cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8020973.v1
title: Bayesian Approach for Assessing Non-Inferiority in Three-Arm Trials for Risk Ratio and Odds Ratio

description: In this article, we consider three-arm noninferiority (NI) trial that includes an experimental, a reference, and a placebo arm. While the risk difference (RD) is the most common and well-explored functional form for testing efficacy (or effectiveness), for binary outcomes, recent FDA guideline suggested other measures, such as relative risk (RR) and odds ratio (OR) on the basis of which NI can be claimed. However, developing test based on these different functions of binary outcomes are challenging since the construction and interpretation of NI margin for such functions are not trivial extensions of RD-based approach. Recently, we have proposed Frequentist approach for testing NI for these functionals. In this article, we further develop Bayesian approaches for testing NI based on effect retention approach for RR and OR. Bayesian paradigm provides a natural path to integrate historical trials’ information, as well as it allows using patients’/clinicians’ opinions as prior information via sequential learning. In addition we discuss, in detail, the sample size/power calculation which could be readily used while designing such trials in practice.
DOI: 10.6084/m9.figshare.8020970
title: “Step-Down Parametric Procedures for Testing Correlated Endpoints in a Group-Sequential Trial” by Yiyong Fu

description: Fu (2018) developed a parametric consonant closed testing procedure for correlated endpoints in a group-sequential design. In their approach, correlations between endpoints are exploited leading to a proportional up-scaling of local significance levels from Holm’s weighting scheme. We challenge the claim that the proposed calculation of the up-scaling factor leads to a test that protects the type I error in the group-sequential setting and outline two alternative approaches which do lead to exact error control.
DOI: 10.6084/m9.figshare.12821081
title: Metadata record for: Project IPAD, a database to catalogue the analysis of Fukushima Daiichi accident fragmental release material

description: This dataset contains key characteristics about the data described in the Data Descriptor Project IPAD, a database to catalogue the analysis of Fukushima Daiichi accident fragmental release material. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format
DOI: 10.6084/m9.figshare.8020898
title: 22ss

description: The details about this dataset and how to use them can be found here: https://aksimhal.github.io/astrocytes-synapses-fxs/
DOI: 10.6084/m9.figshare.8020970.v1
title: “Step-Down Parametric Procedures for Testing Correlated Endpoints in a Group-Sequential Trial” by Yiyong Fu

description: Fu (2018) developed a parametric consonant closed testing procedure for correlated endpoints in a group-sequential design. In their approach, correlations between endpoints are exploited leading to a proportional up-scaling of local significance levels from Holm’s weighting scheme. We challenge the claim that the proposed calculation of the up-scaling factor leads to a test that protects the type I error in the group-sequential setting and outline two alternative approaches which do lead to exact error control.
DOI: 10.6084/m9.figshare.12821081.v1
title: Metadata record for: Project IPAD, a database to catalogue the analysis of Fukushima Daiichi accident fragmental release material

description: This dataset contains key characteristics about the data described in the Data Descriptor Project IPAD, a database to catalogue the analysis of Fukushima Daiichi accident fragmental release material. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format
DOI: 10.6084/m9.figshare.8020856
title: 7ss

description: The details about this dataset and how to use them can be found here: https://aksimhal.github.io/astrocytes-synapses-fxs/
DOI: 10.6084/m9.figshare.8020898.v1
title: 22ss

description: The details about this dataset and how to use them can be found here: https://aksimhal.github.io/astrocytes-synapses-fxs/
DOI: 10.6084/m9.figshare.8020850
title: 6ss

description: The details about this dataset and how to use them can be found here: https://aksimhal.github.io/astrocytes-synapses-fxs/
DOI: 10.6084/m9.figshare.8020856.v1
title: 7ss

description: The details about this dataset and how to use them can be found here: https://aksimhal.github.io/astrocytes-synapses-fxs/
DOI: 10.6084/m9.figshare.8020769
title: Example of square planar copper(II) biuret complex: crystal structure, DNA and protein binding activity and molecular docking study

