cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25625/citojd
title: Household and plot-level survey data on adoption, outcomes, and perceptions of early sown wheat and zero tillage in Northwest India

description: This study collected evidence on the use of early sown wheat varieties and complementary zero tillage technologies in Northwest India. Detailed information on farmers’ knowledge, adoption decisions, personal experience, and perceptions of early sown wheat and zero tillage technologies were collected at the household level using different survey tools. Additional information on agricultural practices during the Rabi Season 2021/22 were collected at the plot level and geocoded. Overall, the dataset comprises responses from 1206 wheat farmers in 70 villages across 7 districts in Punjab and Haryana that were collected between September and October 2022. The villages were selected using stratified random sampling based on a sampling frame of 1722 communities that had been identified as predominantly wheat growing areas based on remote-sensing data from satellite images. The dataset provides rich information that may be used for assessing the diffusion and impact of recently developed wheat varieties designed for early sowing, identifying barriers to the wider adoption of these technologies, and informing policy making aimed at improving adoption and usage decisions of agricultural innovations.
DOI: 10.26179/5cc937513bd6d
title: SA Agulhas II Winter 2017 Cruise: ice edge drifters
DOI: 10.5281/zenodo.10013090
title: BITS-2 Dataset for Fall Detection

description: Data was collected using a custom-built wrist-worn end worn on the left wrist. Qualcomm Snapdragon 820c. We used MAX30102 Heart rate and SP02 sensor, MPU6500, which gives 3-axis acceleration, 3-axis linear acceleration and 3-axis gyroscope data and GY273 Magnetometer chip for data collection. All the sensors are interfaced to the SoC via the I2C interface using a Mezzanine board.
Table, each table having six columns, time-stamp, x-axis data, y-axis data and z-axis data, number of axes and type of sensor(label) except in case of heart-rate where there will be only three columns, time-stamp, beats per minute and label (hrt for heart-rate)
In this data set, the data was collected from a total of 41 volunteers performing 16 ADLs and 8 Falls. Every activity was repeated for five trials.
DOI: 10.5281/zenodo.4429248
title: SH2-containing-inositol-5-phosphatases (INPP5D); A Target Enabling Package

description: SH2-containing-inositol-5-phosphatases (SHIP1 and SHIP2, coded for by genes <em>INPP5D</em> and <em>INPPL1</em>, respectively) dephosphorylate phosphatidylinositol-3,4,5-trisphosphate (PI(3,4,5)P<sub>3</sub>) to produce phosphatidylinositol-3,4-bisphosphate (PI(3,4)P<sub>2</sub>). This is an important part of the PI3K/AKT/mTOR signalling pathway. The SHIPs have been linked to a range of conditions, including cancer, diabetes, hypertension, and graft versus host disease. A link has also been demonstrated by GWAS between a non-coding mutation in the <em>INPP5D</em> (SHIP1) gene and increased risk of late-onset Alzheimer’s disease. The role of SHIP1 in Alzheimer’s disease is believed to be mediated through inflammatory processes such as the regulation of microglia and cytokine release. The distinction between the effects of SHIP1 and SHIP2 on these processes is not fully understood. In this TEP we present an apo structure of the phosphatase and C2 domains of SHIP1 and a structure with a magnesium ion and a phosphate ion bound to the active site. We also present 91 fragment bound structures that may act as starting points for the modulation of SHIP1. We are also able to crystallise an equivalent construct of SHIP2 and purify a range of other inositol-5-phosphatases to serve as a selectivity panel for the development of specific compounds. An assay has also been developed.
description: This document represents version 1 of the TEP datasheet and includes all updates on the project as of November 2020. For more information about TEPs and the TEP Programme, please visit https://thesgc.org/tep.
DOI: 10.6084/m9.figshare.22117559
title: EUSEDcollab.v1

