cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13032740.v2
title: Data and R codes for: Novel trophic interactions under climate change promote alpine plant coexistence

description: ============================================================<br>============================================================<br>============================================================<br><b><br></b><b>When using these datasets, please cite the following references:</b><br>Descombes, P., et al. (2020). Novel trophic interactions under climate change promote alpine plant coexistence. <i>Science</i>, 370(6523), 1469-1473.<br>P. Descombes et al., Data and R codes for: Novel trophic<br>interactions under climate change promote alpine plant<br>coexistence, FigShare (2020); https://doi.org/10.6084/<br>m9.figshare.13032740<br>============================================================<br>============================================================<br>============================================================<br><b><br></b><b>Datasets descriptions:<br></b><b><br></b>Details on the data sampling are fully described in the aforementioned references. The content of each datasets (rows and columns) are described in each datasets "readme" files. <br><br>
DOI: 10.6084/m9.figshare.13656029.v1
title: QUESTIONS ENG.xlsx

description: All complete answers from students partecipating to the survey.One file in English, one file in the original language used (Italian)<br>
DOI: 10.60893/figshare.jcp.28344026.v1
title: Supplemental Information

description: Additional details on the bulk modulus calculations, Green-Kubo approach, structural characterization, and gas diffusivity calculations.
DOI: 10.6084/m9.figshare.1326216.v1
title: Computed list of effective collision strengths for nebular [O III] optical and infrared lines with kappa electron energy distribution

description: The list consists of effective collision strengths in the electron excitation (Upsilon) and de-excitation (Downsilon) with a kappa electron energy distribution as a function of the electron temperature and kappa for 10 forbidden transitions between the five lowest energy levels of the astronomically abundant doubly-ionized oxygen ion, O^{2+}, in an intermediate coupling scheme using the Breit-Pauli relativistic terms as implemented in an R-matrix atomic scattering code. An atomic target for the R-matrix scattering defined by 72 atomic terms is used in these calculations with Gailitis averaging in the region beneath thresholds where the effective quantum number is greater than 10. The raw collision strength data are obtained from a list created previously by the authors (CDS VI/141). The limits of the effective collision strength data are the same as the limits of the original raw collision strength data, that is the data apply for a temperature range between about 100-25000 K with a free electron excitation energy up to about 1.3 Rydberg. These limits are adopted mainly for relevance to planetary nebulae and H II regions. The data can also be obtained from Centre de Donnees astronomiques de Strasbourg (CDS) database. The dataset associates the following publication: P.J. Storey, Taha Sochi. Effective collision strengths for excitation and de-excitation of nebular [O III] optical and infrared lines with kappa-distributed electron energies. Monthly Notices of the Royal Astronomical Society. DOI: 10.1093/mnras/stv484 See this link: http://cdsarc.u-strasbg.fr/viz-bin/qcat?VI/144
DOI: 10.6084/m9.figshare.28816019.v1
title: Good practice.pptx

description: The risks of the concept known as "Good Practice"
DOI: 10.6084/m9.figshare.7517399.v1
title: Combinatorial Analysis: from random method to systematic combinatorics

description: This research seeks to understand the psychogenesis of the combinatorial thought from the perspective of the genetic epistemology of Jean Piaget. It analyzes the mechanisms used by high school students in solving combinatorial analysis of experimental situations in order to understand how this notion is built by them. The thought of the subjects is analyzed emphasizing their similarities, as reasoning structures, when building possibilities. We believe that some school methods can hinder the construction of the formal reasoning, explaining the difficulties of young people in understanding combinatorial mechanisms.
DOI: 10.17632/kzrn9t5n3g
title: Paleoenvironments, Provenance, and Reservoir Characterization: Integrating Litho-Ichnofacies, Petrography, and Geochemistry of Compound Sandstone-Shale in the Jurassic Datta Formation, Western Salt Range, NW Himalayas (DATASET)

description: This dataset provides supporting materials for the manuscript "Paleoenvironments, Provenance, and Reservoir Characterization: Integrating Litho-Ichnofacies, Petrography, and Geochemistry of Compound Sandstone-Shale in the Jurassic Datta Formation, Western Salt Range, NW Himalayas." It includes detailed petrographic data, geochemical analyses, ichnofacies classifications, and sedimentological observations supporting interpretations of depositional environments, provenance, and reservoir potential.
DOI: 10.6084/m9.figshare.19029710.v1
title: Supplementary Material for: The Novel Inducer of Innate Immunity HO53 Stimulates Autophagy in Human Airway Epithelial Cells

