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https://www.readbyqxmd.com/read/29342307/using-phylogenomic-data-to-explore-the-effects-of-relaxed-clocks-and-calibration-strategies-on-divergence-time-estimation-primates-as-a-test-case
#1
Mario Dos Reis, Gregg F Gunnell, José Barba-Montoya, Alex Wilkins, Ziheng Yang, Anne D Yoder
Primates have long been a test case for the development of phylogenetic methods for divergence time estimation. Despite a large number of studies, however, the timing of origination of crown Primates relative to the K-Pg boundary and the timing of diversification of the main crown groups remain controversial. Here we analysed a dataset of 372 taxa (367 Primates and 5 outgroups, 3.4 million aligned base pairs) that includes nine primate genomes. We systematically explore the effect of different interpretations of fossil calibrations and molecular clock models on primate divergence time estimates...
January 12, 2018: Systematic Biology
https://www.readbyqxmd.com/read/29342247/peath-single-individual-haplotyping-by-a-probabilistic-evolutionary-algorithm-with-toggling
#2
Joong Chae Na, Jong-Chan Lee, Je-Keun Rhee, Soo-Yong Shin
Motivation: Single individual haplotyping (SIH) is critical in genomic association studies and genetic diseases analysis. However, most genomic analysis studies do not perform haplotype-phasing analysis due to its complexity. Several computational methods have been developed to solve the SIH problem, but these approaches have not generated sufficiently reliable haplotypes. Results: Here, we propose a novel SIH algorithm, called PEATH (Probabilistic Evolutionary Algorithm with Toggling for Haplotyping), to achieve more accurate and reliable haplotyping...
January 12, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29342241/ipat-intelligent-prediction-and-association-tool-for-genomic-research
#3
Chunpeng James Chen, Zhiwu Zhang
Summary: The ultimate goal of genomic research is to effectively predict phenotypes from genotypes so that medical management can improve human health and molecular breeding can increase agricultural production. Genomic prediction or selection (GS) plays a complementary role to genome-wide association studies (GWAS), which is the primary method to identify genes underlying phenotypes. Unfortunately, most computing tools cannot perform data analyses for both GWAS and GS. Furthermore, the majority of these tools are executed through a command-line interface (CLI), which requires programming skills...
January 11, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29342232/informational-and-linguistic-analysis-of-large-genomic-sequence-collections-via-efficient-hadoop-cluster-algorithms
#4
Umberto Ferraro Petrillo, Gianluca Roscigno, Giuseppe Cattaneo, Raffaele Giancarlo
Motivation: Information theoretic and compositional/linguistic analysis of genomes have a central role in bioinformatics, even more so since the associated methodologies are becoming very valuable also for epigenomic and meta-genomic studies. The kernel of those methods is based on the collection of k-mer statistics, i.e., how many times each k-mer in {A;C; G; T}k occurs in a DNA sequence. Although this problem is computationally very simple and efficiently solvable on a conventional computer, the sheer amount of data available now in applications demands to resort to parallel and distributed computing...
January 12, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29342229/a-rapid-epistatic-mixed-model-association-analysis-by-linear-retransformations-of-genomic-estimated-values
#5
Chao Ning, Dan Wang, Huimin Kang, Raphael Mrode, Lei Zhou, Shizhong Xu, Jian-Feng Liu
Motivation: Epistasis provides a feasible way for probing potential genetic mechanism of complex traits. However, time-consuming computation challenges successful detection of interaction in practice, especially when linear mixed model (LMM) is used to control type I error in the presence of population structure and cryptic relatedness. Results: A rapid epistatic mixed-model association analysis (REMMA) method was developed to overcome computational limitation. This method first estimates individuals' epistatic effects by an extended genomic best linear unbiased prediction (EG-BLUP) model with additive and epistatic kinship matrix, then pairwise interaction effects are obtained by linear retransformations of individuals' epistatic effects...
