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https://www.readbyqxmd.com/read/28087693/de-novo-genome-and-transcriptome-assembly-of-the-canadian-beaver-castor-canadensis
#1
Si Lok, Tara A Paton, Zhuozhi Wang, Gaganjot Kaur, Susan Walker, Ryan K C Yuen, Wilson W L Sung, Joseph Whitney, Janet A Buchanan, Brett Trost, Naina Singh, Beverly Apresto, Nan Chen, Matthew Coole, Travis J Dawson, Karen Y Ho, Zhizhou Hu, Sanjeev Pullenayegum, Kozue Samler, Arum Shipstone, Fiona Tsoi, Ting Wang, Sergio L Pereira, Pirooz Rostami, Carol Ann Ryan, Amy Hin Yan Tong, Karen Ng, Yogi Sundaravadanam, Jared T Simpson, Burton K Lim, Mark D Engstrom, Christopher J Dutton, Kevin C R Kerr, Maria Franke, William Rapley, Richard F Wintle, Stephen W Scherer
The Canadian beaver (Castor canadensis) is the largest indigenous rodent in North America. We report a draft annotated assembly of the beaver genome, the first for a large rodent and the first mammalian genome assembled directly from uncorrected and moderate coverage (< 30 ×) long-reads generated by single-molecule sequencing. The genome size is 2.7 Gb estimated by k-mer analysis. We assembled the beaver genome using the new Canu assembler optimized for noisy reads. The resulting assembly was refined using Pilon supported by shortreads (80 ×) and checked for accuracy by congruency against an independent short-read assembly...
January 13, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28087243/using-deep-learning-to-investigate-the-neuroimaging-correlates-of-psychiatric-and-neurological-disorders-methods-and-applications
#2
REVIEW
Sandra Vieira, Walter H L Pinaya, Andrea Mechelli
Deep learning (DL) is a family of machine learning methods that has gained considerable attention in the scientific community, breaking benchmark records in areas such as speech and visual recognition. DL differs from conventional machine learning methods by virtue of its ability to learn the optimal representation from the raw data through consecutive nonlinear transformations, achieving increasingly higher levels of abstraction and complexity. Given its ability to detect abstract and complex patterns, DL has been applied in neuroimaging studies of psychiatric and neurological disorders, which are characterised by subtle and diffuse alterations...
January 10, 2017: Neuroscience and Biobehavioral Reviews
https://www.readbyqxmd.com/read/28086974/ovarian-cancer-density-equalizing-mapping-of-the-global-research-architecture
#3
Dörthe Brüggmann, Katharina Pulch, Doris Klingelhöfer, Celeste Leigh Pearce, David A Groneberg
BACKGROUND: Despite its impact on female health worldwide, no efforts have been made to depict the global architecture of ovarian cancer research and to understand the trends in the related literature. Hence, it was the objective of this study to assess the global scientific performance chronologically, geographically and in regards to economic benchmarks using bibliometric tools and density equalizing map projections. METHODS: The NewQIS platform was employed to identify all ovarian cancer related articles published in the Web of Science since 1900...
January 13, 2017: International Journal of Health Geographics
https://www.readbyqxmd.com/read/28086959/e-learning-programs-in-oncology-a-nationwide-experience-from-2005-to-2014
#4
Jan Degerfält, Staffan Sjöstedt, Per Fransson, Elisabeth Kjellén, Mads U Werner
BACKGROUND: E-learning is an established concept in oncological education and training. However, there seems to be a scarcity of long-term assessments of E-learning programs in oncology vis-á-vis their structural management and didactic value. This study presents descriptive, nationwide data from 2005 to 2014. E-learning oncology programs in chemotherapy, general oncology, pain management, palliative care, psycho-social-oncology, and radiotherapy, were reviewed from our databases. Questionnaires of self-perceived didactic value of the programs were examined 2008-2014...
