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https://www.readbyqxmd.com/read/28545234/validation-of-splicing-events-in-transcriptome-sequencing-data
#1
Wolfgang Kaisers, Johannes Ptok, Holger Schwender, Heiner Schaal
Genomic alignments of sequenced cellular messenger RNA contain gapped alignments which are interpreted as consequence of intron removal. The resulting gap-sites, genomic locations of alignment gaps, are landmarks representing potential splice-sites. As alignment algorithms report gap-sites with a considerable false discovery rate, validations are required. We describe two quality scores, gap quality score (gqs) and weighted gap information score (wgis), developed for validation of putative splicing events: While gqs solely relies on alignment data wgis additionally considers information from the genomic sequence...
May 23, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28545175/the-effect-of-sagittal-knee-deformity-on-preoperative-measurement-of-coronal-mechanical-alignment-during-total-knee-arthroplasty
#2
Gautam M Shetty, Arun Mullaji, Ahmed Adel Khalifa, Abhik Ray, Vivek Nikumbha
Purpose: The purpose of this prospective study was to determine correlation between coronal mechanical alignment measured on preoperative standing full-length radiographs and navigation during total knee arthroplasty (TKA) in the presence of an associated sagittal deformity (hyperextension and flexion deformity). Materials and Methods: Coronal mechanical alignment measured on preoperative, standing, full-length, hip-to-ankle anteroposterior radiographs was compared with intraoperative measurements recorded with computer navigation in 200 primary navigated TKAs...
June 1, 2017: Knee Surgery & related Research
https://www.readbyqxmd.com/read/28545124/cornet-assigning-function-to-networks-of-co-evolving-residues-by-automated-literature-mining
#3
Tom van den Bergh, Giorgio Tamo, Alberto Nobili, Yifeng Tao, Tianwei Tan, Uwe T Bornscheuer, Remko K P Kuipers, Bas Vroling, René M de Jong, Kalyanasundaram Subramanian, Peter J Schaap, Tom Desmet, Bernd Nidetzky, Gert Vriend, Henk-Jan Joosten
CorNet is a web-based tool for the analysis of co-evolving residue positions in protein super-family sequence alignments. CorNet projects external information such as mutation data extracted from literature on interactively displayed groups of co-evolving residue positions to shed light on the functions associated with these groups and the residues in them. We used CorNet to analyse six enzyme super-families and found that groups of strongly co-evolving residues tend to consist of residues involved in a same function such as activity, specificity, co-factor binding, or enantioselectivity...
2017: PloS One
https://www.readbyqxmd.com/read/28545068/automatically-tracking-neurons-in-a-moving-and-deforming-brain
#4
Jeffrey P Nguyen, Ashley N Linder, George S Plummer, Joshua W Shaevitz, Andrew M Leifer
Advances in optical neuroimaging techniques now allow neural activity to be recorded with cellular resolution in awake and behaving animals. Brain motion in these recordings pose a unique challenge. The location of individual neurons must be tracked in 3D over time to accurately extract single neuron activity traces. Recordings from small invertebrates like C. elegans are especially challenging because they undergo very large brain motion and deformation during animal movement. Here we present an automated computer vision pipeline to reliably track populations of neurons with single neuron resolution in the brain of a freely moving C...
May 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28545064/transcriptomic-analysis-of-the-response-of-pseudomonas-fluorescens-to-epigallocatechin-gallate-by-rna-seq
#5
Xiaoxiang Liu, Bimiao Shen, Peng Du, Nan Wang, Jiaxue Wang, Jianrong Li, Aihua Sun
Epigallocatechin gallate (EGCG) is a main constituent of green tea polyphenols that are widely used as food preservatives and are considered to be safe for consumption. However, the underlying antimicrobial mechanism of EGCG and the bacterial response to EGCG are not clearly understood. In the present study, a genome-wide transcriptional analysis of a typical spoilage bacterium, Pseudomonas fluorescens that responded to EGCG was performed using RNA-seq technology. A total of 26,365,414 and 23,287,092 clean reads were generated from P...
