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https://www.readbyqxmd.com/read/28535294/hgva-the-human-genome-variation-archive
#1
Javier Lopez, Jacobo Coll, Matthias Haimel, Swaathi Kandasamy, Joaquin Tarraga, Pedro Furio-Tari, Wasim Bari, Marta Bleda, Antonio Rueda, Stefan Gräf, Augusto Rendon, Joaquin Dopazo, Ignacio Medina
High-profile genomic variation projects like the 1000 Genomes project or the Exome Aggregation Consortium, are generating a wealth of human genomic variation knowledge which can be used as an essential reference for identifying disease-causing genotypes. However, accessing these data, contrasting the various studies and integrating those data in downstream analyses remains cumbersome. The Human Genome Variation Archive (HGVA) tackles these challenges and facilitates access to genomic data for key reference projects in a clean, fast and integrated fashion...
May 23, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28534797/transition-icons-for-time-series-visualization-and-exploratory-analysis
#2
Paul Nickerson, Raheleh Baharloo, Amal A Wanigatunga, Todd D Manini, Patrick J Tighe, Parisa Rashidi
The modern healthcare landscape has seen the rapid emergence of techniques and devices which temporally monitor and record physiological signals. The prevalence of time series data within the healthcare field necessitates the development of methods which can analyze the data in order to draw meaningful conclusions. Time series behavior is notoriously difficult to intuitively understand due to its intrinsic high-dimensionality, which is compounded in the case of analyzing groups of time series collected from different patients...
May 16, 2017: IEEE Journal of Biomedical and Health Informatics
https://www.readbyqxmd.com/read/28533975/an-exhaustive-survey-of-regular-peptide-conformations-using-a-new-metric-for-backbone-handedness-h
#3
Ranjan V Mannige
The Ramachandran plot is important to structural biology as it describes a peptide backbone in the context of its dominant degrees of freedom-the backbone dihedral angles φ and ψ (Ramachandran, Ramakrishnan & Sasisekharan, 1963). Since its introduction, the Ramachandran plot has been a crucial tool to characterize protein backbone features. However, the conformation or twist of a backbone as a function of φ and ψ has not been completely described for both cis and trans backbones. Additionally, little intuitive understanding is available about a peptide's conformation simply from knowing the φ and ψ values of a peptide (e...
2017: PeerJ
https://www.readbyqxmd.com/read/28533140/3d-interactive-surgical-visualization-system-using-mobile-spatial-information-acquisition-and-autostereoscopic-display
#4
Zhencheng Fan, Yitong Weng, Guowen Chen, Hongen Liao
Three-dimensional (3D) visualization of preoperative and intraoperative medical information becomes more and more important in minimally invasive surgery. We develop a 3D interactive surgical visualization system using mobile spatial information acquisition and autostereoscopic display for surgeons to observe surgical target intuitively. The spatial information of regions of interest (ROIs) is captured by the mobile device and transferred to a server for further image processing. Triangular patches of intraoperative data with texture are calculated with a dimension-reduced triangulation algorithm and a projection-weighted mapping algorithm...
May 19, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28532394/circularlogo-a-lightweight-web-application-to-visualize-intra-motif-dependencies
#5
Zhenqing Ye, Tao Ma, Michael T Kalmbach, Surendra Dasari, Jean-Pierre A Kocher, Liguo Wang
BACKGROUND: The sequence logo has been widely used to represent DNA or RNA motifs for more than three decades. Despite its intelligibility and intuitiveness, the traditional sequence logo is unable to display the intra-motif dependencies and therefore is insufficient to fully characterize nucleotide motifs. Many methods have been developed to quantify the intra-motif dependencies, but fewer tools are available for visualization. RESULT: We developed CircularLogo, a web-based interactive application, which is able to not only visualize the position-specific nucleotide consensus and diversity but also display the intra-motif dependencies...
May 22, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28529964/ultrafast-electron-microscopy-integrated-with-a-direct-electron-detection-camera
#6
Young Min Lee, Young Jae Kim, Ye-Jin Kim, Oh-Hoon Kwon
In the past decade, we have witnessed the rapid growth of the field of ultrafast electron microscopy (UEM), which provides intuitive means to watch atomic and molecular motions of matter. Yet, because of the limited current of the pulsed electron beam resulting from space-charge effects, observations have been mainly made to periodic motions of the crystalline structure of hundreds of nanometers or higher by stroboscopic imaging at high repetition rates. Here, we develop an advanced UEM with robust capabilities for circumventing the present limitations by integrating a direct electron detection camera for the first time which allows for imaging at low repetition rates...
July 2017: Structural Dynamics (Melville, N.Y.)
https://www.readbyqxmd.com/read/28529537/a-web-based-tool-for-automatic-data-collection-curation-and-visualization-of-complex-healthcare-survey-studies-including-social-network-analysis
#7
José Alberto Benítez, José Emilio Labra, Enedina Quiroga, Vicente Martín, Isaías García, Pilar Marqués-Sánchez, Carmen Benavides
There is a great concern nowadays regarding alcohol consumption and drug abuse, especially in young people. Analyzing the social environment where these adolescents are immersed, as well as a series of measures determining the alcohol abuse risk or personal situation and perception using a number of questionnaires like AUDIT, FAS, KIDSCREEN, and others, it is possible to gain insight into the current situation of a given individual regarding his/her consumption behavior. But this analysis, in order to be achieved, requires the use of tools that can ease the process of questionnaire creation, data gathering, curation and representation, and later analysis and visualization to the user...
