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https://www.readbyqxmd.com/read/28107606/dishevelled-segment-polarity-protein-3-dvl3-a-novel-and-easily-applicable-recurrence-predictor-in-localized-prostate-adenocarcinoma
#1
Pil-Jong Kim, Ji Y Park, Hong-Gee Kim, Yong Mee Cho, Heounjeong Go
OBJECTIVE: To identify new biomarkers for the biochemical recurrence (BCR) of prostate adenocarcinoma. PATIENTS AND METHODS: Clinical information of 500 prostate adenocarcinoma patients and their 152 RNA-sequencing and protein-array data from The Cancer Genome Atlas (TCGA) were separated into a discovery-set and a validation-set. Each dataset was analyzed according to the Gleason grade groups reflecting BCR. The results obtained from the analysis using TCGA dataset were confirmed by immunohistochemistry analyses of the confirmation cohort composed of 395 localized prostate adenocarcinoma patients...
January 20, 2017: BJU International
https://www.readbyqxmd.com/read/28107542/temporal-segregation-between-dung-inhabiting-beetle-and-fly-species
#2
Frantisek Xaver Jiri Sladecek, Simon Tristram Segar, Colin Lee, Richard Wall, Martin Konvicka
The coexistence of ecologically similar species (i.e. species utilizing the same resource) is a major topic in ecology. Communities are assembled either through the biotic interactions of ecologically similar species, e.g. competition, or by the abiotic separation of species along gradients of environmental conditions. Here, we investigated the temporal segregation, succession and seasonality of dung-inhabiting Coleoptera and Diptera that utilize an identical resource in exactly the same way. The data were collected from two temperate pastures, one in the United Kingdom and the second in the Czech Republic...
2017: PloS One
https://www.readbyqxmd.com/read/28107530/broad-scale-genetic-diversity-of-cannabis-for-forensic-applications
#3
Christophe Dufresnes, Catherine Jan, Friederike Bienert, Jérôme Goudet, Luca Fumagalli
Cannabis (hemp and marijuana) is an iconic yet controversial crop. On the one hand, it represents a growing market for pharmaceutical and agricultural sectors. On the other hand, plants synthesizing the psychoactive THC produce the most widespread illicit drug in the world. Yet, the difficulty to reliably distinguish between Cannabis varieties based on morphological or biochemical criteria impedes the development of promising industrial programs and hinders the fight against narcotrafficking. Genetics offers an appropriate alternative to characterize drug vs...
2017: PloS One
https://www.readbyqxmd.com/read/28107476/origin-and-dispersal-history-of-two-colonial-ascidian-clades-in-the-botryllus-schlosseri-species-complex
#4
Marie L Nydam, Kirsten B Giesbrecht, Emily E Stephenson
Human-induced global warming and species introductions are rapidly altering the composition and functioning of Earth's marine ecosystems. Ascidians (Phylum Chordata, Subphylum Tunicata, Class Ascidiacea) are likely to play an increasingly greater role in marine communities. The colonial ascidian B. schlosseri is a cryptic species complex comprising five genetically divergent clades (A-E). Clade A is a global species, and Clade E has so far been identified in European waters only. Using the largest mitochondrial cytochrome oxidase I datasets yet assembled, we determine the origin and dispersal history of these species...
2017: PloS One
https://www.readbyqxmd.com/read/28107436/a-micro-ct-study-in-patients-with-breast-microcalcifications-using-a-mathematical-algorithm-to-assess-3d-structure
#5
David Kenkel, Zsuzsanna Varga, Heike Heuer, Konstantin J Dedes, Nicole Berger, Lukas Filli, Andreas Boss
PURPOSE: The aim of this study was to evaluate the relevance of the three-dimensional (3D) structure of breast microcalcifications (MC) as a predictor of malignancy using highly resolved micro-computed tomography (micro-CT) datasets of biopsy samples. MATERIAL AND METHODS: The study included 28 women with suspicious MC in their mammogram undergoing vacuum-assisted biopsy. Directly after the intervention, the specimens were scanned in a micro-CT with an isometric spatial resolution of 9 μm...
