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Selection probability

Sanja Dacic, Liza C Villaruz, Shira Abberbock, Alyssa Mahaffey, Pimpin Incharoen, Marina N Nikiforova
Break-apart ALK FISH probe is the FDA approved approach for detection of ALK rearrangements in lung carcinoma patients who may benefit from ALK kinase inhibitors. The FISH assay can be technically challenging and difficult to interpret. ALK immunohistochemistry and next generation sequencing have been proposed as alternative approaches. In this study, we compared various ALK -FISH patterns to next -generation sequencing (NGS) for gene fusion detection, ALK immunohistochemistry (IHC) and tumor responses to crizotinib...
October 17, 2016: Oncotarget
Wen Yea Hwong, Michiel L Bots, Sharmini Selvarajah, L Jaap Kappelle, Zariah Abdul Aziz, Norsima Nazifah Sidek, Ilonca Vaartjes
BACKGROUND: A shortage of computed tomographic (CT) machines in low and middle income countries often results in delayed CT imaging for patients suspected of a stroke. Yet, time constraint is one of the most important aspects for patients with an ischemic stroke to benefit from thrombolytic therapy. We set out to assess whether application of the Siriraj Stroke Score is able to assist physicians in prioritizing patients with a high probability of having an ischemic stroke for urgent CT imaging...
2016: PloS One
Ashleigh A McGirr, Kevin L Schwartz, Upton Allen, Melinda Solomon, Beate Sander
Background Children with cystic fibrosis (CF) are at higher risk of severe respiratory syncytial virus (RSV) infection, which can lead to a decline in lung function. A monoclonal antibody, palivizumab (PMB), effectively prevents RSV hospitalizations; however, the high cost of PMB, approximately C$10,000 per patient per RSV season, limits its widespread use. We assess the cost-effectiveness of PMB prophylaxis in CF children less than 2 years of age from the Canadian healthcare payer's perspective. Methods In 2014, a Markov cohort model of CF disease and infant RSV infections in the Canadian setting was developed based on literature data...
October 21, 2016: Human Vaccines & Immunotherapeutics
Rui Seixas, Tânia Raquel Santos, Jorge Machado, Luís Tavares, Fernando Bernardo, Teresa Semedo-Lemsaddek, Manuela Oliveira
The increase in prevalence of Salmonella 1,4,[5],12:i:- related infections over the last few years has been considered a public health issue in many European countries, especially as this serovar may be associated with tetraresistance to ampicillin, streptomycin, sulfonamides, and tetracyclines (R-type ASSuT). Salmonella 1,4,[5],12:i:- isolates (n = 187) obtained by the Portuguese National Laboratory from different sources, including human clinical cases (n = 170), veterinary (n = 10), environmental (n = 6), and food samples (n = 1), were collected from 15 districts between 2006 and 2011...
October 21, 2016: Foodborne Pathogens and Disease
Glenn Yiu, Eric Tieu, Anthony T Nguyen, Brittany Wong, Zeljka Smit-McBride
Purpose: To employ type II clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 endonuclease to suppress ocular angiogenesis by genomic disruption of VEGF-A in human RPE cells. Methods: CRISPR sequences targeting exon 1 of human VEGF-A were computationally identified based on predicted Cas9 on- and off-target probabilities. Single guide RNA (gRNA) cassettes with these target sequences were cloned into lentiviral vectors encoding the Streptococcuspyogenes Cas9 endonuclease (SpCas9) gene...
October 1, 2016: Investigative Ophthalmology & Visual Science
Donald J Viglione, Luciano Giromini, Patricia Landis
This article describes the development of the Inventory of Problems-29 (IOP-29), a new, short, paper-and-pencil, self-administered measure of feigned mental and cognitive disorders. Four clinical comparison simulation studies were conducted. Study 1 (n = 451) selected the items and produced an index of potential feigning. Study 2 (n = 331) scaled this index to produce a probability score, and examined its psychometric properties. Study 3 tested the generalizability of Study 2's findings with 2 additional samples (ns = 128 and 90)...
October 21, 2016: Journal of Personality Assessment
Yanling Zhang, Aizhi Liu, Changyin Sun
For large quantities of spatial models, the multi-strategy selection under weak selection is the sum of two competition terms: the pairwise competition and the competition of multiple strategies with equal frequency. Two parameters σ1 and σ2 quantify the dependence of the multi-strategy selection on these two terms, respectively. Unlike previous studies, we here do not require large populations for calculating σ1 and σ2, and perform the first quantitative analysis of the effect of migration on them in group-structured populations of any finite sizes...