2017: PloS One
https://www.readbyqxmd.com/read/28544847/theoretical-determination-of-band-edge-alignments-at-the-water-cuins2-112-semiconductor-interface
#6
Thomas P Senftle, Emily A Carter
Knowledge of a semiconductor electrode's band edge alignment is essential for optimizing processes that occur at the semiconductor/electrolyte interface. Photocatalytic processes are particularly sensitive to such alignments, as they govern the transfer of photo-excited electrons or holes from the surface to reactants in the electrolyte solution. Reconstructions of a semiconductor surface during operation, as well as its interaction with the electrolyte solution, must be considered when determining band edge alignment...
May 25, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28544766/barriers-and-facilitators-of-mentoring-for-trainees-and-early-career-investigators-in-rheumatology-research-current-state-identification-of-needs-and-roadmap-to-an-inter-institutional-adult-rheumatology-mentoring-program
#7
Alexis Ogdie, Jeffrey A Sparks, Sheila T Angeles-Han, Kathleen Bush, Flavia V Castelino, Amit Golding, Yihui Jiang, J Michelle Kahlenberg, Alfred H J Kim, Yvonne C Lee, Kirthi Machireddy, Michael J Ombrello, Ami A Shah, Zachary S Wallace, Peter A Nigrovic, Una E Makris
OBJECTIVES: Determine perceived barriers and facilitators to effective mentoring for early career rheumatology investigators and develop a framework for an inter-institutional mentoring program. METHODS: Focus groups or interviews with rheumatology fellows, junior faculty, and mentors were conducted, audiotaped and transcribed. Content analysis was performed using NVivo software. Themes were grouped into categories (e.g., mentor-mentee relationship, barriers and facilitators of a productive relationship)...
May 23, 2017: Arthritis Care & Research
https://www.readbyqxmd.com/read/28544765/fast-batch-production-of-high-quality-graphene-films-in-a-sealed-thermal-molecular-movement-system
#8
Jianbao Xu, Junxiong Hu, Qi Li, Rubing Wang, Weiwei Li, Yufen Guo, Yongbo Zhu, Fengkui Liu, Zaka Ullah, Guocai Dong, Zhongming Zeng, Liwei Liu
Chemical vapor deposition (CVD) growth of high-quality graphene has emerged as the most promising technique in terms of its integrated manufacturing. However, there lacks a controllable growth method for producing high-quality and a large-quantity graphene films, simultaneously, at a fast growth rate, regardless of roll-to-roll (R2R) or batch-to-batch (B2B) methods. Here, a stationary-atmospheric-pressure CVD (SAPCVD) system based on thermal molecular movement, which enables fast B2B growth of continuous and uniform graphene films on tens of stacked Cu(111) foils, with a growth rate of 1...
May 24, 2017: Small
https://www.readbyqxmd.com/read/28544472/engineering-muscle-cell-alignment-through-3d-bioprinting
#9
Pamela Mozetic, Sara Maria Giannitelli, Manuele Gori, Marcella Trombetta, Alberto Rainer
Processing of hydrogels represents a main challenge for the prospective application of additive manufacturing (AM) to soft tissue engineering. Furthermore, direct manufacturing of tissue precursors with a cell density similar to native tissues has the potential to overcome the extensive in vitro culture required for conventional cell-seeded scaffolds seeking to fabricate constructs with tailored structural and functional properties. In this work, we present a simple AM methodology that exploits the thermoresponsive behavior of a block copolymer (Pluronic®) as a means to obtain good shape retention at physiological conditions and to induce cellular alignment...
May 22, 2017: Journal of Biomedical Materials Research. Part A
https://www.readbyqxmd.com/read/28544464/structural-and-biochemical-insights-into-the-2-o-methylation-of-pyrimidines-34-in-trna
#10
Panjiao Pang, Xiangyu Deng, Zhong Wang, Wei Xie
tRNA molecules undergo extensive modifications during their maturation process and these modifications play important cellular roles. TrmL is a tRNA-modification enzyme that catalyzes the transfer of a methyl group to the 2' hydroxyl group of the pyrimidines at the wobble position 34 in two tRNA(L)(eu) isoacceptors, but the mechanism remains elusive. In this study, we determined the crystal structure of TrmL from Thermus Thermophilus (TtTrmL) to 1.7 Å. The enzyme contains only the conserved minimal SPOUT fold, but displays distinct biochemical behaviors from its Escherichia coli counterpart EcTrmL...
