cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4294838
title: snvphyl_manuscript_synthetic_datasets.tar.gz

description: This package contains synthetic datasets used to evaluate the the SNVPhyl (http://snvphyl.readthedocs.io/) pipeline. This is divided into two separate datasets. Additional details on how these datasets were constructed are available at https://github.com/apetkau/snvphyl-validations.<br><br>1. <b>e-coli-simulated-dataset</b>: Simulated reads for evaluated SNVPhyl's SNV detection accuracy.<br><br>Reads are based off of an E. Coli reference genome (NC_002695), plus two plasmids (NC_002128, NC_002127) which were concatenated into a single fasta file <i>reference-genome/e_coli_sakai_w_plasmids.fasta</i>. Random mutations were introduced to produce the variant genomes present in the genomes under <i>variant-genomes/</i>. Reads were simulated using ART Illumina (http://www.niehs.nih.gov/research/resources/software/biostatistics/art/) to generate the fastq files in this directory.<br><br>2. <b>salmonella-heidelberg-contamination</b>: Simulated reads for evaluating SNVPhyl's performance in the presence of contamination from another genomic sample.<br><br>Reads for the sample SH13-001 (BioSample: SAMN04334637) were downsampled and contaminated with SH12-001 (BioSample: SAMN04334627) at percentages of 5%, 10%, 20%, and 30%.<br>
DOI: 10.6084/m9.figshare.4294838.v1
title: snvphyl_manuscript_synthetic_datasets.tar.gz

description: This package contains synthetic datasets used to evaluate the the SNVPhyl (http://snvphyl.readthedocs.io/) pipeline. This is divided into two separate datasets. Additional details on how these datasets were constructed are available at https://github.com/apetkau/snvphyl-validations.<br><br>1. <b>e-coli-simulated-dataset</b>: Simulated reads for evaluated SNVPhyl's SNV detection accuracy.<br><br>Reads are based off of an E. Coli reference genome (NC_002695), plus two plasmids (NC_002128, NC_002127) which were concatenated into a single fasta file <i>reference-genome/e_coli_sakai_w_plasmids.fasta</i>. Random mutations were introduced to produce the variant genomes present in the genomes under <i>variant-genomes/</i>. Reads were simulated using ART Illumina (http://www.niehs.nih.gov/research/resources/software/biostatistics/art/) to generate the fastq files in this directory.<br><br>2. <b>salmonella-heidelberg-contamination</b>: Simulated reads for evaluating SNVPhyl's performance in the presence of contamination from another genomic sample.<br><br>Reads for the sample SH13-001 (BioSample: SAMN04334637) were downsampled and contaminated with SH12-001 (BioSample: SAMN04334627) at percentages of 5%, 10%, 20%, and 30%.<br>
DOI: 10.6084/m9.figshare.4294553
title: Taking the stock of granule cargo: Platelet releasate proteomics

description: Human platelets are key players in a multitude of physiological and pathological processes. Upon activation they release cargo from different types of granules as well as microparticles in an apparently well-regulated and orchestrated manner. The resulting specific platelet releasates create microenvironments of biologically active compounds and proteins during platelet aggregation and thrombus formation, allowing efficient delivery of growth factors and immune modulators to their sites of effect and enhancing the coagulative response in a positive feedback loop. Thus, platelet releasates play a central role in the regulation of platelet homeostasis and heterotypic cell interaction. Additionally, it recently emerged that both the qualitative and quantitative composition of the releasate as well as release dynamics may be stimulus dependent and therefore more complex than expected. Mass spectrometry-based proteomics is an important asset for studying platelet releasates <i>in vitro</i>, as it allows not only (i) identifying released proteins, but moreover (ii) determining their quantities and the dynamics of release as well as (iii) differentially comparing releasates across a variety of conditions. Though owing to the high sensitivity and comprehensiveness of modern proteomic techniques, a thorough experimental design and a standardized and robust sample preparation are essential to obtain highly confident and reliable insights into platelet biology and pathology. Here, we review releasate proteome studies and crucial sample preparation strategies to summarize possible achievements of state-of-the-art technologies and furthermore discuss potential pitfalls and limitations. We provide a future perspective of platelet releasate proteomics including targeted analyses, post-translational modifications and multi-omics approaches that should be adopted by platelet releasate researchers due to their tremendous depth and comprehensiveness.
DOI: 10.6084/m9.figshare.4294553.v1
title: Taking the stock of granule cargo: Platelet releasate proteomics