October 21, 2016: Scientific Reports
Magali Ranchou-Peyruse, Cyrielle Gasc, Marion Guignard, Thomas Aüllo, David Dequidt, Pierre Peyret, Anthony Ranchou-Peyruse
The formation water of a deep aquifer (853 m of depth) used for geological storage of natural gas was sampled to assess the mono-aromatic hydrocarbons attenuation potential of the indigenous microbiota. The study of bacterial diversity suggests that Firmicutes and, in particular, sulphate-reducing bacteria (Peptococcaceae) predominate in this microbial community. The capacity of the microbial community to biodegrade toluene and m- and p-xylenes was demonstrated using a culture-based approach after several hundred days of incubation...
October 21, 2016: Microbial Biotechnology
Huifang Yin, Michael R Phillips, Klaas J Wardenaar, Guangming Xu, Johan Ormel, Hongjun Tian, Robert A Schoevers
Mental health in China is of growing concern to both policy-makers and researchers. The Tianjin Mental Health Survey (TJMHS) was conducted between July 2011 and March 2012 to assess the prevalence and risk factors of mental disorders in the context of recent economic growth and other socio-demographic changes in Tianjin, a municipality of 13 million on China's eastern seaboard. A multistage cluster random sample selected using probability proportionate to size methods participated in a two-phase screening procedure: 11,748 subjects 18 or older were screened for risk of psychopathology and then an enriched risk-proportional subsample of 4,438 subjects was interviewed by psychiatrists using an expanded Chinese version of the Structured Clinical Interview for Diagnostic and Statistical Manual, Fourth Edition (DSM-IV) Axis I disorders (SCID)...
October 21, 2016: International Journal of Methods in Psychiatric Research
Juan L Reig-Valiente, Juan Viruel, Ester Sales, Luis Marqués, Javier Terol, Marta Gut, Sophia Derdak, Manuel Talón, Concha Domingo
BACKGROUND: After its domestication, rice cultivation expanded from tropical regions towards northern latitudes with temperate climate in a progressive process to overcome limiting photoperiod and temperature conditions. This process has originated a wide range of diversity that can be regarded as a valuable resource for crop improvement. In general, current rice breeding programs have to deal with a lack of both germplasm accessions specifically adapted to local agro-environmental conditions and adapted donors carrying desired agronomical traits...
December 2016: Rice
Janina Jamasbi, Remco T A Megens, Mariaelvy Bianchini, Kerstin Uhland, Götz Münch, Martin Ungerer, Shachar Sherman, Alexander Faussner, Richard Brandl, Christine John, Johannes Buchner, Christian Weber, Reinhard Lorenz, Natalie Elia, Wolfgang Siess
To enhance the antithrombotic properties of recombinant glycoprotein VI fragment crystallizable (GPVI-Fc), the authors incubated GPVI-Fc with anti-human Fc antibodies to cross-link the Fc tails of GPVI-Fc. Cross-linking potentiated the inhibition of human plaque- and collagen-induced platelet aggregation by GPVI-Fc under static and flow conditions without increasing bleeding time in vitro. Cross-linking with anti-human-Fc Fab2 was even superior to anti-human-Fc immunoglobulin G (IgG). Advanced optical imaging revealed a continuous sheath-like coverage of collagen fibers by cross-linked GPVI-Fc complexes...
April 2016: JACC. Basic to Translational Science
Maciej Woźny, Bogdan Lewczuk, Natalia Ziółkowska, Piotr Gomułka, Stefan Dobosz, Alicja Łakomiak, Maciej Florczyk, Paweł Brzuzan
To date, there has been no systematic approach comprehensively describing the sequence of pathological changes in fish during prolonged exposure to microcystin-LR (MC-LR). Towards this aim, juvenile whitefish individuals received an intraperitoneal injection with pure MC-LR, and the injection was repeated every week to maintain continuous exposure for 28days. During the exposure period, growth and condition of the fish were assessed based on biometric measurements. Additionally, selected biochemical markers were analysed in the fishes' blood, and their livers were carefully examined for morphological, ultrastructural, and molecular changes...
October 17, 2016: Toxicology and Applied Pharmacology
Jaime I Davila, Numrah M Fadra, Xiaoke Wang, Amber M McDonald, Asha A Nair, Barbara R Crusan, Xianglin Wu, Joseph H Blommel, Jin Jen, Kandelaria M Rumilla, Robert B Jenkins, Umut Aypar, Eric W Klee, Benjamin R Kipp, Kevin C Halling
BACKGROUND: RNA-seq is a well-established method for studying the transcriptome. Popular methods for library preparation in RNA-seq such as Illumina TruSeq® RNA v2 kit use a poly-A pulldown strategy. Such methods can cause loss of coverage at the 5' end of genes, impacting the ability to detect fusions when used on degraded samples. The goal of this study was to quantify the effects RNA degradation has on fusion detection when using poly-A selected mRNA and to identify the variables involved in this process...
