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https://www.readbyqxmd.com/read/28343098/developmental-validation-of-qiagen-investigator-%C3%A2-24plex-qs-kit-and-investigator-%C3%A2-24plex-go-kit-two-6-dye-multiplex-assays-for-the-extended-codis-core-loci
#1
Melanie Kraemer, Anke Prochnow, Michael Bussmann, Mario Scherer, Ralf Peist, Carolyn Steffen
The original CODIS database based on 13 core STR loci has been overwhelmingly successful for matching suspects with evidence. In order to increase the power of discrimination, reduce the possibility of adventitious matches, and expand global data sharing, the CODIS Core Loci Working Group determined the expansion of the CODIS core loci to 20 STR plus three additional "highly recommended" loci (SE33, DY391, Amelogenin) Hares, 2015, 2012 [1,2]. The QIAGEN Investigator 24plex QS and Investigator 24plex GO! Kits are 6-dye multiplex assays that contain all markers of the expanded 23 CODIS core loci along with a unique internal performance control that is co-amplified with the STR markers...
March 12, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28342724/a-hypergraph-and-arithmetic-residue-based-probabilistic-neural-network-for-classification-in-intrusion-detection-systems
#2
M R Gauthama Raman, Nivethitha Somu, Kannan Kirthivasan, V S Shankar Sriram
Over the past few decades, the design of an intelligent Intrusion Detection System (IDS) remains an open challenge to the research community. Continuous efforts by the researchers have resulted in the development of several learning models based on Artificial Neural Network (ANN) to improve the performance of the IDSs. However, there exists a tradeoff with respect to the stability of ANN architecture and the detection rate for less frequent attacks. This paper presents a novel approach based on Helly property of Hypergraph and Arithmetic Residue-based Probabilistic Neural Network (HG AR-PNN) to address the classification problem in IDS...
February 17, 2017: Neural Networks: the Official Journal of the International Neural Network Society
https://www.readbyqxmd.com/read/28339747/deep-learning-for-pharmacovigilance-recurrent-neural-network-architectures-for-labeling-adverse-drug-reactions-in-twitter-posts
#3
Anne Cocos, Alexander G Fiks, Aaron J Masino
Objective: Social media is an important pharmacovigilance data source for adverse drug reaction (ADR) identification. Human review of social media data is infeasible due to data quantity, thus natural language processing techniques are necessary. Social media includes informal vocabulary and irregular grammar, which challenge natural language processing methods. Our objective is to develop a scalable, deep-learning approach that exceeds state-of-the-art ADR detection performance in social media...
February 22, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/28339176/identification-of-likely-associations-between-cerebral-folate-deficiency-and-complex-genetic-and-metabolic-pathogenesis-of-autism-spectrum-disorders-by-utilization-of-a-pilot-interaction-modeling-approach
#4
Daniel Krsička, Jan Geryk, Markéta Vlčková, Markéta Havlovicová, Milan Macek, Radka Pourová
Recently, cerebral folate deficiency (CFD) was suggested to be involved in the pathogenesis of autism spectrum disorders (ASD). However, the exact role of folate metabolism in the pathogenesis of ASD, identification of underlying pathogenic mechanisms and impaired metabolic pathways remain unexplained. The aim of our study was to develop and test a novel, unbiased, bioinformatics approach in order to identify links between ASD and disturbed cerebral metabolism by focusing on abnormal folate metabolism, which could foster patient stratification and novel therapeutic interventions...
March 24, 2017: Autism Research: Official Journal of the International Society for Autism Research
https://www.readbyqxmd.com/read/28339085/integrated-analysis-of-mrna-and-mirna-expression-profiles-in-pancreatic-ductal-adenocarcinoma
#5
Hongwei Sun, Liang Zhao, Kehua Pan, Zhao Zhang, Mengtao Zhou, Guoquan Cao
In the present study, to investigate the potential molecular mechanism of pancreatic ductal adenocarcinoma (PDAC), mRNA and miRNA expression profiles were integrated for systematic analysis. Results showed that a total of 76 common differentially expressed genes (DEGs) were identified from 2 mRNA expression profiles that contained 39 tumor and 15 normal samples. Notably, the tumor and normal samples were able to be clearly classified into 4 groups based on the DEGs. mRNA‑miRNA regulation network analysis indicated that 22 out of the 76 DEGs including MUC4, RRM2 and CCL2 are regulated by 5 reported miRNAs...
