cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22730483
title: Data used in Manuscript from Carrying eggs uphill: are costs of reproduction stronger on steeper slopes?

description: Locomotor impairment during pregnancy is a well-documented cost of reproduction, but most empirical studies have not incorporated ecological complexity, such as locomotion on sloping inclines rather than horizontal surfaces. Biomechanical factors suggest that carrying a heavy burden—including shifts in the body's centre of mass—may impair locomotor ability even more when an animal is running uphill. If so, then measuring costs of reproduction on horizontal racetracks may underestimate these costs in nature for arboreal species. To evaluate this prediction, we measured the pregnancy-induced reduction in speed for jacky dragons (<i>Amphibolurus muricatus</i>) at inclines ranging from 0 to 45°. Both pregnancy and steeper slopes reduced lizard performance, but pregnancy did not exacerbate the locomotor decrement on steeper racetracks. An ability to maintain mobility on steep slopes during pregnancy may be a target of selection in arboreal taxa. To understand the evolutionary context of locomotion-based costs of reproduction, we also need studies on the relationship between organismal performance and ecologically relevant measures such as predation risk.
DOI: 10.6084/m9.figshare.22730483.v1
title: Data used in Manuscript from Carrying eggs uphill: are costs of reproduction stronger on steeper slopes?

description: Locomotor impairment during pregnancy is a well-documented cost of reproduction, but most empirical studies have not incorporated ecological complexity, such as locomotion on sloping inclines rather than horizontal surfaces. Biomechanical factors suggest that carrying a heavy burden—including shifts in the body's centre of mass—may impair locomotor ability even more when an animal is running uphill. If so, then measuring costs of reproduction on horizontal racetracks may underestimate these costs in nature for arboreal species. To evaluate this prediction, we measured the pregnancy-induced reduction in speed for jacky dragons (<i>Amphibolurus muricatus</i>) at inclines ranging from 0 to 45°. Both pregnancy and steeper slopes reduced lizard performance, but pregnancy did not exacerbate the locomotor decrement on steeper racetracks. An ability to maintain mobility on steep slopes during pregnancy may be a target of selection in arboreal taxa. To understand the evolutionary context of locomotion-based costs of reproduction, we also need studies on the relationship between organismal performance and ecologically relevant measures such as predation risk.
DOI: 10.6084/m9.figshare.22730502.v1
title: <i>In silico</i> study to recognize novel angiotensin-converting-enzyme-I inhibitors by 2D-QSAR and constraint-based molecular simulations

description: Cardiovascular diseases (CVD) such as heart failure, stroke, and hypertension affect 64.3 million people worldwide and are responsible for 30% of all deaths. Primary inhibition of the angiotensin-converting enzyme (ACE) is significant in the management of CVD. In the present study, the genetic algorithm-multiple linear regressions (GA-MLR) method is used to generate highly predictive and statistically significant (<i>R</i><sup>2</sup> = 0.70–0.75, <i>Q</i><sup>2</sup><sub>LOO</sub>=0.67–0.73, <i>Q</i><sup>2</sup><sub>LMO</sub>=0.66–0.72, CCC<sub>ex</sub>=0.70–0.78) quantitative structure-activity relationships (QSAR) models conferring to OECD requirements using a dataset of 255 structurally diverse and experimentally validated ACE inhibitors. The models contain simply illustratable Padel, Estate, and PyDescriptors that correlate structural scaffold requisite for ACE inhibition. Also, constraint-based molecular docking reveals an interaction profile between ligands and enzymes which is then correlated with the essential structural features associated with the QSAR models. The QSAR-based virtual screening was utilized to find novel lead molecules from a designed database of 102 thiadiazole derivatives. The Applicability domain (AD), Molecular Docking, Molecular dynamics, and ADMET analysis suggest two compound D24 and D40 are inflexibly linked to the protein binding site and follows drug-likeness properties. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.22730502
title: <i>In silico</i> study to recognize novel angiotensin-converting-enzyme-I inhibitors by 2D-QSAR and constraint-based molecular simulations