description: The EUropean SEDiments collaboration (EUSEDcollab) database contains a compilation of data contributions from monitored catchments from across multiple European institutions. The focus of the database is small to medium catchments containing water discharge and sediment delivery time series measurements for soil erosion, sediment delivery and runoff studies. These measurements from various institutions provide insights into the processes governing soil erosion and sediment delivery across a spectrum of spatial and temporal scales. The data is aimed at multiple end-user applications, such as providing baseline information for further analytical studies and model application/development, allowing comparison with real measurements of process rates. As a user-orientated EUSO initiative, the contributed data is harmonised with a common metadata and time series structure to allow efficient reuse. This database aims to provide the research community with a starting point for new research opportunities in a range of sediment-related research avenues. Description: EUSEDcollab is available as a single repository containing multiple sub-folders with catchment data: 1) METADATA: A series of files (.csv format) containing the completed metadata inputs for each catchment. 2) Q_SSL: A time series (.csv format) containing time series of water discharge, suspended sediment concentration and total suspended sediment load. 3) Q_SSL_QUALITY_CONTROL: (.json format) containing evaluations of the time series completeness with specific evaluations for the different dataset temporal structures. A description of each data quality check is given in (Data_quality_check_fields.xlsx). 4) PRECIPITATION: Precipitation time series data from catchments with available measurements. 5) SED_RATING_CURVES: Original sediment rating curve data from catchments with available data. 6) ADDITIONAL_FILES: Other auxiliary information for each catchment e.g. readme files with additional information, catchment boundary polygons, land-use information, additional reports. 7) EUSEDcollab_submission_templates: The template files to make a submission to the EUSEDcollab database. See the ESDAC page for details (https://esdac.jrc.ec.europa.eu/content/EUSEDcollab). <br> 2 additional files containing database compilations can also be found in the parent directory: 1) 'ALL_METADATA.csv' - a compilation of all metadata inputs. 2) 'all_timeseries.pickle' - a pickle file containing a dictionary of dataframes for all catchments. This allows the database to be read as one single file and accessed based on the catchment ID number. <br> The accompanying code can be found at: https://github.com/matfran/EUSEDcollab.git <br>
DOI: 10.17632/znks6nsbdj.1
title: 10Be exposure age dating of moraine boulders and glacially polished bedrock surfaces in Karakoram and Ladakh Ranges, NW Himalaya

description: The dataset shows the exposure ages obtained from moraine boulders and glacially polished bedrock surfaces in Karakoram and Ladakh Ranges, NW Himalaya.
DOI: 10.5281/zenodo.5806296
title: Slow Port Scan Test (D2)

description: Ports scan dataset contains approximately 50% benign flow data and 50% malicious flow data. Benign flow data have been generated with the same python scripts used in D1 and has been labeled as '0'. Malicious flow data has been labeled as '1'. Malicious flow data has been generated using Nmap tool. Different types of slow port scans have been launched on both TCP and UDP ports. The scans carried out were: TCP SYN scanning; TCP Connect scanning; UDP scanning; TCP NULL; FIN; Xmas scanning; TCP ACK scanning; TCP Window scanning; and TCP Maimon scanning. Slow port-scanning attacks have been carried out by 100 attack nodes that scanned 65536 ports on 200 victim nodes. Requests are launched with 5 to 10 seconds of slack time among them.
DOI: 10.5281/zenodo.8084059
title: Genome sequencing of 2,000 canids advances the understanding of demography, genome function and architecture

description: <strong>Background: </strong>The international Dog10K project aims to sequence and analyze several thousand canine genomes. Incorporating 20x data from 1,987 individuals, including 1,611 dogs (321 breeds), 309 village dogs, 63 wolves and four coyotes, we identify genomic variation across the canid family, setting the stage for detailed studies of domestication, behavior, morphology, disease susceptibility and genome architecture and function. <strong>Results: </strong>We report the analysis of &gt;48M single nucleotide, indel, and structural variants spanning the autosomes, X chromosome and mitochondria. We discover more than 75% of variation for 239 sampled breeds. Allele sharing analysis indicates that 94.9% of breeds form monophyletic clusters and 25 major clades. German Shepherd Dogs and related breeds show the highest allele sharing with independent breeds from multiple clades. On average, each breed dog differs from the UU_Cfam_GSD_1.0 reference at 26,960 deletions and 14,034 insertions greater than 50bp, with wolves having 14% more variants. Discovered variants include retrogene insertions from 926 parent genes. To aid functional prioritization, single nucleotide variants were annotated with SnpEff and Zoonomia phyloP constraint scores. Constrained positions were negatively correlated with allele frequency. Finally, the utility of the Dog10K data as an imputation reference panel is assessed, generating high confidence calls across varied genotyping platform densities including for breeds not included in the Dog10K collection. <strong>Conclusions:</strong> We have developed a dense dataset of 1,987 sequenced canids that reveals patterns of allele sharing, identifies likely functional variants, informs breed structure, and enables accurate imputation. Dog10K data are publicly available
DOI: 10.5281/zenodo.8357067
title: MCProj interactive applications