March 24, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28339073/identification-of-proteins-in-the-aqueous-humor-associated-with-cataract-development-using-itraq-methodology
#6
Minhong Xiang, Xingru Zhang, Qingsong Li, Hanmin Wang, Zhenyong Zhang, Zhumei Han, Meiqing Ke, Xingxing Chen
Proteins in the aqueous humor (AH) are important in the induction of cataract development. The identification of cataract-associated proteins assists in identifying patients and predisposed to the condition and improve treatment efficacy. Proteomics analysis has previously been used for identifying protein markers associated with eye diseases; however, few studies have examined the proteomic alterations in cataract development due to high myopia, glaucoma and diabetes. The present study, using the isobaric tagging for relative and absolute protein quantification methodology, aimed to examine cataract-associated proteins in the AH from patients with high myopia, glaucoma or diabetes, and controls...
March 21, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28338718/identification-and-characterization-of-gra6-gra7-of-neospora-caninum-in-mdbk-cells
#7
Jingquan Dong, Jianhua Li, Jinpeng Wang, Fei Li, Ju Yang, Pengtao Gong, He Li, Xichen Zhang
Neospora caninum, an apicomplexan parasite, is recognized as a major bovine abortifacient. Dense granule antigens (GRAs) play important roles in the formation and modification of parasitophorous vacuoles (PVs) in Toxoplasma gondii. However, a few studies investigating GRAs have been reported in N. caninum. The aim of the present study was to characterize the dense GRA6/GRA7 of N. caninum in PVs using MDBK cells as a host cell model. Neospora caninum was inoculated into MDBK cells, and changes were observed using a transmission electron microscope (TEM)...
February 24, 2017: Acta Biochimica et Biophysica Sinica
https://www.readbyqxmd.com/read/28337212/identification-of-norway-spruce-myb-bhlh-wdr-transcription-factor-complex-members-linked-to-regulation-of-the-flavonoid-pathway
#8
Miguel Nemesio-Gorriz, Peter B Blair, Kerstin Dalman, Almuth Hammerbacher, Jenny Arnerup, Jan Stenlid, Shahid M Mukhtar, Malin Elfstrand
Transcription factors (TFs) forming MYB-bHLH-WDR complexes are known to regulate the biosynthesis of specialized metabolites in angiosperms through an intricate network. These specialized metabolites participate in a wide range of biological processes including plant growth, development, reproduction as well as in plant immunity. Studying the regulation of their biosynthesis is thus essential. While MYB (TFs) have been previously shown to control specialized metabolism (SM) in gymnosperms, the identity of their partners, in particular bHLH or WDR members, has not yet been revealed...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28335718/rnav-2-0-a-visualization-tool-for-bacterial-srna-mediated-regulatory-networks-mining
#9
Romain Bourqui, Isabelle Dutour, Jonathan Dubois, William Benchimol, Patricia Thébault
BACKGROUND: Bacterial sRNA-mediated regulatory networks has been introduced as a powerful way to analyze the fast rewiring capabilities of a bacteria in response to changing environmental conditions. The identification of mRNA targets of bacterial sRNAs is essential to investigate their functional activities. However, this step remains challenging with the lack of knowledge of the topological and biological constraints behind the formation of sRNA-mRNA duplexes. Even with the most sophisticated bioinformatics target prediction tools, the large proportion of false predictions may be prohibitive for further analyses...
March 23, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28334753/alcohol-screening-among-young-people-a-prospective-study-from-the-swiss-sentinel-surveillance-system-sentinella-of-physicians-a-priori-opinions
#10
Coralie Wenger-Bonny, Adjua Alexandra N'goran, Jérôme Pasquier, Charles Dvorak, Dagmar M Haller, Lilli Herzig
Background.: Systematic screening for excessive alcohol use among young people is recommended but rarely implemented. Family practitioners tend to select patients for screening, based on their preliminary subjective opinions, which may be biased. Objective.: To evaluate the ability of family practitioners to identify excessive alcohol use among young people prior to screening them. Methods.: This prospective study was conducted through Sentinella, an epidemiological network involving 150 family practitioners across Switzerland...
