cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.21253/dmu.9896036
title: Understanding enzyme dosing in AD

description: Dataset underpinning figure and tables of the article "Understanding enzyme dosing in anaerobic digestion". The spreadsheets contain raw data acquired from laboratory work and their manipulation. Biogas reading have been normalised to STD conditions. Volatile solids for long-term experiments have been measured at the start of the experiments only.
DOI: 10.21253/dmu.9896036.v1
title: Understanding enzyme dosing in AD

description: Dataset underpinning figure and tables of the article "Understanding enzyme dosing in anaerobic digestion". The spreadsheets contain raw data acquired from laboratory work and their manipulation. Biogas reading have been normalised to STD conditions. Volatile solids for long-term experiments have been measured at the start of the experiments only.
DOI: 10.6084/m9.figshare.9896009
title: Bacillus subtilis genome-wide transformation

description: This is the VCF dataset for whole genome transformation of Bacillus subtilis.
DOI: 10.6084/m9.figshare.9896009.v2
title: Bacillus subtilis genome-wide transformation

description: This is the VCF dataset for whole genome transformation of Bacillus subtilis.
DOI: 10.6084/m9.figshare.9896009.v1
title: Untitled Item

description: This is the VCF dataset for whole genome transformation of Bacillus subtilis.
DOI: 10.6084/m9.figshare.9895979
title: Improving (Q)SAR predictions by examining bias in the selection of compounds for experimental testing

description: Existing data on structures and biological activities are limited and distributed unevenly across distinct molecular targets and chemical compounds. The question arises if these data represent an unbiased sample of the general population of chemical-biological interactions. To answer this question, we analyzed ChEMBL data for 87,583 molecules tested against 919 protein targets using supervised and unsupervised approaches. Hierarchical clustering of the Murcko frameworks generated using Chemistry Development Toolkit showed that the available data form a big diffuse cloud without apparent structure. In contrast hereto, PASS-based classifiers allowed prediction whether the compound had been tested against the particular molecular target, despite whether it was active or not. Thus, one may conclude that the selection of chemical compounds for testing against specific targets is biased, probably due to the influence of prior knowledge. We assessed the possibility to improve (Q)SAR predictions using this fact: PASS prediction of the interaction with the particular target for compounds predicted as tested against the target has significantly higher accuracy than for those predicted as untested (average ROC AUC are about 0.87 and 0.75, respectively). Thus, considering the existing bias in the data of the training set may increase the performance of virtual screening.
DOI: 10.6084/m9.figshare.9895976
title: Blocking the FKBP12 induced dendrimeric burst in aberrant aggregation of α-synuclein by using the ElteN378 synthetic inhibitor

description: α-Synuclein (α-syn), a disordered cytoplasmatic protein, plays a fundamental role in the pathogenesis of Parkinson’s disease (PD). Here, we have shown, using photophysical measurements, that addition of FKBP12 to α-syn solutions, dramatically accelerates protein aggregation, leading to an explosion of dendritic structures revealed by fluorescence and phase-contrast microscopy. We have further demonstrated that this aberrant α-syn aggregation can be blocked using a recently discovered non-immunosuppressive synthetic inhibitor of FKBP12, ElteN378. The role of FKBP12 and of ElteN378 in the α-syn aggregation mechanism has been elucidated using molecular dynamics simulations based on an effective coarse-grained model. The reported data not only reveal a new potent synthetic drug as a candidate for early stage treatment of α-syn dependent neurodegenerations but also pave the way to a deeper understanding of the mechanism of action of FKBP12 on α-syn oligomeric aggregation, a topic which is still controversial.
DOI: 10.6084/m9.figshare.9895979.v1
title: Improving (Q)SAR predictions by examining bias in the selection of compounds for experimental testing

