cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.723377.v1
title: Simultaneous transcriptional profiling of Chlamydia and their host cells by heterogenous RNA-Seq (hRNA-Seq)

description: Bacterial pathogens subvert host cells by using their gene products to manipulate cellular pathways for survival and replication; in turn, host cells respond to invading pathogens through cascading changes in gene expression. Deciphering this complex temporal and spatial interplay is crucial for improved diagnostics and therapeutics. However, the technical limitations of existing methods of expression profiling, such as microarray analysis, significantly reduce their utility for obtaining both bacterial and host expression profiles from infected cells. We developed the heterogeneous RNA-Seq (hRNA-Seq) method to simultaneously capture prokaryotic and eukaryotic expression profiles of bacteria-infected cells. As proof of principle, hRNA-Seq was applied to <em>Chlamydia</em>-infected cells, successfully obtaining the transcriptomes of both <em>Chlamydia</em> and their host cells at 1 and 24 hours post-infection. Substantial transcription was found in the immediate-early period of infection for both <em>Chlamydia</em> and the host cell. Numerous novel host responses were found; in particular we discovered putative positive feedback mechanisms for <em>Chlamydia</em>-induced fibrotic scarring.
DOI: 10.6084/m9.figshare.7252406.v1
title: Supplementary Material for: Factors Associated with Acceptability, Consideration and Intention of Uptake of Direct-To-Consumer Genetic Testing: A Survey Study

description: <b><i>Background:</i></b> With interest in personalised health care growing, so is interest in personal genetic testing. This is now offered direct-to-consumer, thereby referred to as direct-to-consumer genetic testing (DTC-GT). Criticisms have been expressed on whether a truly informed decision to undergo testing is made with regard to these services. In order to provide relevant information to achieve this, knowing the characteristics of the expected user population is helpful. Therefore, the aim of this study is to identify characteristics of individuals who (1) find the concept of DTC-GT acceptable and (2) consider undergoing DTC-GT in the distant or near future. <b><i>Methods:</i></b> This cross-sectional study investigated factors associated with acceptability, consideration and intention in the Dutch general population. Studied variables included awareness, principles and how-to knowledge, attitude, innovativeness, and multiple demographic characteristics. Generalised linear models were applied to identify associated variables. <b><i>Results:</i></b> Full data was obtained for 836 respondents. Of those, 18.3% found DTC-GT somewhat or totally acceptable, whereas 12.6% considered and 5.5% intended to undergo DTC-GT in the distant or near future. Acceptability was greater with lower principles knowledge, and consideration and intention with lower how-to knowledge. A more positive attitude and greater innovativeness were associated with an increase in all 3 outcomes. <b><i>Conclusion:</i></b> Informed decision making may be hampered as individuals with lower how-to knowledge were found to be more interested in pursuing testing. The identified characteristics can be used in development and distribution of public and personalized information, in order to help consumers make a truly informed decision.
DOI: 10.17632/2c8fhjb9kj
title: Data for: Functional analysis of a polluted river microbiome reveals a metabolic potential for bioremediation of environmental significance pollutants

description: These data contain the list of selected "seed-sequences" for biodegradative and metal-related activities prediction by hidden Markov models (HMM) profiles, in Apatlaco river, Morelos state, Mexico. The Apatlaco river has 63 km in length and provides water to 10 state districts and an average of 2 million of people. The river receives 321 wastewater discharges, of which 49% come from industrial activities, 42% from the domestic sector and just 9% from farming. The aim of this research is to understand the functional and metabolic potential of the microbial communities in the Apatlaco river and highlight its relations with natural bioremediation capabilities. Also, we make publicly available the metagenomic assemblies generated for each of four sites sampled along the river (S1-S4). The assemblies were generated using Megahit v1.1.3 (Li et al., 2015) with the following parameters: --k-min 25 --k-max 75 --k-step 10 -m 0.4 --no-mercy.
DOI: 10.6084/m9.figshare.12830567.v2
title: Body mass records_DOetal.csv

