cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.26248163
title: Supplementary Material for: Prediction of the Signaling Pathway in Polycystic Ovary Syndrome Using an Integrated Bioinformatics Approach

description: Objectives
The purpose of this study was to define the underlying biological mechanisms of PCOS utilizing the protein-protein interaction networks that were constructed based on the putative disease-causing genes for PCOS.
Design
No animals were used in this research because this study is an In-Silico studies which mainly uses softwares and online analysis tools.
Participants/Materials, Settings
Genes datasets related with PCOS were obtained from Genecard. 
Methods
The protein-protein interaction networks (PPIN) of PCOS were created using the String Database after genes related with PCOS were obtained from Genecard. After that, we performed an analysis of the hub-gene clusters extracted from the PPIN using the ShinyGO algorithm. In the final step of this research project, functional enrichment analysis was used to investigate the primary biological activities and signaling pathways that were associated with the hub clusters.
Results
The Genecard database provided the source for the identification of a total of 1072 potential genes related with PCOS. The PPIN that was generated by using the genes that we collected above contained a total of 82 genes and three different types of cluster interaction interactions. In addition, after conducting research on the PPIN with the shinyGO plug-in, 19 of the most important gene clusters were discovered. The primary biological functions that were enriched in the key clusters that were developed were ovarian stereoidogenesis, breast cancer pathway, regulation of lipid and glucose metabolism by AMPK pathway, and ovarian stereoidogenesis. The integrated analysis that was performed in the current study demonstrated that these hub clusters and their connected genes are closely associated to the pathogenesis of PCOS. 
Limitations
Several of the significant genes that were identified in this study, such as ACVR1, SMAD5, BMP6, SMAD3, SMAD4 and AMH. It is necessary to do additional research using large samples, several centers, and multiple ethnicities in order to verify these findings.
Conclusions
The integrated analysis that was performed in the current study demonstrated that these hub clusters and their connected genes are closely associated to the pathogenesis of PCOS. This information may possibly bring unique insights for the treatment of PCOS as well as the investigation of its underlying pathogenic mechanism.
DOI: 10.6084/m9.figshare.27201303
title: List of SNPs found in Liberoid Meranti 1 and 2 samples and supplementary tables

description: List of SNPs found in Liberoid Meranti 1 and 2 samples. Use the following column names to distinguish the varieties:VH01787_14_AACHH5CHV_1_AGAGTCCA is Liberoid Meranti 1, plant 2 - 1_2VH01787_14_AACHH5CHV_1_AGGATAGC is Liberoid Meranti 2, plant 1 - 2_1VH01787_14_AACHH5CHV_1_CGATCGAT is Liberoid Meranti 2, plant 3 - 2_3VH01787_14_AACHH5CHV_1_GATCTTGC is Liberoid Meranti 2, plant 2 - 2_2VH01787_14_AACHH5CHV_1_GCTACTCT is Liberoid Meranti 1, plant 1 - 1_1 VH01787_14_AACHH5CHV_1_GTAGCGTA is Liberoid Meranti 1, plant 3 - 1_3
DOI: 10.6084/m9.figshare.27698967
title: Supplementary Material for: Splenic irradiation preceding allogeneic hematopoietic stem cell transplantation as a possible risk factor of sinusoidal obstruction syndrome: a report of three cases

description: Introduction: Splenomegaly is frequently encountered in patients with myeloproliferative neoplasms. Splenomegaly is associated with an increased incidence of engraftment failure during allogeneic hematopoietic stem cell transplantation (allow-HSCT), and some centers perform prior low-dose splenic irradiation (LDSI) which has been reported to be both safe and effective. However, we report conflicting results by presenting three allo-HSCT patients undergoing LDSI that subsequently developed sinusoidal obstruction syndrome (SOS). Case Presentation: The underlying diseases of the presented cases were atypical chronic myeloid leukemia, secondary myelofibrosis following essential thrombocythemia, and acute myeloid leukemia transforming from myeloproliferative neoplasm, unclassifiable. Endothelial activation and stress index (EASIX) scores of the three patients were 0.40, 3.82, and 4.40. Conclusion: SOS is a potentially fatal complication of allo-HSCT, and the mortality rates of severe cases are reported to be above 80%. LDSI has not been recognized as a risk factor of SOS to date. Alternative management methods of splenomegaly during allo-HSCT such as ruxolitinib administration may be safer compared to LDSI.
DOI: 10.6084/m9.figshare.27952257.v2
title: GETM dataset - The major role of riverine outflows in shaping the current and future habitats of Harmful Algal Blooms : the case of the North Sea