description: Cardiovascular diseases (CVD) such as heart failure, stroke, and hypertension affect 64.3 million people worldwide and are responsible for 30% of all deaths. Primary inhibition of the angiotensin-converting enzyme (ACE) is significant in the management of CVD. In the present study, the genetic algorithm-multiple linear regressions (GA-MLR) method is used to generate highly predictive and statistically significant (<i>R</i><sup>2</sup> = 0.70–0.75, <i>Q</i><sup>2</sup><sub>LOO</sub>=0.67–0.73, <i>Q</i><sup>2</sup><sub>LMO</sub>=0.66–0.72, CCC<sub>ex</sub>=0.70–0.78) quantitative structure-activity relationships (QSAR) models conferring to OECD requirements using a dataset of 255 structurally diverse and experimentally validated ACE inhibitors. The models contain simply illustratable Padel, Estate, and PyDescriptors that correlate structural scaffold requisite for ACE inhibition. Also, constraint-based molecular docking reveals an interaction profile between ligands and enzymes which is then correlated with the essential structural features associated with the QSAR models. The QSAR-based virtual screening was utilized to find novel lead molecules from a designed database of 102 thiadiazole derivatives. The Applicability domain (AD), Molecular Docking, Molecular dynamics, and ADMET analysis suggest two compound D24 and D40 are inflexibly linked to the protein binding site and follows drug-likeness properties. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.22730507
title: Supporting_Data.zip from Low-nutrient diet in <i>Drosophila</i> larvae stage causes enhancement in dopamine modulation in adult brain due epigenetic imprinting

description: Nutrient scarcity is a frequent adverse condition that organisms face during their development. This condition may lead to long-lasting effects on the metabolism and behaviour of adults due to developmental epigenetic modifications. Here, we show that reducing nutrient availability during larval development affects adult spontaneous activity and sleep behaviour, together with changes in gene expression and epigenetic marks in the Mushroom bodies (MBs). We found that open chromatin regions map to 100 of 241 transcriptionally upregulated genes in the adult MBs, these new opening zones are preferentially located in regulatory zones such as promoter-TSS and introns. Importantly, opened chromatin at the Dopamine 1-like receptor 2 transcription start site correlates with increased expression. Thus, adult administration of a dopamine antagonist reverses increased spontaneous activity and diminished sleep time observed in response to early-life nutrient restriction. In comparison, reducing <i>dop1R2</i> expression in MBs also ameliorates these effects, albeit to a lesser degree. These results lead to the conclusion that increased dopamine signalling in the MBs of flies reared in a poor nutritional environment underlies the behavioural changes observed due to this condition during development.
DOI: 10.6084/m9.figshare.22730507.v1
title: Supporting_Data.zip from Low-nutrient diet in <i>Drosophila</i> larvae stage causes enhancement in dopamine modulation in adult brain due epigenetic imprinting

description: Nutrient scarcity is a frequent adverse condition that organisms face during their development. This condition may lead to long-lasting effects on the metabolism and behaviour of adults due to developmental epigenetic modifications. Here, we show that reducing nutrient availability during larval development affects adult spontaneous activity and sleep behaviour, together with changes in gene expression and epigenetic marks in the Mushroom bodies (MBs). We found that open chromatin regions map to 100 of 241 transcriptionally upregulated genes in the adult MBs, these new opening zones are preferentially located in regulatory zones such as promoter-TSS and introns. Importantly, opened chromatin at the Dopamine 1-like receptor 2 transcription start site correlates with increased expression. Thus, adult administration of a dopamine antagonist reverses increased spontaneous activity and diminished sleep time observed in response to early-life nutrient restriction. In comparison, reducing <i>dop1R2</i> expression in MBs also ameliorates these effects, albeit to a lesser degree. These results lead to the conclusion that increased dopamine signalling in the MBs of flies reared in a poor nutritional environment underlies the behavioural changes observed due to this condition during development.
DOI: 10.5281/zenodo.7885485
title: Appendix A

description: Transcription of the third weekend of the Convention on the Constitution.
DOI: 10.5281/zenodo.7885484
title: Appendix A

description: Transcription of the third weekend of the Convention on the Constitution.
DOI: 10.25625/hgghqc
title: B08 - litter and soil density and moisture from Landscape Assessment (2021)

description: Weights of litter and soil (fresh and dry) from ~100 Landscape Assessment plots (2021).
DOI: 10.25625/hgghqc/fuinrm
title: B08_LA_Litter and soil density and moisture.tab

description: :unav
DOI: 10.6084/m9.figshare.22730520
title: Electronic Supplementary Material 2 from Elevated compositional change in plant assemblages linked to invasion

description: Spreadsheet with the rarefied data from BioTIME used for analyses (terrestrial plants, at least 3 years of sampling, abundance data)
DOI: 10.6084/m9.figshare.22730520.v1
title: Electronic Supplementary Material 2 from Elevated compositional change in plant assemblages linked to invasion

