cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15156/bio/sh2743921.08fu
title: SH2743921.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.6084/m9.figshare.8263508
title: D3_varyNe_results

description: D, D3, and bootstrapping results for sims with interlocus variation in Ne
DOI: 10.6084/m9.figshare.8263508.v1
title: D3_varyNe_results

description: D, D3, and bootstrapping results for sims with interlocus variation in Ne
DOI: 10.6084/m9.figshare.8263478
title: Women at Work: Sexual Harassment

description: Over the last two years, awareness about the sexual mistreatment of women has stunned the world. According to analysis by the New York Times, the defeat of Hilary Clinton and election of Donald Trump spurred a women’s movement in the US that began in November of 2016 and resulted in protests across the country, including the largest single-day protest in history on January 21, 2017. Later that year, the #MeToo movement (starting in October 2017) and subsequent #TimesUp movement (starting in January 2018) galvanized women to unite against sexual assault and sexual harassment, which has become the hallmark of the current women’s movement. But has anything changed over this time period in regard to the sexual harassment of women? We examine data from over 500 women at two points in time (September 2016 and September 2018) and found reduced levels of the most egregious forms of sexual harassment (unwanted sexual attention and sexual coercion) but increased levels of gender harassment in 2018 compared to data collected in 2016. More importantly, sexual harassment had a weaker relationship with women’s negative self-views (lower self-esteem, higher self-doubt) in 2018 compared to 2016. Qualitative interviews collected from women in the fall of 2016 and in the fall of 2018 from the same women, support the quantitative data. They suggest that the decrease in the more egregious forms of sexual harassment is due to the increased scrutiny on the topic and the increase in gender harassment is the result of backlash against women. The interviewees also suggest that the diminished relationship between sexual harassment and negative self-views was the result of reduced shame and increased support and empowerment.
DOI: 10.6084/m9.figshare.8263493
title: D3_t1_results

description: D, D3, and bootstrapping results for sims with variation in t1.
DOI: 10.6084/m9.figshare.8263502.v1
title: D3_tm_results

description: D, D3, and bootstrapping results for sims with variation in the timing of introgression.
DOI: 10.6084/m9.figshare.8263469
title: D3_fewersites_results

description: D, D3 and bootstrapping results for simulations with fewer sites.
DOI: 10.6084/m9.figshare.8263493.v1
title: D3_t1_results

description: D, D3, and bootstrapping results for sims with variation in t1.
DOI: 10.6084/m9.figshare.8263469.v1
title: D3_fewersites_results

description: D, D3 and bootstrapping results for simulations with fewer sites.
DOI: 10.6084/m9.figshare.8263445
title: D3_errors_results

description: Results of D3, window analysis, and bootstrapping with sequence bias artificially introduced.
DOI: 10.6084/m9.figshare.8263436
title: D3_v2_results

description: Results of D, D3, the second version of D3 using dAB in the denominator, and bootstrapping.
DOI: 10.6084/m9.figshare.8263478.v1
title: Women at Work_SH.xlsx

description: Over the last two years, awareness about the sexual mistreatment of women has stunned the world. According to analysis by the New York Times, the defeat of Hilary Clinton and election of Donald Trump spurred a women’s movement in the US that began in November of 2016 and resulted in protests across the country, including the largest single-day protest in history on January 21, 2017. Later that year, the #MeToo movement (starting in October 2017) and subsequent #TimesUp movement (starting in January 2018) galvanized women to unite against sexual assault and sexual harassment, which has become the hallmark of the current women’s movement. But has anything changed over this time period in regard to the sexual harassment of women? We examine data from over 500 women at two points in time (September 2016 and September 2018) and found reduced levels of the most egregious forms of sexual harassment (unwanted sexual attention and sexual coercion) but increased levels of gender harassment in 2018 compared to data collected in 2016. More importantly, sexual harassment had a weaker relationship with women’s negative self-views (lower self-esteem, higher self-doubt) in 2018 compared to 2016. Qualitative interviews collected from women in the fall of 2016 and in the fall of 2018 from the same women, support the quantitative data. They suggest that the decrease in the more egregious forms of sexual harassment is due to the increased scrutiny on the topic and the increase in gender harassment is the result of backlash against women. The interviewees also suggest that the diminished relationship between sexual harassment and negative self-views was the result of reduced shame and increased support and empowerment.
DOI: 10.6084/m9.figshare.8263424
title: D3_bigtheta_results

