cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19690618.v1
title: Supplementary Material for: <b><i>Staphylococcus aureus</i></b> Activates the Aryl Hydrocarbon Receptor in Human Keratinocytes

description: <i>Staphylococcus aureus</i> is an important pathogen causing various infections, including – as most frequently isolated bacterium – cutaneous infections. Keratinocytes as the first barrier cells of the skin respond to <i>S. aureus</i> by the release of defense molecules such as cytokines and antimicrobial peptides. Although several pattern recognition receptors expressed in keratinocytes such as Toll-like and NOD-like receptors have been reported to detect the presence of <i>S. aureus</i>, the mechanisms underlying the interplay between <i>S. aureus</i> and keratinocytes are still emerging. Here, we report that <i>S. aureus</i> induced gene expression of CYP1A1 and CYP1B1, responsive genes of the aryl hydrocarbon receptor (AhR). AhR activation by <i>S. aureus</i> was further confirmed by AhR gene reporter assays. AhR activation was mediated by factor(s) &lt;2 kDa secreted by <i>S. aureus</i>. Whole transcriptome analyses and real-time PCR analyses identified IL-24, IL-6, and IL-1beta as cytokines induced in an AhR-dependent manner in <i>S. aureus</i>-treated keratinocytes. AhR inhibition in a 3D organotypic skin equivalent confirmed the crucial role of the AhR in mediating the induction of IL-24, IL-6, and IL-1beta upon stimulation with living <i>S. aureus</i>. Taken together, we further highlight the important role of the AhR in cutaneous innate defense and identified the AhR as a novel receptor mediating the sensing of the important skin pathogen <i>S. aureus</i> in keratinocytes.
DOI: 10.6084/m9.figshare.28829036.v1
title: Abundance_different cats.csv

description: read-based ARG coverage depth table for different ARG categories. ARGs were annotated by RGI bwt (v6.0.0) to align metagenomic reads against CARD’s canonical reference (v3.2.7) and CARD’s Resistomes & Variants database (v4.0.1) under protein homolog model using default settings.
DOI: 10.6084/m9.figshare.15063213.v1
title: Mycorrhizal responsiveness predicts plant community changes in response to long term N and P fertilization

description: It includes data of plant species percentage cover and species with the mycorrhizal responsiveness reported.
DOI: 10.6084/m9.figshare.28269791.v1
title: Supplementary Material for: Relationship Between Podocyte Injury and Renal Outcomes in Patients with Acute Kidney Injury: A Report From a Retrospective Study in China

description: Introduction: Podocyte injury has been proven to be a major cause for poor renal outcomes after acute kidney injury (AKI). However, clinical trial data are still limited. This study aimed to explore the clinical correlations between podocyte injury and renal outcomes in hospitalized AKI patients. Method: This retrospective study analyzed data on 52 AKI patients who were histologically diagnosed with acute tubular necrosis (ATN) or acute interstitial nephritis (AIN) from six centers throughout China between January 2012 and June 2023. Patients were classified into two groups based on the degree of foot process fusion: ≤50% (mild podocyte injury group), and ＞50% (severe podocyte injury group). The outcomes were post-AKI new-onset proteinuria and incident CKD. Results: Among 52 AKI patients (14 male; median age, 49 [30, 56] years), 28 (53.8%) had mild podocyte injury, 24 (46.2%) had severe podocyte injury. After 12-month follow-up, 16(57.1%) had post-AKI proteinuria, and 5(17.9%) had post-AKI incident CKD in mild podocyte injury group. 20 (83.3%) had post-AKI new-onset proteinuria, and 14 (58.3%) had post-AKI incident CKD in severe podocyte injury group. Patients with more severe foot process fusion exhibited significantly higher incidences of post-AKI new-onset proteinuria (83.3% vs. 57.1%, P = 0.041) and incident CKD (58.3% vs. 17.9%, P = 0.003) at 12 months following AKI. The degree of foot process fusion (95%CI 1.013～3.88, P=0.048) and proteinuria at 3 months (95%CI 1.309～5.443, P=0.015) were identified as independent risk factors for post-AKI new-onset proteinuria at 12 months. The degree of foot process fusion (95%CI 1.026～14.196, P=0.048), and the presence of partial renal pathological features, including tubular atrophy (95%CI 1.012～5.958, P=0.030), interstitial inflammation (95%CI 1.005～6.846, P=0.039), interstitial fibrosis (95%CI 1.110～6.075, P=0.043) were independent risk factors for post-AKI incident CKD at 12month. Kaplan-Meier analysis shows severe podocyte injury group had worst renal survival, including post-AKI new-onset proteinuria (P=0.0066) and incident CKD (P=0.0455). Conclusion: The degree of podocyte injury is an independent risk factor for post-AKI new-onset proteinuria and incident CKD in patients, and patients with more severe podocyte injury exhibit a higher incidence of post-AKI new-onset proteinuria and incident CKD.
DOI: 10.6084/m9.figshare.28726667.v1
title: The English Romantic Portrait

