cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12058095
title: DECM Ontology. T-AP Digging into Early Colonial Mexico Project

description: This document contains a tailored ontology that encompassed the complexity of Relaciones Geográficas de la Nueva España (1577-1585), resulting in twenty-one entities or categories (types of information). These entities were defined and linked to DBpedia, a semantic standard, to ensure the interoperability of our dataset. Additionally, most entities contain labels, also defined and linked to DBpedia to enrich the semantic extraction process.<br><br>More information about the use of this ontology in combination with Machine Learning and Natural Language Processing techniques:<br>https://www.academia.edu/41852118/Digital_Approaches_to_Historical_Archaeology_Exploring_the_Geographies_of_16th_Century_New_Spainhttps://www.academia.edu/39912267/Training_NLP_Models_for_the_Analysis_of_16th_century_Latin_American_Historical_Documents_Tagtog_and_the_Geographic_Reports_of_New_Spain
DOI: 10.6084/m9.figshare.12058101.v1
title: Supplementary Material for: Myofibroblast-Derived Exosomes Contribute to Development of a Susceptible Substrate for Atrial Fibrillation

description: <b><i>Objective:</i></b> Atrial fibrosis plays a critical role in atrial fibrillation (AF). A key event in the pathogenesis of fibrosis is the activation of fibroblasts (FBs) into myofibroblasts (MFBs). Paracrine factors released from MFBs lead to ion channel expression changes in cardiomyocytes (CMs). Downregulation of L-type calcium channel Ca<sub>v</sub>1.2 expression is a hallmark of AF-associated ionic remodeling. However, whether exosome (Exo)-mediated crosstalk between MFBs and CMs regulates Ca<sub>v</sub>1.2 expression remains unknown. <b><i>Methods:</i></b> Atrial FBs and CMs were isolated and cultured from neonatal rats by enzymatic digestion. The activation of FBs into MFBs was induced by angiotensin II. Co-culture assay and in vitro Exo treatment were used to determine the effect of MFB-derived Exos on Ca<sub>v</sub>1.2 expression. Confocal Ca<sup>2+</sup> imaging was performed to examine the adrenergic stimulation-elicited Ca<sup>2+</sup> influx signals. The levels of potential Ca<sub>v</sub>1.2-inhibitory microRNAs (miRNAs) were measured by qRT-PCR. <b><i>Results:</i></b> Untreated FBs expressed limited amounts of alpha smooth muscle actin (α-SMA), while angiotensin II induced a significant upregulation of α-SMA-expressing MFBs. Co-cultures of MFBs and CMs resulted in downregulation of Ca<sub>v</sub>1.2 expression in CMs, which was largely abolished by pretreatment of MFBs with exosomal inhibitor GW4869. More importantly, treatment with MFB-derived Exos caused repression of Ca<sub>v</sub>1.2 expression in CMs. Additionally, the adrenergic receptor agonist-elicited Ca<sup>2+</sup> influx signals in CMs were remarkably attenuated by pretreatment with MFB-derived Exos, corresponding to the paralleled change in Ca<sub>v</sub>1.2 expression. Finally, miR-21-3p, a potential Ca<sub>v</sub>1.2-inhibitory miRNA, was enriched in MFB-derived Exos and upregulated in CMs in response to MFB-derived Exos. <b><i>Conclusion:</i></b> We uncover an Exo-mediated crosstalk between MFBs and CMs, contributing to increased vulnerability to AF by reducing the expression of Ca<sub>v</sub>1.2 in CMs.
DOI: 10.6084/m9.figshare.12058083
title: Supplementary Material for: Oral Lactobacilli Related to Caries Status of Children with Primary Dentition

