cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5619637.v1
title: The intron landscape of the mtDNA <i>cytb</i> gene among the Ascomycota: introns and intron-encoded open reading frames

description: Fungal mitochondrial genes are frequently noted for the presence of introns. These introns are self-splicing and can be assigned to either group I or II introns and they can encode open reading frames (ORFs). This study examines the introns present within the cytochrome b (<i>cytb</i>) gene of ascomycetes fungi. Cytochrome b gene sequences were sampled from GenBank and supplemented with our own data for species of <i>Leptographium</i> and <i>Ophiostoma</i>. Group I introns were encountered most frequently, many encoding either LAGLIDADG or GIY-YIG homing endonucleases (HEs). Numerous examples of different intron/ORF arrangements were observed including nested ORFs, multiple ORFs within a single intron and intron ORFs at various stages of erosion due to the accumulation of mutations. In addition, we noted one example of a nested intron and one complex group II intron that could potentially allow for alternative splicing. Documenting the distribution of introns within the same gene across a range of species allows for a better understanding of the evolution of introns and intronic ORFs. Intron landscapes also are a resource that can help in annotating genes and in bioprospecting for potentially active HEs, which are rare-cutting DNA endonucleases with applications in biotechnology.
DOI: 10.6084/m9.figshare.5619577.v1
title: Lake Catchment Set

description: A freely available data set of inflow lakes’ catchments including lakes, location, shape, area, perimeter, etc. over the Qiangtang Plateau which is a main part of the Tibetan Plateau. The data set is derived from Landset8 images, Google Earth and DEM. It will provide important basic information for researchers to study the changes of meteorology, hydrology and environment and its mechanism in Qinghai-Tibet Plateau.
DOI: 10.6084/m9.figshare.5619577.v2
title: Lake Catchment Set

description: A freely available data set of inflow lakes’ catchments including lakes, location, shape, area, perimeter, etc. over the Qiangtang Plateau which is a main part of the Tibetan Plateau. The data set is derived from Landset8 images, Google Earth and DEM. It will provide important basic information for researchers to study the changes of meteorology, hydrology and environment and its mechanism in Qinghai-Tibet Plateau.
DOI: 10.6084/m9.figshare.5619577.v3
title: Lake Catchment Set

description: A freely available data set of inflow lakes’ catchments including lakes, location, shape, area, perimeter, etc. over the Qiangtang Plateau which is a main part of the Tibetan Plateau. The data set is derived from Landset8 images, Google Earth and DEM. It will provide important basic information for researchers to study the changes of meteorology, hydrology and environment and its mechanism in Qinghai-Tibet Plateau.
DOI: 10.6084/m9.figshare.5619577.v4
title: Lake Catchment Set

description: A freely available data set of inflow lakes’ catchments including lakes, location, shape, area, perimeter, etc. over the Qiangtang Plateau which is a main part of the Tibetan Plateau. The data set is derived from Landset8 images, Google Earth and DEM. It will provide important basic information for researchers to study the changes of meteorology, hydrology and environment and its mechanism in Qinghai-Tibet Plateau.
DOI: 10.6084/m9.figshare.5619436
title: Small Cell Lung Cancer

