cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12407735.v1
title: Antibiotic sensitivity data for the bacterial strain LMJ (Bacterium strain clone LIB091_C05_1243 variant 16S ribosomal RNA; GenBank Accession # MN633292.1).

description: The Excel data file, Data S1 LMJ.xlsx contain information about the means and standard deviations of the zones of inhibitions of the bacterial strain LMJ and <i>Chlamydomonas</i>, induced by 4 antibiotics. <br><br>The Excel data file, Data S2 LMJ.xlsx contain statistical analyses of the zones of inhibitions of the bacterial strain LMJ and <i>Chlamydomonas</i>, induced by 4 antibiotics. <br><br>Antibiotics used are: Penicillin, Chloramphenicol, Neomycin & Polymyxin B. Three biological replicates were used for the generation of the data. Two different doses of antibiotics were used: 50 and 100 micrograms of each antibiotic.
DOI: 10.6084/m9.figshare.12407732.v1
title: Journaling Dataset For Upload June 2020.sav

description: These data were collected from multiple classes regarding which themes covered during instruction most influenced their position on evolution.
DOI: 10.6084/m9.figshare.12407795.v1
title: Pereira_et.al_2020

description: Data set for Pereira et al. 2020
DOI: 10.6084/m9.figshare.12407696
title: Table S5 from Disruption of TFIIH activities generates a stress gene expression response and reveals possible new targets against cancer

description: Disruption of the enzymatic activities of the transcription factor TFIIH by the small molecules Triptolide (TPL) or THZ1 could be used against cancer. Here, we used the MCF10A-ErSrc oncogenesis model to compare the effect of TFIIH inhibitors between transformed cells and their progenitors. We report that tumour cells exhibited highly increased sensitivity to TPL or THZ1 and that the combination of both had a synergic effect. TPL affects the interaction between XPB and p52, causing a reduction in the levels of XPB, p52 and p8, but not other TFIIH subunits. RNA-Seq and RNAPII-ChIP-Seq experiments showed that although the levels of many transcripts were reduced, the levels of a significant number were increased after TPL treatment, with maintained or increased RNAPII promoter occupancy. A significant number of these genes encode for factors that have been related to tumour growth and metastasis, suggesting that transformed cells might rapidly develop resistance to TPL/THZ inhibitors. Some of these genes were also overexpressed in response to THZ1, which depletion enhances the toxicity of TPL and are possible new targets against cancer.
DOI: 10.6084/m9.figshare.12407696.v1
title: Table S5 from Disruption of TFIIH activities generates a stress gene expression response and reveals possible new targets against cancer

description: Disruption of the enzymatic activities of the transcription factor TFIIH by the small molecules Triptolide (TPL) or THZ1 could be used against cancer. Here, we used the MCF10A-ErSrc oncogenesis model to compare the effect of TFIIH inhibitors between transformed cells and their progenitors. We report that tumour cells exhibited highly increased sensitivity to TPL or THZ1 and that the combination of both had a synergic effect. TPL affects the interaction between XPB and p52, causing a reduction in the levels of XPB, p52 and p8, but not other TFIIH subunits. RNA-Seq and RNAPII-ChIP-Seq experiments showed that although the levels of many transcripts were reduced, the levels of a significant number were increased after TPL treatment, with maintained or increased RNAPII promoter occupancy. A significant number of these genes encode for factors that have been related to tumour growth and metastasis, suggesting that transformed cells might rapidly develop resistance to TPL/THZ inhibitors. Some of these genes were also overexpressed in response to THZ1, which depletion enhances the toxicity of TPL and are possible new targets against cancer.
DOI: 10.6084/m9.figshare.12407681
title: Table S3 from Disruption of TFIIH activities generates a stress gene expression response and reveals possible new targets against cancer