January 12, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29342208/comparison-of-traffic-injury-related-hospitalisation-between-bicyclists-and-motorcyclists-in-taiwan
#6
Chih-Wei Pai, Hsiao-Yu Lin, Shin-Han Tsai, Ping-Ling Chen
OBJECTIVES: Bicyclists and motorcyclists contribute substantially to the morbidity and mortality rates of road crash casualties. The objective of the study was to investigate the crash characteristics of bicyclist and motorcyclist casualties presented to hospitals in Taiwan resulting from crashes. METHODS: By using linked data from The National Traffic Crash Dataset and the National Health Insurance Database between 2003 and 2012, logistic regression models were used to examine the determinants of hospitalisation among motorcyclist and bicyclist casualties...
2018: PloS One
https://www.readbyqxmd.com/read/29342192/white-matter-tract-specific-quantitative-analysis-in-multiple-sclerosis-comparison-of-optic-radiation-reconstruction-techniques
#7
Chenyu Wang, Alexander Klistorner, Linda Ly, Michael H Barnett
The posterior visual pathway is commonly affected by multiple sclerosis (MS) pathology that results in measurable clinical and electrophysiological impairment. Due to its highly structured retinotopic mapping, the visual pathway represents an ideal substrate for investigating patho-mechanisms in MS. Therefore, a reliable and robust imaging segmentation method for in-vivo delineation of the optic radiations (OR) is needed. However, diffusion-based tractography approaches, which are typically used for OR segmentation are confounded by the presence of focal white matter lesions...
2018: PloS One
https://www.readbyqxmd.com/read/29342165/increased-colon-cancer-risk-after-severe-salmonella-infection
#8
Lapo Mughini-Gras, Michael Schaapveld, Jolanda Kramers, Sofie Mooij, E Andra Neefjes-Borst, Wilfrid van Pelt, Jacques Neefjes
BACKGROUND: Colon cancer constitutes one of the most frequent malignancies. Previous studies showed that Salmonella manipulates host cell signaling pathways and that Salmonella Typhimurium infection facilitates colon cancer development in genetically predisposed mice. This epidemiological study examined whether severe Salmonella infection, usually acquired from contaminated food, is associated with increased colon cancer risk in humans. METHODS AND FINDINGS: We performed a nationwide registry-based study to assess colon cancer risk after diagnosed Salmonella infection...
2018: PloS One
https://www.readbyqxmd.com/read/29342159/prediction-of-novel-target-genes-and-pathways-involved-in-bevacizumab-resistant-colorectal-cancer
#9
Precious Takondwa Makondi, Chia-Hwa Lee, Chien-Yu Huang, Chi-Ming Chu, Yu-Jia Chang, Po-Li Wei
Bevacizumab combined with cytotoxic chemotherapy is the backbone of metastatic colorectal cancer (mCRC) therapy; however, its treatment efficacy is hampered by therapeutic resistance. Therefore, understanding the mechanisms underlying bevacizumab resistance is crucial to increasing the therapeutic efficacy of bevacizumab. The Gene Expression Omnibus (GEO) database (dataset, GSE86525) was used to identify the key genes and pathways involved in bevacizumab-resistant mCRC. The GEO2R web tool was used to identify differentially expressed genes (DEGs)...
2018: PloS One
https://www.readbyqxmd.com/read/29342101/a-novel-methodology-for-improving-plant-pest-surveillance-in-vineyards-and-crops-using-uav-based-hyperspectral-and-spatial-data
#10
Fernando Vanegas, Dmitry Bratanov, Kevin Powell, John Weiss, Felipe Gonzalez
Recent advances in remote sensed imagery and geospatial image processing using unmanned aerial vehicles (UAVs) have enabled the rapid and ongoing development of monitoring tools for crop management and the detection/surveillance of insect pests. This paper describes a (UAV) remote sensing-based methodology to increase the efficiency of existing surveillance practices (human inspectors and insect traps) for detecting pest infestations (e.g., grape phylloxera in vineyards). The methodology uses a UAV integrated with advanced digital hyperspectral, multispectral, and RGB sensors...
January 17, 2018: Sensors
https://www.readbyqxmd.com/read/29342035/systematic-review-of-hearing-preservation-after-radiotherapy-for-vestibular-schwannoma
#11
Adam R Coughlin, Tyler J Willman, Samuel P Gubbels
OBJECTIVE: To determine the long-term hearing preservation rate for spontaneous vestibular schwannoma treated by primary radiotherapy. DATA SOURCES: The MEDLINE/PubMed, Web of Science, Cochrane Reviews, and EMBASE databases were searched using a comprehensive Boolean keyword search developed in conjunction with a scientific librarian. English language papers published from 2000 to 2016 were evaluated. STUDY SELECTION: Inclusion criteria: full articles, pretreatment and posttreatment audiograms or audiogram based scoring system, vestibular schwannoma only tumor type, reported time to follow-up, published after 1999, use of either Gamma Knife or linear accelerator radiotherapy...