description: Aroylated phenylenediamines (APDs) are novel modulators of innate immunity with respect to enhancing the expression of antimicrobial peptides and maintaining epithelial barrier integrity. Here, we present a new study on induction of autophagy in human lung epithelial cells by the APD HO53. Interestingly, HO53 affected autophagy in a dose-dependent manner, demonstrated by increased microtubule-associated proteins 1A/1B light-chain 3B (LC3B) processing in mature polarized bronchial epithelial cells. The quantification of LC3B puncta showed increased autophagy flux and formation of autophagosomes visualized by transmission electron microscopy. The phenotypic changes indicated that autophagy induction was associated with activation of 5′ adenosine monophosphate-activated protein kinase (AMPK), nuclear translocation of transcription factor EB (TFEB), and changes in expression of autophagy-related genes. The kinetics of the explored signaling pathways indicated on activation of AMPK followed by the nuclear translocation of TFEB. Moreover, our data suggest that HO53 modulates epigenetic changes related to induction of autophagy manifested by transcriptional regulation of histone-modifying enzymes. These changes were reflected by decreased ubiquitination of histone 2B at the lysine 120 residue that is associated with autophagy induction. Taken together, HO53 modulates autophagy, a part of the host defense system, through a complex mechanism involving several pathways and epigenetic events.
DOI: 10.17632/p2yryg9k6z
title: Gear wear run-to-failure dataset

description: This run-to-failure test (with and without lubrication) was conducted on the spur gearbox test rig at the University of New South Wales. The vibration signals were acquired regularly, at a 100 kHz sampling frequency and for a duration of 11 seconds. More descriptions can be found in 'Read me for data description'. 

When using this dataset, please give proper citations to our journal papers, which can be found using the related links.
DOI: 10.6084/m9.figshare.11321852.v1
title: Acknowledgement training dataset

description: Acknowledgement training dataset<br>
DOI: 10.6084/m9.figshare.14038334.v1
title: Supplementary Material for: International Observational Survey of the Effectiveness of Personal Protective Equipment during Endoscopic Procedures Performed in Patients with COVID-19

description: <b><i>Introduction and Aims:</i></b> This international survey was performed to evaluate the cumulative incidence of nosocomial novel coronavirus disease 2019 (COVID-19) among healthcare professionals during endoscopic procedures. <b><i>Methods:</i></b> We performed an international web-based self-reported questionnaire survey. Participants completed the questionnaires every week for 12 weeks. The questionnaire elicited responses regarding the development of COVID-19 and details of the personal protective equipment (PPE) used. <b><i>Results:</i></b> All 483 participants were included in the analysis. Participants had a mean age of 42.3 years and comprised 68.3% males. The geographic distribution of the study population was Asia (89.2%), Europe (2.9%), North and South America (4.8%), Oceania (0.6%), and Africa (1.5%). The most common endoscopy-related role of the participants was endoscopist (78.7%), and 74.5% had &gt;10 years of experience. Fourteen participants had performed 83 endoscopic procedures in patients positive for COVID-19. During the mean follow-up period of 4.95 weeks, there were no cases of COVID-19 when treating COVID-19 positive patients. The most common PPE used by participants treating patients with COVID-19 was a surgical mask plus N95 mask plus face shield, goggles, cap, long-sleeved isolation gown, and single pair of gloves. The most common PPE used by participants treating patients without COVID-19 was a surgical mask, no face shield but goggles, cap, long-sleeved isolation gown, and single pair of gloves during all endoscopic procedures. <b><i>Conclusions:</i></b> The risk of COVID-19 transmission during any endoscopic procedure was low in clinical practice.
DOI: 10.6084/m9.figshare.19499360.v1
title: patches and local annotations, slide 039, zoom 248x248 um2

description: patches and local annotations: data for slide with ID of the last 3 characters of the file name: local annotations in csv format and a folder with patches at zoom level indicated at the 6th character of the file name
DOI: 10.6084/m9.figshare.28088009.v1
title: Sequencing data on Inbred mice

description: Sequencing data on Inbred mice
DOI: 10.17632/nx94z23388
title: Data on the association of serum glypican-4 with prevalent and future kidney function