description: <b>What if a portrait could whisper secrets instead of merely displaying a face?</b> <i>The English Romantic Portrait</i> explores the subtle yet profound emotional depth of British Romantic art. It delves into how painters of the era defied the rationality of the Enlightenment, embracing mystery, introspection, and raw sentiment. Through masterful brushwork and enigmatic gazes, these portraits reveal more than they seem—expressing emotions not through direct confrontation but through suggestion and symbolism.
DOI: 10.6084/m9.figshare.14679540.v1
title: mRNAmatrix.txt

description: Transcriptome data were obtained from TCGA liver cancer data set
DOI: 10.6084/m9.figshare.20653908.v1
title: Share dataset about Tumor

description: The share dataset about gene and isoforms.
DOI: 10.6084/m9.figshare.28189751.v1
title: Dataset SSCI 246499298

description: Data related to the paper: "Optimal fusion $\beta$-quaternion filtering from delayed observations and packet losses with compensation strategy under properness".<br>
DOI: 10.6084/m9.figshare.8765492.v1
title: As plantas comestíveis no Brasil dos séculos XVI e XVII segundo relatos de época

description: <b>Apêndice 1 -</b> Plantas alimentícias do Brasil nos séculos XVI e XVII
DOI: 10.26188/5da557cc41ed8
title: EPiC database - Stainless steel extruded

description: This material is part of the free Environmental Performance in Construction (EPiC) Database. The EPiC Database contains embodied environmental flow coefficients for 250+ construction materials using a comprehensive hybrid life cycle inventory approach.<br><br>Steel is a ferrous metal and is an alloy of iron and carbon, as well as potential other elements. It has a very high tensile strength. Steel has been used in the construction industry for over a century. Stainless steel is extremely resistant to corrosion.<br><br>The core material for making steel is iron, which is found in iron ore. Iron is extracted from iron ore in blast furnaces through the smelting process, while controlling for the content of carbon. To render the steel stainless, chromium is needed and is typically added as stainless steel scraps. The molten steel is usually further processed before being extruded into its final shape.<br><br>Steel is commonly used in the construction industry, mainly as a structural material. Extruded stainless steel can be used to produce a range of tubes for structural and finishing purposes as well as pipes.
DOI: 10.6084/m9.figshare.20624376.v1
title: Supplementary Material for: Substance Use, Substance Use Disorders, and Co-Occurring Psychiatric Disorders in Recently Incarcerated Men: A Comparison with the General Population

