumber = {2},\n\tjournal = {J. Comput. Neurosci.},\n\tauthor = {Lopour, Beth A and Tasoglu, Savas and Kirsch, Heidi E and Sleigh, James W and Szeri, Andrew J},\n\tmonth = apr,\n\tyear = {2011},\n\tnote = {Publisher: Springer Science and Business Media LLC},\n\tkeywords = {Savas Scholar},\n\tpages = {471--487},\n}\n\n\n
@article{tasoglu_consequences_2011,\n\ttitle = {The consequences of yield stress on deployment of a non-{Newtonian} anti-{HIV} microbicide gel},\n\tvolume = {166},\n\tissn = {0377-0257},\n\turl = {https://scholar.google.ca/scholar?cluster=13921123107674771522&hl=en&as_sdt=0,5&sciodt=0,5},\n\tdoi = {10.1016/j.jnnfm.2011.06.007},\n\tabstract = {A recent study in South Africa has confirmed, for the first time, that a\nvaginal gel formulation of the antiretroviral drug Tenofovir, when applied\ntopically, significantly inhibits sexual HIV transmission to women [10].\nHowever the gel for this drug, and anti-HIV microbicide gels in general,\nhave not been designed using full understanding of how gel spreading and\nretention in the vagina govern successful drug delivery.\nElastohydrodynamic lubrication theory can be applied to model such\nspreading of microbicide gels, which are inherently non-Newtonian [13,15].\nA yield stress is emerging as one of the important properties of\nmicrobicide gel vehicle deployment, as this may improve retention within\nthe vaginal canal. On the other hand, a yield stress may decrease the\ninitial extent of the coating flow. Here, we first explain a certain yield\nstress paradox observed generally in many lubrication flows. Four\nconditions are determined, via scaling analysis, which mitigate the\ninconsistency in the use of lubrication theory to analyze the specific\nproblem of elastic wall squeezing flow of yield stress fluid. Parameters\ncharacterizing these conditions are obtained experimentally for a test\ngel. Using them, it is shown that the lubrication approximation may be\napplied to the elastic wall-squeezing problem for this gel.},\n\tnumber = {19-20},\n\tjournal = {J. Nonnewton. Fluid Mech.},\n\tauthor = {Tasoglu, Savas and Park, Su Chan and Peters, Jennifer J and Katz, David F and Szeri, Andrew J},\n\tmonth = oct,\n\tyear = {2011},\n\tnote = {Publisher: Elsevier BV},\n\tkeywords = {Savas Scholar},\n\tpages = {1116--1122},\n}\n\n\n
@article{tasoglu_impact_2010,\n\ttitle = {Impact of a compound droplet on a flat surface: {A} model for single cell epitaxy},\n\turl = {https://pubs.aip.org/aip/pof/article/22/8/082103/256539},\n\tabstract = {The impact and spreading of a compound viscous droplet on a flat surface\nare studied computationally using a front-tracking method as a model for\nthe single cell epitaxy. This is a …},\n\tjournal = {Physics of},\n\tauthor = {Tasoglu, S and Kaynak, G and Szeri, A J and Demirci, U and {others}},\n\tyear = {2010},\n\tnote = {Publisher: pubs.aip.org},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{szeri_epithelial_2010,\n\ttitle = {Epithelial coating mechanisms by semi-solid materials: {Application} to microbicide gels},\n\turl = {https://www.cell.com/biophysj/pdf/S0006-3495(09)05095-4.pdf},\n\tabstract = {Many epithelial surfaces have natural coating by polymeric materials, eg\nmucus. Foreign materials may be introduced for coating, eg for lubrication\nor drug delivery: examples are …},\n\tjournal = {Biophysical},\n\tauthor = {Szeri, A J and Park, S C and Tasoglu, S and Verguet, S and Gorham, A and {others}},\n\tyear = {2010},\n\tnote = {Publisher: cell.com},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{muradoglu_front-tracking_2010,\n\ttitle = {A front-tracking method for computational modeling of impact and spreading of viscous droplets on solid walls},\n\tissn = {0045-7930},\n\turl = {https://www.sciencedirect.com/science/article/pii/S0045793009001698},\n\tabstract = {A finite-difference/front-tracking method is developed for computational\nmodeling of impact and spreading of a viscous droplet on dry solid walls.