cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.25971832.v1
title: 839PLWH_clinical_data_mutations.xlsx

description: The implementation of pretreatment drug resistance (PDR) surveillance among people living with HIV-1 (PLWH) is a top priority in countries using efavirenz (EFV)/nevirapine (NVP) for first-line ART. In this study, we assessed the prevalence of PDR among PLWH in Shanghai, China during 2017-2021, and to reveal PDR transmission between Shanghai and other regions of China. A total of 5050 PLWH not on ART during 2017-2021 were included. Partial HIV-1 <i>pol</i> sequences were amplified, sequenced, and analyzed for drug resistance mutations (DRMs). Besides, transmission network of PDR variants was<b> </b>inferred using HIV-TRACE. The overall prevalence of PDR was 4.8% (242/5050; 95% CI, 4.2-5.4). Prevalence of NNRTI-associated PDR was 3.9% (95% CI, 3.4-4.5), higher than those of NRTI-associated (0.8%; 95% CI, 0.5-1.1) and PI-associated PDR (0.9%; 95% CI, 0.6-1.2). High prevalence of PDR (especially high-level resistance) to EFV (132/5050, 2.6%) and NVP (137/5050, 2.7%) were found. CRF01_AE (46.0%) was the predominant HIV-1 genotype with any DRMs, followed by CRF55_01B (21.0%), and CRF07_BC (15.1%). Two NRTI-associated (S68G/N/R and T215A/N/S/Y), five NNRTI-associated (V179D/E/T/L, K103N/R/S/T, E138A/G/K, V106M/I/A and Y181C/I) and two PI-associated mutations (M46I/L/V and Q58E) were the most common observed DRMs in PDR patients in Shanghai. The vast majority of S68G occurred in CRF01_AE (45%). M46I/L/V and Q58E showed a relatively high prevalence in CRF01_AE (4.1%) and CRF07_BC (12.6%). Transmission network analyses demonstrated cross-regional transmission links of PDR variants between Shanghai and other regions of China, which was mainly driven by the potential low-level DRM V179D/E. These results provide crucial information for clinical decision making of first-line ART in PLWH with PDR.
DOI: 10.6084/m9.figshare.12809948.v1
title: Client species accumulation curve for redlip cleaner wrasses

description: Number of client species visiting redlip cleaner wrasses in Mo'orea, French Polynesia
DOI: 10.6084/m9.figshare.5084686.v1
title: Sexual differences in the effect of previous breeding performance on nest-box reuse and mate retention in White-rumped Swallows (<i>Tachycineta leucorrhoa</i>)

description: In birds, the selection of nesting sites and mates has a profound influence on the daily interactions of individuals. Both behaviours are energetically costly and time-consuming and can strongly affect the Darwinian fitness of individuals. Using a 12-year dataset on banded returning breeders, we explored variables associated with nest-box choice and mate choice in the White-rumped Swallow, a socially monogamous migratory passerine. Females reusing nest-boxes, but not males, produced significantly more fledglings than did those that changed nest-boxes. Females and males that retained mates produced significantly more fledglings than did those that divorced. General linear mixed models revealed that the number of fledglings produced in previous seasons significantly explained the reuse of particular nest-boxes by females, but not by males. Mate choice by females was not strongly affected by either past breeding performance or nest-box reuse, but nest-box reuse alone predicted mate choice by males. Nest-box reuse by males was apparently more related to retention of female partners. This study revealed that sexual differences in the nesting and mating decisions were guided by the use of information on past breeding performance in a subtropical, secondary cavity nester.
DOI: 10.6084/m9.figshare.19499393.v1
title: patches and local annotations, slide 045, 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.28714169.v1
title: Metagenome-assembled genomes (MAGs) and viral genomes in the rumen and feces of sheep

description: The rumen and feces MAGs, with ≥50% completeness, and &lt;10% contamination, were reconstructed by metagenomic sequencing from sheep. Additionally, the Rumen and Feces Viruse Genomes (RFVG) include 6224 viral operational taxonomic units (vOTUs) of middle-quality or higher (≥5 kb length and ≥50% completeness).
DOI: 10.15468/dl.2u7mpn
title: Occurrence Download

description: A dataset containing 2601 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Observation, Human Observation, Machine Observation, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Aelia acuminata (Linnaeus, 1758)"
 ]
}