description: <b><i>Introduction:</i></b> The rates of alcohol and illegal drug use and the prevalence of alcohol and illegal drug use disorders (AUDs and DUDs) are high in prison populations, particularly in men entering jail. However, these rates have never been exhaustively assessed and compared to those of the general population in France. <b><i>Methods:</i></b> We based our research on two surveys, conducted in the same French region, which included a total of 630 men entering jail and 5,793 men recruited from the general population. We used the Mini-International Neuropsychiatric Interview to assess alcohol and drug use, AUD, DUD, as well as co-occurring psychiatric disorders, and we examined differences in prevalence rates between the two populations. Logistic regression models were performed to (i) identify the factors associated with AUD and DUD and (ii) test whether the interaction between admission to jail and the presence of AUD, DUD, or both is linked to the presence of at least one co-occurring psychiatric disorder. <b><i>Results:</i></b> Compared to the general population sample, the prevalence of AUD (33.8% vs. 8.7%, <i>p</i> &lt; 0.001) and DUD (at least one type of drug: 28.7% vs. 5.0%, <i>p</i> &lt; 0.001; cannabis: 24.0% vs. 4.7%, <i>p</i> &lt; 0.001; opioids: 6.8% vs. 0.4%, <i>p</i> &lt; 0.001; stimulants: 5.2% vs. 0.8%, <i>p</i> &lt; 0.001) was significantly higher in the jail population sample, as well as the rates of past-year use of various substances (alcohol: 62.1% vs. 56.4%, <i>p</i> = 0.007; at least one type of illegal drug: 50.0% vs. 14.4%, <i>p</i> &lt; 0.001; cannabis: 45.6% vs. 13.9%, opioids: 9.4% vs. 0.7%; stimulants: 8.6% vs. 1.9%). Admission to jail was associated with a higher risk of AUD (aOR = 3.80, 95% CI: 2.89–5.01, <i>p</i> &lt; 0.001) or DUD (aOR = 4.25, 95% CI: 3.10–5.84, <i>p</i> &lt; 0.001). History of trauma was also associated with both AUD (aOR = 1.81, 95% CI: 1.53–2.14, <i>p</i> &lt; 0.001) and DUD (aOR = 2.15, 95% CI: 1.74–2.65, <i>p</i> &lt; 0.001), whereas history of migration was only associated with DUD (aOR = 1.38, 95% CI: 1.12–1.71, <i>p</i> = 0.003). AUDs and DUDs were more strongly associated with co-occurring psychiatric disorders in incarcerated men than in the general population. Among individuals with AUD, DUD, or both, co-occurring anxiety and mood disorders were particularly more frequent in jail than in the general population. <b><i>Discussion/Conclusion:</i></b> As in most countries, AUD and DUD are highly prevalent among men entering jail in France. Our results also suggest that incarceration constitutes an independent vulnerability factor for a dual disorder, which supports a systematic assessment and treatment of psychiatric disorders in men entering jail and diagnosed with an AUD or DUD.
DOI: 10.6084/m9.figshare.8974817.v1
title: HBCx_95_scChIPseq_mm10_50kb.tsv

description: The samples correspond to the mouse cells from patient-derived xenograft (PDX) originating from two different human donors. The HBCx-22 and HBCx-22-TamR datasets correspond to mouse cells from a pair of luminal ER<sup>+</sup> breast PDXs: HBCx-22, responsive to Tamoxifen and HBCx-22-TamR, resistant to Tamoxifen. The HBCx-95 and HBCx-95-CapaR correspond to a triple-negative breast cancer (TNBC) tumor model of acquired resistance to chemotherapy. Row names of the matrices are 50,000-bp binned regions; Column names are barcodes corresponding to single cell; Cells contains raw counts, in mm10 reference.
DOI: 10.17632/5bnrprjgb5
title: Data for: Future water resource availability in Central Asia based on 2,000yBP to present climate records

description: Monthly by-country mean datasets of total precipitation and mean temperature for the countries of Central Asia during the 20th century. Compiled from Global Historical Climatology Network (GHCN) data.
DOI: 10.17632/m55vd9vz78
title: Data for: The maternal brain: Neural responses to infants in mothers with and without mood disorder

description: Search string for articles for systematic review
DOI: 10.17632/pwhtt9jtdn
title: The carbon and hydrogen isotope of microbial PLFAs from soils and peats

