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https://www.readbyqxmd.com/read/28644610/mzmine-2-data-preprocessing-to-enhance-molecular-networking-reliability
#1
Florent Olivon, Gwendal Grelier, Fanny Roussi, Marc Litaudon, David Touboul
Molecular networking is becoming more and more popular into the metabolomic community to organize tandem mass spectrometry (MS2) data. Even though this approach allows the treatment and comparison of large data sets, several drawbacks related to the MS-Cluster tool routinely used on the Global Natural Product Social Molecular Networking platform (GNPS) limit its potential. MS-Cluster cannot distinguish between chromatography well-resolved isomers as retention times are not taken into account. Annotation with predicted chemical formulas is also not implemented and semi-quantification is only based on the number of MS2 scans...
June 23, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28642031/clustering-of-ms-2-spectra-using-unsupervised-methods-to-aid-the-identification-of-secondary-metabolites-from-pseudomonas-aeruginosa
#2
Tobias Depke, Raimo Franke, Mark Brönstrup
Pseudomonas aeruginosa is an important opportunistic pathogen that produces a large arsenal of small molecule virulence factors and quorum sensing signal molecules. The annotation of these secondary metabolites in untargeted, mass spectrometry-based metabolomics is difficult, as many of them cannot be found in common metabolite databases, and as manual annotation is tedious. We therefore developed an algorithm named CluMSID that uses cosine similarities of product ion spectra and neutral loss patterns in combination with unsupervised clustering methods such as multidimensional scaling, density based clustering and hierarchical clustering to group structurally similar compounds and hence facilitate their annotation...
June 4, 2017: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
https://www.readbyqxmd.com/read/28640845/is-self-assessment-of-medical-abortion-using-a-low-sensitivity-pregnancy-test-combined-with-a-checklist-and-phone-text-messages-feasible-in-south-african-primary-healthcare-settings-a-randomized-trial
#3
Deborah Constant, Jane Harries, Kristen Daskilewicz, Landon Myer, Kristina Gemzell-Danielsson
OBJECTIVE: To evaluate feasibility of self-assessment of medical abortion outcome using a low-sensitivity urine pregnancy test, checklist and text messages. The study assessed whether accurate self-assessment required a demonstration of the low-sensitivity urine pregnancy test or if verbal instructions suffice. METHODS: This non-inferiority trial enrolled 525 adult women from six public sector abortion clinics. Eligible women were undergoing medical abortion at gestations within 63 days...
2017: PloS One
https://www.readbyqxmd.com/read/28634630/development-and-validation-of-a-tool-for-non-technical-skills-evaluation-in-robotic-surgery-the-icars-system
#4
Nicholas Raison, Thomas Wood, Oliver Brunckhorst, Takashige Abe, Talisa Ross, Ben Challacombe, Mohammed Shamim Khan, Giacomo Novara, Nicolo Buffi, Henk Van Der Poel, Craig McIlhenny, Prokar Dasgupta, Kamran Ahmed
BACKGROUND: Non-technical skills (NTS) are being increasingly recognised as vital for safe surgical practice. Numerous NTS rating systems have been developed to support effective training and assessment. Yet despite the additional challenges posed by robotic surgery, no NTS rating systems have been developed for this unique surgical environment. This study reports the development and validation of the first NTS behavioural rating system for robotic surgery. METHODS: A comprehensive index of all relevant NTS behaviours in robotic surgery was developed through observation of robotic theatre and interviews with robotic surgeons...
June 20, 2017: Surgical Endoscopy
https://www.readbyqxmd.com/read/28633441/bioqueue-a-novel-pipeline-framework-to-accelerate-bioinformatics-analysis
#5
Li Yao, Heming Wang, Yuanyuan Song, Guangchao Sui
Motivation: With the rapid development of Next-Generation Sequencing, a large amount of data is now available for bioinformatics research. Meanwhile, the presence of many pipeline frameworks makes it possible to analyse these data. However, these tools concentrate mainly on their syntax and design paradigms, and dispatch jobs based on users' experience about the resources needed by the execution of a certain step in a protocol. As a result, it is difficult for these tools to maximize the potential of computing resources, and avoid errors caused by overload, such as memory overflow...
