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https://www.readbyqxmd.com/read/28107396/mixfit-methodology-for-computing-ancestry-related-genetic-scores-at-the-individual-level-and-its-application-to-the-estonian-and-finnish-population-studies
#1
Toomas Haller, Liis Leitsalu, Krista Fischer, Marja-Liisa Nuotio, Tõnu Esko, Dorothea Irene Boomsma, Kirsten Ohm Kyvik, Tim D Spector, Markus Perola, Andres Metspalu
Ancestry information at the individual level can be a valuable resource for personalized medicine, medical, demographical and history research, as well as for tracing back personal history. We report a new method for quantitatively determining personal genetic ancestry based on genome-wide data. Numerical ancestry component scores are assigned to individuals based on comparisons with reference populations. These comparisons are conducted with an existing analytical pipeline making use of genotype phasing, similarity matrix computation and our addition-multidimensional best fitting by MixFit...
2017: PloS One
https://www.readbyqxmd.com/read/28105913/mumal2-improving-sensitivity-in-shotgun-proteomics-using-cost-sensitive-artificial-neural-networks-and-a-threshold-selector-algorithm
#2
Fabio Ribeiro Cerqueira, Adilson Mendes Ricardo, Alcione de Paiva Oliveira, Armin Graber, Christian Baumgartner
BACKGROUND: This work presents a machine learning strategy to increase sensitivity in tandem mass spectrometry (MS/MS) data analysis for peptide/protein identification. MS/MS yields thousands of spectra in a single run which are then interpreted by software. Most of these computer programs use a protein database to match peptide sequences to the observed spectra. The peptide-spectrum matches (PSMs) must also be assessed by computational tools since manual evaluation is not practicable...
December 15, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28104697/male-birthweight-semen-quality-and-birth-outcomes
#3
B W Whitcomb, M S Bloom, S Kim, Z Chen, G M Buck Louis
STUDY QUESTION: What are the relations among birthweight (BW), semen parameters and birth outcomes in a population-based sample? SUMMARY ANSWER: BW is unrelated to semen parameters, which are in turn unrelated to birth outcomes. WHAT IS KNOWN ALREADY: In clinical settings, there has been suggestion that semen parameters are related to BW when comparing fertile and infertile men; however, findings have been less clear in more general populations...
January 18, 2017: Human Reproduction
https://www.readbyqxmd.com/read/28104229/computational-analysis-of-the-safe-zone-for-the-antegrade-lag-screw-in-posterior-column-fixation-with-the-anterior-approach-in-acetabular-fracture-a-cadaveric-study
#4
Gu-Hee Jung, Yongkoo Lee, Joon-Woo Kim, Ji-Wan Kim
OBJECTIVE: The fluoroscopically-guided procedure of antegrade posterior lag screw in posterior column fixation through anterior approach is technique-dependent and requires an experienced surgeon. The purpose of this study was to establish the safe zone for the antegrade posterior lag screw by using computational analysis. METHOD: The virtual three-dimensional model of 178 hemi-pelvises was created from the CT data (DICOM format) by using Mimics(®) program, and were used to measure the safe zone of antegrade lag screw fixation on the inner table of the iliac wing, and the largest diameter of cylindrical implant inside safe zone...
January 13, 2017: Injury
https://www.readbyqxmd.com/read/28103189/dynamic-programming-for-instance-annotation-in-multi-instance-multi-label-learning
#5
Anh Pham, Raviv Raich, Xiaoli Fern
Labeling data for classification requires significant human effort. To reduce labeling cost, instead of labeling every instance, a group of instances (bag) is labeled by a single bag label. Computer algorithms are then used to infer the label for each instance in a bag, a process referred to as instance annotation. This task is challenging due to the ambiguity regarding the instance labels. We propose a discriminative probabilistic model for the instance annotation problem and introduce an expectation maximization framework for inference, based on the maximum likelihood approach...
January 5, 2017: IEEE Transactions on Pattern Analysis and Machine Intelligence
https://www.readbyqxmd.com/read/28103187/convexity-shape-prior-for-binary-segmentation
#6
Lena Gorelick, Olga Veksler, Yuri Boykov, Claudia Nieuwenhuis
Convexity is a known important cue in human vision. We propose shape convexity as a new high-order regularization constraint for binary image segmentation. In the context of discrete optimization, object convexity is represented as a sum of three-clique potentials penalizing any 1- 0- 1 configuration on all straight lines. We show that these non-submodular potentials can be efficiently optimized using an iterative trust region approach. At each iteration the energy is linearly approximated and globally optimized within a small trust region around the current solution...
