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https://www.readbyqxmd.com/read/27914139/genetic-variations-of-the-kiss1r-gene-in-korean-girls-with-central-precocious-puberty
#1
Yeon Joung Oh, Young Jun Rhie, Hyo Kyoung Nam, Hye Ryun Kim, Kee Hyoung Lee
The timing of puberty onset varies greatly among individuals, and much of this variation is modulated by genetic factors. This study aimed to identify the kisspeptin receptor (KISS1R) gene variations and to investigate the associations between these variations and central precocious puberty (CPP). Korean girls with CPP (n = 194) and their healthy controls (n = 99) were included in this study. The entire coding region and the exon-intron boundaries (exon 1 through 5) of the KISS1R gene were directly sequenced...
January 2017: Journal of Korean Medical Science
https://www.readbyqxmd.com/read/27913366/deepr-a-convolutional-net-for-medical-records
#2
Phuoc Nguyen, Truyen Tran, Nilmini Wickramasinghe, Svetha Venkatesh
Feature engineering remains a major bottleneck when creating predictive systems from electronic medical records. At present, an important missing element is detecting predictive regular clinical motifs from irregular episodic records. We present Deepr (short for Deep record), a new end-to-end deep learning system that learns to extract features from medical records and predicts future risk automatically. Deepr transforms a record into a sequence of discrete elements separated by coded time gaps and hospital transfers...
December 1, 2016: IEEE Journal of Biomedical and Health Informatics
https://www.readbyqxmd.com/read/27911958/advantages-of-an-improved-rhesus-macaque-genome-for-evolutionary-analyses
#3
Julien S Gradnigo, Abhishek Majumdar, Robert B Norgren, Etsuko N Moriyama
The rhesus macaque (Macaca mulatta) is widely used in molecular evolutionary analyses, particularly to identify genes under adaptive or unique evolution in the human lineage. For such studies, it is necessary to align nucleotide sequences of homologous protein-coding genes among multiple species. The validity of these analyses is dependent on high quality genomic data. However, for most mammalian species (other than humans and mice), only draft genomes are available. There has been concern that some results obtained from evolutionary analyses using draft genomes may not be correct...
2016: PloS One
https://www.readbyqxmd.com/read/27910444/synthetic-diagnostics-platform-for-fusion-plasmas-invited
#4
L Shi, E J Valeo, B J Tobias, G J Kramer, L Hausammann, W M Tang, M Chen
A Synthetic Diagnostics Platform (SDP) for fusion plasmas has been developed which provides state of the art synthetic reflectometry, beam emission spectroscopy, and Electron Cyclotron Emission (ECE) diagnostics. Interfaces to the plasma simulation codes GTC, XGC-1, GTS, and M3D-C(1) are provided, enabling detailed validation of these codes. In this paper, we give an overview of SDP's capabilities, and introduce the synthetic diagnostic modules. A recently developed synthetic ECE Imaging module which self-consistently includes refraction, diffraction, emission, and absorption effects is discussed in detail...
November 2016: Review of Scientific Instruments
https://www.readbyqxmd.com/read/27910390/validation-of-fast-ion-d-alpha-spectrum-measurements-during-east-neutral-beam-heated-plasmas
#5
J Huang, W W Heidbrink, M G von Hellermann, L Stagner, C R Wu, Y M Hou, J F Chang, S Y Ding, Y J Chen, Y B Zhu, Z Jin, Z Xu, W Gao, J F Wang, B Lyu, Q Zang, G Q Zhong, L Hu, B Wan
To investigate the fast ion behavior, a fast ion D-alpha (FIDA) diagnostic system has been installed on EAST. Fast ion features can be inferred from the Doppler shifted spectrum of Balmer-alpha light from energetic hydrogenic atoms. This paper will focus on the validation of FIDA measurements performed using MHD-quiescent discharges in 2015 campaign. Two codes have been applied to calculate the Dα spectrum: one is a Monte Carlo code, Fortran 90 version FIDASIM, and the other is an analytical code, Simulation of Spectra (SOS)...
