cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/7jvdd7jwks
title: Parasite presence induces gene expression changes in an ant host related to immunity and longevity

description: Most species are either parasites or exploited by parasites, making parasite-host interactions a driver of evolution. Parasites with complex life cycles often evolve strategies to facilitate transmission to the definitive host by manipulating their intermediate host. Such manipulations could explain phenotypic changes in the ant Temnothorax nylanderi, the intermediate host of the cestode Anomotaenia brevis. In addition to behavioral and morphological alterations, infected workers exhibit increased survival, comparable to that of queens, which live up to two decades. We used transcriptomic data from cestodes and ants of different castes and infection status to investigate the molecular underpinnings of phenotypic alterations in infected workers, and whether the extended lifespan of queens and infected workers has a common molecular basis. To this end we sequenced the abdominal RNA of infected and uninfected ants of parasitized nests and queens and workers from unparasitized nests and assembled a transcriptome using StringTie. After filtering the transcriptome for those transcripts with an ORF greater or equal than 150 bp and filtering the gene count matrix for only those genes that had at least 5 counts in at least 3 samples, we first conducted a Principal Component Analysis. We tested each PC for its association with infection status and for the significant PCs we extracted the loadings of each gene (dataset S1). Moreover, we analyzed gene expression using DESeq2, comparing infected workers with their uninfected nestmates and on the other hand queens and their workers from unparasitized nests. The significant upregulated genes in each group can be found in the dataset S2. GO enrichment was performed using topGO on both the genes and their loadings on PC2 using a Kolomogorov-Smirnov test and the upregulated genes compared to the whole transcriptome using Fisher's exact tests (dataset S3). Afterward, we analyzed the overlap between genes upregulated in infected workers and in queens. Infected workers and queens commonly upregulated only six genes, one of them with a known anti-aging function. Our text-mining approach revealed that both groups overexpressed immune genes, although not the same ones. Our findings suggest that the lifespan extension of infected workers is not achieved via the expression of queen-specific genes. To be able to filter the abdominal RNA sequences of infected workers from cestode RNA, we additionally sequenced RNA of 320 cysticercoids and de novo assembled a transcriptome of A. brevis. The analysis of the cestodes’ transcriptome revealed dominant expression of genes of the mitochondrial respiratory transport chain indicating an active metabolism and shedding light on the physiology of the parasite in its cysticercoid stage (dataset S4).
DOI: 10.17632/r4x3n68cw8
title: Arquivo de dados

description: Base de dados; apresentação da proposta do programa para avaliação de aceitabilidade e viabilidade; questionário de avaliação.
DOI: 10.6084/m9.figshare.19474316.v2
title: Fern Tree of Life (FTOL) input data

description: The data included here are used in a pipeline that (mostly) automatically generates a maximally sampled fern phylogenetic tree based on plastid sequences in GenBank (https://github.com/fernphy/ftol). <br> The first step is to download the latest release of GenBank data from the NCBI GenBank FTP site (https://ftp.ncbi.nlm.nih.gov/genbank/) and use it to create a local database of fern sequences. This is done with custom R scripts contained in https://github.com/fernphy/ftol, in particular setup_gb.R (https://github.com/fernphy/ftol/blob/main/R/setup_gb.R). <br> Next, a set of reference FASTA files for 79 target loci (one per locus; ref_aln.tar.gz) is generated. These include 77 protein-coding genes based on a list of 83 genes (Wei et al. 2017) that was filtered to only genes that show no evidence of duplication, plus two spacer regions (trnL-trnF and rps4-trnS). Each FASTA file in ref_aln.tar.gz includes one representative (longest) sequence per avaialable fern genus. This is done with prep_ref_seqs_plan.R (https://github.com/fernphy/ftol/blob/main/prep_ref_seqs_plan.R). <br> Sequences matching the target loci are then extracted from each accession in the local database using the FASTA files contained in ref_aln.tar.gz as references with the “Reference_Blast_Extract.py” script of superCRUNCH (Portik and Wiens 2020). <br> The extracted sequences are aligned with MAFFT (Katoh et al. 2002), phylogenetic analysis is done using IQ-TREE (Nguyen et al. 2015) and divergence times estimated with treePL (Smith and O’Meara 2012). <br> For additional methodological details and references, see the README file included in this dataset and this paper:<br> <br> Nitta JH, Schuettpelz E, Ramírez-Barahona S, Iwasaki W. 2022. An open and continuously updated fern tree of life (FTOL). https://doi.org/10.1101/2022.03.31.486640<br>
DOI: 10.6084/m9.figshare.27133888.v1
title: Supplementary Tables from Quantifying age-specific household contacts in Aotearoa New Zealand for infectious disease modelling

