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https://www.readbyqxmd.com/read/27913756/the-short-term-efficacy-of-vena-cava-filters-for-the-prevention-of-pulmonary-embolism-in-patients-with-venous-thromboembolism-receiving-anticoagulation-meta-analysis-of-randomized-controlled-trials
#1
Jun Jiang, Yuanyong Jiao, Xiwei Zhang
OBJECTIVES: To perform a meta-analysis of randomized controlled trials assessing the effectiveness of inferior vena cava filters in patients with deep vein thrombosis for preventing pulmonary embolism. METHOD: Relevant randomized controlled trials of inferior vena cava filters for the prevention of pulmonary embolism were identified by searching electronic databases updated in February 2016. Relative risks of recurrent pulmonary embolism, recurrent deep vein thrombosis, and mortality at three months were analyzed...
December 2, 2016: Phlebology
https://www.readbyqxmd.com/read/27913255/using-the-bitola-system-to-identify-candidate-molecules-in-the-interaction-between-oral-lichen-planus-and-depression
#2
Yuanbo Zhan, Shuang Zhou, Ying Li, Sen Mu, Xuejing Song, Feng Lin, Ruimin Zhang, Bin Zhang
Exacerbations of oral lichen planus (OLP) have been linked to the periods of psychological stress, anxiety and depression. The specific mechanism of the interaction is unclear. The aim of this study was to explore the candidate genes or molecules that play important roles in the interaction between OLP and depression. The BITOLA system was used to search all intermediate concepts relevant to the "Gene or Gene Product" for OLP and depression, and the gene expression data and tissue-specific gene data along with manual checking were then employed to filter the intermediate concepts...
November 29, 2016: Behavioural Brain Research
https://www.readbyqxmd.com/read/27910970/exploration-of-hydrogen-bond-networks-and-potential-energy-surfaces-of-methanol-clusters-using-a-two-stage-clustering-algorithm
#3
Po-Jen Hsu, Kun-Lin Ho, Sheng-Hsien Lin, Jer-Lai Kuo
The potential energy surface (PES), structures and thermal properties of methanol clusters (MeOH)n with n = 8-15 were explored by replica-exchange molecular dynamics (REMD) simulations with an empirical model and refined using density functional theory (DFT) methods. For a given size, local minima structures were sampled from REMD trajectories and archived by a newly developed molecular database via a two-stage clustering algorithm (TSCA). Our TSCA utilizes both the topology of O-HO hydrogen bonding networks and the similarity of the shapes to filter out duplicates...
December 2, 2016: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/27903464/a-peptide-retrieval-strategy-enables-significant-improvement-of-quantitative-performance-without-compromising-confidence-of-identification
#4
Chengjian Tu, Shichen Shen, Quanhu Sheng, Yu Shyr, Jun Qu
: Reliable quantification of low-abundance proteins in complex proteomes is challenging largely owing to the limited number of spectra/peptides identified. In this study we developed a straightforward method to improve the quantitative accuracy and precision of proteins by strategically retrieving the less confident peptides that were previously filtered out using the standard target-decoy search strategy. The filtered-out MS/MS spectra matched to confidently-identified proteins were recovered, and the peptide-spectrum-match FDR were re-calculated and controlled at a confident level of FDR≤1%, while protein FDR maintained at ~1%...
