cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/fyp26zjgmj
title: Immunogenicity of standard and extended dosing intervals of BNT162b2 mRNA vaccine. Payne et al.

description: Overview

Extension of the interval between vaccine doses for the BNT162b2 mRNA vaccine was introduced in the UK to accelerate 
population coverage with a single dose. At this time, trial data was lacking, and we addressed this in a study of UK 
healthcare workers. We aimed to describe the dynamics of T cell and Ab responses after the first dose of BNT162b2 mRNA
vaccine over an extended dosing interval, and to compare the magnitude of Ab and T cell responses 4 weeks after dose 2 
between short and long vaccination regimens. 

Human sample and metadata collection

HCWs were recruited into the PITCH study at NHS hospitals in five centres in England. All participants received the BNT162b2 
Pfizer/BioNTech vaccine at either the "short" dosing interval (3-5 weeks) or "long" dosing interval (6-14 weeks). Peripheral blood was
collected and peripheral blood mononuclear cells (PBMCs) and plasma were stored by cryopreservation at -140 oC and -80 oC 
respectively. Participants were identified as those with samples collected at timepoints of interest (n=589 participants). 

Long dosing interval accepted timepoints included;
- baseline (anytime prior to first dose of vaccine)
- 28 days after first vaccine dose (+/- 7 days)
- 70 days after first vaccine dose (minimum accepted 40 days. IQR 62/75, range 41 - 129 days), 
- 28 days after the second vaccine dose (+/- 7 days)
- 90 days after the second dose (+/- 7 days)

Short dosing interval accepted timepoints included; 
- baseline (anytime prior to first dose of vaccine)
- 7 days after second dose (+ 7days)
- 28 days after the second vaccine dose (+/- 7 days)
- 90 days after the second dose.

Clinical metadata collected included BNT162b2 immunisation dates, date of any prior SARS-CoV-2 infection defined by a positive 
PCR test and/or detection of antibodies to spike or nucleocapsid protein, presence or absence of symptoms, time between
symptom onset and sampling, age, gender and ethnicity of participant. Other metadata included location of study centre. 
De-identified limited metadata are available here. Options to explore detailed metadata can be sought by contacting the lead author
(Paul Klenerman).

Data collection

Serology and Cellular data were collected from assays using plasma and PBMCs respectively.
Serology:
MSD and ACE2 assay - Two wells run per test; 1:1000 and 1:10,000 dilution
Neutralizing Ab          - Serial dilutions were run per test to calculate reduction in number of infected foci - FRNT50

Cellular:
ELISpot                       - Two or three wells run per test ; mean is shown with background subtraction. Total Spike is calculated by 
                                      adding data from Spike 1 and Spike2
ICS                              - One run per test compared to positive and negative controls.


Results
These data on dynamic cellular and humoral responses indicate that extension of the dosing interval is an effective, immunogenic protocol
DOI: 10.6084/m9.figshare.21174397.v2
title: Phylogenetic reconstructions of Micromonas commoda RCC299 light stress response proteins from the manuscript "Phosphate limitation responses in marine green algae are linked to reprogramming of the tRNA epitranscriptome and codon usage bias"

description: Phylogenetic reconstructions of Micromonas commoda RCC299 light stress response proteins in nexus (*.tre) and pdf format (*.pdf), corresponding to Fig. 4, Fig. S5 and Dataset S3 in the manuscript "Phosphate limitation responses in marine green algae are linked to reprogramming of the tRNA epitranscriptome and codon usage bias". Trees were inferred using IQ-TREE, using the best LG model identified for each alignment separately, node support was calculated using 1000 ultrafast bootstrap replicates. Filenames for phylogenies contain, in that order, the <i>Micromonas commoda</i> RCC299 protein ID(s), the name of the gene(s) as described in the manuscript and the model used for tree reconstruction.
DOI: 10.6084/m9.figshare.21632357.v1
title: Video Data Analysis and Police Body-Worn Footage: Table 1 through 5