description: These data are described in (Ying et al., 1995) and originally collected in (Maksymuik et al., 1994). The patients were randomly assigned to one of two treatments referred to as Arm A and Arm B. Arm A patients received cisplatin (P) followed by etoposide (E), while Arm B patients received (E) followed by (P). There were a total of 62 patients in Arm A with 15 right censored survival times, while Arm B consisted of 59 patients with 8 right censored survival times.<br><br>The variables recorded in the dataset(s) are:<br>- age: age of the patient upon entry (in years)<br>- time: survival time of the patient (in days)<br>- cens: indicator for survival time - 0 if observed, 1 if right censored<br><br>We analyze these data using a Dirichlet Process Mixture Model with a Gamma kernel distribution (Poynor and Kottas, 2017). The primary emphasis of our work is to obtain inference for the mean residual life function. Our code is shared through github (see link in references). <br><br>Journal References:<br><i><br></i><i>Jett, R, J D Earle, J Q Su, F A Diegert, J A Mailliard, C G Kardinal, J E Krook, M H Veeder, and M Wiesenfeld. Sequencing and schedule effects of cisplatin plus etoposide in small-cell lung cancer: results of a North Central Cancer Treatment Group randomized clinical trial</i>. A W Maksymiuk, J Journal of Clinical Oncology 1994 12:1, 70-76<br><br>Poynor V. and Kottas A. (2017). <i>Nonparametric Bayesian Inference for Mean Residual Life Functions in Survival Analysis</i>. Submitted to Biostatistics. arXiv:1411.7481 [stat.ME]. <br><br><i>Ying, Z., S. H. Jung and L. J. Wei. Survival Analysis with Median Regression Models. </i>Journal of the American Statistical Association, Vol. 90, No. 429 (Mar., 1995), pp.178-184<br> <br><br>
DOI: 10.6084/m9.figshare.5619316
title: China's STEM Research Environment: A Snapshot

description: This fileset contains data associated with the following publication: China's STEM Research Environment: A Snapshot. Accessible here: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0195347<br>All identifying information have been removed from the following data sets to protect the privacy of our survey respondents. Original survey questions (in both Mandarin Chinese and English) can be found as supplemental material under a forthcoming publication. If you would like access to the original survey questions prior to the publication or have any questions regarding the fileset, please contact Xueying Han at xhan@ida.org.<br>There are five files in this fileset:<br>1. "All surveys combined.csv" Raw survey data from the 731 completed surveys. Does not include free response answers.<br>2. "Translation and coding for challenges to research environment.xlsx" Free response answers (original text + English translation) to survey question #51 (What challenges, if any, do you think exist in China's current research environment/culture?) File also provides manual coding of each free response answer: 1 = challenge was identified by a survey respondent, 0 = challenge was not identified by a survey respondent. Twelve challenge themes were identified. Each challenge theme consists of a subset of smaller challenges that contributes to the larger challenge. (N = 466 responses) <br>3. "Identified challenges to China's scientific environnment.csv" Contains presence/absence data (1/0) for the 12 challenge themes identified in data set #2. File to be used in R.<br>4. "Translation and coding for opportunities for improvement.xlsx" Free response answers (original text + English translation) to survey question #52 (What changes, if any, do you think would improve the research environment/culture in China?) File also provides manual coding of each free response answer: 1 = recommendation to improve the research environment was identified by a survey respondent, 0 = recommendation was not identified by a survey respondent. Ten overencompassing themes were identified. Each theme consists of a subset of recommendations to improve China's research environment. (N = 443 responses)<br>5. "Opportunities for improving China's research environment.csv" Contains presence/absence data (1/0) for the 10 themes on how to improve China's research environment identified in data set #4. File to be used in R.<br>
DOI: 10.6084/m9.figshare.5619187
title: Lycaon_pictus_Sighting_Catalogue_&_Suppl_Mat_Kafue_Zambia

description: A photographic catalogue of individually identified African wild dogs (Lycaon pictus) and their pack affiliations compiled from sightings made during 2007-2012 in the southern Kafue ecosystem, Zambia.<br>Four video files are provided as Supplemental Material.<br>
DOI: 10.6084/m9.figshare.5619187.v1
title: Lycaon_pictus_Sighting_Catalogue_&_Suppl_Mat_Kafue_Zambia

description: A photographic catalogue of individually identified African wild dogs (Lycaon pictus) and their pack affiliations compiled from sightings made during 2007-2012 in the southern Kafue ecosystem, Zambia.<br>Four video files are provided as Supplemental Material.<br>
DOI: 10.6084/m9.figshare.5616922
title: Ethyl pyruvate ameliorates hepatic injury following blunt chest trauma and hemorrhagic shock by reducing local inflammation, NF-kappaB activation and HMGB1 release