November 2016: Review of Scientific Instruments
https://www.readbyqxmd.com/read/27909036/defining-adolescent-common-mental-disorders-using-electronic-primary-care-data-a-comparison-with-outcomes-measured-using-the-cis-r
#6
Rosie P Cornish, Ann John, Andy Boyd, Kate Tilling, John Macleod
OBJECTIVE: To compare the prevalence of common mental disorders (CMDs) derived from data held in primary care records with that measured using the revised Clinical Interview Schedule (CIS-R) in order to assess the potential robustness of findings based only on routinely collected data. DESIGN AND SETTING: Comparison study using linkage between the Avon Longitudinal Study of Parents and Children (ALSPAC) and electronic primary care records. PARTICIPANTS: We studied 1562 adolescents who had completed the CIS-R in ALSPAC at age 17-18 years and had linkage established to their primary care records...
December 1, 2016: BMJ Open
https://www.readbyqxmd.com/read/27908705/a-novel-method-for-in-silico-identification-of-regulatory-snps-in-human-genome
#7
Rong Li, Dexing Zhong, Ruiling Liu, Hongqiang Lv, Xinman Zhang, Jun Liu, Jiuqiang Han
Regulatory single nucleotide polymorphisms (rSNPs), kind of functional noncoding genetic variants, can affect gene expression in a regulatory way, and they are thought to be associated with increased susceptibilities to complex diseases. Here a novel computational approach to identify potential rSNPs is presented. Different from most other rSNPs finding methods which based on hypothesis that SNPs causing large allele-specific changes in transcription factor binding affinities are more likely to play regulatory functions, we use a set of documented experimentally verified rSNPs and nonfunctional background SNPs to train classifiers, so the discriminating features are found...
November 28, 2016: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/27908188/polymer-gel-dosimetry-for-measuring-the-dose-near-thin-high-z-materials-irradiated-with-high-energy-photon-beams
#8
Leighton L Warmington, N Gopishankar, John H Broadhurst, Yoichi Watanabe
PURPOSE: To investigate the feasibility of three-dimensional (3D) dose measurements near thin high-Z materials placed in a water-like medium by using a polymer gel dosimeter (PGD) when the medium was irradiated with high energy photon beams. METHODS: PGD is potentially a useful tool for this application because it can record the dose around a small object made of a high-Z material in a continuous 3D medium. In this study, the authors manufactured a methacrylic acid-based normoxic PGD, nMAG...
December 2016: Medical Physics
https://www.readbyqxmd.com/read/27908114/self-consistent-implementation-of-meta-gga-functionals-for-the-onetep-linear-scaling-electronic-structure-package
#9
James C Womack, Narbe Mardirossian, Martin Head-Gordon, Chris-Kriton Skylaris
Accurate and computationally efficient exchange-correlation functionals are critical to the successful application of linear-scaling density functional theory (DFT). Local and semi-local functionals of the density are naturally compatible with linear-scaling approaches, having a general form which assumes the locality of electronic interactions and which can be efficiently evaluated by numerical quadrature. Presently, the most sophisticated and flexible semi-local functionals are members of the meta-generalized-gradient approximation (meta-GGA) family, and depend upon the kinetic energy density, τ, in addition to the charge density and its gradient...
November 28, 2016: Journal of Chemical Physics
https://www.readbyqxmd.com/read/27907883/measurement-and-calculation-of-fast-neutron-and-gamma-spectra-in-well-defined-cores-in-lr-0-reactor
#10
Michal Košťál, Zdeněk Matěj, František Cvachovec, Vojtěch Rypar, Evžen Losa, Jiří Rejchrt, Filip Mravec, Martin Veškrna
A well-defined neutron spectrum is essential for many types of experimental topics and is also important for both calibration and testing of spectrometric and dosimetric detectors. Provided it is well described, such a spectrum can also be employed as a reference neutron field that is suitable for validating selected cross sections. The present paper aims to compare calculations and measurements of such a well-defined spectra in geometrically similar cores of the LR-0 reactor with fuel containing slightly different enrichments (2%, 3...
