cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6187244
title: Dataset for: Transcending data gaps: a framework to reduce inferential errors in ecological analyses

description: The analysis of functional diversity has gained increasing importance due to its generality and utility in ecology. In particular, patterns in the spatial distribution and temporal change of functional diversity are being used to predict locations and functional groups that are immediately vulnerable to global changes. A major impediment to the accurate measurement of functional diversity is the pervasiveness of missing data in trait datasets. Whilst such prevalent data gaps can engender misleading inferences in functional diversity analyses, we currently lack any practical guide to handle missing data in trait datasets. Here, we identify significant mismatches between true functional diversity and values derived from datasets that contain missing data. We demonstrate that imputing missing data with a phylogeny-informed approach reduces the risk of misinterpretation of functional diversity patterns, and provides baseline information against which central questions in ecology can be evaluated.
DOI: 10.6084/m9.figshare.6187244.v1
title: Dataset for: Transcending data gaps: a framework to reduce inferential errors in ecological analyses

description: The analysis of functional diversity has gained increasing importance due to its generality and utility in ecology. In particular, patterns in the spatial distribution and temporal change of functional diversity are being used to predict locations and functional groups that are immediately vulnerable to global changes. A major impediment to the accurate measurement of functional diversity is the pervasiveness of missing data in trait datasets. Whilst such prevalent data gaps can engender misleading inferences in functional diversity analyses, we currently lack any practical guide to handle missing data in trait datasets. Here, we identify significant mismatches between true functional diversity and values derived from datasets that contain missing data. We demonstrate that imputing missing data with a phylogeny-informed approach reduces the risk of misinterpretation of functional diversity patterns, and provides baseline information against which central questions in ecology can be evaluated.
DOI: 10.6084/m9.figshare.6185279
title: likert.xlsx

description: Dataser of the Likert Scale in xlsx format
DOI: 10.6084/m9.figshare.6182636
title: Ediacaran (~ 600 Ma) orogenic gold in Egypt: age of the Atalla gold mineralization and its geological significance

description: Integration of a new monazite U–Pb age for the Atalla monzogranite (615 ± 9 Ma) and a <sup>40</sup>Ar/<sup>39</sup>Ar plateau age of hydrothermal white mica (601 ± 5.5 Ma, 2σ) disseminated in gold-bearing quartz veins at the Atalla mine indicates post-intrusion Au-mineralization, overlapping with cooling and regional exhumation ages of the Central Eastern Desert. The mica age is in agreement with published Re–Os age of gold mineralization in the Fawakhir area, ~ 20 km to the south along the Atalla shear zone. The new geochronological data demonstrate lode gold formation during the ~ 600 Ma period, controlled by wrench tectonics along Najd-related structures in the region (620–585 Ma). Fluid focusing and gold deposition during the Ediacaran were promoted by contrasting lithological and rheological properties at the granite-ophiolites contacts. This seems to be a typical setting for gold ores in this part of the Nubian Shield, and can aid exploration for undiscovered resources in the region.
DOI: 10.6084/m9.figshare.6182636.v1
title: Ediacaran (~ 600 Ma) orogenic gold in Egypt: age of the Atalla gold mineralization and its geological significance

description: Integration of a new monazite U–Pb age for the Atalla monzogranite (615 ± 9 Ma) and a <sup>40</sup>Ar/<sup>39</sup>Ar plateau age of hydrothermal white mica (601 ± 5.5 Ma, 2σ) disseminated in gold-bearing quartz veins at the Atalla mine indicates post-intrusion Au-mineralization, overlapping with cooling and regional exhumation ages of the Central Eastern Desert. The mica age is in agreement with published Re–Os age of gold mineralization in the Fawakhir area, ~ 20 km to the south along the Atalla shear zone. The new geochronological data demonstrate lode gold formation during the ~ 600 Ma period, controlled by wrench tectonics along Najd-related structures in the region (620–585 Ma). Fluid focusing and gold deposition during the Ediacaran were promoted by contrasting lithological and rheological properties at the granite-ophiolites contacts. This seems to be a typical setting for gold ores in this part of the Nubian Shield, and can aid exploration for undiscovered resources in the region.
DOI: 10.6084/m9.figshare.6182609
title: Supplementary Data - R code from Does the winner–loser effect determine male mating success?

