cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5415241.v1
title: Computationally Efficient Estimation for the Generalized Odds Rate Mixture Cure Model with Interval Censored Data

description: For semiparametric survival models with interval censored data and a cure fraction, it is often difficult to derive nonparametric maximum likelihood estimation due to the challenge in maximizing the complex likelihood function. In this paper, we propose a computationally efficient EM algorithm, facilitated by a gamma-poisson data augmentation, for maximum likelihood estimation in a class of generalized odds rate mixture cure (GORMC) models with interval censored data. The gamma-poisson data augmentation greatly simplifies the EM estimation and enhances the convergence speed of the EM algorithm. The empirical properties of the proposed method are examined through extensive simulation studies and compared with numerical maximum likelihood estimates. An R package “GORCure” is developed to implement the proposed method and its use is illustrated by an application to the Aerobic Center Longitudinal Study dataset.
DOI: 10.6084/m9.figshare.5415193.v2
title: Species tree

description: Data set of species trees from: https://figshare.com/projects/Evaluating_fast_maximum_likelihood-based_phylogenetic_programs_using_empirical_phylogenomic_data_sets/22040
DOI: 10.6084/m9.figshare.5415193.v1
title: A1.RAxML.ASTRAL.tre

description: Data set of species trees from: https://figshare.com/projects/Evaluating_fast_maximum_likelihood-based_phylogenetic_programs_using_empirical_phylogenomic_data_sets/22040
DOI: 10.6084/m9.figshare.12464465.v1
title: Pathogen-induced recruitment of a beneficial bacterium in wheat

description: <b>Plants are subjected to diverse stresses throughout their lives. Emerging theoretical framework suggests that they may have co-evolved multiple strategies to cooperate with microorganisms to cope with </b><b>stresses. However, empirical evidence underlying co-evolution processes and mutualistic plant-microbial interactions in stress scenarios are limited. In this study, we tested the hypothesis that infection by the soil-borne hemi-biotrophic pathogen <i>Fusarium pseudograminearum</i> (<i>Fp</i>), which causes a devastating crown rot disease on wheat, affects the community structure of the wheat-associated microbiome. Rhizosphere and plant samples were collected from a field experiment where durum wheat (<i>Triticum aestivum</i>) was naturally infected with <i>Fp </i>at different levels for individuals. Phylogenetic marker gene sequencing was used to profile microbial communities and evaluate effects of <i>Fp</i> infection on plant microbiomes. Our data revealed that diseased plants were associated with distinct rhizosphere and root endosphere microbiomes compared with healthy plants. We observed that infected plants had higher abundances of some taxa including a beneficial bacterium <i>Stenotrophomonas rhizophila</i> (SR80) in the rhizosphere soil and root endosphere. T</b><b>his bacterium </b><b>reached 3×10<sup>8</sup> cfu g<sup>-1</sup> in the rhizosphere soil, accounting for up to 12% of the microbes in the root endosphere. Further analyses revealed that the abundance of SR80</b><b> had a positive linear correlation with the <i>Fp</i> load at base stems and expression of </b><b>defense</b><b> genes </b><b>in</b><b> leaves. </b><b>We were able to isolate SR80 from the rhizosphere, which upon re-introduction in soils promoted wheat growth, survival rates, and enhanced defense signaling in plant leaves, but only in the presence of the pathogen. This bacterium seems to have acted as an early warning system for plant defense against the <i>Fp</i>.</b><b> Together, these findings provide novel evidence for the potential protection of plants by a beneficial microbe against pathogens via modulation of the plant immune system.</b>
DOI: 10.6084/m9.figshare.5415055
title: Household Structure Census Data

description: Summary of hosuehold types in 22 countries from IPUMS data<br>See github repo for code. <br><br>See pdf of poster for full factsheet. <br>
DOI: 10.6084/m9.figshare.5415055.v2
title: Household Structure Census Data

description: Summary of hosuehold types in 22 countries from IPUMS data<br>See github repo for code. <br><br>See pdf of poster for full factsheet. <br>
DOI: 10.6084/m9.figshare.5415055.v1
title: summaries.csv