November 17, 2016: Applied Radiation and Isotopes
https://www.readbyqxmd.com/read/27907167/infusion-advancing-discovery-of-fusion-genes-and-chimeric-transcripts-from-deep-rna-sequencing-data
#11
Konstantin Okonechnikov, Aki Imai-Matsushima, Lukas Paul, Alexander Seitz, Thomas F Meyer, Fernando Garcia-Alcalde
Analysis of fusion transcripts has become increasingly important due to their link with cancer development. Since high-throughput sequencing approaches survey fusion events exhaustively, several computational methods for the detection of gene fusions from RNA-seq data have been developed. This kind of analysis, however, is complicated by native trans-splicing events, the splicing-induced complexity of the transcriptome and biases and artefacts introduced in experiments and data analysis. There are a number of tools available for the detection of fusions from RNA-seq data; however, certain differences in specificity and sensitivity between commonly used approaches have been found...
2016: PloS One
https://www.readbyqxmd.com/read/27905972/a-new-parametric-model-to-assess-delay-and-compression-of-mortality
#12
Joop de Beer, Fanny Janssen
BACKGROUND: A decrease in mortality across all ages causes a shift of the age pattern of mortality, or mortality delay, while differences in the rate of decrease across ages cause a change in the shape of the age-at-death distribution, mortality compression or expansion. Evidence exists for both compression and delay of mortality. Existing parametric models to describe the full age pattern of mortality are not able to capture mortality delay versus mortality compression. More recent models that assess delay versus compression mostly focused on the adult or old ages alone and did not distinguish mortality compression below and above the modal age at death, although they represent different mechanisms...
December 1, 2016: Population Health Metrics
https://www.readbyqxmd.com/read/27905953/improving-the-usefulness-of-us-mortality-data-new-methods-for-reclassification-of-underlying-cause-of-death
#13
Kyle J Foreman, Mohsen Naghavi, Majid Ezzati
BACKGROUND: Mortality data are affected by miscertification of the medical cause of death deaths and changes to cause of death classification systems. We present both mappings of ICD9 and ICD10 to a unified list of causes, and a new statistical model for reducing the impact of misclassification of cause of death. METHODS: We propose a Bayesian mixed-effects multinomial logistic model that can be run on individual record level death certificates to reclassify "garbage-coded" deaths onto causes that are more meaningful for public health purposes...
April 28, 2016: Population Health Metrics
https://www.readbyqxmd.com/read/27904452/virtual-modelling-of-novel-applicator-prototypes-for-cervical-cancer-brachytherapy
#14
Primoz Petric, Robert Hudej, Noora Al-Hammadi, Barbara Segedin
BACKGROUND: Standard applicators for cervical cancer Brachytherapy (BT) do not always achieve acceptable balance between target volume and normal tissue irradiation. We aimed to develop an innovative method of Target-volume Density Mapping (TDM) for modelling of novel applicator prototypes with optimal coverage characteristics. Patients and methods. Development of Contour-Analysis Tool 2 (CAT-2) software for TDM generation was the core priority of our task group. Main requests regarding software functionalities were formulated and guided the coding process...