description: This is the raw data of the manuscript entitled “The carbon and hydrogen isotopic composition of microbial fatty acids traces microbial metabolism in soils and peats” submitted to Geochimica et Cosmochimica Acta.
DOI: 10.6084/m9.figshare.12191673.v1
title: A chromosome-level genome of blue tilapia (Actinopterygii: Cichliformes) based on the Oxford nanopore long-read sequencing technology

description: To try to provide a high-quality reference to help to figure out molecular events underlying the unique features of the species, we here provide a nearly chromosomal-level genome of <i>O. aureus</i>, based on the Oxford nanopore long-read sequencing and Hi-C technologies.
DOI: 10.6084/m9.figshare.14839659.v1
title: SleepSource

description: Training data age group 25-59 with label
DOI: 10.6084/m9.figshare.22358599.v5
title: SPIRIT Checklist of Protocol of Efficacy and safety of mizoribine in comparison with cyclophosphamide for treatment of lupus nephritis: a multi-center, open-label, randomized controlled trial

description: This is a completed SPIRIT checklist of the protocol. Protocol of Efficacy and safety of mizoribine in comparison with cyclophosphamide for treatment of lupus nephritis: a multi-center, open-label, randomized controlled trial have fully adhered to the SPIRIT reporting guidelines.
DOI: 10.6084/m9.figshare.24975405.v1
title: Volume measurements of gnathal ganglia for w<sup>1118</sup> control and DfD-Gal4<sup>1</sup> and Dfd-Gal4<sup>2</sup> animals.

description: Gnathal ganglia (GNG) volumes for four animals of each genotype were calculated as described in the published Methods of the paper from individual sections of confocal Z-stacks through the entire nervous system. Areas of outlined GNG neuropil in each Z-section of each animal are shown.
DOI: 10.6084/m9.figshare.4753627.v1
title: Landmark dataset associated with reconstruction of A.L. 288-1 scapula

description: Landmarks used in the GM reconstruction of the scapula of "Lucy" Australopithecus afarenis A.L. 288-1
DOI: 10.6084/m9.figshare.12005508.v1
title: Figshare_Traits _Data.csv

description: Dataset regarding abiotic stressors and plant traits of <i>Spartina anglica</i> in salt marshes. This dataset has been used in the paper "<i>Multiple trait dimensions mediate stress gradient effects on plant biomass allocation, with implications for coastal ecosystem services</i>". This manuscript has been published in the Journal of Ecology.<br>
DOI: 10.6084/m9.figshare.14974623.v1
title: Supplementary information for: Thornton et al., Simulating fully-integrated hydrological dynamics in complex Alpine headwaters

description: Supplementary figures, tables, animations, and model files.
DOI: 10.6084/m9.figshare.20652652.v2
title: Efficacy and safety of Nivolumab in patients with advanced esophageal, gastroesophageal, and gastric cancers: a meta-analysis of randomized controlled trials

description: Immune checkpoint inhibitors (ICI) have revolutionized care in oncology with improved overall survival in several cancer populations. Nivolumab has recently been approved for use in patients with upper gastrointestinal cancers. We quantitatively summarized the efficacy and safety of Nivolumab use in patients with advanced esophageal, gastroesophageal, and gastric carcinoma compared to standard chemotherapy. Systemic search of electronic databases was performed to analyze phase III randomized controlled trials (RCTs) comparing Nivolumab versus standard chemotherapy in patients with advanced upper gastrointestinal cancers. Primary endpoints were overall survival (OS) and progression-free survival (PFS). Data were pooled using random effects model <i>via</i> RevMan 5.4 software. Four RCTs with a total of 3369 patients and a median follow-up of 13 months were included. The patients’ mean age was 61 ± 20 years, 74.6% were males, and 26% had ≥1% PD-L1 expression. Compared to the chemotherapy group, Nivolumab group had a significantly favorable OS and PFS [HR 0.81;95% CI (0.74, 0.89), <i>p</i> &lt; .001], [HR 0.82;95% CI (0.69, 0.98), <i>p</i> = .03], respectively. Nivolumab significant effect was only in patients with ≥1% PD L1 expression [HR 0.72; 95% CI (0.58, 0.89), <i>p</i> &lt; .001]. No statistical difference was detected between groups regarding serious adverse effects (AE) [OR 1.47; 95%CI (0.94,2.31), <i>p</i> = 0.09]. Compared to standard chemotherapy, the use of Nivolumab in patients with advanced esophageal, gastroesophageal, and gastric cancers is associated with improved overall and progression-free survival, with similar rates of AE and AE leading to death. The improvement in survival was significant in patients with ≥1% PD L1 expression.
DOI: 10.6084/m9.figshare.25927159.v1
title: H6_Wh