description: Oral lactobacilli are members of a group of bacteria implicated in caries progression, although information regarding their transmission, colonization, and caries-associated species is not well established. This study isolated oral lactobacilli from a group of children with primary dentition for determination of <i>Lactobacillus</i> prevalence, detection of <i>Streptococcus mutans</i>, a major pathogen of caries initiation, and dental caries status of the children. Species of <i>Lactobacillus</i> isolates were determined from examination of 16S rDNA sequences. Subsequently, the most prevalent species was evaluated for involvement in caries status, and binding ability to type I collagen of all <i>Lactobacillus</i> isolates was determined in association with caries status. Multilocus sequence typing (MLST) of eleven loci was carried out to study strains of the predominant <i>Lactobacillus</i> sp. The detection of oral lactobacilli together with <i>S. mutans</i> was significantly associated with the highest dental caries indices, but there was no involvement of collagen-binding properties of <i>Lactobacillus</i> isolates in caries status. <i>Lactobacillus fermentum</i> was the most prevalent, and its presence was related to high scores of caries indices. MLST analysis of <i>L. fermentum</i> population could not specify a particular clone associated with caries status, but revealed sharing of identical <i>L. fermentum</i> strains among children in the same classrooms. Taken together, the data contributed useful information on the role of oral lactobacilli, in particular <i>L. fermentum</i> in dental caries.
DOI: 10.6084/m9.figshare.12058089.v1
title: Wave fetch GIS layers for Australia at 100m scale

description: This data layer gives values of summed wave fetch in 32 angular sectors around focal cells, using a model modified from that given in Burrows et al (2012 - see reference). Wave fetch is the distance to the nearest land in a defined direction. The model performs a three-scale search for land around each cell in the model, sparsely (every 10km) up to 200km, every 1km up to 20km away, and every 100m up to 1km distant. Fetch is calculated up to 5km from the coastline.<br>Values represent the summed number of grid cells to the nearest land across all 32 11.5° sectors. The file is a GeoTIFF using the WGS84 projection.
DOI: 10.6084/m9.figshare.12058068
title: Supplementary Material for: Predictors of Outcomes in Hypoxic-Ischemic Encephalopathy following Hypothermia: A Meta-Analysis

description: <b><i>Introduction:</i></b> Prediction of neurodevelopmental outcome in infants with hypoxic-ischemic encephalopathy remains an important challenge. Various studies have shown that the predictive ability of different modalities changed after the introduction of therapeutic hypothermia. This paper reviews the diagnostic test accuracy of the different modalities that are being used to predict neurodevelopmental outcomes following therapeutic hypothermia. <b><i>Methods:</i></b> A systematic literature search was performed using Embase and PubMed. Two reviewers independently included eligible studies and extracted data. The quality of the studies was assessed using the Quality in Prognosis Studies Tool. Meta-analyses were performed where possible. <b><i>Results:</i></b> Forty-seven articles and 3 conference abstracts were included, reporting on 3,072<i></i>infants of whom 39% died or had an adverse neurodevelopmental outcome. A meta-analysis could be performed using 37 articles on (amplitude-integrated) electroencephalography (EEG), conventional magnetic resonance imaging (MRI), diffusion-weighted imaging (DWI), and proton magnetic resonance spectroscopy (<sup>1</sup>H-MRS). Amplitude-integrated EEG (aEEG) at 24 and 72 h showed similar high diagnostic OR, while aEEG at 6 h and EEG performed less, both due to a low specificity. For MRI, most studies reported scoring systems in which early (&lt;8 days) MRI performed better than late (≥8 days) MRI. Injury to the posterior limb of the internal capsule on MRI or to the thalami on DWI were strong individual predictors, as was an increased lactate/N-acetylaspartate peak on <sup>1</sup>H-MRS. <b><i>Conclusions:</i></b> In the era of therapeutic hypothermia, the different modalities remain good predictors of neurodevelopmental outcome. However, timing should be taken into account. aEEG may initially be false positive and gets more reliable after 24 h. In contrast, MRI should be used during the first week, as its predictive value decreases afterwards.
DOI: 10.6084/m9.figshare.12058083.v1
title: Supplementary Material for: Oral Lactobacilli Related to Caries Status of Children with Primary Dentition