description: Body mass is one of the most important phenotypic attributes in animal ecology and life history. This trait is widely used in the fields of ecology and macroevolution, since it influences physiology, morphological functions, as well as a myriad of ecological and social interactions. In this data set, our aim was to gather a comprehensive bird and mammal body mass data set from northern South America. We report body mass, discriminated by sex, for 42,022 individual birds and 7,441 mammals representing 1317 bird species (69% of Colombia’s avifauna) and 270 mammal species (51% of Colombian mammals) from the Neotropics. The data was sourced from vouchers collected between 1942 and 2020 and from individuals captured and released at banding stations over the last two decades for birds (2000 – 2020) and the last decade for mammals (2010 – 2020), by ten research groups and institutions in Colombia. This data set fills gaps identified in other similar databases, as it focuses on northern South America, a highly diverse Neotropical region often underrepresented in morphological data sets. We provide wide taxonomic coverage for studies interested in information both at regional and local scales.<br>
DOI: 10.6084/m9.figshare.16655140.v2
title: Indoor plant microbiome

description: Here we report results of experiments performed in a controlled climate chamber to characterize the diversity of bacterial communities inhabiting the growing media and leaves of five indoor plant species, and quantify microbial transfer dynamics and persistence on human skin following simulated touch contact events. To identify bacterial taxa, we sequenced the V3--V4 region of the 16S rRNA gene on an Illumina MiSeq 2X250 platform.
DOI: 10.6084/m9.figshare.29073143.v1
title: Panoramic segmentation

description: oucomes of the panoramic segmentation
DOI: 10.6084/m9.figshare.8014820.v1
title: Dataset of Natural Parasitism Behaviour of Microcharops anticarsiae

description: This is a dataset to describe the results on "Natural Parasitism Behaviour of<i> Microcharops anticarsiae</i> Gupta and its Sex Ratio in the Field and Laboratory".<br>
DOI: 10.6084/m9.figshare.28451807.v1
title: Heaven et al. Table1.xlsx

description: The Impact of Linear Energy Transfer on Micronuclei FormationSupplemental data for Heaven et al. 'Proton vs photon: Unravelling the Impact of Linear Energy Transfer on Micronuclei Formation'. Scientific Reports (2025). For raw data files, please contact precise@manchester.ac.uk.
DOI: 10.6084/m9.figshare.29143991.v1
title: Supplementary material for GPUMC

description: Supplementary material for CAV 2025 Paper:- GPUMC: A Stateless Model Checker for GPU Weak Memory Concurrency.
DOI: 10.6084/m9.figshare.7857050.v1
title: Dataset

description: The data consist of several items:1. PePeNDatabase is a database containing PE- and PEN- word whose multiple semantics roles2. PepenInflectionSingle is a database containing PE- and PEN- words which have inflection in it and single semantic role3. PepenSingleOccurence_NoMorphVar is a database containing PE- and PEN- words which have no inflection in it and single semantic role4. PepenMeberSimple is a database containing words with PE- and PEN- prefixes. This database also includes the base of MEN- prefix, BER- prefix, and monomorphemic words 5. AllVerbs is a database containing Indonesian verbs6. MeBer is a database containing verbs which have MEN- and BER- prefixes7. SimpleWords is a database containing monomorphemic words in the corpus
DOI: 10.17632/ghfycysjt3
title: JAAD Supplementary Materials : Evolution of the spectrum of drugs associated with acute generalized exanthematous pustulosis over time: a pharmacovigilance study

description: This is the Appendix where the supplementary methods, Tables and Figures of the article "Evolution of the spectrum of drugs associated with acute generalized exanthematous pustulosis over time: a pharmacovigilance study" are presented
DOI: 10.17632/vgxy5d9j93
title: Increased house mouse (Mus musculus) abundance in wetlands in response to Typha sp. flowering: implications for understanding wetland occupancy patterns of the eastern grass owl (Tyto longimembris)

description: This data was gathered to test the hypothesis that house mice abundance in south-eastern Australian wetlands during austral summer is due to increased monocot seeds (grass seeds). Data is presented in long-form displaying house mice abundance per wetland per survey in Microsoft Excel. Observations of eastern grass owls (Tyto longimembris) and eastern barn owls (Tyto alba delicatula) are also tabulated. Calculation code is also included which summarizes data per week and per Typha flowering period.
DOI: 10.6084/m9.figshare.11919753.v3
title: Genome-wide CRISPR screens of oral squamous cell carcinoma reveal fitness genes in the Hippo pathway

description: Supplementary dataset and source data for the elife article titled - Genome-wide CRISPR screens of oralsquamous cell carcinoma reveal fitnessgenes in the hippo pathway (https://elifesciences.org/articles/57761)
DOI: 10.6084/m9.figshare.12962291.v1
title: Supplementary Material for: Early Morphofunctional Changes in AngII-Infused Mice Contribute to Regional Onset of Aortic Aneurysm and Dissection

