cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5395567
title: Dataset OROV

description: <b>First outbreak of Oropouche Fever reported in a non-endemic central-western region of the Peruvian Amazon. </b><b>Molecular diagnosis and clinical characteristics. </b><b>Introduction: </b>Oropouche virus (OROV) is an underreported and emerging infectious disease. Its incidence is underestimated mainly due to clinical similarities with other diseases that are also caused by arboviruses present in endemic areas. We report the first outbreak of OROV in the western region of the Peruvian Amazon in the department of Huanuco, Peru. <b>Methods</b>: This outbreak occurred in the region of Huanuco, Peru during July of 2016. Blood samples were taken from 268 patients who presented acute febrile syndrome to be later analyzed for Oropouche Virus via Polymerase Chain Reaction.<b>Results</b>: Of all 268 patients, 46 (17%) cases tested were positive for OROV. the most common symptom reported was headaches with a frequency of 87% (n=40) followed by myalgias with 76% (n=35), arthralgias with 65.2% (n=30), retro-ocular pain 60.8% (n=28) and hyporexia with 50% (n=23). Concerning signs and symptoms that may suggest severe OROV infection, 4.3% (n=2) had low platelet count, 8.6% (n=4) had intense abdominal pain, and only 2.1% (n=1) had a presentation with thoracic pain.
DOI: 10.6084/m9.figshare.5395555
title: Peruvian researchers with UNMSM affiliation in Google Scholar by topic areas [Ago, 2017]

description: Dataset from blog article "Analysis of National University of San Marcos researchers profiles in the Google Academic and its impact on academic community" published in MediaLab UNMSM avaliable at http://medialab.letras.unmsm.edu.pe/.<br>Data was collected on August, 2017.
DOI: 10.6084/m9.figshare.5395555.v1
title: Peruvian researchers with UNMSM affiliation in Google Scholar by topic areas [Ago, 2017]

description: Dataset from blog article "Analysis of National University of San Marcos researchers profiles in the Google Academic and its impact on academic community" published in MediaLab UNMSM avaliable at http://medialab.letras.unmsm.edu.pe/.<br>Data was collected on August, 2017.
DOI: 10.6084/m9.figshare.5395504
title: Red Blood Cell Distribution Width: genome-wide association results in UK Biobank 150K

description: <strong>Pilling LC, Atkins JL, Duff MO, Beaumont RN, Jones SE, et al. (2017). Red Blood Cell Distribution Width: genetic evidence for aging pathways in 116,666 volunteers (PLOS ONE)</strong><strong> Preprint available on bioRxiv https://doi.org/10.1101/128330</strong> Fields are as follows<br> SNP: dnSNP name of genetic marker, if available<br> CHR: chromosome<br> BP: base-pair position on CHR (hg19 / b37)<br> ALLELE1: effect allele<br> ALLELE0: non-effect allele<br> A1FREQ: frequency of ALLELE1<br> INFO: imputation quality/certainty metric from IMPUTE2<br> BETA: effect size from BOLT-LMM approximation to infinitesimal mixed model<br> SE: standard error of effect size<br> P_BOLT_LMM_INF: infinitesimal mixed model association test p-value<br> P_BOLT_LMM: non-infinitesimal mixed model association test p-value If you use these data, please cite the reference above.
DOI: 10.6084/m9.figshare.5395504.v1
title: Red Blood Cell Distribution Width: genome-wide association results in UK Biobank 150K

description: <strong>Pilling LC, Atkins JL, Duff MO, Beaumont RN, Jones SE, et al. (2017). Red Blood Cell Distribution Width: genetic evidence for aging pathways in 116,666 volunteers (PLOS ONE)</strong><strong> Preprint available on bioRxiv https://doi.org/10.1101/128330</strong> Fields are as follows<br> SNP: dnSNP name of genetic marker, if available<br> CHR: chromosome<br> BP: base-pair position on CHR (hg19 / b37)<br> ALLELE1: effect allele<br> ALLELE0: non-effect allele<br> A1FREQ: frequency of ALLELE1<br> INFO: imputation quality/certainty metric from IMPUTE2<br> BETA: effect size from BOLT-LMM approximation to infinitesimal mixed model<br> SE: standard error of effect size<br> P_BOLT_LMM_INF: infinitesimal mixed model association test p-value<br> P_BOLT_LMM: non-infinitesimal mixed model association test p-value If you use these data, please cite the reference above.
DOI: 10.6084/m9.figshare.5395459
title: Data from: Evolution of almond genetic diversity and farmer practices in Lebanon: Impacts of the diffusion of a graft-propagated cultivar in a traditional system based on seed-propagation