January 13, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/28086901/gpu-accelerated-voxel-driven-forward-projection-for-iterative-reconstruction-of-cone-beam-ct
#5
Yi Du, Gongyi Yu, Xincheng Xiang, Xiangang Wang
BACKGROUND: For cone-beam computed tomography (CBCT), which has been playing an important role in clinical applications, iterative reconstruction algorithms are able to provide advantageous image qualities over the classical FDK. However, the computational speed of iterative reconstruction is a notable issue for CBCT, of which the forward projection calculation is one of the most time-consuming components. METHOD AND RESULTS: In this study, the cone-beam forward projection problem using the voxel-driven model is analysed, and a GPU-based acceleration method for CBCT forward projection is proposed with the method rationale and implementation workflow detailed as well...
January 5, 2017: Biomedical Engineering Online
https://www.readbyqxmd.com/read/28086892/pressure-ulcer-image-segmentation-technique-through-synthetic-frequencies-generation-and-contrast-variation-using-toroidal-geometry
#6
Ortiz P David, Daniel Sierra-Sosa, Begoña García Zapirain
BACKGROUND: Pressure ulcers have become subject of study in recent years due to the treatment high costs and decreased life quality from patients. These chronic wounds are related to the global life expectancy increment, being the geriatric and physical disable patients the principal affected by this condition. Injuries diagnosis and treatment usually takes weeks or even months by medical personel. Using non-invasive techniques, such as image processing techniques, it is possible to conduct an analysis from ulcers and aid in its diagnosis...
January 6, 2017: Biomedical Engineering Online
https://www.readbyqxmd.com/read/28086746/mviaeval-a-web-tool-for-comprehensively-evaluating-the-performance-of-a-new-missing-value-imputation-algorithm
#7
Wei-Sheng Wu, Meng-Jhun Jhou
BACKGROUND: Missing value imputation is important for microarray data analyses because microarray data with missing values would significantly degrade the performance of the downstream analyses. Although many microarray missing value imputation algorithms have been developed, an objective and comprehensive performance comparison framework is still lacking. To solve this problem, we previously proposed a framework which can perform a comprehensive performance comparison of different existing algorithms...
January 13, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28081097/laser-beam-self-focusing-in-turbulent-dissipative-media
#8
B Hafizi, J R Peñano, J P Palastro, R P Fischer, G DiComo
A high-power laser beam propagating through a dielectric in the presence of fluctuations is subject to diffraction, dissipation, and optical Kerr nonlinearity. A method of moments was applied to a stochastic, nonlinear enveloped wave equation to analyze the evolution of the long-term spot radius. For propagation in atmospheric turbulence described by a Kolmogorov-von Kármán spectral density, the analysis was benchmarked against field experiments in the low-power limit and compared with simulation results in the high-power regime...
January 15, 2017: Optics Letters
https://www.readbyqxmd.com/read/28081064/using-national-inpatient-death-rates-as-a-benchmark-to-identify-hospitals-with-inaccurate-cause-of-death-reporting-missouri-2009-2012
#9
Jennifer Lloyd, Ehsan Jahanpour, Brian Angell, Craig Ward, Andy Hunter, Cherri Baysinger, George Turabelidze
Reporting causes of death accurately is essential to public health and hospital-based programs; however, some U.S. studies have identified substantial inaccuracies in cause of death reporting. Using CDC's national inpatient hospital death rates as a benchmark, the Missouri Department of Health and Senior Services (DHSS) analyzed inpatient death rates reported by hospitals with high inpatient death rates in St. Louis and Kansas City metro areas. Among the selected hospitals with high inpatient death rates, 45...
January 13, 2017: MMWR. Morbidity and Mortality Weekly Report
https://www.readbyqxmd.com/read/28081058/leading-causes-of-death-in-nonmetropolitan-and-metropolitan-areas-united-states-1999-2014
#10
Ernest Moy, Macarena C Garcia, Brigham Bastian, Lauren M Rossen, Deborah D Ingram, Mark Faul, Greta M Massetti, Cheryll C Thomas, Yuling Hong, Paula W Yoon, Michael F Iademarco
PROBLEM/CONDITION: Higher rates of death in nonmetropolitan areas (often referred to as rural areas) compared with metropolitan areas have been described but not systematically assessed. PERIOD COVERED: 1999-2014 DESCRIPTION OF SYSTEM: Mortality data for U.S. residents from the National Vital Statistics System were used to calculate age-adjusted death rates and potentially excess deaths for nonmetropolitan and metropolitan areas for the five leading causes of death...
