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https://www.readbyqxmd.com/read/29775922/acid-phosphatase-test-on-phadebas-%C3%A2-sheets-an-optimized-method-for-presumptive-saliva-and-semen-detection
#1
Yael Herman, Ilan Feine, Ron Gafny
The precise and efficient detection of semen and saliva in sexual assault case-work items is a critical step in the forensic pipeline. The outcome of this stage may have a profound impact on identifying perpetrators as well as on the investigation process and the final outcome in court. Semen detection is usually based on the activity of acid phosphatase (AP), an enzyme found in high concentration in the seminal plasma. Amylase, an enzyme catalyzing starch hydrolysis is found in high concentrations in saliva and therefore is a useful target for its detection...
April 30, 2018: Forensic Science International
https://www.readbyqxmd.com/read/29775487/a-fiber-optic-pipeline-lets-the-root-circadian-clock-see-the-light
#2
C Robertson McClung
No abstract text is available yet for this article.
May 18, 2018: Plant, Cell & Environment
https://www.readbyqxmd.com/read/29775406/phrase-mining-of-textual-data-to-analyze-extracellular-matrix-protein-patterns-across-cardiovascular-disease
#3
David Alexandre Liem, Sanjana Murali, Dibakar Sigdel, Yu Shi, Xuan Wang, Jiaming Shen, Howard Choi, J Harry Caufield, Wei Wang, Peipei Ping, Jiawei Han
Extracellular matrix (ECM) proteins have been shown to play important roles regulating multiple biological processes in an array of organ systems, including the cardiovascular system. By using a novel bioinformatics text-mining tool, we studied six categories of cardiovascular disease (CVD), namely ischemic heart disease (IHD), cardiomyopathies (CM), cerebrovascular accident (CVA), congenital heart disease (CHD), arrhythmias (ARR), and valve disease (VD), anticipating novel ECM protein-disease and protein-protein relationships hidden within vast quantities of textual data...
May 18, 2018: American Journal of Physiology. Heart and Circulatory Physiology
https://www.readbyqxmd.com/read/29774599/deep-convolutional-neural-network-for-segmentation-of-knee-joint-anatomy
#4
Zhaoye Zhou, Gengyan Zhao, Richard Kijowski, Fang Liu
PURPOSE: To describe and evaluate a new segmentation method using deep convolutional neural network (CNN), 3D fully connected conditional random field (CRF), and 3D simplex deformable modeling to improve the efficiency and accuracy of knee joint tissue segmentation. METHODS: A segmentation pipeline was built by combining a semantic segmentation CNN, 3D fully connected CRF, and 3D simplex deformable modeling. A convolutional encoder-decoder network was designed as the core of the segmentation method to perform high resolution pixel-wise multi-class tissue classification for 12 different joint structures...
May 17, 2018: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
https://www.readbyqxmd.com/read/29774062/-in-vivo-imaging-biomarkers-of-neuroinflammation-in-the-development-and-assessment-of-stroke-therapies-towards-clinical-translation
#5
REVIEW
Bastian Zinnhardt, Maximilian Wiesmann, Lisa Honold, Cristina Barca, Michael Schäfers, Amanda J Kiliaan, Andreas H Jacobs
Modulation of the inflammatory microenvironment after stroke opens a new avenue for the development of novel neurorestorative therapies in stroke. Understanding the spatio-temporal profile of (neuro-)inflammatory imaging biomarkers in detail thereby represents a crucial factor in the development and application of immunomodulatory therapies. The early integration of quantitative molecular imaging biomarkers in stroke drug development may provide key information about (i) early diagnosis and follow-up, (ii) spatio-temporal drug-target engagement (pharmacodynamic biomarker), (iii) differentiation of responders and non-responders in the patient cohort (inclusion/exclusion criteria; predictive biomarkers), and (iv) the mechanism of action...