description: R code used for data analysis
DOI: 10.6084/m9.figshare.6182609.v1
title: Supplementary Data - R code from Does the winner–loser effect determine male mating success?

description: R code used for data analysis
DOI: 10.6084/m9.figshare.6182606
title: Supplementary Dataset from Does the winner–loser effect determine male mating success?

description: The original, raw data collected and used for data analysis
DOI: 10.6084/m9.figshare.6182606.v1
title: Supplementary Dataset from Does the winner–loser effect determine male mating success?

description: The original, raw data collected and used for data analysis
DOI: 10.6084/m9.figshare.6182522.v1
title: Phase1 Daytime pH analysis.R

description: These data and statistics are associated with the following publication: Groner ML, Burge CA, Cox R, Rivlin N, Turner M, Van Alstyne KL, Wyllie-Echeverria S, Bucci J, Staudigel P, and Friedman CS. 2018. Oysters and eelgrass: potential partners in a high pCO2 ocean. Ecology _:_-_. <br>
DOI: 10.6084/m9.figshare.6182522.v2
title: Data and Statistics associated with Groner et al. 2018 Oysters and eelgrass: Potential partners in a high pCO2 ocean

description: These data and statistics are associated with the following publication: Groner ML, Burge CA, Cox R, Rivlin N, Turner M, Van Alstyne KL, Wyllie-Echeverria S, Bucci J, Staudigel P, and Friedman CS. 2018. Oysters and eelgrass: potential partners in a high pCO2 ocean. Ecology _:_-_. <br>
DOI: 10.6084/m9.figshare.6182522.v3
title: Data and statistical code associated with Groner et al. 2018 Oysters and eelgrass: Potential partners in a high pCO2 ocean

description: These data and statistics are associated with the following publication: Groner ML, Burge CA, Cox R, Rivlin N, Turner M, Van Alstyne KL, Wyllie-Echeverria S, Bucci J, Staudigel P, and Friedman CS. 2018. Oysters and eelgrass: potential partners in a high pCO2 ocean. Ecology _:_-_. <br>
DOI: 10.6084/m9.figshare.6182519
title: Anchored phylogenomics uncovers hybridization and ecological adaptation shaping the Lake Tanganyika cichlid radiation

description: Alignments, trees, and networks for the paper "Anchored phylogenomics uncovers hybridization and ecological adaptation shaping the Lake Tanganyika cichlid radiation" published in Nature Communications
DOI: 10.6084/m9.figshare.6182513
title: Supplementary table 3

description: <b>Polar metabolite data</b>Polar metabolite profiling data were generated for a mouse KGC pancreatic tumor line expressing doxycycline-inducible constitutively-active<b> </b>mutant GNAS (GNAS<sup>R201C</sup>) growing in 2D culture in the presence of doxycycline; Dox(+) or absence of doxycycline; Dox(-). The cells were harvested as 5 biological replicates and flash-frozen. The polar metabolites were extracted with 40:40:20 acetonitrile/methanol/water and replicates are denoted as Dox(+)-1, Dox(+)-2, Dox(+)-3, Dox(+)-4, Dox(+)-5 and Dox(-)-1, Dox(-)-2, Dox(-)-3, Dox(-)-4, Dox(-)-5. Polar metabolites were analyzed by QQQ-LC/MS/MSas described in the reference<sup>1.</sup>The ion counts were normalized to the total cell number. Metabolites were quantified by integrating the area under the curve, and then normalized to internal standard values. <sup></sup> 1) Louie, S. M.<i>et al.</i>GSTP1 Is a Driver of Triple-Negative Breast Cancer Cell Metabolism and Pathogenicity. <i>Cell Chem Biol</i><b>23</b>, 567-578, doi:10.1016/j.chembiol.2016.03.017 (2016).
DOI: 10.6084/m9.figshare.6182513.v1
title: Supplementary table 3