description: Oral lactobacilli are members of a group of bacteria implicated in caries progression, although information regarding their transmission, colonization, and caries-associated species is not well established. This study isolated oral lactobacilli from a group of children with primary dentition for determination of <i>Lactobacillus</i> prevalence, detection of <i>Streptococcus mutans</i>, a major pathogen of caries initiation, and dental caries status of the children. Species of <i>Lactobacillus</i> isolates were determined from examination of 16S rDNA sequences. Subsequently, the most prevalent species was evaluated for involvement in caries status, and binding ability to type I collagen of all <i>Lactobacillus</i> isolates was determined in association with caries status. Multilocus sequence typing (MLST) of eleven loci was carried out to study strains of the predominant <i>Lactobacillus</i> sp. The detection of oral lactobacilli together with <i>S. mutans</i> was significantly associated with the highest dental caries indices, but there was no involvement of collagen-binding properties of <i>Lactobacillus</i> isolates in caries status. <i>Lactobacillus fermentum</i> was the most prevalent, and its presence was related to high scores of caries indices. MLST analysis of <i>L. fermentum</i> population could not specify a particular clone associated with caries status, but revealed sharing of identical <i>L. fermentum</i> strains among children in the same classrooms. Taken together, the data contributed useful information on the role of oral lactobacilli, in particular <i>L. fermentum</i> in dental caries.
DOI: 10.6084/m9.figshare.12058095.v2
title: DECM Ontology. T-AP Digging into Early Colonial Mexico Project

description: This document contains a tailored ontology that encompassed the complexity of Relaciones Geográficas de la Nueva España (1577-1585), resulting in twenty-one entities or categories (types of information). These entities were defined and linked to DBpedia, a semantic standard, to ensure the interoperability of our dataset. Additionally, most entities contain labels, also defined and linked to DBpedia to enrich the semantic extraction process.<br><br>More information about the use of this ontology in combination with Machine Learning and Natural Language Processing techniques:<br>https://www.academia.edu/41852118/Digital_Approaches_to_Historical_Archaeology_Exploring_the_Geographies_of_16th_Century_New_Spainhttps://www.academia.edu/39912267/Training_NLP_Models_for_the_Analysis_of_16th_century_Latin_American_Historical_Documents_Tagtog_and_the_Geographic_Reports_of_New_Spain
DOI: 10.6084/m9.figshare.12058062
title: Supplementary Material for: A Validation Study for Recurrence Risk Stratification of Stage II Colon Cancer Using the 55-Gene Classifier

description: <b><i>Introduction:</i></b> DNA microarrays, such as the consensus molecular subtype (CMS) classification using &gt;600 genes, are used to predict cancer patient prognosis. We recently constructed a simple 55-gene classifier (55GC) system to risk stratify colon cancer (CC). <b><i>Objective:</i></b> Here, we validate the 55GC specifically for stage II CC and compare it with CMS categories. <b><i>Methods:</i></b> Tissue sections from 232 stage II CC patients who underwent curative surgery without adjuvant chemotherapy between 2009 and 2012 were subjected to DNA microarray analysis. <b><i>Results:</i></b> Based on the 55GC, patients were classified into microsatellite instability-like (27%), chromosomal instability-like (41%), and stromal (32%) subtypes with 5-year relapse-free survival (RFS) rates of 88.5, 83.3, and 71.2%, respectively (stromal vs. others: <i>p</i> = 0.0049). Multivariate analysis by Cox’s proportional hazard model revealed that the stromal subtype, pT4, and the number of lymph nodes examined (&lt;12) were independent poor prognostic factors. The overall concordance rate between 55GC and CMS was 72%, and 5-year RFS rates of patients with CMS1, CMS2, CMS3, and CMS4 cancers were 100, 85.5, 92.3, and 73.0%, respectively (<i>p</i> = 0.0113). <b><i>Conclusions:</i></b> We conclude that the 55GC is a useful and reproducible grading system for stage II CC recurrence risk stratification.
DOI: 10.6084/m9.figshare.12058038
title: Maqu ELBARA-III dataset_Version1.0: Multiyear in-situ L-band microwave radiometry of land surface processes on the Tibetan Plateau

