cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4763320.v1
title: Diagnosis of smear-negative tuberculosis is greatly improved by Xpert MTB/RIF

description: 5-year (January 2011-December 2015) retrospective analysis of microbiological results for the diagnosis of TB performed at the Unit of Microbiology of the S. Orsola-Malpighi University Hospital in Bologna (Italy). During the study period, 5170 specimens originated from patients with suspected TB have been examined with Xpert MTB/RIF. Database reports smear microscopy, mycobacterial culture, Xpert results (divided by assay version) and Rif detection, sample localization.
DOI: 10.6084/m9.figshare.13117637.v1
title: Supplementary Material for: A Case of Duodenal Tumor Adjacent to the Diverticulum That Was Resected by the Technique of Partial Submucosal Injection Combined with Underwater Endoscopic Mucosal Resection

description: A 66-year-old male was referred to our hospital for treatment of duodenal tumor. The most difficult part was that the lesion was adjacent to duodenal diverticulum. Endoscopic mucosal resection (EMR) was difficult because submucosal injection spread broadly and quickly and makes it difficult to visualize the diverticulum edge of the lesion. Simple underwater EMR (UEMR) had risk for perforation at the diverticulum part because duodenal diverticulum is spurious diverticulum that defects the proper muscle layer. Therefore, to make sufficient distance between diverticulum and the lesion, we performed partial submucosal injection into only the diverticulum side of the lesion combined with simple UEMR. The lesion was resected en bloc without any adverse events. Histopathological diagnosis was tubular adenoma with moderate atypia and surgical margin negative. Partial submucosal injection combined with simple UEMR might be useful for duodenal tumor that has any technical difficulties as in this case.
DOI: 10.6084/m9.figshare.27302049.v1
title: Supplementary Material for: GLOBAL ASSESSMENT OF TRAINING NEEDS IN ADDICTION MEDICINE

description: Introduction
A minority of addiction patients receive appropriate treatment directly from trained professionals in addiction medicine. Most countries have not recognized addiction medicine as a speciality in its own right or within psychiatry/other specialities. Therefore, the effectiveness and organization of addiction medicine training around the world need to be improved. Unfortunately, standard instruments are rarely used in most studies to assess training needs. This study aimed to determine international competencies in addiction medicine (AM) among professionals in as many countries as possible using a standard instrument such as the AM Training Needs Assessment (AM-TNA).
Method We examined competencies in addiction medicine with the AM-TNA using an online survey. A General Competency Level in Addiction Medicine (GLOCIAM30) was calculated by dividing the total score by the number of 30 items. This GLOCIAM30 was used to measure the general level of competency in addiction medicine and to compare individual competencies. 
Results One hundred ninety-nine respondents from 45 countries completed the survey. Ninety-five of the 199 respondents (49.0%) had a GLOCIAM30 higher or equal to 4 (fairly competent). The highest skill level was found for the competency "Assessing substance use problems by taking the patient's history.” Nine of the 45 countries had 8 or more respondents (n=129). After post hoc analysis, there was no difference between these countries. Respondents could reasonably estimate whether the competency level in their country was higher or lower than the world average.
Conclusions This study is the first international attempt to examine competencies in addiction medicine. Although a much larger study population is needed to establish an overall goal for competencies in addiction medicine, our study provided an initial direction for such a gold standard in benchmarking procedures.
DOI: 10.6084/m9.figshare.12217802.v1
title: Anvi'o profiles per individual

description: These anvi'o merged profile databases describe the co-assembly of each individual in the Shaiber et al. study.<br>They lend themselves to visualization of co-assembled contigs and their coverages across metagenomes, and reconstruction of genomes from these metagenomes.
DOI: 10.6084/m9.figshare.14072102.v1
title: Dataset periodontitis y2021m02