description: <b>Polar metabolite data</b>Polar metabolite profiling data were generated for a mouse KGC pancreatic tumor line expressing doxycycline-inducible constitutively-active<b> </b>mutant GNAS (GNAS<sup>R201C</sup>) growing in 2D culture in the presence of doxycycline; Dox(+) or absence of doxycycline; Dox(-). The cells were harvested as 5 biological replicates and flash-frozen. The polar metabolites were extracted with 40:40:20 acetonitrile/methanol/water and replicates are denoted as Dox(+)-1, Dox(+)-2, Dox(+)-3, Dox(+)-4, Dox(+)-5 and Dox(-)-1, Dox(-)-2, Dox(-)-3, Dox(-)-4, Dox(-)-5. Polar metabolites were analyzed by QQQ-LC/MS/MSas described in the reference<sup>1.</sup>The ion counts were normalized to the total cell number. Metabolites were quantified by integrating the area under the curve, and then normalized to internal standard values. <sup></sup> 1) Louie, S. M.<i>et al.</i>GSTP1 Is a Driver of Triple-Negative Breast Cancer Cell Metabolism and Pathogenicity. <i>Cell Chem Biol</i><b>23</b>, 567-578, doi:10.1016/j.chembiol.2016.03.017 (2016).
DOI: 10.6084/m9.figshare.6182501
title: Supplementary table 2.xlsx

description: <b>Lipidomic data </b> <b></b>Lipidomic maps were generated for mouse KGC pancreatic tumor organoid lines expressing doxycycline-inducible constitutively-active<b> </b>mutant GNAS (GNAS<sup>R201C</sup>). The organoids were analyzed in the presence of doxycycline; Dox(+) or absence of doxycycline; Dox(-). LC-MS experiments for non-polar metabolites were performed using a KCG organoid line in triplicate for the +Dox and -Dox conditions and denoted as Dox(+)-1; Dox(+)-2; Dox(+)-3; Dox(-)-1; Dox(-)-2; Dox(-)-3. LC-MS/MS-based lipidomic experiments and data analyses were performed as described in the reference<sup>1</sup>. The data were normalized to the total number of cells in the organoids from replicate wells. Metabolites were quantified by integrating the area under the curve. Lipidation (lipid species detected); Class (class of lipids. see lipid keys in the document)Reference: 1) Smulan, L. J.<i>et al.</i>Cholesterol-Independent SREBP-1 Maturation Is Linked to ARF1 Inactivation. <i>Cell reports</i><b>16</b>, 9-18, doi:10.1016/j.celrep.2016.05.086 (2016).
DOI: 10.6084/m9.figshare.6182501.v1
title: Supplementary table 2.xlsx

description: <b>Lipidomic data </b> <b></b>Lipidomic maps were generated for mouse KGC pancreatic tumor organoid lines expressing doxycycline-inducible constitutively-active<b> </b>mutant GNAS (GNAS<sup>R201C</sup>). The organoids were analyzed in the presence of doxycycline; Dox(+) or absence of doxycycline; Dox(-). LC-MS experiments for non-polar metabolites were performed using a KCG organoid line in triplicate for the +Dox and -Dox conditions and denoted as Dox(+)-1; Dox(+)-2; Dox(+)-3; Dox(-)-1; Dox(-)-2; Dox(-)-3. LC-MS/MS-based lipidomic experiments and data analyses were performed as described in the reference<sup>1</sup>. The data were normalized to the total number of cells in the organoids from replicate wells. Metabolites were quantified by integrating the area under the curve. Lipidation (lipid species detected); Class (class of lipids. see lipid keys in the document)Reference: 1) Smulan, L. J.<i>et al.</i>Cholesterol-Independent SREBP-1 Maturation Is Linked to ARF1 Inactivation. <i>Cell reports</i><b>16</b>, 9-18, doi:10.1016/j.celrep.2016.05.086 (2016).
DOI: 10.6084/m9.figshare.6182381
title: PEPSE for SURE.sav