description: One mononuclear Cu(II) complex Cu(L)<sub>2</sub> (<b>1</b>) of biuret ligand has been synthesized and characterized by spectroscopic as well as single crystal X-ray diffraction study. The interaction of 1 with CT-DNA, BSA and HSA (bovine serum albumin and human serum albumin) was studied by UV-Vis, fluorescence spectral methods. Theoretical molecular docking studies were also carried out to investigate the interaction of metal complex (<b>1</b>) with CT-DNA. From all the study, it is clear that complex <b>1</b> has significant binding ability with CT-DNA and biologically active protein molecules like BSA as well as HSA. High value of intrinsic binding constant suggests classical intercalative binding modes and this intercalative binding modes were also verified by its quenching phenomenon of <b>1</b> with both BSA and HSA.
DOI: 10.6084/m9.figshare.8020850.v1
title: 6ss

description: The details about this dataset and how to use them can be found here: https://aksimhal.github.io/astrocytes-synapses-fxs/
DOI: 10.6084/m9.figshare.8020769.v1
title: Example of square planar copper(II) biuret complex: crystal structure, DNA and protein binding activity and molecular docking study

description: One mononuclear Cu(II) complex Cu(L)<sub>2</sub> (<b>1</b>) of biuret ligand has been synthesized and characterized by spectroscopic as well as single crystal X-ray diffraction study. The interaction of 1 with CT-DNA, BSA and HSA (bovine serum albumin and human serum albumin) was studied by UV-Vis, fluorescence spectral methods. Theoretical molecular docking studies were also carried out to investigate the interaction of metal complex (<b>1</b>) with CT-DNA. From all the study, it is clear that complex <b>1</b> has significant binding ability with CT-DNA and biologically active protein molecules like BSA as well as HSA. High value of intrinsic binding constant suggests classical intercalative binding modes and this intercalative binding modes were also verified by its quenching phenomenon of <b>1</b> with both BSA and HSA.
DOI: 10.6084/m9.figshare.8020736
title: Koutsidi_Moukas_Tzanatos_Table_S1.xls

description: <b>Koutsidi_Moukas_Tzanatos_Table_S1</b>: Niche classification scheme for 205 species of Mediterranean nekton, generated from a Regression tree analysis, using four niche descriptors (distribution, ecology, biology, behaviour). The file includes every combination of traits (ecological niche) generated from the Regression tree analysis (600 terminal nodes in total). The 144 ecological niches are occupied from groups of species examined, while the 456 ecological niches are vacant.
DOI: 10.6084/m9.figshare.8020754
title: Koutsidi_Moukas_Tzanatos_Table_S2.xls

description: <b>Koutsidi_Moukas_Tzanatos_Table_S2</b>: The competition between 205 species of Mediterranean nekton examined, specifically regarding: (a) habitat use, (b) food resources of adult/mature stages, (c) spawning habitat use. Species occurring in the same habitat (Posidonia beds, coralligene formations, lagoons) according to the cited sources are considered as competitors for the specific resource. The excel file has 3 worksheets: (1) <b>habitat_use</b>: This worksheet contains the 205 species examined, sorted by the modalities of the traits (optimal depth, habitat type, seabed type) relevant to habitat use. The trait depth range, appearing at the table (characterizing a species as eurybathic or stenobathic) for habitat use, was added, not to describe resource use, but to indicate the intensity of potential competition. (2) <b>adult_food</b>: This worksheet contains the 205 species examined, sorted by the modalities of the traits (maximum length, trophic level, feeding type, diet) relevant to the use of food resources by mature fish. (3) <b>spawning_habitat</b>: This worksheet contains the 205 species examined, sorted by the modalities of the traits (spawning period, spawning habitat) relevant to spawning habitat use.
DOI: 10.6084/m9.figshare.8020736.v1
title: Koutsidi_Moukas_Tzanatos_Table_S1.xls

description: <b>Koutsidi_Moukas_Tzanatos_Table_S1</b>: Niche classification scheme for 205 species of Mediterranean nekton, generated from a Regression tree analysis, using four niche descriptors (distribution, ecology, biology, behaviour). The file includes every combination of traits (ecological niche) generated from the Regression tree analysis (600 terminal nodes in total). The 144 ecological niches are occupied from groups of species examined, while the 456 ecological niches are vacant.
DOI: 10.6084/m9.figshare.8020754.v1
title: Koutsidi_Moukas_Tzanatos_Table_S2.xls