 The dataset includes 2601 records from 68 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009499-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.25046471.v1
title: USPTO reaction datasets remapped by LocalMapper

description: The atom-to-atom mappings (AAMs) of USPTO reaction datasets, including USPTO-50K and USPTO-full datasets, are remapped by LocalMapper and deposited here.The original reactions are downloaded from https://figshare.com/articles/dataset/Chemical_reactions_from_US_patents_1976-Sep2016_/5104873
DOI: 10.6084/m9.figshare.11346746.v1
title: Supplementary table 4

description: Table 4. Average correlation between CV-accuracy and AR2 metrics and the observed SNP accuracy, major allele accuracy and minor allele accuracy on test sets, by minor allele frequency categories. Values are given for one of the 20 test sets (for the other test sets, almost identical
DOI: 10.6084/m9.figshare.28888286.v1
title: de la Roche et al DATA.zip

description: DATA MATRIX FROM THE ARTICLE. Brown Algae from San Andres Island, Southwest Caribbean: A Nuclear Magnetic Resonance Spectroscopy–Metabolomic Study
DOI: 10.6084/m9.figshare.20039686.v1
title: Bioprocess optimization of interferon β-1-a in Pichia pastoris and its improved inhibitory effect against hepatocellular carcinoma cells

description: Abstract Interferon-β-1a (INF-β-1a) has gained significant attention due to its emerging applications in the treatment of different human diseases. Therefore, many researchers have attempted to produce it in large quantities and also in a biologically active form using different expression systems. In the present study, we aimed to improve the expression level of INF-β-1a by Pichia pastoris using optimization of culture conditions. The codon-optimized INF-β- 1a gene was cloned into pPICZαA plasmid under the control of alcohol oxidase I (AOX1) promoter. The protein expression was induced using different concentrations of methanol at different pHs and temperatures. The biological activity of produced protein was evaluated by anti-proliferative assay. The ideal culture conditions for the expression of INF-β-1a by P. pastoris were found to be induction with 2% methanol at pH 7.0 culture medium at 30 C which yielded a concentration of 15.5 mg/L INF-β-1a in a shake flask. Our results indicate that differences in glycosylation pattern could result in different biological activities as INF- β-1a produced by P. pastoris could significantly more reduce the cell viability of HepG-2 cells, a hepatocellular carcinoma cell line, than a commercially available form of this protein produced by CHO.
DOI: 10.6084/m9.figshare.13641548.v1
title: Modified 69-bus distribution system

description: This file provides the line and load data of modified 69-bus system.<br>
DOI: 10.6084/m9.figshare.20484390.v4
title: LK93 genome

description: The nuclear and mitochondrial genomes of <em>Bipolaris sorokiniana</em> strain LK93, a fungal pathogen causing wheat root rot. Small genetic variations and large structural variants between genomes of LK93 and reference strains
DOI: 10.6084/m9.figshare.25718766.v1
title: Data for the article A Controversial Make-over of a ‘Make-believe’ heritage – The Transformation of Guangrenwang Temple

description: This article discusses issues related to sustainable heritage management in China and problematises two dichotomies in heritage practices and research: the ‘Easter/Western’ approaches and the tangible-intangible divide. It addresses these issues by examining a dramatic ‘make-over’ project of Guangrenwang Temple in Shanxi Province, China. The ‘make-over’ project transformed a small rural temple with a ninth-century timber structure into an architectural history museum, with a combination of private, public, and crowd-sourced funding. A real-estate corporation played a significant role in the project’s initiative and organised a large-scale national and international publicity campaign around the project. Previously unknown to most laypeople in China, the temple attracted much debate since the project’s completion, revolving around its ‘cultural legitimacy’, the design’s appropriateness, the sustainability of the revitalisation, and the implications of the project to its ‘heritage value’ and authenticity. This article traces the opinions, actions, and effects of the temple’s heritage assemblage and reveals the causal powers contributing to the emergence and transformation of associations within. It further questions the project team’s claims regarding the project’s effects on the historic setting’s authenticity and its long-term social impact on the relationship between the temple and its community. It reveals five controversies regarding the choice of its curation theme, architectural language, decision-making, and management models. The complexities manifested in the actor’s actions and effects demonstrate the ambiguous boundaries between the tangible and the intangible, and the perceived ‘Western’ and ‘Eastern’ approaches.
DOI: 10.6084/m9.figshare.27950145.v1
title: Supplementary Material for: Systemic Cancer Hallmarks as Novel Markers Associated with Progression-free Survival in Gastroenteropancreatic Neuroendocrine Tumor Patients Undergoing PRRT

