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Biomedical engineering

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https://www.readbyqxmd.com/read/29036277/pyseqlab-an-open-source-python-package-for-sequence-labeling-and-segmentation
#1
Ahmed Allam, Michael Krauthammer
Motivation: Text and genomic data are composed of sequential tokens, such as words and nucleotides that give rise to higher order syntactic constructs. In this work, we aim at providing a comprehensive Python library implementing conditional random fields (CRFs), a class of probabilistic graphical models, for robust prediction of these constructs from sequential data. Results: Python Sequence Labeling (PySeqLab) is an open source package for performing supervised learning in structured prediction tasks...
July 21, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29035749/chemical-remodeling-cell-surface-glycans-for-immunotargeting-of-tumor-cells
#2
Xuexia Li, Xiaoyan Xu, Xiongjian Rao, Yinping Tian, Wen Yi
Recruitment of human endogenous antibodies to target and eliminate tumor cells is a promising therapeutic strategy in the biomedical field. Current antibody-recruiting molecules are typically bi-functional agents that utilize cell-surface receptor binding property for targeting. This approach has intrinsic limitations due to the heterogeneity of tumor cells and the limited number of receptors on the cell surface. Here we report a targeting strategy based on remodeling of cell surface glycans through metabolic engineering and bioorthogonal chemical ligation...
October 10, 2017: Carbohydrate Research
https://www.readbyqxmd.com/read/29035605/a-two-staged-approach-to-developing-and-evaluating-an-ontology-for-delivering-personalized-education-to-diabetic-patients
#3
Susan Quinn, Raymond Bond, Chris Nugent
Ontologies are often used in biomedical and health domains to provide a concise and consistent means of attributing meaning to medical terminology. While they are novices in terms of ontology engineering, the evaluation of an ontology by domain specialists provides an opportunity to enhance its objectivity, accuracy, and coverage of the domain itself. This paper provides an evaluation of the viability of using ontology engineering novices to evaluate and enrich an ontology that can be used for personalized diabetic patient education...
October 16, 2017: Informatics for Health & Social Care
https://www.readbyqxmd.com/read/29034997/everything-you-always-wanted-to-know-about-poly-l-lysine-dendrigrafts-but-were-afraid-to-ask
#4
Jean-Patrick Francoia, Laurent Vial
Less than a decade ago, dendrigrafts of poly-L-lysine (DGLs) joined the family of polycationic dendritic macromolecules. Resulting from the iterative polycondensation of a N-carboxyanhydride in water, four generations of the dendrigraft can be obtained on a multi-gram scale and without chromatographic purification. DGLs share features with both dendrimers and hyperbranched polymers, but turned out to have unique biophysical and bioactive properties. The macromolecules - in their native form or functionalized - have been extensively characterized by various analytical and computational methods, and already found numerous applications in the biomedical field such as drug and gene delivery, biomaterials, tissue engineering, bioimaging, and biosensing...
October 16, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/29034774/mechanical-enhancement-and-in-vitro-biocompatibility-of-nanofibrous-collagen-chitosan-scaffolds-for-tissue-engineering
#5
Fengjuan Zou, Runrun Li, Jianjun Jiang, Xiumei Mo, Guofeng Gu, Zhongwu Guo, Zonggang Chen
The collagen-chitosan complex with a three-dimensional nanofiber structure was fabricated to mimic native ECM for tissue repair and biomedical applications. Though the three-dimensional hierarchical fibrous structures of collagen-chitosan composites could provide more adequate stimulus to facilitate cell adhesion, migrate and proliferation, and thus have the potential as tissue engineering scaffolding, there are still limitations in their applications due to the insufficient mechanical properties of natural materials...
