Phylotastic! Making Tree-of-Life Knowledge Accessible, Reusable and Convenient

Scientists rarely reuse expert knowledge of phylogeny, in spite of years of effort to assemble a great "Tree of Life" (ToL). A notable exception involves the use of Phylomatic, which provides tools to generate custom phylogenies from a large, pre-computed, expert phylogeny of plant taxa. This suggests great potential for a more generalized system that, starting with a query consisting of a list of any known species, would rectify non-standard names, identify expert phylogenies containing the implicated taxa, prune away unneeded parts, and supply branch lengths and annotations, resulting in a custom phylogeny suited to the user's needs. Such a system could become a sustainable community resource if implemented as a distributed system of loosely coupled parts that interact through clearly defined interfaces. Results: With the aim of building such a "phylotastic" system, the NESCent Hackathons, Interoperability, Phylogenies (HIP) working group recruited 2 dozen scientist-programmers to a weeklong programming hackathon in June 2012. During the hackathon (and a three-month follow-up period), 5 teams produced designs, implementations, documentation, presentations, and tests including: (1) a generalized scheme for integrating components; (2) proof-of-concept pruners and controllers; (3) a meta-API for taxonomic name resolution services; (4) a system for storing, finding, and retrieving phylogenies using semantic web technologies for data exchange, storage, and querying; (5) an innovative new service, DateLife.org, which synthesizes pre-computed, time-calibrated phylogenies to assign ages to nodes; and (6) demonstration projects. These outcomes are accessible via a public code repository (GitHub.com), a website (www.phylotastic.org), and a server image. Conclusions: Approximately 9 person-months of effort (centered on a software development hackathon) resulted in the design and implementation of proof-of-concept software for 4 core phylotastic components, 3 controllers, and 3 end-user demonstration tools. While these products have substantial limitations, they suggest considerable potential for a distributed system that makes phylogenetic knowledge readily accessible in computable form. Widespread use of phylotastic systems will create an electronic marketplace for sharing phylogenetic knowledge that will spur innovation in other areas of the ToL enterprise, such as annotation of sources and methods and third-party methods of quality assessment.NESCent (the National Evolutionary Synthesis Center)NSF EF-0905606iPlant Collaborative (NSF) DBI-0735191Biodiversity Synthesis Center (BioSync) of the Encyclopedia of LifeComputer Science

Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient

Abstract Background Scientists rarely reuse expert knowledge of phylogeny, in spite of years of effort to assemble a great “Tree of Life” (ToL). A notable exception involves the use of Phylomatic, which provides tools to generate custom phylogenies from a large, pre-computed, expert phylogeny of plant taxa. This suggests great potential for a more generalized system that, starting with a query consisting of a list of any known species, would rectify non-standard names, identify expert phylogenies containing the implicated taxa, prune away unneeded parts, and supply branch lengths and annotations, resulting in a custom phylogeny suited to the user’s needs. Such a system could become a sustainable community resource if implemented as a distributed system of loosely coupled parts that interact through clearly defined interfaces. Results With the aim of building such a “phylotastic” system, the NESCent Hackathons, Interoperability, Phylogenies (HIP) working group recruited 2 dozen scientist-programmers to a weeklong programming hackathon in June 2012. During the hackathon (and a three-month follow-up period), 5 teams produced designs, implementations, documentation, presentations, and tests including: (1) a generalized scheme for integrating components; (2) proof-of-concept pruners and controllers; (3) a meta-API for taxonomic name resolution services; (4) a system for storing, finding, and retrieving phylogenies using semantic web technologies for data exchange, storage, and querying; (5) an innovative new service, DateLife.org, which synthesizes pre-computed, time-calibrated phylogenies to assign ages to nodes; and (6) demonstration projects. These outcomes are accessible via a public code repository (GitHub.com), a website ( http://www.phylotastic.org ), and a server image. Conclusions Approximately 9 person-months of effort (centered on a software development hackathon) resulted in the design and implementation of proof-of-concept software for 4 core phylotastic components, 3 controllers, and 3 end-user demonstration tools. While these products have substantial limitations, they suggest considerable potential for a distributed system that makes phylogenetic knowledge readily accessible in computable form. Widespread use of phylotastic systems will create an electronic marketplace for sharing phylogenetic knowledge that will spur innovation in other areas of the ToL enterprise, such as annotation of sources and methods and third-party methods of quality assessment.http://deepblue.lib.umich.edu/bitstream/2027.42/112888/1/12859_2013_Article_5897.pd

