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Bias modification

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https://www.readbyqxmd.com/read/28533032/design-and-synthesis-of-an-immobilized-metal-affinity-chromatography-and-metal-oxide-affinity-chromatography-hybrid-material-for-improved-phosphopeptide-enrichment
#1
Da-Song Yang, Xi-Ying Ding, Hong-Ping Min, Bo Li, Meng-Xiang Su, Miao-Miao Niu, Bin Di, Fang Yan
Reversible phosphorylation of proteins is one of the most important post-translational modifications, while the detection of phosphopeptides is difficult due to their low abundance and the signal suppression of nonphosphorylated peptides. Therefore, selective enrichment of phosphopeptides from highly complicated mixtures is vital for MS-based phosphoproteome analysis. Despite various strategies have been developed, there is no single method that is capable of providing full coverage of the whole phosphoproteome...
May 10, 2017: Journal of Chromatography. A
https://www.readbyqxmd.com/read/28531873/randomized-control-trial-investigating-the-efficacy-of-a-computer-based-intolerance-of-uncertainty-intervention
#2
Mary E Oglesby, Nicholas P Allan, Norman B Schmidt
Intolerance of uncertainty (IU) is an important transdiagnostic variable within various anxiety and mood disorders. Theory suggests that individuals high in IU interpret ambiguous information in a more threatening manner. A parallel line of research has shown that interpretive biases can be modified through cognitive training and previous research aimed at modifying negative interpretations through Cognitive Bias Modification (CBM-I) has yielded promising results. Despite these findings, no research to date has examined the efficacy of an IU-focused CBM-I paradigm...
May 11, 2017: Behaviour Research and Therapy
https://www.readbyqxmd.com/read/28516905/the-effects-of-forest-canopy-shading-and-turbulence-on-boundary-layer-ozone
#3
P A Makar, R M Staebler, A Akingunola, J Zhang, C McLinden, S K Kharol, B Pabla, P Cheung, Q Zheng
The chemistry of the Earth's atmosphere close to the surface is known to be strongly influenced by vegetation. However, two critical aspects of the forest environment have been neglected in the description of the large-scale influence of forests on air pollution: the reduction of photolysis reaction rates and the modification of vertical transport due to the presence of foliage. Here we show that foliage shading and foliage-modified vertical diffusion have a profound influence on atmospheric chemistry, both at the Earth's surface and extending throughout the atmospheric boundary layer...
May 18, 2017: Nature Communications
https://www.readbyqxmd.com/read/28508326/the-association-of-low-penetrance-genetic-risk-modifiers-with-colorectal-cancer-in-lynch-syndrome-patients-a-systematic-review-and-meta-analysis
#4
REVIEW
Neil Donald, Salim Malik, Joshua L McGuire, Kevin J Monahan
Lynch syndrome (LS) is a highly penetrant inherited cancer predisposition syndrome accounting for approximately 1000 cases of colorectal cancer (CRC) in the UK annually. LS is characterised by autosomal dominant inheritance and germline mutations in DNA mismatch repair genes. The penetrance is highly variable and the reasons for this have not been fully elucidated. This study investigates whether low penetrance genetic risk factors may result in phenotype modification in LS patients. To conduct a systematic literature review and meta-analysis to assess the association between low penetrance genetic risk modifiers and CRC in LS patients...
May 15, 2017: Familial Cancer
https://www.readbyqxmd.com/read/28504580/intragastric-administration-of-lactobacillus-casei-bl23-induces-regulatory-foxp3-ror%C3%AE-t-t-cells-subset-in-mice
#5
N G Cortes-Perez, D Lozano-Ojalvo, M A Maiga, S Hazebrouck, K Adel-Patient
Many studies have highlighted the immunomodulatory properties of the probiotic strain Lactobacillus casei BL23. Recently, we demonstrated the ability of this strain to modulate the Th2-oriented immune response in a mouse model of cow's milk allergy based on the induction of a Th17-biased immune response. The probiotic function of L. casei has been also linked to gut-microbiota modifications which could been potentially involved in the immune regulation; however, its precise mechanism of action remains poorly understood...
