cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9973631.v1
title: Community structure – ecosystem function relationships in the Congo Basin methane cycle depend on the physiological scale of function. Meyer et al. 2020 MolEcol.

description: This is the dataset corresponding to Meyer et al. 2020. Molecular Ecology. Community structure – ecosystem function relationships in the Congo Basin methane cycle depend on the physiological scale of function. Please cite this manuscript when using any of these archived contents.<br>Sequences are of the V4 region of the 16S SSU rRNA gene, and were amplified using the 515F-806R primer combination.<br><br>Included here are:1) Quality-filtered fasta files 'seqs.filtered.fasta.gz'2) Meta data file with sample specific barcodes, biogeochemical process rates, soil chemical variables, and habitat category (see below for further details) 'MetaDataMolEcol_archive.txt'3) ASV community matrix of RNA- and DNA-based 16S rRNA gene sequences '16S_ASV_table_MolEcol.txt'4) ASV community matrix of RNA- and DNA-based 16S rRNA gene sequences, subsetted for known methanogens and methanotrophs '16S_Methanotroph_gen_subset_table_MolEcol.txt'5) qPCR data of mcrA gene abundances 'mcrA_qpcr.txt'6) qPCR data of pmoA gene abundances 'pmoA_qpcr.txt'7) Example of R code used to generate results of Meyer et al. 2020 Mol Ecol. 'Meyer_et_al_MolEcol_2020_analysis_example.R'8) Custom R functions that correspond to R code in item 7: 'Rarefy_mean.R' and 'NeedInHaystack_function.R'<br>The following meta data columns correspond to the biogeochemical processes presented in Meyer et al. 2020: 'CH4' is the rate of gross methanogenesis, 'H_CH4_percent' is the percent predominance of the hydrogenotrophic pathway, 'low_final_k' is the rate of high-affinity methanotrophy, and 'Vmax' is the rate of gross methanotrophy. Soil physico-chemical variables include: bulk density 'Bulk_dens', soil moisture content 'Mois_cont', pH 'pH', percent carbon 'C_percent', and percent nitrogen 'N_percent'. See publication for further details.
DOI: 10.17632/6gkkd7cvyb
title: dealy of gratification (SPSS)

description: The data collected for the study "The Impact of Delay of Gratification on EFL Learners' Grit, Self-Regulation, and Language Achievement", which is organized in the SPSS file. The data wad collected via an experimental study conducted in two groups to delve into teachers' application of delay of gratification  and its contribution to students' grit, self-regulation, ad language learning.
DOI: 10.17632/s4gxwzhmfk
title: Bonilla et al., Frontiers In Neuroscience 2024

description: Effects of Chronic Light Cycle Disruption during Adolescence on Circadian Clock, Neuronal Activity Rhythms, and Behavior in Mice
DOI: 10.6084/m9.figshare.28188326.v1
title: <b>Two haplotype-resolved telomere-to-telomere genome assemblies of </b><b><i>Xanthoceras sorbifolium</i></b>

description: Yellowhorn (<i>Xanthoceras sorbifolium</i>) is widely used for landscaping, desertification control, and oil production in northern China. However, the lack of high-quality genomes has hindered breeding and evolutionary studies. Here, we present the first haplotype-resolved, telomere-to-telomere (T2T) yellowhorn genomes of PBN-43 (white single-flowered) and PBN-126 (white double-flowered) using PacBio HiFi and Hi-C data. These assemblies range from 464.34 Mb to 468.97 Mb and include all centromeres and telomeres. Genome annotation revealed that an average of 67.99% (317.09 Mb) of yellowhorn genomic regions consist of repetitive elements across all haplotypes, and the protein-coding genes number range from 35,039 to 35,174 among assemblies, representing an average 50.16% increase compared to the first published yellowhorn genome. Additionally, 93.90% of the annotated genes have functional annotations.
DOI: 10.17632/5hbv6s26fd
title: Supplementary Data for “The Association of Psoriasis with Rheumatic Diseases: A National Cross-Sectional Study”

description: Supplementary tables from the article “The Association of Psoriasis with Rheumatic Diseases: A National Cross-Sectional Study,” published in the Journal of the American Academy of Dermatology
DOI: 10.17632/5p4zbpy8wz
title: SeLLaI Mal-Eng: Sentence Level Language Identification of Malayalam-English Code-Mixed Text