description: Summary of hosuehold types in 22 countries from IPUMS data
DOI: 10.6084/m9.figshare.5414995
title: PH.13.02.FS

description: Household Living Arrangements--FactsheetCode for data import and clean and visualisation of IPUMS data as poster/factsheet and shiny app.
DOI: 10.6084/m9.figshare.5414995.v2
title: PH.13.02.FS

description: Household Living Arrangements--FactsheetCode for data import and clean and visualisation of IPUMS data as poster/factsheet and shiny app.
DOI: 10.6084/m9.figshare.5414950
title: AMPK-TOR Phyletic Profile

description: The phylogenetic profile integrating Feature Architecture Similarity scores for AMPK-TOR pathway components.
DOI: 10.6084/m9.figshare.5414950.v1
title: AMPK-TOR Phyletic Profile

description: The phylogenetic profile integrating Feature Architecture Similarity scores for AMPK-TOR pathway components.
DOI: 10.6084/m9.figshare.5414902
title: Managing your scholarly reputation: the experts speak!

description: In this hour-long webinar (recorded 15 September 2017), experts share their tips and tricks for engaging the public, finding readers for your work, and otherwise sharpening the reputational tools in your outreach toolbox. Featuring public historian and #histcomm (history communication) founder Jason Steinhauer (Villanova University) and science communicator and paleontologist Jon Tennant (ScienceOpen). Moderated by Cat Williams (Altmetric).<br>Included here are the webinar's audio recording and slides.
DOI: 10.6084/m9.figshare.5414902.v1
title: Managing your scholarly reputation: the experts speak!

description: In this hour-long webinar (recorded 15 September 2017), experts share their tips and tricks for engaging the public, finding readers for your work, and otherwise sharpening the reputational tools in your outreach toolbox. Featuring public historian and #histcomm (history communication) founder Jason Steinhauer (Villanova University) and science communicator and paleontologist Jon Tennant (ScienceOpen). Moderated by Cat Williams (Altmetric).<br>Included here are the webinar's audio recording and slides.
DOI: 10.6084/m9.figshare.5414770
title: Evolutionary traceabilities of proteins

description: Supplementary tables for traceabilities estimation of 6352 yeast proteins in three domains of life.
DOI: 10.6084/m9.figshare.5414755
title: Example dataset for bibrep.ado

description: The data file contains the publication set of the author which can be used for testing the bibrep.ado command in Stata.<br>
DOI: 10.6084/m9.figshare.5414770.v1
title: Evolutionary traceabilities of proteins

description: Supplementary tables for traceabilities estimation of 6352 yeast proteins in three domains of life.
DOI: 10.6084/m9.figshare.5414782
title: OPEN RESEARCH: Kyoto University - September 13, 2017

description: Event poster, information and photos of speakers from the Kyoto University event about Open Research: The Future of Scholarly Communication.September 13, 2017Kyoto, Japan<br>Speakers: - Takaaki Aoki - Associate Professor, Institute for Information Management and Communication, Kyoto University- Ed Gerstner - Regional Scientific Director, Greater China, SpringerNature- Nobuko Miyairi - Regional Director, Asia Pacific, ORCiD- Mark Hahnel - Founder and CEO, figshare (part of the Digital Science portfolio)- Yasuhiro Murayama - Research Executive Director of the Strategic Program Office, National Institute of Information and Communications Technology (NICT) <br>
DOI: 10.6084/m9.figshare.5414737
title: Assessing the effects of mowing machinery on seed dispersal pattern: a test of two methods of seed tracking

description: Seed dispersal is a key process that humans can influence in various ways. However, this type of interaction is less studied than dispersal by other animals. In addition, tracking seeds to determine dispersal pattern is a complicated task. We explored the effects of mowing machinery on seed dispersal in roadsides by testing two methods, (i) by marking fruits and diaspore of plants within the standing vegetation (ii) by making fake plants containing estimated quantities of marked seeds. We measured the pattern of dispersal by considering each seed and the centre of seed shadows of each species calculated by two means (i.e. the centroids and the gravity centres). We estimated the distance of dispersal from roadsides, and the deviation angle from the direction of the mowing. We then analysed the variation in dispersal patterns among species, seed mass and width/length ratio by using correlation tests. Seeds coloured within the standing vegetation were detected from 0.5 to 15.51 metres away from roadsides, with deviation angles from the mowing machinery ranging from –153.43° to 161.57°. With the other method we found a mean distance of dispersal ranging from 0.5 to 13.01 metres and deviation angle from –168.69° to 180°. We did not find strong variation in dispersal patterns among species and seed traits, but we demonstrated however that mowing machinery influenced both dispersal distance and deviation angles.
DOI: 10.6084/m9.figshare.5414737.v1
title: Assessing the effects of mowing machinery on seed dispersal pattern: a test of two methods of seed tracking