description: MCView applications from the paper: MCProj: metacell projection for interpretable and quantitative use of transcriptional atlases.
DOI: 10.5281/zenodo.8420032
title: Supplementary Datasets for "Genome-wide CRISPR off-target prediction and optimization using RNA-DNA interaction fingerprints"

description: Supplementary Datasets for "Genome-wide CRISPR off-target prediction and optimization using RNA-DNA interaction fingerprints". The deposition contains training/testing datasets used in the article.
DOI: 10.15156/bio/1264819
title: UNITE QIIME release for eukaryotes

description: Three sets of QIIME files are released, corresponding to the SHs resulting from clustering at the 97% and 99% threshold levels. The third set of files is the result of a dynamic use of clustering thresholds, such that some SHs are delimited at the 97% level, some at the 97.5% level, some at the 98% level, and so on; these choices were made manually by experts of those particular lineages of fungi. The syntax is the same throughout the three sets of files.
DOI: 10.18112/openneuro.ds004507.v1.0.1
title: PMJ BIDS Dataset
DOI: 10.5281/zenodo.5806285
title: Bening Flow Data Train (D1)

description: Train dataset only contains benign traffic, this dataset has been collected using Netflow and implementing a sampling rate of 1 packet out of each 1000 to generate the flows, simulating the conditions of the RedCayle’s routers. The traffic has been generated using three Python scripts. The first one simulates email sending using SMTP protocol. The second script simulates SSH connections. The third script simulates a user browsing the internet using different search engines and different protocols like HTTP and HTTPS.
DOI: 10.6084/m9.figshare.22153475.v1
title: DNB_RTM_LUNAR_RAYLEIGH.rar

description: Dataset containing all pictures in the paper.
DOI: 10.5281/zenodo.8405255
title: Genetic variation of Scots pine in Eurasia: Impact of postglacial recolonisation and human-mediated gene transfer

description: <strong>The dataset comprises nuclear microsatellite data (PCR products lengths) used in the paper "Genetic variation of Scots pine in Eurasia: Impact of postglacial recolonisation and human-mediated gene transfer".</strong> <strong>The pdf file includes the list of populations.</strong> Abstract: Scots pine (<em>Pinus sylvestris</em> L.) seems to be a species of low conservation priority because it has a very wide Eurasian distribution and plays a leading role in many forest tree breeding programs. Nevertheless, considering its economic value, long breeding history, range fragmentation, and increased mortality, which is also projected in the future, it requires a more detailed description of its genetic resources. Our goal was to compare patterns of genetic variation found in biparentally inherited nuclear DNA with previous research carried out with mitochondrial and chloroplast DNA due to their different modes of transmission. We analysed the genetic variation and relationships of 60 populations across the distribution of Scots pine in Eurasia (1,262 individuals) using a set of nuclear DNA markers. We confirmed the high genetic variation and low genetic differentiation of Scots pine spanning large geographical areas. Nevertheless, there was a clear division between European and Asian gene pools. The genetic variation of Asian populations was lower than in Europe. Spain, Turkey, and the Apennines constituted separate gene pools, the latter showing the lowest values of all genetic variation parameters. The analyses showed that most populations experienced genetic bottlenecks in the distant past. Ongoing admixture was found in Fennoscandia. Our results suggest a much simpler recolonization history of the Asian than European part of the Scots pine distribution, with migration from limited sources and possible founder effects. Eastern European stands seem to have descended from the Urals refugium. It appears that Central Europe and Fennoscandia share at least one glacial refugium in the Balkans and migrants from higher latitudes, as well as from southeastern regions. The low genetic structure between Central Europe and Fennoscandia, along with their high genetic admixture, may result at least partially from past human activities related to the transfer of germplasm in the 19<sup>th</sup> and early 20<sup>th</sup> centuries. In light of ongoing climate changes and projected range shifts of Scots pine, conservation strategies are especially needed for marginal and isolated stands of this species. Genetic research should also be complemented in parts of the species distribution that have thus far been poorly studied.
DOI: 10.17632/d2xt5hdm5j.1
title: Genome variation data of Lithuanians

