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https://www.readbyqxmd.com/read/28923003/cleaning-by-clustering-methodology-for-addressing-data-quality-issues-in-biomedical-metadata
#1
Wei Hu, Amrapali Zaveri, Honglei Qiu, Michel Dumontier
BACKGROUND: The ability to efficiently search and filter datasets depends on access to high quality metadata. While most biomedical repositories require data submitters to provide a minimal set of metadata, some such as the Gene Expression Omnibus (GEO) allows users to specify additional metadata in the form of textual key-value pairs (e.g. sex: female). However, since there is no structured vocabulary to guide the submitter regarding the metadata terms to use, consequently, the 44,000,000+ key-value pairs in GEO suffer from numerous quality issues including redundancy, heterogeneity, inconsistency, and incompleteness...
September 18, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28920440/unrestricted-mass-spectrometric-data-analysis-for-identification-localization-and-quantification-of-oxidative-protein-modifications
#2
Martin Rykær, Birte Svensson, Michael J Davies, Per Hägglund
Oxidation generates multiple diverse post-translational modifications resulting in changes in protein structure and function, associated with a wide range of diseases. Of these modifications, carbonylations have often been used as hallmarks of oxidative damage. However, accumulating evidence supports the hypothesis that other oxidation products may be quantitatively more important under physiological conditions. To address this issue we have developed a holistic mass spectrometry-based approach for simultaneous identification, localization and quantification of a broad range of oxidative modifications based on so-called 'dependent peptides'...
September 18, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28916136/mathematical-basis-of-improved-protein-subfamily-classification-by-a-hmm-based-sequence-filter
#3
Siddhartha Kundu
Informative phylogenetic analysis is dependent on the presence of curated and annotated sequences. This may be complemented by the simultaneous availability of empirical data pertaining to their in vivo function. Confounding sequences, with their similarity to more than one functional cluster, can therefore, render any categorization ambiguous, subjective, and imprecise. Here, I analyze and discuss the development of a mathematical expression that can characterize a potential confounding protein sequence. Specifically, statistical descriptors of combinatorially arranged profile HMM scores are computed and evaluated...
September 12, 2017: Mathematical Biosciences
https://www.readbyqxmd.com/read/28914900/cycle-slip-less-low-complexity-phase-recovery-algorithm-for-coherent-optical-receivers
#4
Valery Nobl Rozental, Deming Kong, Benjamin Foo, Bill Corcoran, Arthur James Lowery
We propose and experimentally validate a blind phase recovery algorithm based on tracking low-frequency components of the phase noise, which we call "filtered carrier-phase estimation (F-CPE)." Tracking only the low-frequency components allows F-CPE to reduce the computational complexity by using a frequency-domain equalizer and to simplify the partitioning of a 16 quadrature amplitude modulation (16QAM) constellation. Further, this approach eliminates cycle slips by suppressing the impact of amplified spontaneous emission on phase noise estimation...
September 15, 2017: Optics Letters
https://www.readbyqxmd.com/read/28912666/prevalence-of-low-back-pain-in-iranian-nurses-a-systematic-review-and-meta-analysis
#5
Yosra Azizpour, Ali Delpisheh, Zahra Montazeri, Kourosh Sayehmiri
BACKGROUND: Low back pain (LBP) as a musculoskeletal disorder is one of the most common occupational injuries in nurses but there isn't any valid measure of the prevalence of LBP in Iranian nursing. In order to increase the power and improve the estimates of the prevalence of LBP in Iranian nurses, a comprehensive meta-analysis was carried out. A summary measure of all studies conducted in this field was found and distributions of LBP were evaluated based on different variables. METHODS: Inclusion criteria included articles with prevalence of LBP in Iranian nurses, who had at least six months of work experience without any trauma, injuries to spine, or any underlying disease...
2017: BMC Nursing
https://www.readbyqxmd.com/read/28905217/early-life-arsenic-exposure-infant-and-child-growth-and-morbidity-a-systematic-review
#6
REVIEW
Anisur Rahman, Caroline Granberg, Lars-Åke Persson
Epidemiological studies have suggested a negative association between early life arsenic exposure and fetal size at birth, and subsequently with child morbidity and growth. However, our understanding of the relationship between arsenic exposure and morbidity and growth is limited. This paper aims to systematically review original human studies with an analytical epidemiological study design that have assessed arsenic exposure in fetal life or early childhood and evaluated the association with one or several of the following outcomes: fetal growth, birth weight or other birth anthropometry, infant and child growth, infectious disease morbidity in infancy and early childhood...