January 16, 2018: Otology & Neurotology
https://www.readbyqxmd.com/read/29341344/the-medial-temporal-lobe-functional-connectivity-patterns-associated-with-forming-different-mental-representations
#12
Signy Sheldon, Brian Levine
The medial temporal lobes (MTL), and more specifically the hippocampus, are critical for forming mental representations of past experiences - autobiographical memories - and for forming other 'non-experienced' types of mental representations, such as imagined scenarios. How the MTL coordinate with other brain areas to create these different types of representations is not well understood. To address this issue, we performed a task-based functional connectivity analysis on a previously published dataset in which fMRI data were collected as participants created different types of mental representations under three conditions...
January 17, 2018: Hippocampus
https://www.readbyqxmd.com/read/29341341/prediction-of-activation-patterns-preceding-hallucinations-in-patients-with-schizophrenia-using-machine-learning-with-structured-sparsity
#13
Amicie de Pierrefeu, Thomas Fovet, Fouad Hadj-Selem, Tommy Löfstedt, Philippe Ciuciu, Stephanie Lefebvre, Pierre Thomas, Renaud Lopes, Renaud Jardri, Edouard Duchesnay
Despite significant progress in the field, the detection of fMRI signal changes during hallucinatory events remains difficult and time-consuming. This article first proposes a machine-learning algorithm to automatically identify resting-state fMRI periods that precede hallucinations versus periods that do not. When applied to whole-brain fMRI data, state-of-the-art classification methods, such as support vector machines (SVM), yield dense solutions that are difficult to interpret. We proposed to extend the existing sparse classification methods by taking the spatial structure of brain images into account with structured sparsity using the total variation penalty...
January 16, 2018: Human Brain Mapping
https://www.readbyqxmd.com/read/29341323/test-retest-reliability-and-longitudinal-analysis-of-automated-hippocampal-subregion-volumes-in-healthy-ageing-and-alzheimer-s-disease-populations
#14
Amanda Worker, Danai Dima, Anna Combes, William R Crum, Johannes Streffer, Steven Einstein, Mitul A Mehta, Gareth J Barker, Steve C R Williams, Owen O'daly
The hippocampal formation is a complex brain structure that is important in cognitive processes such as memory, mood, reward processing and other executive functions. Histological and neuroimaging studies have implicated the hippocampal region in neuropsychiatric disorders as well as in neurodegenerative diseases. This highly plastic limbic region is made up of several subregions that are believed to have different functional roles. Therefore, there is a growing interest in imaging the subregions of the hippocampal formation rather than modelling the hippocampus as a homogenous structure, driving the development of new automated analysis tools...
January 16, 2018: Human Brain Mapping
https://www.readbyqxmd.com/read/29341127/discrimination-of-geographical-origin-of-asian-garlic-using-isotopic-and-chemical-datasets-under-stepwise-principal-component-analysis
#15
Tsang-Sen Liu, Jhen-Nan Lin, Tsung-Ren Peng
Isotopic compositions of δ2 H, δ18 O, δ13 C, and δ15 N and concentrations of 22 trace elements from garlic samples were analyzed and processed with stepwise principal component analysis (PCA) to discriminate garlic's country of origin among Asian regions including South Korea, Vietnam, Taiwan, and China. Results indicate that there is no single trace-element concentration or isotopic composition that can accomplish the study's purpose and the stepwise PCA approach proposed does allow for discrimination between countries on a regional basis...