June 19, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28633070/length-and-repeat-sequence-variation-in-58-strs-and-94-snps-in-two-spanish-populations
#6
Ferran Casals, Roger Anglada, Núria Bonet, Raquel Rasal, Kristiaan J van der Gaag, Jerry Hoogenboom, Neus Solé-Morata, David Comas, Francesc Calafell
We have genotyped the 58 STRs (27 autosomal, 24 Y-STRs and 7 X-STRs) and 94 autosomal SNPs in Illumina ForenSeq™ Primer Mix A in 88 Spanish Roma (Gypsy) samples and 143 Catalans. Since this platform is based in massive parallel sequencing, we have used simple R scripts to uncover the sequence variation in the repeat region. Thus, we have found, across 58 STRs, 541 length-based alleles, which, after considering repeat-sequence variation, became 804 different alleles. All loci in both populations were in Hardy-Weinberg equilibrium...
June 16, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28632461/consuming-ecstasy-representations-of-male-and-female-orgasm-in-mainstream-pornography
#7
Léa J Séguin, Carl Rodrigue, Julie Lavigne
Social representations, which appear in a variety of media, can influence the way sexual experiences are perceived and understood. While pornography is not the only medium in which orgasm is portrayed, it is the most explicit, and it is widespread and easily accessible. As such, pornography is an ideal medium for examining representations of male and female orgasm. PornHub's 50 most viewed videos of all time were viewed and coded for the frequency of male and female orgasm, orgasm-inducing sex acts (and whether activity inducing female orgasms included some form of clitoral stimulation), and auditory (verbal, vocal) and visual (bodily) indicators of orgasm...
June 20, 2017: Journal of Sex Research
https://www.readbyqxmd.com/read/28632399/prokaryotic-contig-annotation-pipeline-server-web-application-for-a-prokaryotic-genome-annotation-pipeline-based-on-the-shiny-app-package
#8
Byeonghyeok Park, Min-Jeong Baek, Byoungnam Min, In-Geol Choi
Genome annotation is a primary step in genomic research. To establish a light and portable prokaryotic genome annotation pipeline for use in individual laboratories, we developed a Shiny app package designated as "P-CAPS" (Prokaryotic Contig Annotation Pipeline Server). The package is composed of R and Python scripts that integrate publicly available annotation programs into a server application. P-CAPS is not only a browser-based interactive application but also a distributable Shiny app package that can be installed on any personal computer...
June 20, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28632092/unscripted-exploring-representations-of-older-unpartnered-women-s-sexuality
#9
Beth Montemurro, Lisa Chewning
Images of sexually active women beyond the age of 50 are lacking in popular culture and in particular on television. Dominant sexual scripts depict older women as generally asexual. The television program Hot in Cleveland features unpartnered midlife and older women as main characters. In this article, based on analysis of four seasons of Hot in Cleveland, we look closely at portrayals of sexual activity to see whether they underscore dominant sexual scripts mocking older women's sexual interest, position aging as sexual decline, or reinforce the narrative of "successful" aging/aging as progress...
March 3, 2017: Journal of Women & Aging
https://www.readbyqxmd.com/read/28631479/quantitative-analysis-of-ligand-induced-heterodimerization-of-two-distinct-receptors
#10
Chang Lu, Zhi-Xin Wang
The induced dimerization of two distinct receptors through a heterobifunctional inducer is prevalent among all levels of cellular signaling processes, yet its complexity poses difficulty for systematic quantitative analysis. This paper first shows how to calculate the amount of any possible complex or monomer of heteroligand and two receptors present at equilibrium. The theory is subsequently applied to the determination of three independent equilibrium parameters involved in the rapamycin induced FKBP and FRB dimerization, in which all parameters were simultaneously estimated using one set of fluorescence resonance energy transfer (FRET) experiments...