February 2017: IEEE Transactions on Pattern Analysis and Machine Intelligence
https://www.readbyqxmd.com/read/28102588/three-dimensional-translabial-ultrasound-assessment-of-urethral-supports-and-the-urethral-sphincter-complex-in-stress-urinary-incontinence
#7
Jordi Cassadó Garriga, Antoni Pessarrodona Isern, Monica Rodríguez Carballeira, Mar Pallarols Badia, Manuela Moya Del Corral, Marta Valls Esteve, Eva Huguet Galofré
AIMS: The pathophysiological mechanism of incontinence is multifactorial. We evaluated the role of 3D-4D ultrasound in the assessment of the fascial supports of the urethra and the urethral sphincter complex (USC) for diagnosing stress urinary incontinence. METHODS: Observational case-control study in women with and without stress urinary incontinence attending a urogynecology service and a general gynecology service. All women were interviewed, examined, and classified according to the Pelvic Organ Prolapse Quantification (POP-Q) and underwent a 3D-4D translabial ultrasound...
January 19, 2017: Neurourology and Urodynamics
https://www.readbyqxmd.com/read/28102488/performance-and-side-effects-of-supplementation-with-n-acetylcysteine-a-systematic-review-and-meta-analysis
#8
REVIEW
Kate Rhodes, Andrea Braakhuis
BACKGROUND: N-Acetylcysteine (NAC) is a promising antioxidant supplement with potential as an acute strategy to enhance performance in elite sport, but there are concerns about its side effects with high doses. OBJECTIVE: To review the current literature and evaluate the effects of NAC supplementation on sport performance and the risk of adverse effects. METHODS: The literature up to May 2016 was searched on MEDLINE (PubMed), EMBASE, SPORTDiscus, Google Scholar and Scopus databases to identify all studies investigating the effects of NAC supplementation on exercise performance and/or side effects experienced...
January 19, 2017: Sports Medicine
https://www.readbyqxmd.com/read/28102461/rnahelix-computational-modeling-of-nucleic-acid-structures-with-watson-crick-and-non-canonical-base-pairs
#9
Dhananjay Bhattacharyya, Sukanya Halder, Sankar Basu, Debasish Mukherjee, Prasun Kumar, Manju Bansal
Comprehensive analyses of structural features of non-canonical base pairs within a nucleic acid double helix are limited by the availability of a small number of three dimensional structures. Therefore, a procedure for model building of double helices containing any given nucleotide sequence and base pairing information, either canonical or non-canonical, is seriously needed. Here we describe a program RNAHelix, which is an updated version of our widely used software, NUCGEN. The program can regenerate duplexes using the dinucleotide step and base pair orientation parameters for a given double helical DNA or RNA sequence with defined Watson-Crick or non-Watson-Crick base pairs...
January 19, 2017: Journal of Computer-aided Molecular Design
https://www.readbyqxmd.com/read/28101956/aggregates-finding-structures-in-simulation-results-of-solutions
#10
Carlos E S Bernardes
Molecular Dynamic and Monte-Carlo simulations are widely used to investigate the structure and physical properties of solids and liquids at a molecular level. Tools to extract the most relevant information from the obtained results are, however, in considerable demand. One such tool, the program AGGREGATES, is described in this work. Based on distance criteria, the program searches trajectory files for the presence of molecular clusters and computes several statistical and shape properties for these structures...
January 19, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28101113/evaluating-the-effectiveness-of-pubertal-preparedness-program-in-terms-of-knowledge-and-attitude-regarding-pubertal-changes-among-pre-adolescent-girls
#11
Manisha Rani, Poonam Sheoran, Yogesh Kumar, Navjyot Singh
Objective: To compare the knowledge and attitude regarding pubertal changes among pre - adolescent girls before and after the pubertal preparedness program (PPP) in experimental and comparison group. Materials and methods: A Quasi experimental (non- equivalent comparison group pretest posttest) design was adopted with 104pre-adolescentgirls (52 in each experimental and comparison group) of age 12-14years, selected by purposive sampling from two different Government schools of Ambala District. Knowledge and attitude was assessed using structured knowledge questionnaire (KR-20 = 0...