description: Additional data will be provided upon request
DOI: 10.6084/m9.figshare.5616898
title: EASY_ADA_Separate.txt

description: Easy Separated
DOI: 10.6084/m9.figshare.5616922.v1
title: Ethyl pyruvate ameliorates hepatic injury following blunt chest trauma and hemorrhagic shock by reducing local inflammation, NF-kappaB activation and HMGB1 release

description: Additional data will be provided upon request
DOI: 10.6084/m9.figshare.5619220.v1
title: LAS IMPLICACIONES DE LA INTERVENCIÓN DEL INTÉRPRETE VOLUNTARIO EN LA INTERPRETACIÓN SANITARIA ÁRABE-ESPAÑOL (ANEXO 1: TRANSCRIPCIÓN Y COMENTARIO DE LOS CUATRO CASOS REALES)

description: Este archivo anexo contiene la transcripción comentada de los cuatro casos de estudio analizados en la contribución “<b>Las implicaciones de la intervención del <i>intérprete voluntario</i> en la interpretación sanitaria árabe-español”</b>, por Dr. Bachir Mahyub Rayaa, Universidad de Granada (bachirmr@ugr.es).<br>
DOI: 10.6084/m9.figshare.5616889
title: DIFFICULT_ADA_Separated.txt

description: Difficult Separated
DOI: 10.6084/m9.figshare.5616892
title: EASY_ADA_Integrated.txt

description: Easy Integrated
DOI: 10.6084/m9.figshare.5616898.v1
title: EASY_ADA_Separate.txt

description: Easy Separated
DOI: 10.6084/m9.figshare.5616889.v1
title: DIFFICULT_ADA_Separated.txt

description: Difficult Separated
DOI: 10.6084/m9.figshare.5616892.v1
title: EASY_ADA_Integrated.txt

description: Easy Integrated
DOI: 10.6084/m9.figshare.5616880
title: DIFFICULT_ADA_Integrated.txt

description: Difficult Integrated Condition
DOI: 10.6084/m9.figshare.5616880.v1
title: DIFFICULT_ADA_Integrated.txt

description: Difficult Integrated Condition
DOI: 10.6084/m9.figshare.5616691
title: Come and gone: Description of a new species of Eucharitidae (Hymenoptera) attacking Solenopsis in Texas Fig. 14-17

description: Figs 14–17. Orasema taii. (14) ovipositor, ventral view. (15) lateral view of apex of ovipositor stylets. (16) female pupa, lateral and ventral view. (17) male pupa, lateral and ventral view of abdomen (inset). Except for inset, pupae are at same scale. 59x22mm (300 x 300 DPI)
DOI: 10.6084/m9.figshare.5616700
title: Come and gone: Description of a new species of Eucharitidae (Hymenoptera) attacking Solenopsis in Texas Fig 18-23

description: Figs 18–23. Orasema taii. (18) section through leaf showing egg within oviposition puncture. (19) oviposition on Vachellia (Fabaceae). (20) planidium habitus, dorsal and ventral view. (21) magnified mandibular area of planidium. (22) third instar larva. (23) pupa. 158x164mm (300 x 300 DPI)
DOI: 10.6084/m9.figshare.5616691.v1
title: Come and gone: Description of a new species of Eucharitidae (Hymenoptera) attacking Solenopsis in Texas Fig. 14-17

description: Figs 14–17. Orasema taii. (14) ovipositor, ventral view. (15) lateral view of apex of ovipositor stylets. (16) female pupa, lateral and ventral view. (17) male pupa, lateral and ventral view of abdomen (inset). Except for inset, pupae are at same scale. 59x22mm (300 x 300 DPI)
DOI: 10.6084/m9.figshare.5616688
title: Come and gone: Description of a new species of Eucharitidae (Hymenoptera) attacking Solenopsis in Texas Fig 8-13