June 22, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28628333/coupling-targeted-and-untargeted-mass-spectrometry-for-metabolome-microbiome-wide-association-studies-of-human-fecal-samples
#11
Alexey V Melnik, Pieter C Dorrestein, Ricardo R da Silva, Embriette R Hyde, Alexander A Aksenov, Fernando Vargas, Amina Bouslimani, Ivan Protsyuk, Alan Jarmusch, Anupriya Tripathi, Theodore Alexandrov, Rob Knight
Increasing appreciation of the gut microbiome's role in health motivates understanding the molecular composition of human feces. To analyze such complex samples, we developed a platform coupling targeted and untargeted metabolomics. The approach is facilitated through split flow from one UPLC, joint timing triggered by contact closure relays and a script to retrieve the data. It is designed to detect specific metabolites of interest with high sensitivity, allows for correction of targeted information, enables better quantitation thus providing an advanced analytical tool for exploratory studies...
June 19, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28626438/sensitivity-to-stroke-emerges-in-kindergartners-reading-chinese-script
#12
Su Li, Li Yin
To what extent are young children sensitive to individual stroke, the smallest unit of writing in Chinese that carries no phonological or semantic information? The present study examined Chinese kindergartners' sensitivity to stroke and the contribution of reading ability and age to stroke sensitivity. Fifty five children from Beijing, including 28 4-year-olds (Mage = 4.55 years, SD = 0.28, 16 males) and 29 5-year-olds (Mage = 5.58 years, SD = 0.30, 14 males), were administered an orthographic matching task and assessed on non-verbal IQ and Chinese word reading...
2017: Frontiers in Psychology
https://www.readbyqxmd.com/read/28625936/do-medical-french-students-know-how-to-properly-score-a-mini-mental-state-examination
#13
Intza Hernandorena, Sophie Chauvelier, Jean-Sébastien Vidal, Matthieu Piccoli, Joséphine Coulon, Laurence Hugonot-Diener, Anne-Sophie Rigaud, Olivier Hanon, Emmanuelle Duron
The mini mental state examination (MMSE) is a validated tool to assess global cognitive function. Training is required before scoring. Inaccurate scoring can lead to inappropriate medical decisions. In France, MMSE is usually scored by medical students. To assess if medical French students know how to properly score a mini mental state examination. Two « physician-patient » role playings performed by 2 specialized physicians, were performed in front of University Paris V medical students. Role playing A: Scoring of a MMSE according to a script containing five tricks; Role playing B: Find the 5 errors committed in a pre-filled MMSE form, according to the second script...
June 1, 2017: Gériatrie et Psychologie Neuropsychiatrie du Vieillissement
https://www.readbyqxmd.com/read/28624322/assessing-pragmatic-communication-in-children-with-down-syndrome
#14
Elizabeth Smith, Kari-Anne B Næss, Christopher Jarrold
PURPOSE: Successful communication depends on language content, language form, and language use (pragmatics). Children with Down syndrome (DS) experience communication difficulties, however little is known about their pragmatic profile, particularly during early school years. The purpose of the present study was to explore the nature of pragmatic communication in children with DS. METHOD: Twenty-nine six-year-old children with DS were assessed, in the areas of 1) initiation, 2) scripted language, 3) understanding context and 4) nonverbal communication, as reported by children's parents via the Children's Communication Checklist-2 (Bishop, 2003)...
June 9, 2017: Journal of Communication Disorders
https://www.readbyqxmd.com/read/28621925/kpic2-an-effective-framework-for-mass-spectrometry-based-metabolomics-using-pure-ion-chromatograms
#15
Hongchao Ji, Fanjuan Zeng, Yamei Xu, Hongmei Lu, Zhimin Zhang
Distilling accurate quantitation information of metabolites from liquid chromatography coupled with mass spectrometry (LC-MS) datasets is crucial for further statistical analysis and biomarker identification. However, it is still challenging due to the complexity of biological systems. The concept of pure ion chromatograms (PIC) is an effective way for extracting meaningful ions, but few toolboxes provide full processing workflow for LC-MS datasets based on PIC. In this study, an integrated framework, KPIC2, has been developed for metabolomics studies, which can detect pure ions accurately, align PICs across samples, group PICs to identify isotope and potential adducts, fill missing peaks and do multivariate pattern recognition...