May 15, 2017: Beneficial Microbes
https://www.readbyqxmd.com/read/28499349/epimetheus-a-multi-profile-normalizer-for-epigenomic-sequencing-data
#6
Mohamed-Ashick M Saleem, Marco-Antonio Mendoza-Parra, Pierre-Etienne Cholley, Matthias Blum, Hinrich Gronemeyer
BACKGROUND: Exponentially increasing numbers of NGS-based epigenomic datasets in public repositories like GEO constitute an enormous source of information that is invaluable for integrative and comparative studies of gene regulatory mechanisms. One of today's challenges for such studies is to identify functionally informative local and global patterns of chromatin states in order to describe the regulatory impact of the epigenome in normal cell physiology and in case of pathological aberrations...
May 12, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28499102/alcohol-consumption-and-mortality-from-coronary-heart-disease-an-updated-meta-analysis-of-cohort-studies
#7
Jinhui Zhao, Tim Stockwell, Audra Roemer, Timothy Naimi, Tanya Chikritzhs
OBJECTIVE: Previous meta-analyses estimate that low-volume alcohol consumption protects against coronary heart disease (CHD). Potential errors in studies include systematic misclassification of drinkers as abstainers, inadequate measurement, and selection bias across the life course. METHOD: Prospective studies of alcohol consumption and CHD mortality were identified in scholarly databases and reference lists. Studies were coded for potential abstainer biases and other study characteristics...
May 2017: Journal of Studies on Alcohol and Drugs
https://www.readbyqxmd.com/read/28490552/coffee-including-caffeinated-and-decaffeinated-coffee-and-the-risk-of-hepatocellular-carcinoma-a-systematic-review-and-dose-response-meta-analysis
#8
Oliver John Kennedy, Paul Roderick, Ryan Buchanan, Jonathan Andrew Fallowfield, Peter Clive Hayes, Julie Parkes
OBJECTIVES: To examine the association between coffee, including caffeinated and decaffeinated coffee, with hepatocellular carcinoma (HCC) and assess the influence of HCC aetiology and pre-existing liver disease. DESIGN: We performed a systematic review and meta-analysis. We calculated relative risks (RRs) of HCC according to caffeinated and decaffeinated coffee consumption using a random-effects dose-response meta-analysis. We tested for modification of the effect estimate by HCC aetiology and pre-existing liver disease...
May 9, 2017: BMJ Open
https://www.readbyqxmd.com/read/28487723/genome-silencing-and-elimination-insights-from-a-selfish-b-chromosome
#9
REVIEW
John C Aldrich, Patrick M Ferree
B chromosomes are non-essential components of numerous plant and animal genomes. Because many of these "extra" chromosomes enhance their own transmission in ways that are detrimental to the rest of the genome, they can be thought of as genome parasites. An extreme example is a paternally inherited B chromosome known as paternal sex ratio (PSR), which is found in natural populations of the jewel wasp Nasonia vitripennis. In order to ensure its own propagation, PSR severely biases the wasp sex ratio by converting diploid female-destined embryos into transmitting haploid males...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28486151/causal-inference-framework-for-generalizable-safety-effect-estimates
#10
Jonathan S Wood, Eric T Donnell
This study integrates a causal inference framework to the Empirical Bayes (EB) before-after method to develop generalizable safety effect estimates (i.e., crash modification factor (CMF)). The method considers approaches to estimate the average treatment effect for the treated (ATT), average treatment effect for the untreated (ATU), and average treatment effect (ATE). The current EB method is shown to estimate ATT while ATE is what is typically desired in traffic safety research. Modifications to the current EB method to estimate ATU and ATE are provided...
May 6, 2017: Accident; Analysis and Prevention
https://www.readbyqxmd.com/read/28482000/a-meta-analysis-of-the-effects-of-abdominoplasty-modifications-on-the-incidence-of-postoperative-seroma
#11
Ben Ardehali, Francesca Fiorentino
Background: Seroma is the most common complication of abdominoplasty. Certain modifications to abdominoplasty may reduce the risk of seroma. Objectives: The authors evaluated the incidence of seroma for 3 abdominoplasty techniques: preservation of Scarpa's fascia, placement of progressive tension (or quilting) sutures, and application of fibrin glue. Methods: In this systematic review and meta-analysis, the Cochrane Library, MEDLINE, Embase, and the International Clinical Trials Registry Platform (World Health Organization) were searched to identify studies of patients who underwent abdominoplasty with seroma as a potential "outcome...