February 22, 2017: Family Practice
https://www.readbyqxmd.com/read/28334063/what-role-does-elongation-play-in-tool-specific-activation-and-connectivity-in-the-dorsal-and-ventral-visual-streams
#11
Juan Chen, Jacqueline C Snow, Jody C Culham, Melvyn A Goodale
Images of tools induce stronger activation than images of nontools in a left-lateralized network that includes ventral-stream areas implicated in tool identification and dorsal-stream areas implicated in tool manipulation. Importantly, however, graspable tools tend to be elongated rather than stubby, and so the tool-selective responses in some of these areas may, to some extent, reflect sensitivity to elongation rather than "toolness" per se. Using functional magnetic resonance imaging, we investigated the role of elongation in driving tool-specific activation in the 2 streams and their interconnections...
March 18, 2017: Cerebral Cortex
https://www.readbyqxmd.com/read/28333986/building-the-road-to-a-regional-zoonoses-strategy-a-survey-of-zoonoses-programmes-in-the-americas
#12
Melody J Maxwell, Mary H Freire de Carvalho, Armando E Hoet, Marco A N Vigilato, Julio C Pompei, Ottorino Cosivi, Victor J Del Rio Vilas
BACKGROUND: In recent years, global public health security has been threatened by zoonotic disease emergence as exemplified by outbreaks of H5N1 and H1N1 influenza, SARS, and most recently Ebola and Zika. Additionally, endemic zoonoses, such as rabies, burden countries year after year, placing demands on limited finances and personnel. To survey the baseline status of the emerging and endemic zoonoses programmes of the Latin American and the Caribbean (LAC) countries, the Pan American Health Organization (PAHO) conducted a survey of priority emerging and endemic zoonoses, countries´ prioritization criteria and methodologies, and suggestions to strengthen countries capacities and regional approaches to zoonoses control...
2017: PloS One
https://www.readbyqxmd.com/read/28331816/inhibition-of-fat-cell-differentiation-in-3t3-l1-pre-adipocytes-by-all-trans-retinoic-acid-integrative-analysis-of-transcriptomic-and-phenotypic-data
#13
Katharina Stoecker, Steffen Sass, Fabian J Theis, Hans Hauner, Michael W Pfaffl
The process of adipogenesis is controlled in a highly orchestrated manner, including transcriptional and post-transcriptional events. In developing 3T3-L1 pre-adipocytes, this program can be interrupted by all-trans retinoic acid (ATRA). To examine this inhibiting impact by ATRA, we generated large-scale transcriptomic data on the microRNA and mRNA level. Non-coding RNAs such as microRNAs represent a field in RNA turnover, which is very important for understanding the regulation of mRNA gene expression. High throughput mRNA and microRNA expression profiling was performed using mRNA hybridisation microarray technology and multiplexed expression assay for microRNA quantification...
March 2017: Biomolecular Detection and Quantification
https://www.readbyqxmd.com/read/28328971/mapping-the-n-linked-glycosites-of-rice-oryza-sativa-l-germinating-embryos
#14
Jiezheng Ying, Juan Zhao, Yuxuan Hou, Yifeng Wang, Jiehua Qiu, Zhiyong Li, Xiaohong Tong, Zhaomei Shi, Jun Zhu, Jian Zhang
Germination is a key event in the angiosperm life cycle. N-glycosylation of proteins is one of the most common post-translational modifications, and has been recognized to be an important regulator of the proteome of the germinating embryo. Here, we report the first N-linked glycosites mapping of rice embryos during germination by using a hydrophilic interaction chromatography (HILIC) glycopeptides enrichment strategy associated with high accuracy mass spectrometry identification. A total of 242 glycosites from 191 unique proteins was discovered...
2017: PloS One
https://www.readbyqxmd.com/read/28327601/bcip-a-gene-centered-platform-for-identifying-potential-regulatory-genes-in-breast-cancer
#15
Jiaqi Wu, Shuofeng Hu, Yaowen Chen, Zongcheng Li, Jian Zhang, Hanyu Yuan, Qiang Shi, Ningsheng Shao, Xiaomin Ying
Breast cancer is a disease with high heterogeneity. Many issues on tumorigenesis and progression are still elusive. It is critical to identify genes that play important roles in the progression of tumors, especially for tumors with poor prognosis such as basal-like breast cancer and tumors in very young women. To facilitate the identification of potential regulatory or driver genes, we present the Breast Cancer Integrative Platform (BCIP, http://omics.bmi.ac.cn/bcancer/). BCIP maintains multi-omics data selected with strict quality control and processed with uniform normalization methods, including gene expression profiles from 9,005 tumor and 376 normal tissue samples, copy number variation information from 3,035 tumor samples, microRNA-target interactions, co-expressed genes, KEGG pathways, and mammary tissue-specific gene functional networks...