description: We report a unique multiyear L-band microwave radiometry dataset collected at the Maqu site on the eastern Tibetan Plateau and demonstrate its utilities in advancing our understandings of microwave observations of land surface processes. The presented dataset contains measurements of L-band brightness temperature by an ELBARA-III microwave radiometer in horizontal and vertical polarization, profile soil moisture and soil temperature, turbulent heat fluxes, and meteorological data from the beginning of 2016 till August 2019, while the experiment is still continuing. Auxiliary vegetation and soil texture information collected in dedicated campaigns are also reported. This dataset can be used to validate the Soil Moisture and Ocean Salinity (SMOS) and Soil Moisture Active Passive (SMAP) satellite based observations and retrievals, verify radiative transfer model assumptions and land surface model and reanalysis outputs, retrieve soil properties, as well as to quantify land-atmosphere exchanges of energy, water and carbon and help to reduce discrepancies and uncertainties in current Earth System Models (ESM) parameterizations. Measurement cases in winter, pre-monsoon, monsoon and post-monsoon periods are presented.
DOI: 10.6084/m9.figshare.12058023
title: Utility of micro-TESE in the most severe cases of non-obstructive azoospermia

description: The use of intracytoplasmic sperm injection (ICSI) has been a major breakthrough in the treatment of male infertility. Even patients with non-obstructive azoospermia (NOA) may benefit from the ICSI technique to father a child as long as spermatogenesis is present. There are several techniques to recover testicular sperm in patients with NOA. However, retrieval of spermatozoa is unfortunately still only successful in a subset of patients with NOA, and the most superior sperm retrieval method is still under debate. A more recent technique, microdissection testicular sperm extraction (MD-TESE) with an operative microscope collecting larger and more opaque seminiferous tubules, is a non-blind sperm retrieval technique with theoretical benefits. The MD-TESE procedure seems to be feasible, effective, and safe in NOA patients but also more technically demanding and time-consuming compared with conventional blind techniques. In the present report, we describe our clinical experience and results from our first 159 MD-TESE procedures. The probability to retrieve sperm with the MD-TESE technique is high in NOA cases where earlier sperm retrieval with blind methods such as needle aspiration, percutaneous needle biopsy, or conventional TESE has failed.
DOI: 10.6084/m9.figshare.12058065.v1
title: Solar wind in situ data suitable for machine learning (python numpy arrays): STEREO-A/B, Wind, Parker Solar Probe, Ulysses, Venus Express, MESSENGER

description: **work in progress** don't use yet!<br>These are solar wind in situ data arrays in python pickle suitable for machine learning, i.e. the arrays consist only of numbers, no strings, no datetime objects.<br>Made with https://github.com/cmoestl/heliocats <br><br>Load in python with e.g.:<br>&gt; import pickle&gt; filepsp='psp_2018_2019_numpy.p'&gt; [psp,hpsp]=pickle.load(open(filepsp, "rb" ) ) <br>plot time vs total field&gt; import matplotlib.pyplot as plt&gt; plt.plot(psp[:,0],psp[:,1])<br><br>Times psp[:,0 ]are in matplotlib format. Variable 'hpsp' contains a header with the variable names for each column.<br><br>
DOI: 10.6084/m9.figshare.12058023.v1
title: Utility of micro-TESE in the most severe cases of non-obstructive azoospermia