October 20, 2016: BMC Genomics
Félix LaRoche-Johnston, Caroline Monat, Benoit Cousineau
BACKGROUND: Group II introns are catalytically active RNA and mobile retroelements present in certain eukaryotic organelles, bacteria and archaea. These ribozymes self-splice from the pre-mRNA of interrupted genes and reinsert within target DNA sequences by retrohoming and retrotransposition. Evolutionary hypotheses place these retromobile elements at the origin of over half the human genome. Nevertheless, the evolution and dissemination of group II introns was found to be quite difficult to infer...
October 20, 2016: BMC Evolutionary Biology
Shehla Akbar, Fazal Subhan, Nasiara Karim, Muhammad Shahid, Nisar Ahmad, Gowhar Ali, Wajahat Mahmood, Khwaja Fawad
BACKGROUND: Diabetic neuropathy is the most prevalent, persistent and debilitating complication of diabetes mellitus often coupled with vulvodynia that may present as an isolated symptom or as a part of constellation of other neuropathic abnormalities. OBJECTIVE: Flavonoids have selective affinity for GABA receptors and 6-methoxyflavanone (6-MeOF) is a positive allosteric modulator of GABA responses at human recombinant GABAA receptors. GABAergic and opioidergic system inhibition have been shown to facilitate neuropathic pain...
October 17, 2016: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
Huong Nguyen, Jerome Vanclay, John Herbohn, Jennifer Firn
There is growing interest in multi-species tropical plantations but little information exists to guide their design and silviculture. The Rainforestation Farming system is the oldest tropical polyculture planting system in the Philippines and provides a unique opportunity to understand the underlying processes affecting tree performance within diverse plantings. Data collected from 85 plots distributed across the 18 mixed-species plantations in the Philippines was used to identify the factors influencing growth, probability of harvest, and death of trees in these complex plantings...
2016: PloS One
Ingo Muegge, Prasenjit Mukherjee
A statistical analysis of 203 high-throughput screens was conducted studying the propensity of small molecules in the Boehringer Ingelheim screening deck to show biological activity after having tested inactive previously in a growing number of screening assays. Dark chemical matter (DCM) compounds, which have been tested and found inactive in 50 or more assays, exhibit hit rates that are comparable to those of compounds tested in much fewer assays. Only compounds tested inactive in 125 or more assays start showing a hit rate deterioration of up to 40% compared to compounds tested in less than 25 assays...
October 20, 2016: Journal of Medicinal Chemistry
L Olmo, K Ashley, J R Young, S Suon, P C Thomson, P A Windsor, R D Bush
This study aimed to identify factors associated with cattle reproductive output in rural smallholder farms in Cambodia in order to determine the main causes of reproductive failure and design efficient interventions for improvement. The majority of the nation's beef is produced on smallholder farms where productivity is constrained by poor animal reproductivity reflected in the recent livestock population decline of approximately 13 % from 2009 to 2013. Farmers (n = 240) from 16 villages from five provinces were surveyed in mid-2015 to determine their baseline knowledge, attitude and practices (KAP) associated with cattle reproduction...
October 19, 2016: Tropical Animal Health and Production
Riccardo Bientinesi, Cesare Mancuso, Maria Martire, Pier Francesco Bassi, Emilio Sacco, Diego Currò
Voltage-gated type 7 K(+) (KV7 or KCNQ) channels regulate the contractility of various smooth muscles. With this study, we aimed to assess the role of KV7 channels in the regulation of human detrusor contractility, as well as the gene and protein expression of KV7 channels in this tissue. For these purposes, the isolated organ technique, RT-qPCR, and Western blot were used, respectively. XE-991, a selective KV7 channel blocker, concentration-dependently contracted the human detrusor; mean EC50 and Emax of XE-991-induced concentration-response curve were 14...
October 19, 2016: Naunyn-Schmiedeberg's Archives of Pharmacology
Séverine Fourdrilis, Patrick Mardulyn, Olivier J Hardy, Kurt Jordaens, António Manuel de Frias Martins, Thierry Backeljau
We report the presence of mitochondrial DNA (mtDNA) hyperdiversity in the marine periwinkle Melarhaphe neritoides (Linnaeus, 1758), the first such case among marine gastropods. Our dataset consisted of concatenated 16S-COI-Cytb gene fragments. We used Bayesian analyses to investigate three putative causes underlying genetic variation, and estimated the mtDNA mutation rate, possible signatures of selection and the effective population size of the species in the Azores archipelago. The mtDNA hyperdiversity in M...
2016: PeerJ
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