description: Spreadsheet with the rarefied data from BioTIME used for analyses (terrestrial plants, at least 3 years of sampling, abundance data)
DOI: 10.25625/03gnic
title: B08 - Litter and soil density and water content (core plots, 2016 and 2021)

description: Weights of litter and soil (fresh and dry) from core plots of the second and third EFForTS phase (2016 and 2021).
DOI: 10.25625/03gnic/yswncy
title: B08_2016-2022_Core_Litter and soil density and moisture.tab

description: :unav
DOI: 10.25625/fsgj8v/axj5hp
title: B08_2016_Core_RootBiomass.tab

description: :unav
DOI: 10.25625/fsgj8v
title: B08 - Root biomasses in litter and topsoil (core plots, 2016)

description: Dry biomass of fine and coarse roots in litter and top 5 cm of soil from EFForTS core plots (2016).
DOI: 10.25625/9cer2f/pagtp6
title: B08B13_2013-2016_DataCompilation_AllPlatforms.tab

description: :unav
DOI: 10.25625/9cer2f
title: B08 and B13 - Soil animal collection from 2013-2017 (core plots, BEE, OPMX)

description: Abundances of soil animal taxa (orders, families) from core plots, BEE, and OPMX from the first two EFForTS phases (2013-2017). Samples were collected from litter and soil and extracted using a Kempson extractor.
DOI: 10.25625/lc6fci/luksns
title: B08_LA_Earthworm abundance.tab

description: :unav
DOI: 10.25625/lc6fci
title: B08 - Earthworm abundance from Landscape Assessment (2021)

description: Earthworm collection across ca. 100 plots sampled during Landscape Assessment (2021). Earthworms were hand-sorted, adults were counted separately.
DOI: 10.25625/9q8sgd/77onbp
title: B08_2017_SeasonalChanges_SoilAnimals.tab

description: :unav
DOI: 10.25625/9q8sgd
title: B08 - Soil animal collection from four seasons (core plots, 2017)

description: Soil animal collection from 12 core plots in Harapan landscape, collected in four seasons (2017). Samples were collected from litter and soil and extracted using a Kempson extractor. Animals are sorted to high-rank taxa (orders, families)
DOI: 10.25625/jyfh3y/npeonm
title: B08_2013_SpeciesDataCompillation.tab

description: :unav
DOI: 10.25625/jyfh3y
title: B08 - Community matrices (species-level) of soil animals (core plots, 2013)

description: Species-level identified soil animal taxa from 32 core plots from the first EFForTS phase (mostly 2013). Samples were collected from litter and soil and extracted using a Kempson extractor. The following taxonomic groups were identified to species level and are shared in this dataset: Oribatida, Mesostigmata, Collembola, Pseudoscorpiones, Chilopoda, Carabidae, Araneae (hear extraction), Araneae (litter sieving, B01 data). Morphospecies can be found in Ecotaxonomy web database.
DOI: 10.48758/ufz.12451
title: Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS) data of wastewater effluent organic matter (EfOM).

description: Processed and quality checked FT-ICR MS data for original (nEx) and PPL extracted (Ex), as well as non-ozonated (nOz) and ozonated (Oz) DOM from a waste water treatment plant sample. Sampling and measurement conditions are described in the companion paper (Jennings et al. 2022, doi:10.1021/acs.est.1c04310). Direct infusion (DI) and LC-FTICR MS data are included. For LC data, the segment numbe (Range#) as well as the retention time range (in min) are indicated.
DOI: 10.48758/ufz.13076
title: Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS) data of dissolved organic matter (DOM) and disinfection byproducts (DBP) in drinking water.

description: Processed and quality checked FT-ICR MS data for raw and disinfected drinking water (_DW_) measured by nanoLC-nanoESI-FT-ICR MS. The dataset includes a _raw_ and chlorinated (_DW_) sample for two different drinking water treatment plants, one with Cl2 (_A_) and one with ClO2 (_B_), resulting in two paired samples, _raw_nLC-A_ and _DW_nLC-A_ as well as _raw_nLC-B_ and _DW_nLC-B_. For the first drinking water sample, also a PPL solid phase extracted sample is included (_DW_SPE_nLC-A_). Each LC run was segmented into 0.5 min wide segments (e.g. ..._11_11p5m), yielding 20 individual spectra per sample. Sample details, sample disinfection, measurement conditions and data evaluation workflows are described in the companion paper (Han et al. 2022).
DOI: 10.25625/xn0kmg/ekatg9
title: B08_2013_SoilAnimalCollection.tab

description: :unav
DOI: 10.25625/xn0kmg
title: B08 - Individual-level soil animal collection (core plots, 2013)

description: Individual-level soil animal collection from 32 core plots from the first EFForTS phase (2013). Samples were collected from litter and soil and extracted using a Kempson extractor. Body lengths for most individuals are provided.
DOI: 10.48758/ufz.12908
title: Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS) data of dissolved organic matter (DOM) from soils and streams in the Bavarian Forest National Park, Germany.