January 13, 2017: MMWR. Surveillance Summaries: Morbidity and Mortality Weekly Report. Surveillance Summaries
https://www.readbyqxmd.com/read/28080088/the-effect-of-reactive-emotions-expressed-in-response-to-another-s-anger-on-inferences-of-social-power
#11
Shlomo Hareli, Shlomo David
Social perception of emotions is influenced by the context in which it occurs. One such context is a social interaction involving an exchange of emotions. The way parties to the interaction are perceived is shaped by the combination of emotions exchanged. This idea was examined by assessing the extent to which expressions of anger toward a target-which, in isolation, are perceived as signals of high social power-are influenced by the target's emotional reaction to it (i.e., reactive emotions). Three studies show that the angry person was perceived as having a higher level of social power when this anger was responded by fear or sadness than when it was responded by neutrality or anger...
January 12, 2017: Emotion
https://www.readbyqxmd.com/read/28080054/bond-dissociation-energies-for-diatomic-molecules-containing-3d-transition-metals-benchmark-scalar-relativistic-coupled-cluster-calculations-for-twenty-molecules
#12
Lan Cheng, Jürgen Gauss, Branko Ruscic, Peter B Armentrout, John F Stanton
Benchmark scalar-relativistic coupled-cluster calculations for dissociation energies of the twenty diatomic molecules containing 3d transition metals in the 3dMLBE20 database (Xu et al., J. Chem. Theory Comput. 2015, 11, 2036) ) are reported. Electron correlation and basis set effects are systematically studied. The agreement between theory and experiment is in general satisfactory. For a subset of sixteen molecules, the standard deviation between computational and experimental values is 9 kJ/mol with the maximum deviation being 15 kJ/mol...
January 12, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28080051/prediction-of-bond-dissociation-energies-heat-of-formation-for-diatomic-transition-metal-compounds-ccsd-t-works
#13
Zongtang Fang, Monica Vasiliu, Kirk A Peterson, David A Dixon
It was recently reported (J. Chem. Theory Comput. 2015, 11, 2036-2052) that the coupled cluster singles and doubles with perturbative triples method, CCSD(T), should not be used as a benchmark tool for the prediction of dissociation energies (heats of formation) for the 1st row transition metal diatomics based on a comparison with the experimental thermodynamic values for a set of 20 diatomics. In the present work the bond dissociation energies as well as the heats of formation for those diatomics have been calculated by the Feller-Peterson-Dixon approach at the CCSD(T)/complete basis set (CBS) level of theory including scalar relativistic corrections and correlation of the outer shell of core electrons in addition to the valence electrons...
January 12, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28079887/drp-1-is-required-for-bh3-mimetic-mediated-mitochondrial-fragmentation-and-apoptosis
#14
Mateus Milani, Dominic P Byrne, Georgia Greaves, Michael Butterworth, Gerald M Cohen, Patrick A Eyers, Shankar Varadarajan
The concept of using BH3 mimetics as anticancer agents has been substantiated by the efficacy of selective drugs, such as Navitoclax and Venetoclax, in treating BCL-2-dependent haematological malignancies. However, most solid tumours depend on MCL-1 for survival, which is highly amplified in multiple cancers and a major factor determining chemoresistance. Most MCL-1 inhibitors that have been generated so far, while demonstrating early promise in vitro, fail to exhibit specificity and potency in a cellular context...
January 12, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/28079561/-single-checked-patient-group-directions-during-initial-nurse-assessment-within-paediatric-emergency-departments-of-the-uk-and-ireland
#15
Chris K Bird, Anthony G Sinclair, Stuart Hartshorn
OBJECTIVE: Double checking medications at initial assessment within paediatric emergency departments (EDs) has the potential to delay patient flow, and doubt has been cast on the efficacy of double checking in all but high-risk medications. We aimed to benchmark current practice for the use of Patient Group Direction (PGD) medications at initial assessment in EDs within the Paediatric Emergency Research UK and Ireland (PERUKI) network, with a focus on the use of 'single-checker' PGDs...