description: We sampled a large range of cultivated individuals from different agro-climatic areas in Lebanon, and analyzed them with a set of 15 SSRs markers selected for their producibility and polymorphism in almond and other Prunus species.The most common and oldest cultivar is known as 'Khachabi', it has been cultivated by seeds. The other cultivar called 'Halwani', probably introduced last century, it has been widely propagated by grafts. <br>
DOI: 10.6084/m9.figshare.5395372
title: Six global and local QSPR models of aqueous solubility at pH = 7.4 based on structural similarity and physicochemical descriptors

description: Aqueous solubility at pH = 7.4 is a very important property for medicinal chemists because this is the pH value of physiological media. The present work describes the application of three different methods (support vector machine (SVM), random forest (RF) and multiple linear regression (MLR)) and three local quantitative structure–property relationship (QSPR) models (regression corrected by nearest neighbours (RCNN), arithmetic mean property (AMP) and local regression property (LoReP)) to construct stable QSPRs with clear mechanistic interpretation. Our data set contained experimental values of aqueous solubility at pH = 7.4 of 387 chemicals (349 in the training set and 38 in the test set including 16 own measurements). The initial descriptor pool contained 210 physicochemical descriptors, calculated from the HYBOT, DRAGON, SYBYL and VolSurf+ programs. Six QSPRs with good statistics based on fundamentals of aqueous solubility and optimization of descriptor space were obtained. Those models have an RMSE close to experimental error (0.70), and are amenable to physical interpretation. The QSPR models developed in this study may be useful for medicinal chemists. Global MLR, RF and SVM models may be valuable for consideration of common factors that influence solubility. The RCNN, AMP and LoReP local models may be helpful for the optimization of aqueous solubility in small sets of related chemicals.
DOI: 10.6084/m9.figshare.5395453
title: “Raw data for Version 2 of “Insights into pancreatic β cell energy metabolism using rodent β cell models””.

description: The impact of different glucose concentrations on INS-1 biology linked to the ability of the cells to secrete insulin in response to high levels of glucose
DOI: 10.6084/m9.figshare.5395372.v1
title: Six global and local QSPR models of aqueous solubility at pH = 7.4 based on structural similarity and physicochemical descriptors

description: Aqueous solubility at pH = 7.4 is a very important property for medicinal chemists because this is the pH value of physiological media. The present work describes the application of three different methods (support vector machine (SVM), random forest (RF) and multiple linear regression (MLR)) and three local quantitative structure–property relationship (QSPR) models (regression corrected by nearest neighbours (RCNN), arithmetic mean property (AMP) and local regression property (LoReP)) to construct stable QSPRs with clear mechanistic interpretation. Our data set contained experimental values of aqueous solubility at pH = 7.4 of 387 chemicals (349 in the training set and 38 in the test set including 16 own measurements). The initial descriptor pool contained 210 physicochemical descriptors, calculated from the HYBOT, DRAGON, SYBYL and VolSurf+ programs. Six QSPRs with good statistics based on fundamentals of aqueous solubility and optimization of descriptor space were obtained. Those models have an RMSE close to experimental error (0.70), and are amenable to physical interpretation. The QSPR models developed in this study may be useful for medicinal chemists. Global MLR, RF and SVM models may be valuable for consideration of common factors that influence solubility. The RCNN, AMP and LoReP local models may be helpful for the optimization of aqueous solubility in small sets of related chemicals.
DOI: 10.6084/m9.figshare.5395453.v1
title: “Raw data for Version 2 of “Insights into pancreatic β cell energy metabolism using rodent β cell models””.