September 14, 2017: Archives of Toxicology
https://www.readbyqxmd.com/read/28904269/the-effectiveness-of-specific-risk-mitigation-techniques-used-in-the-production-and-handling-of-manufactured-nanomaterials-a-systematic-review
#7
Toshihiko Myojo, Tomohisa Nagata, Jos Verbeek
Many kinds of manufactured nanomaterials (MNMs) have been developed and used as basic materials of industrial products, and they may pose health risks for workers in not only developed countries but also in developing countries. Few studies have looked at the evidence for effects of controls that mitigate the risk of exposure to MNMs. Therefore, we systematically searched the literature from the year 2000 to 2015. We included studies that compared the use of an exposure control to the situation without such a technique and those that measured the exposure to MNMs as the outcome...
2017: Journal of UOEH
https://www.readbyqxmd.com/read/28891513/electrode-channel-selection-based-on-backtracking-search-optimization-in-motor-imagery-brain-computer-interfaces
#8
Shengfa Dai, Qingguo Wei
Common spatial pattern algorithm is widely used to estimate spatial filters in motor imagery based brain-computer interfaces. However, use of a large number of channels will make common spatial pattern tend to over-fitting and the classification of electroencephalographic signals time-consuming. To overcome these problems, it is necessary to choose an optimal subset of the whole channels to save computational time and improve the classification accuracy. In this paper, a novel method named backtracking search optimization algorithm is proposed to automatically select the optimal channel set for common spatial pattern...
2017: Journal of Integrative Neuroscience
https://www.readbyqxmd.com/read/28888533/an-overview-of-posttraumatic-stress-disorder-genetic-studies-by-analyzing-and-integrating-genetic-data-into-genetic-database-ptsdgene
#9
REVIEW
Kunlin Zhang, Susu Qu, Suhua Chang, Gen Li, Chengqi Cao, Kechi Fang, Miranda Olff, Li Wang, Jing Wang
Posttraumatic stress disorder (PTSD) is a debilitating psychiatric syndrome with complex etiology. Studies aiming to explore genetic susceptibility and environmental triggers of PTSD have been increasing. However, the results are limited and highly heterogeneous. To understand the genetic study status of PTSD and explore more reliable candidates, we obtained 105 PTSD related genetic studies by comprehensively literature searching and filtering 1762 studies. Detailed phenotype and sample information for each study and association results for each genetic marker were extracted...
September 6, 2017: Neuroscience and Biobehavioral Reviews
https://www.readbyqxmd.com/read/28882517/diagnosis-and-genetic-analysis-of-the-worldwide-distributed-rattus-borne-trypanosoma-herpetosoma-lewisi-and-its-allied-species-in-blood-and-fleas-of-rodents
#10
Paola A Ortiz, Herakles A Garcia, Luciana Lima, Flávia Maia da Silva, Marta Campaner, Carlos L Pereira, Sathaporn Jittapalapong, Luis Neves, Marc Desquesnes, Erney P Camargo, Marta M G Teixeira
Trypanosoma (Herpetosoma) lewisi is a cosmopolitan parasite of rodents strongly linked to the human dispersal of Rattus spp. from Asia to the rest of the world. This species is highly phylogenetically related to trypanosomes from other rodents (T. lewisi-like), and sporadically infects other mammals. T. lewisi may opportunistically infect humans, and has been considered an emergent rat-borne zoonosis associated to poverty. We developed the THeCATL-PCR based on Cathepsin L (CATL) sequences to specifically detect T...
September 4, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28877865/developing-a-web-based-geolocated-directory-of-hiv-pre-exposure-prophylaxis-providing-clinics-the-prep-locator-protocol-and-operating-procedures
#11
Aaron J Siegler, Susan Wirtz, Shannon Weber, Patrick S Sullivan
BACKGROUND: Human immunodeficiency virus (HIV) pre-exposure prophylaxis (PrEP) is highly effective in preventing HIV transmission, yet patients interested in learning more about PrEP or in getting a PrEP prescription may not be able to find local medical providers willing to prescribe PrEP. OBJECTIVE: We sought to create a national database of PrEP-providing clinics to allow for patients to have access to a unified, vetted source of PrEP providers in an easily accessible database...
