Interactive Table Research Articles

ToTem: a tool for variant calling pipeline optimization

BackgroundHigh-throughput bioinformatics analyses of next generation sequencing (NGS) data often require challenging pipeline optimization. The key problem is choosing appropriate tools and selecting the best parameters for optimal precision and recall.ResultsHere we introduce ToTem, a tool for automated pipeline optimization. ToTem is a stand-alone web application with a comprehensive graphical user interface (GUI). ToTem is written in Java and PHP with an underlying connection to a MySQL database. Its primary role is to automatically generate, execute and benchmark different variant calling pipeline settings. Our tool allows an analysis to be started from any level of the process and with the possibility of plugging almost any tool or code. To prevent an over-fitting of pipeline parameters, ToTem ensures the reproducibility of these by using cross validation techniques that penalize the final precision, recall and F-measure. The results are interpreted as interactive graphs and tables allowing an optimal pipeline to be selected, based on the user’s priorities. Using ToTem, we were able to optimize somatic variant calling from ultra-deep targeted gene sequencing (TGS) data and germline variant detection in whole genome sequencing (WGS) data.ConclusionsToTem is a tool for automated pipeline optimization which is freely available as a web application at https://totem.software.

MetExplore: collaborative edition and exploration of metabolic networks.

Metabolism of an organism is composed of hundreds to thousands of interconnected biochemical reactions responding to environmental or genetic constraints. This metabolic network provides a rich knowledge to contextualize omics data and to elaborate hypotheses on metabolic modulations. Nevertheless, performing this kind of integrative analysis is challenging for end users with not sufficiently advanced computer skills since it requires the use of various tools and web servers. MetExplore offers an all-in-one online solution composed of interactive tools for metabolic network curation, network exploration and omics data analysis. In particular, it is possible to curate and annotate metabolic networks in a collaborative environment. The network exploration is also facilitated in MetExplore by a system of interactive tables connected to a powerful network visualization module. Finally, the contextualization of metabolic elements in the network and the calculation of over-representation statistics make it possible to interpret any kind of omics data. MetExplore is a sustainable project maintained since 2010 freely available at https://metexplore.toulouse.inra.fr/metexplore2/.

M6ASNP: a tool for annotating genetic variants by m6A function.

BackgroundLarge-scale genome sequencing projects have identified many genetic variants for diverse diseases. A major goal of these projects is to characterize these genetic variants to provide insight into their function and roles in diseases. N6-methyladenosine (m6A) is one of the most abundant RNA modifications in eukaryotes. Recent studies have revealed that aberrant m6A modifications are involved in many diseases.FindingsIn this study, we present a user-friendly web server called “m6ASNP” that is dedicated to the identification of genetic variants that target m6A modification sites. A random forest model was implemented in m6ASNP to predict whether the methylation status of an m6A site is altered by the variants that surround the site. In m6ASNP, genetic variants in a standard variant call format (VCF) are accepted as the input data, and the output includes an interactive table that contains the genetic variants annotated by m6A function. In addition, statistical diagrams and a genome browser are provided to visualize the characteristics and to annotate the genetic variants.ConclusionsWe believe that m6ASNP is a very convenient tool that can be used to boost further functional studies investigating genetic variants. The web server “m6ASNP” is implemented in JAVA and PHP and is freely available at [60].

HYGIENIC REGULATION OF THE USE OF INTERACTIVE EQUIPMENT IN THE CLASSROOM IN KINDERGARTEN

Introduction. The purpose of the study was to assess the hygienic impact of classes with using an interactive whiteboard and an interactive table on the functional state of the body of preschool children aged 6-7 years. Material and methods. The results of studies of the impact of classes using interactive equipment in kindergarten on the functional state of the body of children aged 6-7 years. The interactive whiteboard was used in all classes (two or three) during the day. Continuous duration of its use at each session did not exceed 5 minutes, in total - 15 minutes during play activities used the interactive table which lasted up to 10 min. Results. The comparative analysis of the results of the studies did not reveal any differences in the indices of fatigue and psycho-emotional state of children in the response to developmental activities with and without the use of interactive equipment. The expressed activating influence of occupations with use of the interactive equipment on the activity of the central nervous system is established. This was manifested in a significant increase in the speed of complex sensorimotor responses and a decrease in the probability of an error. Discussion. In our opinion, the approximate response to the novelty, bright and attractive form of information presentation with the interactive equipment lead to the functional mobilization of brain structures involved in the analysis of information, followed by a more pronounced concentration of attention, creates an optimal tone of the central nervous system, providing ease and speed of lockings and functioning of nerve connections underlying learning.