May 25, 2017: FEBS Journal
https://www.readbyqxmd.com/read/28544452/a-conserved-role-for-vegf-signaling-in-specification-of-homologous-mesenchymal-cell-types-positioned-at-spatially-distinct-developmental-addresses-in-early-development-of-sea-urchins
#11
Eric M Erkenbrack, Elizabeth Petsios
Comparative studies of early development in echinoderms are revealing the tempo and mode of alterations to developmental gene regulatory networks and to the cell types they specify. In euechinoid sea urchins, skeletogenic mesenchyme (SM) ingresses prior to gastrulation at the vegetal pole and aligns into a ring-like array with two bilateral pockets of cells, the sites where spiculogenesis will later occur. In cidaroid sea urchins, the anciently diverged sister clade to euechinoid sea urchins, a homologous SM cell type ingresses later in development, after gastrulation has commenced, and consequently at a distinct developmental address...
May 23, 2017: Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution
https://www.readbyqxmd.com/read/28544136/conceptualizations-of-fairness-and-legitimacy-in-the-context-of-ethiopian-health-priority-setting-reflections-on-the-applicability-of-accountability-for-reasonableness
#12
Kadia Petricca, Asfaw Bekele
A critical element in building stronger health systems involves strengthening good governance to build capacity for transparent and fair health planning and priority setting. Over the past 20 years, the ethical framework Accountability for Reasonableness (A4R) has been a prominent conceptual guide in strengthening fair and legitimate processes of health decision-making. While many of the principles embedded within the framework are congruent with Western conceptualizations of what constitutes procedural fairness, there is a paucity in the literature that captures the degree of resonance between these principles and the views of decision makers from non-Western settings; particularly in Africa, where many countries have only recently, within the last 20-30 years, become more democratic...
May 22, 2017: Developing World Bioethics
https://www.readbyqxmd.com/read/28543951/determination-of-genetic-relatedness-from-low-coverage-human-genome-sequences-using-pedigree-simulations
#13
Michael D Martin, Flora Jay, Sergi Castellano, Montgomery Slatkin
We develop and evaluate methods for inferring relatedness among individuals from low-coverage DNA sequences of their genomes, with particular emphasis on sequences obtained from fossil remains. We suggest the major factors complicating the determination of relatedness among ancient individuals are sequencing depth, the number of overlapping sites, the sequencing error rate, and the presence of contamination from present-day genetic sources. We develop a theoretical model that facilitates the exploration of these factors and their relative effects, via measurement of pairwise genetic distances, without calling genotypes, and determine the power to infer relatedness under various scenarios of varying sequencing depth, present-day contamination, and sequencing error...
May 25, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28543877/it-s-time-to-move-on-from-the-bell-curve
#14
Lawrence R Robinson
The bell-curve was first described in the 18(th) century by de Moivre and Gauss to depict the distribution of binomial events, such as coin tossing, or repeated measures of physical objects. In the 19(th) and 20(th) centuries, the bell-curve was appropriated, or perhaps misappropriated, to apply to biologic and social measures across people. For many years we used it to derive reference values for our electrophysiologic studies. There is, however, no reason to believe that electrophysiologic measures should approximate a bell curve distribution, and empiric evidence suggests they do not...
May 23, 2017: Muscle & Nerve
https://www.readbyqxmd.com/read/28543843/white-matter-biomarkers-from-fast-protocols-using-axially-symmetric-diffusion-kurtosis-imaging
#15
Brian Hansen, Ahmad R Khan, Noam Shemesh, Torben E Lund, Ryan Sangill, Simon F Eskildsen, Leif Østergaard, Sune N Jespersen
White matter tract integrity (WMTI) can characterize brain microstructure in areas with highly aligned fiber bundles. Several WMTI biomarkers have now been validated against microscopy and provided promising results in studies of brain development and aging, as well as in a number of brain disorders. Currently, WMTI is mostly used in dedicated animal studies and clinical studies of slowly progressing diseases, and has not yet emerged as a routine clinical tool. To this end, a less data intensive experimental method would be beneficial by enabling high resolution validation studies, and ease clinical applications by speeding up data acquisition compared with typical diffusion kurtosis imaging (DKI) protocols utilized as part of WMTI imaging...