description: Aortic aneurysms and dissections are silent and lethal conditions, whose pathogenesis remains incompletely understood. Although angiotensin II (AngII)-infused ApoE−/− mice have been widely used to study aortic aneurysm and dissection, early morphofunctional alterations preceding the onset of these conditions remain unknown. The goal of this study was to unveil early morphofunctional changes underlying the onset of aneurysm and dissection. At 3 days post-AngII infusion, suprarenal abdominal aorta presented significant volumetric dilatation and microstructural damage. Ex vivo assessment of vascular reactivity of the suprarenal dissection-prone aorta and its side branches, showed an endothelial and contractile dysfunctions that were severe in the suprarenal aorta, moderate distally, and absent in the side branches, mirroring the susceptibility to dissection of these different vascular segments. Early and specific morphofunctional changes of the suprarenal aorta may contribute to the regional onset of aortic aneurysm and dissection by exacerbating the biomechanical burden arising from its side branches.
DOI: 10.6084/m9.figshare.14912838.v1
title: Soils chemical & physical data

description: Two files:<br>1. Bulk density<br>2. Chemical properties & textures report from BC Ministry of Environment analytical chemistry lab, including pH, Nitrogen, Phosphorus, texture, total carbon, active carbon, organic carbon.
DOI: 10.6084/m9.figshare.4822939.v1
title: Supplementary Material for: Poly-(ADP-Ribose) Polymerase-1 Promotes Prothrombin Gene Transcription and Produces Des-Gamma-Carboxy Prothrombin in Hepatocellular Carcinoma

description: <b><i>Background and Aim:</i></b> Although des-gamma-carboxy prothrombin (DCP) is a well-known tumor marker for hepatocellular carcinoma (HCC), the mechanism of DCP production is unclear. This study aimed to investigate the mechanism how DCP is produced in HCC cells. <b><i>Methods:</i></b> Levels of mRNA and DCP were analyzed by real-time polymerase chain reaction and electro-chemiluminescence immunoassay respectively. Secreted alkaline phosphatase (SEAP) expression vectors including deletion mutants of the prothrombin gene promoter were constructed for reporter gene assay. The transcription factors bound to DNA fragments were analyzed by mass spectrometry. An electrophoretic mobility shift assay (EMSA) was performed using a biotin end-labeled DNA. <b><i>Results:</i></b> The prothrombin mRNA levels in all 5 DCP producing cell lines were appreciably high. However, those in 2 DCP non-producing cell lines were below detectable levels. A SEAP vector with -2985 to +27 showed a very high transcription activity in DCP-producing Huh-1 cells. However, transcription abruptly decreased when the vector with -2955 to +27 was transfected, and then remained at the similar levels with larger deletion mutants, indicating the existence of a cis-element at -2985 to -2955 (31-bp). Mass spectrometry analysis identified the protein that bound to the 31-bp DNA as poly-(ADP-ribose) polymerase-1 (PARP-1). Knockdown of the PARP-1 gene by small interfering RNA in Huh-1 cells induced marked inhibition of prothrombin gene transcription. The EMSA clearly showed that PARP-1 specifically binds to the 31-bp DNA fragment in the prothrombin gene promoter. <b><i>Conclusions:</i></b> Our data suggest that PARP-1 activates prothrombin gene transcription and that the excessive prothrombin gene transcription induces DCP production in DCP-producing HCC cells.
DOI: 10.6084/m9.figshare.5129344.v1
title: Supplementary Material for: Estradiol Rapidly Attenuates ORL-1 Receptor-Mediated Inhibition of Proopiomelanocortin Neurons via G<sub>q</sub>-Coupled, Membrane-Initiated Signaling