Highlights of the 2017 European AIDS Clinical Society (EACS) Guidelines for the treatment of adult HIV-positive persons version 9.0.

BackgroundThe European AIDS Clinical Society (EACS) Guidelines have since 2005 provided multidisciplinary recommendations for the care of HIV‐positive persons in geographically diverse areas.Guideline highlightsMajor revisions have been made in all sections of the 2017 Guidelines: antiretroviral treatment (ART), comorbidities, coinfections and opportunistic diseases. Newly added are also a summary of the main changes made, and direct video links to the EACS online course on HIV Management. Recommendations on the clinical situations in which tenofovir alafenamide may be considered over tenofovir disoproxil fumarate are provided, and recommendations on which antiretrovirals can be used safely during pregnancy have been revised. Renal and bone toxicity and hepatitis C virus (HCV) treatment have been added as potential reasons for ART switches in fully virologically suppressed individuals, and dolutegravir/rilpivirine has been included as a treatment option. In contrast, dolutegravir monotherapy is not recommended. New recommendations on non‐alcoholic fatty liver disease, chronic lung disease, solid organ transplantation, and prescribing in elderly are included, and human papilloma virus (HPV) vaccination recommendations have been expanded. All drug–drug interaction tables have been updated and new tables are included. Treatment options for direct‐acting antivirals (DAAs) have been updated and include the latest combinations of sofosbuvir/velpatasvir/voxilaprevir and glecaprevir/pibrentasvir. Recommendations on management of DAA failure and acute HCV infection have been expanded. For treatment of tuberculosis (TB), it is underlined that intermittent treatment is contraindicated, and for resistant TB new data suggest that using a three‐drug combination may be as effective as a five‐drug regimen, and may reduce treatment duration from 18‐24 to 6‐10 months.ConclusionsVersion 9.0 of the EACS Guidelines provides a holistic approach to HIV care and is translated into the six most commonly spoken languages.

Parametric Optimization of WEDM on α-β Titanium Alloy using Desirability Approach

Wire-electro discharge machining (WEDM) is a specialized non-traditional machining process to produce intricate shapes and for producing components which are difficult to machining by conventional machining methods. Modeling and optimization of machining process is one of the important aspects in manufacturing. In order to achieve this, proper planning of experimentation is desirable to analysis the results. In this work, to conduct experiments a central composite face centered (CCF) design has been used in order to optimize the WEDM process. Five input parameters considered as pulse-on time, pulse-off time, peak current, servo voltage and wire feed and responses to be measured as surface roughness and material removal rate. Second order models were developed to establish the relation between responses and process parameters using multiple linear regression. The effect of process parameters on the responses are evaluated and optimum cutting conditions for minimizing surface roughness and maximizing material removal rate were determined using response tables, response graphs, interaction tables, 3-D surface plots and desirability analysis. Further, in-depth analysis of factor affects has been carried out by means of interaction tables and interaction graphs. Backward linear regression option of SPSS, is used to develop the surface roughness (SR) and material removal rate (MRR) models. Simultaneous optimization of responses has been performed using desirability function.

Interactive and Portable Periodic Table Boxed Set with Real Samples

Interactive and Portable Periodic Table Boxed Set with Real Samples

Estimated and Interactively Visualized Female Breast Cancer Incidence Rates in Missouri Senate Districts: 2008-2012.