description: Human platelets are key players in a multitude of physiological and pathological processes. Upon activation they release cargo from different types of granules as well as microparticles in an apparently well-regulated and orchestrated manner. The resulting specific platelet releasates create microenvironments of biologically active compounds and proteins during platelet aggregation and thrombus formation, allowing efficient delivery of growth factors and immune modulators to their sites of effect and enhancing the coagulative response in a positive feedback loop. Thus, platelet releasates play a central role in the regulation of platelet homeostasis and heterotypic cell interaction. Additionally, it recently emerged that both the qualitative and quantitative composition of the releasate as well as release dynamics may be stimulus dependent and therefore more complex than expected. Mass spectrometry-based proteomics is an important asset for studying platelet releasates <i>in vitro</i>, as it allows not only (i) identifying released proteins, but moreover (ii) determining their quantities and the dynamics of release as well as (iii) differentially comparing releasates across a variety of conditions. Though owing to the high sensitivity and comprehensiveness of modern proteomic techniques, a thorough experimental design and a standardized and robust sample preparation are essential to obtain highly confident and reliable insights into platelet biology and pathology. Here, we review releasate proteome studies and crucial sample preparation strategies to summarize possible achievements of state-of-the-art technologies and furthermore discuss potential pitfalls and limitations. We provide a future perspective of platelet releasate proteomics including targeted analyses, post-translational modifications and multi-omics approaches that should be adopted by platelet releasate researchers due to their tremendous depth and comprehensiveness.
DOI: 10.6084/m9.figshare.4294091
title: McClung et al Egg Hunt data.xlsx

description: This data set was produced from a novel optimal foraging paradigm, the Egg Hunt, in which pairs of participants could choose whether to help each other at either no-cost or a cost to themselves. Participants were also allocated to either talking or non-talking conditions. As such it contains data on frequency of helping behaviour as well as data on the frequency with which participants produced different types of utterances when they were able to talk during the hunt. <br>
DOI: 10.6084/m9.figshare.4294085
title: data_anthro_for deposit.pdf

description: The WHO standards are available on the website of WHO (http://www.who.int/childgrowth/en/). You find there the software Anthro2005 for calculation of individual data (Anthro2005). For calculating the z-scores of the new standards the LMS procedure is used. The principle is to get from a table for a certain age and sex 3 values (LMS) which are put into a formula For example WAZ = ((weight/M)^L-1)/(L*S)) e.g.: Female, 9kg, 365 days =&gt; L = -0.2022, M = 8.9462, S = 0.12267 WAZ = ((9/M)^L-1)/(L*S) = ((9/8.9462)^-0.2022-1)/(-0.2022*0.12267) = 0.04885 Z-scores On the WHO website you find only the LMS values for each month. Wt L M S 9 -0.2022 8.9462 0.12267 0.048847178 To calculate the actual weight from the LSM statistics at any cut off point use the following formula: wt = M * ((Z * S * L) +1)^(1/L)Where Z = Zscore you are trying to obtainThis is the reverse of the formula to calculate WAZ etc.And will give the standard to more decimal places for interpolation [purposesI have taken 10 boys and 10 girls at 0.5 cm intervals from 60 to 110cm in height with weight for height mean at -1Z with SD or 1.0. These are in the sheet WFH_Population. For the simulation I have now added a random variable to the weight or the height in the POP_weight and the POP_height sheets.
DOI: 10.6084/m9.figshare.4294076
title: Management of childhood asthma

description: A small, controlled trial of joint treatment of childhood asthma by a doctor, a physiotherapist, a psychologist, and a social worker, working together in the family setting, demonstrated an improvement in ventilatory capacity. The limited scope of Oded Kariti trial does not permit more general conclusions as to the effect of such treatment on the severity and frequency of attacks, but the observation that some measurable physiological improvement occurred suggests that the place of multidisciplinary nonpharmaceutical management of childhood asthma should be investigated in more detail.
DOI: 10.6084/m9.figshare.4294079
title: Biofeedback-aided relaxation studies

