cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8312366.v1
title: Variation in different measures of diversity during primary succession on a tropical coastal dune

description: <b>Background</b>: The understanding of the processes that govern community assembly during ecological succession helps determine the ecological attributes in restoration and monitoring programmes. <b>Aims</b>: The aim of this long-term study of primary succession was to analyse changes in species richness, diversity, taxonomic distinctness and functional types to understand community assembly processes. <b>Methods</b>: For 25 years, species turnover was monitored in 150 permanent plots in a dune system on the coast of the Gulf of Mexico. <b>Results</b>: Earliest successional states had low species diversity and richness, a high unevenness in the taxonomic tree structure, and a lower number of functional groups, with psammophytes being dominant. Richness and diversity increased in a humped-back shape with intermediate states reaching the highest values. Succession generated taxonomic trees that became less uneven and more diverse, and the diversity of functional groups increased. <b>Conclusions</b>: The processes underlying community assembly are complex during succession: sand movement acts as an environmental filter affecting the dominant functional groups, and species interactions probably change from facilitation to competition. The understanding of the combined processes affecting the different measures of diversity over time can improve the effectiveness of restoration and conservation practice in dune systems.
DOI: 10.6084/m9.figshare.8312372.v1
title: tree newick

description: the alignment and tree files of phylogenetic analysis
DOI: 10.6084/m9.figshare.8312372.v2
title: tree newick

description: the alignment and tree files of phylogenetic analysis
DOI: 10.6084/m9.figshare.8312216
title: IRLA-CL

description: datasets contain records of dead people which collected from ssdmf.info
DOI: 10.6084/m9.figshare.8312207
title: IRLA-CL

description: datasets contain records of dead people which collected from ssdmf.info
DOI: 10.6084/m9.figshare.8312216.v1
title: IRLA-CL

description: datasets contain records of dead people which collected from ssdmf.info
DOI: 10.6084/m9.figshare.8312201
title: DataIn_15_E1000k2.txt

description: datasets contain records of dead people which collected from ssdmf.info
DOI: 10.6084/m9.figshare.8312198
title: DataIn_15_E1000k3.txt

description: datasets contain records of dead people which collected from ssdmf.info
DOI: 10.6084/m9.figshare.8312195
title: DataIn_15_E1000k5.txt

description: datasets contain records of dead people which collected from ssdmf.info
DOI: 10.6084/m9.figshare.8312201.v1
title: DataIn_15_E1000k2.txt

description: datasets contain records of dead people which collected from ssdmf.info
DOI: 10.6084/m9.figshare.8312192
title: DataIn1000k1.txt

description: datasets contain records of dead people which collected from ssdmf.info
DOI: 10.6084/m9.figshare.8312195.v1
title: DataIn_15_E1000k5.txt

description: datasets contain records of dead people which collected from ssdmf.info
DOI: 10.6084/m9.figshare.8312207.v2
title: IRLA-CL

description: datasets contain records of dead people which collected from ssdmf.info
DOI: 10.6084/m9.figshare.8312192.v1
title: DataIn1000k1.txt

description: datasets contain records of dead people which collected from ssdmf.info
DOI: 10.6084/m9.figshare.8312198.v1
title: DataIn_15_E1000k3.txt

description: datasets contain records of dead people which collected from ssdmf.info
DOI: 10.6084/m9.figshare.8312207.v1
title: datasets contain records of dead people which collected from ssdmf.info

description: datasets contain records of dead people which collected from ssdmf.info
DOI: 10.6084/m9.figshare.8312186
title: DataIn_15_E1000k1.txt

description: datasets contain records of dead people which collected from ssdmf.info
DOI: 10.6084/m9.figshare.8312186.v1
title: DataIn_15_E1000k1.txt

description: datasets contain records of dead people which collected from ssdmf.info
DOI: 10.6084/m9.figshare.8312189
title: DataIn_15_E1000k4.txt

description: datasets contain records of dead people which collected from ssdmf.info
DOI: 10.6084/m9.figshare.8312168
title: Baltic Sea sea level trends for 10, 50 and 100 year periods

description: The data set contains Baltic Sea sea level trends for 10, 50 and 100 year periods with uncertainties<br><br>
DOI: 10.6084/m9.figshare.8312183
title: Trained neural network models