November 26, 2016: Journal of Proteomics
https://www.readbyqxmd.com/read/27899677/the-mouse-gene-expression-database-gxd-2017-update
#5
Jacqueline H Finger, Constance M Smith, Terry F Hayamizu, Ingeborg J McCright, Jingxia Xu, Meiyee Law, David R Shaw, Richard M Baldarelli, Jon S Beal, Olin Blodgett, Jeff W Campbell, Lori E Corbani, Jill R Lewis, Kim L Forthofer, Pete J Frost, Sharon C Giannatto, Lucie N Hutchins, Dave B Miers, Howie Motenko, Kevin R Stone, Janan T Eppig, James A Kadin, Joel E Richardson, Martin Ringwald
The Gene Expression Database (GXD; www.informatics.jax.org/expression.shtml) is an extensive and well-curated community resource of mouse developmental expression information. Through curation of the scientific literature and by collaborations with large-scale expression projects, GXD collects and integrates data from RNA in situ hybridization, immunohistochemistry, RT-PCR, northern blot and western blot experiments. Expression data from both wild-type and mutant mice are included. The expression data are combined with genetic and phenotypic data in Mouse Genome Informatics (MGI) and made readily accessible to many types of database searches...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899614/suba4-the-interactive-data-analysis-centre-for-arabidopsis-subcellular-protein-locations
#6
Cornelia M Hooper, Ian R Castleden, Sandra K Tanz, Nader Aryamanesh, A Harvey Millar
The SUBcellular location database for Arabidopsis proteins (SUBA4, http://suba.live) is a comprehensive collection of manually curated published data sets of large-scale subcellular proteomics, fluorescent protein visualization, protein-protein interaction (PPI) as well as subcellular targeting calls from 22 prediction programs. SUBA4 contains an additional 35 568 localizations totalling more than 60 000 experimental protein location claims as well as 37 new suborganellar localization categories. The experimental PPI data has been expanded to 26 327 PPI pairs including 856 PPI localizations from experimental fluorescent visualizations...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899575/ensembl-2017
#7
Bronwen L Aken, Premanand Achuthan, Wasiu Akanni, M Ridwan Amode, Friederike Bernsdorff, Jyothish Bhai, Konstantinos Billis, Denise Carvalho-Silva, Carla Cummins, Peter Clapham, Laurent Gil, Carlos García Girón, Leo Gordon, Thibaut Hourlier, Sarah E Hunt, Sophie H Janacek, Thomas Juettemann, Stephen Keenan, Matthew R Laird, Ilias Lavidas, Thomas Maurel, William McLaren, Benjamin Moore, Daniel N Murphy, Rishi Nag, Victoria Newman, Michael Nuhn, Chuang Kee Ong, Anne Parker, Mateus Patricio, Harpreet Singh Riat, Daniel Sheppard, Helen Sparrow, Kieron Taylor, Anja Thormann, Alessandro Vullo, Brandon Walts, Steven P Wilder, Amonida Zadissa, Myrto Kostadima, Fergal J Martin, Matthieu Muffato, Emily Perry, Magali Ruffier, Daniel M Staines, Stephen J Trevanion, Fiona Cunningham, Andrew Yates, Daniel R Zerbino, Paul Flicek
Ensembl (www.ensembl.org) is a database and genome browser for enabling research on vertebrate genomes. We import, analyse, curate and integrate a diverse collection of large-scale reference data to create a more comprehensive view of genome biology than would be possible from any individual dataset. Our extensive data resources include evidence-based gene and regulatory region annotation, genome variation and gene trees. An accompanying suite of tools, infrastructure and programmatic access methods ensure uniform data analysis and distribution for all supported species...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27898627/publishing-trends-in-the-field-of-pediatric-emergency-medicine-from-2004-to-2013
#8
Nancy S Rixe, Jeffrey Rixe, Joshua Glick, Erik Lehman, Robert P Olympia
OBJECTIVE: To identify publishing trends within the field of pediatric emergency medicine between 2004 and 2013. METHODS: We conducted a MEDLINE search of pediatric emergency medicine articles, filtered by clinical trial, published between 2004 and 2013 in ten journals from the fields of pediatrics, emergency medicine, general medicine, and pediatric emergency medicine. Each article was classified by journal type, study design, results (positive or negative/equivocal), age/type of subjects, and major topic (based on the objective of the study)...
December 2016: Pediatric Emergency Care
https://www.readbyqxmd.com/read/27897151/effect-of-intermittent-hypoxic-training-on-hypoxia-tolerance-based-on-brain-functional-connectivity
#9
Guang Li, Tinglin Zhang, Xiaojian Chen, Chungang Shang, You Wang
The difference of brain functional connectivity between hypoxic and normal states was studied. The impact of intermittent hypoxic training on the hypoxia tolerance of the brain was explored. Multivariable empirical mode decomposition was applied to extract common inherent modes of multichannel EEG adaptively instead of a priori selection of filter bandwidth, and the first two scales of intrinsic mode functions expressed the differences in brain connectivity. To quantify synchronization and search for consistent performance, coherence, phase locking value and synchronization likelihood were all utilized...
November 29, 2016: Physiological Measurement
https://www.readbyqxmd.com/read/27893379/blasst-band-limited-atomic-sampling-with-spectral-tuning-with-applications-to-utility-line-noise-filtering
#10
Kenneth R Ball, W David Hairston, Piotr J Franaszczuk, Kay A Robbins
OBJECTIVE: In this paper we present and test a new method for the identification and removal of non-stationary utility line noise from biomedical signals. METHODS: The method, Band Limited Atomic Sampling with Spectral Tuning (BLASST), is an iterative approach that is designed to (1) fit non-stationarities in line noise by searching for best-fit Gabor atoms at predetermined time points, (2) self-modulate its fit by leveraging information from frequencies surrounding the target frequency, and (3) terminate based on a convergence criterion obtained from the same surrounding frequencies...