October 16, 2017: Journal of Biomaterials Science. Polymer Edition
https://www.readbyqxmd.com/read/29027284/polydopamine-particles-reinforced-poly-vinyl-alcohol-hydrogel-with-nir-light-triggered-shape-memory-and-self-healing-capability
#6
Li Yang, Zhanhua Wang, Guoxia Fei, Hesheng Xia
This study focuses on developing a facile approach to prepare biocompatible poly(vinyl alcohol) (PVA) composite hydrogels containing polydopamine particles (PDAPs) with ultrafast near-infrared (NIR) light-triggered shape memory and self-healing capability. The PVA-PDAPs composite hydrogels with excellent mechanical properties can be achieved after freezing/thawing treatment, and the formation of physically cross-linked networks from the hydrogen bonding (H-bonding) between PVA and PDAPs. Due to the excellent photothermal effect of polydopamine, the composited hydrogel can achieve rapid shape recovery and efficient self-healing properties under NIR light exposure in a short time...
October 13, 2017: Macromolecular Rapid Communications
https://www.readbyqxmd.com/read/29026204/engineering-and-physical-sciences-in-oncology-challenges-and-opportunities
#7
REVIEW
Michael J Mitchell, Rakesh K Jain, Robert Langer
The principles of engineering and physics have been applied to oncology for nearly 50 years. Engineers and physical scientists have made contributions to all aspects of cancer biology, from quantitative understanding of tumour growth and progression to improved detection and treatment of cancer. Many early efforts focused on experimental and computational modelling of drug distribution, cell cycle kinetics and tumour growth dynamics. In the past decade, we have witnessed exponential growth at the interface of engineering, physics and oncology that has been fuelled by advances in fields including materials science, microfabrication, nanomedicine, microfluidics, imaging, and catalysed by new programmes at the National Institutes of Health (NIH), including the National Institute of Biomedical Imaging and Bioengineering (NIBIB), Physical Sciences in Oncology, and the National Cancer Institute (NCI) Alliance for Nanotechnology...
October 13, 2017: Nature Reviews. Cancer
https://www.readbyqxmd.com/read/29025157/chronic-pain-after-traumatic-brain-injury-pathophysiology-and-pain-mechanisms
#8
Karen-Amanda Irvine, J David Clark
Background: Traumatic brain injury refers to a broad range of neurological, cognitive, and emotional factors that result from the application of an external force to the head. Individuals recovering from traumatic brain injury will frequently experience acute and chronic pain. Objective: The objective of this paper is to discuss the pathophysiological changes resulting from traumatic brain injury and how these may be involved in the development and persistence of pain after injury...
August 29, 2017: Pain Medicine: the Official Journal of the American Academy of Pain Medicine
https://www.readbyqxmd.com/read/29020614/gene-editing-in-rat-embryonic-stem-cells-to-produce-in%C3%A2-vitro-models-and-in%C3%A2-vivo-reporters
#9
Yaoyao Chen, Sonia Spitzer, Sylvia Agathou, Ragnhildur Thora Karadottir, Austin Smith
Rat embryonic stem cells (ESCs) offer the potential for sophisticated genome engineering in this valuable biomedical model species. However, germline transmission has been rare following conventional homologous recombination and clonal selection. Here, we used the CRISPR/Cas9 system to target genomic mutations and insertions. We first evaluated utility for directed mutagenesis and recovered clones with biallelic deletions in Lef1. Mutant cells exhibited reduced sensitivity to glycogen synthase kinase 3 inhibition during self-renewal...
October 10, 2017: Stem Cell Reports
https://www.readbyqxmd.com/read/28993220/silk-fibroin-hydroxyapatite-composites-for-bone-tissue-engineering
#10
REVIEW
Mehdi Farokhi, Fatemeh Mottaghitalab, Saeed Samani, Mohammad Ali Shokrgozar, Subhas C Kundu, Rui L Reis, Yousef Fattahi, David L Kaplan
Silk fibroin (SF) is a natural fibrous polymer with strong potential for many biomedical applications. SF has attracted interest in the field of bone tissue engineering due to its extraordinary characteristics in terms of elasticity, flexibility, biocompatibility and biodegradability. However, low osteogenic capacity has limited applications for SF in the orthopedic arena unless suitably functionalized. Hydroxyapatite (HAp) is a well-established bioceramic with biocompatibility and appropriate for constructing orthopedic and dental substitutes...