description: <b>Koutsidi_Moukas_Tzanatos_Table_S2</b>: The competition between 205 species of Mediterranean nekton examined, specifically regarding: (a) habitat use, (b) food resources of adult/mature stages, (c) spawning habitat use. Species occurring in the same habitat (Posidonia beds, coralligene formations, lagoons) according to the cited sources are considered as competitors for the specific resource. The excel file has 3 worksheets: (1) <b>habitat_use</b>: This worksheet contains the 205 species examined, sorted by the modalities of the traits (optimal depth, habitat type, seabed type) relevant to habitat use. The trait depth range, appearing at the table (characterizing a species as eurybathic or stenobathic) for habitat use, was added, not to describe resource use, but to indicate the intensity of potential competition. (2) <b>adult_food</b>: This worksheet contains the 205 species examined, sorted by the modalities of the traits (maximum length, trophic level, feeding type, diet) relevant to the use of food resources by mature fish. (3) <b>spawning_habitat</b>: This worksheet contains the 205 species examined, sorted by the modalities of the traits (spawning period, spawning habitat) relevant to spawning habitat use.
DOI: 10.6084/m9.figshare.8020622
title: Lipid membranes accelerate amyloid formation in the mouse model of AA amyloidosis

description: <b>Introduction:</b> AA amyloidosis develops as a result of prolonged inflammation and is characterized by deposits of N-terminal proteolytic fragments of the acute phase reactant serum amyloid A (SAA). Macrophages are usually found adjacent to amyloid, suggesting their involvement in the formation and/or degradation of the amyloid fibrils. Furthermore, accumulating evidence suggests that lipid membranes accelerate the fibrillation of different amyloid proteins. <b>Methods:</b> Using an experimental mouse model of AA amyloidosis, we compared the amyloidogenic effect of liposomes and/or amyloid-enhancing factor (AEF). Inflammation was induced by subcutaneous injection of silver nitrate followed by intravenous injection of liposomes and/or AEF to accelerate amyloid formation. <b>Results:</b> We showed that liposomes accelerate amyloid formation in inflamed mice, but the amyloidogenic effect of liposomes was weaker compared with AEF. Regardless of the induction method, amyloid deposits were mainly found in the marginal zones of the spleen and coincided with the depletion of marginal zone macrophages, while red pulp macrophages and metallophilic marginal zone macrophages proved insensitive to amyloid deposition. <b>Conclusions:</b> We conclude that increased intracellular lipid content facilitates AA amyloid fibril formation and show that the mouse model of AA amyloidosis is a suitable system for further mechanistic studies.
DOI: 10.6084/m9.figshare.8020631
title: Teaching modes and social-epistemological dimensions in medical Massive Open Online Courses: Lessons for integration in campus education

description: <b>Purpose:</b> Medical Massive Open Online Courses (MOOCs) have been integrated into formal campus teaching by several universities. However, teaching attributes of medical MOOCs have not been systematically investigated. Additionally, guidelines are needed to inform integration practices. This study systematically investigated the available teaching modes and social-epistemological dimensions of medical MOOCs. <b>Methods:</b> An overview of MOOCs on a medical topic was compiled and inclusion criteria were developed. A data collection tool was composed and calibrated. For data collection, out of 410 MOOCs 33 were selected based on these criteria. Investigators enrolled in selected MOOCs and analyzed teaching modes after examination of all course pages. Teaching modes were categorized in social-epistemological dimensions according to the Teaching Approach Framework. <b>Results:</b> Twenty-nine different teaching modes were found, showing wide distributions. Analysis of social-epistemological dimensions showed medical MOOCs focus on constructivist and individual teaching modes as opposed to objectivist and group modes. <b>Conclusions:</b> Medical MOOCs do not have a universal teaching mode profile. They contain a rich variety of teaching modes for integration in campus education of which videos, discussion boards, and multiple choice questions are used regularly. Constructivist teaching modes are readily available in medical MOOCs and can support educational innovation of formal campus teaching when integrated.
DOI: 10.6084/m9.figshare.8020622.v1
title: Lipid membranes accelerate amyloid formation in the mouse model of AA amyloidosis