description: Existing data on structures and biological activities are limited and distributed unevenly across distinct molecular targets and chemical compounds. The question arises if these data represent an unbiased sample of the general population of chemical-biological interactions. To answer this question, we analyzed ChEMBL data for 87,583 molecules tested against 919 protein targets using supervised and unsupervised approaches. Hierarchical clustering of the Murcko frameworks generated using Chemistry Development Toolkit showed that the available data form a big diffuse cloud without apparent structure. In contrast hereto, PASS-based classifiers allowed prediction whether the compound had been tested against the particular molecular target, despite whether it was active or not. Thus, one may conclude that the selection of chemical compounds for testing against specific targets is biased, probably due to the influence of prior knowledge. We assessed the possibility to improve (Q)SAR predictions using this fact: PASS prediction of the interaction with the particular target for compounds predicted as tested against the target has significantly higher accuracy than for those predicted as untested (average ROC AUC are about 0.87 and 0.75, respectively). Thus, considering the existing bias in the data of the training set may increase the performance of virtual screening.
DOI: 10.6084/m9.figshare.9895976.v1
title: Blocking the FKBP12 induced dendrimeric burst in aberrant aggregation of α-synuclein by using the ElteN378 synthetic inhibitor

description: α-Synuclein (α-syn), a disordered cytoplasmatic protein, plays a fundamental role in the pathogenesis of Parkinson’s disease (PD). Here, we have shown, using photophysical measurements, that addition of FKBP12 to α-syn solutions, dramatically accelerates protein aggregation, leading to an explosion of dendritic structures revealed by fluorescence and phase-contrast microscopy. We have further demonstrated that this aberrant α-syn aggregation can be blocked using a recently discovered non-immunosuppressive synthetic inhibitor of FKBP12, ElteN378. The role of FKBP12 and of ElteN378 in the α-syn aggregation mechanism has been elucidated using molecular dynamics simulations based on an effective coarse-grained model. The reported data not only reveal a new potent synthetic drug as a candidate for early stage treatment of α-syn dependent neurodegenerations but also pave the way to a deeper understanding of the mechanism of action of FKBP12 on α-syn oligomeric aggregation, a topic which is still controversial.
DOI: 10.6084/m9.figshare.9895943
title: Fig 6 Strain Data

description: This file contains the averaged strain data measured radially from the apex of the LV for mice that underwent sham, 30 minutes ischemia-reperfusion, and permanent ligation surgery
DOI: 10.6084/m9.figshare.9895943.v1
title: Fig 6 Strain Data

description: This file contains the averaged strain data measured radially from the apex of the LV for mice that underwent sham, 30 minutes ischemia-reperfusion, and permanent ligation surgery
DOI: 10.6084/m9.figshare.9895742
title: Systematic review (meta-aggregation) of qualitative studies on the experiences of family members caring for individuals with early psychosis

description: Despite the importance of the role of caregivers of people with psychosis being widely recognized, comprehensive understanding of their experience is limited. A thorough understanding of the experience of caregivers over the journey of the illness, particularly during its early stages, is crucial. Qualitative studies published between 1 January 1949 and 31 January 2018 were obtained from seven databases based on PICo search strategy. Meta-aggregation methodology of the Joanna Briggs Institute (JBI) was adopted to aggregate existing qualitative findings about caregivers’ experiences. Twenty-eight qualitative studies on 635 caregivers and family members were included in the review. Six inter-related categories—‘stigma’, ‘help-seeking’, ‘service encounter’, ‘emotional challenges’, ‘on becoming a caregiver’ and ‘making sense of experience’—were aggregated from 129 themes from the sub-acute stage, the acute stage and the recovery or residual stage. Three statements about caregivers’ experiences of their relative’s first episode of psychosis were synthesized from the findings. Results highlighted the need of incorporating caregiver intervention into the existing services to support the emotional challenges, uncertainty, and stigma-related burden along the caregiving journey.
DOI: 10.6084/m9.figshare.9895715
title: HCMV seroprevalence, Blue Nile State, Sudan

description: This data contain information about seroprevalence of HCMV among aborted pregnant women in Blue Nile State, Sudan. permission was taken from Faculty of Medical Laboratory Sciences, University of Gezira, and Ministry of Health, Blue Nile State, Sudan. Laboratory analysis was performed by ELISA for IgG and IgM titre. <br>
DOI: 10.6084/m9.figshare.9895715.v1
title: HCMV seroprevalence, Blue Nile State, Sudan

description: This data contain information about seroprevalence of HCMV among aborted pregnant women in Blue Nile State, Sudan. permission was taken from Faculty of Medical Laboratory Sciences, University of Gezira, and Ministry of Health, Blue Nile State, Sudan. Laboratory analysis was performed by ELISA for IgG and IgM titre. <br>
DOI: 10.6084/m9.figshare.9895742.v2
title: Systematic review (meta-aggregation) of qualitative studies on the experiences of family members caring for individuals with early psychosis