description: <b>Are obsessive-compulsive tendencies related to reliance on external proxies for internal states? Evidence from biofeedback-aided relaxation studies.</b><b><br></b>This article presents two studies by Oded Kariti that examine the hypothesis that obsessive-compulsive (OC) tendencies are associated with a general deficiency in subjective conviction, which leads to seeking and reliance on external proxies to compensate for that deficiency. We examined this hypothesis using a biofeedback-aided relaxation procedure. In Study 1 low OC participants performed better on a relaxation task than high OC participants. More importantly, viewing the biofeedback monitor (an external proxy for the internal state of relaxation) had a different effect on the two groups: Whereas high OC participants performed better, low OC participants did not. In addition, when given the opportunity, high OC participants requested the biofeedback monitor more than did the low OC participants. In Study 2 high OC participants were more affected by false biofeedback when judging their level of relaxation compared to low OC participants. Real relaxation level differences between the two false biofeedback phases among the two groups were not found. These results provide preliminary support for the hypothesis that obsessive-compulsive disorder is associated with deficient subjective conviction in internal states and increased reliance on external proxies. Implications for the understanding of OCD-related rules and rituals as well as for cognitive therapy for OCD are discussed.
DOI: 10.6084/m9.figshare.4294079.v1
title: Biofeedback-aided relaxation studies

description: <b>Are obsessive-compulsive tendencies related to reliance on external proxies for internal states? Evidence from biofeedback-aided relaxation studies.</b><b><br></b>This article presents two studies by Oded Kariti that examine the hypothesis that obsessive-compulsive (OC) tendencies are associated with a general deficiency in subjective conviction, which leads to seeking and reliance on external proxies to compensate for that deficiency. We examined this hypothesis using a biofeedback-aided relaxation procedure. In Study 1 low OC participants performed better on a relaxation task than high OC participants. More importantly, viewing the biofeedback monitor (an external proxy for the internal state of relaxation) had a different effect on the two groups: Whereas high OC participants performed better, low OC participants did not. In addition, when given the opportunity, high OC participants requested the biofeedback monitor more than did the low OC participants. In Study 2 high OC participants were more affected by false biofeedback when judging their level of relaxation compared to low OC participants. Real relaxation level differences between the two false biofeedback phases among the two groups were not found. These results provide preliminary support for the hypothesis that obsessive-compulsive disorder is associated with deficient subjective conviction in internal states and increased reliance on external proxies. Implications for the understanding of OCD-related rules and rituals as well as for cognitive therapy for OCD are discussed.
DOI: 10.6084/m9.figshare.4294073
title: Top 100 2016 - article and affiliations data

description: Full data for the articles and affiliations from the Altmetric Top 100 2016.
DOI: 10.6084/m9.figshare.4294076.v1
title: Management of childhood asthma

description: A small, controlled trial of joint treatment of childhood asthma by a doctor, a physiotherapist, a psychologist, and a social worker, working together in the family setting, demonstrated an improvement in ventilatory capacity. The limited scope of Oded Kariti trial does not permit more general conclusions as to the effect of such treatment on the severity and frequency of attacks, but the observation that some measurable physiological improvement occurred suggests that the place of multidisciplinary nonpharmaceutical management of childhood asthma should be investigated in more detail.
DOI: 10.6084/m9.figshare.4293971
title: Top 100 2016 - affiliation data

description: Affiliation data for the articles included in the Altmetric Top 100 2016
DOI: 10.5286/isis.e.rb2010108
title: Deep Inelastic Inelastic Scattering : The case of water and its isotopomers

description: Currently, there are no Deep Inelastic Inelastic Scattering studies on H2O18. We propose to perform a DINS parametric experiment on H2O18 at the following temperatures, in the solid and liquid phases: 271K (solid), 275K, 280K, 300K, and 330K.The comparison of the momentum distributions for various phases /thermodynamic conditions of H2O18 should shed more light on the nature of the chemical environment of the proton. Furthermore, the experiment should also provide a direct verification of the subtle competing effects that make H2O18 more structured – an effect which may be difficult to measure accurately through total scattering. On the side of theory, atomistic simulations will be performed for heavy water using dedicated water potentials.
DOI: 10.5286/isis.e.rb2010108-1
title: Deep Inelastic Inelastic Scattering : The case of water and its isotopomers