description: This includes an SPSS command file (.sps) that will execute, with comments, a series of descriptive statistics against the data file (.sav) that correspond to tables 1-5 in the manuscript *McCluskey, John and Craig Uchida (2023) "Video Data Analysis and Police Body-Worn Camera Footage" Sociological Methods and Research. The data are based on observers' assessments of BWC audio and video channels of LAPD officers' footage from encounters and events. <br> The syntax file should be run against the .sav file in the archive. The syntax is saved in the .txt file and should offer a guidance in how the results might be obtained in Excel or another program such as R or STATA using the CSV file stored here. <br>
DOI: 10.6084/m9.figshare.7695554.v2
title: Comparing Machine Learning and Heuristic Approaches for Metric-Based Code Smell Detection

description: Code smells represent poor implementation choices applied by developers when enhancing source code. Their negative impact on source code maintainability and comprehensibility has been widely shown in the past and several techniques to automatically detect them have been devised. Most of these techniques are based on heuristics, namely they compute a set of code metrics and combine them by creating detection rules; while they have a reasonable accuracy, a recent trend is represented by the use of machine learning where code metrics are used as predictors of the smelliness of code artifacts. Despite the recent advances in the field, there is still a noticeable lack of knowledge of whether machine learning can actually be more accurate than traditional heuristic-based approaches. To fill this gap, in this paper we propose a large-scale study to empirically compare the performance of heuristic-based and machine-learning-based techniques for metric-based code smell detection. We consider six code smell types and compare machine learning models with Decor, a state-of-the-art heuristic-based approach. Key findings emphasise the need of further research aimed at improving the effectiveness of machine learning to code smell detection. Indeed, on the one hand​, machine-learning-based-techniques generally achieve better performance without requiring any threshold definitions, while on the other hand for some specific code smell types sometimes the training data are not enough to make the models able to discriminate the smelliness of code components.
DOI: 10.17632/vjzrrzm5wm
title: Bearing 6213 OR Dataset

description: Vibration of rolling ball bearings under various speed conditions. For detailed explaination, please, see *.docx.
DOI: 10.6084/m9.figshare.13489929.v1
title: Data S12-16

description: EEG Data
DOI: 10.6084/m9.figshare.26704182.v1
title: Additional file 5 of Psychometric evaluation of the near activity visual questionnaire presbyopia (NAVQ-P) and additional patient-reported outcome items

description: Supplementary Material 5
DOI: 10.6084/m9.figshare.28208555.v1
title: County-level monthly CO2 emissions

description: County-level monthly CO2 emissions
DOI: 10.6084/m9.figshare.12469118.v1
title: Student_Availability_2020.xlsx

description: Students submitted their availability to me and I compiled them into this spreadsheet.
DOI: 10.6084/m9.figshare.28087799.v1
title: 20-90 Ach Sweating(repository).xlsx

description: Original dataset for the study entitled "Biological aging and sex differences in cholinergic sweating: From young adults to the elderly in their 80s and beyond".
DOI: 10.6084/m9.figshare.28091654.v1
title: code & data for GeoEvo

description: The code and data for manuscript Geographic evolutionary multi-task optimization framework for automated hyperparameters tuning on spatially stratified machine learning models.
DOI: 10.6084/m9.figshare.25288210.v1
title: Attitudinally-positioned European sample dataset

description: These files provide a dataset of attitudinally positioned populations of social media users in Europe. Building on recent advancements on large-scale multi-dimensional political attitude inference in social networks and text, we show how to create a European sample of attitudinally-positioned users along a Left-Right and a Anti-elite dimension measuring attitudes towards elites and trust in institutions. These two dimensions are shown to be relevant to conduct both traditional political analysis on social media and analyses accounting for new forms of polarization related to democratic backsliding. This dataset of users will serve as a frame of reference for the development of case studies exploring different links between activity in online platforms, evidence and impacts in politics in other tasks of the project.
DOI: 10.6084/m9.figshare.17304221.v3
title: Solar and wind power data from the Chinese State Grid Renewable Energy Generation Forecasting Competition

description: Two years (2019, 2020) on-site data with time granularity of 15 minutes of six wind farms and eight solar stations in China was recorded, which includes weather conditions and power generation information.
DOI: 10.6084/m9.figshare.3522281.v1
title: Appendix A. Rank correlation (Kendall's Tau) matrix of annual sound seed production.