description: Compressed folder containing Supplementary Table .csv files
DOI: 10.17632/htrzgc377c
title: MCC-specific survival for sex, chemotherapy, disease stage, and polyomavirus status

description: Supplemental Figure 3 for "Disease presentation and outcomes in Merkel cell carcinoma: A retrospective tertiary center cohort study"
DOI: 10.17632/jw6pz4krrh
title: STUDENTS' OPINIONS ON REMOTE LEARNING/ HALLGATÓI VÉLEMÉNYEK A TÁVOLLÉTI OKTATÁSRÓL

description: We aim to highlight the significant differences in the effectiveness of traditional teaching and emergency remote teaching. We formulated the hypotheses from the point of view of the students. Our study was registered and approved by ELTE PPK under number KEB-2020/102. H.1. Students are not too happy about online learning due to changes in their successful academic progress, lifestyle, and living conditions. H.2. Although the availability of ICT tools and the development of digital competencies are dispersed among students, those have a positive effect on the smooth transition H.3. Students have a general positive belief that their professors have handled subject activities and requirements with acceptable flexibility although the increase in the number of subjects and instructors is coupled with a more negative perception of faculty flexibility. Our research sample consists of 478 higher education students participating in voluntary data provision, who had the opportunity to be reached through personal acquaintance and various community of social media. Due to the low number of items and the strong inter-institutional dispersion of the respondents, our data are not representative, therefore they do not allow for national findings or comparisons between different higher education institutions. Our results point out the extraordinary efforts of students to stand up in remote learning as well as the differences in terms of the efficiency/organization of online education. In addition, some neuralgic points in the success of distance education, such as student and faculty anomalies in the knowledge and use of ICT tools, are highlighted. Our data also shed light on the shortcomings of the digital readiness of Hungarian higher education on the student and teacher side and the areas to be developed.
DOI: 10.6084/m9.figshare.23968008.v1
title: Meruelo UAV

description: RGB and TIR images of the Meruelo landfill photogrammetric flight.
DOI: 10.6084/m9.figshare.27259218.v1
title: Ethical committee attestation for the in vivo biological activities

description: This document contains the ethics committee's attestation for the study involving the biological activities of the essential oil of <i>Pelargonium graveolens</i> (PFEO). The document confirms that all in vivo and in vitro experiments conducted during the research complied with the ethical guidelines and standards applicable to scientific research. This attestation guarantees that the study complied with the required ethical considerations, particularly with regard to the use of animal models in the evaluation of the anti-inflammatory and analgesic properties of PFEO.
DOI: 10.6084/m9.figshare.22811765.v1
title: Changes in NPX values

description: Description The archive contains files with the changes (delta) in NPX values (one file for each of the four contrasted timepoints). dNPX_accpost Represent the effect of acclimation in the hyperthermic state. It was generated by subtracting the NPX values on day 1 (post) [<strong>hyperthermic, pre-acclimation</strong>] from the NPX values on day 7 (post) [<strong>hyperthermic, post-acclimation</strong>]. dNPX_accpre Represent the effect of acclimation in the normothermic state. It was generated by subtracting the NPX values on day 1 (pre) [<strong>normothermic, pre-acclimation</strong>] from the NPX values on day 7 (pre) [<strong>normothermic, post-acclimation</strong>]. dNPX_hd1 Represent the effect of heat exposure prior to acclimation. It was generated by subtracting the NPX values on day 1 (pre) [<strong>normothermic, pre-acclimation</strong>] from the NPX values on day 1 (post) [<strong>hyperthermic, pre-acclimation</strong>]. dNPX_hd7 Represent the effect of heat exposure post-acclimation. It was generated by subtracting the NPX values on day 7 (pre) [<strong>normothermic, post-acclimation</strong>] from the NPX values on day 7 (post) [<strong>hyperthermic, post-acclimation</strong>].
DOI: 10.17632/ckgb9zv7cg
title: Male rock hyraxes that maintain an isochronous song rhythm achieve higher reproductive success

description: Male hyrax reproductive success and categorical song rhythm ratios dataset. The data consists of three data objects: 

CV data: a summary of male annual reproductive success, body weights, social status and calculated coefficient of inter-call interval variance for songs recorded in the given year. 