description: These neural network models were trained on an EyePACS set distributed by Kaggle, and were used in a study in an attempt to replicate methods of JAMA 2016; 316(22), and reproduce their results. We used Tensorflow and Keras.<br>The source code of the replication/reproduction study, and instructions to classify retinal fundus images by using these models are described here: https://github.com/mikevoets/jama16-retina-replication#evaluation<br>Our study is published here: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0217541<br>
DOI: 10.6084/m9.figshare.8312156
title: b2m-10.vasp

description: fssfsfd
DOI: 10.6084/m9.figshare.8312168.v1
title: Baltic Sea sea level trends for 10, 50 and 100 year periods

description: The data set contains Baltic Sea sea level trends for 10, 50 and 100 year periods with uncertainties<br><br>
DOI: 10.6084/m9.figshare.8312189.v1
title: DataIn_15_E1000k4.txt

description: datasets contain records of dead people which collected from ssdmf.info
DOI: 10.6084/m9.figshare.8312153
title: Appendix II

description: Attributable fraction of fractures to low bone mineral density in men and women (T-scores ≤ -2.5)
DOI: 10.6084/m9.figshare.8312147
title: Appendix I.docx

description: Incidence of fracture by age, "low bone mineral density" status and prior fracture<br>
DOI: 10.6084/m9.figshare.8312156.v1
title: b2m-10.vasp

description: fssfsfd
DOI: 10.6084/m9.figshare.8312156.v2
title: b2m-10.vasp

description: fssfsfd
DOI: 10.6084/m9.figshare.8311994
title: Data from: Estimating snakebite incidence from mathematical models: A test in Costa Rica

description: Data used to perform the study. All files must be unzipped in the same folder, and the working directory in the code must be this folder. Maxent file is the java file, which must be located in the dismo folder inside R packages.
DOI: 10.6084/m9.figshare.8311994.v1
title: Data and code used for this study

description: Data used to perform the study. All files must be unzipped in the same folder, and the working directory in the code must be this folder. Maxent file is the java file, which must be located in the dismo folder inside R packages.
DOI: 10.6084/m9.figshare.8311904
title: Predicted distribution for Bothrops asper

description: Predicted distribution for Bothrops asper in Costa Rica. This file must be located in the same folder than Rcode.
DOI: 10.6084/m9.figshare.8311907
title: Pacific and Caribbean boundaries

description: Raster with information about Caribbean or Pacific versant. This file must be located in the same folder than Rcode.
DOI: 10.6084/m9.figshare.8311907.v1
title: Pacific and Caribbean boundaries

description: Raster with information about Caribbean or Pacific versant. This file must be located in the same folder than Rcode.
DOI: 10.6084/m9.figshare.8311892
title: Districts boundaries

description: You must unzip this file inside the folder where the r code is located.
DOI: 10.6084/m9.figshare.8311895
title: Incidence dataset

description: Incidence dataset for Costa Rica. This file must be located in the same folder than rcode.
DOI: 10.6084/m9.figshare.8311889
title: Costa Rica boundaries

description: You must unzip this file inside the folder where the code is located.
DOI: 10.6084/m9.figshare.8311892.v1
title: Districts boundaries

description: You must unzip this file inside the folder where the r code is located.
DOI: 10.6084/m9.figshare.8311889.v1
title: Costa Rica boundaries

description: You must unzip this file inside the folder where the code is located.
DOI: 10.6084/m9.figshare.8311886
title: Presence locations for Bothrops asper in Costa Rica

description: Presence locations for Bothrops asper in Costa Rica. You must place this file in the folder where you have the code.
DOI: 10.6084/m9.figshare.8311574
title: Antifungal Mechanism of Action of Lauryl Betaine Against Skin-Associated Fungus <i>Malassezia restricta</i>

