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https://www.readbyqxmd.com/read/29149658/evaluating-casama-contextualized-semantic-maps-for-summarization-of-lung-cancer-studies
#1
Jean I Garcia-Gathright, Nicholas J Matiasz, Carlos Adame, Karthik V Sarma, Lauren Sauer, Nova F Smedley, Marshall L Spiegel, Jennifer Strunck, Edward B Garon, Ricky K Taira, Denise R Aberle, Alex A T Bui
OBJECTIVE: It is crucial for clinicians to stay up to date on current literature in order to apply recent evidence to clinical decision making. Automatic summarization systems can help clinicians quickly view an aggregated summary of literature on a topic. Casama, a representation and summarization system based on "contextualized semantic maps," captures the findings of biomedical studies as well as the contexts associated with patient population and study design. This paper presents a user-oriented evaluation of Casama in comparison to a context-free representation, SemRep...
November 3, 2017: Computers in Biology and Medicine
https://www.readbyqxmd.com/read/29146731/organic-anion-transporting-polypeptide-1b3-as-a-dual-reporter-gene-for-fluorescence-and-magnetic-resonance-imaging
#2
Menq-Rong Wu, Hon-Man Liu, Chen-Wen Lu, Way-Hone Shen, I-Jou Lin, Li-Wen Liao, Yi-You Huang, Ming-Jium Shieh, Jong-Kai Hsiao
Reporter proteins have broad applications in visualizing molecular events at the cellular, tissue and whole-body levels. Transmembrane transporters recognizing specific molecular domains are of particular interest because they enable the migration of signal-source molecules from the extracellular space to the cytoplasm for subsequent application in multimodality imaging. Organic anion-transporting polypeptides (OATPs) have demonstrated their MRI reporter efficacy. We further expanded their use as a dual-modality reporter in MRI and noninvasive in vivo imaging system (IVIS)...
November 16, 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/29140916/gender-disparities-in-medical-student-research-awards-a-thirteen-year-study-from-the-yale-school-of-medicine
#3
Joseph T King, Nancy R Angoff, John N Forrest, Amy C Justice
PURPOSE: Instruction in research conduct is currently required, and many U.S. medical schools require students to complete a research project. Each year all Yale School of Medicine (YSM) graduating students submit a research thesis, and ~5% are awarded highest honors. Gender disparities exist in areas related to physician research productivity, including academic rank, research funding, and publications. The authors asked whether gender disparities exist for medical student research. METHOD: The authors conducted a retrospective review of 1,120 theses submitted by graduating medical students from 2003-2015 at YSM and collected data on gender, mentoring, research type, sponsoring department, and other characteristics...
November 14, 2017: Academic Medicine: Journal of the Association of American Medical Colleges
https://www.readbyqxmd.com/read/29139537/planaria-an-animal-model-that-integrates-development-regeneration-and-pharmacology
#4
Oné R Pagán
Although planarians are established model organisms in developmental biology and regeneration studies, in the last forty years or so, they have caught the attention of pharmacologists, especially to study the pharmacology of drugs of abuse. This review covers the following topics: some fundamentals of the history of animal models and planarians in biomedical research; an abbreviated story of systematic pharmacology research using planarians as a model organism; an example of how planarians are contributing to the search for compounds against acute cocaine toxicity; an analysis of the number of papers on planarians and pharmacological topics from 1900-2016; some perspectives on pharmacology in developmental and regeneration studies, arguing in favor of the planarian model as a leading subject for this interdisciplinary area of research, and finally some concluding thoughts...
2017: International Journal of Developmental Biology
https://www.readbyqxmd.com/read/29134422/hiv-prevention-among-young-women-in-south-africa-understanding-multiple-layers-of-risk
#5
Christina Psaros, Cecilia Milford, Jennifer A Smit, Letitia Greener, Nzwakie Mosery, Lynn T Matthews, Abigail Harrison, Janna R Gordon, Matthew Mimiaga, David R Bangsberg, Steven A Safren
Despite concerted prevention efforts, young South African women remain at the epicenter of the HIV epidemic. Although these women have grown up in a community powerfully affected by HIV, systematic investigation into how this "second generation" of HIV-affected youth navigates HIV risk is lacking. This study qualitatively explored a complex interplay of factors influencing HIV risk among young pregnant women in KwaZulu-Natal, South Africa. We conducted in-depth interviews with 35 pregnant women (22 HIV-uninfected and 13 HIV-infected) aged 18-21, 18 healthcare providers, and focus groups with 19 community stakeholders...