Singing effort data: summary of male annual reproductive success, body weights, social status and singing effort (singing events/total behavioral events) 

Rhythmic proportions data: summary of male annual reproductive success, body weights, social status and calculated proportions between on-integer and off integer inter-call-interval ratios.
The provided data was used as an input for statistical analysis detailed in the paper and for drafting the corresponding figures. 

Scripts folder: an R script used for calculating Inter-call-interval rations, categorizing and normalizing them. A sample data set is provided
DOI: 10.17632/ndystc5t45
title: HO-Diagram Data

description: Data and Calculation Details for paper submitted to Case Studies in Thermal Engineering: Pels Leusden, C., Universal graphical representation of combustion processes for hydrocarbon fuels
DOI: 10.17632/xh4wmzxxg5
title: Data for: Agent-based modelling of interactions between air pollutants and greenery using a case study of Yerevan, Armenia

description: 1. List of activities of enterprises of Yerevan, Armenia 2. List of main enterprises of Yerevan, Armenia 3. List of main kindergartens of Yerevan, Armenia 4. List of node coordinates of main roads of Yerevan, Armenia 5. Data on initial radiuses of agent-emissions 6. Data on harmful emissions produced by enterprises of Yerevan, Armenia 7. Data on absorption characteristics of trees planted in Yerevan, Armenia
DOI: 10.17632/yxrfp9mszd
title: Geotagging Images using Geosetter in Google Earth Environment

description: Attachment: Methodology flow diagram & Final Outputs in kmz Coordinates were required to be assigned to a set of 50 images which were to be taken manually by the user. So, Images had to be procured, their locations were to be known and the location was required to be inscribed in the Image Metadata. Step 1: Obtaining Images + Location Google Earth has Google Photos which are uploaded by Individual users. These photos were enabled in Google Earth and each image was copied and pasted in MS Paint and then saved with an appropriate name At each image, the location pins were placed to mark the coordinates for each image Step 2: Extracting the coordiantes The marked pin locations in Google Earth were saved as: Save My Places -&gt; .kml This kml file was uploaded to https://mygeodata.cloud/converter/kml-to-csv to convert it into csv file to read the lat & long for each pinned markings Step 3: Embedding Coordinates in Image Metadata Geosetter Software enables us to embed coordinated in each Image file. Images were loaded in Geosetter and the subsequent coordinates were added with the Edit Data dialogue. The location name of each image was added in Object Name. The Images were then exported with thumbnail size=2000 and thumbnail={Object_Name}
DOI: 10.17632/gvkjpp87xj
title: Salazie - Reunion Island - landslide inventory

description: This repository contains the shapefiles of the landslides mapped in the study of Rault et al untitled Landslide processes involved in volcano dismantling from past to present: the remarkable open-air laboratory of the cirque of Salazie (La Réunion Island)), currently in review. 
Three shapefiles are given : 
- The shapefile of the landslides triggered during 1978-1984 mainly caused by Cyclone Hyacinthe (1980) 
- The shapefile of inactive landslide (not exaustive)
- The shapefile of active landslide

In addition, the shapefile of the limit of the cirque of Salazie used is provided. 

