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https://www.readbyqxmd.com/read/28641385/development-of-an-electronic-medical-record-based-child-physical-abuse-alert-system
#1
Rachel P Berger, Richard A Saladino, Janet Fromkin, Emily Heineman, Srinivasan Suresh, Tom McGinn
Objective: Physical abuse is a leading cause of pediatric morbidity and mortality. Physicians do not consistently screen for abuse, even in high-risk situations. Alerts in the electronic medical record may help improve screening rates, resulting in early identification and improved outcomes. Methods: Triggers to identify children < 2 years old at risk for physical abuse were coded into the electronic medical record at a freestanding pediatric hospital with a level 1 trauma center...
June 21, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/28641268/newgoa-predicting-new-go-annotations-of-proteins-by-bi-random-walks-on-a-hybrid-graph
#2
Guoxian Yu, Guangyuan Fu, Jun Wang, Yingwen Zhao
A remaining key challenge of modern biology is annotating the functional roles of proteins. Various computational models have been proposed for this challenge. Most of them assume the annotations of annotated proteins are complete. But in fact, many of them are incomplete. We proposed a method called NewGOA to predict new Gene Ontology (GO) annotations for incompletely annotated proteins and for completely un-annotated ones. NewGOA employs a hybrid graph, composed of two types of nodes (proteins and GO terms), to encode interactions between proteins, hierarchical relationships between terms and available annotations of proteins...
June 15, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28641048/updates-and-current-challenges-in-microrna-research-for-personalized-medicine-in-ovarian-cancer
#3
Victoria Mandilaras, Mégane Vernon, Matthieu Meryet-Figuière, Katherine Karakasis, Bernard Lambert, Laurent Poulain, Amit Oza, Christophe Denoyelle, Stephanie Lheureux
Ovarian cancer (OC) is the second most common and the most lethal of the gynecological malignancies. Currently, there exists no effective screening tool for OC. MicroRNAs (miRNAs) are endogenous 18-23 nucleotide non-coding RNAs that refine gene expression. MiRNAs have been found to be aberrantly expressed in OC tumor tissue as well as detectable in biological fluids such as the blood, urine, and ascites and have been proposed as biomarkers and therapeutic targets for OC. Areas covered: This review summarizes the current knowledge regarding the application of miRNAs as diagnostic, prognostic, and predictive biomarkers in OC...
June 22, 2017: Expert Opinion on Biological Therapy
https://www.readbyqxmd.com/read/28640671/regulation-of-a-muralytic-enzyme-encoding-gene-by-two-non-coding-rnas
#4
Renée J St-Onge, Marie A Elliot
Non-coding regulatory RNAs fine-tune gene expression post-transcriptionally. In the streptomycetes, rpfA - encoding a muralytic enzyme required for establishing and exiting dormancy - is flanked by non-coding regulatory RNA elements both upstream (riboswitch) and downstream [antisense small RNA (sRNA)]. In Streptomyces coelicolor, the upstream riboswitch decreases rpfA transcript abundance in response to the second messenger cyclic di-AMP, itself involved in cell wall metabolism and dormancy. There is, however, no obvious expression platform associated with this riboswitch and consequently, its mechanism of action is entirely unknown...
June 22, 2017: RNA Biology
https://www.readbyqxmd.com/read/28637323/evolution-of-transcription-activator-like-effectors-in-xanthomonas-oryzae
#5
Annett Erkes, Maik Reschke, Jens Boch, Jan Grau
Transcription activator-like effectors (TALEs) are secreted by plant-pathogenic Xanthomonas bacteria into plant cells where they act as transcriptional activators and, hence, are major drivers in reprogramming the plant for the benefit of the pathogen. TALEs possess a highly repetitive DNA-binding domain of typically 34 amino acid tandem repeats, where amino acid 12 and 13, termed repeat variable di-residue (RVD), determine target specificity. Different Xanthomonas strains possess different repertoires of TALEs...
