cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4805719.v2
title: Structural Equation Models for Dealing With Spatial Confounding

description: In regression analyses of spatially structured data, it is common practice to introduce spatially correlated random effects into the regression model to reduce or even avoid unobserved variable bias in the estimation of other covariate effects. If besides the response the covariates are also spatially correlated, the spatial effects may confound the effect of the covariates or vice versa. In this case, the model fails to identify the true covariate effect due to multicollinearity. For highly collinear continuous covariates, path analysis and structural equation modeling techniques prove to be helpful to disentangle direct covariate effects from indirect covariate effects arising from correlation with other variables. This work discusses the applicability of these techniques in regression setups, where spatial and covariate effects coincide at least partly and classical geoadditive models fail to separate these effects. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.4805719.v1
title: Structural Equation Models for Dealing with Spatial Confounding

description: In regression analyses of spatially structured data, it is common practice to introduce spatially correlated random effects into the regression model in order to reduce or even avoid unobserved variable bias in the estimation of other covariate effects. If besides the response the covariates are also spatially correlated, the spatial effects may confound the effect of the covariates or vice versa. In this case, the model fails to identify the true covariate effect due to multicollinearity. For highly collinear continuous covariates, path analysis and structural equation modeling techniques prove to be helpful to disentangle direct covariate effects from indirect covariate effects arising from correlation with other variables. This work discusses the applicability of these techniques in regression setups where spatial and covariate effects coincide at least partly and classical geoadditive models fail to separate these effects.
DOI: 10.6084/m9.figshare.4805656
title: salamander feeding experiment data.xlsx

description: Excel file of weights of salamanders
DOI: 10.6084/m9.figshare.4805707.v2
title: The Wilcoxon–Mann–Whitney Procedure Fails as a Test of Medians

description: To illustrate and document the tenuous connection between the Wilcoxon–Mann–Whitney (WMW) procedure and medians, its relationship to mean ranks is first contrasted with the relationship of a <i>t</i>-test to means. The quantity actually tested: Pr ^(X1&lt;X2)+ Pr ^(X1=X2)/2 is then described and recommended as the basis for an alternative summary statistic that can be employed instead of medians. In order to graphically represent an estimate of the quantity: Pr(<i>X</i><sub>1</sub> &lt; <i>X</i><sub>2</sub>) + Pr(<i>X</i><sub>1</sub> = <i>X</i><sub>2</sub>)/2, use of a bubble plot, an ROC curve and a dominance diagram are illustrated. Several counter-examples (real and constructed) are presented, all demonstrating that the WMW procedure fails to be a test of medians. The discussion also addresses another, less common and perhaps less clear cut, but potentially even more important misconception: that the WMW procedure requires continuous data in order to be valid. Discussion of other issues surrounding the question of the WMW procedure and medians is presented, along with the authors' teaching experience with the topic. SAS code used for the examples is included as supplementary material.
DOI: 10.6084/m9.figshare.4805749.v2
title: Bengalese Finch song repository

description: This is a collection of song from four Bengalese finches recorded in the Sober lab at Emory University. The song has been hand-labeled by two of the authors. We share it as a means of testing different machine learning algorithms for classifying the elements of birdsong, known as syllables. A Python package, hybrid-vocal-classifier (HVC), has been tested using this dataset: https://github.com/NickleDave/hybrid-vocal-classifier. <br>The actual sound files have the extension .cbin and were collected using the program EvTAF. They can be loaded with the `load_cbin` function in the `evfuncs` module of HVC. Each .cbin file has an associated .cbin.not.mat file that contains song syllable onsets, offsets, labels, etc. These files can be opened with the `load_notmat` function in the `evfuncs` module. Each .cbin file also has associated .tmp and .rec files also created by EvTAF. Those files are not strictly required to work with this dataset but are included for completeness.<br>
DOI: 10.6084/m9.figshare.4805707.v1
title: The Wilcoxon-Mann-Whitney procedure fails as a test of medians