description: The present study included 456 patients who were referred to elective coronary angiography. Serum GPC4 levels were measured with a commercially available ELSIA kit. Glomerular filtration rate (GFR) was estimated (eGFR) using the ‘Chronic Kidney Disease Epidemiology Collaboration’ (CKD-EPI) serum creatinine equation. GFR categories were defined as follows: G1: eGFR≥90 mL/min/1.73 m2; G2: eGFR=60-89 mL/min/1.73 m2; G3a: eGFR=45-59 mL/min/1.73 m2; G3b: eGFR=30-44 mL/min/1.73 m2; G4: eGFR=15-29 mL/min/1.73 m2. Urinary albumin excretion was expressed as ACR in a random morning urine specimen. ACR levels lower than 30 mg/g (category A1) were defined as normal and albuminuria was diagnosed as an ACR of 30 mg/g or greater. CKD was diagnosed in case of eGFR ˂ 60 mL/min/1.73 m2 or albuminuria. After a mean period of 3.5 years, patients were re-invited to undergo a follow-up investigation and kidney function was reassessed. The Table includes baseline characteristics and GPC4 values as well as parameters of kidney function.
DOI: 10.4121/uuid:aa4a6ad5-e92c-468e-841b-de07f7133786
title: Global Tide and Surge Reanalysis (GTSR)

description: GTSR (Global Tide and Surge Reanalysis) is the first global reanalysis of storm surges and extreme sea levels based on hydrodynamic modelling. GTSR covers the entire world's coastline and provides estimates of extreme sea levels with a 1-in-100 year return period.
DOI: 10.6084/m9.figshare.11604195.v1
title: Supplementary Material for: SERINC5 Is an Unconventional HIV Restriction Factor That Is Upregulated during Myeloid Cell Differentiation

description: Classical antiviral restriction factors promote cellular immunity by their ability to interfere with virus replication and induction of their expression by proinflammatory cytokines such as interferons. The serine incorporator proteins SERINC3 and SERINC5 potently reduce the infectivity of HIV-1 particles when overexpressed, and RNA interference or knockout approaches in T cells have indicated antiviral activity also of the endogenous proteins. Due to lack of reagents for detection of endogenous SERINC proteins, it is still unclear whether SERINC3/5 are expressed to functionally relevant levels in different primary target cells of HIV infection and how the expression levels of these innate immunity factors are regulated. In the current study, analysis of <i>SERINC3/5</i> mRNA steady-state levels in primary lymphoid and monocyte-derived cells revealed selective induction of their expression upon differentiation of myeloid cells. Contrary to classical antiviral restriction factors, various antiviral α-interferon subtypes and proinflammatory interleukins had no effect on <i>SERINC</i> levels, which were also not dysregulated in CD4+ T cells and monocytes isolated from patients with chronic HIV-1 infection. Notably, HIV-1 particles produced by terminally differentiated monocyte-derived macrophages with high <i>SERINC5</i> expression, but not by low-expressing monocytes, showed a Nef-dependent infectivity defect. Overall, these findings suggest endogenous expression of SERINC5 to antivirally active levels in macrophages. Our results classify SERINC5 as an unconventional HIV-1 restriction factor whose expression is specifically induced upon differentiation of cells towards the myeloid lineage.
DOI: 10.6084/m9.figshare.24550819.v1
title: Supplementary Material for: Progression of Acute Lung Injury in Intratracheal LPS Rat Model: Efficacy of Fluticasone, Dexamethasone, and Pirfenidone