A Pilot Study of Abnormal Growth in Autism Spectrum Disorders and Other Childhood Psychiatric Disorders

The aims of the current study were to examine whether early growth abnormalities are (a) comparable in autism spectrum disorders (ASD) and other childhood psychiatric disorders, and (b) specific to the brain or generalized to the whole body. Head circumference, height, and weight were measured during the first 19 months of life in 129 children with ASD and 59 children with non-ASD psychiatric disorders. Both groups showed comparable abnormal patterns of growth compared to population norms, especially regarding height and head circumference in relation to height. Thus abnormal growth appears to be related to psychiatric disorders in general and is mainly expressed as an accelerated growth of height not matched by an increase in weight or head circumference

Sex differences in short-term mate preferences and behavioral mimicry: A semi-naturalistic experiment

Item does not contain fulltextStudies on short-term mating (STM) yield sex differences regarding preferences for attractiveness (important towomen, very important to men) and social status (very important to women, not to men) in potential mates. Additionally, men generally report a greater desire to engage in STM than women. So far, this evidence is primarily based on studies using vignettes or surveys. The current study extended the findings on sex differences in STM by examining actual behavior and STM-desires towards real people of the opposite sex. It investigated whether (1) sex differences exist in STM-desire, (2) whether this desire was affected by a confederate's attractiveness and status, and (3) if these sex differences were also reflected in interpersonal behavior (mimicry). In a pub-like laboratory, single heterosexual participants performed a task alongside a confederate of the opposite sex, who differed in attractiveness and social status. Mimicry was observed and explicit STM-desire was assessed. Results showed that men only desired STM more than women in the case of an attractive partner. Women's STMdesire did not vary as a function of status or ttractiveness of the potential partner. Men’s, but not women's, mimicry paralleled these differential STM-desires. These results underline the conditionality of sex differences in STM-desire and provide a useful paradigm to further investigate STM.10 p

An Experimental Comparison of Selected Blue Flame Pyrotechnics

In this research, 10 different pyrotechnic blue flame compositions were designed and compared. Chromaticity and luminosity parameters of the flame were measured using Ocean Optics JAZ‐ULM VIS‐Spectrometer equipped with a cosine corrector. Color saturation, luminous intensity, specific luminous intensity, oxygen balance, burn rate, actual and theoretical maximum density, color coordinates (X, Y) are presented and discussed

Data on plug-based large-bore arteriotomy vascular closure device related access complications

This article provides supplementary tables and figures to the research article: Frequency, Impact and Predictors of Access Complications with Plug-Based Large-Bore Arteriotomy Closure - A patient level meta-analysis [1]. The data provide insight in the type and management of access complications related to the plug-based MANTA vascular closure device (VCD) for large-bore catheter-based cardiovascular interventions. Since MANTA is mostly used in transcatheter aortic valve replacement (TAVR) procedures, this article also contains a sub-group analysis on TAVR procedures using contemporary valve-platforms. Further, data describing MANTA hemostasis times and mortality causes are included. For this dataset, individual patient data were derived from a European and a North American device approval study (the Conformite Européene [CE] mark study and the investigational device exemption SAFE-MANTA study [2,3]) in addition to a post-approval registry (the MARVEL registry [4]) covering a total of 891 patients who were enrolled between 2015 and 2019 across 28 investigational sites. Eligibility criteria were most stringent in the SAFE MANTA study (38% of patients) whereas the MARVEL registry applied liberal and only relative exclusion criteria (56% of patients). A total of 78 Roll-in cases (i.e. first or second time operator use of the MANTA VCD) who were excluded from analysis in SAFE MANTA were included in the present to evaluate a potential learning curve effect. Therefore, this dataset reflects the largest study population undergoing arteriotomy closure with the MANTA VCD by operators at various levels of experience, which can be valuable to further build on research regarding percutaneous large-bore arteriotomy management