description: Energy related data for House 6
DOI: 10.17632/k2zj6xk63p
title: RFM analysis for customer segmentation using feature generation and accelerated deep learning for prediction

description: In this project, we propose a feature generation method for customer segmentation using an online retail store dataset. Also, we perform a comparative cluster analysis between the proposed method and the traditional method with K-means. We show that among the top-7 classifiers reported in previous studies, Multi-layer Perceptron (MLP) is the best. Then, we use the Genetic Algorithm (GA) to improve the speed and accuracy of MLP during the prediction phase.
DOI: 10.21942/uva.11771190.v2
title: Dataset for MS1. Yang et al. 2018. Soil organic carbon stocks controlled by lithology and soil depth in a Peruvian alpine grassland of the Andes. Catena 171, 11–21. https://doi.org/10.1016/j.catena.2018.06.038

description: The soil is the largest carbon (C) pool in the terrestrial ecosystem, and soil organic carbon (SOC) stocks play an important role in global C dynamics. Alpine grasslands of the Andes are characterized by high SOC stocks. Quantifying SOC stocks and unraveling key factors controlling SOC stocks, is necessary to obtain a better un- derstanding of the dynamics of the large C stocks in this environment. However, most studies on C dynamics of the Andes focus on volcanic-ash soils, whereas information about non-volcanic ash soils in this region is scarce. Our objectives were: (i) to estimate SOC stocks in an alpine grassland of the Peruvian Andes (7° 11′S, 78° 35′W) with parent materials other than volcanic ash, and (ii) to identify the underlying soil formation and environ- mental (SFE) factors and soil properties explaining observed patterns of SOC stocks. We sampled 69 plots up to the parent material to measure soil properties and to calculate SOC stocks, in relation to lithology, land use, grazing intensity, slope angle, slope position and altitude. We applied linear models to identify key factors controlling SOC stocks. Our results showed that total SOC stocks had a mean value of 215 ± 21 T ha−1, whereas SOC stocks of the upper 10 cm and 40 cm comprised 29.3% and 80.0% of total SOC stocks respectively. The variation of the total SOC stocks was mainly explained by soil depth and soil moisture. When soil depth and soil moisture were controlled as conditional variables, lithology became the key factor controlling the total SOC stocks. For the SOC stocks of the upper 10 cm, soil moisture explained a large part of the variation, whereas lithology, grazing intensity and altitude were also significant predictors. Our results also show that when soils are sampled with limited depths instead of the entire soil profile, SOC stocks can be underestimated, and the effects of the SFE factors on SOC stocks can be overestimated.<br>
DOI: 10.6084/m9.figshare.12807872.v1
title: Study data and dictionary - Evaluation of Pneumococcal Serotyping of Nasopharyngeal- Carriage Isolates by Latex Agglutination, Whole-Genome Sequencing (PneumoCaT), and DNA Microarray in a High- Pneumococcal-Carriage-Prevalence Population in Malawi

description: Serotyping results with relevant metadata and dictionary used for evaluating concordance between three serotyping methods
DOI: 10.17605/osf.io/uzdwp
title: Metaphorical Motion in Arabic

description: Data Collection Metadata

Who:
Data was collected by myself, Dr. Waleed Ahmad Othman.