description: GETM experiment data supporting the article : "Duteil, O., Macias, D., Stips, A., & Polimene, L. (2024). The major role of riverine outflows in shaping the current and future habitats of Harmful Algal Blooms : the case of the North Sea. In Environmental Research Communications. IOP Publishing. https://doi.org/10.1088/2515-7620/ad97ab"This study investigates the extension of the potential habitat of Harmful Algal Blooms (HABs) in the North Sea using observational data and model experiments under current and future climate scenarios. We assess the combined effects of temperature, salinity, and nutrient availability, particularly the nitrogen-to-phosphorus ratio, on HABs in the region. Climate change projections indicate a decrease in salinity concomitant with an increase in surface temperature, potentially leading to an offshore extension of HAB habitat. Reducing nitrogen and phosphorus loads in rivers differentially affects dissolved inorganic nitrogen (DIN) and phosphorus (DIP) levels, with DIN being more sensitive to load reduction, thereby constraining HAB habitat extension. Our study underscores the importance of considering both physical and biogeochemical factors in assessing HAB habitat dynamics and the potential impacts of climate change and nutrient reduction measures on HAB expansion in the North Sea. These findings have significant implications for environmental policy and management.
DOI: 10.6084/m9.figshare.27985751
title: Supplementary Material for: Thyroid function and brain structure: insight from a Mendelian randomization study

description: Background: Thyroid hormones play a critical role in brain development. However, the precise causal associations between thyroid function and structural changes in specific brain regions remain uncertain. Methods: We applied the univariate Mendelian randomization (UVMR) method to assess the causal effects of thyroid function on brain structure. Genome-wide association study (GWAS) data on thyroid-related traits from the ThyroidOmics consortium, including free thyroxine (FT4), free triiodothyronine (FT3), thyroid-stimulating hormone (TSH), FT3/FT4 ratio, as well as dichotomized high and low TSH levels were used as exposures. GWAS data on cortical thickness, surface area, and volume of subcortical structures served as outcomes. Inverse-variance weighted (IVW) was the main estimate method. Subsequently, multivariable MR (MVMR) was conducted to validate significant causal associations identified in UVMR. Results: UVMR analysis identified 1 significant and 13 nominal significant causal relationships (P&lt;0.05). Genetically predicted FT4 showed a statistically significant inverse association with putamen volume (β= -71.91, 95% confidence interval: -112.11 to -31.71). These findings were robust in sensitivity analysis. MVMR analysis further confirmed a persistent causal relationship between FT4 and putamen volume after adjusting for FT3, TSH, and neuropsychiatric disorders. Functional enrichment analyses indicated the pathways by which FT4 influences putamen volume may be related to thyroid hormone signaling pathway, sodium-independent organic anion transport, and Rap1 signaling pathway. Conclusion: MR analysis provides evidence for causal relationships between thyroid function and brain structural alterations, particularly highlighting the impact of FT4 on putamen volume. Further research is warranted to elucidate the underlying mechanisms by which thyroid hormones modulate brain structure.
DOI: 10.11570/24.0092
title: Filament Accretion and Fragmentation in the Perseus Molecular Cloud
DOI: 10.14469/hpc/14586
title: Calicheamicin, full system, reactant, wB97XD/Def2-svpp G = -5768.785232

description: Gaussian 16 (C01) calculation
DOI: 10.15468/xa7mmc
title: Some finds of birds, mammals, insects, amphibians and reptiles in July 2014 in Georgia

description: The dataset includes finds of birds (Aves), mammals (Mammalia), insects (Insecta), amphibians (Amphibia) and reptiles (Reptilia) in some western, central, southwestern and southeastern regions of Georgia.
DOI: 10.1594/pangaea.947073
title: Stable carbon and nitrogen isotopes in bulk samples and nitrogen isotopes in amino acids of mesozooplankton (200 - 2000 µm) of NW Spain (NE Atlantic) during 2001 and 2017