description: <sup>Background</sup><sup> </sup><sup>In western countries, men who have sex with men (MSM) are most affected by HIV and increasingly likely to engage in risky sexual behaviour. MSM who experience a potential sexual exposure to HIV (PEPSE) and receive a preventative regimen of anti-HIV treatment are at particularly high risk of acquiring HIV and could potentially benefit from targeted risk reduction behavioural interventions such as motivational interviewing (MI).</sup><sup> </sup><sup>Purpose</sup><sup> </sup><sup>The aim of this trial was to examine the impact of augmented MI (MI plus information provision and behavioural skills building), over and above routine care, on reducing risky sexual behaviour in MSM prescribed PEPSE. Secondary aims of the research were to examine whether the intervention reduced sexually transmitted infections (STI) and further requests for PEP. </sup><sup> </sup><sup>Methods</sup><sup> </sup><sup>A parallel-group pragmatic randomised controlled trial was conducted with 175 MSM recruited from five sexual health (SH) clinics in the south east of England. The intervention was two fixed-duration sessions of telephone administered augmented MI. A manual guided the selection of individualised persuasive communication strategies based on underlying change mechanisms specified by the Information, Motivation and Behavioural Skills (IMB) model. Primary outcomes were the number of receptive and active anal intercourse (AI) partners, the use of condoms every time during receptive and active AI and the use of condoms sometimes during receptive and active AI.</sup><sup> </sup><sup>Results</sup><sup> </sup><sup>There were no significant impacts on sexual risk behaviour or any of the psychological measures, and no discernible reduction in requests for repeat PEP or rates of STIs within a year. </sup><sup> </sup><sup>Conclusion</sup><sup> </sup><sup>Our behavioural intervention of augmented MI did not affect risky sexual behaviour, rates of further PEP and STIs, and psychological factors, in MSM prescribed PEPSE.</sup>
DOI: 10.6084/m9.figshare.6182381.v1
title: PEPSE for SURE.sav

description: <sup>Background</sup><sup> </sup><sup>In western countries, men who have sex with men (MSM) are most affected by HIV and increasingly likely to engage in risky sexual behaviour. MSM who experience a potential sexual exposure to HIV (PEPSE) and receive a preventative regimen of anti-HIV treatment are at particularly high risk of acquiring HIV and could potentially benefit from targeted risk reduction behavioural interventions such as motivational interviewing (MI).</sup><sup> </sup><sup>Purpose</sup><sup> </sup><sup>The aim of this trial was to examine the impact of augmented MI (MI plus information provision and behavioural skills building), over and above routine care, on reducing risky sexual behaviour in MSM prescribed PEPSE. Secondary aims of the research were to examine whether the intervention reduced sexually transmitted infections (STI) and further requests for PEP. </sup><sup> </sup><sup>Methods</sup><sup> </sup><sup>A parallel-group pragmatic randomised controlled trial was conducted with 175 MSM recruited from five sexual health (SH) clinics in the south east of England. The intervention was two fixed-duration sessions of telephone administered augmented MI. A manual guided the selection of individualised persuasive communication strategies based on underlying change mechanisms specified by the Information, Motivation and Behavioural Skills (IMB) model. Primary outcomes were the number of receptive and active anal intercourse (AI) partners, the use of condoms every time during receptive and active AI and the use of condoms sometimes during receptive and active AI.</sup><sup> </sup><sup>Results</sup><sup> </sup><sup>There were no significant impacts on sexual risk behaviour or any of the psychological measures, and no discernible reduction in requests for repeat PEP or rates of STIs within a year. </sup><sup> </sup><sup>Conclusion</sup><sup> </sup><sup>Our behavioural intervention of augmented MI did not affect risky sexual behaviour, rates of further PEP and STIs, and psychological factors, in MSM prescribed PEPSE.</sup>
DOI: 10.6084/m9.figshare.6182243
title: Supplementary Material for: Diagnostic Accuracy of Latex Agglutination Turbidimetric Immunoassay in Screening Adolescents for <b><i>Helicobacter pylori</i></b> Infection in Japan