description: Despite the importance of the role of caregivers of people with psychosis being widely recognized, comprehensive understanding of their experience is limited. A thorough understanding of the experience of caregivers over the journey of the illness, particularly during its early stages, is crucial. Qualitative studies published between 1 January 1949 and 31 January 2018 were obtained from seven databases based on PICo search strategy. Meta-aggregation methodology of the Joanna Briggs Institute (JBI) was adopted to aggregate existing qualitative findings about caregivers’ experiences. Twenty-eight qualitative studies on 635 caregivers and family members were included in the review. Six inter-related categories—‘stigma’, ‘help-seeking’, ‘service encounter’, ‘emotional challenges’, ‘on becoming a caregiver’ and ‘making sense of experience’—were aggregated from 129 themes from the sub-acute stage, the acute stage and the recovery or residual stage. Three statements about caregivers’ experiences of their relative’s first episode of psychosis were synthesized from the findings. Results highlighted the need of incorporating caregiver intervention into the existing services to support the emotional challenges, uncertainty, and stigma-related burden along the caregiving journey.
DOI: 10.6084/m9.figshare.9895742.v1
title: Systematic review (meta-aggregation) of qualitative studies on the experiences of family members caring for individuals with early psychosis

description: Despite the importance of the role of caregivers of people with psychosis being widely recognized, comprehensive understanding of their experience is limited. A thorough understanding of the experience of caregivers over the journey of the illness, particularly during its early stages, is crucial. Qualitative studies published between 1 January 1949 and 31 January 2018 were obtained from seven databases based on PICo search strategy. Meta-aggregation methodology of the Joanna Briggs Institute (JBI) was adopted to aggregate existing qualitative findings about caregivers’ experiences. Twenty-eight qualitative studies on 635 caregivers and family members were included in the review. Six inter-related categories—‘stigma’, ‘help-seeking’, ‘service encounter’, ‘emotional challenges’, ‘on becoming a caregiver’ and ‘making sense of experience’—were aggregated from 129 themes from the sub-acute stage, the acute stage and the recovery or residual stage. Three statements about caregivers’ experiences of their relative’s first episode of psychosis were synthesized from the findings. Results highlighted the need of incorporating caregiver intervention into the existing services to support the emotional challenges, uncertainty, and stigma-related burden along the caregiving journey.
DOI: 10.6084/m9.figshare.9895670
title: Hydrological linkages between different water resources from two contrasting ecosystems of western peninsular India: a stable isotope perspective

description: Water scarcity is a leading concern in both developing and developed nations. Coping with water scarcity requires an understanding of various hydrological processes that act upon precipitation, surface and groundwater at a local scale. We measured isotopic signatures of several water samples from two distinct ecosystems, i.e. tropical savanna in the West and the warm semi-arid region in the East lying across the Western Ghats mountain range, India, to understand the hydrological processes. The results show that the hydrogeological conditions strongly influence the isotopic characteristics of water of different resources, governed by different hydrological processes, even at close spatial scales. Based on the local evaporation lines of different water resources within a particular ecosystem, it is inferred that the water resources are well linked at one site, but have diverse connectivity at the other site. Further, the isotopic signatures of all the water resources are systematically affected by the monsoon precipitation. In addition, anomalously depleted isotopic signatures are observed during known hailstorm events. This may provide a means to trace their signature in the existing water resources.
DOI: 10.6084/m9.figshare.9895670.v1
title: Hydrological linkages between different water resources from two contrasting ecosystems of western peninsular India: a stable isotope perspective

description: Water scarcity is a leading concern in both developing and developed nations. Coping with water scarcity requires an understanding of various hydrological processes that act upon precipitation, surface and groundwater at a local scale. We measured isotopic signatures of several water samples from two distinct ecosystems, i.e. tropical savanna in the West and the warm semi-arid region in the East lying across the Western Ghats mountain range, India, to understand the hydrological processes. The results show that the hydrogeological conditions strongly influence the isotopic characteristics of water of different resources, governed by different hydrological processes, even at close spatial scales. Based on the local evaporation lines of different water resources within a particular ecosystem, it is inferred that the water resources are well linked at one site, but have diverse connectivity at the other site. Further, the isotopic signatures of all the water resources are systematically affected by the monsoon precipitation. In addition, anomalously depleted isotopic signatures are observed during known hailstorm events. This may provide a means to trace their signature in the existing water resources.
DOI: 10.6084/m9.figshare.9895490
title: Differentially regulated isoforms in iPSC d14 vs. d7 cardiomyocyte differentiation