November 23, 2016: IEEE Transactions on Bio-medical Engineering
https://www.readbyqxmd.com/read/27881112/photoprotective-potential-in-some-medicinal-plants-used-to-treat-skin-diseases-in-sri-lanka
#11
Mayuri Tharanga Napagoda, Benthota Malavi Arachchige Shamila Malkanthi, Subasinghe Appuhamillage Kaumudi Abayawardana, Mohomed Mallique Qader, Lalith Jayasinghe
BACKGROUND: The constant exposure to solar ultraviolet radiation (UV) has a variety of harmful effects on human health. Although synthetic sunscreen products have been introduced as a preventive/therapeutic strategy, with the realization of their adverse side effects, the recent trend is to search for human friendly alternative formulations especially of plant origin. Therefore, the present study focuses on evaluation of photoprotective activity of aqueous extracts (1 mg/ml) of eleven medicinal plants in Sri Lanka that have been widely employed in traditional medicine as treatment options for various skin diseases and to improve the complexion...
November 24, 2016: BMC Complementary and Alternative Medicine
https://www.readbyqxmd.com/read/27871726/identification-and-determination-of-chlorinated-azoles-in-sludge-using-liquid-chromatography-quadrupole-time-of-flight-and-triple-quadrupole-mass-spectrometry-platforms
#12
G Castro, M Roca, I Rodríguez, M Ramil, R Cela
Four antimycotic drugs (tioconazole, TCZ; sertaconazole, STZ; fenticonazole, FTZ and itraconazole, ITZ) and the fungicide imazalil (IMZ) are determined in sludge from sewage treatment plants (STPs) following a bottom-up analytical strategy. First, sludge extracts, obtained under different sample preparation conditions, were analyzed by liquid chromatography (LC) quadrupole time-of-flight (QTOF) mass spectrometry (MS). A non-target search strategy, combined with the use of the chlorine mass filter, permitted to detect several chlorinated pollutants including the above referred azoles, which either had not been previously reported (TCZ, STZ, FTZ and ITZ), or scarcely investigated (IMZ), in this environmental compartment...
December 9, 2016: Journal of Chromatography. A
https://www.readbyqxmd.com/read/27866497/neurodevelopmental-outcomes-in-infants-exposed-in-utero-to-antipsychotics-a-systematic-review-of-published-data
#13
Salvatore Gentile, Maria Luigia Fusco
The proportion of pregnancies exposed to either second-generation antipsychotics (SGAs) or first-generation antipsychotics (FGAs) varies between 0.3%-2% of all pregnancies, but, until now, little is known about the potential neurobehavioral teratogenicity of antipsychotics. Assessing this safety facet is the aim of this article. PubMed, Scopus, and Google Scholar were searched for eligible articles. PubMed (1954 to May 2016) was searched using several medical subject headings, variously combined. PubMed search results were also limited using the search filter for human studies published in English...
November 21, 2016: CNS Spectrums
https://www.readbyqxmd.com/read/27865782/application-of-nano-lc-maldi-tof-tof-ms-for-proteomic-analysis-of-microvesicles
#14
Joanna Kasprzyk, Ewa Stępień, Wojciech Piekoszewski
Activated platelets and platelet derived microvesicles (PMVs) emerged recently to be promising biomarkers. There is no universal procedure to carry out the proteomic analysis on microvesicles. In this study we proposed a nano-liquid chromatography (nano-LC) technique coupled off-line with a spectrometric measurement MALDI-TOF-MS/MS as a throughput and time-saving procedure. In this study we developed a simplified method to evaluate the protein composition of platelet organelles and PMVs. Platelet-rich plasma (PRP) was collected from healthy donors...
November 16, 2016: Clinical Biochemistry
https://www.readbyqxmd.com/read/27855179/analysis-of-web-spam-for-non-english-content-toward-more-effective-language-based-classifiers
#15
Mansour Alsaleh, Abdulrahman Alarifi
Web spammers aim to obtain higher ranks for their web pages by including spam contents that deceive search engines in order to include their pages in search results even when they are not related to the search terms. Search engines continue to develop new web spam detection mechanisms, but spammers also aim to improve their tools to evade detection. In this study, we first explore the effect of the page language on spam detection features and we demonstrate how the best set of detection features varies according to the page language...