May 6, 2017: Aesthetic Surgery Journal
https://www.readbyqxmd.com/read/28481891/the-decay-of-motor-adaptation-to-novel-movement-dynamics-reveals-an-asymmetry-in-the-stability-of-motion-state-dependent-learning
#12
Eghbal A Hosseini, Katrina P Nguyen, Wilsaan M Joiner
Motor adaptation paradigms provide a quantitative method to study short-term modification of motor commands. Despite the growing understanding of the role motion states (e.g., velocity) play in this form of motor learning, there is little information on the relative stability of memories based on these movement characteristics, especially in comparison to the initial adaptation. Here, we trained subjects to make reaching movements perturbed by force patterns dependent upon either limb position or velocity. Following training, subjects were exposed to a series of error-clamp trials to measure the temporal characteristics of the feedforward motor output during the decay of learning...
May 8, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28465827/does-level-of-motivation-for-change-impact-post-treatment-outcomes-in-the-eating-disorders-protocol-for-a-systematic-review-with-quantitative-analysis
#13
Jeanne Sansfaçon, Howard Steiger, Lise Gauvin, Émilie Fletcher, Mimi Israël
BACKGROUND: Eating Disorders are highly prevalent and widespread mental health problems, with marked risk of chronicity and refractoriness to treatment. Affected individuals are hesitant to change their behaviours and therefore struggle to maintain motivation for therapy. This review aims to produce the first high-quality meta-analysis of the literature on the impact of level of motivation for change on post-treatment outcomes in anorexia nervosa, bulimia nervosa, binge-eating disorder, and other specified feeding or eating disorder (OSFED)...
2017: Journal of Eating Disorders
https://www.readbyqxmd.com/read/28460010/molecular-and-functional-bases-of-selection-against-a-mutation-bias-in-an-rna-virus
#14
Ignacio de la Higuera, Cristina Ferrer-Orta, Ana I de Ávila, Celia Perales, Macarena Sierra, Kamalendra Singh, Stefan G Sarafianos, Yves Dehouck, Ugo Bastolla, Nuria Verdaguer, Esteban Domingo
The selective pressures acting on viruses that replicate under enhanced mutation rates are largely unknown. Here, we describe resistance of foot-and-mouth disease virus to the mutagen 5-fluorouracil (FU) through a single polymerase substitution that prevents an excess of A to G and U to C transitions evoked by FU on the wild-type foot-and-mouth disease virus, while maintaining the same level of mutant spectrum complexity. The polymerase substitution inflicts upon the virus a fitness loss during replication in absence of FU but confers a fitness gain in presence of FU...
May 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28455123/neighborhood-environment-and-cognition-in-older-adults-a-systematic-review
#15
REVIEW
Lilah M Besser, Noreen C McDonald, Yan Song, Walter A Kukull, Daniel A Rodriguez
CONTEXT: Some evidence suggests that treating vascular risk factors and performing mentally stimulating activities may delay cognitive impairment onset in older adults. Exposure to a complex neighborhood environment may be one mechanism to help delay cognitive decline. EVIDENCE ACQUISITION: PubMed, Web of Science, and ProQuest Dissertation and Theses Global database were systematically reviewed, identifying 25 studies published from February 1, 1989 to March 5, 2016 (data synthesized, May 3, 2015 to October 7, 2016)...