description: This dataset contains the values of natural abundance of stable carbon and nitrogen isotopes in bulk samples and of nitrogen isotopes in amino acids measured in 22 samples of mesozooplankton (200–2000 µm) from a shelf station off A Coruña (NW Spain, NE Atlantic). The samples were collected by double oblique tows between the surface and 50 m depth with a Juday-Bogorov net (0.5 m Ø, mesh size 200 µm), at approximately monthly intervals during the years 2001 and 2017. The net was equipped with a General Oceanic Flowmeter for the calculation of water filtered and a depth recorder. All samples were collected between 10:00 and 14:00 (local time) and were preserved dried (50 °C, 24h). Large specimens (particularly gelatinous plankton) were excluded by filtration through a 2000 µm sieve. Stable isotope determinations were made by isotope-ratio mass spectrometry using and elemental analyzer (bulk samples) or a gas-chromatograph (derivatized amino acids) as the inlet device.
description: Further Projects:ANILE project (Incorporación de N antropogénico en los sistemas litorales: bases para el seguimiento mediante isótopos estables), Award: CTM2009-08396 by Plan Nacional de I+D+I (Spain).
DOI: 10.1594/pangaea.965602
title: Sediment core dating to estimate carbon burial rates below seaweed farms

description: Sediment cores were collected below seaweed farms between October 2020 and October 2021, in order to estimate the carbon burial rates and to compare them to reference sediments beyond the farm and/or prior to the farm operation. Sampling sites represented a total of 20 farms located in 11 different countries distributed globally, including the Americas, Europe, Africa and Asia. The majority of cores were taken manually by divers in shallow waters at &lt;10 m depth. The sampling strategy consisted in collecting 3 cores within the farm area and 2 cores beyond it, as reference sites, which yielded a total of 108 cores. Cores were sliced at 0.5 cm, 1 cm and 2 cm thickness and analyzed for Pb-210, Ra-226, organic carbon and delta C-13. Pb-210 and Ra-226 were used to estimate the excess lead and to model the sedimentation rates over a time period of up to 100 years. Combined with the measurements of organic carbon concentration, carbon burial rates could be calculated at both farm and reference sites.
DOI: 10.24432/c59c74
title: Parkinsons
DOI: 10.24432/c5q01s
title: Parkinson Disease Spiral Drawings Using Digitized Graphics Tablet
DOI: 10.25423/cmcc/blksea_multiyear_phy_007_004
title: Black Sea Physical Reanalysis (CMEMS BLK-Physics, E3R1 system)

description: The CMEMS Black Sea (BLK) reanalysis physical system is based NEMO v3.6 ocean circulation model, online coupled with OceanVar data assimilation scheme, able to assimilate temperature and salinity vertical profiles provided by the CMEMS INS TAC and satellite SLA along track data from CMEMS SL TAC. The model solutions are relaxed to satellite SST data provided by CMEMS SST TAC. Prognostic equations are solved on a 1/36˚ x 1/27˚ regular horizontal grid resolution and 31 unevenly spaced vertical levels. BLK reanalysis product timeseries is updated twice per year. This product refers to the BLK-MFC Physics Production Unit.
DOI: 10.25597/0mxm-7t30
title: Replication material for: Bornatici, C., & Zinn, I. (In press). Beyond Tradition? How gender ideology impacts employment and family arrangements in Swiss couples. Gender & Society
DOI: 10.5066/f78w3c7w
title: Time-series Coral-cover Data from Hawaii, Florida, Mo'orea, and the Virgin Islands