2017: Computational and Mathematical Methods in Medicine
https://www.readbyqxmd.com/read/28528932/robot-assisted-gynaecological-cancer-surgery-complications-and-prevention
#8
REVIEW
Ka Yu Tse, Hextan Yuen Sheung Ngan, Peter Christopher Lim
Ever since the US Food and Drug Administration approval of the use of da Vinci surgical systems (Intuitive Surgical Inc., Sunnyvale, California) in gynaecology in 2005, robot-assisted surgery has been widely adopted in different countries. Some of the applications in benign and oncological gynaecology include myomectomy, sacrocolpopexy, tubal anastomosis, simple hysterectomy, radical hysterectomy, radical trachelectomy, pelvic and/or para-aortic lymphadenectomy and even debulking surgery for ovarian cancer and pelvic exenteration for recurrent cervical and vaginal cancer...
April 23, 2017: Best Practice & Research. Clinical Obstetrics & Gynaecology
https://www.readbyqxmd.com/read/28528640/ec-clem-a-multidimension-multimodel-software-to-correlate-intermodal-images-with-a-focus-on-light-and-electron-microscopy
#9
Xavier Heiligenstein, Perrine Paul-Gilloteaux, Graça Raposo, Jean Salamero
Correlative light and electron microscopy (CLEM) is a scientific method covered by a broad range of techniques. The path taken to explore a scientific question is often driven both by the question and the technology available. Yet, one common step to all CLEM workflows is the registration of the multimodal images to assign a fluorescent signal to an ultrastructure. The manual relocation and registration of light microscopy and electron microscopy images can be challenging and time-consuming (Muller-Reichert & Verkade, 2014)...
2017: Methods in Cell Biology
https://www.readbyqxmd.com/read/28528639/matrix-maps-an-intuitive-software-to-acquire-analyze-and-annotate-light-microscopy-data-for-clem
#10
Martin Schorb, Frank Sieckmann
Matrix MAPS provides an intuitive interface for acquiring light microscopy data during a correlative light and electron microscopy experiment either at room or cryogenic temperatures. First, the user graphically defines the geometry of the acquisition region on top of preview images. Multiple independent regions can then be imaged in an automated way, each with individual settings. The same interface allows the user to mark and select points or regions of interest whose coordinates can subsequently be transferred directly to the electron microscope...
2017: Methods in Cell Biology
https://www.readbyqxmd.com/read/28527449/correlated-matrix-fluctuation-mediated-activated-transport-of-dilute-penetrants-in-glass-forming-liquids-and-suspensions
#11
Rui Zhang, Kenneth S Schweizer
We formulate a microscopic, force-level statistical mechanical theory for the activated diffusion of dilute penetrants in dense liquids, colloidal suspensions, and glasses. The approach explicitly and self-consistently accounts for coupling between penetrant hopping and matrix dynamic displacements that actively facilitate the hopping event. The key new ideas involve two mechanistically (at a stochastic trajectory level) coupled dynamic free energy functions for the matrix and spherical penetrant particles...
May 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28527318/activating-analytic-thinking-enhances-the-value-given-to-individualizing-moral-foundations
#12
Onurcan Yilmaz, S Adil Saribay
Two central debates within Moral Foundations Theory concern (1) which moral foundations are core and (2) how conflict between ideological camps stemming from valuing different moral foundations can be resolved. Previous studies have attempted to answer the first question by imposing cognitive load on participants to direct them toward intuitive and automatic thought. However, this method has limitations and has produced mixed findings. In the present research, in two experiments, instead of directing participants toward intuitive thought, we tested the effects of activating high-effort, analytic thought on participants' moral foundations...
May 17, 2017: Cognition
https://www.readbyqxmd.com/read/28527138/application-of-hyper-branched-rolling-circle-amplification-hrca-and-hrca-based-strip-test-for-the-detection-of-chattonella-marina
#13
Xiaoli Nie, Chunyun Zhang, Yuanyuan Wang, Changlu Guo, Jin Zhou, Guofu Chen
Harmful algal blooms (HABs) are global threats to marine ecosystems, fisheries, and human health. Therefore, developing effective and accurate methods for identifying causative algae and monitoring seawater quality is urgent. However, traditional, microscopy-based methods are complex, inaccurate, and time-consuming. Here, we present a novel method for effective and sensitive detection of Chattonella marina using hyper-branched rolling circle amplification (HRCA) and HRCA-based strip test (HBST). The large subunit (LSU) ribosomal DNA (rDNA) D1-D2 region of C...