October 6, 2017: Biotechnology Advances
https://www.readbyqxmd.com/read/28992698/monitoring-of-heparin-activity-in-live-rats-using-metal-organic-framework-nanosheets-as-peroxidase-mimics
#11
Hanjun Cheng, Yufeng Liu, Yihui Hu, Yubin Ding, Shichao Lin, Wen Cao, Qian Wang, Jiangjiexing Wu, Faheem Muhammad, Xiaozhi Zhao, Dan Zhao, Zhe Li, Hang Xing, Hui Wei
Metal-organic framework (MOF) nanosheets are a class of two-dimensional (2D) porous and crystalline materials that hold promise for catalysis and biodetection. Although 2D MOF nanosheets have been utilized for in vitro assays, ways of engineering them into diagnostic tools for live animals are much less explored. In this work, a series of MOF nanosheets are successfully engineered into a highly sensitive and selective diagnostic platform for in vivo monitoring of heparin (Hep) activity. The iron-porphyrin derivative is selected as ligand to synthesize a series of archetypical MOF nanosheets with intrinsic heme-like catalytic sites, mimicking pe-roxidase...
October 10, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28977499/addressable-configurations-of-dna-nanostructures-for-rewritable-memory
#12
Arun Richard Chandrasekaran, Oksana Levchenko, Dhruv S Patel, Molly MacIsaac, Ken Halvorsen
DNA serves as nature's information storage molecule, and has been the primary focus of engineered systems for biological computing and data storage. Here we combine recent efforts in DNA self-assembly and toehold-mediated strand displacement to develop a rewritable multi-bit DNA memory system. The system operates by encoding information in distinct and reversible conformations of a DNA nanoswitch and decoding by gel electrophoresis. We demonstrate a 5-bit system capable of writing, erasing, and rewriting binary representations of alphanumeric symbols, as well as compatibility with 'OR' and 'AND' logic operations...
August 30, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28976996/beyond-funding-acknowledgement-patterns-in-biomedical-natural-and-social-sciences
#13
Adèle Paul-Hus, Adrián A Díaz-Faes, Maxime Sainte-Marie, Nadine Desrochers, Rodrigo Costas, Vincent Larivière
For the past 50 years, acknowledgments have been studied as important paratextual traces of research practices, collaboration, and infrastructure in science. Since 2008, funding acknowledgments have been indexed by Web of Science, supporting large-scale analyses of research funding. Applying advanced linguistic methods as well as Correspondence Analysis to more than one million acknowledgments from research articles and reviews published in 2015, this paper aims to go beyond funding disclosure and study the main types of contributions found in acknowledgments on a large scale and through disciplinary comparisons...
2017: PloS One
https://www.readbyqxmd.com/read/28976521/cardiac-microphysiological-devices-with-flexible-thin-film-sensors-for-higher-throughput-drug-screening
#14
Johan U Lind, Moran Yadid, Ian Perkins, Blakely B O'Connor, Feyisayo Eweje, Christophe O Chantre, Matthew A Hemphill, Hongyan Yuan, Patrick H Campbell, Joost J Vlassak, Kevin K Parker
Microphysiological systems and organs-on-chips promise to accelerate biomedical and pharmaceutical research by providing accurate in vitro replicas of human tissue. Aside from addressing the physiological accuracy of the model tissues, there is a pressing need for improving the throughput of these platforms. To do so, scalable data acquisition strategies must be introduced. To this end, we here present an instrumented 24-well plate platform for higher-throughput studies of engineered human stem cell-derived cardiac muscle tissues that recapitulate the laminar structure of the native ventricle...
October 4, 2017: Lab on a Chip
https://www.readbyqxmd.com/read/28975171/injectable-nanoengineered-stimuli-responsive-hydrogels-for-on-demand-and-localized-therapeutic-delivery
#15
Nima A Jalili, Manish K Jaiswal, Charles W Peak, Lauren M Cross, Akhilesh K Gaharwar
"Smart" hydrogels are an emerging class of biomaterials that respond to external stimuli and have been investigated for a range of biomedical applications, including therapeutic delivery and regenerative engineering. Stimuli-responsive nanogels constructed of thermoresponsive polymers such as poly(N-isopropylacrylamide-co-acrylamide) (poly(NIPAM-co-AM)) and magnetic nanoparticles (MNPs) have been developed as "smart carriers" for on-demand delivery of therapeutic biomolecules via magneto-thermal activation...