description: SeLLaI Mal-Eng is a thoroughly curated and annotated dataset designed for sentence-level language identification in Malayalam-English code-mixed text. The dataset comprises 22,400 sentences composed using English alphabets. The dataset file is organized into two columns: sentence and language. The language annotation is categorized into three distinct classes: Manglish, Code-Mixed, and English. The sentences that belong to the Malayalam language and are composed using English alphabets are annotated as Manglish. Manglish sentences may consist of either only Malayalam words written in English alphabets or a combination of Malayalam and English words. Sentences containing words formed by combining Malayalam and English words where Malayalam suffixes are added to the end of English words or parts of English to enhance comprehension for Malayalam speakers are annotated as Code-Mixed. Sentences belonging to the English language and easily recognizable by English speakers are annotated as English.
DOI: 10.17632/zys8crj7jw
title: Business Cycle Synchronization and Asymmetry in the Eurozone

description: This code and data replicate the results in the Manuscript ECMODE-D-23-00367R2 "Business Cycle Synchronization and Asymmetry in the European Union" written by Vladimir Arčabić, Irina B. Panovska and Josip Tica. The ReadMe File provides the instructions for replicating the results. The user will need RATS version 10.0 and Stata version 17 to replicate the main results. Other than that, R version 4.1.3 and Gauss version 19 or later are required to replicate results regarding principal component, individual nonlinear output gaps, and the Phillips curve coherent output gap and its weights. It will take up to 15 minutes to replicate the main results. 

Data sources: Quarterly seasonally adjusted data for real GDP, inflation, employment, and the unemployment rate are obtained from the Eurostat and OECD databases. Data and sources are explained in detail in the paper in section 3.1 Data. The raw data are saved in Excel files Data - GDP.xlsx, Data - Employment.xlsx, Data - Unemployment.xlsx, and Data - Inflation.xlsx in Linear gaps estimation folder and in the file Data_GDP_R1.xlsx in the Nonlinear gaps estimation folder. All data is publicly available and obtained from EUROSTAT and OECD. 

The replication files are organized in five folders: Linear gaps estimation, Nonlinear gaps estimation, Replication of Figures 3, 4 and 10, Replication of Figures 1-2, 5-8, 13 and Tables 1 and 2, Replication of Figures 9, 11 and 12
DOI: 10.6084/m9.figshare.19410476.v2
title: City climate and landscape structure shape pollinators, nectar and transported pollen along a gradient of urbanization

description: The datasets contain field and laboratory data used in the publication entitled "City climate and landscape structure shape pollinators, nectar and transported pollen along a gradient of urbanization" by Biella et al, Journal of Applied Ecology, 2022.<br>Pollinator abudance, nectar sugar and plant richness in pollen are given with site and coordinates.<br>Landscape and climate data can be obtained from public repositories as indicated in the Supporting Information, Appendix A1 of the publication.
DOI: 10.17632/7kyx4vwpc6
title: online case discussion combined data

description: quantitative data for research project that investigated the effect of group size and group composition on online case-based instruction
DOI: 10.6084/m9.figshare.12998417.v1
title: Supplementary Material for: The Gut Microbiome of Adults with Allergic Rhinitis Is Characterised by Reduced Diversity and an Altered Abundance of Key Microbial Taxa Compared to Controls

description: <b><i>Introduction:</i></b> Unique gut microbial colonisation patterns are associated with the onset of allergic disease in infants; however, there is insufficient evidence to determine if aberrant microbial composition patterns persist in adult allergic rhinitis (AR) sufferers. <b><i>Objective:</i></b> To compare the gut microbiome composition between adult AR sufferers and controls. <b><i>Methods:</i></b> Gut microbial composition in stool samples was compared between 57 adult AR sufferers (39.06 ± 13.29 years) and 23 controls (CG; 36.55 ± 10.51 years) via next-generation sequencing of the V3–V4 hypervariable regions of the 16S rRNA gene. Taxonomic classification and identity assignment was performed using a reference-based approach with the NCBI database of 16S rRNA gene sequences. <b><i>Results:</i></b> Species richness determined via the Shannon index was significantly reduced in the AR cohort compared to the CG (4.35 ± 0.59 in AR vs. 4.65 ± 0.55 in CG, <i>p</i> = 0.037); trends for reductions in operational taxonomic unit (OTU) counts, inverse Simpson, and CHAO1 diversity indices were also noted. Bacteroidetes (<i>p</i> = 0.014) was significantly more abundant in the AR group than in the CG. In contrast, the Firmicutes phylum was significantly less abundant in the AR group than in the CG (<i>p</i> = 0.006). An increased abundance of <i>Parabacteroides</i> (<i>p</i> = 0.008) and a reduced abundance of <i>Oxalobacter</i> (<i>p</i> = 0.001) and Clostridiales (<i>p</i> = 0.005) were also observed in the AR cohort compared to the CG. <b><i>Conclusion:</i></b> Adult AR sufferers have a distinct gut microbiome profile, marked by a reduced microbial diversity and altered abundance of certain microbes compared to controls. The results of this study provide evidence that unique gut microbial patterns occur in AR sufferers in adulthood and warrant further examination in the form of mechanistic studies.
DOI: 10.6084/m9.figshare.27239001.v2
title: Meta Dataset