description: Rank correlation (Kendall's Tau) matrix of annual sound seed production.
DOI: 10.6084/m9.figshare.24866091.v1
title: pretrained_models_and_data.zip

description: Stakeholders of machine learning models desire explainable artificial intelligence (XAI) to produce human-understandable and consistent interpretations. In computational toxicity, augmentation of text-based molecular representations has been used successfully for transfer learning on downstream tasks. Augmentations of molecular representations can also be used at inference to compare differences between multiple representations of the same ground-truth.In this study, we investigate the robustness of eight XAI methods using test-time augmentation for a molecular-representation model in the field of computational toxicity prediction.We report significant differences between explanations for different representations of the same ground-truth, and show that randomized models have similar variance. We hypothesize that text-based molecular representations in this and past research reflect tokenization more than learned parameters. Furthermore, we see a greater variance between in-domain predictions than out-of-domain predictions, indicating XAI measures something other than learned parameters. Finally, we investigate the relative importance given to expert-derived structural alerts and find similar importance given irregardless of applicability domain, randomization and varying training procedures. We therefore caution future research to validate their methods using a similar comparison to human intuition without further investigation.
DOI: 10.17632/vk7r3r7bz8
title: SINGINT: Automatic numerical integration of singular integrands

description: Abstract We explore the combination of deterministic and Monte Carlo methods to facilitate efficient automatic numerical computation of multidimensional integrals with singular integrands. Two adaptive algorithms are presented that employ recursion and are runtime and memory optimized, respectively. SINGINT, a C implementation of the algorithms, is introduced and its utilization in the calculation of particle scattering amplitudes is exemplified. Title of program: SINGINT Catalogue Id: ADRQ_v1_0 Nature of problem Efficient, robust and automatic numerical computation of multidimensional integrals with singular integrands, for example occurring in the calculation of particle scattering amplitudes in perturbative field theory. Versions of this program held in the CPC repository in Mendeley Data ADRQ_v1_0; SINGINT; 10.1016/S0010-4655(03)00160-7 This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2019)
DOI: 10.17632/zkjdv33xnm
title: Incidence of dermatofibrosarcoma protuberans stratified by age group, sex, and race

description: Supplementary figure 2: Incidence of dermatofibrosarcoma protuberans stratified by age group, sex, and race.
DOI: 10.6084/m9.figshare.27984770.v1
title: The first de novo genome assembly and annotation of a green-blooded skink (Prasinohaema aff. flavipes)

description: The scincid genus <i>Prasinohaema</i> represents the only group of amniotes to possess green blood, resulting from the accumulation of the bile pigment biliverdin. Recent phylogenetic analyses have shown <i>Prasinohaema</i> to be polyphyletic with 4 independent origins for green blood. It is unknown why this trait has evolved in multiple instances and how <i>Prasinohaema</i> species are able to tolerate such high concentrations of a cytotoxic bile pigment. Here, we report the first de novo genome assembly and annotation for a green blooded skink, <i>Prasinohaema aff. flavipes</i>, which was sequenced from an ethanol preserved specimen that was collected more than 20 years ago. Our assembly comprises 907 contigs spanning 1.52 Gbp with contig N50 of 3.2 Mbp. The genome is highly complete, with a BUSCO completeness score of 97.76%, and will be a valuable source in examining the key genes, regulatory mechanisms, and functional mutations involved in the elevated biliverdin levels.
DOI: 10.17632/32w7fw9ysm
title: FCwx.csv

description: Weather data from Fort Collins, Colorado, U.S.A. from 1900 to 1999. Source: Katz, R. W., Parlange, M. B. and Naveau, P. (2002) Statistics of extremes in hydrology. Advances in Water Resources, 25, 1287–1304. Data frame with components: Year: integer years from 1900 to 1999, Mn: integer months from 1 to 12, Dy: integer days of the month (i.e., from 1 to 28, 29, 30 or 31 depending on the month/year), MxT: integer valued daily maximum temperature (degrees Fahrenheit), MnT: integer valued daily minimum temperature (degrees Fahrenheit), Prec: numeric giving the daily accumulated precipitation (inches), Snow: numeric daily accumulated snow amount, SnCv: numeric daily snow cover amount
DOI: 10.6084/m9.figshare.23501529.v1
title: Annotation of two barley genome