description: Introduction: Gastroenteropancreatic neuroendocrine tumors (GEP-NETs) are a heterogeneous group of tumors often detected at the metastatic stage. The aim of this study was to profile the peripheral blood transcriptome through RNA-Seq and investigate the association of the systemic cancer hallmarks with progression-free survival in PRRT-treated GEP-NET patients. Methods: The cohorts were: discovery cohort [PRRT-naïve well-differentiated GEP-NETs, n=59; age- and sex-matched healthy individuals, n=38], and independent evaluation cohort [GEP-NETs, n=66]. Peripheral blood transcriptomes were profiled through RNA sequencing and cancer hallmarks were identified via Gene Set Enrichment Analysis (GSEA). Activities of cancer hallmarks in each sample were calculated using Gene Set Variation Analysis (GSVA). Differentially expressed genes were identified with DESeq2. Progression-free survival was used as a primary endpoint and prognostic association was evaluated using univariate and multivariate COXPH analyses. Results: RNA-Seq captured global changes in the peripheral blood transcriptome of GEP-NET patients. Peripheral blood transcriptome of NET patients showed differential enrichment of 30 systemic cancer hallmarks viz., TNF-α signaling via NF-κB, IL2/STAT5 signaling, TNF-α response, TNF-γ response, IL6/JAK/STAT signaling, TGF-β signaling, heme metabolism. etc. In the univariate analyses, two cancer hallmarks were prognostically significant (p&lt;0.05) in GEP-NETs. Heme metabolism and IL2/STAT5 signaling were statistically significant in the Discovery cohort (n=58) and independent evaluation cohort (n=66). In multivariate COXPH analyses, heme metabolism and IL2/STAT5 signaling were independently associated with PFS in GEP-NET patients undergoing PRRT. Conclusions: This study provides comprehensive coverage of the peripheral blood transcriptome of GEP-NET patients via RNA-Seq and identifies systemic cancer hallmarks as independent prognostic factors in NETs.
DOI: 10.6084/m9.figshare.27988586.v1
title: Newixk file for dendrogram for yeast phylogenomics

description: Newick file of a dendrogram showing the phylogenomic position of sequenced isolates in comparison to clades described in literature.
DOI: 10.6084/m9.figshare.11423013.v3
title: Data for Dalerum at el. 2019. Frontiers in Ecology and Evolution 7:507. doi: 10.3389/fevo.2019.00507

description: Data for Dalerum F, Selby LOK and Pirk CWW (2019) Relationships between livestock damages and large carnivore densities in Sweden. Front. Ecol. Evol. 7:507. doi: 10.3389/fevo.2019.00507<br>
DOI: 10.6084/m9.figshare.15074067.v1
title: Supplementary Material for: Association between Vitamin D and Risk of Stroke: A PRISMA-Compliant Systematic Review and Meta-Analysis