description: <b>Description and susceptibility of periodontopathic bacteria with severe chronic periodontitis among a group of Peruvian patients: A pilot study</b> <b> </b> <b>ABSTRACT</b> <b>Background</b>: Severe periodontal disease is highly prevalent worldwide, affecting 20 % of the population between the ages of 35 and 44 years old. The etiological epidemiology in Peru is scarce, even though some studies describe a prevalence of 48.5 % of periodontal disease in the general population. Periodontitis is one of the most prevalent oral diseases associated with site-specific changes in the oral microbiota and it has been associated to socioeconomic state. This study aimed to determine the etiology and resistance profile of bacteria identified in a group of patients with chronic severe periodontitis. <b>Methods</b>: Six subgingival plaque samples were collected from eight patients with chronic severe periodontitis. Bacterial identification was carried out by an initial culture, PCR amplification and subsequently DNA sequencing. We evaluated the antibiotic susceptibility by disk diffusion method. <b>Results</b>: Variable diversity in oral microbiota was identified in each one the eight patients. The bacterial genus most frequently found was <i>Streptococcus </i>spp. (15/48, 31.3 %) followed by <i>Rothia </i>spp. (11/48, 22.9 %), <i>Actinomyces</i> spp. (9/48, 18.8 %), and <i>Eikenella</i> spp. (4/48, 8.3 %). The most common species found was <i>Rothia dentocariosa</i> (8/48, 16.7 %). The antimicrobial susceptibility assay varied according to the species tested, however, among all the isolates evaluated <i>Actinomyces naeslundii</i> was resistant to penicillin and tetracycline; <i>Eikenella corrodens</i> resistant to dicloxacillin; and <i>Rothia dentocariosa</i> was resistant to amoxicillin + clavulanic acid and metronidazole but also susceptible to trimethoprim-sulfamethoxazole. <b>Conclusions</b>: Bacterial species of importance medical were detected in patients with chronic severe periodontitis, especially <i>Rothia dentocariosa</i>, most prevalent in this study. Specific antimicrobial therapy is required to improve the treatment outcomes of patients with periodontal disease and to avoid the development of antibiotic resistance.
DOI: 10.6084/m9.figshare.19499213.v1
title: patches and local annotations, slide 089, 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.12859577.v1
title: Supplementary Material for: Use of Continuous Physiological Monitor Data to Evaluate Doxapram Therapy in Preterm Infants

description: <b><i>Introduction:</i></b> Evaluation of pharmacotherapy during intensive care treatment is commonly based on subjective, intermittent interpretations of physiological parameters. Real-time visualization and analysis may improve drug effect evaluation. We aimed to evaluate the effects of the respiratory stimulant doxapram objectively in preterm infants using continuous physiological parameters. <b><i>Methods:</i></b> In this longitudinal observational study, preterm infants who received doxapram therapy were eligible for inclusion. Physiological data (1 Hz) were used to assess respiration and to evaluate therapy effects. The oxygen saturation (SpO<sub>2</sub>)/fraction of inspired oxygen (FiO<sub>2</sub>) ratio and the area under the 89% SpO<sub>2</sub> curve (duration × saturation depth below target) were calculated as measures of hypoxemia. Regression analyses were performed in 1-h timeframes to discriminate therapy failure (intubation or death) from success (no intubation). <b><i>Results:</i></b> Monitor data of 61 patients with a median postmenstrual age (PMA) at doxapram initiation of 28.7 (IQR 27.6–30.0) weeks were available. The success rate of doxapram therapy was 56%. Doxapram pharmacodynamics were reflected in an increased SpO<sub>2</sub> and SpO<sub>2</sub>/FiO<sub>2</sub> ratio as well as a decrease in episodes with saturations below target (SpO<sub>2</sub> &lt;89%). The SpO<sub>2</sub>/FiO<sub>2</sub> ratio, corrected for PMA and mechanical ventilation before therapy start, discriminated best between therapy failure and success (highest AUC ROC of 0.83). <b><i>Conclusion:</i></b> The use of continuous physiological monitor data enables objective and detailed interpretation of doxapram in preterm infants. The SpO<sub>2</sub>/FiO<sub>2</sub> ratio is the best predictive parameter for therapy failure or success. Further implementation of real-time data analysis and treatment algorithms would provide new opportunities to treat newborns.
DOI: 10.6084/m9.figshare.26927398.v1
title: Raw data of the LMO and LFP batteries

description: The raw data for paper "Unlocking ultrafast diagnosis of retired batteries via interpretable machine learning and optical fiber sensors"
DOI: 10.6084/m9.figshare.12127221.v1
title: Diagnostic prediction model for levodopa-induced dyskinesia in Parkinson’s disease