description: Disruption of the enzymatic activities of the transcription factor TFIIH by the small molecules Triptolide (TPL) or THZ1 could be used against cancer. Here, we used the MCF10A-ErSrc oncogenesis model to compare the effect of TFIIH inhibitors between transformed cells and their progenitors. We report that tumour cells exhibited highly increased sensitivity to TPL or THZ1 and that the combination of both had a synergic effect. TPL affects the interaction between XPB and p52, causing a reduction in the levels of XPB, p52 and p8, but not other TFIIH subunits. RNA-Seq and RNAPII-ChIP-Seq experiments showed that although the levels of many transcripts were reduced, the levels of a significant number were increased after TPL treatment, with maintained or increased RNAPII promoter occupancy. A significant number of these genes encode for factors that have been related to tumour growth and metastasis, suggesting that transformed cells might rapidly develop resistance to TPL/THZ inhibitors. Some of these genes were also overexpressed in response to THZ1, which depletion enhances the toxicity of TPL and are possible new targets against cancer.
DOI: 10.6084/m9.figshare.12407684
title: Table S1 from Disruption of TFIIH activities generates a stress gene expression response and reveals possible new targets against cancer

description: Disruption of the enzymatic activities of the transcription factor TFIIH by the small molecules Triptolide (TPL) or THZ1 could be used against cancer. Here, we used the MCF10A-ErSrc oncogenesis model to compare the effect of TFIIH inhibitors between transformed cells and their progenitors. We report that tumour cells exhibited highly increased sensitivity to TPL or THZ1 and that the combination of both had a synergic effect. TPL affects the interaction between XPB and p52, causing a reduction in the levels of XPB, p52 and p8, but not other TFIIH subunits. RNA-Seq and RNAPII-ChIP-Seq experiments showed that although the levels of many transcripts were reduced, the levels of a significant number were increased after TPL treatment, with maintained or increased RNAPII promoter occupancy. A significant number of these genes encode for factors that have been related to tumour growth and metastasis, suggesting that transformed cells might rapidly develop resistance to TPL/THZ inhibitors. Some of these genes were also overexpressed in response to THZ1, which depletion enhances the toxicity of TPL and are possible new targets against cancer.
DOI: 10.6084/m9.figshare.12407687
title: Table S2 from Disruption of TFIIH activities generates a stress gene expression response and reveals possible new targets against cancer

description: Disruption of the enzymatic activities of the transcription factor TFIIH by the small molecules Triptolide (TPL) or THZ1 could be used against cancer. Here, we used the MCF10A-ErSrc oncogenesis model to compare the effect of TFIIH inhibitors between transformed cells and their progenitors. We report that tumour cells exhibited highly increased sensitivity to TPL or THZ1 and that the combination of both had a synergic effect. TPL affects the interaction between XPB and p52, causing a reduction in the levels of XPB, p52 and p8, but not other TFIIH subunits. RNA-Seq and RNAPII-ChIP-Seq experiments showed that although the levels of many transcripts were reduced, the levels of a significant number were increased after TPL treatment, with maintained or increased RNAPII promoter occupancy. A significant number of these genes encode for factors that have been related to tumour growth and metastasis, suggesting that transformed cells might rapidly develop resistance to TPL/THZ inhibitors. Some of these genes were also overexpressed in response to THZ1, which depletion enhances the toxicity of TPL and are possible new targets against cancer.
DOI: 10.6084/m9.figshare.12407690
title: Table S4 from Disruption of TFIIH activities generates a stress gene expression response and reveals possible new targets against cancer

description: Disruption of the enzymatic activities of the transcription factor TFIIH by the small molecules Triptolide (TPL) or THZ1 could be used against cancer. Here, we used the MCF10A-ErSrc oncogenesis model to compare the effect of TFIIH inhibitors between transformed cells and their progenitors. We report that tumour cells exhibited highly increased sensitivity to TPL or THZ1 and that the combination of both had a synergic effect. TPL affects the interaction between XPB and p52, causing a reduction in the levels of XPB, p52 and p8, but not other TFIIH subunits. RNA-Seq and RNAPII-ChIP-Seq experiments showed that although the levels of many transcripts were reduced, the levels of a significant number were increased after TPL treatment, with maintained or increased RNAPII promoter occupancy. A significant number of these genes encode for factors that have been related to tumour growth and metastasis, suggesting that transformed cells might rapidly develop resistance to TPL/THZ inhibitors. Some of these genes were also overexpressed in response to THZ1, which depletion enhances the toxicity of TPL and are possible new targets against cancer.
DOI: 10.6084/m9.figshare.12407687.v1
title: Table S2 from Disruption of TFIIH activities generates a stress gene expression response and reveals possible new targets against cancer