2017: PloS One
https://www.readbyqxmd.com/read/28107266/early-fluid-overload-prolongs-mechanical-ventilation-in-children-with-viral-lower-respiratory-tract-disease
#6
Sarah A Ingelse, Hanke M G Wiegers, Job C Calis, Job B van Woensel, Reinout A Bem
OBJECTIVES: Viral-lower respiratory tract disease is common in young children worldwide and is associated with high morbidity. Acute respiratory failure due to viral-lower respiratory tract disease necessitates PICU admission for mechanical ventilation. In critically ill patients in PICU settings, early fluid overload is common and associated with adverse outcomes such as prolonged mechanical ventilation and increased mortality. It is unclear, however, if this also applies to young children with viral-lower respiratory tract disease induced acute respiratory failure...
January 19, 2017: Pediatric Critical Care Medicine
https://www.readbyqxmd.com/read/28107264/readmission-and-late-mortality-after-critical-illness-in-childhood
#7
Mary E Hartman, Mohammed J Saeed, Tellen Bennett, Katri Typpo, Renee Matos, Margaret A Olsen
OBJECTIVES: Little is known about the ongoing mortality risk and healthcare utilization among U.S. children after discharge from a hospitalization involving ICU care. We sought to understand risks for hospital readmission and trends in mortality during the year following ICU discharge. DESIGN: Retrospective observational cohort study. SETTING: This study was performed using administrative claims data from 2006-2013 obtained from the Truven Health Analytics MarketScan Database...
January 19, 2017: Pediatric Critical Care Medicine
https://www.readbyqxmd.com/read/28107038/prevalence-of-and-factors-associated-with-sarcopenia-in-korean-cancer-survivors-based-on-data-obtained-by-the-korea-national-health-and-nutrition-examination-survey-knhanes-2008-2011
#8
Eun Young Kim, Kirang Kim, Young Saing Kim, Hee Kyung Ahn, Yu Mi Jeong, Jeong Ho Kim, Won-Jun Choi
Using a representative dataset from the Korea National Health and Nutrition Examination Survey (KNHANES) from 2008 to 2011, we analyzed anthropometric and dual-energy X-ray absorptiometry (DXA)-determined body composition findings for 493 cancer survivors (mean age a61.1 ± 12.6 years; 35.7% male). A much higher proportion of men (30.1%) than women (0.6%) met the criteria of sarcopenia. Subjects with a history of lung cancer, genitourinary cancer, or gastric cancer were prone to develop sarcopenia (31.6%, 26...
January 20, 2017: Nutrition and Cancer
https://www.readbyqxmd.com/read/28106916/a-bayesian-analysis-of-quantal-bioassay-experiments-incorporating-historical-controls-via-bayes-factors
#9
Luis G León Novelo, Andrew Womack, Hongxiao Zhu, Xiaowei Wu
This paper addresses model-based Bayesian inference in the analysis of data arising from bioassay experiments. In such experiments, increasing doses of a chemical substance are given to treatment groups (usually rats or mice) for a fixed period of time (usually 2 years). The goal of such an experiment is to determine whether an increased dosage of the chemical is associated with increased probability of an adverse effect (usually presence of adenoma or carcinoma). The data consists of dosage, survival time, and the occurrence of the adverse event for each unit in the study...
January 20, 2017: Statistics in Medicine
https://www.readbyqxmd.com/read/28106819/modeling-aboveground-biomass-in-hulunber-grassland-ecosystem-by-using-unmanned-aerial-vehicle-discrete-lidar
#10
Dongliang Wang, Xiaoping Xin, Quanqin Shao, Matthew Brolly, Zhiliang Zhu, Jin Chen
Accurate canopy structure datasets, including canopy height and fractional cover, are required to monitor aboveground biomass as well as to provide validation data for satellite remote sensing products. In this study, the ability of an unmanned aerial vehicle (UAV) discrete light detection and ranging (lidar) was investigated for modeling both the canopy height and fractional cover in Hulunber grassland ecosystem. The extracted mean canopy height, maximum canopy height, and fractional cover were used to estimate the aboveground biomass...
January 19, 2017: Sensors
https://www.readbyqxmd.com/read/28106794/a-thoroughly-validated-virtual-screening-strategy-for-discovery-of-novel-hdac3-inhibitors
#11
Huabin Hu, Jie Xia, Dongmei Wang, Xiang Simon Wang, Song Wu
Histone deacetylase 3 (HDAC3) has been recently identified as a potential target for the treatment of cancer and other diseases, such as chronic inflammation, neurodegenerative diseases, and diabetes. Virtual screening (VS) is currently a routine technique for hit identification, but its success depends on rational development of VS strategies. To facilitate this process, we applied our previously released benchmarking dataset, i.e., MUBD-HDAC3 to the evaluation of structure-based VS (SBVS) and ligand-based VS (LBVS) combinatorial approaches...