November 13, 2017: Archives of Sexual Behavior
https://www.readbyqxmd.com/read/29132408/using-semantics-for-representing-experimental-protocols
#6
Olga Giraldo, Alexander García, Federico López, Oscar Corcho
BACKGROUND: An experimental protocol is a sequence of tasks and operations executed to perform experimental research in biological and biomedical areas, e.g. biology, genetics, immunology, neurosciences, virology. Protocols often include references to equipment, reagents, descriptions of critical steps, troubleshooting and tips, as well as any other information that researchers deem important for facilitating the reusability of the protocol. Although experimental protocols are central to reproducibility, the descriptions are often cursory...
November 13, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/29132014/a-genetic-algorithm-for-simulating-correlated-binary-data-from-biomedical-research
#7
Jochen Kruppa, Bernd Lepenies, Klaus Jung
Correlated binary data arise in a large variety of biomedical research. In order to evaluate methods for their analysis, computer simulations of such data are often required. Existing methods can often not cover the full range of possible correlations between the variables or are not available as implemented software. We propose a genetic algorithm that approaches the desired correlation structure under a given marginal distribution. The procedure generates a large representative matrix from which the probabilities of individual observations can be derived or from which samples can be drawn directly...
October 31, 2017: Computers in Biology and Medicine
https://www.readbyqxmd.com/read/29131162/the-3d-orbisims-label-free-metabolic-imaging-with-subcellular-lateral-resolution-and-high-mass-resolving-power
#8
Melissa K Passarelli, Alexander Pirkl, Rudolf Moellers, Dmitry Grinfeld, Felix Kollmer, Rasmus Havelund, Carla F Newman, Peter S Marshall, Henrik Arlinghaus, Morgan R Alexander, Andy West, Stevan Horning, Ewald Niehuis, Alexander Makarov, Colin T Dollery, Ian S Gilmore
We report the development of a 3D OrbiSIMS instrument for label-free biomedical imaging. It combines the high spatial resolution of secondary ion mass spectrometry (SIMS; under 200 nm for inorganic species and under 2 μm for biomolecules) with the high mass-resolving power of an Orbitrap (>240,000 at m/z 200). This allows exogenous and endogenous metabolites to be visualized in 3D with subcellular resolution. We imaged the distribution of neurotransmitters-gamma-aminobutyric acid, dopamine and serotonin-with high spectroscopic confidence in the mouse hippocampus...
November 13, 2017: Nature Methods
https://www.readbyqxmd.com/read/29131160/human-primary-liver-cancer-derived-organoid-cultures-for-disease-modeling-and-drug-screening
#9
Laura Broutier, Gianmarco Mastrogiovanni, Monique Ma Verstegen, Hayley E Francies, Lena Morrill Gavarró, Charles R Bradshaw, George E Allen, Robert Arnes-Benito, Olga Sidorova, Marcia P Gaspersz, Nikitas Georgakopoulos, Bon-Kyoung Koo, Sabine Dietmann, Susan E Davies, Raaj K Praseedom, Ruby Lieshout, Jan N M IJzermans, Stephen J Wigmore, Kourosh Saeb-Parsy, Mathew J Garnett, Luc Jw van der Laan, Meritxell Huch
Human liver cancer research currently lacks in vitro models that can faithfully recapitulate the pathophysiology of the original tumor. We recently described a novel, near-physiological organoid culture system, wherein primary human healthy liver cells form long-term expanding organoids that retain liver tissue function and genetic stability. Here we extend this culture system to the propagation of primary liver cancer (PLC) organoids from three of the most common PLC subtypes: hepatocellular carcinoma (HCC), cholangiocarcinoma (CC) and combined HCC/CC (CHC) tumors...
November 13, 2017: Nature Medicine
https://www.readbyqxmd.com/read/29129805/rare-genetic-diseases-update-on-diagnosis-treatment-and-online-resources
#10
REVIEW
Robert E Pogue, Denise P Cavalcanti, Shreya Shanker, Rosangela V Andrade, Lana R Aguiar, Juliana L de Carvalho, Fabrício F Costa
Rare genetic diseases collectively impact a significant portion of the world's population. For many diseases there is limited information available, and clinicians can find difficulty in differentiating between clinically similar conditions. This leads to problems in genetic counseling and patient treatment. The biomedical market is affected because pharmaceutical and biotechnology industries do not see advantages in addressing rare disease treatments, or because the cost of the treatments is too high. By contrast, technological advances including DNA sequencing and analysis, together with computer-aided tools and online resources, are allowing a more thorough understanding of rare disorders...