How:
The data comprises instances of motion verbs extracted from Arabic fiction works published between 1970 and 2022. The works were selected based on their availability as freely downloadable PDF files. The Ctrl+F feature in PDF readers was utilized to locate instances of the selected motion verbs within the texts.

Why:
The purpose of this data collection was to investigate the use of motion verbs in conceptual metaphors in contemporary Arabic fiction. This study aims to contribute to the understanding of how motion is expressed metaphorically in Arabic literary contexts.

When and Where:
Data collection occurred over a period of three months, from July 2023 to September 2023. The process was conducted online, with access from both home and office environments.

Funding:
No external funding was required for this data collection process.
DOI: 10.17632/8gx48tmvjr
title: nGVS_MAP_HR_ELD2020

description: Dataset; nGVS_MAP_HR_ELD2020
DOI: 10.23641/asha.25529371.v1
title: Nonword repetition in Cantonese (Fu et al., 2024)

description: <b>Purpos</b><b>e: </b>Nonword repetition (NWR) has been described as a clinical marker of developmental language disorder (DLD), as NWR tasks consistently discriminate between DLD and typical development (TD) cross-linguistically, with Cantonese as the only reported exception. This study reexamines whether NWR is able to generate TD/DLD group differences in Cantonese-speaking children by reporting on a novel set of NWR stimuli that take into account factors known to affect NWR performance and group differentiation, including lexicality, sublexicality, length, and syllable complexity.<b>Method: </b>Sixteen Cantonese-speaking children with DLD and 16 age-matched children with TD repeated two sets of high-lexicality nonwords, where all constituent syllables are morphemic in Cantonese but meaningless when combined, and one set of low-lexicality nonwords, where all constituent syllables are nonmorphemic. Low-lexicality nonwords were further classified on sublexicality in terms of consonant–vowel (CV) combination attestedness (whether or not CV combinations in nonword syllables occur in real Cantonese words).<b>Results: </b>Children with DLD scored significantly below their peers with TD. Effect sizes showed that high-lexicality nonwords and nonword syllables with attested CV combinations offered the greatest TD/DLD group differentiation. Nonword length and syllable complexity did not affect TD/DLD group differentiation.<b>Conclusions: </b>NWR can capture TD/DLD group differences in Cantonese-speaking children. Lexicality and sublexicality effects must be considered in designing NWR stimuli for TD/DLD group differentiation. Future studies should replicate the present study on a larger sample size and a younger population as well as examine the diagnostic accuracy of this NWR test.<b>Supplemental Material S1. </b>Full list of NWR stimuli.Fu, N. C., Chen, S., Polišenská, K., Chan, A., Kan, R., & Chiat, S. (2024). Nonword repetition in children with developmental language disorder: Revisiting the case of Cantonese. <i>Journal of Speech, Language, and Hearing Research, 67</i>(6), 1772–1784<i>. </i>https://doi.org/10.1044/2024_JSLHR-22-00397
DOI: 10.5522/04/16573640.v1
title: Multi-region scRNA and scTCR data on ADAPTeR patient cohort

description: scRNA and scTCR data for the manuscript '<b>Determinants of anti-PD-1 response and resistance in clear cell renal cell carcinoma'</b><br>Samples: Tumour infiltrating lymphocyes taken from two ccRCC patients post anti-PD-1 (nivolumab) treatment. One responder patient, one non-responder patient. For each patient cells were split by IgG4 binding (IgG4 = proxy for nivolumab binding), followed by 10x paired scRNA and scTCR sequencing.<br>Data analysis: sequencing files were demultiplexed and mapped to the hg38 genome and VDJ reference using cellranger count and cellranger vdj respectively. Expression matrices and VDJ annotations are provided in this submission. Also provided is cell metadata containing UMAP co-ordinates and other information pertinent to this study.<br>Files types: .mtx, .tsv, .csv<br>FIle size (compressed) 183.5MB