January 18, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28106793/hybrid-intelligent-system-to-perform-fault-detection-on-bis-sensor-during-surgeries
#12
José-Luis Casteleiro-Roca, José Luis Calvo-Rolle, Juan Albino Méndez Pérez, Nieves Roqueñí Gutiérrez, Francisco Javier de Cos Juez
This paper presents a new fault detection system in hypnotic sensors used for general anesthesia during surgery. Drug infusion during surgery is based on information received from patient monitoring devices; accordingly, faults in sensor devices can put patient safety at risk. Our research offers a solution to cope with these undesirable scenarios. We focus on the anesthesia process using intravenous propofol as the hypnotic drug and employing a Bispectral Index (BIS(TM)) monitor to estimate the patient's unconsciousness level...
January 18, 2017: Sensors
https://www.readbyqxmd.com/read/28106764/effective-alternating-direction-optimization-methods-for-sparsity-constrained-blind-image-deblurring
#13
Naixue Xiong, Ryan Wen Liu, Maohan Liang, Di Wu, Zhao Liu, Huisi Wu
Single-image blind deblurring for imaging sensors in the Internet of Things (IoT) is a challenging ill-conditioned inverse problem, which requires regularization techniques to stabilize the image restoration process. The purpose is to recover the underlying blur kernel and latent sharp image from only one blurred image. Under many degraded imaging conditions, the blur kernel could be considered not only spatially sparse, but also piecewise smooth with the support of a continuous curve. By taking advantage of the hybrid sparse properties of the blur kernel, a hybrid regularization method is proposed in this paper to robustly and accurately estimate the blur kernel...
January 18, 2017: Sensors
https://www.readbyqxmd.com/read/28106546/a-common-variant-of-il-6r-is-associated-with-elevated-il-6-pathway-activity-in-alzheimer-s-disease-brains
#14
Patrick C G Haddick, Jessica L Larson, Nisha Rathore, Tushar R Bhangale, Qui T Phung, Karpagam Srinivasan, David V Hansen, Jennie R Lill, Margaret A Pericak-Vance, Jonathan Haines, Lindsay A Farrer, John S Kauwe, Gerard D Schellenberg, Carlos Cruchaga, Alison M Goate, Timothy W Behrens, Ryan J Watts, Robert R Graham, Joshua S Kaminker, Marcel van der Brug
The common p.D358A variant (rs2228145) in IL-6R is associated with risk for multiple diseases and with increased levels of soluble IL-6R in the periphery and central nervous system (CNS). Here, we show that the p.D358A allele leads to increased proteolysis of membrane bound IL-6R and demonstrate that IL-6R peptides with A358 are more susceptible to cleavage by ADAM10 and ADAM17. IL-6 responsive genes were identified in primary astrocytes and microglia and an IL-6 gene signature was increased in the CNS of late onset Alzheimer's disease subjects in an IL6R allele dependent manner...
January 18, 2017: Journal of Alzheimer's Disease: JAD
https://www.readbyqxmd.com/read/28106377/chemical-proteomics-maps-brain-region-specific-activity-of-endocannabinoid-hydrolases
#15
Marc P Baggelaar, Annelot van Esbroeck, Eva van Rooden, Bogdan I Florea, Herman S Overkleeft, Giovanni Marsicano, Francis Chaouloff, Mario van der Stelt
The biosynthetic and catabolic enzymes of the endocannabinoids tightly regulate endocannabinoid-mediated activation of the cannabinoid CB1 receptor. Monitoring the activities of these endocannabinoid hydrolases in different brain regions is, therefore, key to gain insight in spatiotemporal control of CB1 receptor-mediated physiology. We have employed a comparative chemical proteomics approach to quantitatively map the activity profile of endocannabinoid hydrolases in various mouse brain regions at the same time...
January 20, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28105958/dmirnet-inferring-direct-microrna-mrna-association-networks
#16
Minsu Lee, HyungJune Lee
BACKGROUND: MicroRNAs (miRNAs) play important regulatory roles in the wide range of biological processes by inducing target mRNA degradation or translational repression. Based on the correlation between expression profiles of a miRNA and its target mRNA, various computational methods have previously been proposed to identify miRNA-mRNA association networks by incorporating the matched miRNA and mRNA expression profiles. However, there remain three major issues to be resolved in the conventional computation approaches for inferring miRNA-mRNA association networks from expression profiles...