description: D, D3, and bootstrap results from simulations using a higher value of theta.
DOI: 10.6084/m9.figshare.8263436.v1
title: D3_v2_results

description: Results of D, D3, the second version of D3 using dAB in the denominator, and bootstrapping.
DOI: 10.6084/m9.figshare.8263445.v1
title: D3_errors_results

description: Results of D3, window analysis, and bootstrapping with sequence bias artificially introduced.
DOI: 10.6084/m9.figshare.8263403
title: D_D3_bootstrap_main_results

description: D, D3, and bootstrapping for the main results figure of Hahn & Hibbins. Used to make the plot.
DOI: 10.6084/m9.figshare.8263424.v1
title: D3_bigtheta_results

description: D, D3, and bootstrap results from simulations using a higher value of theta.
DOI: 10.6084/m9.figshare.8263337
title: Data.xlsx

description: embryo transfer
DOI: 10.6084/m9.figshare.8263337.v1
title: Data.xlsx

description: embryo transfer
DOI: 10.6084/m9.figshare.8263403.v1
title: D_D3_bootstrap_main_results

description: D, D3, and bootstrapping for the main results figure of Hahn & Hibbins. Used to make the plot.
DOI: 10.6084/m9.figshare.8263265
title: Dribble

description: Collision between a ball and a half space at a sonic velocity<br>
DOI: 10.6084/m9.figshare.8263265.v1
title: Dribble

description: Collision between a ball and a half space at a sonic velocity<br>
DOI: 10.6084/m9.figshare.8263163
title: Supplementary Material for: Clinical Considerations in Physician-Assisted Death for Probable Alzheimer’s Disease: Decision-Making Capacity, Anosognosia, and Suffering

description: <b><i>Background:</i></b> Requests for physician-assisted death (PAD) in patients with cognitive impairment are complex and require careful consideration. Of particular difficulty is determination of whether the request is voluntary and well considered. <b><i>Results:</i></b> Euthanasia and physician-assisted suicide (PAS) are both legal in The Netherlands, Luxemburg, Colombia, and Canada. Euthanasia is legal in Belgium, while PAS is legal in Switzerland and Oregon, Washington, Montana, Vermont, and California (USA). Upon a PAD request, evaluation of the capacity to consent medical treatment is relevant for the decision-making process, while evaluation of testamentary capacity is appropriate before an advance euthanasia directive is written. Anosognosia assessment throughout the Alzheimer’s disease continuum provides essential and relevant information regarding the voluntary and well-considered nature of the PAD request; meanwhile, early assessment of hypernosognosia or subjective cognitive decline assists in formulation of a clinical prognosis. Furthermore, the assessment of physical and psychological suffering should incorporate verbal and nonverbal cues as well as consideration of the psychosocial factors that might affect due care criteria. <b><i>Conclusion:</i></b> The clinical approach to a PAD request should consider the legal framework and the decision-making capacity, assess memory deficit awareness and the perception of suffering, and evaluate mental competency when considered pertinent.
DOI: 10.6084/m9.figshare.8263070
title: Master Sheet TLR

description: Thermolimit respirometry data under hypoxia and normoxia
DOI: 10.6084/m9.figshare.8263070.v1
title: Master Sheet TLR

description: Thermolimit respirometry data under hypoxia and normoxia
DOI: 10.6084/m9.figshare.8262788
title: Dataset Linking YouTube and university ranking.xlsx

description: Research performance for a list of world class and overall universities according to ARWU, THE, Webometrics, U-Multirank rankings, as well as Youtube metrics.
DOI: 10.6084/m9.figshare.8262779
title: The phylogenetic range of bacterial and viral pathogens of vertebrates: dataset and supplementary material