December 1, 2016: Radiology and Oncology
https://www.readbyqxmd.com/read/27899558/pathdip-an-annotated-resource-for-known-and-predicted-human-gene-pathway-associations-and-pathway-enrichment-analysis
#15
Sara Rahmati, Mark Abovsky, Chiara Pastrello, Igor Jurisica
Molecular pathway data are essential in current computational and systems biology research. While there are many primary and integrated pathway databases, several challenges remain, including low proteome coverage (57%), low overlap across different databases, unavailability of direct information about underlying physical connectivity of pathway members, and high fraction of protein-coding genes without any pathway annotations, i.e. 'pathway orphans'. In order to address all these challenges, we developed pathDIP, which integrates data from 20 source pathway databases, 'core pathways', with physical protein-protein interactions to predict biologically relevant protein-pathway associations, referred to as 'extended pathways'...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27897201/long-intergenic-non-coding-rna-expression-signature-in-human-breast-cancer
#16
Yanfeng Zhang, Erin K Wagner, Xingyi Guo, Isaac May, Qiuyin Cai, Wei Zheng, Chunyan He, Jirong Long
Breast cancer is a complex disease, characterized by gene deregulation. There is less systematic investigation of the capacity of long intergenic non-coding RNAs (lincRNAs) as biomarkers associated with breast cancer pathogenesis or several clinicopathological variables including receptor status and patient survival. We designed a two-stage study, including 1,000 breast tumor RNA-seq data from The Cancer Genome Atlas (TCGA) as the discovery stage, and RNA-seq data of matched tumor and adjacent normal tissue from 50 breast cancer patients as well as 23 normal breast tissue from healthy women as the replication stage...
November 29, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27896993/frequent-subgraph-mining-of-personalized-signaling-pathway-networks-groups-patients-with-frequently-dysregulated-disease-pathways-and-predicts-prognosis
#17
Arda Durmaz, Tim A D Henderson, Douglas Brubaker, Gurkan Bebek
MOTIVATION: Large scale genomics studies have generated comprehensive molecular characterization of numerous cancer types. Subtypes for many tumor types have been established; however, these classifications are based on molecular characteristics of a small gene sets with limited power to detect dysregulation at the patient level. We hypothesize that frequent graph mining of pathways to gather pathways functionally relevant to tumors can characterize tumor types and provide opportunities for personalized therapies...
2016: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/27896982/predictive-modeling-of-hospital-readmission-rates-using-electronic-medical-record-wide-machine-learning-a-case-study-using-mount-sinai-heart-failure-cohort
#18
Khader Shameer, Kipp W Johnson, Alexandre Yahi, Riccardo Miotto, L I Li, Doran Ricks, Jebakumar Jebakaran, Patricia Kovatch, Partho P Sengupta, Sengupta Gelijns, Alan Moskovitz, Bruce Darrow, David L David, Andrew Kasarskis, Nicholas P Tatonetti, Sean Pinney, Joel T Dudley
Reduction of preventable hospital readmissions that result from chronic or acute conditions like stroke, heart failure, myocardial infarction and pneumonia remains a significant challenge for improving the outcomes and decreasing the cost of healthcare delivery in the United States. Patient readmission rates are relatively high for conditions like heart failure (HF) despite the implementation of high-quality healthcare delivery operation guidelines created by regulatory authorities. Multiple predictive models are currently available to evaluate potential 30-day readmission rates of patients...
2016: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/27896969/reproducible-drug-repurposing-when-similarity-does-not-suffice
#19
Emre Guney
Repurposing existing drugs for new uses has attracted considerable attention over the past years. To identify potential candidates that could be repositioned for a new indication, many studies make use of chemical, target, and side effect similarity between drugs to train classifiers. Despite promising prediction accuracies of these supervised computational models, their use in practice, such as for rare diseases, is hindered by the assumption that there are already known and similar drugs for a given condition of interest...
2016: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/27896873/identifying-fallacious-arguments-in-a-qualitative-study-of-antipsychotic-prescribing-in-dementia
#20
Parastou Donyai
BACKGROUND: Dementia can result in cognitive, noncognitive and behavioural symptoms which are difficult to manage. Formal guidelines for the care and management of dementia in the UK state that antipsychotics should only be prescribed where fully justified. This is because inappropriate use, particularly problematic in care-home settings, can produce severe side effects including death. The aim of this study was to explore the use of fallacious arguments in professionals' deliberations about antipsychotic prescribing in dementia in care-home settings...
November 29, 2016: International Journal of Pharmacy Practice
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