description: Limma generated table for differential expression of protein isoform quantified between human induced pluripotent stem cell derived cardiomyocytes (day 14 of differentiation) and early cardiomyocytes (day 7 of differentiation). Entries correspond to custom heart database.
DOI: 10.6084/m9.figshare.9895115
title: MOESM8 of Overlapping transcriptional expression response of wheat zinc-induced facilitator-like transporters emphasize important role during Fe and Zn stress

description: Additional file 8: Table S7. List of the primers used during the current study.
DOI: 10.6084/m9.figshare.9895490.v1
title: Differentially regulated isoforms in iPSC d14 vs. d7

description: Limma generated table for differential expression of protein isoform quantified between human induced pluripotent stem cell derived cardiomyocytes (day 14 of differentiation) and early cardiomyocytes (day 7 of differentiation). Entries correspond to custom heart database.
DOI: 10.6084/m9.figshare.9895109
title: MOESM6 of Overlapping transcriptional expression response of wheat zinc-induced facilitator-like transporters emphasize important role during Fe and Zn stress

description: Additional file 6: Table S5. Cis-elements of wheat ZIFL genes along with their positions in the promoter. HMREâ heavy metal responsive element, IRO2â iron related transcription factor 2, MRE: metal responsive element, IDE1: iron-deficiency responsive element binding factor 1.
DOI: 10.6084/m9.figshare.9895112
title: MOESM7 of Overlapping transcriptional expression response of wheat zinc-induced facilitator-like transporters emphasize important role during Fe and Zn stress

description: Additional file 7: Table S6. Table listing the details and expression values extracted from expVIP for different developmental stages and tissues, as well as fold change values obtained after processing the TPM values for the stress conditions (Abiotic stress: phosphate deficiency; heat, drought, combined heat-drought stress, & Biotic stress: Fusarium heat blight, Septoria tritici, stripe Rust and Powdery mildew).
DOI: 10.6084/m9.figshare.9895115.v1
title: MOESM8 of Overlapping transcriptional expression response of wheat zinc-induced facilitator-like transporters emphasize important role during Fe and Zn stress

description: Additional file 8: Table S7. List of the primers used during the current study.
DOI: 10.6084/m9.figshare.9895103
title: MOESM5 of Overlapping transcriptional expression response of wheat zinc-induced facilitator-like transporters emphasize important role during Fe and Zn stress

description: Additional file 5: Table S4. ZIFL Signature motifs (Cys, His, MFS and MFS antiporter) and their locations in all wheat ZIFL proteins. The motif positions were mapped to the TM-HMM predicted TaZIFL protein structures to obtain the location of motifs.
DOI: 10.6084/m9.figshare.9895109.v1
title: MOESM6 of Overlapping transcriptional expression response of wheat zinc-induced facilitator-like transporters emphasize important role during Fe and Zn stress

description: Additional file 6: Table S5. Cis-elements of wheat ZIFL genes along with their positions in the promoter. HMREâ heavy metal responsive element, IRO2â iron related transcription factor 2, MRE: metal responsive element, IDE1: iron-deficiency responsive element binding factor 1.
DOI: 10.6084/m9.figshare.9895103.v1
title: MOESM5 of Overlapping transcriptional expression response of wheat zinc-induced facilitator-like transporters emphasize important role during Fe and Zn stress

description: Additional file 5: Table S4. ZIFL Signature motifs (Cys, His, MFS and MFS antiporter) and their locations in all wheat ZIFL proteins. The motif positions were mapped to the TM-HMM predicted TaZIFL protein structures to obtain the location of motifs.
DOI: 10.6084/m9.figshare.9895112.v1
title: MOESM7 of Overlapping transcriptional expression response of wheat zinc-induced facilitator-like transporters emphasize important role during Fe and Zn stress

description: Additional file 7: Table S6. Table listing the details and expression values extracted from expVIP for different developmental stages and tissues, as well as fold change values obtained after processing the TPM values for the stress conditions (Abiotic stress: phosphate deficiency; heat, drought, combined heat-drought stress, & Biotic stress: Fusarium heat blight, Septoria tritici, stripe Rust and Powdery mildew).
DOI: 10.6084/m9.figshare.9895085
title: MOESM3 of Overlapping transcriptional expression response of wheat zinc-induced facilitator-like transporters emphasize important role during Fe and Zn stress