November 10, 2017: Drug Discovery Today
https://www.readbyqxmd.com/read/29129632/synthesis-characterization-of-zno-chitosan-nanocomposites-and-evaluation-of-its-antifungal-activity-against-pathogenic-candida-albicans
#11
S H S Dananjaya, R Saravana Kumar, Minyang Yang, Chamilani Nikapitiya, Jehee Lee, Mahanama De Zoysa
In this study, we investigated the antifungal activity and cytotoxicity of ZnO-chitosan nanocomposites against Candida albicans and human epithelial type 2 (HEp2) cells, respectively. The crystalline phase, morphology, composition, particle size and optical absorption properties of the synthesized ZnO-C NCs were systematically investigated by various contemporary methods The X-ray diffraction analysis results showed characteristic diffraction peaks corresponding to both ZnO and chitosan, while field-emission scanning electron microscopy (FESEM) displayed clusters of spherical shaped particulate morphology...
November 9, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29127902/a-survey-of-machine-learning-applications-in-hiv-clinical-research-and-care
#12
REVIEW
Kuteesa R Bisaso, Godwin T Anguzu, Susan A Karungi, Agnes Kiragga, Barbara Castelnuovo
A wealth of genetic, demographic, clinical and biomarker data is collected from routine clinical care of HIV patients and exists in the form of medical records available among the medical care and research communities. Machine learning (ML) methods have the ability to identify and discover patterns in complex datasets and predict future outcomes of HIV treatment. We survey published studies that make use of ML techniques in HIV clinical research and care. An advanced search relevant to the use of ML in HIV research was conducted in the PubMed biomedical database...
November 8, 2017: Computers in Biology and Medicine
https://www.readbyqxmd.com/read/29126854/biomedical-applications-of-glyconanoparticles-based-on-quantum-dots
#13
REVIEW
C R A Cunha, A D P R Oliveira, T V C Firmino, D P L A Tenório, G Pereira, L B Carvalho, B S Santos, M T S Correia, A Fontes
BACKGROUND: Quantum dots (QDs) are outstanding nanomaterials of great interest to life sciences. Their conjugation versatility added to unique optical properties, highlight these nanocrystals as very promising fluorescent probes. Among uncountable new nanosystems, in the last years, QDs conjugated to glycans or lectins have aroused a growing attention and their application as a tool to study biological and functional properties has increased. SCOPE OF REVIEW: This review describes the strategies, reported in the literature, to conjugate QDs to lectins or carbohydrates, providing valuable information for the elaboration, improvement, and application of these nanoconjugates...
November 7, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29125054/nitrogen-and-phosphorus-release-from-organic-wastes-and-suitability-as-bio-based-fertilizers-in-a-circular-economy
#14
S D C Case, L S Jensen
The drive for a more circular economy has led to an increasing interest in recycling organic wastes as bio-based fertilizers, including those from urban settings, and food or biomedical industries. However, there is a lack of knowledge as to their fertilizer value and whether further processing could make these waste materials more valuable as bio-based fertilizers. This study screened 15 different organic waste materials including manures, digestates, sludges, composts, industry byproducts, and struvites. Nitrogen (N) and phosphorous (P) release was compared following addition to soil...
November 10, 2017: Environmental Technology
https://www.readbyqxmd.com/read/29124084/second-harmonic-generation-imaging-of-collagen-in-ancient-bone
#15
B Thomas, D McIntosh, T Fildes, L Smith, F Hargrave, M Islam, T Thompson, R Layfield, D Scott, B Shaw, C L Burrell, S Gonzalez, S Taylor
Second-harmonic generation imaging (SHG) captures triple helical collagen molecules near tissue surfaces. Biomedical research routinely utilizes various imaging software packages to quantify SHG signals for collagen content and distribution estimates in modern tissue samples including bone. For the first time using SHG, samples of modern, medieval, and ice age bones were imaged to test the applicability of SHG to ancient bone from a variety of ages, settings, and taxa. Four independent techniques including Raman spectroscopy, FTIR spectroscopy, radiocarbon dating protocols, and mass spectrometry-based protein sequencing, confirm the presence of protein, consistent with the hypothesis that SHG imaging detects ancient bone collagen...