description: <b><i>Background:</i></b> Previous studies have shown inconsistent results for associations between vitamin D and risk of stroke. We gathered the existing published articles and conducted this meta-analysis with the aim to explore the association between vitamin D and risk of stroke. <b><i>Methods:</i></b> We searched for articles exploring the association between vitamin D and risk of stroke and published before April 2021 in the following databases: PubMed, Web of Science, MEDLINE, EMBASE, and Google Scholar. All statistical analyses were made using STATA 12.0 software. Q test and <i>I</i><sup><i>2</i></sup> were applied to examine heterogeneities between studies. <b><i>Results:</i></b> For the association between serum levels of 25(OH) vitamin D and risks of stroke, the present analysis included 20 cohort studies (including 213,276 participants) and a case-control analysis (including 13,642 participants). Additionally, the analysis included 15 studies (including 41,146 participants given vitamin D supplementation and 41,163 participants given placebo) to evaluate the influence of vitamin D supplementation on risk of stroke. Higher circulating levels of 25(OH) vitamin D were associated with a reduced risk of stroke (odds ratio/relative risk = 0.78, 95% confidence interval [CI]: 0.70–0.86, <i>I</i><sup><i>2</i></sup> = 41.5%, <i>p</i> = 0.025). However, the present analysis showed that vitamin D supplementation did not influence the risk of stroke (hazard ratio = 1.05, 95% CI: 0.96–1.14, <i>I</i><sup>2</sup> = 2.3%, <i>p</i> = 0.425). <b><i>Conclusions:</i></b> Our analysis indicated that lower circulating level of vitamin D was associated with an elevated risk of stroke, but extra supplement of vitamin D failed to show benefit in decreasing the risk of stroke. Further research and study are also needed to show the role of vitamin D in relation to stroke.
DOI: 10.6084/m9.figshare.12597773.v1
title: GL setup intake genomes processing dir script

description: GL setup intake genomes processing dir script<br>detailed on this page: https://hackmd.io/@astrobiomike/GL-genome-intake-processing<br>
DOI: 10.6084/m9.figshare.4535564.v1
title: Supplementary Material for: A RIG-I 2CARD-MAVS200 Chimeric Protein Reconstitutes IFN-β Induction and Antiviral Response in Models Deficient in Type I IFN Response

description: RIG-I-like receptors (RLRs) are cellular sensor proteins that detect certain RNA species produced during viral infections. RLRs activate a signaling cascade that results in the production of IFN-β as well as several other cytokines with antiviral and proinflammatory activities. We explored the potential of different constructs based on RLRs to induce the IFN-β pathway and create an antiviral state in type I IFN-unresponsive models. A chimeric construct composed of RIG-I 2CARD and the first 200 amino acids of MAVS (2CARD-MAVS200) showed an enhanced ability to induce IFN-β when compared to other stimulatory constructs. Furthermore, this human chimeric construct showed a superior ability to activate IFN-β expression in cells from various species. This construct was found to overcome the restrictions of blocking IFN-β induction or signaling by a number of viral IFN-antagonist proteins. Additionally, the antiviral activity of this chimera was demonstrated in influenza virus and HBV infection mouse models using adeno-associated virus (AAV) vectors as a delivery vehicle. We propose that AAV vectors expressing 2CARD-MAVS200 chimeric protein can reconstitute IFN-β induction and recover a partial antiviral state in different models that do not respond to recombinant IFN-β treatment.
DOI: 10.6084/m9.figshare.19091771.v1
title: Alzheimer's disease and Schizophrenia

description: Dataset from the paper "EEG functional connectivity and deep learning for automatic diagnosis of brain disorders: Alzheimer's disease and schizophrenia".<br>Schizophrenia dataset also available in: http://brain.bio.msu.ru/eeg_schizophrenia.htm<br>
DOI: 10.6084/m9.figshare.24337138.v1
title: Ephydroidea_phylogeny_IqTree

description: The blind and wingless bee louse fly (Braula coeca) is an aberrant member of the family Drosophilidae that lives as a parasitic inquiline in the hive of the Western honey bee (Apis mellifera). The analysis of its genome identifies a case of horizontal transposon transfer and a striking parallel evolution in a set of ecologically-relevant gene families.
DOI: 10.6084/m9.figshare.3749235.v1
title: The ecology and management of urban pondscapes