description: Betaine derivatives are considered major ingredients of shampoos and are commonly used as antistatic and viscosity-increasing agents. Several studies have also suggested that betaine derivatives can be used as antimicrobial agents. However, the antifungal activity and mechanism of action of betaine derivatives have not yet been fully understood. In this study, we investigated the antifungal activity of six betaine derivatives against <i>Malassezia restricta</i>, which is the most frequently isolated fungus from the human skin and is implicated in the development of dandruff. We found that, among the six betaine derivatives, lauryl betaine showed the most potent antifungal activity. The mechanism of action of lauryl betaine was studied mainly using another phylogenetically close model fungal organism, <i>Cryptococcus neoformans</i>, because of a lack of available genetic manipulation and functional genomics tools for <i>M. restricta</i>. Our genome-wide reverse genetic screening method using the <i>C. neoformans</i> gene deletion mutant library showed that the mutants with mutations in genes for cell membrane synthesis and integrity, particularly ergosterol synthesis, are highly sensitive to lauryl betaine. Furthermore, transcriptome changes in both <i>C. neoformans</i> and <i>M. restricta</i> cells grown in the presence of lauryl betaine were analyzed and the results indicated that the compound mainly affected cell membrane synthesis, particularly ergosterol synthesis. Overall, our data demonstrated that lauryl betaine influences ergosterol synthesis in <i>C. neoformans</i> and that the compound exerts a similar mechanism of action on <i>M. restricta</i>.
DOI: 10.6084/m9.figshare.8311574.v1
title: Antifungal Mechanism of Action of Lauryl Betaine Against Skin-Associated Fungus <i>Malassezia restricta</i>

description: Betaine derivatives are considered major ingredients of shampoos and are commonly used as antistatic and viscosity-increasing agents. Several studies have also suggested that betaine derivatives can be used as antimicrobial agents. However, the antifungal activity and mechanism of action of betaine derivatives have not yet been fully understood. In this study, we investigated the antifungal activity of six betaine derivatives against <i>Malassezia restricta</i>, which is the most frequently isolated fungus from the human skin and is implicated in the development of dandruff. We found that, among the six betaine derivatives, lauryl betaine showed the most potent antifungal activity. The mechanism of action of lauryl betaine was studied mainly using another phylogenetically close model fungal organism, <i>Cryptococcus neoformans</i>, because of a lack of available genetic manipulation and functional genomics tools for <i>M. restricta</i>. Our genome-wide reverse genetic screening method using the <i>C. neoformans</i> gene deletion mutant library showed that the mutants with mutations in genes for cell membrane synthesis and integrity, particularly ergosterol synthesis, are highly sensitive to lauryl betaine. Furthermore, transcriptome changes in both <i>C. neoformans</i> and <i>M. restricta</i> cells grown in the presence of lauryl betaine were analyzed and the results indicated that the compound mainly affected cell membrane synthesis, particularly ergosterol synthesis. Overall, our data demonstrated that lauryl betaine influences ergosterol synthesis in <i>C. neoformans</i> and that the compound exerts a similar mechanism of action on <i>M. restricta</i>.
DOI: 10.6084/m9.figshare.8311532
title: edgeR gene expression tables from Sociality emerges from solitary behaviours and reproductive plasticity in the orchid bee <i>Euglossa dilemma</i>

description: Contains the edgeR output for each pairwise behavioural comparison conducted in the study.
DOI: 10.6084/m9.figshare.8311523
title: Sample information, oviposition observations, selected toolkit gene expression, David analysis, and Behavioural data from Sociality emerges from solitary behaviours and reproductive plasticity in the orchid bee <i>Euglossa dilemma</i>

description: Tables S4-S10, which contain information about the individual samples, oviposition observations, expression information for selected toolkit genes, David functional annotation analysis of brain and ovary DEGs, and data from behavioural observations.
DOI: 10.6084/m9.figshare.8311526
title: Cross study gene list overlaps from Sociality emerges from solitary behaviours and reproductive plasticity in the orchid bee <i>Euglossa dilemma</i>

description: Contains the gene lists and hypergeometric test results of overlap tests done with Megalopta genalis and Apis mellifera data. Also contains the gene list conversions used for each species.
DOI: 10.6084/m9.figshare.8311532.v1
title: edgeR gene expression tables from Sociality emerges from solitary behaviours and reproductive plasticity in the orchid bee <i>Euglossa dilemma</i>

description: Contains the edgeR output for each pairwise behavioural comparison conducted in the study.
DOI: 10.6084/m9.figshare.8311523.v1
title: Sample information, oviposition observations, selected toolkit gene expression, David analysis, and Behavioural data from Sociality emerges from solitary behaviours and reproductive plasticity in the orchid bee <i>Euglossa dilemma</i>

description: Tables S4-S10, which contain information about the individual samples, oviposition observations, expression information for selected toolkit genes, David functional annotation analysis of brain and ovary DEGs, and data from behavioural observations.
DOI: 10.6084/m9.figshare.8311526.v1
title: Cross study gene list overlaps from Sociality emerges from solitary behaviours and reproductive plasticity in the orchid bee <i>Euglossa dilemma</i>