December 5, 2016: BMC Systems Biology
https://www.readbyqxmd.com/read/28105940/integrated-single-cell-data-analysis-reveals-cell-specific-networks-and-novel-coactivation-markers
#17
Shila Ghazanfar, Adam J Bisogni, John T Ormerod, David M Lin, Jean Y H Yang
BACKGROUND: Large scale single cell transcriptome profiling has exploded in recent years and has enabled unprecedented insight into the behavior of individual cells. Identifying genes with high levels of expression using data from single cell RNA sequencing can be useful to characterize very active genes and cells in which this occurs. In particular single cell RNA-Seq allows for cell-specific characterization of high gene expression, as well as gene coexpression. RESULTS: We offer a versatile modeling framework to identify transcriptional states as well as structures of coactivation for different neuronal cell types across multiple datasets...
December 5, 2016: BMC Systems Biology
https://www.readbyqxmd.com/read/28105922/differential-expression-of-alternatively-spliced-transcripts-related-to-energy-metabolism-in-colorectal-cancer
#18
Anastasiya Vladimirovna Snezhkina, George Sergeevich Krasnov, Andrew Rostislavovich Zaretsky, Alex Zhavoronkov, Kirill Mikhailovich Nyushko, Alexey Alexandrovich Moskalev, Irina Yurievna Karpova, Anastasiya Isaevna Afremova, Anastasiya Valerievna Lipatova, Dmitriy Vladimitovich Kochetkov, Maria Sergeena Fedorova, Nadezhda Nikolaevna Volchenko, Asiya Fayazovna Sadritdinova, Nataliya Vladimirovna Melnikova, Dmitry Vladimirovich Sidorov, Anatoly Yurievich Popov, Dmitry Valerievich Kalinin, Andrey Dmitrievich Kaprin, Boris Yakovlevich Alekseev, Alexey Alexandrovich Dmitriev, Anna Viktorovna Kudryavtseva
BACKGROUND: Colorectal cancer (CRC) is one of the most common malignant tumors worldwide. CRC molecular pathogenesis is heterogeneous and may be followed by mutations in oncogenes and tumor suppressor genes, chromosomal and microsatellite instability, alternative splicing alterations, hypermethylation of CpG islands, oxidative stress, impairment of different signaling pathways and energy metabolism. In the present work, we have studied the alterations of alternative splicing patterns of genes related to energy metabolism in CRC...
December 28, 2016: BMC Genomics
https://www.readbyqxmd.com/read/28105918/mirnacle-machine-learning-with-smote-and-random-forest-for-improving-selectivity-in-pre-mirna-ab-initio-prediction
#19
Yuri Bento Marques, Alcione de Paiva Oliveira, Ana Tereza Ribeiro Vasconcelos, Fabio Ribeiro Cerqueira
BACKGROUND: MicroRNAs (miRNAs) are key gene expression regulators in plants and animals. Therefore, miRNAs are involved in several biological processes, making the study of these molecules one of the most relevant topics of molecular biology nowadays. However, characterizing miRNAs in vivo is still a complex task. As a consequence, in silico methods have been developed to predict miRNA loci. A common ab initio strategy to find miRNAs in genomic data is to search for sequences that can fold into the typical hairpin structure of miRNA precursors (pre-miRNAs)...
December 15, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28105915/spectral-consensus-strategy-for-accurate-reconstruction-of-large-biological-networks
#20
Séverine Affeldt, Nataliya Sokolovska, Edi Prifti, Jean-Daniel Zucker
BACKGROUND: The last decades witnessed an explosion of large-scale biological datasets whose analyses require the continuous development of innovative algorithms. Many of these high-dimensional datasets are related to large biological networks with few or no experimentally proven interactions. A striking example lies in the recent gut bacterial studies that provided researchers with a plethora of information sources. Despite a deeper knowledge of microbiome composition, inferring bacterial interactions remains a critical step that encounters significant issues, due in particular to high-dimensional settings, unknown gut bacterial taxa and unavoidable noise in sparse datasets...
December 13, 2016: BMC Bioinformatics
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