description: Currently, there are no Deep Inelastic Inelastic Scattering studies on H2O18. We propose to perform a DINS parametric experiment on H2O18 at the following temperatures, in the solid and liquid phases: 271K (solid), 275K, 280K, 300K, and 330K.The comparison of the momentum distributions for various phases /thermodynamic conditions of H2O18 should shed more light on the nature of the chemical environment of the proton. Furthermore, the experiment should also provide a direct verification of the subtle competing effects that make H2O18 more structured – an effect which may be difficult to measure accurately through total scattering. On the side of theory, atomistic simulations will be performed for heavy water using dedicated water potentials.
DOI: 10.6084/m9.figshare.4294073.v2
title: Top 100 2016 - article and affiliations data

description: Full data of the articles and affiliations from the Altmetric Top 100 2016.
DOI: 10.6084/m9.figshare.4293959
title: data_qm9.pkl.tar.gz

description: compressed python pickle file for qm9 dataset
DOI: 10.6084/m9.figshare.4293611
title: In front of a mirror: visual displays may not be aggressive signals in nocturnal tree frogs

description: Some evidence indicates that in anuran amphibians, visual signalling can be important during social interactions such as territorial disputes among males, especially in diurnal species. The correct identification of a signal is not a trivial matter. A visual signal provides a visual cue during a social interaction, and to be effective it must elicit an immediate response in the receiver. We tested the hypothesis that visual displays in an agonistic context constitute aggressive signals, in three nocturnal species of Hylidae. We predicted that the production of visual displays would increase in the presence of a conspecific intruder male. Males of <i>Hypsiboas raniceps</i>, <i>Dendropsophus nanus</i> and <i>Lysapsus limellum</i> were submitted to two treatments: (1) Self Image, a reflection in a mirror, simulating the presence of an intruder; and (2) Control, a black rectangle covering the mirror. We observed three visual displays: vocal-sac display (inflate the vocal sac and maintain it inflated for some time), limb lifting (rapid up-and-down movements of one or more limbs), and toe/finger trembling (rapid up-and-down movements of one or more toes and/or fingers). This last display was observed only in <i>H. raniceps</i> males. Contrary to our hypothesis, the emission rates of all visual displays of the focal animals did not differ between treatments; and the behavioural response did not differ among species. Therefore, we suggest that these behaviours could not be used directly for communication in agonistic contexts, and may represent displacement activities (involuntary responses). Alternatively, an aggressive bimodal stimulus may be necessary to trigger a behavioural response by using visual signals during territory defence in these three species.
DOI: 10.6084/m9.figshare.4293611.v1
title: In front of a mirror: visual displays may not be aggressive signals in nocturnal tree frogs

description: Some evidence indicates that in anuran amphibians, visual signalling can be important during social interactions such as territorial disputes among males, especially in diurnal species. The correct identification of a signal is not a trivial matter. A visual signal provides a visual cue during a social interaction, and to be effective it must elicit an immediate response in the receiver. We tested the hypothesis that visual displays in an agonistic context constitute aggressive signals, in three nocturnal species of Hylidae. We predicted that the production of visual displays would increase in the presence of a conspecific intruder male. Males of <i>Hypsiboas raniceps</i>, <i>Dendropsophus nanus</i> and <i>Lysapsus limellum</i> were submitted to two treatments: (1) Self Image, a reflection in a mirror, simulating the presence of an intruder; and (2) Control, a black rectangle covering the mirror. We observed three visual displays: vocal-sac display (inflate the vocal sac and maintain it inflated for some time), limb lifting (rapid up-and-down movements of one or more limbs), and toe/finger trembling (rapid up-and-down movements of one or more toes and/or fingers). This last display was observed only in <i>H. raniceps</i> males. Contrary to our hypothesis, the emission rates of all visual displays of the focal animals did not differ between treatments; and the behavioural response did not differ among species. Therefore, we suggest that these behaviours could not be used directly for communication in agonistic contexts, and may represent displacement activities (involuntary responses). Alternatively, an aggressive bimodal stimulus may be necessary to trigger a behavioural response by using visual signals during territory defence in these three species.
DOI: 10.6084/m9.figshare.4293377
title: A Method for Finding Metabolic Pathways Using Atomic Group Tracking

description: The data and program for AGPathFinder.
DOI: 10.6084/m9.figshare.4293377.v1
title: A Method for Finding Metabolic Pathways Using Atomic Group Tracking