description: Seed dispersal is a key process that humans can influence in various ways. However, this type of interaction is less studied than dispersal by other animals. In addition, tracking seeds to determine dispersal pattern is a complicated task. We explored the effects of mowing machinery on seed dispersal in roadsides by testing two methods, (i) by marking fruits and diaspore of plants within the standing vegetation (ii) by making fake plants containing estimated quantities of marked seeds. We measured the pattern of dispersal by considering each seed and the centre of seed shadows of each species calculated by two means (i.e. the centroids and the gravity centres). We estimated the distance of dispersal from roadsides, and the deviation angle from the direction of the mowing. We then analysed the variation in dispersal patterns among species, seed mass and width/length ratio by using correlation tests. Seeds coloured within the standing vegetation were detected from 0.5 to 15.51 metres away from roadsides, with deviation angles from the mowing machinery ranging from –153.43° to 161.57°. With the other method we found a mean distance of dispersal ranging from 0.5 to 13.01 metres and deviation angle from –168.69° to 180°. We did not find strong variation in dispersal patterns among species and seed traits, but we demonstrated however that mowing machinery influenced both dispersal distance and deviation angles.
DOI: 10.6084/m9.figshare.5414755.v1
title: Example dataset for bibrep.ado

description: The Excel file contains the publication set of the author which can be used for testing the bibrep.ado command in Stata.<br>
DOI: 10.6084/m9.figshare.5414755.v2
title: Example dataset for bibrep.ado

description: The data file contains the publication set of the author which can be used for testing the bibrep.ado command in Stata.<br>
DOI: 10.6084/m9.figshare.5414755.v3
title: Example dataset for bibrep.ado

description: The data file contains the publication set of the author which can be used for testing the bibrep.ado command in Stata.<br>
DOI: 10.6084/m9.figshare.5414599
title: OTUs taxonomy for picoplanktonic samples from the Gulf of Gabès

description: Taxonomy of each OTU obtained in the V4-survey from picoplanktonic samples collected during three cruises carried out in the Gulf of Gabès (south-eastern Mediterranean<b>)</b> in June of 2008, April of 2009 and November of 2009.
DOI: 10.6084/m9.figshare.5414599.v1
title: OTUs taxonomy for picoplanktonic samples from the Gulf of Gabès

description: Taxonomy of each OTU obtained in the V4-survey from picoplanktonic samples collected during three cruises carried out in the Gulf of Gabès (south-eastern Mediterranean<b>)</b> in June of 2008, April of 2009 and November of 2009.
DOI: 10.6084/m9.figshare.5414590
title: Downscaling climate-model output in mountainous terrain using local topographic lapse rates for hydrologic modeling of climate-change impacts

description: One of the challenges in using general circulation model (GCM) output is the need to downscale beyond the model’s coarse spatial grid for use in hydrologic modeling of climate-change impacts. In mountainous terrain, using elevation as a primary control on temperature and precipitation at the local scale provides the potential for topographic variables to be used to adjust climate-model output. Here, local topographic lapse rates (LTLR) were estimated from gridded climate data for the Pacific Northwest of the United States and used to downscale GCM output. Skill scores were calculated for the LTLR-downscaled climate-model output relative to an existing set of model output downscaled using the established statistical downscaling technique of localized constructed analogs (LOCA). The results indicate that the LTLR method performs well in the mountainous study region relative to the LOCA method. LTLR downscaling offers a promising method for downscaling climate-model output in regions in which elevation strongly controls climate, particularly for studying impacts of future climate change on water resources.
DOI: 10.6084/m9.figshare.5414578
title: OTUs sequences for picoplanktonic samples from the Gulf of Gabès