description: Figs 8–13. Orasema taii, female. (8) apex of antenna (lateral). (9) mandibles (posterior). (10) mesosoma (lateral). (11) mesosoma (dorsal). (12) petiole (dorsal). (13) fore wing. 197x256mm (300 x 300 DPI)
DOI: 10.6084/m9.figshare.5616700.v1
title: Come and gone: Description of a new species of Eucharitidae (Hymenoptera) attacking Solenopsis in Texas Fig 18-23

description: Figs 18–23. Orasema taii. (18) section through leaf showing egg within oviposition puncture. (19) oviposition on Vachellia (Fabaceae). (20) planidium habitus, dorsal and ventral view. (21) magnified mandibular area of planidium. (22) third instar larva. (23) pupa. 158x164mm (300 x 300 DPI)
DOI: 10.6084/m9.figshare.5616688.v1
title: Come and gone: Description of a new species of Eucharitidae (Hymenoptera) attacking Solenopsis in Texas Fig 8-13

description: Figs 8–13. Orasema taii, female. (8) apex of antenna (lateral). (9) mandibles (posterior). (10) mesosoma (lateral). (11) mesosoma (dorsal). (12) petiole (dorsal). (13) fore wing. 197x256mm (300 x 300 DPI)
DOI: 10.6084/m9.figshare.5616631
title: Raw data and Supplement: Spontaneous rhythms in a harbor seal pup calls

description: This entry contains all raw data files and Supplementary Table for the manuscript: Spontaneous rhythms in a harbor seal pup calls
DOI: 10.6084/m9.figshare.5616631.v1
title: Raw data and Supplement: Spontaneous rhythms in a harbor seal pup calls

description: This entry contains all raw data files and Supplementary Table for the manuscript: Spontaneous rhythms in a harbor seal pup calls
DOI: 10.6084/m9.figshare.5616571
title: Dataset Plosone.xlsx

description: Psychophysics data on detection threshold and suprathreshold intensity for maltodextrin, oligofructose, sweeteners and 4 basic taste qualities.
DOI: 10.6084/m9.figshare.5616490
title: Maternal attraction calls of seal pup: rhythm and timing of spontaneous vocalisations

description: This dataset contains timing/rhythm data of seal pup mother attraction calls, plus a supplementary table presenting simple descriptive statistics and distribution of the data.<br>Data are provided in openly-accessible <b>.csv</b> text files and <b>.pdf</b> formats, code in Python language and .py file format. This dataset contains the following files:<br><b>durations_all.csv </b>- all call durations in milliseconds<b>IOI_all</b><b>.csv </b>- inter-onset intervals (IOIs): the time elapsed between the onsets of two successive calls, in milliseconds<b>IOI_short</b><b>.csv </b>- IOIs within approximately 4 times the minimum value, in milliseconds <b>IPI_all</b><b>.csv </b>- inter-peak intervals (IPIs): the time between the maximum-intensity peak of one call and the maximum-intensity peak of the next call, in milliseconds <b>IPI_short</b><b>.csv </b>- IPIs within approximately 4 times the minimum value, in milliseconds <b>textgrid_IOI_IPI_dur_01.py </b>- this script receives, as input, a wave file (.wav) and its corresponding Praat Textgrid file (.TextGrid). These two files must have the same name and be both in the same directory as this script. The script extract durational information of seal pups' calls from annotated wav files.<br><b>supplement_datanote01 - </b>descriptive statistics and distribution for the durations and intervals in the files listed above<b>: </b>sample size, mean, median and standard deviation<br>The purpose of the threshold (4 times minimum value) in the <b>IOI_short</b><b>.csv </b>and <b>IPI_short</b><b>.csv</b> files was to focus on the timing within vocalization bouts, as opposed to the pooled timing within and between bouts in <b>IOI_all</b><b>.csv </b>and <b>IPI_all</b><b>.csv</b>.<br><b>Background</b><br>The data presents timing of spontaneous vocal rhythms in a harbor seal pup (<i>Phoca vitulina</i>). Data were collected to find spontaneous vocal rhythms in this individual in order to design individually-adapted and ecologically-relevant stimuli for a later playback experiment.<b><br></b>The calls of one seal pup were recorded. The audio recordings were annotated using Praat, a sound analysis software. The annotated onsets and offsets of vocalizations were then imported in a Python script. The script extracted three types of timing information for each call: the duration of calls, the intervals between calls’ onsets, and the intervals between calls’ maximum-intensity peaks. Based on the annotated data, available to download, I provide simple descriptive statistics for these temporal measures, and compare their distributions.
DOI: 10.6084/m9.figshare.5616490.v1
title: Maternal attraction calls of seal pup: rhythm and timing of spontaneous vocalisations

