cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5287/ora-erx7kmw6a
title: Larger colony sizes favoured the evolution of more worker castes in ants

description: Data consists of a single Excel file that contains trait information for 794 species of ants. References for the data are contained in a separate file within this repository. We also upload the list of species that were excluded from the analysis with the justification for doing so provided in the supplementary material of the paper.

We collected data on five ant traits: (i) the number of discrete physical worker castes; (ii) colony size (number of workers in mature colonies); (iii) effective queen mating frequency (estimated number of mates weighted by the proportion of offspring sired by each male; referred to as ‘queen mating frequency’); (iv) observed number of queens per colony; and (v) variation in worker size. We started by gathering data from major reviews, comparative studies, and books, and then performed a topic search of the primary literature using Web of Science. In total, we collected data for 794 species from 160 different genera.

All analyses performed in either R or BayesTraits V4.

Code can be found at GitHub:

https://github.com/LouisBell-Roberts/Larger_colony_sizes_favoured_the_evolution_of_more_worker_castes_in_ants
DOI: 10.6084/m9.figshare.27061261
title: Supplementary Material for: Wilson Disease and Nevus of Ota in a Child – Case Report

description: Introduction
 Wilson's disease is a rare autosomal recessive disorder that disrupts copper metabolism. It presents with distinctive ocular manifestations. Oculodermal melanosis, commonly referred to as Nevus of Ota, is a painless condition characterized by hyperpigmentation in and around the eye. In this case report, we describe the unique occurrence of both conditions in this pediatric patient.
Case presentation
A ten-year-old girl exhibited classic ocular signs associated with Wilson's disease, including Kayser-Fleischer rings and sunflower-type cataracts. Additionally, she displayed unilateral confluent gray-blue hyperpigmentation consistent with a nevus of Ota. As of now, the patient remains asymptomatic, with preserved visual acuity.
Conclusion
To the best of our knowledge, this case represents the first report of Nevus of Ota in a child diagnosed with Wilson's disease.
DOI: 10.17026/dans-xnc-h2fu
title: ITCVD Dataset

description: ITCVD dataset is a large-scale, well annotated and challenging vehicle detection dataset.The images were taken from an airplane platform which flied over Enschede, The Netherlands, in the height of ca $330$m above the ground.The images are taken in both nadir view and oblique view.The tilt angle of oblique view is 45 degrees.The Ground Sampling Distance of the nadir images is 10cm.In total, 173 images are selected among which 135 images with 23543 vehicles are used for training and the remaining 38 images with 5545 vehicles for testing.Each vehicle in the dataset is manually annotated using a bounding box.
DOI: 10.17632/gydhpktxjk.2
title: Test to Graph

description: This Excel Spreadsheet contains some macros. It is developed to automize the whole kinematic calculations for the LVI impact test.
İmportant Notes:
1. These codes were generated for PCB M202B Quartz Force Ring sensor. If anyone uses any other force sensor, he/she must change the conversion factor in the codes.
2. The LVI rig has 15.5 kg mass of a impactor.  If anyone uses different from the existing one, he/she must change the mass of the impactor. The password of the "Template" sheet is "a".
DOI: 10.5066/p9gd8i7a
title: Predicting water temperature in the Delaware River Basin

description: Daily temperature predictions in the Delaware River Basin (DRB) can inform decision makers who can use cold-water reservoir releases to maintain thermal habitat for sensitive fish and mussel species. This data release supports a variety of flow and water temperature modeling efforts and provides the inputs and outputs of both machine learning and process-based modeling methods across 456 river reaches and 2 reservoirs in the DRB. The data are organized into these items: This research was funded by the USGS. Waterbody Information - One shapefile of polylines for the 456 river segments in this study, a reservoir polygon metadata file, and one shapefile of reservoir polygons for the Pepacton and Cannonsville reservoirs Observations - Water temperature and streamflow observations for river reaches used in this study. Water temperature and streamflow observations for inflow and outflow reaches of the Pepacton and Cannonsville reservoirs. Water temperature, water level, and release observations for the Pepacton and Cannonsville reservoirs. Model Configurations - Model parameters and metadata used to configure GLM 3.1 reservoir models Model Inputs - Data used to drive predictive models (distance matrices, river reach metadata, daily meteorology for river reaches and reservoirs, observed reservoir diversions and releases) Model Predictions - PRMS-SNTemp predictions of water temperature for inflow and outflow reaches of the Pepacton and Cannonsville reservoirs, GLM 3.1 predictions of ourflow and water temperature for reservoir outflow reaches, GLM 3.1 predictions of in-reservoir water temperatures at the depth of reservoir outlets, stream temperature predictions from the distance-weighted-average lotic-lentic input network, and 7-day ahead deep learning water temperature forecasts at 5 priority sites.
DOI: 10.5281/zenodo.10424148
title: Utilização da lógica fuzzy para a produção de um substrato específico para a alface
DOI: 10.5281/zenodo.11204059
title: Effect of Soil Moisture on Future Heatwaves over Eastern China: Convection-Permitting Regional Climate Simulations