description: Annotation files of high-quality genome sequencing and assembly of 2 wild barley from Evolutionary Canyon
DOI: 10.6084/m9.figshare.1538644.v1
title: Brazilian Fungi Database

description: This database is supplementary material of the article "Diversity of Brazilian Fungi" published in the Journal Rodriguésia in 2015 (DOI: 10.1590 / 2175-7860201566407).
DOI: 10.6084/m9.figshare.24910881.v2
title: Experiment 1: All d-MPs found by the presented algorithm for the large network from Fig. 5

description: The 'Ex_3_Kd.csv' file contains the results of the numerical experiments described in Section 4.1. Experiment 1.Experiment 1: All d-MPs found by the presented algorithm for the large network from Fig. 5
DOI: 10.6084/m9.figshare.28779272.v1
title: Supplementary materials for the paper "Analysis of macrozoobenthic species associations in the Eastern European Plain under changing climatic zone conditions" by Golovatyuk L.V., Seleznev D.G. and Kurina E.M.

description: The Initial datasets, river parameters and analysis results for the paper "Analysis of macrozoobenthic species associations in the Eastern European Plain under changing climatic zone conditions" by Golovatyuk L.V., Seleznev D.G. and Kurina E.M.Table 1 - Hydrographic characteristics of the studied small rivers;Table 2 - Meteorological and geomorphological indicators of the sampling stations;Table 3 - Species occurrence;Table 4 - PermANOVA analysis results.
DOI: 10.6084/m9.figshare.29039882.v1
title: Supplemental Data for: Bed Shear Stress Modelling for Experimental Flash Floods using Dimensional Analysis

description: Table S1: Data used for calibration for case (i) and case (ii).Table S2: Data used for validation for case (i), case (ii) and comparison with uniform flow model.
DOI: 10.6084/m9.figshare.3181495.v3
title: Academic Identity: An Overview

description: The article describe about the academic identity and its important in the scholarly communication
DOI: 10.6084/m9.figshare.25012616.v3
title: Date : HRV horses during transport

description: Date : HRV horses during transport ATF; Air-conditioned truck with a full loadATS; Air-conditioned truck with a space loadN-ATF; non-air-conditioned truck with a full loadN-ATS; non-air-conditioned truck with a space load
DOI: 10.6084/m9.figshare.28853453.v1
title: <b>Blended Learning as a Novel Teaching Learning Activity: Student Perceptions, Engagement, and Performance Outcomes- data collected via the LMS and data collected through a google form </b>

description: <b>Blended Learning as a Novel Teaching Learning Activity: Student Perceptions, Engagement, and Performance Outcomes</b>- this contain data collected via a google form circulate through the students and data collected via the LMS
DOI: 10.4121/18996992.v1
title: Simulation files of PhD dissertation 'Molecular Simulation of Deep Eutectic Solvents'

description: The files here correspond to simulations performed for the PhD dissertation 'Molecular Simulation of Deep Eutectic Solvents'. For each chapter of the dissertation, the simulation input and output files of a single system are provided. Within each simulation folder, a README.txt file exists, in which the details of the simulation and the files are explained.
DOI: 10.6084/m9.figshare.14193761.v3
title: Atlantic salmon stocks_Baltic Sea_39Stocks_BMM.xlsx

description: Atlantic salmon genetic data for 39 river stocks in the Baltic Sea and 18 characters used in Bayesian mixture modeling. Characters include smolt age class and 17 genetic loci.
DOI: 10.6084/m9.figshare.8030762.v1
title: Amino-acid Sequences of HMM Hits

description: Amino-acid sequences matching HMM search across samples.<br>Supplementary file for publication:Lavy et. al., (2019) Microbial communities across a hillslope-riparian transect shaped by proximity to the stream, groundwater table, and weathered bedrock
DOI: 10.17605/osf.io/3tm8p
title: Adaptation and Validation of the Modified Weight Bias Internalization Scale (WBIS-M) in Brazilian Adults
DOI: 10.17632/63t5c7xb4c
title: SARS-CoV-2 GISAID isolates (2020-06-17) genotyping VCF