December 2017: Bone Reports
https://www.readbyqxmd.com/read/29123331/aptamer-functionalized-hydrogel-for-self-programmed-protein-release-via-sequential-photoreaction-and-hybridization
#16
Jinping Lai, Pinliang Jiang, Erin R Gaddes, Nan Zhao, Lidya Abune, Yong Wang
A dynamic hydrogel that sequentially responds to two independent but interrelated physical and biomolecular signals was reported in this work. Once hit by an external light signal, an immobilized internal molecular signal is activated and freed via photoreaction; and subsequently the freed molecular signal works as a self-programming factor of the hydrogel to induce the dissociation of a biomolecular complex to release protein via hybridization reaction. Notably, pulsatile external light input can be converted to periodical protein output from the hydrogel to regulate cell migration...
July 25, 2017: Chemistry of Materials: a Publication of the American Chemical Society
https://www.readbyqxmd.com/read/29117781/a-joint-model-for-multivariate-hierarchical-semicontinuous-data-with-replications
#17
Wondwosen Kassahun-Yimer, Paul S Albert, Leah M Lipsky, Tonja R Nansel, Aiyi Liu
Longitudinal data are often collected in biomedical applications in such a way that measurements on more than one response are taken from a given subject repeatedly overtime. For some problems, these multiple profiles need to be modeled jointly to get insight on the joint evolution and/or association of these responses over time. In practice, such longitudinal outcomes may have many zeros that need to be accounted for in the analysis. For example, in dietary intake studies, as we focus on in this paper, some food components are eaten daily by almost all subjects, while others are consumed episodically, where individuals have time periods where they do not eat these components followed by periods where they do...
January 1, 2017: Statistical Methods in Medical Research
https://www.readbyqxmd.com/read/29112744/research-roadmap-for-tuberculosis-transmission-science-where-do-we-go-from-here-and-how-will-we-know-when-we-re-there
#18
REVIEW
Sara C Auld, Anne G Kasmar, David W Dowdy, Barun Mathema, Neel R Gandhi, Gavin J Churchyard, Roxana Rustomjee, N Sarita Shah
High rates of tuberculosis transmission are driving the ongoing global tuberculosis epidemic, and there is a pressing need for research focused on understanding and, ultimately, halting transmission. The ongoing tuberculosis-human immunodeficiency virus (HIV) coepidemic and rising rates of drug-resistant tuberculosis in parts of the world add further urgency to this work. Success in this research will require a concerted, multidisciplinary effort on the part of tuberculosis scientists, clinicians, programs, and funders and must span the research spectrum from biomedical sciences to the social sciences, public health, epidemiology, cost-effectiveness analyses, and operations research...
November 3, 2017: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/29110182/new-complexity-measures-reveal-that-topographic-loops-of-human-alpha-phase-potentials-are-more-complex-in-drowsy-than-in-wake
#19
Aleksandar Kalauzi, Aleksandra Vuckovic, Tijana Bojić
A number of measures, stemming from nonlinear dynamics, exist to estimate complexity of biomedical objects. In most cases they are appropriate, but sometimes unconventional measures, more suited for specific objects, are needed to perform the task. In our present work, we propose three new complexity measures to quantify complexity of topographic closed loops of alpha carrier frequency phase potentials (CFPP) of healthy humans in wake and drowsy states. EEG of ten adult individuals was recorded in both states, using a 14-channel montage...
November 7, 2017: Medical & Biological Engineering & Computing
https://www.readbyqxmd.com/read/29107917/differential-effects-of-graphene-oxide-nanosheets-on-candida-albicans-phagocytosis-by-murine-peritoneal-macrophages
#20
R Diez-Orejas, M J Feito, M Cicuéndez, J M Rojo, M T Portolés
Macrophages, as effector cells involved in the innate and adaptive immunity, play a key role in the response to nanomaterials as graphene oxide (GO) and in their cellular uptake. The interactions at the interface of GO nanosheets, macrophages and microbial pathogens need to be assessed to determine the possible impairment of the immune system induced by biomedical treatments with this nanomaterial. Here, we have evaluated by flow cytometry and confocal microscopy the ability of murine peritoneal macrophages to phagocytose the fungal pathogen Candida albicans, alive or heat-killed, after treatment with poly(ethylene glycol-amine)-derivatized GO nanosheets (PEG-GO)...
October 28, 2017: Journal of Colloid and Interface Science
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