description: Coral reefs around the world have degraded over the last half-century as evidenced by loss of live coral cover. This ubiquitous observation led to the establishment of long-term, ecological monitoring programs in several regions with sizable coral-reef resources. As part of the of the U.S. Geological Survey (USGS) John Wesley Powell Center for Analysis and Synthesis working group "Local-scale ecosystem resilience amid global-scale ocean change: the coral reef example," scientists gathered resultant data from four of these programs in the main Hawaiian Islands, the Florida Keys, Mo'orea in French Polynesia, and St. John in the U.S. Virgin Islands to examine among-site, within-region spatial and temporal variation in coral cover. Data from the four focal regions represent spatial scales ranging from ~80 to 17,000 km2. The surveys chosen for the analysis were carried out at fixed sites between 1992 and 2015. Survey durations differed among focal regions and extended from 11 years at Mo'orea to 24 years at some of the sites in St. John. 123 fixed sites (defined here as distinct surveys carried out within a defined reef habitat, depth range, or area of shoreline) were surveyed repeatedly (annually or every few years) in each focal region. Only sites with surveys extending over a decade or more and with at least three years of surveys were used so as to capture a variety of disturbance events (for example, El Nino events, major storms, etc.). Each focal region has experienced disturbances such as overfishing, disease pandemics, thermal stress, pollution, invasive species, predator outbreaks, and major storms. The data gathered for analysis are provided in this data release and are interpreted in Guest and others (2018). Guest, J.R., Edmunds, P.J., Gates, R.D., Kuffner, I.B., Andersson, A.J., Barnes, B.B., Chollett, I., Elahi, R., Courtney, T.A., Gross, K., Lenz, E.A., Mitarai, S., Mumby, P.J., Nelson, H.R., Parker, B.A., Putnam, H.M., and Toth, L.T., 2018, A framework for identifying and characterising coral-reef "oases" against a backdrop of degradation: Journal of Applied Ecology, https://doi.org/10.1111/1365-2664.13179.
DOI: 10.5067/glossac-l3-v2.0
title: Global Space-based Stratospheric Aerosol Climatology Version 2.0
DOI: 10.5281/zenodo.10820563
title: Multi-scale soil moisture data and process-based modeling reveal the importance of lateral groundwater flow in a subarctic catchment

description: Hydrological data measured in Lompolonjängänoja (LJO) catchment and used in Nousu et al.

 

ET_fluxes.csv- Eddy-covariance based, daily evapotranspiration (ET) fluxes [mm/d] at Kenttärova (NFOR) and Lompolojänkkä (NWET) stations

GW_levels.csv- Observed groundwater levels [m] relative to the ground surface measured around the LJO catchment

Q_runoff.csv- Observed specific discharge [mm/d] at the LJO catchment outlet

THETA_kenttarova.csv- Automatically measured soil moisture (i.e. volumetric water content [m3/m3]) around Kenttärova stations

THETA_spatial.csv- Manually measured soil moisture (i.e. volumetric water content [m3/m3]) around the LJO catchment
DOI: 10.5281/zenodo.14195020
title: Effects of Grass Cover on the Overland Soil Erosion Mechanism under Simulated Rainfall

description: Grass cover has a complex influence on overland soil erosion. This study quantified the impact of grass cover on overland soil erosion using a dimensionless water flow path index. It systematically analyzed the response mechanism among overland soil erosion, slope gradient, rainfall intensity, and hydrodynamic parameters, aiming to identify the optimal hydrodynamic parameters capable of characterizing overland soil erosion. A predictive model for soil erosion was constructed based on general dimensionless water flow intensity parameters, comprehensively evaluating the mechanism of soil erosion on grass-covered overland under simulated rainfall conditions. The results indicate that the model constructed using dimensionless parameters exhibits strong adaptability and can be effectively validated in other experiments.
DOI: 10.5281/zenodo.14539904
title: Dataset and source code for "Explanation and optimizing multi-model blending algorithm using random variables theory"

description: this dataset contain: 



2m temperature de-biased model forecast data on station location, ECMWF, NCEP, JP and CMA

2m temperature observaton data, obs_t2m

24H QPF model forecast data on station location, ECMWF, NCEP, CMA-GFS, in raw_data_r24.zip

24H precipitation data, in raw_data_r24.zip

source code (in python)


 

how to use it: 

1. prepare data and python environment    1.1 if you want to run [Station_FCST_MMWB.py] or [Station_FCST_MMWB_r24.py] , please download the station forecast and observation data    1.2 neet meteva package to read/write micaps-3 format data: https://github.com/nmcdev/meteva    1.3 need cartopy to draw picture FigS01. 

2. try the 2m temperature blending methods <optional>    2.1 unzip the [CMA.zip, ECMWF.zip, jp.zip, NCEP.zip, obs_t2m.zip] file into ./raw_data/    2.2 run the Station_FCST_MMWB.py in python environment 

3. try the 24h QPF multi blending methods <optional>    3.1 unzip the [raw_data_r24.zip] file into ./raw_data_r24/    3.2 run the Station_FCST_MMWB_r24.py in python environment