description: Contains the gene lists and hypergeometric test results of overlap tests done with Megalopta genalis and Apis mellifera data. Also contains the gene list conversions used for each species.
DOI: 10.6084/m9.figshare.8311436
title: Relationship between immune response to pneumococcal conjugate vaccines in infants and indirect protection after vaccine implementation

description: <b>Introduction</b>: <i>Streptococcus pneumoniae</i> is a leading cause of morbidity and mortality worldwide. Widespread infant vaccination with pneumococcal conjugate vaccines (PCVs) substantially reduced vaccine-serotype pneumococcal disease by direct protection of immunized children and indirect protection of the community via decreased nasopharyngeal carriage and transmission. Essential to grasping the public health implications of pediatric PCV immunization is an understanding of how PCV formulations impact carriage. <b>Areas covered</b>: Using clinical evidence, this review examines how the immune response to PCVs is associated with subsequent nasopharyngeal carriage reduction in vaccinated infants and toddlers. By combining direct and indirect protection, carriage reduction results in a reduced spread of vaccine serotypes, and eventually, a decrease in vaccine serotype disease incidence in community members of all ages. <b>Expert opinion</b>: The current review presents some of the aspects that influence the overall impact of PCVs on vaccine-serotype carriage, and thus, spread. The link between reduction of vaccine-serotype carriage and the eventual reduction of vaccine-serotype disease in the wider community is described by comparing data from current PCVs, specifically with respect to their ability to reduce carriage of some cross-reacting serotypes (i.e. 6A versus 6B and 19A versus 19F).
DOI: 10.6084/m9.figshare.8311436.v2
title: Relationship between immune response to pneumococcal conjugate vaccines in infants and indirect protection after vaccine implementation

description: <b>Introduction</b>: <i>Streptococcus pneumoniae</i> is a leading cause of morbidity and mortality worldwide. Widespread infant vaccination with pneumococcal conjugate vaccines (PCVs) substantially reduced vaccine-serotype pneumococcal disease by direct protection of immunized children and indirect protection of the community via decreased nasopharyngeal carriage and transmission. Essential to grasping the public health implications of pediatric PCV immunization is an understanding of how PCV formulations impact carriage. <b>Areas covered</b>: Using clinical evidence, this review examines how the immune response to PCVs is associated with subsequent nasopharyngeal carriage reduction in vaccinated infants and toddlers. By combining direct and indirect protection, carriage reduction results in a reduced spread of vaccine serotypes, and eventually, a decrease in vaccine serotype disease incidence in community members of all ages. <b>Expert opinion</b>: The current review presents some of the aspects that influence the overall impact of PCVs on vaccine-serotype carriage, and thus, spread. The link between reduction of vaccine-serotype carriage and the eventual reduction of vaccine-serotype disease in the wider community is described by comparing data from current PCVs, specifically with respect to their ability to reduce carriage of some cross-reacting serotypes (i.e. 6A versus 6B and 19A versus 19F).
DOI: 10.6084/m9.figshare.8311436.v1
title: Relationship between immune response to pneumococcal conjugate vaccines in infants and indirect protection after vaccine implementation

description: <b>Introduction</b>: <i>Streptococcus pneumoniae</i> is a leading cause of morbidity and mortality worldwide. Widespread infant vaccination with pneumococcal conjugate vaccines (PCVs) substantially reduced vaccine-serotype pneumococcal disease by direct protection of immunized children and indirect protection of the community via decreased nasopharyngeal carriage and transmission. Essential to grasping the public health implications of pediatric PCV immunization is an understanding of how PCV formulations impact carriage. <b>Areas covered</b>: Using clinical evidence, this review examines how the immune response to PCVs is associated with subsequent nasopharyngeal carriage reduction in vaccinated infants and toddlers. By combining direct and indirect protection, carriage reduction results in a reduced spread of vaccine serotypes, and eventually, a decrease in vaccine serotype disease incidence in community members of all ages. <b>Expert opinion</b>: The current review presents some of the aspects that influence the overall impact of PCVs on vaccine-serotype carriage, and thus, spread. The link between reduction of vaccine-serotype carriage and the eventual reduction of vaccine-serotype disease in the wider community is described by comparing data from current PCVs, specifically with respect to their ability to reduce carriage of some cross-reacting serotypes (i.e. 6A versus 6B and 19A versus 19F).
DOI: 10.6084/m9.figshare.8311370
title: Fitzpatrick et al code from Tail loss and telomeres: consequences of large-scale tissue regeneration in a terrestrial ectotherm