June 14, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28634911/novel-insights-into-a-reputably-irreversible-process-combined-mrna-and-mirna-profiling-of-tissue-from-vesicourethral-anastomotic-stenosis-after-radical-prostatectomy
#6
T S Worst, K Daskalova, A Steidler, K Berner-Leischner, R Röth, B Niesler, C-A Weis, M C Kriegmair, P Erben, D Pfalzgraf
PURPOSE: Until recently, tissue fibrosis-ultimately leading to permanent scaring-has been considered an irreversible process. However, recent findings indicate that it may be reversible after all. Vesicourethral anastomotic stenosis (VUAS) as fibrous narrowing is a frequent complication after radical prostatectomy with high recurrence rates and requires invasive treatment. The pathophysiology is poorly understood. Therefore, a combined mRNA and miRNA transcription profiling in tissue from VUAS was performed using nCounter technology...
June 20, 2017: World Journal of Urology
https://www.readbyqxmd.com/read/28634715/regulatory-element-based-prediction-identifies-new-susceptibility-regulatory-variants-for-osteoporosis
#7
Shi Yao, Yan Guo, Shan-Shan Dong, Ruo-Han Hao, Xiao-Feng Chen, Yi-Xiao Chen, Jia-Bin Chen, Qing Tian, Hong-Wen Deng, Tie-Lin Yang
Despite genome-wide association studies (GWASs) have identified many susceptibility genes for osteoporosis, it still leaves a large part of missing heritability to be discovered. Integrating regulatory information and GWASs could offer new insights into the biological link between the susceptibility SNPs and osteoporosis. We generated five machine learning classifiers with osteoporosis-associated variants and regulatory features data. We gained the optimal classifier and predicted genome-wide SNPs to discover susceptibility regulatory variants...
June 20, 2017: Human Genetics
https://www.readbyqxmd.com/read/28634438/computational-models-of-anterior-cingulate-cortex-at-the-crossroads-between-prediction-and-effort
#8
Eliana Vassena, Clay B Holroyd, William H Alexander
In the last two decades the anterior cingulate cortex (ACC) has become one of the most investigated areas of the brain. Extensive neuroimaging evidence suggests countless functions for this region, ranging from conflict and error coding, to social cognition, pain and effortful control. In response to this burgeoning amount of data, a proliferation of computational models has tried to characterize the neurocognitive architecture of ACC. Early seminal models provided a computational explanation for a relatively circumscribed set of empirical findings, mainly accounting for EEG and fMRI evidence...
2017: Frontiers in Neuroscience
https://www.readbyqxmd.com/read/28634437/latent-growth-curve-models-for-biomarkers-of-the-stress-response
#9
REVIEW
John M Felt, Sarah Depaoli, Jitske Tiemensma
Objective: The stress response is a dynamic process that can be characterized by predictable biochemical and psychological changes. Biomarkers of the stress response are typically measured over time and require statistical methods that can model change over time. One flexible method of evaluating change over time is the latent growth curve model (LGCM). However, stress researchers seldom use the LGCM when studying biomarkers, despite their benefits. Stress researchers may be unaware of how these methods can be useful...
2017: Frontiers in Neuroscience
https://www.readbyqxmd.com/read/28634436/dual-coding-theory-explains-biphasic-collective-computation-in-neural-decision-making
#10
Bryan C Daniels, Jessica C Flack, David C Krakauer
A central question in cognitive neuroscience is how unitary, coherent decisions at the whole organism level can arise from the distributed behavior of a large population of neurons with only partially overlapping information. We address this issue by studying neural spiking behavior recorded from a multielectrode array with 169 channels during a visual motion direction discrimination task. It is well known that in this task there are two distinct phases in neural spiking behavior. Here we show Phase I is a distributed or incompressible phase in which uncertainty about the decision is substantially reduced by pooling information from many cells...