September 2016: Journal of Family & Reproductive Health
https://www.readbyqxmd.com/read/28100791/the-reliability-and-stability-of-an-inferred-phylogenetic-tree-from-empirical-data
#12
Yukako Katsura, Craig E Stanley, Sudhir Kumar, Masatoshi Nei
The reliability of a phylogenetic tree obtained from empirical data is usually measured by the bootstrap probability (Pb) of interior branches of the tree. If the bootstrap probability is high for most branches, the tree is considered to be reliable. If some interior branches show relatively low bootstrap probabilities, we are not sure that the inferred tree is really reliable. Here we propose another quantity measuring the reliability of the tree called the stability of a subtree. This quantity refers to the probability of obtaining a subtree (Ps) of an inferred tree obtained...
January 18, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28100095/shoulder-kinetics-during-start-up-and-propulsion-with-a-manual-wheelchair-within-the-initial-phase-of-uninstructed-training
#13
Samuel Hybois, Alice Siegel, Joseph Bascou, Nicolas Eydieux, Philippe Vaslin, Hélène Pillet, Pascale Fodé, Christophe Sauret
PURPOSE: Wheelchair locomotion is constraining for the upper limbs and involves a set of motor tasks that need to be learnt by a novice user. To understand this integration process, we investigated the evolution of shoulder kinetics during start-up and propulsion within the initial phase of low-intensity uninstructed training. MATERIALS AND METHODS: Seventeen novice able-bodied subjects performed a 120-min uninstructed practice distributed over 4 weeks. During the initial and final sessions, upper limbs kinematics and hand-rim kinetics were continuously collected...
January 19, 2017: Disability and Rehabilitation. Assistive Technology
https://www.readbyqxmd.com/read/28097472/proceedings-of-the-third-international-molecular-pathological-epidemiology-mpe-meeting
#14
REVIEW
Peter T Campbell, Timothy R Rebbeck, Reiko Nishihara, Andrew H Beck, Colin B Begg, Alexei A Bogdanov, Yin Cao, Helen G Coleman, Gordon J Freeman, Yujing J Heng, Curtis Huttenhower, Rafael A Irizarry, N Sertac Kip, Franziska Michor, Daniel Nevo, Ulrike Peters, Amanda I Phipps, Elizabeth M Poole, Zhi Rong Qian, John Quackenbush, Harlan Robins, Peter K Rogan, Martha L Slattery, Stephanie A Smith-Warner, Mingyang Song, Tyler J VanderWeele, Daniel Xia, Emily C Zabor, Xuehong Zhang, Molin Wang, Shuji Ogino
Molecular pathological epidemiology (MPE) is a transdisciplinary and relatively new scientific discipline that integrates theory, methods, and resources from epidemiology, pathology, biostatistics, bioinformatics, and computational biology. The underlying objective of MPE research is to better understand the etiology and progression of complex and heterogeneous human diseases with the goal of informing prevention and treatment efforts in population health and clinical medicine. Although MPE research has been commonly applied to investigating breast, lung, and colorectal cancers, its methodology can be used to study most diseases...
January 17, 2017: Cancer Causes & Control: CCC
https://www.readbyqxmd.com/read/28097056/rhea-a-transparent-and-modular-r-pipeline-for-microbial-profiling-based-on-16s-rrna-gene-amplicons
#15
Ilias Lagkouvardos, Sandra Fischer, Neeraj Kumar, Thomas Clavel
The importance of 16S rRNA gene amplicon profiles for understanding the influence of microbes in a variety of environments coupled with the steep reduction in sequencing costs led to a surge of microbial sequencing projects. The expanding crowd of scientists and clinicians wanting to make use of sequencing datasets can choose among a range of multipurpose software platforms, the use of which can be intimidating for non-expert users. Among available pipeline options for high-throughput 16S rRNA gene analysis, the R programming language and software environment for statistical computing stands out for its power and increased flexibility, and the possibility to adhere to most recent best practices and to adjust to individual project needs...