description: The use of intracytoplasmic sperm injection (ICSI) has been a major breakthrough in the treatment of male infertility. Even patients with non-obstructive azoospermia (NOA) may benefit from the ICSI technique to father a child as long as spermatogenesis is present. There are several techniques to recover testicular sperm in patients with NOA. However, retrieval of spermatozoa is unfortunately still only successful in a subset of patients with NOA, and the most superior sperm retrieval method is still under debate. A more recent technique, microdissection testicular sperm extraction (MD-TESE) with an operative microscope collecting larger and more opaque seminiferous tubules, is a non-blind sperm retrieval technique with theoretical benefits. The MD-TESE procedure seems to be feasible, effective, and safe in NOA patients but also more technically demanding and time-consuming compared with conventional blind techniques. In the present report, we describe our clinical experience and results from our first 159 MD-TESE procedures. The probability to retrieve sperm with the MD-TESE technique is high in NOA cases where earlier sperm retrieval with blind methods such as needle aspiration, percutaneous needle biopsy, or conventional TESE has failed.
DOI: 10.6084/m9.figshare.12058005
title: Supporting data for "Effect of transport measures and curfew against COVID-19 spread on air pollution (TSP) in Ecuador’s three most populous cities"

description: This dataset includes:-sampling points data, <br>-raw data for particulate matter calculation, namely: Weight PM10 (μg); PM10 Conc.(μg/m3); Weight PM2,5 (μg); PM2,5 Conc. (μg/m3)
DOI: 10.6084/m9.figshare.12058065.v2
title: Solar wind in situ data suitable for machine learning (python numpy structured arrays): STEREO-A/B, Wind, Parker Solar Probe, Ulysses, Venus Express, MESSENGER

description: These are solar wind in situ data arrays in python pickle format suitable for machine learning, i.e. the arrays consist only of numbers, no strings and no datetime objects.<br><br>See AAREADME_insitu_ML.txt for more explanation.<br>If you use these data for peer reviewed scientific publications, please get in touch concerning usage and possible co-authorship by the authors (C. Möstl, A. J. Weiss, R. L. Bailey, A. Isavnin): christian.moestl@oeaw.ac.at or twitter @chrisoutofspace <br>Made with https://github.com/cmoestl/heliocats <br><br>Load in python with e.g. for Parker Solar Probe data:<br>&gt; import pickle&gt; filepsp='psp_2018_2019_sceq_ndarray.p'&gt; [psp,hpsp]=pickle.load(open(filepsp, "rb" ) ) <br>plot time vs total field&gt; import matplotlib.pyplot as plt&gt; plt.plot(psp['time'],psp['bt'])<br><br>Times psp[:,0 ] or psp['time'] are in matplotlib format. Variable 'hpsp' contains a header with the variable names and units for each column. Coordinate systems for magnetic field components are RTN (Ulysses), SCEQ (Parker Solar Probe, STEREO-A/B, VEX, MESSENGER), HEEQ (Wind)<br>available parameters:<br>bt = total magnetic fieldbxyz = magnetic field componentsvt = total proton speedvxyz = velocity components (only for PSP)np = proton densitytp = proton temperaturexyz = spacecraft position in HEEQr, lat, lon = spherical coordinates of position in HEEQ<br><br><br><br>
DOI: 10.6084/m9.figshare.12058005.v1
title: Supporting data for "Effect of transport measures and curfew against COVID-19 spread on air pollution (TSP) in Ecuador’s three most populous cities"

description: This dataset includes:-sampling points data, <br>-raw data for particulate matter calculation, namely: Weight PM10 (μg); PM10 Conc.(μg/m3); Weight PM2,5 (μg); PM2,5 Conc. (μg/m3)
DOI: 10.6084/m9.figshare.12057966
title: HSV transcript annotation

description: Meta-analysis HSV transcriptome
DOI: 10.6084/m9.figshare.12057966.v2
title: HSV transcript annotation

description: Meta-analysis HSV transcriptome
DOI: 10.6084/m9.figshare.12058065.v3
title: Solar wind in situ data suitable for machine learning (python numpy structured arrays): STEREO-A/B, Wind, Parker Solar Probe, Ulysses, Venus Express, MESSENGER