ObjectivesTo measure and interactively visualize female breast cancer (FBC) incidence rates in Missouri by age, race, stage and grade, and senate district of residence at diagnosis from 2008 to 2012.MethodsAn observational epidemiological study. The FBC cases in counties split by senate districts were geocoded. Population database was created. A database was created within SEER*Stat. The incidence rates and the 95% Confidence Interval (CI) were age standardized using US 2000 Standard Population. The Census Bureau’s Cartographic Boundary Files were used to create maps showing Missouri senate districts. Incidence results were loaded along with the maps into InstantAtlas™ software to produce interactive reports.ResultsCancer profiles were created for all 34 Missouri senate districts. An area profile and a double map that included interactive maps, graphs, and tables for the 34 Missouri senate districts were built.ConclusionThe results may provide an estimation of social inequality within the state and could provide clues about the impact of level of coverage and accessibility to screening and health care services on disease prevention and early diagnosis.

Tibetan Magmatism Database

AbstractA database containing previously published geochronologic, geochemical, and isotopic data on Mesozoic to Quaternary igneous rocks in the Himalayan‐Tibetan orogenic system are presented. The database is intended to serve as a repository for new and existing igneous rock data and is publicly accessible through a web‐based platform that includes an interactive map and data table interface with search, filtering, and download options. To illustrate the utility of the database, the age, location, and ɛHft composition of magmatism from the central Gangdese batholith in the southern Lhasa terrane are compared. The data identify three high‐flux events, which peak at 93, 50, and 15 Ma. They are characterized by inboard arc migration and a temporal and spatial shift to more evolved isotopic compositions.

Abstract A10: CRISPR-AnalyzeR (caR): Web-based, interactive and exploratory analysis and documentation of pooled CRISPR/Cas9 screens

Abstract Since the availability of the CRISPR/Cas9 gene editing technique, pooled CRISPR/Cas9 screens have become a powerful and versatile tool for the investigation of functional genomics in a variety of organisms. Pooled CRISPR/Cas9 screens are cost-effective and do not require lab automation, which allows even small labs to perform genome-wide genetic perturbation screens. The analysis of such screens so far requires in-depth knowledge in either bioinformatics or data analysis as there is a limited availability of end-to-end data analysis pipelines (Li et al., 2014; Winter et al., 2015). Moreover, the explorative analysis of screening data using end-to-end analysis tools often comes with certain limitations. Either these pipelines require sufficient computing power on the user machine or have to be run in command-line mode on dedicated machines, which constrains the usability. A special need for wet-lab scientists is the availability of analysis pipelines which allow them to analyze the screening data on their own, knowing best about potential candidates and the biological background. Here we describe the CRISPR-AnalyzeR (caR), which is a web-based and fully-interactive tool to analyze pooled CRISPR/Cas9 screens meant for wet-lab scientists. caR combines both, end-to-end data analysis and explorative screen analysis that can be accessed via a regular web-browser such as Google Chrome or Firefox from any device - allowing the user to analyze the data in a comfortable, convenient and exploratory way. Moreover, caR uses latest visualization technologies to provide interactive plots and tables, allowing even novice users to analyze their own screens in an exploratory way. caR performs hit-calling using six different analysis methods, which gives the user the power and flexibility to select appropriate follow-up candidates. caR provides an easy-to-follow workflow and guides the user through the whole analysis process, which includes quality control, hit calling, in-depth gene information, data annotation enrichment and downloadable interactive reports to provide a comprehensive documentation. Since caR is a web-based tool, it can be used via a provided web-server at http://crispr-analyzer.dkfz.de or can be downloaded for a local network installation. Citation Format: Jan Winter, Marc Schwering, Benedikt Rauscher, Florian Heigwer, Michael Boutros. CRISPR-AnalyzeR (caR): Web-based, interactive and exploratory analysis and documentation of pooled CRISPR/Cas9 screens [abstract]. In: Proceedings of the AACR Precision Medicine Series: Opportunities and Challenges of Exploiting Synthetic Lethality in Cancer; Jan 4-7, 2017; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2017;16(10 Suppl):Abstract nr A10.

Globe Browsing: Contextualized Spatio-Temporal Planetary Surface Visualization.