description: Estradiol rapidly regulates the activity of arcuate nucleus (ARH) proopiomelanocortin (POMC) neurons that project to the medial preoptic nucleus (MPN) to regulate lordosis. Orphanin FQ/nociceptin (OFQ/N) acts via opioid receptor-like (ORL)-1 receptors to inhibit these POMC neurons. Therefore, we tested the hypothesis that estradiol excites POMC neurons by rapidly attenuating inhibitory ORL-1 signaling in these cells. Hypothalamic slices through the ARH were prepared from ovariectomized rats injected with Fluorogold into the MPN. Electrophysiological recordings were generated in ARH neurons held at or near -60 mV, and neuronal phenotype was determined post hoc by immunohistofluorescence. OFQ/N application induced robust outward currents and hyperpolarizations via G protein-gated, inwardly rectifying K<sup>+</sup> (GIRK) channels that were attenuated by pretreatment with either 17-β estradiol (E<sub>2</sub>) or E<sub>2</sub> conjugated to bovine serum albumin. This was blocked by the estrogen receptor (ER) antagonist ICI 182,780 and mimicked by the G<sub>q</sub>-coupled membrane ER (G<sub>q</sub>-mER) ligand STX and the ERα agonist PPT. Inhibiting phosphatidylinositol-3-kinase (PI3K) blocked the estrogenic attenuation of ORL-1/GIRK currents. Antagonizing either phospholipase C (PLC), protein kinase C (PKC), protein kinase A (PKA) or neuronal nitric oxide synthase (nNOS) also abrogated E<sub>2</sub> inhibition of ORL-1/GIRK currents, whereas activation of PKC, PKA, protein kinase B (Akt) and nNOS substrate L-arginine all attenuated the OFQ/N response. This was observed in 92 MPN-projecting, POMC-positive ARH neurons. Thus, ORL-1 receptor-mediated inhibition of POMC neurons is rapidly and negatively modulated by E<sub>2</sub>, an effect which is stereoselective and membrane initiated via G<sub>q</sub>-mER and ERα activation that signals through PLC, PKC, PKA, PI3K and nNOS.
DOI: 10.6084/m9.figshare.7339043.v1
title: Supplementary Material for: Long-Term Effect of Rifaximin with and without Lactulose on the Active Bacterial Assemblages in the Proximal Small Bowel and Faeces in Patients with Minimal Hepatic Encephalopathy

description: <b><i>Background:</i></b> Gut microbiota play an essential role in the pathogenesis of hepatic encephalopathy (HE). Treatment strategies are directed to modulate intestinal microbiota profiles and their function by the administration of the non-absorbable disaccharide lactulose and the non-absorbable antibiotic rifaximin, which are required for long terms, but little is known on their long-term effect on gut microbiota composition and function. <b><i>Aim:</i></b> To characterize the active bacterial assemblages in duodenum and faeces in patients with minimal HE (MHE) before, during and after long-term therapy with rifaximin. <b><i>Methods:</i></b> We analysed the microbiota composition in 5 patients with liver cirrhosis and MHE treated either with rifaximin 550 mg bid alone continuously for a period of 3 months or combined with lactulose 30–60 mL daily for 3 months. In addition to clinical assessments of HE, biopsies from duodenum and stool samples were analysed for their specific bacterial community applying NGS after RNA isolation before treatment, after 3 months of treatment and 3 months after the end of treatment. <b><i>Results:</i></b> All 5 patients had a significant improvement of their MHE. Bacterial communities were different and distinct in duodenal samples and faeces. No statistically significant changes were found in the bacterial community profile at the different time points. <b><i>Conclusion:</i></b> Rifaximin therapy with and without lactulose over a period of 3 months does not affect the bacterial community composition. The improvement of HE with rifaximin is lasting also after the end of treatment and therefore a prolonged effect on microbiota metabolic function is suggested.
DOI: 10.17632/vfwgmp5pnz
title: Data for: Effect of community-based lifestyle interventions on weight loss and cardiometabolic risk factors in obese elderly in China: a randomized controlled trial
DOI: 10.17632/x6j2f3fvsx
title: MuFA (Multi-type Fourier Analyzer): A tool for batch generation of MuMax3 input scripts and multi-type Fourier analysis from micromagnetic simulation output data

description: We present a tool for batch generation of input scripts and multi-type Fourier analysis from simulation results for the micromagnetic software MuMax3. The introduction of graphical user interface and parameter-sweeping functionality strongly speed up the input scripts creation and accelerate model optimization processes consequently. Three types of important Fourier analysis methods are provided for the acquisition of the quantitative frequency compositions, the spin-wave dispersion curve and the spatial distribution of spin-wave powers at different frequencies, respectively. Since the Fourier analysis is accelerated by parallel computations, the time cost is reduced to an acceptable level even in the presentation of tens of gigabytes data. With the MuMax3 and our proposal, a complete micromagnetic simulating tool chain from scripts generation to post analysis has been developed.
DOI: 10.25452/figshare.plus.24573268.v1
title: Oxfordshire human bloodstream infection isolate sequence data