June 16, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28621157/predicting-individual-differences-in-reading-and-spelling-skill-with-artificial-script-based-letter-speech-sound-training
#16
Sebastián Aravena, Jurgen Tijms, Patrick Snellings, Maurits W van der Molen
In this study, we examined the learning of letter-speech sound correspondences within an artificial script and performed an experimental analysis of letter-speech sound learning among dyslexic and normal readers vis-à-vis phonological awareness, rapid automatized naming, reading, and spelling. Participants were provided with 20 min of training aimed at learning eight new basic letter-speech sound correspondences, followed by a short assessment of mastery of the correspondences and word-reading ability in this unfamiliar script...
June 1, 2017: Journal of Learning Disabilities
https://www.readbyqxmd.com/read/28617790/clinical-management-and-patient-persistence-with-antibiotic-course-in-suspected-group-a-streptococcal-pharyngitis-for-primary-prevention-of-rheumatic-fever-the-perspective-from-a-new-zealand-emergency-department
#17
Jeremy J Mathan, Jozsef Ekart, Anthony Houlding, Gary Payinda, Clair Mills
AIM: Rates of acute rheumatic fever in the Northland region are historically among the highest in New Zealand, impacting disproportionately on Māori children and youth. The primary aim of this study was to determine patient persistence to antibiotic treatment for group A streptococcus (GAS) pharyngitis in patients presenting with sore throat to the Whangarei Hospital Emergency Department. Secondarily, this study sought to determine prescriber adherence to the national antibiotic guideline for sore throat management...
June 16, 2017: New Zealand Medical Journal
https://www.readbyqxmd.com/read/28610849/dynamic-spatial-organization-of-the-occipito-temporal-word-form-area-for-second-language-processing
#18
Yue Gao, Yafeng Sun, Chunming Lu, Guosheng Ding, Taomei Guo, Jeffrey G Malins, James R Booth, Danling Peng, Li Liu
Despite the left occipito-temporal region having shown consistent activation in visual word form processing across numerous studies in different languages, the mechanisms by which word forms of second languages are processed in this region remain unclear. To examine this more closely, 16 Chinese-English and 14 English-Chinese late bilinguals were recruited to perform lexical decision tasks to visually presented words in both their native and second languages (L1 and L2) during functional magnetic resonance imaging scanning...
June 10, 2017: Neuropsychologia
https://www.readbyqxmd.com/read/28608193/do-alternating-color-words-facilitate-reading-aloud-text-in-chinese-evidence-with-developing-and-adult-readers
#19
Manuel Perea, Xiaoyun Wang
Prior research has shown that colors induce perceptual grouping and, hence, colors can be used as word dividers during reading (Pinna & Deiana, 2014). This issue is particularly important for those writing systems that do not employ interword spaces (e.g., Chinese). The rationale is that alternating colors across words in these scripts may facilitate the process of word identification without altering the spatial distribution of text. Here, we tested whether color alternation across words produces a benefit in a reading-aloud task in native speakers of Chinese...
June 12, 2017: Memory & Cognition
https://www.readbyqxmd.com/read/28608168/a-unique-path-to-callous-unemotional-traits-for-children-who-are-temperamentally-fearless-and-unconcerned-about-transgressions-a-longitudinal-study-of-typically-developing-children-from-age-2-to-12
#20
Kathryn C Goffin, Lea J Boldt, Sanghag Kim, Grazyna Kochanska
Despite the acknowledged significance of callous-unemotional (CU) traits in developmental psychopathology, few studies have examined their early antecedents in typically developing children, in long-term longitudinal designs, using observational measures. In 102 community mothers, fathers, and children (N = 51 girls), we examined main and interactive effects of children's fearless temperament and low concern about transgressions from toddler to early school age as predictors of CU traits in middle childhood and early preadolescence...
June 13, 2017: Journal of Abnormal Child Psychology
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