For more information please contact us.
DOI: 10.17632/7wzxh93p9z
title: Dosage- and site-dependent retention of black carbon and polycyclic aromatic hydrocarbons in farmland soils via long-term biochar addition

description: The supplementary material contains descriptions of the methods and relevant parameters of health risk assessment about polycyclic aromatic hydrocarbons, elemental composition of soil and biochar, contents of benzene polycarboxylic acid (BPCA) species and polycyclic aromatic hydrocarbon (PAH) species in the soil and biochar, scanning electron microscopy (SEM) image of fresh biochar, ontents of black carbon (BCBPCA), benzene polycarboxylic acid (BPCA) species, 18 polycyclic aromatic hydrocarbons (18PAHs) and polycyclic aromatic hydrocarbon (PAH) species in biochar.
DOI: 10.17632/bn46knt28h
title: TerraDactyl v1.0 software archive

description: TerraDactyl allows for the extraction of map layer data, currently curated by Google Earth Engine (GEE), at a set of point in space and time. It has been developed in tandem with eDNAExplorer.org as a means of automatically associated biodiversity data, derived from environmental DNA, with environmental conditions associated with each sample. However, these extracted environmental data can be associated with other types of data collected, not just biodiversity measurements.

Quick overview of this archive:
1. Example input file for TerraDactyl: TerraDactyl_ExampleInput.csv
2. Example output file from TerraDactyl: TerraDactyl_ExampleOutput.csv
3. Overview of environmental data sets utilized by TerraDactyl: TerraDactyl_Metadata.xlsx
4. Python requirements: requirements.txt
5. Script for processing environmental maps in raster format: RasterDataset.py
6. Script for processing environmental maps in vector format: VectorDataset.py
7. The TerraDactly script: terradactyl.py
8. Shell script for running terradactyl.py in parallel over input rows of metadata (These describe sample locations and dates).
DOI: 10.17632/ntr7r59p79
title: Dataset: Air Quality Index (AQI) of Major Indian Cities and Stations 25/4/2024

description: The dataset contains air quality information for various cities across India. It includes parameters such as Air Quality Index (AQI), concentrations of particulate matter (PM2.5 and PM10), ozone (O3), nitrogen dioxide (NO2), sulfur dioxide (SO2), carbon monoxide (CO), as well as geographical coordinates and time stamps. This dataset enables analysis and comparison of air quality levels among different cities, aiding in understanding environmental health impacts and informing policy decisions.
DOI: 10.17632/sf9mw4c5vv
title: Synergistic Integration of Leonardite coal derived humic acid assisted Graphene Oxide with Cerium oxide on LFP Cathodes

description: This study explores the impact of cerium oxide on improving the electrochemical performance and durability of lithium iron phosphate composite cathodes with reduced graphene oxide. The graphene oxide, derived from humic acid in leonardite coal, provides a sustainable alternative to conventional sources. CeO2 integration enhances cycling stability and rate capability, with CeO2-inlaid LFP achieving a good discharge capacity after 100 cycles, maintaining 99.99% capacity retention rate. These findings highlight CeO2’s potential in enhancing lithium-ion battery electrode materials.
DOI: 10.6084/m9.figshare.12331400.v2
title: Reference carbon cycle dataset for typical Chinese forests via colocated observations and data assimilation

description: Chinese forests cover most of the representative forest types in the Northern Hemisphere and function as a large carbon (C) sink in the global C cycle. The availability of long-term C dynamics observations is key to evaluating and understanding C sequestration of these forests. The Chinese Ecosystem Research Network has conducted normalized and systematic monitoring of the soil-biology-atmosphere-water cycle in Chinese forests since 2000. For the first time, a reference dataset of the decadal C cycle dynamics was produced for 10 typical Chinese forests after strict quality control, including biomass, leaf area index, litterfall, soil organic C, and the corresponding meteorological data. Based on these basic but time-discrete C-cycle elements, an assimilated dataset of key C cycle parameters and time-continuous C sequestration functions was generated via model-data fusion, including C allocation, turnover, and soil, vegetation, and ecosystem C storage. These reference data could be used as a benchmark for model development, evaluation and C cycle research under global climate change for typical forests in the Northern Hemisphere.
DOI: 10.6084/m9.figshare.14748471.v1
title: High temporal and spatial resolution of bioclimatic variables on central chile for different climate change scenarios and global circulation models