September 6, 2017: JMIR Public Health and Surveillance
https://www.readbyqxmd.com/read/28875981/unraveling-genetic-predisposition-to-familial-or-early-onset-gastric-cancer-using-germline-whole-exome-sequencing
#12
Ingrid P Vogelaar, Rachel S van der Post, J Han Jm van Krieken, Liesbeth Spruijt, Wendy Ag van Zelst-Stams, C Marleen Kets, Jan Lubinski, Anna Jakubowska, Urszula Teodorczyk, Cora M Aalfs, Liselotte P van Hest, Hugo Pinheiro, Carla Oliveira, Shalini N Jhangiani, Donna M Muzny, Richard A Gibbs, James R Lupski, Joep de Ligt, Lisenka E L M Vissers, Alexander Hoischen, Christian Gilissen, Maartje van de Vorst, Jelle J Goeman, Hans K Schackert, Guglielmina N Ranzani, Valeria Molinaro, Encarna B Gómez García, Frederik J Hes, Elke Holinski-Feder, Maurizio Genuardi, Margreet G E M Ausems, Rolf H Sijmons, Anja Wagner, Lizet E van der Kolk, Inga Bjørnevoll, Hildegunn Høberg-Vetti, Ad Geurts van Kessel, Roland P Kuiper, Marjolijn J L Ligtenberg, Nicoline Hoogerbrugge
Recognition of individuals with a genetic predisposition to gastric cancer (GC) enables preventive measures. However, the underlying cause of genetic susceptibility to gastric cancer remains largely unexplained. We performed germline whole-exome sequencing on leukocyte DNA of 54 patients from 53 families with genetically unexplained diffuse-type and intestinal-type GC to identify novel GC-predisposing candidate genes. As young age at diagnosis and familial clustering are hallmarks of genetic tumor susceptibility, we selected patients that were diagnosed below the age of 35, patients from families with two cases of GC at or below age 60 and patients from families with three GC cases at or below age 70...
September 6, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28875396/the-reliability-of-bariatric-surgery-videos-in-youtube-platform
#13
Hasan Erdem, Abdullah Sisik
BACKGROUND: The growing number of bariatric surgery videos shared on YouTube highlights the need for content and quality assessment. The aim of this study was to answer the question 'Is watching these videos useful to surgeons and patients?' METHODS: YouTube was searched using the keywords 'obesity surgery', 'bariatric surgery' and 'weight loss surgery', and 100 videos retrieved using each keyword were classified based on their 'usefulness score' as very useful, useful and not useful...
September 5, 2017: Obesity Surgery
https://www.readbyqxmd.com/read/28873587/untargeted-screening-of-sulfonamides-and-their-metabolites-in-salmon-using-liquid-chromatography-coupled-to-quadrupole-orbitrap-mass-spectrometry
#14
Wei Jia, Lin Shi, Xiaogang Chu
An analytical method for the non-target screening of sulfonamides and metabolites in salmon was developed, using automated on-line extraction procedure followed by ultra-high performance liquid chromatography coupled to electrospray ionization quadrupole Orbitrap high-resolution mass spectrometry (UHPLC Q-Orbitrap), including three systematic workflows (i) fully non-targeted data acquisition with fragmentation, (ii) suspect library spectra searching followed by characteristic structural fragments filtering and (iii) confirmation of non-target analytes and structural characterization of unknown analytes based on the availability of reference standards...
January 15, 2018: Food Chemistry
https://www.readbyqxmd.com/read/28873439/crispr-focus-a-web-server-for-designing-focused-crispr-screening-experiments
#15
Qingyi Cao, Jian Ma, Chen-Hao Chen, Han Xu, Zhi Chen, Wei Li, X Shirley Liu
The recently developed CRISPR screen technology, based on the CRISPR/Cas9 genome editing system, enables genome-wide interrogation of gene functions in an efficient and cost-effective manner. Although many computational algorithms and web servers have been developed to design single-guide RNAs (sgRNAs) with high specificity and efficiency, algorithms specifically designed for conducting CRISPR screens are still lacking. Here we present CRISPR-FOCUS, a web-based platform to search and prioritize sgRNAs for CRISPR screen experiments...