description: The impact of different glucose concentrations on INS-1 biology linked to the ability of the cells to secrete insulin in response to high levels of glucose
DOI: 10.17608/k6.auckland.5395336
title: Hamilton et al. 2017. Accounting for uncertainty in duplicate identification and group size judgments in mark-recapture distance sampling

description: Please see the file MRDS-with-uncertain-dups.R for full description and instructions for using the code. <br>
DOI: 10.6084/m9.figshare.5395459.v2
title: Data from: Evolution of almond genetic diversity and farmer practices in Lebanon: Impacts of the diffusion of a graft-propagated cultivar in a traditional system based on seed-propagation

description: We sampled a large range of cultivated individuals from different agro-climatic areas in Lebanon, and analyzed them with a set of 15 SSRs markers selected for their producibility and polymorphism in almond and other Prunus species.The most common and oldest cultivar is known as 'Khachabi', it has been cultivated by seeds. The other cultivar called 'Halwani', probably introduced last century, it has been widely propagated by grafts. <br>
DOI: 10.17608/k6.auckland.5395336.v1
title: Hamilton et al. 2017. Accounting for uncertainty in duplicate identification and group size judgments in mark-recapture distance sampling

description: Please see the file MRDS-with-uncertain-dups.R for full description and instructions for using the code. <br>
DOI: 10.6084/m9.figshare.5395459.v1
title: 509-datainput.csv

description: We sampled a large range of cultivated individuals from different agro-climatic areas in Lebanon, and analyzed them with a set of 15 SSRs markers selected for their producibility and polymorphism in almond and other Prunus species.The most common and oldest cultivar is known as 'Khachabi', it has been cultivated by seeds. The other cultivar called 'Halwani', probably introduced last century, it has been widely propagated by grafts. <br>
DOI: 10.6084/m9.figshare.5395270
title: Filtered Data

description: Filtered Data (iMap4 analysis)<br>
DOI: 10.6084/m9.figshare.5395249
title: Additive Gaussian Process for Computer Models With Qualitative and Quantitative Factors

description: Computer experiments with qualitative and quantitative factors occur frequently in various applications in science and engineering. Analysis of such experiments is not yet completely resolved. In this work, we propose an additive Gaussian process model for computer experiments with qualitative and quantitative factors. The proposed method considers an additive correlation structure for qualitative factors, and assumes that the correlation function for each qualitative factor and the correlation function of quantitative factors are multiplicative. It inherits the flexibility of unrestrictive correlation structure for qualitative factors by using the hypersphere decomposition, embracing more flexibility in modeling the complex systems of computer experiments. The merits of the proposed method are illustrated by several numerical examples and a real data application. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.5395270.v1
title: Filtered Data

description: Filtered Data (iMap4 analysis)<br>
DOI: 10.6084/m9.figshare.5395249.v1
title: Additive Gaussian Process for Computer Models With Qualitative and Quantitative Factors

description: Computer experiments with qualitative and quantitative factors occur frequently in various applications in science and engineering. Analysis of such experiments is not yet completely resolved. In this work, we propose an additive Gaussian process model for computer experiments with qualitative and quantitative factors. The proposed method considers an additive correlation structure for qualitative factors, and assumes that the correlation function for each qualitative factor and the correlation function of quantitative factors are multiplicative. It inherits the flexibility of unrestrictive correlation structure for qualitative factors by using the hypersphere decomposition, embracing more flexibility in modeling the complex systems of computer experiments. The merits of the proposed method are illustrated by several numerical examples and a real data application. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.5395234
title: Raw Data

description: Raw data for project<br>
DOI: 10.6084/m9.figshare.5395234.v1
title: Raw Data

description: Raw data for project<br>
DOI: 10.6084/m9.figshare.5395138
title: Figures

description: Figures of the paper Interactions of Estuarine Shoreline Infrastructure with Multiscale Sea-level Variability
DOI: 10.6084/m9.figshare.5395138.v1
title: Figures

description: Figures of the paper Interactions of Estuarine Shoreline Infrastructure with Multiscale Sea-level Variability
DOI: 10.6084/m9.figshare.5395093
title: Abstract text for Journal articles (76)

description: This file contains the text from abstracts of 76 published journal articles analyzed in the following manuscript:Han BA, Ostfeld RS. 2019. Topic modeling of major research themes in disease ecology of mammals. J Mammal 100:1008–1018.
DOI: 10.6084/m9.figshare.5395093.v1
title: Abstract text for Journal articles (76)

description: This file contains the text from abstracts of 76 published journal articles analyzed in the following manuscript:Han BA, Ostfeld RS. 2019. Topic modeling of major research themes in disease ecology of mammals. J Mammal 100:1008–1018.
DOI: 10.6084/m9.figshare.5395066
title: Abstract text for Review articles (62)