2017: Frontiers in Neuroscience
https://www.readbyqxmd.com/read/28633662/orthored-a-rapid-and-accurate-orthology-prediction-tool-with-low-computational-requirement
#11
Kai Battenberg, Ernest K Lee, Joanna C Chiu, Alison M Berry, Daniel Potter
BACKGROUND: Identifying orthologous genes is an initial step required for phylogenetics, and it is also a common strategy employed in functional genetics to find candidates for functionally equivalent genes across multiple species. At the same time, in silico orthology prediction tools often require large computational resources only available on computing clusters. Here we present OrthoReD, an open-source orthology prediction tool with accuracy comparable to published tools that requires only a desktop computer...
June 21, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28633642/prediction-and-analysis-of-three-gene-families-related-to-leaf-rust-puccinia-triticina-resistance-in-wheat-triticum-aestivum-l
#12
Fred Y Peng, Rong-Cai Yang
BACKGROUND: The resistance to leaf rust (Lr) caused by Puccinia triticina in wheat (Triticum aestivum L.) has been well studied over the past decades with over 70 Lr genes being mapped on different chromosomes and numerous QTLs (quantitative trait loci) being detected or mapped using DNA markers. Such resistance is often divided into race-specific and race-nonspecific resistance. The race-nonspecific resistance can be further divided into resistance to most or all races of the same pathogen and resistance to multiple pathogens...
June 20, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28632384/finite-field-method-for-nonlinear-optical-property-prediction-using-rational-function-approximants
#13
Anand H G Patel, Ahmed A K Mohammed, Peter A Limacher, Paul Woodson Ayers
The finite-field (FF) method is a quick, easy-to-implement tool for the prediction of nonlinear optical properties. Here, we present and explore a novel variant of the FF method, which uses a rational function to fit a molecule's energy with respect to an electric field. Similarly to previous FF methods, factors crucial for the method's accuracy were tuned. These factors include: the number of terms in the function, the distribution of fields used to construct the approximation, and the initial field in the approximation...
June 20, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28629385/administrative-algorithms-to-identify-avascular-necrosis-of-bone-among-patients-undergoing-upper-or-lower-extremity-magnetic-resonance-imaging-a-validation-study
#14
Medha Barbhaiya, Yan Dong, Jeffrey A Sparks, Elena Losina, Karen H Costenbader, Jeffrey N Katz
BACKGROUND: Studies of the epidemiology and outcomes of avascular necrosis (AVN) require accurate case-finding methods. The aim of this study was to evaluate performance characteristics of a claims-based algorithm designed to identify AVN cases in administrative data. METHODS: Using a centralized patient registry from a US academic medical center, we identified all adults aged ≥18 years who underwent magnetic resonance imaging (MRI) of an upper/lower extremity joint during the 1...
June 19, 2017: BMC Musculoskeletal Disorders
https://www.readbyqxmd.com/read/28629368/identification-and-characterization-of-long-intergenic-noncoding-rnas-in-bovine-mammary-glands
#15
Chao Tong, Qiaoling Chen, Lili Zhao, Junfei Ma, Eveline M Ibeagha-Awemu, Xin Zhao
BACKGROUND: Mammary glands of dairy cattle produce milk for the newborn offspring and for human consumption. Long intergenic noncoding RNAs (lincRNAs) play various functions in eukaryotic cells. However, types and roles of lincRNAs in bovine mammary glands are still poorly understood. RESULTS: Using computational methods, 886 unknown intergenic transcripts (UITs) were identified from five RNA-seq datasets from bovine mammary glands. Their non-coding potentials were predicted by using the combination of four software programs (CPAT, CNCI, CPC and hmmscan), with 184 lincRNAs identified...