description: Processed and quality checked FT-ICR MS data for dissolved organic matter extracted from piezometers located in forest soils (FSx) and from the Hinterer Schachtenbach (HS) sampled during a precipitation event. Sampling locations, sample processing and measurement conditions are described in the companion paper (Blaurock et al. 2022, ID: 2022JG006831RRR).
DOI: 10.48758/ufz.12914
title: Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS) data of dissolved organic matter (DOM) from streams in the Ammer and Steinlach catchments, Germany.

description: Processed and quality checked FT-ICR MS data for dissolved organic matter samples during events and baseflow condition in two catchments (Ammer and Steinlach, South-East Germany) during the Swabian MOSES campaign. Sampling locations, sample processing and measurement conditions as well as other sample data are described in the companion paper (Glaser et al. 2023).
DOI: 10.7303/syn51169055
title: LPP Sleeve
DOI: 10.5281/zenodo.7876343
title: FEP benchmark HIF2A FEP+ fmp and trajectory files

description: Full FEP+ fmp file and related trajectory files for HIF2A FEP+ calculations related to dataset https://github.com/MCompChem/fep-benchmark
DOI: 10.5281/zenodo.7876342
title: FEP benchmark HIF2A FEP+ fmp and trajectory files

description: Full FEP+ fmp file and related trajectory files for HIF2A FEP+ calculations related to dataset https://github.com/MCompChem/fep-benchmark
DOI: 10.5281/zenodo.7639960
title: CLUSTER anti-TNF clinical dataset

description: This data dictionary describes the CLUSTER anti-TNF clinical dataset. It contains key variables of interest for measuring treatment response to tumour necrosis factor inhibitors (anti-TNF) in juvenile idiopathic arthritis (JIA) patients at baseline/timepoint 1 (start of anti-TNF treatment or up to 3 months before) and timepoint 2 (6 months after baseline, within a 3-12 month window). If a patient had multiple visits within a timepoint window, the one closest to baseline/6 months was selected. There are 2401 patients in this dataset. CLUSTER has brought together data from 4 UK observational JIA research cohort studies: the UK JIA Biologics Register, the Childhood Arthritis Prospective Study (CAPS) and the Childhood Arthritis Response to Medication Study (CHARMS). Clinical data from these studies was pooled to create the CLUSTER anti-TNF clinical dataset. More details of CLUSTER's clinical data harmonisation process are available here: &lt;link&gt; We are open to collaborating and sharing data with researchers who have research questions that may be answered by our data. Access to CLUSTER data is regulated according to the conditions of patient consent, study ethics and the CLUSTER Consortium’s policies. Access is available to researchers via an application to the CLUSTER data access committee - more details are available on CLUSTER's website.
DOI: 10.5281/zenodo.7639959
title: CLUSTER anti-TNF clinical dataset

description: This data dictionary describes the CLUSTER anti-TNF clinical dataset. It contains key variables of interest for measuring treatment response to tumour necrosis factor inhibitors (anti-TNF) in juvenile idiopathic arthritis (JIA) patients at baseline/timepoint 1 (start of anti-TNF treatment or up to 3 months before) and timepoint 2 (6 months after baseline, within a 3-12 month window). If a patient had multiple visits within a timepoint window, the one closest to baseline/6 months was selected. There are 2401 patients in this dataset. CLUSTER has brought together data from 4 UK observational JIA research cohort studies: the UK JIA Biologics Register, the Childhood Arthritis Prospective Study (CAPS) and the Childhood Arthritis Response to Medication Study (CHARMS). Clinical data from these studies was pooled to create the CLUSTER anti-TNF clinical dataset. More details of CLUSTER's clinical data harmonisation process are available here: &lt;link&gt; We are open to collaborating and sharing data with researchers who have research questions that may be answered by our data. Access to CLUSTER data is regulated according to the conditions of patient consent, study ethics and the CLUSTER Consortium’s policies. Access is available to researchers via an application to the CLUSTER data access committee - more details are available on CLUSTER's website.
DOI: 10.5281/zenodo.7639899
title: CLUSTER MTX Clinical Dataset

