cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5129593.v1
title: Supplementary Material for: Q787Q EGFR Polymorphism as a Prognostic Factor for Lung Squamous Cell Carcinoma

description: <b><i>Objective:</i></b> EGFR genetic polymorphisms have been investigated for carcinogenesis in various tumors including lung cancer. We evaluated EGFR mutations in four exons, with an emphasis on the Q787Q EGFR polymorphism in non-small-cell lung cancer. <b><i>Methods:</i></b> To determine the presence of the Q787Q polymorphism in patients with lung cancer, we performed direct sequencing analyses of four exons for 83 squamous cell carcinomas and 80 adenocarcinomas untreated with EGFR tyrosine kinase inhibitors. <b><i>Results:</i></b> The Q787Q EGFR polymorphism was more frequently detected in squamous cell carcinoma patients than in adenocarcinoma patients (24 vs. 15.9%). The group of patients with the Q787Q EGFR polymorphism included more males and heavy smokers compared with other patient groups. The presence of the Q787Q EGFR polymorphism significantly and negatively affected the overall survival rate among patients with non-small-cell carcinoma (p = 0.011), particularly those with squamous cell carcinoma (p = 0.037). Among stage I and II squamous cell carcinoma patients, those with the Q787Q EGFR polymorphism had a poor prognosis (p = 0.032). <b><i>Conclusions:</i></b> The Q787Q EGFR polymorphism allows stratifying lung squamous cell carcinoma patients and could be an independent prognostic marker, particularly among those in stages I and II.
DOI: 10.6084/m9.figshare.24432148.v1
title: Data for Manuscript

description: Digital Inclusive Finance and Agricultural Carbon Emissions
DOI: 10.6084/m9.figshare.19588756.v1
title: Supplementary Material for: Evaluation of a bariatric monitoring pass for primary care physicians

description: Introduction There is a growing number of patients undergoing bariatric surgery requiring lifelong follow-up. Therefore, follow-up care can no longer be covered by specialized outpatient clinics alone due to the sharp rise in the number of bariatric patients. BagEL (Bariatric Patients in Primary Care: Post-operative Nutrition and Lifestyle Management) is a survey to evaluate a newly developed structured disease management program including nutrition and lifestyle management in primary care. Methods The study is conceived as a randomized cohort study with a control group. An expert questionnaire for general practitioners (GPs) was developed to assess the usability of a structured post-operative care system regarding nutrition and lifestyle management for bariatric patients in primary care. A structured follow-up program in primary care with a so-called “bariatric monitoring passport” (BMP) was provided for patients in the intervention group (INT) and the existing information sheet “Metabolic surgery and perioperative care” for the control group (CON). 124 patients, who met inclusion criteria and who underwent a bariatric procedure first time, served as ambassadors for delivery of the expert questionnaire and study documents to their individual GPs. Results A total of 39 (31,5%) different GPs from 124 ambassador patients responded. For the primary outcome “Does the aftercare-booklets support treatment of bariatric patients?” GPs of the INT group rated the new designed aftercare booklet (INT) significantly more helpful for treating bariatric patients than the one from the CON group (p=0,041). Discussion/Conclusion These results suggest that GPs are welcoming supportive tools like our BMP to improve the care of long-term follow-up of bariatric patients and should actively participate in the development of lifelong disease management plans necessary to cope with the rapidly growing number of patients.
DOI: 10.6084/m9.figshare.16773202.v1
title: clinical data.xlsx

description: TCGA clinical data
DOI: 10.6084/m9.figshare.16323666.v2
title: Sharon (Co-assembly) dataset and binning results

description: Sharon dataset from the preborn infant gut metagenome (Sharon <i>et. al</i>, 2013). Contains the following files.<br>- Contigs file- Paths file (metaSPAdes)- Assembly graph file (metaSPAdes)- Abundance file- Binning results (including CheckM results)
DOI: 10.6084/m9.figshare.21844845.v1
title: Clinical and immunological features of an APLAID patient caused by a novel 1 mutation in PLCG2