description: To illustrate and document the tenuous connection between the Wilcoxon-Mann-Whitney (WMW) procedure and medians, its relationship to mean ranks is first contrasted with the relationship of a t-test to means. The quantity actually tested: Pr ^(X<sub>1</sub>2) + Pr ^(X<sub>1</sub> = X<sub>2</sub>)/2 is then described and recommended as the basis for an alternative summary statistic that can be employed instead of medians. In order to graphically represent an estimate of the quantity: Pr(X<sub>1</sub>2) + Pr( X<sub>1</sub> = X<sub>2</sub>)/2, use of a bubble plot, an ROC curve and a dominance diagram are illustrated. Several counter-examples (real and constructed) are presented, all demonstrating that the WMW procedure fails to be a test of medians. The discussion also addresses another, less common and perhaps less clear cut, but potentially even more important misconception: that the WMW procedure requires continuous data in order to be valid. Discussion of other issues surrounding the question of the WMW procedure and medians is presented, along with the authors' teaching experience with the topic. SAS code used for the examples is included as supplementary material.
DOI: 10.6084/m9.figshare.4805749.v3
title: Bengalese Finch song repository

description: This is a collection of song from four Bengalese finches recorded in the Sober lab at Emory University. The song has been hand-labeled by two of the authors. We share it as a means of testing different machine learning algorithms for classifying the elements of birdsong, known as syllables. A Python package, hybrid-vocal-classifier (HVC), has been tested using this dataset: https://github.com/NickleDave/hybrid-vocal-classifier. <br>The actual sound files have the extension .cbin and were collected using the program EvTAF. They can be loaded with the `load_cbin` function in the `evfuncs` module of HVC. Each .cbin file has an associated .cbin.not.mat file that contains song syllable onsets, offsets, labels, etc. These files can be opened with the `load_notmat` function in the `evfuncs` module. Each .cbin file also has associated .tmp and .rec files also created by EvTAF. Those files are not strictly required to work with this dataset but are included for completeness.<br>
DOI: 10.6084/m9.figshare.4805563
title: Logistics of Mathematical Modeling-Focused Projects

description: This article addresses the logistics of implementing projects in an undergraduate mathematics class and is intended both for new instructors and for instructors who have had negative experiences implementing projects in the past. Project implementation is given for both lower- and upper-division mathematics courses with an emphasis on mathematical modeling and data collection. Projects provide tangible connections to course content, which can motivate students to learn at a deeper level. Logistical pitfalls and insights are highlighted, as well as descriptions of several key implementation resources. Effective assessment tools, which allowed a smooth adjustment to student feedback, are demonstrated for a sample class. As I smoothed the transition into each project and guided students through the use of the technology, their negative feedback on projects decreased and more students noted how the projects had enhanced their understanding of the course topics. Best practices learned over the years are given, along with project summaries and sample topics. These projects were implemented at a small liberal arts university, but advice is given to extend them to larger classes for broader use.
DOI: 10.6084/m9.figshare.4805563.v1
title: Logistics of Mathematical Modeling-Focused Projects

description: This article addresses the logistics of implementing projects in an undergraduate mathematics class and is intended both for new instructors and for instructors who have had negative experiences implementing projects in the past. Project implementation is given for both lower- and upper-division mathematics courses with an emphasis on mathematical modeling and data collection. Projects provide tangible connections to course content, which can motivate students to learn at a deeper level. Logistical pitfalls and insights are highlighted, as well as descriptions of several key implementation resources. Effective assessment tools, which allowed a smooth adjustment to student feedback, are demonstrated for a sample class. As I smoothed the transition into each project and guided students through the use of the technology, their negative feedback on projects decreased and more students noted how the projects had enhanced their understanding of the course topics. Best practices learned over the years are given, along with project summaries and sample topics. These projects were implemented at a small liberal arts university, but advice is given to extend them to larger classes for broader use.
DOI: 10.6084/m9.figshare.4805539
title: Direct Numerical Simulation of Boron Particle Agglomeration in Combustion of Boron-Containing Solid Propellants

description: The available experimental data on boron particles agglomeration during combustion of boron-containing solid propellants and a mechanism of the boron particles agglomeration are discussed. The model and the method of direct numerical simulation of the boron particles agglomeration have been suggested and developed. The calculation consists of two stages: the first stage is a simulation of a heterogeneous structure of solid propellant; the second stage is a calculation of a behavior of each boron particle, taking into account its interaction with other particles and with flow of gaseous combustion products of solid propellant. A mechanism of the adhesive bonds between the boron particles is suggested and the criterion of conglomerate detachment from the burning surface has been determined. The dependence of the strength of the adhesive bonds between the boron particles on the propellant burning rate and pressure is analyzed. The calculations of the boron particles agglomeration, which demonstrates the effect of the strength of adhesive bonds between boron particles on the intensity of agglomeration, have been carried out.
DOI: 10.6084/m9.figshare.4805539.v1
title: Direct Numerical Simulation of Boron Particle Agglomeration in Combustion of Boron-Containing Solid Propellants