description: These are solar wind in situ data arrays in python pickle format suitable for machine learning, i.e. the arrays consist only of numbers, no strings and no datetime objects.<br><br>See AAREADME_insitu_ML.txt for more explanation.<br>If you use these data for peer reviewed scientific publications, please get in touch concerning usage and possible co-authorship by the authors (C. Möstl, A. J. Weiss, R. L. Bailey, A. Isavnin): christian.moestl@oeaw.ac.at or twitter @chrisoutofspace <br>Made with https://github.com/cmoestl/heliocats <br><br>Load in python with e.g. for Parker Solar Probe data:<br>&gt; import pickle&gt; filepsp='psp_2018_2019_sceq_ndarray.p'&gt; [psp,hpsp]=pickle.load(open(filepsp, "rb" ) ) <br>plot time vs total field&gt; import matplotlib.pyplot as plt&gt; plt.plot(psp['time'],psp['bt'])<br><br>Times psp[:,0 ] or psp['time'] are in matplotlib format. Variable 'hpsp' contains a header with the variable names and units for each column. Coordinate systems for magnetic field components are RTN (Ulysses), SCEQ (Parker Solar Probe, STEREO-A/B, VEX, MESSENGER), HEEQ (Wind)<br>available parameters:<br>bt = total magnetic fieldbxyz = magnetic field componentsvt = total proton speedvxyz = velocity components (only for PSP)np = proton densitytp = proton temperaturexyz = spacecraft position in HEEQr, lat, lon = spherical coordinates of position in HEEQ<br><br><br><br>
DOI: 10.6084/m9.figshare.12057966.v1
title: HSV transcript annotation

description: Meta-analysis HSV transcriptome
DOI: 10.6084/m9.figshare.12057951
title: Dynamic change of lymphocyte count in COVID-19 patients

description: Lymphopenia is associated with COVID-19 severity. Herein we describe the dynamic changes in lymphocyte count during hospitalization and explore a possible association with the severity of COVID-19.In this retrospective study, 13 non-severe COVID-19 patients diagnosed at admission were enrolled. One patient progressed to severe disease. Dynamic changes in lymphocyte count and CT score of all patients were analyzed.
DOI: 10.6084/m9.figshare.12058065.v4
title: Solar wind in situ data suitable for machine learning (python numpy structured arrays): STEREO-A/B, Wind, Parker Solar Probe, Ulysses, Venus Express, MESSENGER

description: These are solar wind in situ data arrays in python pickle format suitable for machine learning, i.e. the arrays consist only of numbers, no strings and no datetime objects.<br><br>See AAREADME_insitu_ML.txt for more explanation.<br>If you use these data for peer reviewed scientific publications, please get in touch concerning usage and possible co-authorship by the authors (C. Möstl, A. J. Weiss, R. L. Bailey, A. Isavnin): christian.moestl@oeaw.ac.at or twitter @chrisoutofspace <br>Made with https://github.com/cmoestl/heliocats <br><br>Load in python with e.g. for Parker Solar Probe data:<br>&gt; import pickle&gt; filepsp='psp_2018_2019_sceq_ndarray.p'&gt; [psp,hpsp]=pickle.load(open(filepsp, "rb" ) ) <br>plot time vs total field&gt; import matplotlib.pyplot as plt&gt; plt.plot(psp['time'],psp['bt'])<br><br>Times psp[:,0 ] or psp['time'] are in matplotlib format. Variable 'hpsp' contains a header with the variable names and units for each column. Coordinate systems for magnetic field components are RTN (Ulysses), SCEQ (Parker Solar Probe, STEREO-A/B, VEX, MESSENGER), HEEQ (Wind)<br>available parameters:<br>bt = total magnetic fieldbxyz = magnetic field componentsvt = total proton speedvxyz = velocity components (only for PSP)np = proton densitytp = proton temperaturexyz = spacecraft position in HEEQr, lat, lon = spherical coordinates of position in HEEQ<br><br><br><br>