description: The single-cell sequencing results of an APLAID patient and a healthy control.
DOI: 10.6084/m9.figshare.7006421.v1
title: Questionnaire3.docx

description: Second amendment to opinion of merolla replication
DOI: 10.6084/m9.figshare.5126413.v1
title: Supplementary Material for: Postnatal Weight and Height Growth Modeling and Prediction of Body Mass Index as a Function of Time for the Study of Growth Determinants

description: Weight, height and body mass index (BMI) growth trajectories have been associated with several chronic diseases in later life. Our aim was to describe a method to model individual weight and height growth curves during infancy and to show how it can be used to study their determinants and relationships with later health outcomes as well as to predict BMI trajectories. In the EDEN mother-child cohort, we collected 17 measurements of weight and 16 of length/height per child between birth and 3 years of age in 1,900 infants from their health care booklet and during the study clinical examinations at 1 and 3 years; 1,436 (76%) had at least 1 measurement between 2 and 3 years. We fitted individual weight and height growth trajectories using the Jenss nonlinear model including random effects using the ‘SAEMIX' package (R software). We studied whether individual growth model parameters were associated with gender in one- and two-step approaches. We indirectly calculated BMI increase against time from both weight and height growth models combined and compared the fit with a direct multilevel spline model. By modeling observed growth data, we homogenized the data in terms of number and age of measurements and were able to calculate other specific parameters as growth velocities.
DOI: 10.6084/m9.figshare.7071848.v1
title: Supplementary Material for: Temporal Regulation of Glomerular and Cortical Tubulointerstitial Genes Involved in the Development of Nephrotoxic Serum Nephritis

description: <b><i>Background/Aims:</i></b> Murine nephrotoxic nephritis (NTN) is a well-established model resembling chronic kidney disease. Investigating gene expression patterns separately in the glomerular and cortical tubulointerstitial structure could provide new knowledge about structure-specific changes in expression of genes in the NTN model. <b><i>Methods:</i></b> Glomerular, cortical tubulointerstitial and whole kidney tissues from mice subjected to nephrotoxic serum (NTS) or phosphate buffered saline (PBS) were collected on day 7, 21 and 42 using laser microdissection (LMD). Total RNA was extracted and subjected to nCounter NanoString. Histology, immunohistochemistry, in situ hybridization and/or quantitative real time PCR (qRT PCR) were performed to confirm regulation of selected genes. <b><i>Results:</i></b> LMD provided detailed information about genes that were regulated differently between structures over time. Some of the fibrotic and inflammatory genes (<i>Col1a1</i>, <i>Col3a1</i> and <i>Ccl2</i>) were upregulated in both structures, whereas other genes such as <i>Spp1</i> and <i>Grem1</i> were differentially regulated suggesting spatial pathogenic mechanisms in the kidney. Downregulation of cortical tubulointerstitium genes involved in iron metabolism was detected along with iron accumulation. <b><i>Conclusion:</i></b> This study demonstrates several regulated genes in pathways important for the pathogenesis of the NTN model and that LMD identifies structure-specific changes in gene expression during disease development. Furthermore, this study shows the benefits of isolating glomeruli and cortical tubulointerstitium in order to identify gene regulation.
DOI: 10.6084/m9.figshare.14130239.v1
title: MLVA COVID-19

description: ARF files of the top 100 features obtained through feature selection (FS) for all tested vocal tasks in all study groups
DOI: 10.6084/m9.figshare.25249405.v1
title: Supplementary Material for: Musculoskeletal health worsened from carnitine supplementation and not impacted by a novel individualized treadmill training protocol