description: The data and program for AGPathFinder.
DOI: 10.6084/m9.figshare.4292921
title: Data - LINKING ANIMAL CONTESTS AND COMMUNITY STRUCTURE USING ROCKPOOL FISHES AS A MODEL SYSTEM.xlsx

description: This Data is supplementary for a Functional Ecology Paper - LINKING ANIMAL CONTESTS AND COMMUNITY STRUCTURE USING ROCKPOOL FISHES AS A MODEL SYSTEM.
DOI: 10.6084/m9.figshare.4292921.v1
title: Data - LINKING ANIMAL CONTESTS AND COMMUNITY STRUCTURE USING ROCKPOOL FISHES AS A MODEL SYSTEM.xlsx

description: This Data is supplementary for a Functional Ecology Paper - LINKING ANIMAL CONTESTS AND COMMUNITY STRUCTURE USING ROCKPOOL FISHES AS A MODEL SYSTEM.
DOI: 10.6084/m9.figshare.4292897
title: Table. BBD 16S rRNA bacteria and T4 bacteriophage composition.

description: <b>Part of supplementary material for paper:<br><br></b>Novel T4 bacteriophages associated with black band disease in corals.<br>
DOI: 10.6084/m9.figshare.4292897.v1
title: Table. BBD 16S rRNA bacteria and T4 bacteriophage composition.

description: <b>Part of supplementary material for paper:<br><br>T4-bacteriophage communities associated with black band disease show few uniquely abundant OTUs</b><br>
DOI: 10.6084/m9.figshare.4292897.v3
title: Table. BBD 16S rRNA bacteria and T4 bacteriophage composition.

description: <b>Part of supplementary material for paper:<br><br></b>Novel T4 bacteriophages associated with black band disease in corals.<br>
DOI: 10.6084/m9.figshare.4292897.v2
title: Table. BBD 16S rRNA bacteria and T4 bacteriophage composition.

description: <b>Part of supplementary material for paper:<br><br>T4-bacteriophage communities associated with black band disease show few uniquely abundant OTUs</b><br>
DOI: 10.4225/03/5848bb75cfaf4
title: Non Anti-Coagulant Factors Associated with Filter Life in Continuous Renal Replacement Therapy (CRRT): A systematic review and meta-analysis. Study Data

description: This is the data summary from Comprehensive Meta-analysis used to construct all tables and figures in the review.
DOI: 10.6084/m9.figshare.4292891.v1
title: Reduced chemical kinetic models for butanol isomers

description: This dataset contains reduced chemical kinetic models for the isomers of butanol, generated using the directed relation graph with error propagation (DRGEP) and DRGEP and sensitivity analysis (DRGEPSA). Two separate detailed models for the butanol isomers were reduced: the Sarathy and Merchant models (see README for associated references).<br>The reduction_output archive contains the metadata for the reduction, and the necessary thermodynamic and transport data files are included for each set of model files.
DOI: 10.17608/k6.auckland.4292870
title: Data File - TCoA-III Long Secondary Schools

description: The SPSS data file containing all data information collected from the TCoA-III Long questionnaire administered in 2007 for secondary schools. <br>The long version of the data was not used for reporting, please see the TCoA-IIIA for secondary schools for data that was reported on. <br><br><br>
DOI: 10.17608/k6.auckland.4292870.v1
title: Data File - TCoA-III Long Secondary Schools

description: The SPSS data file containing all data information collected from the TCoA-III Long questionnaire administered in 2007 for secondary schools. <br>The long version of the data was not used for reporting, please see the TCoA-IIIA for secondary schools for data that was reported on. <br><br><br>
DOI: 10.17608/k6.auckland.4292831
title: Automating R Demonstration Videos

description: This document describes a proof-of-concept for producing R demonstration videos in a fully-automated manner. The “script” for the video consists of a text file containing code chunks paired with text commentary. The video is produced by running the code while recording a screen capture, using text-to-speech software to record audio of the commentary, then combining video and audio with appropriate timings and pauses.
DOI: 10.17608/k6.auckland.4292831.v1
title: Automating R Demonstration Videos

description: This document describes a proof-of-concept for producing R demonstration videos in a fully-automated manner. The “script” for the video consists of a text file containing code chunks paired with text commentary. The video is produced by running the code while recording a screen capture, using text-to-speech software to record audio of the commentary, then combining video and audio with appropriate timings and pauses.