description: Abstract Background: There are currently no methods to predict the development of levodopa-induced dyskinesia (LID), a frequent complication of Parkinson's disease (PD) treatment. Clinical predictors and single nucleotide polymorphisms (SNP) have been associated to LID in PD. Objective: To investigate the association of clinical and genetic variables with LID and to develop a diagnostic prediction model for LID in PD. Methods: We studied 430 PD patients using levodopa. The presence of LID was defined as an MDS-UPDRS Part IV score ≥1 on item 4.1. We tested the association between specific clinical variables and seven SNPs and the development of LID, using logistic regression models. Results: Regarding clinical variables, age of PD onset, disease duration, initial motor symptom and use of dopaminergic agonists were associated to LID. Only CC genotype of ADORA2A rs2298383 SNP was associated to LID after adjustment. We developed two diagnostic prediction models with reasonable accuracy, but we suggest that the clinical prediction model be used. This prediction model has an area under the curve of 0.817 (95% confidence interval [95%CI] 0.77‒0.85) and no significant lack of fit (Hosmer-Lemeshow goodness-of-fit test p=0.61). Conclusion: Predicted probability of LID can be estimated with reasonable accuracy using a diagnostic clinical prediction model which combines age of PD onset, disease duration, initial motor symptom and use of dopaminergic agonists.
DOI: 10.6084/m9.figshare.21529227.v1
title: Dataset on the changes in liver transcriptomics of T1D mice receiving the gut microbiota from normal control mice

description: <strong>Abstract</strong> After 1 week of acclimation, mice were injected with streptozocin (STZ) for 5 days to develop type 1 diabetic (T1D) mice and then administered with a 5-day antibiotic (Abx) treatment after 8 weeks. Subsequently, faecal material from normal control mice was transferred to Abx-treated T1D mice (FMT) for 2 weeks. The transcriptomics changes in the liver of T1D mice receiving the gut microbiota from normal control mice were presented in this dataset. The detailed information including the development of T1D mouse model, FMT, sample collection and transcriptomics analysis were provided in the file named “Protocols for Transcriptomics”. <br> <strong>Acknowledgements</strong> This work was supported by the National Natural Science Foundation of China (Nos. 21974096, 22074106，82000384). We would also like to acknowledge the Scientific Research Center and the Laboratory Animal Center of Wenzhou Medical University for Technical Services.
DOI: 10.6084/m9.figshare.1599742.v1
title: Gaussian Job Archive for C6H16ClNO5

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.21136489.v1
title: RData File for Differential Expression

description: RData file containing processed data and DESeq2 normalized counts for differential expression. Counts have been adjusted for sequencing platform, RIN, and site of sample collection covariates.
DOI: 10.6084/m9.figshare.1537406.v1
title: Music Training Increases Phonological Awareness and Reading Skills in Developmental Dyslexia

description: These data refer to the Article "Music Training Increases Phonological Awareness and Reading Skills in Developmental Dyslexia: a Randomized Control Trial", by Elena Flaugnacco, Luisa Lopez, Chiara Terribili, Marcella Montico, Stefania Zoia, Daniele Schön
DOI: 10.6084/m9.figshare.23251535.v1
title: Neogobius melanostomus Nm3.tif

description: X-ray of Neogobius melanostomus, scale bar 1 cm
DOI: 10.6084/m9.figshare.5917267.v1
title: Stream invertebrate data and local habitat variables from 120 New Zealand streams

description: Benthic invertebrate data, accompanied by local habitat variables. Collected February-April 2006. Details of units and sampling can be found in the preprint at bioRxiv (https://doi.org/10.1101/084673). <br>
DOI: 10.6084/m9.figshare.14109701.v1
title: TABLA 1- Productions of Netflix and HBO in the post- MeToo era.docx

description: Productions of Netflix and HBO in the post- MeToo era
DOI: 10.6084/m9.figshare.21758303.v1
title: Brassicogethes_aenues.xlsx

description: Annotation reports of transcriptome assemblies of five insect pests of euorpean oilseed rape
DOI: 10.6084/m9.figshare.4106805.v1
title: PowerPoint Slides for: Efficacy of Prophylactic Antibiotics at Peritoneal Catheter Insertion on Early Peritonitis: Data from the Catheter Section of the French Language Peritoneal Dialysis Registry