October 4, 2017: Nanoscale
https://www.readbyqxmd.com/read/28972947/the-peritoneum-health-disease-and-perspectives-regarding-tissue-engineering-and-cell-therapies
#16
Ronaldo J F C do Amaral, Kátia D Arcanjo, Márcia C El-Cheikh, Felipe L de Oliveira
There are several pathologies associated with the peritoneum, such as mesothelioma and peritonitis. Moreover, the peritoneum is widely used in ultrafiltration procedures, i.e., peritoneal dialysis, presenting advantages over hemodialysis. On the other hand, ultrafiltration failure may lead to dialysis-induced fibrosis and hypervolemia. Therefore, the pathophysiological study of this tissue is of extreme biomedical importance. Studies investigating the biology of the cells dwelling in the peritoneum wall provide evidence of their plasticity and progenitor features...
October 4, 2017: Cells, Tissues, Organs
https://www.readbyqxmd.com/read/28967940/nanocellulose-as-a-sustainable-biomass-material-structure-properties-present-status-and-future-prospects-in-biomedical-applications
#17
REVIEW
Yan Xue, Zihao Mou, Huining Xiao
Nanocellulose, extracted from the most abundant biomass material cellulose, has proved to be an environmentally friendly material with excellent mechanical performance owing to its unique nano-scaled structure, and has been used in a variety of applications as engineering and functional materials. The great biocompatibility and biodegradability, in particular, render nanocellulose promising in biomedical applications. In this review, the structure, treatment technology and properties of three different nanocellulose categories, i...
October 12, 2017: Nanoscale
https://www.readbyqxmd.com/read/28966980/predicting-silk-fiber-mechanical-properties-through-multiscale-simulation-and-protein-design
#18
Nae-Gyune Rim, Erin G Roberts, Davoud Ebrahimi, Nina Dinjaski, Matthew M Jacobsen, Zaira Martín-Moldes, Markus J Buehler, David L Kaplan, Joyce Y Wong
Silk is a promising material for biomedical applications, and much research is focused on how application-specific, mechanical properties of silk can be designed synthetically through proper amino acid sequences and processing parameters. This protocol describes an iterative process between research disciplines that combines simulation, genetic synthesis, and fiber analysis to better design silk fibers with specific mechanical properties. Computational methods are used to assess the protein polymer structure as it forms an interconnected fiber network through shearing and how this process affects fiber mechanical properties...
August 14, 2017: ACS Biomaterials Science & Engineering
https://www.readbyqxmd.com/read/28962799/engineering-pectin-based-hollow-nanocapsules-for-delivery-of-anticancer-drug
#19
Feng Ji, Junjie Li, Zhihui Qin, Boguang Yang, Ershuai Zhang, Dianyu Dong, Jinmei Wang, Yan Wen, Liang Tian, Fanglian Yao
Multifunctional capsules have great applications in biomedical fields. In this study, novel polysaccharide-based nanocapsules were prepared via a layer-by-layer technique using silica as the templates. The shell was constructed based on the electrostatic interactions between pectin and chitosan. The pectin-chitosan nanocapsules ((Pec/Cs)3Pec) could keep good colloidal stability within 96h in PBS solution and 48h in BSA solution. Meanwhile, the nanocapsules exhibited a high drug loading and pH-sensitive release property for doxorubicin hydrochloride...
December 1, 2017: Carbohydrate Polymers
https://www.readbyqxmd.com/read/28961432/interfacially-mediated-oxygen-inhibition-for-precise-and-continuous-poly-ethylene-glycol-diacrylate-pegda-particle-fabrication
#20
Daniel Debroy, John Oakey, Dongmei Li
Hydrogels based on poly(ethylene glycol) diacrylate (PEGDA) have been engineered for a variety of biomedical applications including drug delivery, cell delivery, and tissue engineering. The miniaturization of these materials to nanoscale and microscale particles has been a subject of intense activity, and promises to extend their range of applicability. In general, however, these efforts have been frustrated by the inhibition of chain growth polymerization by oxygen, an effect that is exacerbated as target length scales are reduced...
September 22, 2017: Journal of Colloid and Interface Science
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