description: This dataset contains timing/rhythm data of seal pup mother attraction calls, plus a supplementary table presenting simple descriptive statistics and distribution of the data.<br>Data are provided in openly-accessible <b>.csv</b> text files and <b>.pdf</b> formats, code in Python language and .py file format. This dataset contains the following files:<br><b>durations_all.csv </b>- all call durations in milliseconds<b>IOI_all</b><b>.csv </b>- inter-onset intervals (IOIs): the time elapsed between the onsets of two successive calls, in milliseconds<b>IOI_short</b><b>.csv </b>- IOIs within approximately 4 times the minimum value, in milliseconds <b>IPI_all</b><b>.csv </b>- inter-peak intervals (IPIs): the time between the maximum-intensity peak of one call and the maximum-intensity peak of the next call, in milliseconds <b>IPI_short</b><b>.csv </b>- IPIs within approximately 4 times the minimum value, in milliseconds <b>textgrid_IOI_IPI_dur_01.py </b>- this script receives, as input, a wave file (.wav) and its corresponding Praat Textgrid file (.TextGrid). These two files must have the same name and be both in the same directory as this script. The script extract durational information of seal pups' calls from annotated wav files.<br><b>supplement_datanote01 - </b>descriptive statistics and distribution for the durations and intervals in the files listed above<b>: </b>sample size, mean, median and standard deviation<br>The purpose of the threshold (4 times minimum value) in the <b>IOI_short</b><b>.csv </b>and <b>IPI_short</b><b>.csv</b> files was to focus on the timing within vocalization bouts, as opposed to the pooled timing within and between bouts in <b>IOI_all</b><b>.csv </b>and <b>IPI_all</b><b>.csv</b>.<br><b>Background</b><br>The data presents timing of spontaneous vocal rhythms in a harbor seal pup (<i>Phoca vitulina</i>). Data were collected to find spontaneous vocal rhythms in this individual in order to design individually-adapted and ecologically-relevant stimuli for a later playback experiment.<b><br></b>The calls of one seal pup were recorded. The audio recordings were annotated using Praat, a sound analysis software. The annotated onsets and offsets of vocalizations were then imported in a Python script. The script extracted three types of timing information for each call: the duration of calls, the intervals between calls’ onsets, and the intervals between calls’ maximum-intensity peaks. Based on the annotated data, available to download, I provide simple descriptive statistics for these temporal measures, and compare their distributions.
DOI: 10.6084/m9.figshare.5616571.v2
title: Dataset Plosone.xlsx

description: Psychophysics data on detection threshold and suprathreshold intensity for maltodextrin, oligofructose, sweeteners and 4 basic taste qualities.
DOI: 10.6084/m9.figshare.5616571.v1
title: Dataset Plosone.xlsx

description: Psychophysics data on detection threshold and suprathreshold intensity for maltodextrin, oligofructose, sweeteners and 4 basic taste qualities.
DOI: 10.6084/m9.figshare.5616439
title: Americas-Data.xlsx

description: The data presented here is analysed in 'Why does freshwater fish species richness differ between Atlantic and Pacific drainages of the Americas?' to be published in Journal of Biogeography. A detailed description of the procedures is described there.<br>
DOI: 10.6084/m9.figshare.5616427
title: Demo datasets for fMLC and DiVE