May 22, 2017: NMR in Biomedicine
https://www.readbyqxmd.com/read/28543666/high-resolution-melting-analysis-assay-for-identification-of-fonsecaea-species
#16
Minglan Shi, Xiqing Li, Jiao Feng, Shulin Jia, Xing Xiao, Chunmei Chen, Cindy Fransisca, Liyan Xi, Junmin Zhang
BACKGROUND: Chromoblastomycosis (CBM) is a chronic fungal disease. In China, the principle etiologic agent was a group of dematiaceous fungi, including Fonsecaea monophora, Fonsecaea nubica, and Cladophialophora carrionii. Although the Fonsecaea species have similar morphology, their pathogenicity is quite different. This study aims to establish a new solution for early identification of Fonsecaea species because of their distinctive potential infection risk. METHODS: Five reference strains and 35 clinical isolates from patients with CBM, preserved in our laboratory, were used in this study...
May 22, 2017: Journal of Clinical Laboratory Analysis
https://www.readbyqxmd.com/read/28542739/afternoon-cortisol-provides-a-link-between-self-regulated-anger-and-peer-reported-aggression-in-typically-developing-children-in-the-school-context
#17
Eva Oberle, Kaitlyn McLachlan, Nicole L A Catherine, Ursula Brain, Kimberly A Schonert-Reichl, Joanne Weinberg, Tim F Oberlander
Aggression jeopardizes positive development in children and predicts social and academic maladjustment in school. The present study determined the relationships among anger dysregulation (a marker of emotion regulation), cortisol activity (a biomarker of stress), and peer-nominated aggression in typically developing children in their everyday classroom setting (N = 151, Mean age = 10.86, SD =.74). Salivary cortisol was collected at 09:15, 11:45, and 14:45 hr across 4 consecutive days. Children provided self-reports of anger regulation; peers reported proactive and reactive aggressive behaviors...
May 22, 2017: Developmental Psychobiology
https://www.readbyqxmd.com/read/28542716/improving-needle-tip-identification-during-ultrasound-guided-procedures-in-anaesthetic-practice
#18
REVIEW
H J Scholten, A Pourtaherian, N Mihajlovic, H H M Korsten, R A Bouwman
Ultrasound guidance is becoming standard practice for needle-based interventions in anaesthetic practice, such as vascular access and peripheral nerve blocks. However, difficulties in aligning the needle and the transducer can lead to incorrect identification of the needle tip, possibly damaging structures not visible on the ultrasound screen. Additional techniques specifically developed to aid alignment of needle and probe or identification of the needle tip are now available. In this scoping review, advantages and limitations of the following categories of those solutions are presented: needle guides; alterations to needle or needle tip; three- and four-dimensional ultrasound; magnetism, electromagnetic or GPS systems; optical tracking; augmented (virtual) reality; robotic assistance; and automated (computerised) needle detection...
May 22, 2017: Anaesthesia
https://www.readbyqxmd.com/read/28542704/trabecular-and-cortical-bone-structure-of-the-talus-and-distal-tibia-in-pan-and-homo
#19
Zewdi J Tsegai, Matthew M Skinner, Andrew H Gee, Dieter H Pahr, Graham M Treece, Jean-Jacques Hublin, Tracy L Kivell
OBJECTIVES: Internal bone structure, both cortical and trabecular bone, remodels in response to loading and may provide important information regarding behavior. The foot is well suited to analysis of internal bone structure because it experiences the initial substrate reaction forces, due to its proximity to the substrate. Moreover, as humans and apes differ in loading of the foot, this region is relevant to questions concerning arboreal locomotion and bipedality in the hominoid fossil record...
May 24, 2017: American Journal of Physical Anthropology
https://www.readbyqxmd.com/read/28542435/development-and-evaluation-of-a-bioinformatics-approach-for-designing-molecular-assays-for-viral-detection
#20
Pierre H H Schneeberger, Joël F Pothier, Andreas Bühlmann, Brion Duffy, Christian Beuret, Jürg Utzinger, Jürg E Frey
BACKGROUND: Viruses belonging to the Flaviviridae and Bunyaviridae families show considerable genetic diversity. However, this diversity is not necessarily taken into account when developing diagnostic assays, which are often based on the pairwise alignment of a limited number of sequences. Our objective was to develop and evaluate a bioinformatics workflow addressing two recurrent issues of molecular assay design: (i) the high intraspecies genetic diversity in viruses and (ii) the potential for cross-reactivity with close relatives...
2017: PloS One
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