description: <b>Introduction:</b> AA amyloidosis develops as a result of prolonged inflammation and is characterized by deposits of N-terminal proteolytic fragments of the acute phase reactant serum amyloid A (SAA). Macrophages are usually found adjacent to amyloid, suggesting their involvement in the formation and/or degradation of the amyloid fibrils. Furthermore, accumulating evidence suggests that lipid membranes accelerate the fibrillation of different amyloid proteins. <b>Methods:</b> Using an experimental mouse model of AA amyloidosis, we compared the amyloidogenic effect of liposomes and/or amyloid-enhancing factor (AEF). Inflammation was induced by subcutaneous injection of silver nitrate followed by intravenous injection of liposomes and/or AEF to accelerate amyloid formation. <b>Results:</b> We showed that liposomes accelerate amyloid formation in inflamed mice, but the amyloidogenic effect of liposomes was weaker compared with AEF. Regardless of the induction method, amyloid deposits were mainly found in the marginal zones of the spleen and coincided with the depletion of marginal zone macrophages, while red pulp macrophages and metallophilic marginal zone macrophages proved insensitive to amyloid deposition. <b>Conclusions:</b> We conclude that increased intracellular lipid content facilitates AA amyloid fibril formation and show that the mouse model of AA amyloidosis is a suitable system for further mechanistic studies.
DOI: 10.6084/m9.figshare.8020631.v2
title: Teaching modes and social-epistemological dimensions in medical Massive Open Online Courses: Lessons for integration in campus education

description: <b>Purpose:</b> Medical Massive Open Online Courses (MOOCs) have been integrated into formal campus teaching by several universities. However, teaching attributes of medical MOOCs have not been systematically investigated. Additionally, guidelines are needed to inform integration practices. This study systematically investigated the available teaching modes and social-epistemological dimensions of medical MOOCs. <b>Methods:</b> An overview of MOOCs on a medical topic was compiled and inclusion criteria were developed. A data collection tool was composed and calibrated. For data collection, out of 410 MOOCs 33 were selected based on these criteria. Investigators enrolled in selected MOOCs and analyzed teaching modes after examination of all course pages. Teaching modes were categorized in social-epistemological dimensions according to the Teaching Approach Framework. <b>Results:</b> Twenty-nine different teaching modes were found, showing wide distributions. Analysis of social-epistemological dimensions showed medical MOOCs focus on constructivist and individual teaching modes as opposed to objectivist and group modes. <b>Conclusions:</b> Medical MOOCs do not have a universal teaching mode profile. They contain a rich variety of teaching modes for integration in campus education of which videos, discussion boards, and multiple choice questions are used regularly. Constructivist teaching modes are readily available in medical MOOCs and can support educational innovation of formal campus teaching when integrated.
DOI: 10.6084/m9.figshare.8020631.v1
title: Teaching modes and social-epistemological dimensions in medical Massive Open Online Courses: Lessons for integration in campus education

description: <b>Purpose:</b> Medical Massive Open Online Courses (MOOCs) have been integrated into formal campus teaching by several universities. However, teaching attributes of medical MOOCs have not been systematically investigated. Additionally, guidelines are needed to inform integration practices. This study systematically investigated the available teaching modes and social-epistemological dimensions of medical MOOCs. <b>Methods:</b> An overview of MOOCs on a medical topic was compiled and inclusion criteria were developed. A data collection tool was composed and calibrated. For data collection, out of 410 MOOCs 33 were selected based on these criteria. Investigators enrolled in selected MOOCs and analyzed teaching modes after examination of all course pages. Teaching modes were categorized in social-epistemological dimensions according to the Teaching Approach Framework. <b>Results:</b> Twenty-nine different teaching modes were found, showing wide distributions. Analysis of social-epistemological dimensions showed medical MOOCs focus on constructivist and individual teaching modes as opposed to objectivist and group modes. <b>Conclusions:</b> Medical MOOCs do not have a universal teaching mode profile. They contain a rich variety of teaching modes for integration in campus education of which videos, discussion boards, and multiple choice questions are used regularly. Constructivist teaching modes are readily available in medical MOOCs and can support educational innovation of formal campus teaching when integrated.
DOI: 10.25380/iastate.8020583
title: Longitudinal Shoe Study: Paper + Powder images