description: Disruption of the enzymatic activities of the transcription factor TFIIH by the small molecules Triptolide (TPL) or THZ1 could be used against cancer. Here, we used the MCF10A-ErSrc oncogenesis model to compare the effect of TFIIH inhibitors between transformed cells and their progenitors. We report that tumour cells exhibited highly increased sensitivity to TPL or THZ1 and that the combination of both had a synergic effect. TPL affects the interaction between XPB and p52, causing a reduction in the levels of XPB, p52 and p8, but not other TFIIH subunits. RNA-Seq and RNAPII-ChIP-Seq experiments showed that although the levels of many transcripts were reduced, the levels of a significant number were increased after TPL treatment, with maintained or increased RNAPII promoter occupancy. A significant number of these genes encode for factors that have been related to tumour growth and metastasis, suggesting that transformed cells might rapidly develop resistance to TPL/THZ inhibitors. Some of these genes were also overexpressed in response to THZ1, which depletion enhances the toxicity of TPL and are possible new targets against cancer.
DOI: 10.6084/m9.figshare.12407690.v1
title: Table S4 from Disruption of TFIIH activities generates a stress gene expression response and reveals possible new targets against cancer

description: Disruption of the enzymatic activities of the transcription factor TFIIH by the small molecules Triptolide (TPL) or THZ1 could be used against cancer. Here, we used the MCF10A-ErSrc oncogenesis model to compare the effect of TFIIH inhibitors between transformed cells and their progenitors. We report that tumour cells exhibited highly increased sensitivity to TPL or THZ1 and that the combination of both had a synergic effect. TPL affects the interaction between XPB and p52, causing a reduction in the levels of XPB, p52 and p8, but not other TFIIH subunits. RNA-Seq and RNAPII-ChIP-Seq experiments showed that although the levels of many transcripts were reduced, the levels of a significant number were increased after TPL treatment, with maintained or increased RNAPII promoter occupancy. A significant number of these genes encode for factors that have been related to tumour growth and metastasis, suggesting that transformed cells might rapidly develop resistance to TPL/THZ inhibitors. Some of these genes were also overexpressed in response to THZ1, which depletion enhances the toxicity of TPL and are possible new targets against cancer.
DOI: 10.6084/m9.figshare.12407684.v1
title: Table S1 from Disruption of TFIIH activities generates a stress gene expression response and reveals possible new targets against cancer

description: Disruption of the enzymatic activities of the transcription factor TFIIH by the small molecules Triptolide (TPL) or THZ1 could be used against cancer. Here, we used the MCF10A-ErSrc oncogenesis model to compare the effect of TFIIH inhibitors between transformed cells and their progenitors. We report that tumour cells exhibited highly increased sensitivity to TPL or THZ1 and that the combination of both had a synergic effect. TPL affects the interaction between XPB and p52, causing a reduction in the levels of XPB, p52 and p8, but not other TFIIH subunits. RNA-Seq and RNAPII-ChIP-Seq experiments showed that although the levels of many transcripts were reduced, the levels of a significant number were increased after TPL treatment, with maintained or increased RNAPII promoter occupancy. A significant number of these genes encode for factors that have been related to tumour growth and metastasis, suggesting that transformed cells might rapidly develop resistance to TPL/THZ inhibitors. Some of these genes were also overexpressed in response to THZ1, which depletion enhances the toxicity of TPL and are possible new targets against cancer.
DOI: 10.5522/04/12407567
title: Digitized Thin Blood Films for Sickle Cell Disease Detection

description: If you plan on using this dataset, please cite : P. Manescu, C. Bendkowski, R. Claveau, M. Elmi, B.J. Brown, V. Pawar, M. Shaw and D. Fernandez-Reyes, <b>A weakly supervised deep learning approach for detecting malaria and sickle cells in blood films </b>, MICCAI (2020). <br><b> Image acquistion</b>Images were captured with custom built brightfield microscope fitted with a 100X/1.4NA objective lens, a motorized x-y sample positioning stage and a color camera.z-stacks were projected onto a single (xy) plane using a wavelet-based Extended Depth of Field (EDoF) algorithm.<br><b>Clinical diagnosis</b>Hemoglobin electrophoresis was used to obtain the haemoglobin phenotype and test patients for Sickle Cell Disease (SCD). sickle_slides_new_march.txt contains the corresponding labels. <br><br><b>Ethical Statement. <br></b>The internationally recognized ethics committee at the Institute for Advanced Medical Research and Training (IAMRAT) of the College of Medicine, University of Ibadan (COMUI) approved this research with permit numbers: UI/EC/10/0130, UI/EC/19/0110. Parents and/or guardians of study participants gave informed written consent in accordance with the World Medical Association ethical principles for research involving human subjects.<br><br><br>
DOI: 10.6084/m9.figshare.12407360
title: analyticdata_deathsMA3.xlsx