\nThe contact angle is specified …},\n\tjournal = {Comput. Fluids},\n\tauthor = {Muradoglu, M and Tasoglu, S},\n\tyear = {2010},\n\tnote = {Publisher: Elsevier},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{szeri_coating_2010,\n\ttitle = {Coating flow of an anti-{HIV} microbicide gel: boundary dilution and yield stress},\n\tvolume = {63},\n\tshorttitle = {Coating flow of an anti-{HIV} microbicide gel},\n\turl = {https://ui.adsabs.harvard.edu/abs/2010APS..DFD.RF002S},\n\tabstract = {A recent study has confirmed, for the first time, that a vaginal gel formulation of the antiretroviral drug Tenofovir, when topically applied, significantly inhibits sexual HIV transmission to women [1]. However, the gel for this drug, and anti-HIV microbicide gels in general, have not been designed using an understanding of how gel spreading govern successful drug delivery. Elastohydrodynamic lubrication theory can be applied to model spreading of microbicide gels [2]. Here, we extend our initial analysis: we incorporate a yield stress, and we model the effects of gel dilution due to contact with vaginal fluid produced at the gel-tissue interface. Our model developed in [2] is supplemented with a convective-diffusive transport equation to characterize dilution, and solved using a multi-step scheme in a moving domain. The association between local dilution of gel and rheological properties is obtained experimentally. To model the common yield stress property of gels, we proceed by scaling analysis first. This establishes the conditions for validity of lubrication theory of a shear thinning yield stress fluid. This involves further development of the model in [2], incorporating a biviscosity model.[4pt] [1] Karim, et al., Science, 2010.[0pt] [2] Szeri, et al., Phy. of Fluids, 2008.},\n\turldate = {2023-09-29},\n\tauthor = {Szeri, Andrew J. and Tasoglu, Savas and Park, Su Chan and Katz, David F.},\n\tmonth = nov,\n\tyear = {2010},\n\tnote = {Conference Name: APS Division of Fluid Dynamics Meeting Abstracts\nADS Bibcode: 2010APS..DFD.RF002S},\n\tpages = {RF.002},\n}\n\n\n
@article{muradoglu_impact_2009,\n\ttitle = {Impact and {Spreading} of a {Microdroplet} on a {Solid} {Wall}},\n\turl = {https://asmedigitalcollection.asme.org/ICNMM/proceedings-abstract/ICNMM2009/1095/341113},\n\tabstract = {Impact and spreading of a viscous micro droplet on dry solid surfaces are\nstudied computationally using a finite-difference/front-tracking method.\nThe problem is motivated by …},\n\tjournal = {International},\n\tauthor = {Muradoglu, M and Tasoglu, S},\n\tyear = {2009},\n\tnote = {Publisher: asmedigitalcollection.asme.org},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{ross_plasmon_2009,\n\ttitle = {Plasmon resonance differences between the near-and far-field and implications for molecular detection},\n\turl = {https://www.spiedigitallibrary.org/conference-proceedings-of-spie/7394/739422/Plasmon-resonance-differences-between-the-near--and-far-field/10.1117/12.826804.short},\n\tabstract = {The localized surface plasmon resonance (LSPR) of a nanoplasmonic particle\nis often considered to occur at a single resonant wavelength. However, the\nphysical measures of …},\n\tjournal = {: Metallic Nanostructures and …},\n\tauthor = {Ross, B M and Tasoglu, S and Lee, L P},\n\tyear = {2009},\n\tnote = {Publisher: spiedigitallibrary.org},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{tasoglu_impact_2009,\n\ttitle = {Impact and {Spreading} of a {Compound} {Droplet}: {A} {Model} for {Single} {Cell} {Epitaxi}},\n\tvolume = {62},\n\tshorttitle = {Impact and {Spreading} of a {Compound} {Droplet}},\n\turl = {https://ui.adsabs.harvard.edu/abs/2009APS..DFD.BH007T},\n\tabstract = {In recent years, there has been a growing interest in generating compound droplets mainly due to their potential commercial value [1] and applications in emerging technologies such as single cell epitaxi [2]. Ejecting encapsulated cells on a rigid surface is a promising way to produce 2D/3D tissues [2]. However, this gained experimental capability requires a true understanding of the impact dynamics of the encapsulated cells on solid surfaces for further development. In the present study, a finite-volume/front-tracking method is used to model the impact and spreading of a viscous compound droplet on a flat solid surface as a first step in developing a model for the single cell epitaxi. The cell, the encapsulating droplet and ambient fluid are all assumed to be Newtonian. Simulations are performed for a range of dimensionless parameters and their effects on deformation of inner droplet are investigated. These results provide initial insight about the optimum parameter ranges for highest viability of cells. [1] Utada, Lorenceau, Link, et al., Science, 308(5721), (2005). [2] Demirci and Montesano, Lab Chip, 7, (2007).},\n\turldate = {2023-09-29},\n\tauthor = {Tasoglu, Savas and Kaynak, Gozde and Muradoglu, Metin},\n\tmonth = nov,\n\tyear = {2009},\n\tnote = {Conference Name: APS Division of Fluid Dynamics Meeting Abstracts\nADS Bibcode: 2009APS..DFD.BH007T},\n\tpages = {BH.007},\n}\n\n\n