April 25, 2017: American Journal of Preventive Medicine
https://www.readbyqxmd.com/read/28453890/less-is-more-patient-level-meta-analysis-reveals-paradoxical-dose-response-effects-of-a-computer-based-social-anxiety-intervention-targeting-attentional-bias
#16
REVIEW
Rebecca B Price, Jennie M Kuckertz, Nader Amir, Yair Bar-Haim, Per Carlbring, Meredith L Wallace
BACKGROUND: The past decade of research has seen considerable interest in computer-based approaches designed to directly target cognitive mechanisms of anxiety, such as attention bias modification (ABM). METHODS: By pooling patient-level datasets from randomized controlled trials of ABM that utilized a dot-probe training procedure, we assessed the impact of training "dose" on relevant outcomes among a pooled sample of 693 socially anxious adults. RESULTS: A paradoxical effect of the number of training trials administered was observed for both posttraining social anxiety symptoms and behavioral attentional bias (AB) toward threat (the target mechanism of ABM)...
April 28, 2017: Depression and Anxiety
https://www.readbyqxmd.com/read/28451256/lc-ms-ms-suggests-that-hole-hopping-in-cytochrome-c-peroxidase-protects-its-heme-from-oxidative-modification-by-excess-h2o2
#17
Meena Kathiresan, Ann M English
We recently reported that cytochrome c peroxidase (Ccp1) functions as a H2O2 sensor protein when H2O2 levels rise in respiring yeast. The availability of its reducing substrate, ferrocytochrome c (Cyc(II)), determines whether Ccp1 acts as a H2O2 sensor or peroxidase. For H2O2 to serve as a signal it must modify its receptor so we employed high-performance LC-MS/MS to investigate in detail the oxidation of Ccp1 by 1, 5 and 10 M eq. of H2O2 in the absence of Cyc(II) to prevent peroxidase activity. We observe strictly heme-mediated oxidation, implicating sequential cycles of binding and reduction of H2O2 at Ccp1's heme...
February 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/28449301/the-profile-and-dynamics-of-rna-modifications-in-animals
#18
Pieter van Delft, Alper Akay, Sabrina M Huber, Christoph Bueschl, Konrad L M Rudolph, Tomás Di Domenico, Rainer Schuhmacher, Eric A Miska, Shankar Balasubramanian
More than a hundred distinct modified nucleosides have been identified in RNA, but little is known about their distribution across different organisms, their dynamic nature and their response to cellular and environmental stress. Mass-spectrometry-based methods have been at the forefront of identifying and quantifying modified nucleosides. However, they often require synthetic reference standards, which do not exist in the case of many modified nucleosides, and this therefore impedes their analysis. Here we use a metabolic labelling approach to achieve rapid generation of bio-isotopologues of the complete Caenorhabditis elegans transcriptome and its modifications and use them as reference standards to characterise the RNA modification profile in this multicellular organism through an untargeted liquid-chromatography tandem high-resolution mass spectrometry (LC-HRMS) approach...
March 16, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28448460/assessing-greenhouse-gas-emissions-and-health-co-benefits-a-structured-review-of-lifestyle-related-climate-change-mitigation-strategies
#19
REVIEW
Vivian G M Quam, Joacim Rocklöv, Mikkel B M Quam, Rebekah A I Lucas
This is the first structured review to identify and summarize research on lifestyle choices that improve health and have the greatest potential to mitigate climate change. Two literature searches were conducted on: (1) active transport health co-benefits, and (2) dietary health co-benefits. Articles needed to quantify both greenhouse gas emissions and health or nutrition outcomes resulting from active transport or diet changes. A data extraction tool (PRISMA) was created for article selection and evaluation...
April 27, 2017: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/28446635/a-motif-and-amino-acid-bias-bioinformatics-pipeline-to-identify-hydroxyproline-rich-glycoproteins
#20
Kim L Johnson, Andrew M Cassin, Andrew Lonsdale, Antony Bacic, Monika Susanne Doblin, Carolyn J Schultz
Intrinsically disordered proteins (IDPs) are functional proteins that lack a well-defined three dimensional structure. The study of IDPs is a rapidly growing area as the crucial biological functions of more of these proteins are uncovered. In plants, IDPs are implicated in plant stress responses, signalling and regulatory processes. A superfamily of cell wall proteins, the hydroxyproline-rich glycoproteins (HRGPs), have characteristic features of IDPs. Their protein backbones are rich in the disordering amino acid proline, they contain repeated sequence motifs and extensive post-translational modifications (glycosylation) and have been implicated in many biological functions...
April 26, 2017: Plant Physiology
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