description: [N.B. This is an archived version of the code and data repository available at https://github.com/liampshaw/Pathogen-host-range.]<br><b>Associated preprint</b>: The phylogenetic range of bacterial and viral pathogens of vertebrates<br><b>doi</b>: https://doi.org/10.1101/670315<br><b>Authors</b>: Liam P. Shaw*, Alethea Wang*, David Dylus, Magda Meier, Grega Pogacnik, Christophe Dessimoz, Francois Balloux (* co-first authors)<br>This repository contains code to reproduce all figures and analyses in the associated paper analysing the host range of pathogen species. This is bundled together in the Rmarkdown notebook (Supplementary Text 1 of the manuscript). It also contains several data files. The image above is a schematic for the manual literature review used to construct the database of host-pathogen associations. For more information on the dataset collection methods and analysis, please see the preprint.<br>The main dataset contains a human-curated database of 12,212 host-pathogen associations: 2,595 bacterial and viral pathogens infecting 2,656 vertebrate host species across 90 host orders. It also contains a mitochondrial genome phylogeny for the host species.<br><br>Code can be altered to change any of the figures. Some explanatory text is provided, but not much. Any questions can be addressed via email (liam.philip.shaw at gmail dot com).<br>Unless otherwise stated, data related to viruses is plotted in red and bacteria in black. The code should take &lt;10 minutes to run on a standard laptop.<br><b>Note</b>: At several points code is adapted/reused from the supplementary code repository made available by Olival et. al. (2017):<br>- Olival et al. (2017) paper: Host and viral traits predict zoonotic spillover from mammals https://doi.org/10.1038/nature22975- Code repository: https://github.com/ecohealthalliance/HP3- MIT License: https://opensource.org/licenses/MIT<br>This mainly applies to several scripts in the `scripts' directory relating to the fitting and plotting of generalized additive models (GAMs) - more information is included where appropriate. All code here is also made available under the MIT License.
DOI: 10.6084/m9.figshare.8262779.v1
title: The phylogenetic range of bacterial and viral pathogens of vertebrates: dataset and supplementary material

description: This dataset contains a human-curated database of 12,212 host-pathogen associations: 2,595 bacterial and viral pathogens infecting 2,656 vertebrate host species across 90 host orders. It also contains a mitochondrial genome phylogeny for the host species. <br><br>An R markdown notebook (Supplementary-Text-1) is included to reproduce all analyses included in the associated manuscript. <br><br>For more details, please see the associated publication;<br>The phylogenetic range of bacterial and viral pathogens of vertebrates <br>Liam P. Shaw*, Alethea Wang*, David Dylus, Magda Meier, Grega Pogacnik, Christophe Dessimoz, Francois Balloux(* co-first authors)<br>
DOI: 10.6084/m9.figshare.8262662
title: Supplementary Material for: Effects of Weighted Hula-Hooping Compared to Walking on Abdominal Fat, Trunk Muscularity, and Metabolic Parameters in Overweight Subjects: A Randomized Controlled Study

description: <b><i>Background:</i></b> Weighted hula-hoops have gained popularity, but whether they indeed reshape the trunk or have beneficial metabolic effects in overweight subjects is unknown. <b><i>Objectives:</i></b> To determine effects of hula-hooping and walking matched for energy expenditure on android fat %, trunk muscle mass, and metabolic parameters in a randomized cross-over study. <b><i>Design:</i></b> We recruited 55 overweight nondiabetic subjects, who were randomized to hula-hooping (HULA) for 6 weeks using a 1.5-kg weighted hula-hoop followed by walking (WALK) for another 6 weeks or vice versa. The increments in energy expenditure were similar by HULA and WALK. Body composition (dual-energy X-ray absorptiometry) and metabolic parameters were measured at baseline and after HULA and WALK. The primary endpoint was the change in fat % in the android region. <b><i>Results:</i></b> A total of 53<i></i>subjects (waist 92 ± 1 cm, body mass index 28 ± 1 kg/m<sup>2</sup>) completed the study. Body weight changed similarly (–0.6 ± 0.2 vs. –0.5 ± 0.2 kg, nonsignificant; HULA vs. WALK). During the intervention the subjects hula-hooped on average 12.8 ± 0.5 min/day and walked 9,986 ± 376 steps/day. The % fat in the android region decreased significantly by HULA but not by WALK (between-group change <i>p</i> &lt; 0.001). Trunk muscle mass increased more by HULA than by WALK (<i>p</i> &lt; 0.05). Waist circumference decreased more by HULA than by WALK (–3.1 ± 0.3 cm vs. –0.7 ± 0.4 cm, <i>p</i> &lt; 0.001; HULA vs. WALK). WALK but not HULA significantly lowered systolic blood pressure and increased HDL cholesterol while HULA significantly decreased LDL cholesterol. <b><i>Conclusions:</i></b> Hula-hooping with a weighted hula-hoop can be used to decrease abdominal fat % and increase trunk muscle mass in overweight subjects. Its LDL lowering effect resembles that described for resistance training.
DOI: 10.6084/m9.figshare.8262497
title: Filtered Norway

