SciCombinator

Discover the most talked about and latest scientific content & concepts.

Concept: Web application framework

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DAME (Dynamic Assessment of Microbial Ecology) is a Shiny-based web application for interactive analysis and visualization of microbial sequencing data. DAME provides researchers not familiar with R programming the ability to access the most current R functions utilized for ecology and gene sequencing data analyses. Currently, DAME supports group comparisons of several ecological estimates of α-diversity and β-diversity, along with differential abundance analysis of individual taxa. Using the Shiny framework, the user has complete control of all aspects of the data analysis, including sample/experimental group selection and filtering, estimate selection, statistical methods, and visualization parameters. Furthermore, graphical and tabular outputs are supported by R packages using D3.js and are fully interactive.

Concepts: Scientific method, Evolution, Statistics, Mathematics, Data, PHP, Web 2.0, Web application framework

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Few studies have discussed how the increasing ambient air pollution may affect policy-related attitudes. Medical professionals constitute an important interest group who analyse and solve public issues within a medicalised framework. The current study investigates whether ambient air pollution is associated with a greater likelihood of supporting tobacco control measures among medical students.

Concepts: Pollution, Cultural studies, The Current, National Ambient Air Quality Standards, Air pollution, Web application framework

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A stereocontrolled approach to the cis-decalin framework of clerodane diterpenes and biologically active quinone sesquiterpenes is reported. Starting from an inexpensive optically pure tetrahydroindanone, Birch reductive alkylation builds two new contiguous chiral centers-one of which is quaternary and all-carbon-substituted. Also featured is a highly regioselective diazoalkane-carbonyl homologation reaction to prepare the 6,6-bicyclic skeleton. Therein, the utility of Sc(OTf)₃ as a mild catalyst for formal 1C insertion in complex settings is demonstrated.

Concepts: DNA, Chemical reaction, Enantiomer, Field, Terpene, Gary Numan, Sesquiterpene, Web application framework

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Colorectal cancer (CRC) is a leading cause of cancer-related mortality. CRC incidence and mortality can be reduced by several screening strategies, including colonoscopy, but randomized CRC prevention trials face significant obstacles such as the need for large study populations with long follow-up. Therefore, CRC screening strategies will likely be designed and optimized based on computer simulations. Several computational microsimulation tools have been reported for estimating efficiency and cost-effectiveness of CRC prevention. However, none of these tools is publicly available. There is a need for an open source framework to answer practical questions including testing of new screening interventions and adapting findings to local conditions.

Concepts: Cancer, Colorectal cancer, Ulcerative colitis, Monte Carlo method, Open source, Free software, Computational science, Web application framework

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In the presence of a cationic Ru catalyst, 1,6-diynes bearing a terminal styryl moiety underwent [2+2+2] cyclization to produce dehydrobiphenylenes fused with a five-membered ring. Although the cycloadducts were unstable toward purification, their one-pot iodine-mediated ring expansion successfully afforded unprecedented bridged ketone products containing a benzo-fused bicyclo[3.2.1] framework.

Concepts: Alcohol, Carbonyl, Web application framework

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A catalyst containing small (ca. 2.5 nm) and crystalline Pt nanoparticles embedded into the walls of a mesostructured silica framework was found to be highly active in alkene hydrosilylation reaching TONs of ca. 10(5). More importantly, no Pt leaching was detected. This result is remarkable because Pt leaching is a recurrent problem in alkene hydrosilylation, which often prevents heterogeneous catalysts from being used industrially. This result is in contrast to the significant Pt leaching observed for other Pt/SiO2 catalysts.

Concepts: Ultraviolet, Catalysis, Heterogeneous catalysis, Hydrogenation, Olefin metathesis, Solid, Web application framework

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An indium based metal-porphyrinic framework, denoted NUPF-3, was prepared based on a new amido-decorated porphyrin ligand. NUPF-3 possesses a rarely seen 4-fold interpenetrated pts framework with segmented pores and dense metalloporphyrin central sites. The structure can retain its crystallinity in commonly used solvents, as well as acidic/alkaline solutions with pH ranging from 1 to 12 for 48 h, exhibiting high chemical stability. Meanwhile, thermal analysis reveals that NUPF-3 possesses relatively high thermal stability. Owing to the presence of amido groups, structural interpenetration and a charged framework, NUPF-3 exhibits relatively high CO2 uptake. Moreover, NUPF-3 could be used as a good heterogeneous catalyst for cycloaddition of CO2 and epoxides, under relatively mild conditions, with good recyclability.

Concepts: Hemoglobin, Carbon dioxide, Structure, Catalysis, Nitrogen, Materials science, Exhibition, Web application framework

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With continuously increasing scale and depth of coverage in affinity proteomics (AP-MS) data, the analysis and visualization is becoming more challenging. A number of tools have been developed to identify high confidence interactions; however, a cohesive and intuitive pipeline for analysis and visualization is still needed. Here, we present Automated Processing of SAINT Templated Layouts (APOSTL), a freely available, Galaxy-integrated software suite and analysis pipeline for reproducible, interactive analysis of AP-MS data. APOSTL contains a number of tools woven together using Galaxy workflows, which are intuitive for the user to move from raw data to publication-quality figures within a single interface. APOSTL is an evolving software project with the potential to customize individual analyses with additional Galaxy tools and widgets using the R web application framework, Shiny. The source code, data and documentation are freely available from GitHub (https://github.com/bornea/APOSTL) and other sources.

Concepts: Scientific method, Computer program, Source code, Analysis, Source, Web application framework, Software framework, Project management software

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Rational catalyst design is one of the most fundamental goals in heterogeneous catalysis. Herein, we briefly review our previous design work, and then introduce a general optimization framework, which converts catalyst design into an optimization problem. Furthermore, an example is given using the gradient ascent method to show how this framework can be used for rational catalyst design. This framework may be applied to other design schemes.

Concepts: Mathematics, Catalysis, Heterogeneous catalysis, Optimization, Gradient descent, Web application framework

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The Consensus Constrained TOPology prediction (CCTOP; http://cctop.enzim.ttk.mta.hu) server is a web-based application providing transmembrane topology prediction. In addition to utilizing 10 different state-of-the-art topology prediction methods, the CCTOP server incorporates topology information from existing experimental and computational sources available in the PDBTM, TOPDB and TOPDOM databases using the probabilistic framework of hidden Markov model. The server provides the option to precede the topology prediction with signal peptide prediction and transmembrane-globular protein discrimination. The initial result can be recalculated by (de)selecting any of the prediction methods or mapped experiments or by adding user specified constraints. CCTOP showed superior performance to existing approaches. The reliability of each prediction is also calculated, which correlates with the accuracy of the per protein topology prediction. The prediction results and the collected experimental information are visualized on the CCTOP home page and can be downloaded in XML format. Programmable access of the CCTOP server is also available, and an example of client-side script is provided.

Concepts: Protein, World Wide Web, PHP, Web page, Sequence alignment, Server, Web application framework, Client