January 10, 2017: European Journal of Emergency Medicine: Official Journal of the European Society for Emergency Medicine
https://www.readbyqxmd.com/read/28079527/binary-moving-blocker-based-scatter-correction-in-cone-beam-computed-tomography-with-width-truncated-projections-proof-of-concept
#16
Ho Lee, Benjamin Fahimian, Lei Xing
This paper proposes a binary moving-blocker (BMB)-based technique for scatter correction in cone-beam computed tomography (CBCT). In concept, a beam blocker consisting of lead strips, mounted in front of the x-ray tube, moves rapidly in and out of the beam during a single gantry rotation. The projections are acquired in alternating phases of blocked and unblocked cone beams, where the blocked phase results in a stripe pattern in the width direction. To derive the scatter map from the blocked projections, one-dimensional B-Spline interpolation/extrapolation is applied by using the detected information in the shaded regions...
January 12, 2017: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/28079526/a-measurement-based-generalized-source-model-for-monte-carlo-dose-simulations-of-ct-scans
#17
Xin Ming, Yuanming Feng, Ransheng Liu, Chengwen Yang, Li Zhou, Hezheng Zhai, Jun Deng
The goal of this study is to present a generalized source model (GSM) for accurate Monte Carlo dose simulations of CT scans based solely on the measurement data without a priori knowledge of scanner specifications. The proposed generalized source model consists of an extended circular source located at x-ray target level with its energy spectrum, source distribution and fluence distribution derived from a set of measurement data conveniently available in the clinic. Specifically, the central axis percent depth dose (PDD) curves measured in water and the cone output factors measured in air were used to derive the energy spectrum and the source distribution respectively with a Levenberg-Marquardt algorithm...
January 12, 2017: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/28079322/-incidence-of-non-work-related-sickness-absence-in-spain-by-economic-activity-of-the-company
#18
Fernando G Benavides, Elena Zaballa, Xavier Duran, Victòria Sanchez-Niubo, David Gimeno Ruiz de Porras
INTRODUCTION: The management of sickness absence due to non-work-related diseases in Spain has typically focused on the control of its duration. The goal of this study was to provide estimates for the incidence of sickness absence due to nonwork-related diseases by economic activity to help shift the focus of management of sickness absence towards prevention. METHODS: Retrospective study based on 646,337 workers and 133,812 episodes of sickness absence started in 2009, from the Working Continuous Life Sample...
January 2017: Archivos de Prevención de Riesgos Laborales
https://www.readbyqxmd.com/read/28079135/predicting-drug-target-interactions-by-dual-network-integrated-logistic-matrix-factorization
#19
Ming Hao, Stephen H Bryant, Yanli Wang
In this work, we propose a dual-network integrated logistic matrix factorization (DNILMF) algorithm to predict potential drug-target interactions (DTI). The prediction procedure consists of four steps: (1) inferring new drug/target profiles and constructing profile kernel matrix; (2) diffusing drug profile kernel matrix with drug structure kernel matrix; (3) diffusing target profile kernel matrix with target sequence kernel matrix; and (4) building DNILMF model and smoothing new drug/target predictions based on their neighbors...
January 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28077692/reference-curves-for-the-australian-canadian-hand-osteoarthritis-index-in-the-middle-aged-dutch-population
#20
Féline P B Kroon, Sofia Ramiro, Patrick Royston, Saskia Le Cessie, Frits R Rosendaal, Margreet Kloppenburg
OBJECTIVE: The aim was to establish reference curves of the Australian/Canadian Hand Osteoarthritis Index (AUSCAN), a widely used questionnaire assessing hand complaints. METHODS: Analyses were performed in a population-based sample, The Netherlands Epidemiology of Obesity study (n = 6671, aged 45-65 years). Factors associated with AUSCAN scores were analysed with ordered logistic regression, because AUSCAN data were zero inflated, dividing AUSCAN into three categories (0 vs 1-5 vs >5)...
January 11, 2017: Rheumatology
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