description: Sequences of each OTU obtained in the V4-survey from picoplanktonic samples collected during three cruises carried out in the Gulf of Gabès (south-eastern Mediterranean<b>)</b> in June of 2008, April of 2009 and November of 2009.
DOI: 10.6084/m9.figshare.5414590.v1
title: Downscaling climate-model output in mountainous terrain using local topographic lapse rates for hydrologic modeling of climate-change impacts

description: One of the challenges in using general circulation model (GCM) output is the need to downscale beyond the model’s coarse spatial grid for use in hydrologic modeling of climate-change impacts. In mountainous terrain, using elevation as a primary control on temperature and precipitation at the local scale provides the potential for topographic variables to be used to adjust climate-model output. Here, local topographic lapse rates (LTLR) were estimated from gridded climate data for the Pacific Northwest of the United States and used to downscale GCM output. Skill scores were calculated for the LTLR-downscaled climate-model output relative to an existing set of model output downscaled using the established statistical downscaling technique of localized constructed analogs (LOCA). The results indicate that the LTLR method performs well in the mountainous study region relative to the LOCA method. LTLR downscaling offers a promising method for downscaling climate-model output in regions in which elevation strongly controls climate, particularly for studying impacts of future climate change on water resources.
DOI: 10.6084/m9.figshare.5414569
title: Subproteomic signature comparison of <i>in vitro</i> selected fluoroquinolone resistance and ciprofloxacin stress in <i>Salmonella</i> Typhimurium DT104B

description: <b>Background</b>: Fluoroquinolone resistance in nontyphoidal <i>Salmonella</i> is a situation of serious and international concern, particularly in <i>S.</i> Typhimurium DT104B multiresistant strains. Although known to be multifactorial, fluoroquinolone resistance is still far from a complete understanding. <b>Methods</b>: Subproteome changes between an experimentally selected fluoroquinolone-resistant strain (Se6-M) and its parent strain (Se6), and also in Se6-M under ciprofloxacin (CIP) stress, were evaluated in order to give new insights into the mechanisms involved. Proteomes were compared at the intracellular and membrane levels by a 2-DE~LC-MS/MS and a shotgun LC-MS/MS approach, respectively. <b>Results</b>: In total, 35 differentially abundant proteins were identified when comparing Se6 with Se6-M (25 more abundant in Se6 and 10 more abundant in Se6-M) and 82 were identified between Se6-M and Se6-M+CIP (51 more abundant in Se6-M and 31 more abundant under ciprofloxacin stress). <b>Conclusion</b>: Several proteins with known and possible roles in quinolone resistance were identified which provide important information about mechanism-related differential protein expression, supporting the current knowledge and also leading to new testable hypotheses on the mechanism of action of fluoroquinolone drugs.
DOI: 10.6084/m9.figshare.5414569.v1
title: Subproteomic signature comparison of <i>in vitro</i> selected fluoroquinolone resistance and ciprofloxacin stress in <i>Salmonella</i> Typhimurium DT104B

description: <b>Background</b>: Fluoroquinolone resistance in nontyphoidal <i>Salmonella</i> is a situation of serious and international concern, particularly in <i>S.</i> Typhimurium DT104B multiresistant strains. Although known to be multifactorial, fluoroquinolone resistance is still far from a complete understanding. <b>Methods</b>: Subproteome changes between an experimentally selected fluoroquinolone-resistant strain (Se6-M) and its parent strain (Se6), and also in Se6-M under ciprofloxacin (CIP) stress, were evaluated in order to give new insights into the mechanisms involved. Proteomes were compared at the intracellular and membrane levels by a 2-DE~LC-MS/MS and a shotgun LC-MS/MS approach, respectively. <b>Results</b>: In total, 35 differentially abundant proteins were identified when comparing Se6 with Se6-M (25 more abundant in Se6 and 10 more abundant in Se6-M) and 82 were identified between Se6-M and Se6-M+CIP (51 more abundant in Se6-M and 31 more abundant under ciprofloxacin stress). <b>Conclusion</b>: Several proteins with known and possible roles in quinolone resistance were identified which provide important information about mechanism-related differential protein expression, supporting the current knowledge and also leading to new testable hypotheses on the mechanism of action of fluoroquinolone drugs.
DOI: 10.6084/m9.figshare.5414578.v1
title: OTUs sequences for picoplanktonic samples from the Gulf of Gabès