description: The available experimental data on boron particles agglomeration during combustion of boron-containing solid propellants and a mechanism of the boron particles agglomeration are discussed. The model and the method of direct numerical simulation of the boron particles agglomeration have been suggested and developed. The calculation consists of two stages: the first stage is a simulation of a heterogeneous structure of solid propellant; the second stage is a calculation of a behavior of each boron particle, taking into account its interaction with other particles and with flow of gaseous combustion products of solid propellant. A mechanism of the adhesive bonds between the boron particles is suggested and the criterion of conglomerate detachment from the burning surface has been determined. The dependence of the strength of the adhesive bonds between the boron particles on the propellant burning rate and pressure is analyzed. The calculations of the boron particles agglomeration, which demonstrates the effect of the strength of adhesive bonds between boron particles on the intensity of agglomeration, have been carried out.
DOI: 10.6084/m9.figshare.4805749.v4
title: Bengalese Finch song repository

description: This is a collection of song from four Bengalese finches recorded in the Sober lab at Emory University. The song has been hand-labeled by two of the authors. We share it as a means of testing different machine learning algorithms for classifying the elements of birdsong, known as syllables. A Python package, hybrid-vocal-classifier (HVC), has been tested using this dataset: https://github.com/NickleDave/hybrid-vocal-classifier. <br>The actual sound files have the extension .cbin and were collected using the program EvTAF. They can be loaded with the `load_cbin` function in the `evfuncs` module of HVC. Each .cbin file has an associated .cbin.not.mat file that contains song syllable onsets, offsets, labels, etc. These files can be opened with the `load_notmat` function in the `evfuncs` module. Each .cbin file also has associated .tmp and .rec files also created by EvTAF. Those files are not strictly required to work with this dataset but are included for completeness.<br>
DOI: 10.6084/m9.figshare.4805497
title: Genomic and Chemical Diversity in <i>Cannabis</i>

description: Plants of the <i>Cannabis</i> genus are the only prolific producers of phytocannabinoids, compounds that strongly interact with the evolutionarily ancient endocannabinoid receptors shared by most bilaterian taxa. For millennia, the plant has been cultivated not only for these compounds, but also for food, rope, paper, and clothing. Today, specialized varieties yielding high-quality textile fibers, nutritional seed oil, or high cannabinoid content are cultivated across the globe. However, the genetic identities and histories of these diverse populations remain largely obscured. We analyzed the nuclear genomic diversity among 340 <i>Cannabis</i> varieties, including fiber and seed oil hemp, high cannabinoid drug-types, and feral populations. These analyses demonstrate the existence of at least three major groups of diversity with European hemp varieties more closely related to narrow leaflet drug-types (NLDTs) than to broad leaflet drug-types (BLDTs). The BLDT group appears to encompass less diversity than the NLDT, which reflects the larger geographic range of NLDTs, and suggests a more recent origin of domestication of the BLDTs. As well as being genetically distinct, hemp, NLDT, and BLDT genetic groups produce unique cannabinoid and terpenoid content profiles. This combined analysis of population genomic and trait variation informs our understanding of the potential uses of different genetic variants for medicine and agriculture, providing valuable insights and tools for a rapidly emerging valuable industry.
DOI: 10.6084/m9.figshare.4805611
title: Reconsidering cluster bias (isomorphism) in multilevel data: A Monte Carlo comparison of free and constrained baseline approaches

description: V3. Fixes problem so that level-2 violator effects vary in line with ICC levels to keep bias at 1% and 5% across ICC levels.<br>V2. Fixes problem with previous upload where some folders were incomplete. Adds simulation conditions where referent indicator is biased. Changes free baseline model conditions so that free baseline is always minimally identifiable. <br>V1: This file contains accompanying materials for this Monte Carlo study on free baseline testing for cluster bias (in review). The cell design and parameters excel file describes the parameters used in each of the cells of the design. The inputs and outputs for generation and analysis are included, along with the summary files that the save data command produces. The python scripts are short pieces of code that will extract the summary parameters and fit statistics from the outputs of each run that the Mplus save data output line generates. Run them from the command line. You can request the line you want according to the listing at the end of the Mplus summary files, the fit statistics turn out to be lines 6 and 7 for fixed baseline and 8 and 9 for free baseline conditions.
DOI: 10.6084/m9.figshare.4805299
title: Effect of Obesogenic Diet on Raphe Gene Expression.Old monkeys.Taqman.Prism5