2017: PeerJ
https://www.readbyqxmd.com/read/28096683/clinicopathological-and-immunohistochemical-features-of-lung-invasive-mucinous-adenocarcinoma-based-on-computed-tomography-findings
#16
Katsuhiko Shimizu, Riki Okita, Shinsuke Saisho, Ai Maeda, Yuji Nojima, Masao Nakata
BACKGROUND: We performed an analysis to clarify differences in clinicopathological and molecular features of lung invasive mucinous adenocarcinoma (IMA) based on computed tomography (CT) findings and their impact on prognosis. PATIENTS AND METHODS: On the basis of CT findings, we divided lung IMA into three subtypes: solid, bubbling, and pneumonic. We then investigated differences in clinicopathological characteristics, prognosis, and the expressions of well-identified biomarkers, including cyclooxygenase-2 (Cox-2), excision repair cross-complementation group 1 (ERCC1), ribonucleotide reductase M1 (RRM1), class III beta-tubulin, thymidylate synthase (TS), secreted protein acidic and rich in cysteine (SPARC), programmed cell death-1 ligand-1 (PD-L1), and epidermal growth factor receptor mutation, among the three subtypes...
2017: OncoTargets and Therapy
https://www.readbyqxmd.com/read/28095715/an-overview-of-aldehyde-oxidase-an-enzyme-of-emerging-importance-in-novel-drug-discovery
#17
Mohammad-Reza Rashidi, Somaieh Soltani
Given the rising trend in medicinal chemistry strategy to reduce cytochrome P450-dependent metabolism, aldehyde oxidase (AOX) has recently gained increased attention in drug discovery programs and the number of drug candidates that are metabolized by AOX is steadily growing. Areas covered: Despite the emerging importance of AOX in drug discovery, there are certain major recognized problems associated with AOX-mediated metabolism of drugs. Intra- and inter-species variations in AOX activity, the lack of reliable and predictive animal models using the common experimental animals, and failure in the predictions of in vivo metabolic activity of AOX using traditional in vitro methods are among these issues that are covered in this article...
January 17, 2017: Expert Opinion on Drug Discovery
https://www.readbyqxmd.com/read/28095555/megasessions-for-robotic-hair-restoration
#18
Joa O Carlos Pereira, Joa O Carlos Pereira Filho, Joa O Pedro Cabrera Pereira
A robotic system can select and remove individual hair follicles from the donor area with great precision and without fatigue. This report describes the use of the robotic system in a megasession for hair restoration. Patients were instructed to cut their hair to 1.0 to 1.2 mm before surgery. The robot selected and removed 600 to 800 grafts per hour so the follicular units (FU)s could be transplanted manually to recipient sites. The robot arm consists of a sharp inner punch and a blunt outer punch which together separate FUs from the sur- rounding tissue...
November 1, 2016: Journal of Drugs in Dermatology: JDD
https://www.readbyqxmd.com/read/28094689/quantification-of-rectifications-for-the-northwestern-university-flexible-sub-ischial-vacuum-socket
#19
Stefania Fatone, William Brett Johnson, Lilly Tran, Kerice Tucker, Christofer Mowrer, Ryan Caldwell
BACKGROUND: The fit and function of a prosthetic socket depend on the prosthetist's ability to design the socket's shape to distribute load comfortably over the residual limb. We recently developed a sub-ischial socket for persons with transfemoral amputation: the Northwestern University Flexible Sub-Ischial Vacuum Socket. OBJECTIVE: This study aimed to quantify the rectifications required to fit the Northwestern University Flexible Sub-Ischial Vacuum Socket to teach the technique to prosthetists as well as provide a computer-aided design-computer-aided manufacturing option...
January 1, 2017: Prosthetics and Orthotics International
https://www.readbyqxmd.com/read/28093413/persistence-of-cardiac-remodeling-in-preadolescents-with-fetal-growth-restriction
#20
Sebastian Imre Sarvari, Merida Rodriguez-Lopez, Marta Nuñez-Garcia, Marta Sitges, Alvaro Sepulveda-Martinez, Oscar Camara, Constantine Butakoff, Eduard Gratacos, Bart Bijnens, Fatima Crispi
BACKGROUND: Fetal growth restriction (FGR) affects 5% to 10% of newborns and is associated with increased cardiovascular mortality in adulthood. We evaluated whether prenatal cardiovascular changes previously demonstrated in FGR persist into preadolescence. METHODS AND RESULTS: A cohort study of 58 FGR (defined as birth weight below 10th centile) and 94 normally grown fetuses identified in utero and followed-up into preadolescence (8-12 years of age) by echocardiography and 3-dimensional shape computational analysis...
January 2017: Circulation. Cardiovascular Imaging
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