description: VCF file containing filtered mutated sites in SARS-CoV-2 genomes obtained from GISAID EpiCoV, separated by individual mutations. The columns correspond to viral genome accession ID, nucleotide position in the genome, mutation ID (left blank in all rows), reference nucleotide, identified mutation, quality, filter, and information columns (all left blank), format (GT in all rows), column corresponding to reference genome (all 0, referring to reference nucleotide column), and columns corresponding to isolate genomes, with each row identifying the nucleotide in the POS column, and whether it is non-mutant (0), or the mutant indicated in the identified mutation column (1). The file is tab delimited, with 22546 rows including the names, and 30690 columns. The file was generated to test the hypothesis whether the five most common mutations in the SARS-CoV-2 genome replication complex proteins, nsps 7, 8, 12, and 14, significantly affect the mutation density of the virus over time and whether these affect the synonymous and nonsynonymous mutation densities differently. We discovered that mutations in nsp14, an exonuclease with error correcting capabilities, are most likely to be correlated with increased mutational load across the genome compared to wildtype SARS-CoV-2. These results were obtained by identifying the frequency of mutations across all isolates in genomic regions of interest, analyzing which of the twenty mutations (five per nsp) have a statistically meaningful relationship with the mutation density in the M and E genes (chosen due to being under little selective pressure), and identifying the synonymous and nonsynonymous genomic SNV density for isolates with any of the statistically meaningful mutations, as well as isolates with none of the identified mutations.
DOI: 10.17632/j4yr5fmhv4
title: Brushless DC Motor sound dataset for PdM

description: This dataset contains 43 .wav files of approximately 10 seconds each, with a 16 kHz sampling frequency containing the sound of four A2212 BLDC motors submitted to different categories: healthy motors, propeller failure and bearing failure. These audio files may be useful for signal processing and ML applications in PdM
DOI: 10.6084/m9.figshare.25006589.v1
title: <b>A Machine Learning Dengue Dataset from an Endemic Region of Colombia</b>

description: This repository contains a folder with two datasets (original and preprocessed) of dengue data from Medellin, Colombia between 2008 and 2021. Additionally, it contains the R code project used for the preprocessing and generation of the plots.
DOI: 10.6084/m9.figshare.5123005.v1
title: Supplementary Material for: Anorexigenic and Orexigenic Hormone Modulation of Mammalian Target of Rapamycin Complex 1 Activity and the Regulation of Hypothalamic Agouti-Related Protein mRNA Expression

description: Activation of mammalian target of rapamycin 1 (mTORC1) by nutrients, insulin and leptin leads to appetite suppression (anorexia). Contrastingly, increased AMP-activated protein kinase (AMPK) activity by ghrelin promotes appetite (orexia). However, the interplay between these mechanisms remains poorly defined. The relationship between the anorexigenic hormones, insulin and leptin, and the orexigenic hormone, ghrelin, on mTORC1 signalling was examined using S6 kinase phosphorylation as a marker for changes in mTORC1 activity in mouse hypothalamic GT1-7 cells. Additionally, the contribution of AMPK and mTORC1 signalling in relation to insulin-, leptin- and ghrelin-driven alterations to mouse hypothalamic agouti-related protein (AgRP) mRNA levels was examined. Insulin and leptin increase mTORC1 activity in a phosphoinositide-3-kinase (PI3K)- and protein kinase B (PKB)-dependent manner, compared to vehicle controls, whereas increasing AMPK activity inhibits mTORC1 activity and blocks the actions of the anorexigenic hormones. Ghrelin mediates an AMPK-dependent decrease in mTORC1 activity and increases hypothalamic AgRP mRNA levels, the latter effect being prevented by insulin in an mTORC1-dependent manner. In conclusion, mTORC1 acts as an integration node in hypothalamic neurons for hormone-derived PI3K and AMPK signalling and mediates at least part of the assimilated output of anorexigenic and orexigenic hormone actions in the hypothalamus.
DOI: 10.6084/m9.figshare.14633430.v1
title: Plastid NDH pseudogenization and gene loss in a recently derived lineage from the largest hemiparasitic plant genus Pedicularis (Orobanchaceae)

description: Annotated plastome sequences for the paper published in Plant and Cell Physiology entitled "Plastid NDH pseudogenization and gene loss in a recently derived lineage from the largest hemiparasitic plant genus Pedicularis (Orobanchaceae) ".