2018: Theranostics
https://www.readbyqxmd.com/read/29774017/identifying-group-specific-sequences-for-microbial-communities-using-long-k-mer-sequence-signatures
#6
Ying Wang, Lei Fu, Jie Ren, Zhaoxia Yu, Ting Chen, Fengzhu Sun
Comparing metagenomic samples is crucial for understanding microbial communities. For different groups of microbial communities, such as human gut metagenomic samples from patients with a certain disease and healthy controls, identifying group-specific sequences offers essential information for potential biomarker discovery. A sequence that is present, or rich, in one group, but absent, or scarce, in another group is considered " group-specific " in our study. Our main purpose is to discover group-specific sequence regions between control and case groups as disease-associated markers...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29771371/allele-phasing-greatly-improves-the-phylogenetic-utility-of-ultraconserved-elements
#7
Tobias Andermann, Alexandre M Fernandes, Urban Olsson, Mats Töpel, Bernard Pfeil, Bengt Oxelman, Alexandre Aleixo, Brant C Faircloth, Alexandre Antonelli
Advances in high-throughput sequencing techniques now allow relatively easy and affordable sequencing of large portions of the genome, even for non-model organisms. Many phylogenetic studies reduce costs by focusing their sequencing efforts on a selected set of targeted loci, commonly enriched using sequence capture. The advantage of this approach is that it recovers a consistent set of loci, each with high sequencing depth, which leads to more confidence in the assembly of target sequences. High sequencing depth can also be used to identify phylogenetically informative allelic variation within sequenced individuals, but allele sequences are infrequently assembled in phylogenetic studies...
May 15, 2018: Systematic Biology
https://www.readbyqxmd.com/read/29771109/the-therapeutic-pipeline-for-pseudomonas-aeruginosa-infections
#8
Lori L Burrows
Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen, designated by the World Health Organization as a critical priority for development of new therapeutics due to high levels of intrinsic and acquired antibiotic resistance. Other challenges include its versatility (it can persist in the environment and most strains are capable of causing disease in compromised hosts), robust efflux mechanisms that limit drug penetration, and the propensity to form antimicrobial-tolerant biofilms. Novel therapeutics in development to prevent or treat P...
May 17, 2018: ACS Infectious Diseases
https://www.readbyqxmd.com/read/29770249/snorkel-rapid-training-data-creation-with-weak-supervision
#9
Alexander Ratner, Stephen H Bach, Henry Ehrenberg, Jason Fries, Sen Wu, Christopher Ré
Labeling training data is increasingly the largest bottleneck in deploying machine learning systems. We present Snorkel, a first-of-its-kind system that enables users to train state-of- the-art models without hand labeling any training data. Instead, users write labeling functions that express arbitrary heuristics, which can have unknown accuracies and correlations. Snorkel denoises their outputs without access to ground truth by incorporating the first end-to-end implementation of our recently proposed machine learning paradigm, data programming...
November 2017: Proceedings of the VLDB Endowment
https://www.readbyqxmd.com/read/29769672/pancreas-regeneration
#10
REVIEW
Qiao Zhou, Douglas A Melton
The pancreas is made from two distinct components: the exocrine pancreas, a reservoir of digestive enzymes, and the endocrine islets, the source of the vital metabolic hormone insulin. Human islets possess limited regenerative ability; loss of islet β-cells in diseases such as type 1 diabetes requires therapeutic intervention. The leading strategy for restoration of β-cell mass is through the generation and transplantation of new β-cells derived from human pluripotent stem cells. Other approaches include stimulating endogenous β-cell proliferation, reprogramming non-β-cells to β-like cells, and harvesting islets from genetically engineered animals...
May 2018: Nature
https://www.readbyqxmd.com/read/29769594/touchscreen-typing-pattern-analysis-for-detecting-fine-motor-skills-decline-in-early-stage-parkinson-s-disease
#11
Dimitrios Iakovakis, Stelios Hadjidimitriou, Vasileios Charisis, Sevasti Bostantzopoulou, Zoe Katsarou, Leontios J Hadjileontiadis
Parkinson's disease (PD) is a degenerative movement disorder causing progressive disability that severely affects patients' quality of life. While early treatment can produce significant benefits for patients, the mildness of many early signs combined with the lack of accessible high-frequency monitoring tools may delay clinical diagnosis. To meet this need, user interaction data from consumer technologies have recently been exploited towards unsupervised screening for PD symptoms in daily life. Similarly, this work proposes a method for detecting fine motor skills decline in early PD patients via analysis of patterns emerging from finger interaction with touchscreen smartphones during natural typing...