2017: PloS One
https://www.readbyqxmd.com/read/28863564/a-one-dimensional-search-method-with-stable-1-norm-solution-for-linear-prediction
#16
M K Jayesh, C S Ramalingam
In this paper a simple iterative algorithm that is guaranteed to produce a stable all-pole filter when minimizing the 1-norm of the linear prediction error signal is proposed. The approach works for both the autocorrelation and covariance frameworks, involves only a one-dimensional search at each step, and obviates the need for linear programming based methods. Based on simulation studies, it was observed that the performance of the algorithm is nearly optimal, i.e., very close to the estimates obtained using interior point methods...
August 2017: Journal of the Acoustical Society of America
https://www.readbyqxmd.com/read/28863359/novel-chemotypes-targeting-tubulin-at-the-colchicine-binding-site-and-unbiasing-p-glycoprotein
#17
Giuseppe Felice Mangiatordi, Daniela Trisciuzzi, Domenico Alberga, Nunzio Denora, Rosa Maria Iacobazzi, Domenico Gadaleta, Marco Catto, Orazio Nicolotti
Retrospective validation studies carried out on three benchmark databases containing a small fraction (that is 2.80%) of known tubulin binders permitted us to develop a computational platform very effective in selecting easier manageable subsets showing by far higher percentages of actives (about 25%). These studies relied on the hierarchical application of multilayer in silico screenings employing filters implying molecular shape similarity; a structure-based pharmacophore model and molecular docking campaigns...
July 21, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28859915/viral-bronchiolitis-in-young-infants-new-perspectives-for-management-and-treatment
#18
REVIEW
Mauricio T Caballero, Fernando P Polack, Renato T Stein
OBJECTIVE: The aim of this review was to address advances in management and treatment of acute viral bronchiolitis in infants. SOURCES: A systematic review search was made including all articles published in English between 2010 and 2017, and available in the electronic databases PubMed and Cochrane Central Register of Controlled Trials (CENTRAL) and specialized register of the Acute Respiratory Infections Group (Cochrane review group). The following MESH terms in English were included, using different Boolean operators for the search strategy: "bronchiolitis, viral," "diagnosis," "epidemiology," "etiology," "therapy," "virology," "prevention and control," "respiratory syncytial virus, human...
August 30, 2017: Jornal de Pediatria
https://www.readbyqxmd.com/read/28851433/systematic-review-of-effectiveness-of-universal-self-regulation-based-interventions-and-their-effects-on-distal-health-and-social-outcomes-in-children-and-adolescents-review-protocol
#19
Anuja Pandey, Daniel Hale, Anne-Lise Goddings, Sarah-Jayne Blakemore, Russell Viner
BACKGROUND: Growing evidence suggests that childhood and adolescence self-regulation contributes to multiple health, educational and social outcomes. Considering the potential impact of self-regulation skills on improved life chances in conjunction with evidence suggesting that self-regulation can be modified by interventions, there is a need to identify interventions which are most effective in improving childhood and adolescence self-regulation. The present systematic review was designed to determine the effectiveness of universal interventions focused on enhancing the self-regulation of children and adolescents...
August 29, 2017: Systematic Reviews
https://www.readbyqxmd.com/read/28843717/variables-associated-with-pulmonary-thromboembolism-in-injured-patients-a-systematic-review
#20
Ryan Shuster, Joseph Mathew, Alexander Olaussen, Dashiell Gantner, Dinesh Varma, Jim Koukounaras, Mark C Fitzgerald, Peter A Cameron, Biswadev Mitra
BACKGROUND: Pulmonary thromboembolism (PTE) is a dangerous complication of traumatic injury, with varied risk profiles and treatment options. This review aims to describe reported incidence and variables associated with PTE among severely injured patients. METHODS: Searches were conducted using PubMed, Cochrane and MEDLINE. Relevant studies were identified by two independent reviewers based on predetermined inclusion criteria. Incidence of PTE was the primary outcome measure...
August 18, 2017: Injury
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