description: Additional file 3: Table S2. Detailed information for 35 putative wheat ZIFLs identified. Table includes gene IDs, chromosomal locations, CDS and protein lengths, molecular weight and pI for each of the obtained putative TaZIFLs.
DOI: 10.6084/m9.figshare.9895079
title: Additional file 2: of Amplified fragment length polymorphism and whole genome sequencing: a comparison of methods in the investigation of a nosocomial outbreak with vancomycin resistant enterococci

description: Table S1. All available characteristics of the isolates included in either AFLP, WGS or both analysis methods. NLD = Netherlands, PRT = Portugal, GRC = Greece, DK = Denmark. Phenotypic vancomycin susceptibility testing per typed isolate by VITEK and confirmatory E-test (EUCAST clinical cut-off &gt; 4 mg/L). *The same isolate grown on another plate had an e-test MIC of 8 mg/L. **E-test not done. Same isolate grown on another plate had an e-test MIC of 16 mg/L. Table S2. Core-SNP matrix indicating core-SNP differences between each isolate. Boxed are the core-SNP differences between the Index isolate S01 and all other isolates. (XLSX 23 kb)
DOI: 10.6084/m9.figshare.9895085.v1
title: MOESM3 of Overlapping transcriptional expression response of wheat zinc-induced facilitator-like transporters emphasize important role during Fe and Zn stress

description: Additional file 3: Table S2. Detailed information for 35 putative wheat ZIFLs identified. Table includes gene IDs, chromosomal locations, CDS and protein lengths, molecular weight and pI for each of the obtained putative TaZIFLs.
DOI: 10.6084/m9.figshare.9895070
title: MOESM1 of Overlapping transcriptional expression response of wheat zinc-induced facilitator-like transporters emphasize important role during Fe and Zn stress

description: Additional file 1: Table S1. List of 179 wheat sequence IDs extracted for MFS_1 family, Pfam ID: PF07690 using ensembl wheat database.
DOI: 10.6084/m9.figshare.9895079.v1
title: Additional file 2: of Amplified fragment length polymorphism and whole genome sequencing: a comparison of methods in the investigation of a nosocomial outbreak with vancomycin resistant enterococci

description: Table S1. All available characteristics of the isolates included in either AFLP, WGS or both analysis methods. NLD = Netherlands, PRT = Portugal, GRC = Greece, DK = Denmark. Phenotypic vancomycin susceptibility testing per typed isolate by VITEK and confirmatory E-test (EUCAST clinical cut-off &gt; 4 mg/L). *The same isolate grown on another plate had an e-test MIC of 8 mg/L. **E-test not done. Same isolate grown on another plate had an e-test MIC of 16 mg/L. Table S2. Core-SNP matrix indicating core-SNP differences between each isolate. Boxed are the core-SNP differences between the Index isolate S01 and all other isolates. (XLSX 23 kb)
DOI: 10.6084/m9.figshare.9895070.v1
title: MOESM1 of Overlapping transcriptional expression response of wheat zinc-induced facilitator-like transporters emphasize important role during Fe and Zn stress

description: Additional file 1: Table S1. List of 179 wheat sequence IDs extracted for MFS_1 family, Pfam ID: PF07690 using ensembl wheat database.
DOI: 10.6084/m9.figshare.9895025
title: data for Figure 5D-F, intermediate section

description: process quantified RNAscope data for image set 042317_Htr7_Tac1_Th_B5614_S11_MIP_stitched
DOI: 10.6084/m9.figshare.9895025.v1
title: data for Figure 5D-F, intermediate section

description: process quantified RNAscope data for image set 042317_Htr7_Tac1_Th_B5614_S11_MIP_stitched
DOI: 10.6084/m9.figshare.9895007
title: Additional file 3: of Best-worst scaling improves measurement of first impressions

description: csv files containing data and design details for Study 3: required by the R scripts in Additional File 2. (ZIP 58 kb)
DOI: 10.6084/m9.figshare.9895007.v1
title: Additional file 3: of Best-worst scaling improves measurement of first impressions

description: csv files containing data and design details for Study 3: required by the R scripts in Additional File 2. (ZIP 58 kb)