description: The data used in this study is from https://health.hydra.africa/. The data consists of daily reported COVID-19 deaths in South Africa for the period 27 March 2020 to 20 May 2020. The data was used in the paper " Statistical distribution fitting to the number of COVID-19 deaths in South Africa" which is still under review and is posted on: https://doi.org/10.13140/RG.2.2.25635.27682<br>
DOI: 10.6084/m9.figshare.12407360.v1
title: analyticdata_deathsMA3.xlsx

description: The data used in this study is from https://health.hydra.africa/. The data consists of daily reported COVID-19 deaths in South Africa for the period 27 March 2020 to 20 May 2020. The data was used in the paper " Statistical distribution fitting to the number of COVID-19 deaths in South Africa" which is still under review and is posted on: https://doi.org/10.13140/RG.2.2.25635.27682<br>
DOI: 10.6084/m9.figshare.12407066
title: Domain Affinity Scores

description: Over the years, several methods have been proposed for the computational PPI prediction with different performance evaluation strategies. While attempting to benchmark performance scores, most of these methods often suffer with ill-treated cross-validation strategies, adhoc selection of positive/negative samples etc. To address these issues, in our proposed multi-level feature based PPI prediction approach <i>JUPPI</i>, using sequence, domain and GO information as features, a refined evaluation strategy has been introduced. During the evaluation process, we first extract high quality negative data using three-stage filtering, and then introduce a pair-input based cross validation strategy with three difficulty levels for test-set predictions. Our proposed evaluation strategy reduces the component-level overlapping issue in test sets. Performance of <i>JUPPI</i> is compared with those of the <i>state-of-the-art</i> approaches in this domain and tested on six independent PPI datasets. In almost all the datasets, <i>JUPPI</i> outperforms the <i>state-of-the-art</i> not only at human proteome level for PPI prediction, but also for prediction of interactors for intrinsic disordered human proteins.
DOI: 10.6084/m9.figshare.12407069
title: GO Annotations

description: Over the years, several methods have been proposed for the computational PPI prediction with different performance evaluation strategies. While attempting to benchmark performance scores, most of these methods often suffer with ill-treated cross-validation strategies, adhoc selection of positive/negative samples etc. To address these issues, in our proposed multi-level feature based PPI prediction approach <i>JUPPI</i>, using sequence, domain and GO information as features, a refined evaluation strategy has been introduced. During the evaluation process, we first extract high quality negative data using three-stage filtering, and then introduce a pair-input based cross validation strategy with three difficulty levels for test-set predictions. Our proposed evaluation strategy reduces the component-level overlapping issue in test sets. Performance of <i>JUPPI</i> is compared with those of the <i>state-of-the-art</i> approaches in this domain and tested on six independent PPI datasets. In almost all the datasets, <i>JUPPI</i> outperforms the <i>state-of-the-art</i> not only at human proteome level for PPI prediction, but also for prediction of interactors for intrinsic disordered human proteins.
DOI: 10.6084/m9.figshare.12404492
title: Instructiontousage.sav

description: This is the dataset for the article "Impacts of Library Instruction on Material Circulation and Database usage at a Small Midwest Community College," submitted to College and Undergraduate Libraries.
DOI: 10.6084/m9.figshare.12404492.v1
title: Instructiontousage.sav

description: This is the dataset for the article "Impacts of Library Instruction on Material Circulation and Database usage at a Small Midwest Community College," submitted to College and Undergraduate Libraries.
DOI: 10.6084/m9.figshare.12405014
title: Lyons et al. - Vegetation data