description: Introduction: Chronic kidney disease (CKD) negatively affects musculoskeletal health, leading to reduced mobility and quality of life. In healthy populations, carnitine supplementation and aerobic exercise have been reported to improve musculoskeletal health. However, there are inconclusive results regarding their effectiveness and safety in CKD. We hypothesized that carnitine supplementation and individualized treadmill exercise would improve musculoskeletal health in CKD. Methods: We used a spontaneously progressive CKD rat model (Cy/+ rat) (n=11-12/gr): 1) Cy/+ (CKD-Ctrl), 2) CKD-carnitine (CKD-Carn), and 3) CKD-treadmill (CKD-TM). Carnitine (250mg/kg) was injected daily for 10-weeks. Rats in the treadmill group ran 4 days/week on a 5° incline for 10-weeks progressing from 30 min/day for week one to 40 min/day for week two to 50 min/day for the remaining eight weeks. At 32 weeks of age, we assessed overall cardiopulmonary fitness, muscle function, bone histology and architecture, and kidney function. Data was analyzed by one-way ANOVA with Tukey’s multiple comparisons tests. Results: Moderate to severe CKD was confirmed by biochemistries for blood urea nitrogen (mean 43±5 mg/dl CKD-Ctrl), phosphorus (mean 8±1 mg/dl CKD-Ctrl), parathyroid hormone (PTH; mean 625±185 pg/ml CKD-Ctrl), and serum creatinine (mean 1.1±0.2 mg/ml CKD-Ctrl). Carnitine worsened phosphorous (mean 11±3 mg/dl CKD-Carn; p&lt;0.0001), PTH (mean 1738±1233 pg/ml CKD-Carn; p&lt;0.0001), creatinine (mean 1±0.3 mg/dl CKD-Carn; p&lt;0.0001), cortical bone thickness (mean 0.5±0.1 mm CKD-Ctrl, 0.4±0.1 mm CKD-Carn; p&lt;0.05). Treadmill running significantly improve maximal aerobic capacity when compared to CKD-Ctrl (mean 14±2 min CKD-TM, 10±2 min CKD-Ctrl; p&lt;0.01). Conclusion: Carnitine supplementation worsened CKD progression, mineral metabolism biochemistries and cortical porosity, and did not have an impact on physical function. Individualized treadmill running improved maximal aerobic capacity but did not have an impact on CKD progression or bone properties. Future studies should seek to better understand carnitine doses in conditions of compromised renal function to prevent toxicity which may result from elevated carnitine levels and to optimize exercise prescriptions for musculoskeletal health.
DOI: 10.6084/m9.figshare.5128027.v1
title: Supplementary Material for: Comparison of Stromal/Stem Cells Isolated from Human Omental and Subcutaneous Adipose Depots: Differentiation and Immunophenotypic Characterization

description: The emerging field of regenerative medicine has identified adipose tissue as an abundant source of stromal/stem cells for tissue engineering applications. Therefore, we have compared the differentiation and immunophenotypic features of adipose-derived stromal/stem cells (ASC) isolated from either omental or subcutaneous adipose depots.<b> </b>Human tissue samples were obtained from bariatric and plastic surgical practices at a university-affiliated teaching hospital and a private practice, respectively, with informed patient consent.<b> </b>Primary cultures of human ASC were isolated from adipose specimens within 24 h of surgery and culture expanded in vitro. The passaged ASC were induced to undergo adipogenic or osteogenic differentiation as assessed by histochemical methods or evaluated for surface antigen expression profiles by flow cytometry. ASC yields per unit weight of tissue were comparable between omental and subcutaneous depots. At passage 0, the immunophenotype of omental and subcutaneous ASC were not significantly different with the exception of CD105 and endoglin, a component of the transforming growth factor β receptor. The adipogenic differentiation of omental ASC was less robust than that of subcutaneous ASC based on in vitro histochemical and PCR assays. Although the yield and immunophenotype of ASC from omental adipose depots resembled that of subcutaneous ASC, omental ASC displayed significantly reduced adipogenic differentiation capacity following chemical induction. Further studies are necessary to evaluate and optimize the differentiation function of omental ASC in vitro and in vivo. Pending such analyses, omental ASC should not be used interchangeably with subcutaneous ASC for regenerative medical applications.
DOI: 10.6084/m9.figshare.9117095.v3
title: secondary_structures_of_eukaryotic_group_II_introns_rfam_set(no_yadd)