4. draw figures    4.1 run Fig01.py in python environment     4.2 run Fig02.py in python environment     4.3 run Fig03.py in python environment     4.4 run FigA01.py in python environment     4.5 run FigS01.py in python environment
DOI: 10.5517/ccdc.csd.cc1ljsws
title: CCDC 1475906: Experimental Crystal Structure Determination

description: Related Article: Mark E. Light, Sarah Bain, Jeremy Kilburn|2016|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.6084/m9.figshare.26062966
title: Obtaining a PhD in Portugal. Determinants of Success and Subsequent Career Paths

description: This study analysed the career paths of 5800 individuals who benefited from a doctoral scholarship, using four cohorts of scholarships which began in 1995-1997, 2001-2002, 2006, and 2012. The following research questions were addressed:1. How do different groups of scholarship recipients compare in terms of success rate and time to obtain a degree, based on variables such as gender, nationality, age at the start of the scholarship, field of study, and location of the awarding university?2. What is the persistence of these doctoral graduates in the Portuguese R&D system and what are the characteristics of their post-doctoral careers?
DOI: 10.6084/m9.figshare.27902247
title: PRISMA Checklist and Flow Diagram for "Systematic literature review: Servant leadership in public sectors"

description: This dataset includes the PRISMA 2020 checklist and flowchart, supporting the systematic review titled "Systematic literature review: Servant leadership in public sectors." These materials are provided to enhance the transparency and reproducibility of the study.
DOI: 10.6084/m9.figshare.27917280
title: Data sheet

description: Death due to hanging is commonly seen. Sometime the ligature mark will be very prominent and in some cases it might not. In those cases, the post-mortem examination with its gross morphological findings and histopathological analysis, becomes significantly important. Objective: The objective of this study was to identify the patterns of epidemiological, gross morphological, and histopathological features in hanging cases.The study was conducted on 46 cases of hanging. Their sociodemographic features were collected. Gross morphological analysis of the ligature mark and various measurements were taken. Later tissue from the ligature mark was sent for histopathological analysis. Statistical analysis was performed on the collected parameters.Significant male preponderance was observed in hanging cases. The maximum number of cases of hanging were observed in the fourth decade of life. Daily wage workers were the most significantly affected population. Depression was cited as the cause of suicide in most cases. Carotid intimal tears and injuries to bony and cartilaginous structures were present in smaller numbers. Vital reaction was observed in all 46 cases. Classification of wound vitality showed a correlation to known time since injury.The results of the present study showed that socio-demographic factors play a significant role in the circumstances leading to suicidal deaths. Therefore, in reducing the burden of suicidal deaths, these factors must be addressed. To identify the cause of death as hanging analysis of various gross features and histopathology are very important and should be conducted carefully.
DOI: 10.6084/m9.figshare.28283828.v1
title: DPN - Security in UAE

description: The purpose of this study was to investigate the prevalence of Diabetes Mellitus (DM) and associated complications such as Diabetic Peripheral Neuropathy (DPN), and Peripheral Vascular Disease (PVD) among security personnel in the United Arab Emirates (UAE).
DOI: 10.6084/m9.figshare.956082
title: Gaussian Job Archive for C7H11Cl

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.5281/zenodo.14886327
title: Now that your System has been Reproduced, What does this Mean for the Users?

description: This data repository corresponds to our reproducibility experiment entitled "Now that your System has been Reproduced, What does this Mean for the Users?". It contains the ranking results that were used in the online experiments (rankings.json). The corresponding source code to generate the rankings can be found in the zipped src folder and also on the GitHub repository. The retrieval pipeline is based on a two-stage approach with BM25 [1] as a lexical first-stage retriever and monoT5 [2] as a second-stage reranker. For each stage, this repository holds a separate zipped directory with: 

- plain files: rankings in TREC-formatted style,- compressed files: the above in a compressed format (tar.gz),- jsonl files: the top 10 results for each query in JSON format.

The final rankings used for the online experiments with additional metadata, including the retrieval effectiveness and reproducibility scores, as well as the generated passage title are contained in the rankings.json file. Please take a look at the GitHub repository regarding further information of how to run the scripts in order to reproduce the data artifacts.

[1] Robertson et al. 1994. Okapi at TREC-3. NIST. http://trec.nist.gov/pubs/trec3/papers/city.ps.gz[2] Pradeep et al. 2021. The Expando-Mono-Duo Design Pattern for Text Ranking with Pretrained Sequence-to-Sequence Models. arXiv. https://arxiv.org/abs/2101.05667