description: Raw data belongs to 'Simulate climate warming increases plant community heterogeneity in two types of central Canadian boreal peatlands.' Journal of Vegetation Science, 2020, Lyons, Branfireun, McLaughlin, and Lindo.
DOI: 10.6084/m9.figshare.12405014.v1
title: Lyons et al. - Vegetation data

description: Raw data belongs to 'Simulate climate warming increases plant community heterogeneity in two types of central Canadian boreal peatlands.' Journal of Vegetation Science, 2020, Lyons, Branfireun, McLaughlin, and Lindo.
DOI: 10.6084/m9.figshare.12407069.v1
title: GO Annotations

description: Over the years, several methods have been proposed for the computational PPI prediction with different performance evaluation strategies. While attempting to benchmark performance scores, most of these methods often suffer with ill-treated cross-validation strategies, adhoc selection of positive/negative samples etc. To address these issues, in our proposed multi-level feature based PPI prediction approach <i>JUPPI</i>, using sequence, domain and GO information as features, a refined evaluation strategy has been introduced. During the evaluation process, we first extract high quality negative data using three-stage filtering, and then introduce a pair-input based cross validation strategy with three difficulty levels for test-set predictions. Our proposed evaluation strategy reduces the component-level overlapping issue in test sets. Performance of <i>JUPPI</i> is compared with those of the <i>state-of-the-art</i> approaches in this domain and tested on six independent PPI datasets. In almost all the datasets, <i>JUPPI</i> outperforms the <i>state-of-the-art</i> not only at human proteome level for PPI prediction, but also for prediction of interactors for intrinsic disordered human proteins.
DOI: 10.6084/m9.figshare.12404462
title: Native-invasive seed-light competition trials

description: <b>Purpose</b>To explore the importance of interactions, light limitations, and density in annual plant species in the San Joaquin Desert.<br><b>Dates</b>Trials from October to December 2018 under controlled, high-light conditions in greenhouse at York University.<br><b>Meta-data</b>pot label label on the pot<br>census census number<br>calendar date DD/MM/YY<br>rep replicate<br>density planted number of seeds of native species (Plantago insularis, Phacelia tanacetifolia, and Salvia columbariae planted in the pot (additive study/with replacement)<br>light treatment factor Light as a factor at 2 levels: ambient light or shaded (to replicate shrub canopy) conditions brome treatment factor Exotic brome density as a factor at 2 levels: low Bromus madritensis (density of 5 per pot) and high Bromus madritensis (density of 10 per pot)<br>brome The number of germinated individuals of Bromus madritensis in the pot<br>morphometric metrics list mean values per pot per species<br>biomass for each species after drying for 48hrs at 67F<br>light measured between noon and 1pm using a Licor LI-250A light meter with a LI-190R quantum sensor in µmol of photons m-2 s-1.
DOI: 10.6084/m9.figshare.12404480
title: Regularized Optimal Transport of Covariates and Outcomes in Data Recoding

description: When databases are constructed from heterogeneous sources, it is not unusual that different encodings are used for the same outcome. In such case, it is necessary to recode the outcome variable before merging two databases. The method proposed for the recoding is an application of optimal transportation where we search for a bijective mapping between the distributions of such variable in two databases. In this article, we build upon the work by Garés et al., where they transport the distributions of categorical outcomes assuming that they are distributed equally in the two databases. Here, we extend the scope of the model to treat all the situations where the covariates explain the outcomes similarly in the two databases. In particular, we do not require that the outcomes be distributed equally. For this, we propose a model where joint distributions of outcomes and covariates are transported. We also propose to enrich the model by relaxing the constraints on marginal distributions and adding an <i>L</i><sup>1</sup> regularization term. The performances of the models are evaluated in a simulation study, and they are applied to a real dataset. The code used in the computational assessment and in the simulation of test cases is publicly available on Github repository: https://github.com/otrecoding/OTRecod.jl.
DOI: 10.6084/m9.figshare.12404432
title: RRaw Questionnaire Raw Data.xlsx

description: Questionnaire results presented to current dog owners or caregivers to ascertain their perspectives and opinions around feeding raw meat based diets to their canine pets. The questionnaire was formatted in Google forms and distributed via Facebook. Approval was sought and granted by University of Glasgow College of Medical, Veterinary & Life Sciences Ethics Committee for Non-Clinical Research Involving Human Participants.