description: This study measured gene expression with qRT-PCR in small blocks of brain tissue containing the serotonergic dorsal raphe nucleus. Old female monkeys were ovo-hysterectomized (OvH; spayed) and maintained on a western style diet (WSD) that is high in fat and refined sugar (TAD, Lab Chow, Inc) or maintained on normal monkey chow that is low in fat and refined sugar in 3 treatment groups. Group 1 received placebo; group 2 received estradiol (E) immediately after OvH; and group 3 received placebo for 2 years and E for 6 months. Tissue was obtained from all animals at 2.5 years and processed for qRT-PCR using an ABI Custom Taqman Expression Array. This study was approved by the IACUC of the Oregon National Primate Research Center and conducted in accordance with the 2011 Eighth Edition of the National Institute of Health Guide for the Care and Use of Laboratory Animals. Animals were euthanized according to procedures recommended by the 2013 Edition of the American Veterinary Medical Association Guidelines for the Euthanasia of Animals.
DOI: 10.6084/m9.figshare.4803184
title: repoDB Additional Files

description: Additional files for reproducing repoDB.
DOI: 10.6084/m9.figshare.4805299.v1
title: Effect of Obesogenic Diet on Raphe Gene Expression.Old monkeys.Taqman.Prism5

description: This study measured gene expression with qRT-PCR in small blocks of brain tissue containing the serotonergic dorsal raphe nucleus. Old female monkeys were ovo-hysterectomized (OvH; spayed) and maintained on a western style diet (WSD) that is high in fat and refined sugar (TAD, Lab Chow, Inc) or maintained on normal monkey chow that is low in fat and refined sugar in 3 treatment groups. Group 1 received placebo; group 2 received estradiol (E) immediately after OvH; and group 3 received placebo for 2 years and E for 6 months. Tissue was obtained from all animals at 2.5 years and processed for qRT-PCR using an ABI Custom Taqman Expression Array. This study was approved by the IACUC of the Oregon National Primate Research Center and conducted in accordance with the 2011 Eighth Edition of the National Institute of Health Guide for the Care and Use of Laboratory Animals. Animals were euthanized according to procedures recommended by the 2013 Edition of the American Veterinary Medical Association Guidelines for the Euthanasia of Animals.
DOI: 10.6084/m9.figshare.4803172
title: Data Set for "An Empirical Study of the Personnel Overhead of Continuous Integration"

description: This is the data set and code related to our paper entitled "An Empirical Study of the Personnel Overhead of Continuous Integration" to appear in International Conference on Mining Software Repositories, Mining Challenge.<br>
DOI: 10.6084/m9.figshare.4803184.v1
title: repoDB Additional Files

description: Additional files for reproducing repoDB.
DOI: 10.6084/m9.figshare.4802959
title: clown data.xls

description: <b>Clown-care Reduces Pain in Children with Cerebral Palsy Undergoing Recurrent Botulinum Toxin Injections- a Quasi-Randomized Controlled Crossover Study</b>
DOI: 10.6084/m9.figshare.4803172.v1
title: Data Set for "An Empirical Study of the Personnel Overhead of Continuous Integration"

description: This is the data set and code related to our paper entitled "An Empirical Study of the Personnel Overhead of Continuous Integration" to appear in International Conference on Mining Software Repositories, Mining Challenge.<br>
DOI: 10.6084/m9.figshare.4802959.v1
title: clown data.xls

description: <b>Clown-care Reduces Pain in Children with Cerebral Palsy Undergoing Recurrent Botulinum Toxin Injections- a Quasi-Randomized Controlled Crossover Study</b>
DOI: 10.6084/m9.figshare.4802392
title: Combined modality therapy improves overall survival for angiosarcoma