description: Whole genome sequencing variation data from 50 unrelated adult participants of Lithuanian nationality. The final dataset included 1,461,557 SNPs.
DOI: 10.17632/2p7mbbhn47.1
title: Design and Validation of an Open-Sourced Automation System for Vertical Farming

description: The Modular Automated Crop Array Online System (MACARONS) is a scalable, customiseable and open-sourced platform designed for plant care, monitoring, and transportation. It offers specific dosing for individual plants, automated data logging of temperature, humidity, and images, and custom behaviours programmable in Python. Monitoring and control of the system is achieved through a web-interface. The system was validated by autonomously caring for five lettuce plants over a five-week period. The system is estimated to perform the tasks required 30% faster than a human operator and can handle payloads of up to 5kg with a maximum footprint of 750mm x 500mm. The designs are released and meets the requirements of CERN-OSH-W, which includes step-by-step graphical build instructions and can be built at a cost of GBP 2241.72.
DOI: 10.17632/mns8vgkxvk.1
title: Flower visits of cockroaches (Insecta: Blattodea) in the Iberian Peninsula: are they neglected pollinators?

description: We have reviewed all photographs of cockroaches visiting wildflowers in the Iberian Peninsula uploaded on Biodiversidad Virtual (BV; https://www.biodiversidadvirtual.org/) and iNaturalist (iNat; https://www.inaturalist.org/) until 31th September of 2022. This data was complemented with our own records or photographs provided by other authors specifically for this study. All cockroaches were identified attending to diagnostic characters of the Iberian fauna. In all the flower-visit events, we have tried to include the cockroach and the plant species (or, at least, the lowest taxonomic level possible), the month of the observation, the location and whether the cockroaches are carrying pollen grains. Furthermore, we measured the floral reflectance spectra in the UV and visible light spectrum of plant species visited by cockroaches in the Iberian Peninsula with a spectrophotometer. Reflectance data was processed using PAVO package in R Studio. We also assesed the presence of UV or visible colour patterns in flowers and measure its reflectance spectra.
DOI: 10.17632/mns8vgkxvk.2
title: Flower visits of cockroaches (Insecta: Blattodea) in the Iberian Peninsula: are they neglected pollinators?

description: We have reviewed all photographs of cockroaches visiting wildflowers in the Iberian Peninsula uploaded on Biodiversidad Virtual (BV; https://www.biodiversidadvirtual.org/) and iNaturalist (iNat; https://www.inaturalist.org/) until 31th September of 2022. This data was complemented with our own records or photographs provided by other authors specifically for this study. All cockroaches were identified attending to diagnostic characters of the Iberian fauna. In all the flower-visit events, we have tried to include the cockroach and the plant species (or, at least, the lowest taxonomic level possible), the month of the observation, the location and whether the cockroaches are carrying pollen grains. Furthermore, we measured the floral reflectance spectra in the UV and visible light spectrum of plant species visited by cockroaches in the Iberian Peninsula with a spectrophotometer. Reflectance data was processed using PAVO package in R Studio. We also assesed the presence of UV or visible colour patterns in flowers and measure its reflectance spectra.
DOI: 10.17632/pb6fw2ctth.1
title: Pingyin Rose Essential Oil Restores Intestinal Barrier Integrity in DSS-induced Mice Colitis Model