description: eye-tracking data
DOI: 10.6084/m9.figshare.8262497.v1
title: Filtered Norway

description: eye-tracking data
DOI: 10.6084/m9.figshare.8262482
title: New fossils of early and middle Miocene <i>Choerolophodon</i> from northern China reveal a Holarctic distribution of Choerolophodontidae

description: As one of the three major groups of gomphotheres, the Miocene Choerolophodontidae were long considered to have been distributed in Europe, Africa, and South Asia, with a few localities in East Asia, whereas choerolophodontids never extended into North America during the Miocene. In this paper, we report new <i>Choerolophodon</i> fossil materials from the early and middle Miocene of China, which suggest morphological similarities to the enigmatic North American <i>Gnathabelodon thorpei</i>. The new fossils were recovered from the lower Miocene of Linxia (<i>C. guangheensis</i>) and the middle Miocene of Junggar (<i>Choerolophodon</i> sp.) basins, suggesting the persistence of this genus in East Asia during the early–middle Miocene. The cheek tooth morphology of the new specimens resembles that of early–middle Miocene <i>Choerolophodon</i> from elsewhere (i.e., <i>C. palaeindicus</i>, <i>C. kisumuensis</i>, and <i>C. chioticus</i>), in addition to striking affinities with <i>Gnathabelodon thorpei</i>. The upper tusk and mandibular characters of <i>G. thorpei</i>, which include upwardly bent maxillary tusks without enamel bands, and elongated and trough-like mandibular symphysis without mandibular tusks, also support its relationship with the choerolophodontids. The occurrence of a possible member of Choerolophodontidae in the late Miocene of North America (i.e., <i>G. thorpei</i>) reveals intercontinental dispersals of choerolophodontids from East Asia across Beringia possibly between 16.0 and 11.0 Ma, at roughly the same time as other proboscideans, e.g., Mammutidae, Amebelodontidae, and Gomphotheriidae. Together, these new materials significantly revise previously established models of the geographic distribution, taxonomic diversity, and ecological adaptations of Choerolophodontidae within China and elsewhere across the Holarctic.
DOI: 10.6084/m9.figshare.8262488
title: FCS Files

description: Raw FCS files from which data and results were extracted for the paper: "STAT6 knockdown using multiple siRNA sequences inhibits proliferation and induces apoptosis of human colorectal and breast cancer cell lines"
DOI: 10.6084/m9.figshare.8262482.v1
title: New fossils of early and middle Miocene <i>Choerolophodon</i> from northern China reveal a Holarctic distribution of Choerolophodontidae

description: As one of the three major groups of gomphotheres, the Miocene Choerolophodontidae were long considered to have been distributed in Europe, Africa, and South Asia, with a few localities in East Asia, whereas choerolophodontids never extended into North America during the Miocene. In this paper, we report new <i>Choerolophodon</i> fossil materials from the early and middle Miocene of China, which suggest morphological similarities to the enigmatic North American <i>Gnathabelodon thorpei</i>. The new fossils were recovered from the lower Miocene of Linxia (<i>C. guangheensis</i>) and the middle Miocene of Junggar (<i>Choerolophodon</i> sp.) basins, suggesting the persistence of this genus in East Asia during the early–middle Miocene. The cheek tooth morphology of the new specimens resembles that of early–middle Miocene <i>Choerolophodon</i> from elsewhere (i.e., <i>C. palaeindicus</i>, <i>C. kisumuensis</i>, and <i>C. chioticus</i>), in addition to striking affinities with <i>Gnathabelodon thorpei</i>. The upper tusk and mandibular characters of <i>G. thorpei</i>, which include upwardly bent maxillary tusks without enamel bands, and elongated and trough-like mandibular symphysis without mandibular tusks, also support its relationship with the choerolophodontids. The occurrence of a possible member of Choerolophodontidae in the late Miocene of North America (i.e., <i>G. thorpei</i>) reveals intercontinental dispersals of choerolophodontids from East Asia across Beringia possibly between 16.0 and 11.0 Ma, at roughly the same time as other proboscideans, e.g., Mammutidae, Amebelodontidae, and Gomphotheriidae. Together, these new materials significantly revise previously established models of the geographic distribution, taxonomic diversity, and ecological adaptations of Choerolophodontidae within China and elsewhere across the Holarctic.
DOI: 10.6084/m9.figshare.8262458
title: In search of a single standardised system for reporting complications in craniofacial surgery: a comparison of three different classifications