description: This data dictionary describes the CLUSTER MTX clinical dataset. It contains key variables of interest for measuring treatment response to methotrexate (MTX) in juvenile idiopathic arthritis (JIA) patients at baseline/timepoint 1 (start of MTX treatment or up to 3 months before) and timepoint 2 (6 months after baseline, within a 3-12 month window). If a patient had multiple visits within a timepoint window, the one closest to baseline/6 months was selected. There are 2899 patients in this dataset. CLUSTER has brought together data from 4 UK observational JIA research cohort studies: the UK JIA Biologics Register, the Childhood Arthritis Prospective Study (CAPS) and the Childhood Arthritis Response to Medication Study (CHARMS). Clinical data from these studies was pooled to create the CLUSTER MTX clinical dataset. More details of CLUSTER's clinical data harmonisation process are available here: &lt;link&gt; We are open to collaborating and sharing data with researchers who have research questions that may be answered by our data. Access to CLUSTER data is regulated according to the conditions of patient consent, study ethics and the CLUSTER Consortium’s policies. Access is available to researchers via an application to the CLUSTER data access committee - more details are available on CLUSTER's website.
DOI: 10.5281/zenodo.7639898
title: CLUSTER MTX Clinical Dataset

description: This data dictionary describes the CLUSTER MTX clinical dataset. It contains key variables of interest for measuring treatment response to methotrexate (MTX) in juvenile idiopathic arthritis (JIA) patients at baseline/timepoint 1 (start of MTX treatment or up to 3 months before) and timepoint 2 (6 months after baseline, within a 3-12 month window). If a patient had multiple visits within a timepoint window, the one closest to baseline/6 months was selected. There are 2899 patients in this dataset. CLUSTER has brought together data from 4 UK observational JIA research cohort studies: the UK JIA Biologics Register, the Childhood Arthritis Prospective Study (CAPS) and the Childhood Arthritis Response to Medication Study (CHARMS). Clinical data from these studies was pooled to create the CLUSTER MTX clinical dataset. More details of CLUSTER's clinical data harmonisation process are available here: &lt;link&gt; We are open to collaborating and sharing data with researchers who have research questions that may be answered by our data. Access to CLUSTER data is regulated according to the conditions of patient consent, study ethics and the CLUSTER Consortium’s policies. Access is available to researchers via an application to the CLUSTER data access committee - more details are available on CLUSTER's website.
DOI: 10.5281/zenodo.7885563
title: FEP benchmark SYK FEP+ fmp and trajectory files

description: Full FEP+ fmp file and related trajectory files for SYK FEP+ calculations related to dataset https://github.com/MCompChem/fep-benchmark
DOI: 10.5281/zenodo.7885562
title: FEP benchmark SYK FEP+ fmp and trajectory files

description: Full FEP+ fmp file and related trajectory files for SYK FEP+ calculations related to dataset https://github.com/MCompChem/fep-benchmark
DOI: 10.6084/m9.figshare.22730066
title: Raw and processed data for vegetable production in reducing child stunting

description: Raw and processed data for the manuscript "Contribution of Home Garden Vegetables on Reducing Stunting Among 6-23 Months old Age Children in South Tigray, Northern Ethiopia.
DOI: 10.5281/zenodo.7885580
title: Data for paper: Assessment of ChatGPT's ability to detect variability in requirements

description: Data for paper: Assessment of ChatGPT's ability to detect variability in requirements
DOI: 10.5281/zenodo.7885579
title: Data for paper: Assessment of ChatGPT's ability to detect variability in requirements

description: Data for paper: Assessment of ChatGPT's ability to detect variability in requirements
DOI: 10.4121/8616f5ea-f0e6-4f48-9627-03a3acafe89c
title: City Maps belonging to the paper: Characterizing Residential Segregation in Cities Using Intensity, Separation, and Scale Indicators

description: Maps of Dutch municipalities representing the spatial distribution of 2 social groups, along with regions obtained with a regionalization method.
DOI: 10.4121/8616f5ea-f0e6-4f48-9627-03a3acafe89c.v1
title: City Maps belonging to the paper: Characterizing Residential Segregation in Cities Using Intensity, Separation, and Scale Indicators

description: Maps of Dutch municipalities representing the spatial distribution of 2 social groups, along with regions obtained with a regionalization method.