description: Underlying data and CONSORT checklist for assessing effectiveness of Helfer skin Tap Technique on Pain among Infants undergoing Intramuscular Vaccination – A Randomized Controlled Trial.This RCT study examined the difference in pain score between groups receiving the following interventions: (1) Standard injection technique (2) Helfer skin tap technique. For this, a post-test control design was adopted.
DOI: 10.6084/m9.figshare.28045298.v1
title: Supplementary Material for: Therapy-related leukaemia Following docetaxel Chemotherapy for Metastatic Hormone-Sensitive Prostate Cancer: a case report

description: Introduction: Docetaxel is the first-line drug that has been proved to improve the overall survival of men with mHSPC. For patients who survive the prostate cancer, they may be at risk of secondary neoplasm, especially for the t-MDS or t-AML. Case presentation: We reported a 44-year-old man with prostate cancer (cT4N1M1c) who developed t-AML following docetaxel chemotherapy. Typically, the t-AML in our case was characterized by a aberrant karyotype t(15;17)(q22;q21).Conclusions: This case is, to our knowledge, the first time to report a patient with mHSPC who developed therapy-related acute promyelocytic leukemia following docetaxel chemotherapy, suggesting that docetaxel might contribute to the induction of t-AML.
DOI: 10.21233/5n1s-jp71
title: Lake Biwa, North Basin ostracode surface sample dataset

description: Raw data for the Lake Biwa, North Basin ostracode surface sample dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.6084/m9.figshare.19945478.v2
title: Census_1_and_2_stem_abundance

description: Dataset to examine stem abundance differences across two full censuses of Pālama Nui ForestGEO FDP.
DOI: 10.6084/m9.figshare.26300041.v1
title: Energy consumption

description: The dataset is related to the environmental conditions in the building and includes the type of room (living room or bedroom), time stamps, measured and modeled IATs, and error calculations. The dataset consists of 338 instances without missing values. Below is a detailed description of each column:· Type of room: living room or bedroom.· Date: This column records the date of the measurement or observation. The format is standard date format (e.g., YYYY-MM-DD). · Time: This column records the time of the measurement or observation. The format is in a standard time format (e.g., HH:MM).· Measured IAT: This column contains the measured indoor air temperature (IAT) at the given date and time.· Simulated IAT: This column contains the simulated indoor air temperature (IAT) generated by a simulation model at the given date and time.· err: This column represents the error between the measured IAT and the simulated IAT. It is calculated as the difference between the two values.
DOI: 10.6084/m9.figshare.16657456.v1
title: Supplementary Material for: Biomarkers in the Prediction of Hemorrhagic Transformation in Acute Stroke: A Systematic Review and Meta-Analysis