June 19, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28628647/an-efficient-coding-theory-for-a-dynamic-trajectory-predicts-non-uniform-allocation-of-entorhinal-grid-cells-to-modules
#16
Noga Mosheiff, Haggai Agmon, Avraham Moriel, Yoram Burak
Grid cells in the entorhinal cortex encode the position of an animal in its environment with spatially periodic tuning curves with different periodicities. Recent experiments established that these cells are functionally organized in discrete modules with uniform grid spacing. Here we develop a theory for efficient coding of position, which takes into account the temporal statistics of the animal's motion. The theory predicts a sharp decrease of module population sizes with grid spacing, in agreement with the trend seen in the experimental data...
June 19, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28628559/the-mir-1206-microrna-variant-is-associated-with-methotrexate-induced-oral-mucositis-in-pediatric-acute-lymphoblastic-leukemia
#17
Angela Gutierrez-Camino, Natanja Oosterom, Marissa A H den Hoed, Elixabet Lopez-Lopez, Idoia Martin-Guerrero, Saskia M F Pluijm, Rob Pieters, Robert de Jonge, Wim J E Tissing, Sandra G Heil, Africa García-Orad, Marry M van den Heuvel-Eibrink
Five-year survival rates of pediatric acute lymphoblastic leukemia (ALL) have reached 90% in the developed countries. However, toxicity because of methotrexate (MTX) occurs frequently. Variety in the occurrence of toxicity is partly determined by single nucleotide polymorphisms (SNPs) in coding regions. Recently, five SNPs in non-coding pre-microRNAs and microRNA processing (miRNA) genes were identified in association with MTX-induced oral mucositis. This study aimed to replicate the association of these miRNA variants in relation to MTX-induced oral mucositis in a prospective childhood ALL cohort...
June 16, 2017: Pharmacogenetics and Genomics
https://www.readbyqxmd.com/read/28626813/hallucinations-as-top-down-effects-on-perception
#18
Albert R Powers, Megan Kelley, Philip R Corlett
The problem of whether and how information is integrated across hierarchical brain networks embodies a fundamental tension in contemporary cognitive neuroscience, and by extension, cognitive neuropsychiatry. Indeed, the penetrability of perceptual processes in a 'top-down' manner by higher-level cognition-a natural extension of hierarchical models of perception-may contradict a strictly modular view of mental organization. Furthermore, some in the cognitive science community have challenged cognitive penetration as an unlikely, if not impossible, process...
September 2016: Biological Psychiatry: Cognitive Neuroscience and Neuroimaging
https://www.readbyqxmd.com/read/28626165/identification-and-functional-profiling-of-differentially-expressed-long-non-coding-rnas-in-nasal-mucosa-with-allergic-rhinitis
#19
Zhiqi Ma, Yaoshu Teng, Xiang Liu, Jing Li, Jiangwei Mo, Min Sha, Yong Li
Long non-coding RNAs (lncRNAs) have been proved to play important roles in a variety of human immune diseases. However, their pathological effects on the development of allergic rhinitis (AR) have not been clearly understood. The aim of this study was to determine the expression profile of lncRNAs in nasal mucosa of AR patients by lncRNA microarray and to predict potential roles of specific lncRNAs in the pathogenic mechanisms of AR by analysis of lncRNA-mRNA co-expression network, Gene Ontology (GO) and pathway...
2017: Tohoku Journal of Experimental Medicine
https://www.readbyqxmd.com/read/28625800/arsenic-alters-transcriptional-responses-to-pseudomonas-aeruginosa-infection-and-decreases-antimicrobial-defense-of-human-airway-epithelial-cells
#20
B C Goodale, E J Rayack, B A Stanton
Arsenic contamination of drinking water and food threatens the health of hundreds of millions of people worldwide by increasing the risk of numerous diseases. Arsenic exposure has been associated with infectious lung disease in epidemiological studies, but it is not yet understood how ingestion of low levels of arsenic increases susceptibility to bacterial infection. Accordingly, the goal of this study was to examine the effect of arsenic on gene expression in primary human bronchial epithelial (HBE) cells and to determine if arsenic altered epithelial cell responses to Pseudomonas aeruginosa, an opportunistic pathogen...
June 15, 2017: Toxicology and Applied Pharmacology
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