description: Sequences of each OTU obtained in the V4-survey from picoplanktonic samples collected during three cruises carried out in the Gulf of Gabès (south-eastern Mediterranean<b>)</b> in June of 2008, April of 2009 and November of 2009.
DOI: 10.6084/m9.figshare.5414539
title: Postcranial anatomy of <i>Yinlong downsi</i> (Dinosauria: Ceratopsia) from the Upper Jurassic Shishugou Formation of China and the phylogeny of basal ornithischians

description: Ceratopsia includes some of the best-known ornithischian dinosaurs. Many species are erected based on cranial elements alone, and the postcranial skeletons are either missing or undescribed in many taxa. Here we provide the first detailed postcranial description of <i>Yinlong downsi</i> based on the holotype and eight other well-preserved skeletons. <i>Yinlong downsi</i> from the early Late Jurassic Shishugou Formation of the Wucaiwan area, Xinjiang, China, represents one of the most basal ceratopsians. The detailed study of the postcranial skeleton reveals one feature unique to it among ceratopsians: a blade-like prepubic process of the pubis with an elongate notch near its ventral margin. The postcranial material of <i>Yinlong</i> shares some unique features with that of the ornithischian <i>Stenopelix valdensis</i> from the Early Cretaceous of Germany, and provides further evidence that the latter is a basal ceratopsian. A comprehensive phylogenetic analysis of basal ornithischians was built based on 72 taxa and 380 characters. Most of the characters are illustrated for the first time in order to clarify character states. The new ornithischian phylogeny confirms that <i>Yinlong</i> belongs to Chaoyangsauridae. Chaoyangsaurids and <i>Psittacosaurus</i> form a monophyletic group that is sister to all other ceratopsians. The new phylogeny also supports <i>Stenopelix valdensis</i> as a basal ceratopsian, and <i>Mosaiceratops</i> to be close to Coronosauria. Additionally, the new phylogeny agrees with other recent analyses that place heterodontosaurids as the most basal ornithischians rather than with marginocephalians. Furthermore, <i>Isaberrysaura</i>, which has been hypothesized to be a basal ornithopod, is recovered as one of the most basal stegosaurs for the first time. The former ‘hypsilophodontid’ taxa are recovered within Ornithopoda rather than outside Cerapoda, and Jeholosauridae is shown to be valid in this analysis.
DOI: 10.6084/m9.figshare.5414527
title: OTUs abundance for picoplanktonic samples from the Gulf of Gabès

description: Abundance of each OTU obtained in the V4-survey from picoplanktonic samples collected during three cruises carried out in the Gulf of Gabès (south-eastern Mediterranean) in June of 2008, April of 2009 and November of 2009. <br>
DOI: 10.6084/m9.figshare.5414527.v1
title: OTUs abundance for picoplanktonic samples from the Gulf of Gabès

description: Abundance of each OTU obtained in the V4-survey from picoplanktonic samples collected during three cruises carried out in the Gulf of Gabès (south-eastern Mediterranean) in June of 2008, April of 2009 and November of 2009. <br>
DOI: 10.6084/m9.figshare.5414497
title: Data used in study. from Earless toads sense low frequencies but miss the high notes

description: Hearing and vibration sensitivity for all animals in study.
DOI: 10.6084/m9.figshare.5414497.v1
title: Data used in study. from Earless toads sense low frequencies but miss the high notes

description: Hearing and vibration sensitivity for all animals in study.
DOI: 10.6084/m9.figshare.5414491
title: Mathematica code that can produce the all figures from Population cycles emerging through multiple interaction types

description: Mathematica code that can produce the all figures is shown.
DOI: 10.6084/m9.figshare.5414491.v1
title: Mathematica code that can produce the all figures from Population cycles emerging through multiple interaction types

description: Mathematica code that can produce the all figures is shown.