May 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29769129/a-powerful-nonparametric-method-for-detecting-differentially-co-expressed-genes-distance-correlation-screening-and-edge-count-test
#12
Qingyang Zhang
BACKGROUND: Differential co-expression analysis, as a complement of differential expression analysis, offers significant insights into the changes in molecular mechanism of different phenotypes. A prevailing approach to detecting differentially co-expressed genes is to compare Pearson's correlation coefficients in two phenotypes. However, due to the limitations of Pearson's correlation measure, this approach lacks the power to detect nonlinear changes in gene co-expression which is common in gene regulatory networks...
May 16, 2018: BMC Systems Biology
https://www.readbyqxmd.com/read/29769048/functional-insights-from-proteome-wide-structural-modeling-of-treponema-pallidum-subspecies-pallidum-the-causative-agent-of-syphilis
#13
Simon Houston, Karen Vivien Lithgow, Kara Krista Osbak, Chris Richard Kenyon, Caroline E Cameron
BACKGROUND: Syphilis continues to be a major global health threat with 11 million new infections each year, and a global burden of 36 million cases. The causative agent of syphilis, Treponema pallidum subspecies pallidum, is a highly virulent bacterium, however the molecular mechanisms underlying T. pallidum pathogenesis remain to be definitively identified. This is due to the fact that T. pallidum is currently uncultivatable, inherently fragile and thus difficult to work with, and phylogenetically distinct with no conventional virulence factor homologs found in other pathogens...
May 16, 2018: BMC Structural Biology
https://www.readbyqxmd.com/read/29768981/a-scalable-pipeline-for-high-throughput-flow-cytometry
#14
Aaron C Wilson, Ioannis K Moutsatsos, Gary Yu, Javier J Pineda, Yan Feng, Douglas S Auld
Flow cytometry (FC) provides high-content data for a variety of applications, including phenotypic analysis of cell surface and intracellular markers, characterization of cell supernatant or lysates, and gene expression analysis. Historically, sample preparation, acquisition, and analysis have presented as a bottleneck for running such types of assays at scale. This article will outline the solutions that have been implemented at Novartis which have allowed high-throughput FC to be successfully conducted and analyzed for a variety of cell-based assays...
May 1, 2018: SLAS Discovery
https://www.readbyqxmd.com/read/29768462/a-comparative-study-of-rna-seq-and-microarray-data-analysis-on-the-two-examples-of-rectal-cancer-patients-and-burkitt-lymphoma-cells
#15
Alexander Wolff, Michaela Bayerlová, Jochen Gaedcke, Dieter Kube, Tim Beißbarth
BACKGROUND: Pipeline comparisons for gene expression data are highly valuable for applied real data analyses, as they enable the selection of suitable analysis strategies for the dataset at hand. Such pipelines for RNA-Seq data should include mapping of reads, counting and differential gene expression analysis or preprocessing, normalization and differential gene expression in case of microarray analysis, in order to give a global insight into pipeline performances. METHODS: Four commonly used RNA-Seq pipelines (STAR/HTSeq-Count/edgeR, STAR/RSEM/edgeR, Sailfish/edgeR, TopHat2/Cufflinks/CuffDiff)) were investigated on multiple levels (alignment and counting) and cross-compared with the microarray counterpart on the level of gene expression and gene ontology enrichment...
2018: PloS One
https://www.readbyqxmd.com/read/29767967/structure-guided-modification-of-heterocyclic-antagonists-of-the-p2y-14-receptor
#16
Jinha Yu, Antonella Ciancetta, Steven Dudas, Sierra Duca, Justine Lottermoser, Kenneth A Jacobson
The P2Y14 receptor (P2Y14 R) mediates inflammatory activity by activating neutrophil motility, but few classes of antagonists are known. We have explored the structure-activity relationship of a 3-(4-phenyl-1 H-1,2,3-triazol-1-yl)-5-(aryl)benzoic acid antagonist scaffold, assisted by docking and molecular dynamics (MD) simulation at a P2Y14 R homology model. A computational pipeline using the High Throughput MD Python environment guided the analogue design. Selection of candidates was based upon ligand-protein shape and complementarity and the persistence of ligand-protein interactions over time...