description: R code used to run the statistical analyses.
DOI: 10.6084/m9.figshare.8311364
title: SeminarEvaluationData.xlsx

description: Dataset from Seminar Evaluation
DOI: 10.6084/m9.figshare.8311370.v1
title: Fitzpatrick et al code from Tail loss and telomeres: consequences of large-scale tissue regeneration in a terrestrial ectotherm

description: R code used to run the statistical analyses.
DOI: 10.6084/m9.figshare.8311364.v1
title: SeminarEvaluationData.xlsx

description: Dataset from Seminar Evaluation
DOI: 10.6084/m9.figshare.8311301
title: Supplementary Tables

description: Supplementary Tables from <b><br></b><b>"Global distribution of Trebouxiophyceae diversity explored by high-throughput sequencing and phylogenetic approaches"</b><b><br></b>We explored the global diversity of a group of photosynthetic eukaryotes with a major importance both for academic (study of photosymbiosis) and applied research (biotechnology). Based on a worldwide collection of sequences from freshwater, marine and soil samples, we characterize the extension of Trebouxiophyceae diversity, and identify the most promising environments for new findings.<br>
DOI: 10.6084/m9.figshare.8311289
title: Table S1

description: Table S1: Sequences retrived from public databases with all their information obteined by genbank and culture collections databases.
DOI: 10.6084/m9.figshare.8311301.v2
title: Supplementary Tables

description: Supplementary Tables from <b><br></b><b>"Global distribution of Trebouxiophyceae diversity explored by high-throughput sequencing and phylogenetic approaches"</b><b><br></b>We explored the global diversity of a group of photosynthetic eukaryotes with a major importance both for academic (study of photosymbiosis) and applied research (biotechnology). Based on a worldwide collection of sequences from freshwater, marine and soil samples, we characterize the extension of Trebouxiophyceae diversity, and identify the most promising environments for new findings.<br>
DOI: 10.6084/m9.figshare.8311292
title: Table S4

description: Table S4: Trebouxiophyceae OTUs contribution to each sample.
DOI: 10.6084/m9.figshare.8311292.v1
title: Table S4

description: Table S4: Trebouxiophyceae OTUs contribution to each sample.
DOI: 10.6084/m9.figshare.8311301.v1
title: Supplementary Tables

description: Supplementary Tables from <b><br></b><b>"Global distribution of Trebouxiophyceae diversity explored by high-throughput sequencing and phylogenetic approaches"</b><b><br></b>We explored the global diversity of a group of photosynthetic eukaryotes with a major importance both for academic (study of photosymbiosis) and applied research (biotechnology). Based on a worldwide collection of sequences from freshwater, marine and soil samples, we characterize the extension of Trebouxiophyceae diversity, and identify the most promising environments for new findings.<br>
DOI: 10.6084/m9.figshare.8311277
title: Analyzing aggregation propensities of clinically relevant PTEN mutants: a new culprit in pathogenesis of cancer and other PTENopathies

description: While studies on pathological protein aggregation are largely limited to neurodegenerative disease, emerging evidence suggests that other diseases are also associated with pathogenic protein aggregation. For example, tumor suppressor protein p53, and its mutant conformers, undergo protein aggregation, exacerbating the cancer phenotype. These findings raise the possibility that inactivation of tumor suppressors via protein aggregation may participate in cancer and other disease pathologies. Since tumor suppressor protein PTEN has similar functions to p53, and is mutated in multiple diseases, we examined the aggregation propensity of PTEN wild-type and 1523 clinically relevant PTEN mutants. Applying computational tools to PTEN mutation databases revealed that PTEN wild-type protein can aggregate under physiological conditions, and 274 distinct PTEN mutants had increased aggregation propensity. To understand the mechanism underlying PTEN conformer aggregation, we analyzed the physicochemical properties of these 274 PTEN mutants and defined their aggregation potential. We conclude that increased aggregation propensity of select PTEN mutants may contribute to disease phenotypes. Our studies have built the foundation for interrogating the aggregation potential of these select mutants in cancers and in PTENopathies. Elucidating the pathogenic mechanisms associated with aggregation-prone PTEN conformers will aid in developing therapies that target PTEN-aggregates in multiple diseases. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.8311274
title: Broadband Japan

description: Eye-tracking Data Broadband Face Japan