description: The "small" dataset contains ~4000 ITS yeast sequences, checked and validated by the specialists at the Westerdijk Fungal Biodiversity Institute. This dataset were analyzed and released in Vu D. et al. 2016. The "large" dataset contains ~350K ITS fungal sequences downloaded from GenBank (https://www.ncbi.nlm.nih.gov/) which was used in Vu D. et al. 2014 to evaluate the speed of MLC. <br>
DOI: 10.6084/m9.figshare.5616439.v2
title: Americas-Data.xlsx

description: The data presented here is analysed in 'Why does freshwater fish species richness differ between Atlantic and Pacific drainages of the Americas?' to be published in Journal of Biogeography. A detailed description of the procedures is described there.<br>
DOI: 10.6084/m9.figshare.5616418
title: Discrete and Continuous encoding in RL

description: Illustration of the differences in observation and Q-values encoding between a tabular and a neural network implementation of a Q-learning algorithm.<br>
DOI: 10.6084/m9.figshare.5616427.v2
title: Demo datasets for fMLC and DiVE

description: The "small" dataset contains ~4000 ITS yeast sequences, checked and validated by the specialists at the Westerdijk Fungal Biodiversity Institute. This dataset were analyzed and released in Vu D. et al. 2016. The "large" dataset contains ~350K ITS fungal sequences downloaded from GenBank (https://www.ncbi.nlm.nih.gov/) which was used in Vu D. et al. 2014 to evaluate the speed of MLC. <br>
DOI: 10.6084/m9.figshare.5616412
title: Dataset for: <i>Lactobacillus reuteri </i>strains protect epithelial barrier integrity of IPEC-J2 monolayers from the detrimental effect of Enterotoxigenic <i>Escherichia coli</i> (ETEC).

description: <i>Lactobacillus reuteri</i> is an inhabitant of the gastrointestinal (GI) tract of mammals and birds and several strains of this species are known to be effective probiotics. The mechanisms by which <i><i>L. reuteri</i></i> confers its health-promoting effects are far from being fully understood, but protection of the mucosal barrier is thought to be important. Leaky gut is a state of abnormal intestinal permeability with implications for the pathophysiology of various gastrointestinal disorders. Enterotoxigenic<i><i> Escherichia coli </i></i>(ETEC) can invade the intestinal mucosa and induce changes in barrier function by producing enterotoxin or by direct invasion of the intestinal epithelium.Our hypothesis was that<i> L. reuteri </i>can protect the mucosal barrier, and the goal of the study was to challenge this hypothesis by monitoring the protective effect of <i>L. reuteri </i>strains on epithelial dysfunction caused by ETEC. This study examined the potential of <i><i>Lactobacillus reuteri</i></i> to attenuate the effect of ETEC strain 853/67 on mucosal permeability. Using an infection model based on the porcine intestinal cell line IPEC-J2, it was demonstrated that pre-treatment of the cells with human-derived <i>L. reuteri </i>strains (ATCC PTA 6475, DSM 17938 and 1563F) and a rat strain (R2LC) reduced the detrimental effect of ETEC in a dose-dependent manner, as monitored by permeability of FITC-dextran and transepithelial electrical resistance (TEER). Moreover, the results revealed that ETEC up-regulated pro-inflammatory cytokines IL-6 and TNFα and decreased expression of the shorter isoform of ZO-1 (187 kDa) and E-cadherin. In contrast, pre-treatment with<i> L. reuteri</i> DSM 17938 and 1563F downregulated expression of IL-6 and TNFα, and led to an increase in production of the longer isoform of ZO-1 (195 kDa) and maintained E-cadherin expression. Interestingly, expression of ZO-1 (187 kDa) was preserved only when the infected cells were pre-treated with strain 1563F. These findings demonstrate that <i><i>L. reuteri</i></i> strains exert a protective effect against ETEC-induced mucosal integrity disruption.