description: <b><i>Background:</i></b> Hemorrhagic transformation (HT) is a complication that occurs spontaneously or after thrombolysis in acute ischemic stroke (AIS) and can increase morbidity and mortality. The association of biomarkers with the risk of HT has been variably reported. We conducted a systematic review of the literature and meta-analysis and sought to compare blood biomarkers associated with HT and its subtypes by evaluating its predictability and correlation with outcome in AIS. <b><i>Methods:</i></b> The study protocol was registered in the PROSPERO database (CRD42020201334) and adhered to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. Among 2,230 articles identified from Cochrane Library, PubMed, and Web of Science databases, 30 quality-appraised articles were found eligible. Meta-analysis was conducted for matrix metalloproteinase-9 (MMP-9), cellular fibronectin (c-Fn), ferritin, S100 calcium-binding protein B (S100B), and neutrophil-lymphocyte ratio (NLR). We also reviewed biomarkers for correlation with the functional outcome at 90 days from stroke onset (poor outcome modified Rankin scale &gt;2). <b><i>Results:</i></b> The pooled diagnostic odds ratio (DOR<sub>pooled</sub>) was the highest for baseline c-Fn levels (299.253 [95% CI, 20.508–4,366.709]), followed by MMP-9 (DOR<sub>pooled</sub>, 29.571 [95% CI 17.750–49.267]) and ferritin (DOR<sub>pooled</sub>, 24.032 [95% CI 2.557–225.871]). However, wide confidence intervals for ferritin and c-Fn suggested lesser reliability of the markers. Patients with MMP-9 levels ≥140 ng/mL were 29.5 times at higher risk of developing symptomatic HT after AIS (area under the curve = 0.881). S100B (DOR<sub>pooled</sub>, 6.286 [95% CI, 1.861–21.230]) and NLR (DOR<sub>pooled</sub>, 5.036 [95% CI, 2.898–8.749]) had lower diagnostic accuracies. Among the markers not included for meta-analysis, caveolin-1, thrombin-activated fibrinolysis inhibitor, plasminogen activator inhibitor-1, and soluble ST2 were highly sensitive. Elevated levels of MMP-9, ferritin, and NLR were found to be associated with poor functional outcomes and mortality. <b><i>Conclusion:</i></b> Of the 5 biomarkers, there was enough evidence that MMP-9 has higher diagnostic accuracy for predicting the risk of HT before thrombolysis. MMP-9, ferritin, and NLR also predicted poor short-term outcomes.
DOI: 10.6084/m9.figshare.19103030.v1
title: Supplementary Material for: New Report of a Different Clinical Presentation of <b><i>CD151</i></b> Splicing Mutation (c.351+2T&gt;C): Could <b><i>TSPAN11</i></b> be Considered as a Potential Modifier Gene for <b><i>CD151</i></b>?

description: CD151, a member of the tetraspanin family, is essential for normal development of skin and kidney. To date, only 2 pathogenic variants of the <i>CD151</i> gene have been identified in a related disorder with recessive inheritance. Here, in the third study of <i>CD151</i> mutations, we report 3 affected siblings presenting variable degrees of renal and dermal symptoms. Whole exome sequencing (WES) was performed on the proband, followed by data analysis and in silico assessments. Confirmation of the mutation in the other patients were carried out using Sanger sequencing. The consequence of the <i>CD151</i> mutation was investigated by RNA extraction and Sanger sequencing of PCR products from cDNA. Multiple computational tools were applied for protein alignment, homology modeling, and molecular interaction analysis. WES revealed the variant c.351+2T&gt;C, NM_139029 (GRCh37) in <i>CD151</i>, and this was confirmed by Sanger sequencing in all patients. This variant is the result of a substitution of nucleotide T with C that changes the position +2 of the donor splice site in intron 5, leading to total loss of exon 5 from the transcript. The mentioned variant was not found in population allele frequency databases, and prediction tools concurred in its damaging effect on the protein. Based on the criteria from ACMG guidelines, this variant is pathogenic. Interestingly, in terms of clinical findings, symptoms and severity of the disease in the patients in this study were different compared to the previous report of the mutation and the disease. In addition, in silico analysis in this study appears to suggest a candidate protein, Tetraspanin-11 (TSPAN11), that could partially modify CD151 functions. This study supports the pathogenic effect of the <i>CD151</i> variant c.351+2T&gt;C, highlights the extensive variable expressivity amongst patients, reinforces the contribution of genomic content to clinical characteristics of <i>CD151</i> mutations, and accentuates the importance of modifier genes.
DOI: 10.6084/m9.figshare.5128141.v1
title: Supplementary Material for: A Comprehensive Atlas of the Adult Mouse Penis

description: Mice are routinely used to study the development of the external genitalia and, in particular, the process of male urethral closure. This is because misplacement of the male penile urethra, or hypospadias, is amongst the most common birth defects reported in humans. While mice present a tractable model to study penile development, several structures differ between mice and humans, and there is a lack of consensus in the literature on their annotation and developmental origins. Defining the ontology of the mouse prepuce is especially important for the relevance and interpretation of mouse models of hypospadias to human conditions. We have developed a detailed annotation of the adult mouse penis that addresses these differences and enables an accurate comparison of murine and human hypospadias phenotypes. Through MRI data, gross morphology and section histology, we define the origin of the mouse external and internal prepuces, their relationship to the single human foreskin as well as provide a comprehensive view of the various structures of the mouse penis and their associated muscle attachments within the body. These data are combined to annotate structures in a novel 3D adult penis atlas that can be downloaded, viewed at any angle, and manipulated to examine the relationship of various structures.
DOI: 10.6084/m9.figshare.5576407.v1
title: The taxonomic position and breeding range of Golden Nightjar <i>Caprimulgus eximius</i> (Caprimulgidae)