description: The original data set corresponds to the bioclimatic variables developed by Nix (1986) and used by Higmans (2005) to global data sets for Central Chile at a resolution of 500 meters.<br>The data was generated using daily data of mean minimum and maximum temperatures and precipitation was collected between 1980 and 2017. Temperature data from 103 and precipitation from 321 weather stations, respectively. Data quality control was performed to correct anomaly data, such as repeated values, unrealistic data within the time series. In addition, processing was applied for missing data in the time series that consisted of identifying the station with the least number of missing data, then applying multiple linear regression using the observed data related to the nearest stations. The atmospheric variables of Modern-Era Retrospective Analysis for Research and Applications, Version 2 (MERRA-2) reanalysis that are available for the entire period were included in the regression variables. This process was done iteratively to all required weather stations to complete missing data.<br>Statistical downscaling was performed using regressions that included geographic position and topography and subsequently a correction for bias using data assimilation. This method was applied to a set of CMIP5 GCMs that perform well in Central Chile. 14 GCMs were selected that by including their different assemblies make a total of 33 common data sets for the RCP26 and RCP85 scenarios.<br>To each of these data sets, the annual bioclimatic variables were calculated from 1980 to 2070. The data set was added at a resolution of 2 kilometers per repository capacity limit, but the original data is available upon request from gonzalo.carrasco@arauco.com <br>
DOI: 10.6084/m9.figshare.19188110.v1
title: Supplementary Table 2 from Lack of age-related mosaic loss of W chromosome in long-lived birds

description: Normalized coverage of W and Z chromosomes in females of with different ages for the Blue-footed Booby and the Magnificent Frigatebird
DOI: 10.6084/m9.figshare.25282735.v2
title: Source_data.xlsx

description: Aquaculture systems are expected to act as potential hotspots for nitrous oxide (N<sub>2</sub>O) emissions, largely attributed to substantial nutrient loading from aquafeed applications. However, the specific dynamics and contributions of N<sub>2</sub>O fluxes from these systems to the global emissions inventory are not well characterized due to limited data. This study delves into the N<sub>2</sub>O flux patterns across 127 freshwater systems to elucidate the role of aquaculture ponds and lakes/reservoirs in the N<sub>2</sub>O emission landscape. Our findings reveal that the average N<sub>2</sub>O flux from aquaculture ponds, at 28.73 μg N<sub>2</sub>O m<sup>‒2</sup> h<sup>‒1</sup>, is markedly elevated compared to that from lakes/reservoirs, which average 15.65 μg N<sub>2</sub>O m<sup>‒2</sup> h<sup>‒1</sup>. This translates to an increase of 3.63 and 3.05 times, respectively, over their non-aquaculture counterparts. Smaller aquaculture ponds, in particular, stand out as significant N<sub>2</sub>O emission hotspots, disproportionately emitting higher N<sub>2</sub>O fluxes relative to their area, a result of both elevated nutrient concentrations and more vigorous biogeochemical cycles. By integrating data from 40 published literature with our field measurements, we estimated China's freshwater aquaculture contributes 9,562 ± 3,061 Mg N<sub>2</sub>O per year (an increase of 35% from 2003 to 2022), equivalent to 25.2% of total N<sub>2</sub>O emissions from China’s inland water. After subtracting background emissions from natural water bodies, the net N<sub>2</sub>O emissions arising from aquaculture in China freshwater reach as high as 7,589 ± 2,409 Mg N<sub>2</sub>O per year, highlighting the significant impact of in situ aquaculture as a hotspot for freshwater N<sub>2</sub>O fluxes. In the context of the rapid global expansion of freshwater aquaculture, our findings underscore the critical need to factor in aquaculture's contribution to global N<sub>2</sub>O emissions from inland water bodies and its implications for achieving a low-carbon future.
DOI: 10.17632/vctnmwycht
title: Dataset for: Structural analysis of a novel N-carbamoyl-D-amino acid amidohydrolase from a Brazilian Bradyrhizobium japonicum strain: In silico insights by molecular modelling, docking and molecular dynamics.

description: 3D structures of D-NCAase after 50 ns of molecular dynamics simulations and ligands for virtual screening experiment.
DOI: 10.17632/jjjd7n8gyp
title: Dysbiosis of gut microbiota in pregnant women with pre-gestational type 2 diabetes mellitus

description: The clinical data of the participants which can be mathed to microbiome data by the same set of anonymized identifiers, the STORMS checklist is also provided.