description: Combined modality therapy improves overall survival for angiosarcoma
DOI: 10.6084/m9.figshare.4802392.v1
title: Combined modality therapy improves overall survival for angiosarcoma

description: Combined modality therapy improves overall survival for angiosarcoma
DOI: 10.6084/m9.figshare.4802320
title: Datasets, results and models for nanoQSAR & docking of SWCNs with Mitochondrial VDAC

description: Multiple files for Strong and Weak Single Walled Carbon Nanotubes Interactions with Mitochondrial Voltage-Dependent Anion Channel Based on Docking Perturbation Theory Approaches.
DOI: 10.6084/m9.figshare.4802317
title: DNA and AFLP matrices used in the paper "Sweet vernal grasses (Anthoxanthum) colonized African mountains along two fronts in the Late Pliocene, followed by secondary contact, polyploidization and local extinction in the Pleistocene", accepted for publication in Molecular Ecology

description: Concatenated DNA (nuclear; ITS and ETS and plastid, trnLF and trnTL) and AFLP matrices used in the paper "<i>Sweet vernal grasses (Anthoxanthum) colonized African mountains along two fronts in the Late Pliocene, followed by secondary contact, polyploidization and local extinction in the Pleistocene</i>" by Felly Mugizi Tusiime, Abel Gizaw, Tigist Wondimu, Catherine Aloyce Masao, Ahmed Abdikadir Abdi, Vincent Muwanika, Pavel Trávníček, Sileshi Nemomissa, Magnus Popp, Gerald Eilu, Christian Brochmann and Manuel Pimentel, accepted for publication in <i>Molecular Ecology</i>
DOI: 10.6084/m9.figshare.4802320.v2
title: Datasets, results and models for nanoQSAR & docking of SWCNs with Mitochondrial VDAC

description: Multiple files for Strong and Weak Single Walled Carbon Nanotubes Interactions with Mitochondrial Voltage-Dependent Anion Channel Based on Docking Perturbation Theory Approaches.
DOI: 10.6084/m9.figshare.4802320.v1
title: Datasets, results and models for nanoQSAR & docking of SWCNs with Mitochondrial VDAC

description: Multiple files for Strong and Weak Single Walled Carbon Nanotubes Interactions with Mitochondrial Voltage-Dependent Anion Channel Based on Docking Perturbation Theory Approaches.
DOI: 10.6084/m9.figshare.4802317.v1
title: DNA matrices used in the paper "Sweet vernal grasses (Anthoxanthum) colonized African mountains along two fronts in the Late Pliocene, followed by secondary contact, polyploidization and local extinction in the Pleistocene", accepted for publication in Molecular Ecology

description: Concatenated DNA matrices (nuclear; ITS and ETS and plastid, trnLF and trnTL) used in the paper "<i>Sweet vernal grasses (Anthoxanthum) colonized African mountains along two fronts in the Late Pliocene, followed by secondary contact, polyploidization and local extinction in the Pleistocene</i>" by Felly Mugizi Tusiime, Abel Gizaw, Tigist Wondimu, Catherine Aloyce Masao, Ahmed Abdikadir Abdi, Vincent Muwanika, Pavel Trávníček, Sileshi Nemomissa, Magnus Popp, Gerald Eilu, Christian Brochmann and Manuel Pimentel,<sup></sup><b></b> accepted for publication in <i>Molecular Ecology</i>
DOI: 10.6084/m9.figshare.4802317.v3
title: DNA and AFLP matrices used in the paper "Sweet vernal grasses (Anthoxanthum) colonized African mountains along two fronts in the Late Pliocene, followed by secondary contact, polyploidization and local extinction in the Pleistocene", accepted for publication in Molecular Ecology

description: Concatenated DNA (nuclear; ITS and ETS and plastid, trnLF and trnTL) and AFLP matrices used in the paper "<i>Sweet vernal grasses (Anthoxanthum) colonized African mountains along two fronts in the Late Pliocene, followed by secondary contact, polyploidization and local extinction in the Pleistocene</i>" by Felly Mugizi Tusiime, Abel Gizaw, Tigist Wondimu, Catherine Aloyce Masao, Ahmed Abdikadir Abdi, Vincent Muwanika, Pavel Trávníček, Sileshi Nemomissa, Magnus Popp, Gerald Eilu, Christian Brochmann and Manuel Pimentel, accepted for publication in <i>Molecular Ecology</i>