description: Data used in the manuscript "Effect of Soil Moisture on Future Heatwaves Over Eastern China: Convection-Permitting Regional Climate Simulations" which will be submitted to Journal of Geophysical Research: Atmospheres.
DOI: 10.5281/zenodo.11486725
title: Haplotype-resolved and near-T2T assembly of the African catfish (Clarias gariepinus)

description: Airbreathing catfishes are a group of stenohaline freshwater fish that can withstand various environmental conditions and farming practices, including the ability to breathe atmospheric oxygen. This unique ability has allowed them to thrive in semi-terrestrial habitats. However, the genomic mechanisms underlying their adaptation to adverse ecological conditions remain to fully investigate, due to the absence of gold standard reference genomes. The present study aimed to sequence and characterize the genome of the African catfish (Clarias gariepinus), a representative air-breathing catfish, to elucidate the genomic underpinnings of its remarkable adaptability. By generating a near telomere-to-telomere (T2T) assembly with high-resolution haplotypes, we sought to identify genomic and evolutionary features that may have contributed to its ability to withstand adverse conditions and transition to semi-terrestrial life. \textbf{Methods:} We conducted a comprehensive genomic analysis of the African catfish using a multi-platform sequencing approach, integrating Oxford Nanopore, PacBio HiFi, Illumina, and Hi-C technologies to achieve a haplotype-resolved chromosome-scale genome assembly. Functional annotations and comparative genomic analyses, including gene family evolution and positive selection studies, were performed to identify the genomic mechanisms underlying the species' resilience and adaptation to diverse environments. Results: This multifaceted approach has provided novel insights into the African catfish's complex genomic architecture and adaptive strategies. The near-T2T diploid assembly yielded 48 contigs spanning 969.62 Mb with a contig N50 of 33.71 Mb. We report 25,655 predicted protein-coding genes and 43.94\% repetitive elements in the African catfish genome. Several gene families involved in ion transport, osmoregulation, oxidative stress response, and muscle metabolism were expanded and positively selected in clariids, suggesting a potential role in their transition and adaptation to semi-terrestrial habitats. Conclusion: Our study provides a comprehensive genomic resource for \textit{Clarias gariepinus}, shedding light on the genetic and genomic mechanisms of clariids' adaptation to adverse ecological environments. The findings enhance our understanding of resilience in C. gariepinus and offer valuable insights for improving aquaculture and studying related teleosts.
DOI: 10.5281/zenodo.12250382
title: Raw Data of Polymerase Chain Reaction (qPCR) results of SCUBE3 and TGF-B expression

description: This raw data presents the qPCR results of SCUBE3 and TGF-B expression from each sample taken from the patient's pleural tissue. Each sample was divided into 14 groups consisting of two main control groups (control group with 1x1 cm preparation and 2x2 cm preparation) and 12 groups divided based on the length of incubation time (group incubated for 24 hours and group incubated for 72 hours). Each of these groups consisted of two groups divided by preparation size, namely the group with 1x1 cm preparation and 2x2 preparation. Each preparation group was further divided into three small groups based on treatment, namely the control group, the group with 50 µg EGCG administration, and 100 µg EGCG administration.
DOI: 10.5281/zenodo.12626856
title: ERA5 data to run example tutorials in RASCAL

description: This is data from 2000 to 2023 to run some examples of reconstructions with the RASCAL model. It contains the geopotential height at 925hPa, and the temperature at 2m
DOI: 10.5281/zenodo.12682958
title: BattModels/DiffMix-NatCommData: v1.0.2

description: Minor updates on README file and removing .DS_Store.
DOI: 10.5281/zenodo.13194967
title: Methane concentrations and oxidation rates in land-terminating glacial runoff: measurements from three glacial rivers and a paraglacial lake in Iceland and a literature review

description: This dataset contains methane measurements from Icelandic lakes and rivers during the summer of 2018 and 2019. This includes data from net methane oxidation assays with sediment and overlying water from one paraglacial lake and one glacial river, and surface methane concentration data from grab samples in 3 glacial streams and 15 Icelandic lakes (1 of which is paraglacial).  The dataset also contains methane concentration data from a synthesis of relevant aquatic ecosystems, used to compare against the original measurements collected. 