description: <b>If you use this data, please cite:</b> Matlock, William, and Lipworth, Samuel et al. "Enterobacterales plasmid sharing amongst human bloodstream infections, livestock, wastewater, and waterway niches in Oxfordshire, UK." <i>Elife</i> 12 (2023): e85302.This dataset contains sequence data for <i>n</i>=738 human bloodstream Enterobacterales isolates collected from Oxfordshire, UK in 2008-2018:<b>assemblies.tar.gz:</b> Hybrid assemblies for all isolates, totalling 2618 circularised contigs (chromosomes and plasmids)<b>long_reads.tar.gz:</b> ONT long-reads for all isolates<b>short_reads.tar.gz:</b> Illumina paired-end short-reads for all isolates<br>
DOI: 10.6084/m9.figshare.27111262.v1
title: Extended_data.xlsx

description: This data refers to the paper titled "Iron’s role in soil organic carbon (de)stabilization in mangroves under land use change" (https://doi.org/10.21203/rs.3.rs-4650556/v1).
DOI: 10.6084/m9.figshare.5306497.v3
title: Data for: "Evolutionary history of Coleoptera revealed by extensive sampling of genes and species"

description: The raw sequences, concatenated datasets and phylogenetic results generated from the study "Zhang ert al. (2017) Evolutionary history of Coleoptera revealed by extensive sampling of genes and species"
DOI: 10.11583/dtu.27143514.v1
title: Monthly Surface Elevation Changes over the Greenland Ice Sheet from January 2011 to July 2024

description: Gridded monthly surface elevation changes covering the Greenland Ice Sheet
DOI: 10.17632/5cvszt4s3f
title: Actual operation data of electric vehicles form the NSMC-EV in Beijing

description: Actual operation data of electric vehicles form the National Electric Vehicle Service and Management Center (NSMC-EV) in Beijing, China.
DOI: 10.6084/m9.figshare.26321968.v1
title: SH2 domain related data by CoDIAC analysis

description: CoDIAC-derived data is included in this archive, including the reference human SH2-ome, annotated structures from PDB and AlphaFold, post-translational modifications, contact map features, mutations, etc.
DOI: 10.6084/m9.figshare.4903784.v2
title: Data and code for the Validation of a Spanish Questionnaire Implementing the Stanford Educational Framework for Evaluation of Clinical Teachers: MEDUC30

description: <b>Introduction</b>. Although there are instruments in Spanish to evaluate teacher performance during the initial basic science training years or during medical specialization; there are few instruments for the clinical training years, in which the main role of the teacher is to facilitate experiential learning. The MEDUC30 questionnaire is a Spanish instrument developed by the xx University School of Medicine. It was built using the Stanford Faculty Development Program (SFDP) educational framework for evaluation of clinical teachers’ effectiveness by students. MEDUC30 has been used since 2004 at Xx University and was previously studied with exploratory methods. <b>Objective</b>. To provide satisfying evidence of validity and reliability to support MEDUC30’s usefulness in Spanish-speaking contexts, using confirmatory analytical methods. <b>Method</b>. This is an analytical, longitudinal and retrospective study, in which 24,681 MEDUC30 questionnaires evaluating 579 clinical teachers were analysed. They were completed by medical students from 3rd to 7th year of study, from 2004 throughout 2015. The questionnaire’s structure was studied by exploratory (EFA) and confirmatory factor analysis (CFA). Measurement invariance was evaluated with multi-group CFA. <b>Results</b>. Four different models were compared; a bi-factor model was the best alternative to explain the data’s structure. It was composed of one general and six domain-specific factors: [i] Patient-Based Teaching, [ii] Communication of Goals, [iii] Evaluation and Feedback, [iv] Promotion of Understanding, Retention and Self-directed Learning, [v] Control of the Session, and [vi] Learning Climate. The overall reliability of MEDUC30 scores was excellent (Cronbach’s α = .98, McDonald’s ω = .98) and that of the six specific factors was very good (Cronbach’s α =.88-.95, McDonald’s ω = .78-.94). Measurement invariance extended over teacher gender, date, semester, year of study, clinical teaching setting, and length of clinical rotation; all of these variables were sources of population heterogeneity. <b>Conclusions</b>. MEDUC30 is a valid and reliable Spanish instrument to evaluate clinical teachers. It can be used to provide formative feedback of general and domain-specific effectiveness to clinical teachers and to provide accurate information to department heads and program directors for resource allocation and promotion purposes, and ultimately to improve clinical teaching quality.
DOI: 10.6084/m9.figshare.5155735.v1
title: Raw metabolomics data.csv

description: Serum metabolomic data from Black Angus steers