description: <b><i>Background:</i></b> International guidelines recommend the use of a prophylactic antibiotic before the peritoneal dialysis (PD) catheter can be inserted. The main objective of this study was to assess whether this practice is associated with a lower risk of early peritonitis and to estimate the magnitude of the centre effect. <b><i>Methods:</i></b> A retrospective, multi-centric study was conducted, in which data from the French Language Peritoneal Dialysis Registry was analysed. Patients were separated into 2 groups based on whether or not prophylactic antibiotics were used prior to catheter placement. <b><i>Results:</i></b> Out of the 2,014 patients who had a PD catheter placed between February 1, 2012 and December 31, 2014, 1,105 were given a prophylactic antibiotic. In a classical logit model, the use of prophylactic antibiotics was found to protect the individual against the risk of early peritonitis (OR 0.67, 95% CI 0.49-0.92). However, this association lost significance in a mixed logistic regression model with centre as a random effect: OR 0.73 (95% CI 0.48-1.09). Covariates associated with the risk of developing early peritonitis were age over 65: OR 0.73 (95% CI 0.39-0.85), body mass index over 35 kg/m<sup>2</sup>: OR 1.99 (95% CI 1.13-3.47), transfer to PD due to graft failure: OR 2.24 (95% CI 1.22-4.11), assisted PD: OR 1.96 (95% CI 1.31-2.93), and the use of the Moncrief technique: OR 3.07 (95% CI 1.85-5.11). <b><i>Conclusion:</i></b> There is a beneficial effect of prophylactic antibiotic used prior to peritoneal catheter placement, on the occurence of early peritonitis. However, the beneficial effect could be masked by a centre effect.<br>
DOI: 10.6084/m9.figshare.26892340.v3
title: Supplementary Material for: Eye-tracking–based cognitive assessment efficiently detects mild cognitive decline in the predementia stage

description: Introduction: The early detection of cognitive decline is key to maximizing the benefits of preventive and therapeutic interventions against dementia. Generally, dementia is first assessed by interview-based neuropsychological tests, but the lengthy interview and mental stress during the assessment process make screenings inefficient. We previously developed a rapid screening test for dementia using an eye-tracking technology (eye tracking–based cognitive assessment, ETCA) and reported its utility for clinically detecting cognitive impairment in dementia cases. However, the ETCA’s performance in detecting people with mild cognitive decline, which is the major target population for dementia-prevention strategies, remains insufficiently examined. Therefore, this study aimed to evaluate the ETCA’s performance in individuals aged 40 years and older (n = 94, mean age; 61.0 [SD 13.1] years) without being formally diagnosed with dementia. 
Methods: All participants underwent both the ETCA and neuropsychological tests, including the Mini-Mental State Examination (MMSE), Rivermead Behavioral Memory Test (RBMT), and Addenbrooke’s Cognitive Examination-III (ACE-III) on the same day. We examined the correlations in scores between the ETCA and each neuropsychological test. Furthermore, we selected participants who earned normal scores in each neuropsychological test and evaluated the ETCA’s performance in this subgroup.
Results: Participants’ ETCA scores correlated significantly with their scores on neuropsychological tests, including the MMSE, RBMT, and ACE-III. Notably, the ETCA scores correlated with the RBMT or ACE-III scores in individuals who showed normal scores in each neuropsychological test. 
Conclusion: The ETCA has the potential to screen mild cognitive decline efficiently at the predementia stage in nonclinical settings.
DOI: 10.6084/m9.figshare.14267498.v1
title: R. speratus caste RNA-seq

description: Caste-specific RNA-seq analysis of Reticulitermes speratus. Workers, soldiers and reproductives (queens and kings) were analyzed. Two files are included:<br><br>Rspe_caste_RNAseq_cpm.txt -- CPM (count-per-million) count matrix for each gene and category. Tab-delimited text.<br>RNAseq_sample_info.txt -- Sample information of the libraries used. Column names in Rspe_caste_RNAseq_cpm.txt file are explained in this file.<br>Raw sequence data have been deposited in the DDBJ database under BioProject accessions PRJDB5589. <br><br>
DOI: 10.6084/m9.figshare.26629444.v1
title: Environmental communication.csv

description: This research paper aims to identify the research trends, themes and patterns in the field of environmental communication by conducting a bibliometric analysis, a quantitative method to analyse published academic literature in the Web 2.0 era (2004 - July 2024). A total of 604 articles have been extracted from the Scopus database based on pre-determined criteria for the study. VOS viewer and <i>biblioshiny</i> (R studio) software are used for mapping the keywords, cartographic analysis, thematic mapping and clustering of keywords, thereby the impact, influence and evolution of environmental communication have been studied. The study has been aimed at (i) Identifying the most impactful author and the country with the most scientific production in the field of environmental communication, (ii) the Evolution of Trends over the specified period of the study as measured by co-occurrences analysis of keywords (iii) Thematic evolution in the domain of environmental communication.
DOI: 10.6084/m9.figshare.28059686.v1
title: A list of Saudi Arabian variants and their allele frequencies