Data and Literature Review Synthesis is supplement to Strock et al. 2024 Oxidation is a potentially significant methane sink in land-terminating glacial runoff published in Nature Scientific Reports. 



This study was funded by: National Geographic Society Changing Polar Systems grant (CP4-162R-18); In-kind support from the U.S. Geological Survey; Dickinson College Research and Development; Churchill Exploration Fund at Dickinson College
DOI: 10.5281/zenodo.3715312
title: Reproducibility archive for MeDIP analyses of plasma DNA from brain tumour patients.

description: This contains the starting points, intermediate objects, and the code used to produce them that were used to generate the figures in the associated paper. For execution, please extract the contents of both the data and the markdowns/scripts folder into the same folder.
DOI: 10.5281/zenodo.4646970
title: Pharmacokinetic Named Entity Recognition Benchmark

description: Annotated data to perform Named Entity Recognition (NER) of pharmacokinetic (PK) parameters in scientific text. 

Training, development and test files are released in JSONL format and store the annoated data for training and evaluating NER models. 

Each line in the JSONL files corresponds to an annotated sentence with the following information: 



text: Raw sentence

spans: List of entities mentioned in the sentence, specifying: (1) the character-level boundaries and (2) the entity type of each annotation

SID: Unique sentence ID

metadata: Metadata with unique article, paragraph and sentence identifiers and the article section from which the sentence was extracted
DOI: 10.5281/zenodo.57102
title: Financial Capability Scale (Fcs)

description: The University of Wisconsin’s Center for Financial Security developed the Financial Capability Scale (FCS) with the support and Annie E. Casey Foundation in 2011 with the goal of developing a standardized client financial capability scale that could be used in the field with clients as well as in evaluation studies. In 2013, the Center conducted field testing to establish the reliability and validity of the scale. The FCS has been shown to be associated with credit use, credit scores, savings and financial attitudes. Although designed for financial coaching, the FCS can be applied to other financial capability services and programs.
description: Users may make small changes to the scale items as needed, including the reference period for questions (3 months in the most recent versions). These types of minor changes generally will not degrade the validity of the scale.
DOI: 10.5281/zenodo.7338401
title: Predictive modelling of brain metastasis risk and non-invasive biomarker detection using DNA methylation signatures

description: Methylated cell-free DNA was sequenced for 123 BM plasma and compared to plasma methylomes from 107 gliomas, central nervous system (CNS) lymphomas (CNSL), and non-CNS tumor controls. Plasma methylome-based classifiers of BM from other entities were built in fifty 80% discovery set iterations of 92/123 BM samples. External publicly-available tissue methylation data on 442 LUAD, 85 BM, and 146 glioma/CNSL/control samples were acquired for validation and the remaining 31/123 BM plasma samples were used for additional validation.
DOI: 10.5281/zenodo.8405311
title: Non-redundant metagenome-assembled genomes of activated sludge reactors at different disturbances and scales

description: Metagenome-assembled genomes (MAGs) are microbial genomes reconstructed from metagenomic data and can be assigned to known taxa or lead to uncovering novel ones. MAGs can provide insights into how microbes interact with the environment. Here, we performed genome-resolved metagenomics on sequencing data from four studies using sequencing batch reactors at microcosm (~25 mL) and mesocosm (~4 L) scales inoculated with sludge from full-scale wastewater treatment plants. These studies investigated how microbial communities in such plants respond to two environmental disturbances: the presence of toxic 3-chloroaniline and changes in organic loading rate. We report 839 non-redundant MAGs with at least 50% completeness and 10% contamination (MIMAG medium-quality criteria). From these, 399 are of putative high-quality, while sixty-seven meet the MIMAG high-quality criteria. MAGs in this catalogue represent the microbial communities in sixty-eight laboratory-scale reactors used for the disturbance experiments, and in the full-scale wastewater treatment plant which provided the source sludge. This dataset can aid meta-studies aimed at understanding the responses of microbial communities to disturbances, particularly as ecosystems confront rapid environmental changes.
DOI: 10.6084/m9.figshare.26039878
title: Chromosome-level baobab genome illuminates its evolutionary trajectory and environmental adaptation