description: Introduction: We investigated the potential of LPS (10-300 µg/rat) administered i.t. to induce reproducible features of acute lung injury (ALI) and compared the pharmacological efficacy of anti-inflammatory glucocorticoids and antifibrotic to reduce disease. Additionally, we studied the time dependent progression of ALI in this LPS rat model. Methods: We conducted 1. Dose effect studies of LPS administered i.t. at 10, 30, 100, 300 µg/rat on ALI at 4 hr timepoint; 2. Pharmacological interventions using i.t. fluticasone (100, 300 µg/rat), i.t. pirfenidone (4000 µg/rat), and peroral dexamethasone (1 mg/kg) at 4 hr timepoint; 3. Kinetic studies at 0, 2, 4, 6, 8, 10 and 24 hr post LPS challenge. Phenotype or pharmacological efficacy was assessed using predetermined ALI features such as pulmonary inflammation, edema, and inflammatory mediators. Results: All LPS doses induced a similar increase of inflammation, edema, and inflammatory mediators e.g., IL6, IL1β, TNFα and CINC-1. In pharmacological intervention studies, we showed fluticasone and dexamethasone ameliorated ALI by inhibiting inflammation (&gt;60-80%), edema (&gt;70-100%), and the increase of cytokines IL6, IL1β, TNFα (≥70-90%). We also noticed some inhibition of CINC-1 (25-35%) and TIMP1 (57%) increase with fluticasone and dexamethasone. Conversely, pirfenidone failed to inhibit inflammation, edema, and mediators of inflammation. Lastly, in ALI kinetic studies, we observed progressive pulmonary inflammation and TIMP1 levels, which peaked at 6 hr and remained elevated up to 24 hr. Progressive pulmonary edema started between 2-4 hr and was sustained at later timepoints. On average, levels of IL6 (peak at 6-8 hr), IL1β (peak at 2-10 hr), TNFα (peak at 2 hr), CINC-1 (peak at 2-6 hr), and TGFβ1 (peak at 8 hr) were elevated between 2-10 hr and declined towards 24 hr post LPS challenge. Discussion/Conclusion: Our data show that 10 µg/rat LPS achieved a robust, profound, and reproducible experimental ALI phenotype. Glucocorticoids ameliorated key ALI features at the 4 hr timepoint but the antifibrotic pirfenidone failed. Progressive inflammation and sustained pulmonary edema were present up to 24 hr, whereas levels of inflammatory mediators were dynamic during ALI progression. This study data might be helpful in designing appropriate experiments to test the potential of new therapeutics to cure ALI.
DOI: 10.17632/pnrbbbfc6f
title: Dados sobre publicações decoloniais indexadas nas bases Scopus, Web of Science e OpenAlex

description: Este conjunto de dados foi gerado em 30/01/2025 a partir de buscas realizadas nas bases Scopus, Web of Science, Lens e OpenAlex. A pesquisa considerou publicações do ano de 2024 que contêm o termo "decolonial" nos títulos. Os dados foram processados para a elaboração do artigo correspondente. Os arquivos disponíveis neste repositório são: 1) vilker.pessin(decolonialScopus).csv – Dados extraídos da base Scopus; 2) vilker.pessin(decolonialWoS).xlsx – Dados extraídos da base Web of Science; 3) vilker.pessin(decolonialOAlex).csv – Dados extraídos da base OpenAlex; Esses dados podem ser utilizados para análises adicionais sobre a produção acadêmica relacionada à perspectiva decolonial em 2024.
Este conjunto de dados foi utilizado para contextualizar a produção científica sobre o tema decolonial, analisando como esse campo do conhecimento está indexado em diferentes bases de dados acadêmicas. A pesquisa teve como objetivo comparar a indexação das publicações que contêm o termo "decolonial" nos títulos, identificando padrões e discrepâncias entre as bases Scopus, Web of Science e OpenAlex. Além disso, a análise buscou compreender o predomínio do idioma inglês na disseminação internacional da produção acadêmica sobre o tema, verificando a proporção de publicações em diferentes idiomas e como elas são representadas nas bases indexadoras. Os dados coletados e processados permitiram uma reflexão sobre a visibilidade e acessibilidade do conhecimento "decolonial" no cenário global.
DOI: 10.6084/m9.figshare.11688327.v2
title: The genome sequence of Collichthys lucidus v2.0

description: The updated genome sequence of <i>Collichthys lucidus</i> from NCBI SCMI00000000. Moditifed some contigs position on chromosomes.
DOI: 10.6084/m9.figshare.16680679.v1
title: ALL D-Loop sequence.fas

description: d-loop sequence
DOI: 10.6084/m9.figshare.7857185.v1
title: STRING database ver.10.5 archive 9606 data sets

description: This data collection contains the data sets related to human (9606) that were previously deposed as separate datasets in STRING ver.10.5 before changing the download files structure with release of ver.11.0.<br>
DOI: 10.6084/m9.figshare.16543107.v2
title: Handcrafted features for fundus image classification