Results of planetary mapping are often shared openly for use in scientific research and mission planning. In its raw format, however, the data is not accessible to non-experts due to the difficulty in grasping the context and the intricate acquisition process. We present work on tailoring and integration of multiple data processing and visualization methods to interactively contextualize geospatial surface data of celestial bodies for use in science communication. As our approach handles dynamic data sources, streamed from online repositories, we are significantly shortening the time between discovery and dissemination of data and results. We describe the image acquisition pipeline, the pre-processing steps to derive a 2.5D terrain, and a chunked level-of-detail, out-of-core rendering approach to enable interactive exploration of global maps and high-resolution digital terrain models. The results are demonstrated for three different celestial bodies. The first case addresses high-resolution map data on the surface of Mars. A second case is showing dynamic processes, such as concurrent weather conditions on Earth that require temporal datasets. As a final example we use data from the New Horizons spacecraft which acquired images during a single flyby of Pluto. We visualize the acquisition process as well as the resulting surface data. Our work has been implemented in the OpenSpace software [8], which enables interactive presentations in a range of environments such as immersive dome theaters, interactive touch tables, and virtual reality headsets.

ITTVis: Interactive Visualization of Table Tennis Data.

The rapid development of information technology paved the way for the recording of fine-grained data, such as stroke techniques and stroke placements, during a table tennis match. This data recording creates opportunities to analyze and evaluate matches from new perspectives. Nevertheless, the increasingly complex data poses a significant challenge to make sense of and gain insights into. Analysts usually employ tedious and cumbersome methods which are limited to watching videos and reading statistical tables. However, existing sports visualization methods cannot be applied to visualizing table tennis competitions due to different competition rules and particular data attributes. In this work, we collaborate with data analysts to understand and characterize the sophisticated domain problem of analysis of table tennis data. We propose iTTVis, a novel interactive table tennis visualization system, which to our knowledge, is the first visual analysis system for analyzing and exploring table tennis data. iTTVis provides a holistic visualization of an entire match from three main perspectives, namely, time-oriented, statistical, and tactical analyses. The proposed system with several well-coordinated views not only supports correlation identification through statistics and pattern detection of tactics with a score timeline but also allows cross analysis to gain insights. Data analysts have obtained several new insights by using iTTVis. The effectiveness and usability of the proposed system are demonstrated with four case studies.

Stereochemistry of a Second Riolozane and Other Diterpenoids from Jatropha dioica.

The dichloromethane extract of the roots of Jatropha dioica afforded riolozatrione (1) and a C-6 epimer of riolozatrione, 6-epi-riolozatrione (2), as a new structure and only the second reported riolozane diterpenoid. The two known diterpenoids jatrophatrione (3) and citlalitrione (4) were also isolated and characterized. Both epimers 1 and 2 are genuine plant constituents, with 2 likely being the biosynthesis precursor of 1 due to the tendency for the quantitative transformation of 2 into 1 under base catalysis. The structural characterization and distinction of the stereoisomers utilized 1H iterative full-spin analysis, yielding complete J-correlation maps that were represented as quantum interaction and linkage tables. The absolute configuration of compounds 1-4 was established by means of vibrational circular dichroism and via X-ray diffraction analysis for 1, 2, and 4. Additionally, the cytotoxic and antiherpetic in vitro activities of the isolates were evaluated.

The Reader's Guide to Optimal Monetary Policy

This document serves as an update with discussion of the accompanying new interactive visualization and table tool. Recently, multiple economists have banded together to suggest to the Federal Reserve that the inflation target needs to be changed. The inflation target is the core through which monetary policy makers rationalize their decisions while following the dual mandate of maximum employment and price stability. Understanding the rationale for its level, 2%, and understanding the academic literature related to optimal inflation dynamics seems more important than ever before. This survey takes into account every optimal monetary policy paper made available to the public since the mid-1990s and provides a careful discussion on the most important costs and benefits of inflation.

CompMS2Miner: An Automatable Metabolite Identification, Visualization, and Data-Sharing R Package for High-Resolution LC-MS Data Sets.