May 16, 2018: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/29766023/adeno-associated-virus-genome-population-sequencing-achieves-full-vector-genome-resolution-and-reveals-human-vector-chimeras
#17
Phillip W L Tai, Jun Xie, Kaiyuen Fong, Matthew Seetin, Cheryl Heiner, Qin Su, Michael Weiand, Daniella Wilmot, Maria L Zapp, Guangping Gao
Recombinant adeno-associated virus (rAAV)-based gene therapy has entered a phase of clinical translation and commercialization. Despite this progress, vector integrity following production is often overlooked. Compromised vectors may negatively impact therapeutic efficacy and safety. Using single molecule, real-time (SMRT) sequencing, we can comprehensively profile packaged genomes as a single intact molecule and directly assess vector integrity without extensive preparation. We have exploited this methodology to profile all heterogeneic populations of self-complementary AAV genomes via bioinformatics pipelines and have coined this approach AAV-genome population sequencing (AAV-GPseq)...
June 15, 2018: Molecular Therapy. Methods & Clinical Development
https://www.readbyqxmd.com/read/29765940/a-comparative-survey-of-methods-for-remote-heart-rate-detection-from-frontal-face-videos
#18
Chen Wang, Thierry Pun, Guillaume Chanel
Remotely measuring physiological activity can provide substantial benefits for both the medical and the affective computing applications. Recent research has proposed different methodologies for the unobtrusive detection of heart rate (HR) using human face recordings. These methods are based on subtle color changes or motions of the face due to cardiovascular activities, which are invisible to human eyes but can be captured by digital cameras. Several approaches have been proposed such as signal processing and machine learning...
2018: Frontiers in Bioengineering and Biotechnology
https://www.readbyqxmd.com/read/29765675/-leishmania-naiffi-and-leishmania-guyanensis-reference-genomes-highlight-genome-structure-and-gene-evolution-in-the-viannia-subgenus
#19
Simone Coughlan, Ali Shirley Taylor, Eoghan Feane, Mandy Sanders, Gabriele Schonian, James A Cotton, Tim Downing
The unicellular protozoan parasite Leishmania causes the neglected tropical disease leishmaniasis, affecting 12 million people in 98 countries. In South America, where the Viannia subgenus predominates, so far only L. ( Viannia ) braziliensis and L. ( V. ) panamensis have been sequenced, assembled and annotated as reference genomes. Addressing this deficit in molecular information can inform species typing, epidemiological monitoring and clinical treatment. Here, L. ( V. ) naiffi and L. ( V. ) guyanensis genomic DNA was sequenced to assemble these two genomes as draft references from short sequence reads...
April 2018: Royal Society Open Science
https://www.readbyqxmd.com/read/29765391/abciximab-reopro-dosing-strategy-for-the-management-of-acute-intraprocedural-thromboembolic-complications-during-pipeline-flow-diversion-treatment-of-intracranial-aneurysms
#20
Li-Mei Lin, Bowen Jiang, Jessica K Campos, Narlin B Beaty, Matthew T Bender, Rafael J Tamargo, Judy Huang, Geoffrey P Colby, Alexander L Coon
Background: Flow diversion with the Pipeline embolization device (PED) is an effective neuro-endovascular method and increasingly accepted for the treatment of cerebral aneurysms. Acute in situ thrombosis is a known complication of PED procedures. There is limited experience in the flow diversion literature on the use of abciximab (ReoPro) for the management of acute thrombus formation in PED cases. Methods: Data were collected retrospectively on patients who received intra-arterial (IA) ReoPro with or without subsequent intravenous (IV) infusion during PED flow diversion treatment of intracranial aneurysms...
April 2018: Interventional Neurology
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