description: Our study delves into the evolutionary history of the baobab tree, one of Earth's oldest non-clonal plants. Motivated by FDA recognition of baobab for food use and reports of historic tree deaths, we sought to provide genome-based insights. We began with skim sequencing and genome size estimation for all eight baobab species. Using Illumina and Oxford Nanopore Technologies, we created two chromosome-scale haploid Adansonia digitata assemblies and several long-read contig assemblies for baobabs from Namibia, Sudan, and Madagascar. Additionally, we collected leaf samples from 25 Adansonia digitata specimens across Africa for population genetics analyses. Despite challenges in seed germination and DNA extraction, we refined our methods to obtain high-quality DNA and RNA.Our research unveiled that Adansonia digitata is autotetraploid, unlike the other seven diploid species, and highlighted a proliferation of DNA transposable elements over long terminal repeat retrotransposons. We identified a whole-genome duplication event about 30 million years ago, leading to up to 16 copies of genes related to flower development, chromatin/transcription, and exocytosis. We hypothesize that genes associated with UV-B light perception and chromatin regulation contribute to the baobab's longevity. Additionally, our study revealed distinct baobab populations in Namibia linked to specific watersheds, suggesting geographical barriers to gene flow. These findings enhance our understanding of baobab diversity and inform breeding strategies.By sequencing and providing quality genomic data, we aim to advance conservation efforts and understanding of the baobab's evolutionary trajectory amidst climate change. Our chromosome-resolved genome assembly for Adansonia digitata represents a significant improvement over previous fragmented assemblies.
DOI: 10.6084/m9.figshare.27087523.v1
title: Geochemistry data MD07-3117_IX

description: High resolution spectrophotometric and magnetic susceptibility (MS) data acquired with the Multi-Sensor Core Logger (MSCL) of Ghent University. Elemental (C and N) and stable isotope (δ13C) data measured by Isotope Bioscience Laboratory (ISOFYS) of Ghent University (using EA-IRMS).
DOI: 10.6084/m9.figshare.27178938
title: Supplementary Material for: Impairment of Renal Function in Hermansky-Pudlak Syndrome

description: Introduction
Hermansky-Pudlak syndrome (HPS) is a rare autosomal recessive disorder characterized by defective biogenesis of lysosome-related organelles. The genetic types of HPS are associated with a spectrum of multisystemic clinical manifestations. Phenotypic features of HPS type 1 (HPS-1) or HPS-4, which are associated with defects in biogenesis of lysosome-related organelles complex-3 (BLOC-3), are generally more severe than those of HPS-3, HPS-5, or HPS-6, which are associated with defects in BLOC-2. A paucity of information is available about renal impairment in HPS. The objective of this study is to expand the understanding of kidney disease in HPS.
Methods
Medical records and clinical data of patients with HPS evaluated at the National Institutes of Health Clinical Center from 1995 to 2020 were retrospectively reviewed. For patients with more than one visit, the most recent renal function and urinalysis tests were analyzed. Estimated glomerular filtration rate (eGFR) was calculated using standard equations (i.e., Chronic Kidney Disease Epidemiology Collaboration, Modification of Diet in Renal Disease). Kidney tissue sections from five patients with HPS-1 and one patient with HPS-6 were examined.
Results
Records from 205 adults and 52 children with HPS were reviewed. Calculated eGFR of adult patients with different HPS types differed significantly, and calculated eGFR of pediatric and adult patients with BLOC-3 disorders was significantly lower than that of patients with BLOC-2 disorders. Linear regression analysis showed that renal function progressively decreases with age in patients with BLOC-3 or BLOC-2 disorders, but the rate of decline was more rapid in patients with BLOC-3 disorders compared to patients with BLOC-2 disorders. In adult patients with HPS-1, glucosuria was found in 4%, proteinuria in 12%, hematuria in 15%, high levels of urinary β2MG in 24%, and elevated urinary albumin to creatinine ratios in 9%. Histological examination of kidney tissue in showed accumulation of intracellular deposits of ceroid lipofuscin in proximal renal tubular epithelial cells in patients with HPS-1. There was no evidence of fibrosis, and glomeruli, distal renal tubular epithelial cells, and interstitial regions appeared histologically normal.
Conclusion
Mild impairment of renal function is a feature of HPS. Kidneys of patients with HPS-1 contain Proximal renal tubular intracellular deposits and no histologic evidence of fibrosis. Consistent with other manifestations of HPS, the phenotype of renal impairment is relatively more pronounced in patients with BLOC-3 disorders than in patients with BLOC-2 disorders. Strategies to avoid nephrotoxicity or renal tubular injury and to protect renal function should be considered for patients with HPS irrespective of age.
DOI: 10.6084/m9.figshare.27185751
title: Supplementary Material for: HUMAN PAPILLOMA VIRUS-RELATED ORAL MUCOSAL LESIONS IN TURKEY: A RETROSPECTIVE COHORT STUDY