A long-standing challenge of untargeted metabolomic profiling by ultrahigh-performance liquid chromatography-high-resolution mass spectrometry (UHPLC-HRMS) is efficient transition from unknown mass spectral features to confident metabolite annotations. The compMS2Miner (Comprehensive MS2 Miner) package was developed in the R language to facilitate rapid, comprehensive feature annotation using a peak-picker-output and MS2 data files as inputs. The number of MS2 spectra that can be collected during a metabolomic profiling experiment far outweigh the amount of time required for pain-staking manual interpretation; therefore, a degree of software workflow autonomy is required for broad-scale metabolite annotation. CompMS2Miner integrates many useful tools in a single workflow for metabolite annotation and also provides a means to overview the MS2 data with a Web application GUI compMS2Explorer (Comprehensive MS2 Explorer) that also facilitates data-sharing and transparency. The automatable compMS2Miner workflow consists of the following steps: (i) matching unknown MS1 features to precursor MS2 scans, (ii) filtration of spectral noise (dynamic noise filter), (iii) generation of composite mass spectra by multiple similar spectrum signal summation and redundant/contaminant spectra removal, (iv) interpretation of possible fragment ion substructure using an internal database, (v) annotation of unknowns with chemical and spectral databases with prediction of mammalian biotransformation metabolites, wrapper functions for in silico fragmentation software, nearest neighbor chemical similarity scoring, random forest based retention time prediction, text-mining based false positive removal/true positive ranking, chemical taxonomic prediction and differential evolution based global annotation score optimization, and (vi) network graph visualizations, data curation, and sharing are made possible via the compMS2Explorer application. Metabolite identities and comments can also be recorded using an interactive table within compMS2Explorer. The utility of the package is illustrated with a data set of blood serum samples from 7 diet induced obese (DIO) and 7 nonobese (NO) C57BL/6J mice, which were also treated with an antibiotic (streptomycin) to knockdown the gut microbiota. The results of fully autonomous and objective usage of compMS2Miner are presented here. All automatically annotated spectra output by the workflow are provided in the Supporting Information and can alternatively be explored as publically available compMS2Explorer applications for both positive and negative modes ( https://wmbedmands.shinyapps.io/compMS2_mouseSera_POS and https://wmbedmands.shinyapps.io/compMS2_mouseSera_NEG ). The workflow provided rapid annotation of a diversity of endogenous and gut microbially derived metabolites affected by both diet and antibiotic treatment, which conformed to previously published reports. Composite spectra (n = 173) were autonomously matched to entries of the Massbank of North America (MoNA) spectral repository. These experimental and virtual (lipidBlast) spectra corresponded to 29 common endogenous compound classes (e.g., 51 lysophosphatidylcholines spectra) and were then used to calculate the ranking capability of 7 individual scoring metrics. It was found that an average of the 7 individual scoring metrics provided the most effective weighted average ranking ability of 3 for the MoNA matched spectra in spite of potential risk of false positive annotations emerging from automation. Minor structural differences such as relative carbon-carbon double bond positions were found in several cases to affect the correct rank of the MoNA annotated metabolite. The latest release and an example workflow is available in the package vignette ( https://github.com/WMBEdmands/compMS2Miner ) and a version of the published application is available on the shinyapps.io site ( https://wmbedmands.shinyapps.io/compMS2Example ).

Interactive plant functional group and water table effects on decomposition and extracellular enzyme activity in Sphagnum peatlands

Peatland decomposition may be altered by hydrology and plant functional groups (PFGs), but exactly how the latter influences decomposition is unclear, as are potential interactions of these factors. We used a factorial mesocosm experiment with intact 1 m3 peat monoliths to explore how PFGs (sedges vs Ericaceae) and water table level individually and interactively affect decomposition processes. Decomposition was measured using litter bags at three depths filled with cellulose strips to mimic decomposition of a simple plant-derived structure, and Sphagnum tissue to simulate decomposition of the most abundant recalcitrant material in peatlands. We also analyzed the potential activity of five hydrolytic extracellular enzymes at an intermediate depth. We found lowered water table reduced activity of several enzymes and increased cellulose and Sphagnum decomposition. Presence of Ericaceae reduced decomposition of the recalcitrant Sphagnum tissue, whereas higher activity of chitinase was found in the combined presence of sedges and Ericaceae. We found no relationship between any potential enzyme activity and Sphagnum decomposition rate. Overall our results showed a dominating role of water table controlling decomposition processes, as well as support for the hypothesis that the presence of mycorrhizal Ericaceae can slow decomposition processes of complex plant tissues in peatlands.