description: <b><i>Background/Aims:</i></b> Serologic tests are commonly used for screening <i>Helicobacter pylori</i> infection because they not only provide quick results but also are inexpensive. A new latex agglutination serum antibody assay (LZ test) has been developed and it is expected to be as effective as conventional assays. This study aimed to calculate a reliable cutoff value for the LZ test and to estimate the sensitivity and specificity of the cutoff value in screening adolescents for <i>H. pylori</i> infection in Japan. <b><i>Methods:</i></b> We screened junior high school students in Akita Prefecture, Japan, for <i>H. pylori</i> infection. We used the data of 213 such students who underwent <i>H. pylori</i> stool antigen (HpSA) tests in 2016. The students who had positive results with HpSA tests were diagnosed with <i>H. pylori</i> infection. Of the 213 students, 209 underwent the LZ test. <b><i>Results:</i></b> The prevalence rate of<i> H. pylori</i> infection was 3.8% (8/209). The area under the curve for the LZ test was 0.88. The cutoff value of the LZ test was determined to be 3.1 U/mL. At this value, the sensitivity and specificity were 87.5 and 91.5%, respectively. <b><i>Conclusion:</i></b> The accuracy of the LZ test in adolescents was well balanced for sensitivity and specificity as well as for tolerable results.
DOI: 10.6084/m9.figshare.6182243.v1
title: Supplementary Material for: Diagnostic Accuracy of Latex Agglutination Turbidimetric Immunoassay in Screening Adolescents for <b><i>Helicobacter pylori</i></b> Infection in Japan

description: <b><i>Background/Aims:</i></b> Serologic tests are commonly used for screening <i>Helicobacter pylori</i> infection because they not only provide quick results but also are inexpensive. A new latex agglutination serum antibody assay (LZ test) has been developed and it is expected to be as effective as conventional assays. This study aimed to calculate a reliable cutoff value for the LZ test and to estimate the sensitivity and specificity of the cutoff value in screening adolescents for <i>H. pylori</i> infection in Japan. <b><i>Methods:</i></b> We screened junior high school students in Akita Prefecture, Japan, for <i>H. pylori</i> infection. We used the data of 213 such students who underwent <i>H. pylori</i> stool antigen (HpSA) tests in 2016. The students who had positive results with HpSA tests were diagnosed with <i>H. pylori</i> infection. Of the 213 students, 209 underwent the LZ test. <b><i>Results:</i></b> The prevalence rate of<i> H. pylori</i> infection was 3.8% (8/209). The area under the curve for the LZ test was 0.88. The cutoff value of the LZ test was determined to be 3.1 U/mL. At this value, the sensitivity and specificity were 87.5 and 91.5%, respectively. <b><i>Conclusion:</i></b> The accuracy of the LZ test in adolescents was well balanced for sensitivity and specificity as well as for tolerable results.
DOI: 10.6084/m9.figshare.6182216
title: Cylindrospermopsin toxicity in mice following a 90-d oral exposure