description: Introduction: The human papillomavirus (HPV) is the aetiological agent of a variety of oral mucosal benign and pre/malignant lesions, which demonstrate a wide range of prevalence according to geographic regions.
Material and Methods: This study specifically examined the typing of HPV-associated oral mucosal lesions in Turkish patients. The DNA from FFPE blocks of 228 lesions was utilised for this purpose. A total of 87 oral mucosal lesions were classified as benign, 68 as premalignant, and 73 as malignant. DNA from these lesions was amplified using PCR, and genotypes were identified using restriction fragment length polymorphisms (RFLP). 
Results: HPV DNA was identified in 17 out of 228 patients, indicating a prevalence incidence of 7.4%. In benign oral lesions, the prevalence of HPV DNA was 9.2% (8/87 cases), whereas in premalignant, oral epithelial dysplasia (OED) and oral squamous cell carcinoma (OSCC) lesions, it was 6.9% (9/141 cases). A significant statistical difference was found between patients who tested positive for HPV and those who tested negative in terms of the location of the lesion and the age of the patients (p=0.0097, p=0.02, respectively).
Conclusions: This study underscores the considerable prevalence of HPV infection in oral mucosal lesions among individuals in Central Anatolia, Turkey.
DOI: 10.6084/m9.figshare.27200919
title: Supplementary Material for: Ultrarare Variants in DNA Damage Repair Genes in Pediatric Acute-Onset Neuropsychiatric Syndrome or Acute Behavioral Regression in Neurodevelopmental Disorders

description: Acute onset of severe psychiatric symptoms or regression may occur in children with premorbid neurodevelopmental disorders, although typically developing children can also be affected. Infections or other stressors are likely triggers. The underlying causes are unclear, but a current hypothesis suggests the convergence of genes that influence neuronal and immunological function. We previously identified 11 genes in Pediatric Acute-Onset Neuropsychiatry Syndrome (PANS), in which two classes of genes related to either synaptic function or the immune system were found. Among the latter, three affect the DNA damage response (DDR): PPM1D, CHK2, and RAG1. We now report an additional 17 cases with mutations in PPM1D and other DDR genes in patients with acute onset of psychiatric symptoms and/or regression that their clinicians classified as PANS or another inflammatory brain condition. The genes include clusters affecting p53 DNA repair (PPM1D, ATM, ATR, 53BP1, and RMRP), and the Fanconi Anemia Complex (FANCE, SLX4/FANCP, FANCA, FANCI, and FANCC). We hypothesize that defects in DNA repair genes, in the context of infection or other stressors, could contribute to decompensated states through an increase in genomic instability with a concomitant accumulation of cytosolic DNA in immune cells triggering DNA sensors, such as cGAS-STING and AIM2 inflammasomes, as well as central deficits on neuroplasticity. In addition, increased senescence and defective apoptosis affecting immunological responses could be playing a role. These compelling preliminary findings motivate further genetic and functional characterization as the downstream impact of DDR deficits may point to novel treatment strategies.
DOI: 10.6084/m9.figshare.972912
title: Proof by synthesis: Tobacco mosaic virus

description: Zipped tandem mass spectrum RAW files: 1-34CE-BSMV CP-30_Nben.RAW 1-34CE-ToMV CP-30_NNLL1.RAW 1-34CE-ToMV CP-30_NNLL2.RAW 1-34CE-ToMVnoorf6-30_Nben.RAW