description: This csv file contains the complete text of the abstracts of 62 articles exported from a search conducted in Web of Science for the string "disease ecology" AND "mammal". This search only includes articles marked by Web of Science as Reviews articles.
DOI: 10.6084/m9.figshare.5395003
title: Data from: Brain size does not impact shoaling dynamics in unfamiliar groups of guppies (Poecilia reticulata)

description: Sample videos, tracked data and derived measures for statistical testing.<br>Files follow the naming convention T[trial number]-[sex][group size]-r[replicate]-b[1/0:large/small brain]<br>Sample videos are taken from 5:00 to 5:30 in each of the full videos, with lower resolution than the original. Glitches at the ~1 second mark are artefacts of the conversion software.
DOI: 10.6084/m9.figshare.5395066.v1
title: Abstract text for Review articles (62)

description: This csv file contains the complete text of the abstracts of 62 articles exported from a search conducted in Web of Science for the string "disease ecology" AND "mammal". This search only includes articles marked by Web of Science as Reviews articles.
DOI: 10.6084/m9.figshare.5395003.v1
title: Data from: Brain size does not impact shoaling dynamics in unfamiliar groups of guppies (Poecilia reticulata)

description: Sample videos, tracked data and derived measures for statistical testing.<br>Files follow the naming convention T[trial number]-[sex][group size]-r[replicate]-b[1/0:large/small brain]<br>Sample videos are taken from 5:00 to 5:30 in each of the full videos, with lower resolution than the original. Glitches at the ~1 second mark are artefacts of the conversion software.
DOI: 10.6084/m9.figshare.5394925
title: Electrophysiological Indices of Audiovisual Speech Perception: Beyond the McGurk Effect and Speech in Noise. Supplementary Material

description: Visual information on a talker’s face can influence what a listener hears. Commonly used approaches to study this include mismatched audiovisual stimuli (e.g., McGurk type stimuli) or visual speech in auditory noise. In this paper we discuss potential limitations of these approaches and introduce a novel visual phonemic restoration method. This method always presents the same visual stimulus (e.g., /ba/) dubbed with a matched auditory stimulus (/ba/) or one that has weakened consonantal information and sounds more /a/-like). When this reduced auditory stimulus (or /<i>a</i>/) is dubbed with the visual /ba/, a visual influence will result in effectively ‘restoring’ the weakened auditory cues so that the stimulus is perceived as a /ba/. An oddball design in which participants are asked to detect the /<i>a</i>/ among a stream of more frequently occurring /ba/s while either a speaking face or face with no visual speech was used. In addition, the same paradigm was presented for a second contrast in which participants detected /pa/ among /ba/s, a contrast which should be unaltered by the presence of visual speech. Behavioral and some ERP findings reflect the expected phonemic restoration for the /ba/ vs. /<i>a</i>/ contrast; specifically, we observed reduced accuracy and P300 response in the presence of visual speech. Further, we report an unexpected finding of reduced accuracy and P300 response for both speech contrasts in the presence of visual speech, suggesting overall modulation of the auditory signal in the presence of visual speech. Consistent with this, we observed a mismatch negativity (MMN) effect for the /ba/ vs. /pa/ contrast only that was larger in absence of visual speech.We discuss the potential utility for this paradigm for listeners who cannot respond actively, such as infants and individuals with developmental disabilities.
DOI: 10.6084/m9.figshare.5394895
title: GENOMIC DIVERSITY AND POPULATION STRUCTURE OF THE MEXICAN AND SPANISH BOVINE LIDIA BREED

description: This dataset repository contains the files of the Lidia breed individuals used for the genomic analyses made out from SNP data. <br>
DOI: 10.6084/m9.figshare.5394925.v1
title: Electrophysiological Indices of Audiovisual Speech Perception: Beyond the McGurk Effect and Speech in Noise. Supplementary Material