description: Cylindrospermopsin (CYN) is a toxin associated with numerous species of freshwater cyanobacteria throughout the world. It is postulated to have caused an episode of serious illnesses in Australia through treated drinking water, as well as lethal effects in livestock exposed to water from farm ponds. Toxicity included effects indicative of both hepatic and renal dysfunction. In humans, symptoms progressed from initial hepatomegaly, vomiting, and malaise to acidosis and hypokalemia, bloody diarrhea, and hyperemia in mucous membranes. Laboratory animal studies predominantly involved the intraperitoneal (i.p.) route of administration and confirmed this pattern of toxicity with changes in liver enzyme activities and histopathology consistent with hepatic injury and adverse renal effects. The aim of this study was designed to assess subchronic oral exposure (90 d) of purified CYN from 75 to 300 µg/kg/d in mouse. At the end of the dosing period, examinations of animals noted (1) elevated organ to body weight ratios of liver and kidney at all dose levels, (2) treatment-related increases in serum alanine aminotransferase (ALT) activity, (3) decreased blood urea nitrogen (BUN) and cholesterol concentrations in males, and (4) elevated monocyte counts in both genders. Histopathological alterations included hepatocellular hypertrophy and cord disruption in the liver, as well as renal cellular hypertrophy, tubule dilation, and cortical tubule lesions that were more prominent in males. A series of genes were differentially expressed including Bax (apoptosis), Rpl6 (tissue regeneration), Fabp4 (fatty acid metabolism), and Proc (blood coagulation). Males were more sensitive to many renal end points suggestive of toxicity. At the end of exposure, toxicity was noted at all dose levels, and the 75 µg/kg group exhibited significant effects in liver and kidney/body weight ratios, reduced BUN, increased serum monocytes, and multiple signs of histopathology indicating that a no-observed-adverse-effect level could not be determined for any dose level.
DOI: 10.6084/m9.figshare.6182216.v1
title: Cylindrospermopsin toxicity in mice following a 90-d oral exposure

description: Cylindrospermopsin (CYN) is a toxin associated with numerous species of freshwater cyanobacteria throughout the world. It is postulated to have caused an episode of serious illnesses in Australia through treated drinking water, as well as lethal effects in livestock exposed to water from farm ponds. Toxicity included effects indicative of both hepatic and renal dysfunction. In humans, symptoms progressed from initial hepatomegaly, vomiting, and malaise to acidosis and hypokalemia, bloody diarrhea, and hyperemia in mucous membranes. Laboratory animal studies predominantly involved the intraperitoneal (i.p.) route of administration and confirmed this pattern of toxicity with changes in liver enzyme activities and histopathology consistent with hepatic injury and adverse renal effects. The aim of this study was designed to assess subchronic oral exposure (90 d) of purified CYN from 75 to 300 µg/kg/d in mouse. At the end of the dosing period, examinations of animals noted (1) elevated organ to body weight ratios of liver and kidney at all dose levels, (2) treatment-related increases in serum alanine aminotransferase (ALT) activity, (3) decreased blood urea nitrogen (BUN) and cholesterol concentrations in males, and (4) elevated monocyte counts in both genders. Histopathological alterations included hepatocellular hypertrophy and cord disruption in the liver, as well as renal cellular hypertrophy, tubule dilation, and cortical tubule lesions that were more prominent in males. A series of genes were differentially expressed including Bax (apoptosis), Rpl6 (tissue regeneration), Fabp4 (fatty acid metabolism), and Proc (blood coagulation). Males were more sensitive to many renal end points suggestive of toxicity. At the end of exposure, toxicity was noted at all dose levels, and the 75 µg/kg group exhibited significant effects in liver and kidney/body weight ratios, reduced BUN, increased serum monocytes, and multiple signs of histopathology indicating that a no-observed-adverse-effect level could not be determined for any dose level.
DOI: 10.6084/m9.figshare.6182192
title: Membrane Potential (Windows version)

description: Membrane Potential is a computer program that lets you study some of the factors that affect the value of the membrane potential in mammalian cells as well as to explore the basis for action potentials and synaptic potentials in excitable cells.
DOI: 10.6084/m9.figshare.6182192.v2
title: Membrane Potential (Windows version)

description: Membrane Potential is a computer program that lets you study some of the factors that affect the value of the membrane potential in mammalian cells as well as to explore the basis for action potentials and synaptic potentials in excitable cells.