@article{szeri_effects_2009,\n\ttitle = {Effects of dilution on elastohydrodynamic coating flow of an anti-{HIV} microbicide vehicle},\n\tvolume = {62},\n\turl = {https://ui.adsabs.harvard.edu/abs/2009APS..DFD.HQ005S},\n\tabstract = {Elastohydrodynamic lubrication over soft substrates characterizes the drug delivery of anti-HIV topical microbicides carried in gel vehicles. These gels are under development to prevent HIV transmission into vulnerable vaginal mucosa during intercourse. Their effectiveness depends on completeness and durability of coating, as well as on the active ingredients. Here we investigate the influence of dilution by vaginal fluid on the coating flows that serve to protect the user. The effects of dilution by vaginal fluid simulant are assessed through rheological experiments at variable dilution of the gel vehicle. This involves determination of the way parameters in a Carreau model of a shear-thinning gel are modified by dilution. The changes in coating are determined from a computational model, based on dilution rheology measured in the laboratory. The elastohydrodynamic lubrication model of Szeri, et al. Physics of Fluids (2008) is supplemented with a convective-diffusive transport equation to handle dilution, and solved using a multi-step scheme in a moving domain.},\n\turldate = {2023-09-29},\n\tauthor = {Szeri, Andrew and Park, Su Chan and Tasoglu, Savas and Katz, David F.},\n\tmonth = nov,\n\tyear = {2009},\n\tnote = {Conference Name: APS Division of Fluid Dynamics Meeting Abstracts\nADS Bibcode: 2009APS..DFD.HQ005S},\n\tpages = {HQ.005},\n}\n\n\n
@article{tasoglu_effect_2008,\n\ttitle = {The effect of soluble surfactant on the transient motion of a buoyancy-driven bubble},\n\tissn = {1070-6631},\n\turl = {https://pubs.aip.org/aip/pof/article/20/4/040805/257430},\n\tabstract = {The effect of soluble surfactants on the unsteady motion and deformation\nof a bubble rising in an otherwise quiescent liquid contained in an\naxisymmetric tube is computationally …},\n\tjournal = {Phys. Fluids},\n\tauthor = {Tasoglu, S and Demirci, U and Muradoglu, M},\n\tyear = {2008},\n\tnote = {Publisher: pubs.aip.org},\n\tkeywords = {Savas Scholar},\n}\n\n\n
@article{muradoglu_impact_2008,\n\ttitle = {Impact and {Spreading} of a {Compound} {Droplet} on a {Solid} {Wall}},\n\tvolume = {61},\n\turl = {https://ui.adsabs.harvard.edu/abs/2008APS..DFD.BG005M},\n\tabstract = {Impact and spreading of a compound viscous droplet are studied computationally using a finite-difference/front-tracking method. The problem is motivated by single cell epitaxy developed for printing biological cells on a solid substrate using ink-jet printer technology. In this study, the biological cell is modeled as a highly viscous Newtonian liquid encapsulated by a less viscous droplet. The substrate is partially wettable for the encapsulating droplet and non- wettable for the inner droplet. The contact angle is specified dynamically for the encapsulating droplet using the empirical correlation given by Kistler (1993). In addition, a precursive film model is also used especially for the highly wettable cases, i.e., the static contact angle is smaller than 30{\\textasciicircum}o due to numerical difficulty of resolving thin liquid later penetrating into surrounding gas near the solid surface. The numerical method is first applied to simple droplet spreading and the results are compared with experimental data of Sikalo et al. (2005). Then the impact and spreading dynamic of a compound droplet is studied in details. The effects of governing non-dimensional numbers on the spreading rate and apparent contact angle of the outer droplet as well as on the pressure force and deformation of the inner droplet (cell) are investigated.},\n\turldate = {2023-09-29},\n\tauthor = {Muradoglu, Metin and Tasoglu, Savas},\n\tmonth = nov,\n\tyear = {2008},\n\tnote = {Conference Name: APS Division of Fluid Dynamics Meeting Abstracts\nADS Bibcode: 2008APS..DFD.BG005M},\n\tpages = {BG.005},\n}\n\n\n