description: A text file containing allele frequencies of Saudi Arabian variants based on whole genome sequencing of 302 individuals
DOI: 10.6084/m9.figshare.14139278.v1
title: AE_waves.zip

description: This dataset contains the AE waveforms of Brazilian splitting and uniaxial compression experiments described in "rock fracture pattern recognition based on neural network". This data is in “. CSV” format, you can open it with Excel and other tools.
DOI: 10.25413/sun.24658668.v1
title: RNAseq data from Arabidopsis and BC204 treatment

description: BC204 is a citrus-based plant extract applied as a plant biostimulant on a variety of plant species in South Africa, China and Australia. Although there are reports that it elicits physiological responses such as an increase in crop yield and fruit quality, no molecular data is available to explain the specific mechanisms associated with these effects. In this study, an RNA-seq approach was adopted to elucidate the effects of BC204 at the molecular level in <em>Arabidopsis thaliana</em>. BC204, applied via a soil drench at low concentrations of 0.01% (v/v), stimulated above-ground biomass production whilst eliciting a large change in gene expression levels across several biochemical pathways. Of the entire transcriptomic profile examined, 8.212% of genes were significantly differentially expressed between the treated and control groups, of which 5.136% were upregulated and 3.076% downregulated. Most notably, genes involved in photosynthesis, several aspects of cell wall biogenesis, remodelling and restructuring, carbohydrate metabolism, signalling, stress and secondary metabolism were upregulated, which could explain the observed increase in plant growth. Genes related to transcription and RNA regulation were both strongly up- and downregulated, which suggests that BC204 plays a role in inducing and suppressing several pathways. This novel study provides valuable information to be used as starting point for targeted future research.
DOI: 10.6084/m9.figshare.27989324.v2
title: my code

description: my image dehazing net
DOI: 10.6084/m9.figshare.5985742.v1
title: Additional file 1: of Anatomy of a Neotropical insect radiation

description: Spreadsheet with list of permits obtained for research, collection, export and import of specimens used in this study, and respective granting agencies. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.9272579.v1
title: Supplementary Material for: Differential Organ-Specific Tumor Response to Immune Checkpoint Inhibitors in Hepatocellular Carcinoma

description: <b><i>Background and Aims:</i></b> Immune checkpoint inhibitors (ICIs) exhibit significant clinical activity in patients with advanced hepatocellular carcinoma (HCC). This study explored whether tumor response to ICIs in HCC varies among different organs. <b><i>Methods:</i></b> We reviewed the data of patients with advanced HCC who had received ICIs. Patients with measurable diseases were enrolled. Organ-specific response criteria, adapted from RECIST 1.1 and immune-related RECIST, were used to evaluate the objective response to ICIs in tumors located in the liver, lung, lymph node, and other intra-abdominal sites. <b><i>Results:</i></b> Of the 75 enrolled patients with advanced HCC, 51 and 11 patients had chronic hepatitis B virus and chronic hepatitis C virus infection, respectively. Regarding ICI treatment, 58, 1, and 16 patients had undergone anti-PD-1/anti-PD-L1 monoclonal antibody (mAb) alone, anti-CTLA4 mAb alone, and anti-PD-1 mAb plus anti-CTLA4 mAb, respectively; 20 and 55 patients had received ICIs as first-line or ≥second-line therapy. The overall objective response rate (ORR) was 28.0%. In total, 58, 34, 19, and 18 patients had measurable hepatic tumors and lung, lymph node, and other intra-abdominal metastases, and the corresponding organ-specific ORRs were 22.4, 41.2, 26.3, and 38.9%, respectively. Of the 39 patients who had both hepatic and extrahepatic tumors, 12 had disease control in extrahepatic tumors while progressive disease (PD) in hepatic tumors, whereas only 4 exhibited disease control in hepatic tumors while PD in extrahepatic tumors (<i>p</i> = 0.046, McNemar test). Of the 16 patients with only evaluable tumors in the liver and lungs at baseline, 8 had disease control in the lungs while PD in the liver, and none experienced disease control in the liver while PD in the lungs (<i>p</i> = 0.005). <b><i>Conclusions:</i></b> The hepatic tumors of HCC may be less responsive to ICIs than extrahepatic lesions. Lung metastases responded most favorably to ICIs. The mechanisms underlying this differential response to ICIs warrant further investigation.