2016: PloS One
https://www.readbyqxmd.com/read/27853484/filtered-circular-fingerprints-improve-either-prediction-or-runtime-performance-while-retaining-interpretability
#16
Martin Gütlein, Stefan Kramer
BACKGROUND: Even though circular fingerprints have been first introduced more than 50 years ago, they are still widely used for building highly predictive, state-of-the-art (Q)SAR models. Historically, these structural fragments were designed to search large molecular databases. Hence, to derive a compact representation, circular fingerprint fragments are often folded to comparatively short bit-strings. However, folding fingerprints introduces bit collisions, and therefore adds noise to the encoded structural information and removes its interpretability...
2016: Journal of Cheminformatics
https://www.readbyqxmd.com/read/27848076/identifying-gene-gene-interactions-that-are-highly-associated-with-four-quantitative-lipid-traits-across-multiple-cohorts
#17
Rishika De, Shefali S Verma, Emily Holzinger, Molly Hall, Amber Burt, David S Carrell, David R Crosslin, Gail P Jarvik, Helena Kuivaniemi, Iftikhar J Kullo, Leslie A Lange, Matthew B Lanktree, Eric B Larson, Kari E North, Alex P Reiner, Vinicius Tragante, Gerard Tromp, James G Wilson, Folkert W Asselbergs, Fotios Drenos, Jason H Moore, Marylyn D Ritchie, Brendan Keating, Diane Gilbert-Diamond
Genetic loci explain only 25-30 % of the heritability observed in plasma lipid traits. Epistasis, or gene-gene interactions may contribute to a portion of this missing heritability. Using the genetic data from five NHLBI cohorts of 24,837 individuals, we combined the use of the quantitative multifactor dimensionality reduction (QMDR) algorithm with two SNP-filtering methods to exhaustively search for SNP-SNP interactions that are associated with HDL cholesterol (HDL-C), LDL cholesterol (LDL-C), total cholesterol (TC) and triglycerides (TG)...
November 15, 2016: Human Genetics
https://www.readbyqxmd.com/read/27835957/leaf-transcriptome-of-two-highly-divergent-genotypes-of-urochloa-humidicola-poaceae-a-tropical-polyploid-forage-grass-adapted-to-acidic-soils-and-temporary-flooding-areas
#18
Bianca Baccili Zanotto Vigna, Fernanda Ancelmo de Oliveira, Guilherme de Toledo-Silva, Carla Cristina da Silva, Cacilda Borges do Valle, Anete Pereira de Souza
BACKGROUND: Urochloa humidicola (Koronivia grass) is a polyploid (6x to 9x) species that is used as forage in the tropics. Facultative apospory apomixis is present in most of the genotypes of this species, although one individual has been described as sexual. Molecular studies have been restricted to molecular marker approaches for genetic diversity estimations and linkage map construction. The objectives of the present study were to describe and compare the leaf transcriptome of two important genotypes that are highly divergent in terms of their phenotypes and reproduction modes: the sexual BH031 and the aposporous apomictic cultivar BRS Tupi...
November 11, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27834134/elucidation-of-antiangiogenic-potential-of-vitexin-obtained-from-cucumis-sativus-targeting-hsp90-protein-a-novel-multipathway-targeted-approach-to-restrain-angiogenic-phenomena
#19
Neha Sharma, Salman Akhtar, Qazi M Sajid Jamal, Mohammad A Kamal, M Kalim A Khan, M Haris Siddiqui, Usman Sayeed
BACKGROUND: Angiogenesis involves the process of sprouting of microvessels from preexisting microvasculature and is held responsible for the growth, malignancy and metastasis of cancer. Heat shock protein Hsp90 has been proven responsible for indirectly inducing multiple pathways leading to angiogenesis and metastasis in cancer. Recent researches shift towards proposing novel phytochemicals as possible antiangiogenic agents. OBJECTIVE: The study aims towards Virtual screening of compounds from Cucurbitaceae family and their Druglikeliness and PreADMET filtering in search of potent lead as Vitexin, targeting Hsp90 and hence restraining angiogenesis...
November 11, 2016: Medicinal Chemistry
https://www.readbyqxmd.com/read/27832110/systematic-design-of-a-metal-ion-biosensor-a-multi-objective-optimization-approach
#20
Chih-Yuan Hsu, Bor-Sen Chen
With the recent industrial expansion, heavy metals and other pollutants have increasingly contaminated our living surroundings. Heavy metals, being non-degradable, tend to accumulate in the food chain, resulting in potentially damaging toxicity to organisms. Thus, techniques to detect metal ions have gradually begun to receive attention. Recent progress in research on synthetic biology offers an alternative means for metal ion detection via the help of promoter elements derived from microorganisms. To make the design easier, it is necessary to develop a systemic design method for evaluating and selecting adequate components to achieve a desired detection performance...
2016: PloS One
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