Frequency, Impact, and Predictors of Access Complications With Plug-Based Large-Bore Arteriotomy Closure - A Patient-Level Meta-Analysis

Background/purpose: The MANTA is a dedicated plug-based large-bore vascular closure device (VCD) providing safe hemostasis in most patients, but data on the clinical impact and mechanisms of MANTA related complications are limited. This study sought to determine the frequency, impact and predictors of MANTA-related access complications. Methods/materials: This patient-level meta-analysis included data from 2 medical device approval studies and 1 post-approval registry. The primary endpoint was the composite of major and minor access complications. Technical success was defined as hemostasis with MANTA closure device without need for vascular surgery or stenting. Results: Eight hundred ninety-one patients (mean age 80) underwent transcatheter aortic valve replacement (n = 814), endovascular aortic repair (n = 71), balloon aortic valvuloplasty (n = 4) or mechanical circulatory support (n = 2). Technical success was 96.4% and median time to hemostasis was 31 (interquartile range: 17–76) seconds. The primary endpoint occurred 9.1% and bailout vascular surgery or stenting was necessary in 32 patients (3.6%). Female gender (OR: 2.63, CI: 1.46–4.73, p = 0.001), left femoral access (OR: 2.18, CI: 1.17–4.06, p = 0.015) and unfavorable arteriotomy phenotype (combination of a small femoral artery diameter with a deep arteriotomy; OR 2.27: 1.26–4.10, p = 0.006) independently predicted access complications. Access complications most often consisted of vessel dissection, stenosis or occlusion and predominantly occurred in patients with an unfavorable arteriotomy phenotype. Conclusions: Large-bore arteriotomy closure with MANTA VCD provided fast and safe hemostasis with an acceptable complication rate. Refined procedure planning and risk-stratification may further improve MANTA VCD performance

Exercise and Type 2 Diabetes Mellitus:Changes in Tissue-specific Fat Distribution and Cardiac Function

Purpose: To prospectively assess the effects of an exercise intervention on organ-specific fat accumulation and cardiac function in type 2 diabetes mellitus. Materials and Methods: Written informed consent was obtained from all participants, and the study protocol was approved by the medical ethics committee. The study followed 12 patients with type 2 diabetes mellitus (seven men; mean age, 46 years 6 2 [standard error]) before and after 6 months of moderate-intensity exercise, followed by a high-altitude trekking expedition with exercise of long duration. Abdominal, epicardial, and paracardial fat volume were measured by using magnetic resonance (MR) imaging. Cardiac function was quantified with cardiac MR, and images were analyzed by a researcher who was supervised by a senior researcher (4 and 21 years of respective experience in cardiac MR). Hepatic, myocardial, and intramyocellular triglyceride (TG) content relative to water were measured with proton MR spectroscopy at 1.5 and 7 T. Two-tailed paired t tests were used for statistical analysis. Results: Exercise reduced visceral abdominal fat volume from 348 mL +/- 57 to 219 mL +/- 33 (P <.01), and subcutaneous abdominal fat volume remained unchanged (P = .9). Exercise decreased hepatic TG content from 6.8% +/- 2.3 to 4.6% +/- 1.6 (P <.01) and paracardial fat volume from 4.6 mL +/- 0.9 to 3.7 mL +/- 0.8 (P = .02). Exercise did not change epicardial fat volume (P = .9), myocardial TG content (P = .9), intramyocellular lipid content (P = .3), or cardiac function (P = .5). Conclusion: A 6-month exercise intervention in type 2 diabetes mellitus decreased hepatic TG content and visceral abdominal and paracardial fat volume, which are associated with increased cardiovascular risk, but cardiac function was unaffected. Tissue-specific exercise-induced changes in body fat distribution in type 2 diabetes mellitus were demonstrated in this study. (C) RSNA, 201