description: This dataset contains the hand-crafted features extracted for a number of images originating from the following public datasets: Kaggle DR and Messidor datasets,Indian Diabetic Retinopathy Image Dataset (IDRiD).
DOI: 10.21954/ou.rd.22123220.v1
title: RAW_SmallRingTensileTest_StainlessSteel316L_ExtensionRate1_1mmMin

description: This is a part of the test dataset (Digital Image Correlation Images and CSV data) that describes the experiments done at The Open University for the Small Ring Tensile Testing of SS316L performed at various displacement rates. Unprocessed images (.NEF format) start with the prefix 'RAW' while processed images (.TIF format) start with the prefix 'CLEAN'. The following letters after that describe the test type (Small Ring Test or Uniaxial Test), followed by the material. Lastly, after the material, the crosshead extension rate is described. For instance, 'Extension Rate0_3mmMin' refers to an extension rate of 0.3 mm/min and so on. The 'RAW' folders also contain the unprocessed CSV files. The 'CLEAN' folders contain the camera information (capture interval, ISO, etc) as well as the denoised CSV experimental files. The CSV files are denoised with the help of a Butterworth filter.
DOI: 10.6084/m9.figshare.24551530.v1
title: TEST files

description: TEST 11 bw files
DOI: 10.6084/m9.figshare.25755336.v1
title: Supplementary Material for: Navigating Challenges in a Case of Unusual Hepatic and Pulmonar Sarcoidosis: A Comprehensive Clinical Journey

description: Introduction: Sarcoidosis, a systemic granulomatous disorder with uncertain etiology, commonly involves the lungs and, to a lesser extent, the liver. 
Case report/presentation: A previously healthy 35-year-old Congolese female was admitted with a 7-month history of jaundice, itching and weight loss. Despite markedly mixed hepatitis of a cholestatic pattern of liver injury, liver function tests remained normal in admission lab work. Enlarged ethiological study was negative for infections, autoimmunity, heavy metal poisoning and metabolic diseases. Imaging aligned with compatible biopsy histology led to the diagnosis of hepatic and pulmonary sarcoidosis with vanishing bile duct syndrome. Despite initial treatment with ursodeoxycholic acid and corticosteroid therapy, the patient exhibited an unexpected exacerbation of liver enzymes, prompting a careful consideration of second-line interventions. Following discussion with a tertiary center and a comprehensive review of the literature, it was determined not to intensify therapy due to an inadequate response. Recognizing the persistent challenge of managing advanced cases and the potential progressive course of the disease, the patient was referred to a tertiary transplant center. Currently, she is under outpatient follow-up, clinical and analytically stable with no targeted therapy. 
Discussion/conclusion: This case report details a rare presentation of hepatic sarcoidosis with an unusual laboratory pattern, emphasizing diagnostic and management challenges in recognizing atypical presentations of hepatic sarcoidosis. The complexity of managing advanced cases warrants a multidisciplinary approach and the limited literature on this subject emphasizes the urgency for a more comprehensive understanding of sarcoidosis to improve diagnostic accuracy and refine therapeutic approaches.
DOI: 10.6084/m9.figshare.26548255.v1
title: SAR202 bacteria genomes

description: SAR202 is a group of Chloroflexota bacteria that are diverse and abundant in the ocean. SAR202 bacteria contain unique genomic features for degrading and transforming complex organic molecules, particularly for recalcitrant organic compounds (RDOM). Earlier studies have suggested that SAR202 bacteria are active and could play an important role in carbon cycling in the dark ocean. Metagenomics has recovered more SAR202 genomes from the deep ocean than the surface ocean due to their relatively high abundance in the deep water. This resulted in a less systematic understanding of SAR202 bacteria in the euphotic zone, in terms of their distribution, diversity, and genomic characteristics.
DOI: 10.17632/jp78ghsyv3
title: PDD Dataset

description: PDD dataset contains the response of 137 individuals from India based on the CDRS rating scale's questions based on behavioural characteristics of dysthymia.
DOI: 10.6084/m9.figshare.12593396.v3
title: dataset C21.xlsx

description: surface TRKBpTRKBcontextual fear conditioningelevated plus maze
DOI: 10.6084/m9.figshare.26128603.v1
title: Annotated variant files

description: Integrated risk models for prediction of hypertrophic cardiomyopathy in patients with unclassified variants
DOI: 10.6084/m9.figshare.13338101.v4
title: modified IEEE system parameter.docx

description: IEEE 33-bus, 123-bus data