description: Images of 160 shoe prints (“Nike Winflo 4” or “Adidas Seeley”; 4 sizes each) made using fingerprint powder on paper, with associated measurements and data about shoe wear, surfaces, and wearers.<br><br>Each pair of shoes was worn for at least 10,000 steps per week over a 6-month period, with multiple measurements of the shoe soles taken initially and during three check-in periods spaced at approximately 5 week intervals.<br><br>The images are accompanied by 3 CSV files describing the shoes, visit (information collected from surveys along with the shoes), and individual images. The codebooks contain descriptions of the variables in each of the CSV files as well as a more extensive description of the file naming scheme outlined in the README.<br><br>These files can be used to examine wear pattern development, to look for the presence of identifying characteristics among shoes with similar features, and to develop algorithms for matching shoes based on individualizing characteristics. In addition, the paper prints include manipulations of the kinematic effects of the shoe print process: different actions were recorded including careful stepping, jumping, smudging, and walking. These prints may be useful when developing algorithms to match prints across different types of motion.
DOI: 10.25380/iastate.8020583.v1
title: Longitudinal Shoe Study: Paper + Powder images

description: Images of 160 shoe prints (“Nike Winflo 4” or “Adidas Seeley”; 4 sizes each) made using fingerprint powder on paper, with associated measurements and data about shoe wear, surfaces, and wearers.<br><br>Each pair of shoes was worn for at least 10,000 steps per week over a 6-month period, with multiple measurements of the shoe soles taken initially and during three check-in periods spaced at approximately 5 week intervals.<br><br>The images are accompanied by 3 CSV files describing the shoes, visit (information collected from surveys along with the shoes), and individual images. The codebooks contain descriptions of the variables in each of the CSV files as well as a more extensive description of the file naming scheme outlined in the README.<br><br>These files can be used to examine wear pattern development, to look for the presence of identifying characteristics among shoes with similar features, and to develop algorithms for matching shoes based on individualizing characteristics. In addition, the paper prints include manipulations of the kinematic effects of the shoe print process: different actions were recorded including careful stepping, jumping, smudging, and walking. These prints may be useful when developing algorithms to match prints across different types of motion.
DOI: 10.6084/m9.figshare.8020427
title: Supplementary Material - Arroyo et al., unpublished

description: Arroyo AS, Lannes R, de Vargas C, Bapteste E, Ruiz-Trillo I. "Gene similarity networks from the<i> Tara </i>Oceans expedition unveil geographical distribution, ecological interactions, and novel diversity among unicellular relatives of animals." <i>Unpublished</i>.<br>- Supplementary Material 1: Detailed information on network metrics- Supplementary Material 2: Alignments and the phylogenetic tree from Figure 3D. - Supplementary Material 3: Alignments and the phylogenetic tree from Figure 4B. - Supplementary Material 4: Starting dataset and networks of unicellular Holozoa. - Supplementary Material 5: Alignment and reference Holozoa tree.- Supplementary Table: Control test, assortativity values of ENV <i>vs</i> REF, assortativity values computed for geographical location, laters in the water column, and size fractions.
DOI: 10.6084/m9.figshare.8020418
title: Leprosy Microbiome OTU Level Abundance Data (Filtered Set)

description: OTU level microbial abundance data set obtained using vsearch v2.8.0_linux_x86_64 for Leprosy Microbiome Study. The dataset contains 89 samples and 28321 unique OTUs. A total of 161,695 OTUs were identified using vsearch based de-novo classification, which were filtered to 28,321 unique OTUs by omitting the population level singletons.
DOI: 10.6084/m9.figshare.8020421
title: Leprosy Microbiome OTU Level Abundance Data (Unfiltered, raw set)

description: OTU level microbial abundance data set obtained using vsearch v2.8.0_linux_x86_64 for Leprosy Microbiome Study. The dataset contains 89 samples and 161,695 unique OTUs.
DOI: 10.6084/m9.figshare.8020424
title: Metadata for Leprosy Microbiome Study

description: Comprehensive metadata information table corresponding to all collected samples in the study.