January 16, 2018: Journal of Forensic Sciences
https://www.readbyqxmd.com/read/29340952/rfathm6a-a-new-tool-for-predicting-m6a-sites-in-arabidopsis-thaliana
#16
Xiaofeng Wang, Renxiang Yan
We curated a reliable dataset of m6A sites in Arabidopsis thaliana, built competitive models for predicting m6A sites, extracted predominant rules from the prediction models and analyzed the most important features. In biological RNA, approximately 150 chemical modifications have been discovered, of which N6-methyladenine (m6A) is the most prevalent and abundant. This modification plays an essential role in a myriad of biological mechanisms and regulates RNA localization, nuclear export, translation, stability, alternative splicing, and other processes...
January 16, 2018: Plant Molecular Biology
https://www.readbyqxmd.com/read/29340885/quantifying-diastolic-function-from-e-waves-as-triangles-to-physiologic-contours-via-the-geometric-method
#17
Mikhail Golman, William Padovano, Leonid Shmuylovich, Sándor J Kovács
Conventional echocardiographic diastolic function (DF) assessment approximates transmitral flow velocity contours (Doppler E-waves) as triangles, with peak (Epeak), acceleration time (AT), and deceleration time (DT) as indexes. These metrics have limited value because they are unable to characterize the underlying physiology. The parametrized diastolic filling (PDF) formalism provides a physiologic, kinematic mechanism based characterization of DF by extracting chamber stiffness (k), relaxation (c), and load (x o ) from E-wave contours...
January 16, 2018: Cardiovascular Engineering and Technology
https://www.readbyqxmd.com/read/29340810/ureteral-stents-increase-risk-of-postoperative-acute-kidney-injury-following-colorectal-surgery
#18
Taryn E Hassinger, J Hunter Mehaffey, Matthew G Mullen, Alex D Michaels, Nathan R Elwood, Shoshana T Levi, Traci L Hedrick, Charles M Friel
BACKGROUND: Ureteral stents are commonly placed before colorectal resection to assist in identification of ureters and prevent injury. Acute kidney injury (AKI) is a common cause of morbidity and increased cost following colorectal surgery. Although previously associated with reflex anuria, prophylactic stents have not been found to increase AKI. We sought to determine the impact of ureteral stents on the incidence of AKI following colorectal surgery. METHODS: All patients undergoing colon or rectal resection at a single institution between 2005 and 2015 were reviewed using American College of Surgeons National Surgical Quality Improvement Program dataset...
January 16, 2018: Surgical Endoscopy
https://www.readbyqxmd.com/read/29340580/population-specific-biomarkers-of-human-aging-a-big-data-study-using-south-korean-canadian-and-eastern-european-patient-populations
#19
Polina Mamoshina, Kirill Kochetov, Evgeny Putin, Franco Cortese, Alexander Aliper, Won-Suk Lee, Sung-Min Ahn, Lee Uhn, Neil Skjodt, Olga Kovalchuk, Morten Scheibye-Knudsen, Alex Zhavoronkov
Accurate and physiologically meaningful biomarkers for human aging are key to assessing anti-aging therapies. Given ethnic differences in health, diet, lifestyle, behaviour, environmental exposures and even average rate of biological aging, it stands to reason that aging clocks trained on datasets obtained from specific ethnic populations are more likely to account for these potential confounding factors, resulting in an enhanced capacity to predict chronological age and quantify biological age. Here we present a deep learning-based hematological aging clock modeled using the large combined dataset of Canadian, South Korean and Eastern European population blood samples that show increased predictive accuracy in individual populations compared to population-specific hematologic aging clocks...
January 11, 2018: Journals of Gerontology. Series A, Biological Sciences and Medical Sciences
https://www.readbyqxmd.com/read/29340289/automatic-segmentation-method-of-pelvic-floor-levator-hiatus-in-ultrasound-using-a-self-normalizing-neural-network
#20
Ester Bonmati, Yipeng Hu, Nikhil Sindhwani, Hans Peter Dietz, Jan D'hooge, Dean Barratt, Jan Deprest, Tom Vercauteren
Segmentation of the levator hiatus in ultrasound allows the extraction of biometrics, which are of importance for pelvic floor disorder assessment. We present a fully automatic method using a convolutional neural network (CNN) to outline the levator hiatus in a two-dimensional image extracted from a three-dimensional ultrasound volume. In particular, our method uses a recently developed scaled exponential linear unit (SELU) as a nonlinear self-normalizing activation function, which for the first time has been applied in medical imaging with CNN...
April 2018: Journal of Medical Imaging
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