Human Computer Interaction Based on an Integrated Design of Real and Virtual World

This research has focused on the idea of Groupware Matrix and Roomware and placed them in the field of integrated design of real, physical, architectural spaces and virtual, digital information spaces. Roomware main idea is the computer-augmented components in rooms, e.g. furniture. The general approach is to gather information via examples from i-LAND project where developing various Roomware devices to introduce the meaning and the use of interactive information and cooperation design. It describe i-LAND that consists of DynaWall, Interact able, and ComChair. i-LAND requires and provides other components of human-computer interaction and new forms of computer-supported cooperative work (CSCW). This helps the designer to gather information from architectural spaces and implement a new work practices and design. i-LAND also consists of various “Roomware” components, i.e. computer-augmented objects integrating room elements with information technology. It present the current realization of i-LAND as an interactive electronic wall, an interactive table, and two computer-enhanced chairs.

Gene expression profile of whole blood cells differs in pregnant women with positive screening and negative diagnosis for gestational diabetes

ObjectiveTo evaluate the gene expression profile of whole blood cells in pregnant women without diabetes (with positive screening and negative diagnosis for gestational diabetes mellitus (GDM)) compared with pregnant women...

Predicting Responses in Multiple Environments: Issues in Relation to Genotype × Environment Interactions

Prediction of the phenotypes for a set of genotypes across multiple environments is a fundamental task in any plant breeding program. Genomic prediction (GP) can assist selection decisions by combining incomplete phenotypic information over multiple environments (MEs) with dense sets of markers. We compared a range of ME‐GP models differing in the way environment‐specific genetic effects were modeled. Information among environments was shared either implicitly via the response variable, or by the introduction of explicit environmental covariables. We discuss the models not only in the light of their accuracy, but also in their ability to predict the different parts of the incomplete genotype × environment interaction (G × E) table: (Gt; Et), (Gu; Et), (Gt; Eu), and (Gu; Eu), where G is genotype, E is environment, both tested (t; in one or more instances) and untested (u). Using the ‘Steptoe’ × ‘Morex’ barley (Hordeum vulgare L.) population as an example, we show the advantage of ME‐GP models that account for G × E. In addition, for our example data set, we show that for prediction in the most challenging scenario of untested environments (Eu), the use of explicit environmental information is preferable over the simpler approach of predicting from a main effects model. Besides producing the most general ME‐GP model, the use of environmental covariables naturally links with ecophysiological and crop‐growth models (CGMs) for G × E. We conclude with a list of future research topics in ME‐GP, where we see CGMs playing a central role.

Bayesian estimation of the orthogonal decomposition of a contingency table

In a multinomial sampling, contingency tables can be parametrized by probabilities of each cell. These probabilities constitute the joint probability function of two or more discrete random variables. These probability tables have been previously studied from a compositional point of view. The compositional analysis of probability tables ensures coherence when analysing sub-tables. The main results are:(1) given a probability table, the closest independent probability table is the product of their geometric marginals;(2) the probability table can be orthogonally decomposed into an independent table and an interaction table;(3) the departure of independence can be measured using simplicial deviance, which is the Aitchison square norm of the interaction table.In previous works, the analysis has been performed from a frequentist point of view. This contribution is aimed at providing a Bayesian assessment of the decomposition. The resulting model is a log-linear one, which parameters are the centered log-ratio transformations of the geometric marginals and the interaction table.Using a Dirichlet prior distribution of multinomial probabilities, the posterior distribution of multinomial probabilities is again a Dirichlet distribution. Simulation of this posterior allows to study the distribution of marginal and interaction parameters, checking the independence of the observed contingency table and cell interactions.The results corresponding to a two-way contingency table example are presented.