description: Comparing complication rates between centres is difficult due to the lack of unanimous criteria regarding what adverse events should be defined as complications and how these events should be compiled. This study analysed all adverse events in a cohort of craniofacial (CF) operations over a 10-year period and applied three different scales (Clavien-Dindo, Leeds and Oxford) for systematic comparison. A total of 1023 consecutive CF procedures in 641 patients was identified. The Clavien-Dindo scale captured 74 complications in 74 procedures (7.2%), whereas the Leeds and Oxford scales captured 163 complications in 134 procedures (13.1%) and 85 complications in 83 procedures (8.1%), respectively. The Clavien-Dindo scale appeared less suitable for CF surgery, because it is predominantly adapted to severe complications and also regards blood transfusion as a complication. The Leeds scale provided a detailed picture of all complications, as well as minor events, whereas the Oxford scale captured all major complications well but applied less accurate definitions for the minor events. Our findings contribute to the benchmarking of complications between CF centres and suggest that both the Leeds and the Oxford scale appear relevant, depending on the emphasis required for major and minor complications and inter-centre audits, respectively.
DOI: 10.6084/m9.figshare.8262458.v1
title: In search of a single standardised system for reporting complications in craniofacial surgery: a comparison of three different classifications

description: Comparing complication rates between centres is difficult due to the lack of unanimous criteria regarding what adverse events should be defined as complications and how these events should be compiled. This study analysed all adverse events in a cohort of craniofacial (CF) operations over a 10-year period and applied three different scales (Clavien-Dindo, Leeds and Oxford) for systematic comparison. A total of 1023 consecutive CF procedures in 641 patients was identified. The Clavien-Dindo scale captured 74 complications in 74 procedures (7.2%), whereas the Leeds and Oxford scales captured 163 complications in 134 procedures (13.1%) and 85 complications in 83 procedures (8.1%), respectively. The Clavien-Dindo scale appeared less suitable for CF surgery, because it is predominantly adapted to severe complications and also regards blood transfusion as a complication. The Leeds scale provided a detailed picture of all complications, as well as minor events, whereas the Oxford scale captured all major complications well but applied less accurate definitions for the minor events. Our findings contribute to the benchmarking of complications between CF centres and suggest that both the Leeds and the Oxford scale appear relevant, depending on the emphasis required for major and minor complications and inter-centre audits, respectively.
DOI: 10.6084/m9.figshare.8262359
title: Data Set to Short term sleep fragmentation enhances anxiety related behvior: the role of hormonal alterations

description: Data set to article "Sleep fragmentation enhances anxiety - related behavior: the role of hormonal alterations" by Zeljko Grubac, Nikola Sutulovic, Anida Ademovic, Milica Velimirovic, Aleksandra Rasic Markovic, Djuro Macut, Natasa Petronijevic, Olivera Stanojlovic and Dragan Hrncic, published in PLOS ONE 2019<br>
DOI: 10.6084/m9.figshare.8262359.v1
title: Data Set to Short term sleep fragmentation enhances anxiety related behvior: the role of hormonal alterations

description: Data set to article "Sleep fragmentation enhances anxiety - related behavior: the role of hormonal alterations" by Zeljko Grubac, Nikola Sutulovic, Anida Ademovic, Milica Velimirovic, Aleksandra Rasic Markovic, Djuro Macut, Natasa Petronijevic, Olivera Stanojlovic and Dragan Hrncic, published in PLOS ONE 2019<br>
DOI: 10.6084/m9.figshare.8262272
title: Apéndice 1.pdf

description: Apéndice 1 del trabajo de fin de máster. Máster en Traducción y Estudios Interculturales, Universitat Autònoma de Barcelona, 2019