May 19, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28526850/drought-and-child-mortality-a-meta-analysis-of-small-scale-surveys-from-ethiopia
#14
Tefera Darge Delbiso, Chiara Altare, Jose Manuel Rodriguez-Llanes, Shannon Doocy, Debarati Guha-Sapir
Despite the intuitive connection between drought and mortality, we still lack a sound quantitative synthesis of evidence drawn from the available data. In this study, we estimate the pooled under-five death rates (U5DR) and assess the effect of drought on child death in Ethiopia. Small-scale mortality surveys were searched from the Complex Emergency Database and then aggregated spatially and temporally with drought exposure data from the Global Drought Monitor and food insecurity data from the Famine Early Warning Systems Network...
May 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28526721/health-care-resource-utilization-and-associated-costs-among-metastatic-cutaneous-melanoma-patients-treated-with-ipilimumab-intuition-study
#15
Grant A McArthur, Peter Mohr, Paolo Antonio Ascierto, Ana Arance, Ana Banos Hernaez, Peter Kaskel, Michael Weichenthal, Reshma Shinde, Kendall Stevinson
BACKGROUND: There are limited real-world data on health care resource utilization (HCRU) among advanced melanoma patients. The objective of this study was to describe HCRU and health care costs associated with the management of advanced melanoma patients receiving ipilimumab. METHODS: This retrospective multinational, observational study included advanced melanoma patients from Australia, Germany, Italy, and Spain who had received at least 1 dose of ipilimumab. Data extracted from medical charts included inpatient admissions, outpatient visits, surgical procedures, laboratory investigations, radiation therapy, imaging studies, and concomitant medications...
May 19, 2017: Oncologist
https://www.readbyqxmd.com/read/28523364/-structured-patient-handovers-in-perioperative-medicine-rationale-and-implementation-in-clinical-practice
#16
M J Merkel, V von Dossow, B Zwißler
Clear and consistent communication is pivotal for well-functioning teamwork, in operating theatres as well as intensive care units. However, patient handovers significantly vary between specialties and locations. If communication is not well structured, it might increase the risk for mishaps and malpractice. Therefore, implementing structured handover protocols is pivotal. The perioperative setting is a high-risk environment that is prone to communication failures due to operational design (frequent change of shift due to working time restrictions) and a high work load and multitasking (operating room management, short surgery times, concurrent emergencies)...
May 18, 2017: Der Anaesthesist
https://www.readbyqxmd.com/read/28522848/method-to-estimate-relative-risk-using-exposed-proportion-and-case-group-data
#17
Yoichi Yada
A change in risk of an event occurring, which is affected with a factor, is a common issue in many research fields, and relative risk is widely used because of intuitive interpretation. Estimating relative risk has required data from two follow-up groups and can thus be cost and time consuming. Subjects for whom an event occurred (case group) are often observed but generally analyzed in comparison to those for whom an event did not (control group); however, estimating relative risk using case group data without approximation is hindered...
May 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28520846/patient-specific-augmentation-rhinoplasty-using-a-three-dimensional-simulation-program-and-three-dimensional-printing
#18
Yim Don Choi, Youngjun Kim, EunSoo Park
Background: The convergence of three-dimensional (3D) simulation, tissue engineering, and 3D printing technology is creating a paradigm shift in plastic surgery. In augmentation rhinoplasty, determining the ideal material and design method has been a critical issue for many years. Thus, these technologies are expected to make important contributions to augmentation rhinoplasty. Objectives: We sought to validate the feasibility of the 3D carving simulation and patient-specific implant fabrication system (3D carving system) in a clinical trial using reproducibility tests...
May 17, 2017: Aesthetic Surgery Journal
https://www.readbyqxmd.com/read/28517613/a-quantitative-method-to-the-analysis-of-mlc-leaf-position-and-speed-based-on-epid-and-ebt3-film-for-dynamic-imrt-treatment-with-different-types-of-mlc
#19
Yinghui Li, Lixin Chen, Jinhan Zhu, Bin Wang, Xiaowei Liu
A quantitative method based on the electronic portal imaging system (EPID) and film was developed for MLC position and speed testing; this method was used for three MLC types (Millennium, MLCi, and Agility MLC). To determine the leaf position, a picket fence designed by the dynamic (DMLC) model was used. The full-width half-maximum (FWHM) values of each gap measured by EPID and EBT3 were converted to the gap width using the FWHM versus nominal gap width relationship. The algorithm developed for the picket fence analysis was able to quantify the gap width, the distance between gaps, and each individual leaf position...
May 18, 2017: Journal of Applied Clinical Medical Physics
https://www.readbyqxmd.com/read/28516209/foreign-language-effect-and-psychological-distance
#20
Hong Im Shin, Juyoung Kim
Does using a foreign language result in forming different moral decisions than using our mother tongue? Two studies were conducted to investigate whether there is a relationship between foreign language effects (differences between native vs. foreign language conditions) and psychological distance. Study 1 tested four moral dilemmas adapted from Greene et al. (Cognition 107: 1144-1155, 2008). Non-fluent Korean-English bilingual participants (N = 161) indicated decisions regarding four moral dilemmas in either Korean or English languages...
May 17, 2017: Journal of Psycholinguistic Research
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