description: Small water bodies provide valuable ‘blue space’ in urban environments, creating a network of semi-natural habitat patches for wildlife as well as providing a wide range of ecosystem services. However, the diverse and interacting anthropogenic stressors imposed by the urban environment pose considerable challenges for the effective management of these habitats. We outline some of the key factors that appear to influence urban pond biodiversity: land use with the local (and often small-scale) catchment, the connectivity of ponds through the landscape, and the nature of emergent and riparian vegetation. We argue that all three factors can be incorporated into a landscape-scale planning framework that can target particular areas for creation and amelioration of pond habitats. Such a joined-up approach is currently lacking from most urban planning frameworks, but could provide an opportunity to maximise services provided by urban wetlands at the landscape scale. We emphasise the application of recent ecological advances in our understanding of urban ponds to management guidelines, which have largely come in the form of gardening guides. This management will be required not only to enhance the biodiversity value of urban ponds, but also to control the less desirable elements of aquatic biodiversity such as invasive species and disease vectors that may pose a particular risk in urban environments. Finally, we note the lack of a comprehensive conservation strategy for ponds and highlight key legislation and guidance that can help to fill the gap. The fact that pond value lies in the aggregation of multiple habitats distributed through the landscape challenges our existing approach to habitat protection. However, contemporary approaches to pond creation for mitigation through planning processes and programmes of pond creation provide an opportunity to implement truly large-scale strategic habitat management. It is imperative that ecologists and conservationists are involved in the future planning process and its implementation.
DOI: 10.6084/m9.figshare.5126404.v1
title: Supplementary Material for: Xeroderma Pigmentosum/De Sanctis-Cacchione Syndrome: Unusual Cause of Ataxia

description: <b><i>Introduction:</i></b> Xeroderma pigmentosum (XP) is a rare autosomal recessive disorder of DNA repair, with a prevalence of 1 in 1 million. It may also be a cause of neurological symptoms including sensorineural hearing loss, peripheral neuropathy, ataxia, and chorea. Severe neurological symptoms including mental retardation, short stature, and hypogonadism invoke De Sanctis-Cacchione syndrome (DCS). <b><i>Case Report:</i></b> The patient was a 55-year-old woman with a history of mental retardation who developed chorea at age 32 and ataxia at age 37. She had numerous facial scars from 10 prior basal cell carcinoma excisions as well as diminished deep tendon reflexes, bilateral hearing loss, dysphagia, and skin freckling. Brain MRI revealed severe cortical, cerebellar, and brainstem atrophy. Supportive treatment and prevention of further damage from UV light is the mainstay of treatment in XP and DCS. <b><i>Conclusion:</i></b> XP and related disorders should be considered in the setting of neurological disorder and multiple cutaneous cancers.
DOI: 10.6084/m9.figshare.19968315.v1
title: Protected fat supplementation for early weaned beef cows maintained in nature pasture

description: The objective of this work was to evaluate the productive and reproductive performance of beef cows, as well as the performance of their calves according to the following dietary treatments: PRE: supplemented with protected fat (PF) during 45 days prepartum; PREPOS: supplemented with PF during 45 days prepartum and 63 days postpartum; POS: supplemented with PF during 63 days postpartum; PN: without supplementation. The productive performance of cows was not influenced by feed management (P&gt;0.05), except for body condition score (BCS), which was lower for PRE and PREPOS cows at the end of mating season, with the latter cows having similar BCS POS and PN. The calving interval (CI) was shorter for cows supplemented in PREPOS - 376 days -, and did not differ in cows maintained in PN - 383 days. Supplemented PREPOS cows weaned 4.4% more pounds of calf per 100kg of cow at calving - 22.6kg - than the PRE and POS cows - 21.6kg and 21.6kg, respectively - and 8,4% more pounds of calf per 100 of cow at calving than the cows maintained in native pasture - 20.7kg. The fat protected supplementation during pre and/or postpartum periods did not affect the performance of cows and calves.
DOI: 10.6084/m9.figshare.26562718.v1
title: Dataset Posture specific behaviour and BMI

description: This dataset was used for the study with the aims to explore the compositional associations between posture-specific behaviours and obesity risk in younger (M = 67.35 ± 2.03 years) and older (M = 75.73 ± 4.17 years) seniors and investigate the differences in BMI associated with replacing time spent in lying, sitting and standing with moving or walking.<b> </b>The study involved 309 older adults aged 65 and above from Czech Republic. Participants' movement behaviours, including lying, sitting, standing, moving, and walking, were measured using accelerometers. The data were analysed using compositional data analysis (CoDA) and isotemporal substitution models to assess the impact of reallocating time between different activities on body mass index (BMI).