description: Visual information on a talker’s face can influence what a listener hears. Commonly used approaches to study this include mismatched audiovisual stimuli (e.g., McGurk type stimuli) or visual speech in auditory noise. In this paper we discuss potential limitations of these approaches and introduce a novel visual phonemic restoration method. This method always presents the same visual stimulus (e.g., /ba/) dubbed with a matched auditory stimulus (/ba/) or one that has weakened consonantal information and sounds more /a/-like). When this reduced auditory stimulus (or /<i>a</i>/) is dubbed with the visual /ba/, a visual influence will result in effectively ‘restoring’ the weakened auditory cues so that the stimulus is perceived as a /ba/. An oddball design in which participants are asked to detect the /<i>a</i>/ among a stream of more frequently occurring /ba/s while either a speaking face or face with no visual speech was used. In addition, the same paradigm was presented for a second contrast in which participants detected /pa/ among /ba/s, a contrast which should be unaltered by the presence of visual speech. Behavioral and some ERP findings reflect the expected phonemic restoration for the /ba/ vs. /<i>a</i>/ contrast; specifically, we observed reduced accuracy and P300 response in the presence of visual speech. Further, we report an unexpected finding of reduced accuracy and P300 response for both speech contrasts in the presence of visual speech, suggesting overall modulation of the auditory signal in the presence of visual speech. Consistent with this, we observed a mismatch negativity (MMN) effect for the /ba/ vs. /pa/ contrast only that was larger in absence of visual speech.We discuss the potential utility for this paradigm for listeners who cannot respond actively, such as infants and individuals with developmental disabilities.
DOI: 10.6084/m9.figshare.5394871
title: Computational design of Phe-Tyr dipeptide and preparation, characterization, cytotoxicity studies of Phe-Tyr dipeptide loaded PLGA nanoparticles for the treatment of hypertension

description: Phe-Tyr dipeptide which was investigated in Wakame food with greatest ACE-inhibitory activity is used as a pharmaceutical drug for the treatment of hypertension, cardiovascular diseases, and diabetic nephropathy. To improve the bioavailability of Phe-Tyr, a delivery system based on poly (lactic-co-glycolic acid) (PLGA) nanoparticles loaded with Phe-Tyr (Phe-Tyr-PLGA NPs) for treating hypertension and cardiovascular diseases was prepared in this study. In the experiments, poly(lactic-co-glycolic acid) (PLGA) and Phe-Tyr dipeptide-loaded PLGA nanoparticles were prepared using the double emulsion (w/o/w) method. The characterizations of the nanoparticles were performed with a UV–vis spectrometer, the Zeta-sizer system, and FTIR spectrometer. The optimum size of the Phe-Tyr dipeptide-loaded PLGA nanoparticle was obtained with a 213.8 nm average particle size, and a 0.061 polydispersity index, −19.5 mV zeta potential, 34% of loaded and 90.09% of encapsulation efficiency. From TEM analysis, it was clearly seen that the dipeptide loaded nanoparticles had the spherical and non-aggregated morphology and Phe-Tyr dipeptide loaded-PLGA nanoparticles were obtained successfully. Cell toxicity of nanoparticles at different concentrations was assayed with XTT methods on L929 fibroblast cells. This study determined that the nanoparticles have low toxicity at lower concentration and toxicity augmented with increasing concentration of dipeptide. To analyze the effect of solvents on structure of Phe-Tyr, Molecular dynamics simulation was performed with GROMACS program and molecular orbital calculations were carried out to obtain structural and electronic properties of dipeptide. Moreover, molecular docking calculations were also employed to model and predict protein–drug interactions.
DOI: 10.6084/m9.figshare.5394865
title: 001_OTB1_Tow.xlsx

description: Recently the climate-abusing effects of exhaust gases from combustion processes have been increasingly focused. This is underlining the importance of improving the energy efficiency. Nowadays, fishing fleet is in most cases not efficient because of outdated technology. Maintaining an adequate level of energy efficiency requires a continuous monitoring of the energy profile of the vessel. Any causes of energy inefficiency can be identified, being able to act on them promptly and effectively. A proper system of energy use monitoring is therefore essential for maintaining high-energy efficiency. Once energy use has been related to each operating condition, fishers can minimize fuel use. Energy efficiency in fisheries can be investigated through Energy Audit, which allows obtaining an extensive energy profile of the fishing vessels monitored. Vessel Energy Audit assesses the energy consumption of each energy user (e.g. propulsion system, electric- and hydraulic-user). Energy audits have been conducted for fishing vessels, which lead to recommendations for improved efficiencies to solve present and possible future fuel cost increases.