description: Golden Nightjar <i>Caprimulgus eximius</i> is an apparently sedentary sub-Saharan species with a breeding range extending from Senegal and Mauritania to Sudan. Although genetic studies of nightjars and related Caprimulgiformes have been published previously, none has included Golden Nightjar. In this study, mitochondrial and nuclear DNA of a Golden Nightjar found dead in Western Sahara in April 2016 was sequenced and compared with other species in the genus <i>Caprimulgus</i>. It was concluded with strong support that Golden Nightjar is closely related to Egyptian Nightjar <i>C. aegyptius</i>. It is hypothesised that Golden and Egyptian Nightjars may have arisen by splitting of a single ancestral species into migratory and sedentary populations.
DOI: 10.17632/p8t3wxbs2r
title: Data for: Statistical and Geostatistical Spatial and Temporal Variability of Physico-Chemical Parameters, Nutrients, and Contaminants in the Tenango Dam, Puebla, Mexico.

description: The database contains information related to environmental variables of the Tenango dam, Puebla, 2015.
DOI: 10.17632/x5d5tfntrn
title: Supplementary Table 2

description: Types of treatment administered to melanoma patients (n=309)
DOI: 10.6084/m9.figshare.7105325
title: Supplementary Material for: Analysis of lncRNA-Associated ceRNA Network Reveals Potential lncRNA Biomarkers in Human Colon Adenocarcinoma

description: <b><i>Background/Aims:</i></b> Long non-coding RNAs (lncRNAs) acting as competing endogenous RNAs (ceRNAs) play significant roles in the development of tumors, but the functions of specific lncRNAs and lncRNA-related ceRNA networks have not been fully elucidated for colon adenocarcinoma (COAD). In this study, we aimed to clarify the lncRNA-microRNA (miRNA)-mRNA ceRNA network and potential lncRNA biomarkers in COAD. <b><i>Methods:</i></b> We extracted data from The Cancer Genome Atlas (TCGA) and identified COAD-specific mRNAs, miRNAs, and lncRNAs. The biological processes in Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) were analyzed for COAD-specific mRNAs. We then constructed a ceRNA network of COAD-specific mRNAs, miRNAs and lncRNAs and analyzed the correlation between expression patterns and clinical features of the lncRNAs involved. After identifying potential mRNA targets of 4 lncRNAs related to overall survival (OS), we conducted stepwise analysis of these targets through GO and KEGG. Using tissue samples from our own patients, we also verified certain analytical results using quantitative real-time PCR (qRT-PCR). <b><i>Results:</i></b> Data from 521 samples (480 tumor tissue and 41 adjacent non-tumor tissue samples) were extracted from TCGA. A total of 258 specific lncRNAs, 206 specific miRNAs, and 1467 specific mRNAs were identified (absolute log<sub>2</sub> [fold change] &gt; 2, false discovery rate &lt; 0.01). Analysis of KEGG revealed that specific mRNAs were enriched in cancer-related pathways. The ceRNA network was constructed with 64 lncRNAs, 18 miRNAs, and 42 mRNAs. Among these lncRNAs involved in the network, 3 lncRNAs (LINC00355, HULC, and IGF2-AS) were confirmed to be associated with certain clinical features and 4 lncRNAs (HOTAIR, LINC00355, KCNQ1OT1, and TSSC1-IT1) were found to be negatively linked to OS (log-rank p &lt; 0.05). KEGG showed that the potential mRNA targets of these 4 lncRNAs may be concentrated in the MAPK pathway. Certain results were validated by qRT-PCR. <b><i>Conclusion:</i></b> This study providing novel insights into the lncRNA-miRNA-mRNA ceRNA network and reveals potential lncRNA biomarkers in COAD.
DOI: 10.6084/m9.figshare.26038246.v4
title: First exploration of using geodetic GNSS sites to synchronously retrieve freeze-thaw state and unfrozen water content of seasonally frozen soil

description: This is the dataset supporting the paper "First exploration of using geodetic GNSS sites to synchronously retrieve freeze-thaw state and unfrozen water content of seasonally frozen soil" . See readme for details.
DOI: 10.6084/m9.figshare.13169498.v1
title: Binary Collisions Data

description: Data from experiments investigating attrition due to binary collision of two particles.