description: Introduction: Rosa rugosa cv. Plena is a ‘drug homologous food’ in China with a long history. Pingyin rose essential oil (PREO) is a mixture of compounds extracted from blooming R. rugosa cv. Plena. With its elegant smell and excellent effects on oxidative stress and inflammation alleviation, PREO is wildly used in the food industry as a popular additive. We aimed to decipher if the PREO could alleviate and restore DSS-induced barrier integrity damages. The results showed that a 7-day PREO treatment alleviated the colitis symptoms and improved permeability depending on gene expressions. Methods: There are total five groups: Control (S1-S3), DSS model group(S4-S6), Mesalazine (60mg/kg) standard drug group(S7-S9) , 5μL/kg PREO group (S10-S12) and 15μL/kg PREO group (S13-S15).The distal colon sample was divided into two parts and was collected in RNase-free 1.5 mm tubes. One part (n=3) was subjected to transcriptome analysis from each group. According to sequencing by synthesis (SBS) Technology, the Illumina high-throughput sequencing platform sequenced the cDNA library where base quality scores can reach or exceed Q30. The edgeR was used for analysis between sample groups to attain differentially expressed gene (DEG) sets between two biological conditions. To detect DEGs, the Fold Change=1.5 and p-value≤0.05 were determined as the screening criteria. False Discovery Rate (FDR) was obtained through a significant difference in p-value calibration. Pathway significant enrichment analysis was done by taking Pathway in the KEGG database as the unit, to find pathways that are significantly enriched in DEGs compared with the background of the entire genome(Kanehisa et al., 2008). Results: According to our extensive transcriptome analysis, PREO revealed their relevancy in anti-inflammation significantly. DSS upregulated 1041 DEGs than the control group while PREO downregulated 670 DEGs compared to the DSS group (p≤0.05; FC=1.5). The KEGG enrichment presented in DSS-induced mice showed high enrichment in different inflammatory pathways while PREO and mesalazine lowered the enrichments. PREO (15μL/kg) revealed the downregulation of most of the DEGs involved in inflammatory responses . According to transcriptome analysis, Lbp, Prss3, Reg2, Reg3b, Reg3g, CxCl9, and CxCl10 were the significant genes that were over-expressed by LPS. There were several inflammatory signaling pathways like MAPK, NF-κB, IL-17, Chemokine signaling, JAK-STAT, TNF-α, Mucin biosynthesis, tight Junction, etc. Several digestive pathways, such as carbohydrate, cholesterol, and protein metabolisms, were also significantly upregulated by LPS. However, proteins from Lbp, Prss3, Reg2, Reg3b, Reg3g, CxCl9, and CxCl10 were connected in one protein-protein interaction network (PPI). PREO remarkably downregulated all these genes and pathways.
DOI: 10.48577/jpl.dafnha
title: Microwave Radiometer Calibration Using Deep Learning with Reduced Reference Information and Two-Dimensional Spectral Features

description: The accuracy of geophysical retrievals from ra- diometers relies on the quality of calibrations, which encompasses both absolute radiometric accuracy and spectral consistency. Ra- diometers have employed various calibration techniques, which include the utilization of external calibration targets, vicarious sources, and internal calibrators like noise diodes or matched reference loads. Calibration techniques pose several significant challenges such as frequency dependence, instrumental effects, environmental influences, drift, aging, and radio frequency in- terference. Recent advancements in hardware and processing units have enabled passive radiometers to collect raw samples of the observed scene that contain both temporal and spectral information. Leveraging advanced modeling techniques such as deep learning (DL) architecture can detect subtle correlations, non-linear dependencies, and higher-order interactions within the data. This capability allows them to extract valuable information that may have been difficult to capture using conventional methods. This study will utilize NASA’s Soil Moisture Active Passive (SMAP) satellite’s level 1A and level 1B data products to develop a DL-based radiometer calibrator to estimate antenna temperature. Spectrograms of second raw moments equivalent to power carrying the two-dimensional spectral features will be the primary input in a supervised convolutional neural network- based architecture. DL-based calibrator has demonstrated high R2 and low root mean square error when incorporating spectral information from both reference and noise diodes and when not considering this information. The findings from this analysis will suggest that the ancillary features in DL-based calibrators such as internal thermistor temperature and loss elements exhibit sufficient accuracy in estimating antenna temperature to compen- sate for variations in receiver noise temperature and short-term gain fluctuations in the absence of the reference load and noise diode power. The proposed calibration technique with reduced reference information might enable radiometers for a higher number of antenna scene observations within a footprint.