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28327092/metax-a-flexible-and-comprehensive-software-for-processing-metabolomics-data
#16
Bo Wen, Zhanlong Mei, Chunwei Zeng, Siqi Liu
BACKGROUND: Non-targeted metabolomics based on mass spectrometry enables high-throughput profiling of the metabolites in a biological sample. The large amount of data generated from mass spectrometry requires intensive computational processing for annotation of mass spectra and identification of metabolites. Computational analysis tools that are fully integrated with multiple functions and are easily operated by users who lack extensive knowledge in programing are needed in this research field...
March 21, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28325001/reliability-of-a-cortical-surface-based-analysis-with-subcortical-regression-in-the-identification-of-resting-state-functional-networks
#17
R Lopes, P Besson, R Viard, C Bournonville, C Delmaire, X Leclerc
Many methods exist for identifying brain networks in resting-state functional magnetic resonance imaging. During the last decade, there was a growing interest in functional connectivity using surface-based analysis. However, the advantages of this approach against volume-based analysis in a data-driven model are unclear. In this study, we propose an independent component analysis based method to extract the resting-state networks directly on the cortical surface. The components associated with the subcortical regions are identified by multiple linear regressions between the signals in subcortical voxels and independent components time courses...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28323865/the-microrna-302b-inhibited-insulin-like-growth-factor-binding-protein-2-signaling-pathway-induces-glioma-cell-apoptosis-by-targeting-nuclear-factor-ia
#18
Chin-Cheng Lee, Peng-Hsu Chen, Kuo-Hao Ho, Chwen-Ming Shih, Chia-Hsiung Cheng, Cheng-Wei Lin, Kur-Ta Cheng, Ann-Jeng Liu, Ku-Chung Chen
MicroRNAs are small noncoding RNAs that post-transcriptionally control the expression of genes involved in glioblastoma multiforme (GBM) development. Although miR-302b functions as a tumor suppressor, its role in GBM is still unclear. Therefore, this study comprehensively explored the roles of miR-302b-mediated gene networks in GBM cell death. We found that miR-302b levels were significantly higher in primary astrocytes than in GBM cell lines. miR-302b overexpression dose dependently reduced U87-MG cell viability and induced apoptosis through caspase-3 activation and poly(ADP ribose) polymerase degradation...
2017: PloS One
https://www.readbyqxmd.com/read/28323150/systematic-expression-profiling-analysis-mines-dys-regulated-modules-in-active-tuberculosis-based-on-re-weighted-protein-protein-interaction-network-and-attract-algorithm
#19
Ying Sun, Yan Weng, Ying Zhang, Xiang Yan, Lei Guo, Jia Wang, Xin Song, Ying Yuan, Fu-Ye Chang, Chun-Ling Wang
About 90% of tuberculosis (TB) patients latently infected with Mycobacterium tuberculosis (Mtb) show no symptoms, yet have a 10% chance in lifetime to progress active TB. Nevertheless, current diagnosis approaches need improvement in efficiency and sensitivity. The objective of this work was to detect potential signatures for active TB to further improve the understanding of the biological roles of functional modules involved in this disease. First, targeted networks of active TB and control groups were established via re-weighting protein-protein interaction (PPI) networks using Pearson's correlation coefficient (PCC)...
March 18, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/28323125/minocycline-hepatotoxicity-clinical-characterization-and-identification-of-hla-b%C3%A2-35-02-as-a-risk-factor
#20
Thomas Jacob Urban, Paola Nicoletti, Naga Chalasani, Jose Serrano, Andrew Stolz, Ann Daly, Guruprasad Aithal, John Dillon, Victor Navarro, Joseph Odin, Huiman Barnhart, David Ostrov, Nanye Long, Elizabeth Theresa Cirulli, Paul Brent Watkins, Robert John Fontana
BACKGROUND & AIMS: Minocycline hepatotoxicity can present with prominent autoimmune features in previously healthy individuals. The aim of this study was to identify genetic determinants of minocycline DILI in a well-phenotyped cohort of patients. METHODS: Caucasian patients with minocycline DILI underwent genome-wide genotyping and were compared to unexposed population controls. Human leukocyte antigen (HLA) binding of minocycline was assessed using AutoDock Vina...
March 17, 2017: Journal of Hepatology
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