description: secondary structures of eukaryotic group II introns rfam set (no yadd)
DOI: 10.6084/m9.figshare.22179071.v7
title: Supplementary material of the project "Tracking the intensity of the mechanism to produce antigenic diversity by subtelomeric ectopic recombination across the phylogeny of Plasmodium parasites"

description: <strong>Supplementary material datasets: </strong> <strong>Dataset 1:</strong> Database for phylogenetic reconstruction of the genus <em>Plasmodium.</em> <strong>Dataset 2:</strong> Trees of the genus <em>Plasmodium</em> generated with six phylogenetic tools (Majority-rule consensus tree of the 6 trees obtained). <strong>Dataset 3:</strong> Database for chromosome mapping of gene conservation. <strong>Dataset 4:</strong> List of predominant gene families in young regions per species. <strong>Dataset 5: </strong>Classification of gene families (with the highest number of sequences in young regions) based on the nature of its products. <strong>Dataset 6: </strong>Chromosome maps showing the gene conservation profile, presence of young regions, and distribution of antigenic genes in 19 <em>Plasmodium</em> species. <strong>Supplementary material:</strong> <strong>Table S1: </strong>Criteria to define the four levels in which <em>Plasmodium</em> species are classified based on evidence of the intensity of production of antigenic diversity through ectopic recombination. <strong>Table S2:</strong> Number of species present in each major clade and in their respective minor clades. <strong>Figure S1:</strong> Proportion of species-specific or young genes excluded from chromosome mapping analysis.
DOI: 10.6084/m9.figshare.15177567.v1
title: Supplementary Material for: Antibiotic Prophylaxis against Surgical Site Infection after Open Hernia Surgery: A Systematic Review and Meta-Analysis

description: <b><i>Objective:</i></b> The role of antibiotic prophylaxis (AP) in the prevention of surgical site infection (SSI) after hernia repair is debated. We conducted this systematic review and meta-analysis to assess the evidence on the value of prophylactic antibiotics in reducing the risks of SSI after open hernia surgery. <b><i>Methods:</i></b> We ran an online and manual search to identify relevant randomized controlled trials that compared prophylactic antibiotics to nonantibiotic controls in patients undergoing open surgical hernia repair. Data on SSI risk were extracted and pooled as risk ratios (RRs) with 95% confidence intervals (95% CIs), using RevMan software. We further used the Cochrane risk of bias tool and GRADE assessment to evaluate the quality of generated evidence. <b><i>Results:</i></b> Twenty-nine studies (<i>N</i> = 8,616 patients) were included in the current analysis. Antibiotic prophylaxis reduced the risk of SSI in open hernia repair patients (RR = 0.65, 95% CI = 0.53, 0.79). Subgroup analysis showed a significant benefit for antibiotics in mesh repair patients (RR = 0.60, 95% CI = 0.48, 0.76) yet no significant difference in SSI risk after herniorrhaphy (RR = 0.86, 95% CI = 0.54, 1.36). In addition, AP was associated with a significant reduction in superficial SSI risk (RR = 0.56, 95% CI = 0.43, 0.72) but not deep SSI (RR = 0.70, 95% CI = 0.30, 1.62). Further analysis showed a significant reduction in SSI risk with amoxicillin/clavulanic acid and cefazolin but not with cefuroxime. <b><i>Conclusion:</i></b> The present meta-analysis suggests that AP is beneficial prior to open mesh hernia repair. However, the quality of evidence was low, and further well-designed trials are needed.
DOI: 10.6084/m9.figshare.6503111.v1
title: Susceptibility of Clonal Seedlings of Eucalyptus spp. to Powdery Mildew Disease

description: ABSTRACT Powdery mildew is one of the main diseases in eucalyptus clonal nursery. The present work aimed to confirm the identity of the causal agent of powdery mildew in clonal seedlings of Eucalyptus spp., and to evaluate the susceptibility reaction of clones to this disease. Conidia were collected in minigardens for molecular identification of the pathogen. We assessed susceptibility by testing 4 clones: Clone 1 (Eucalyptus benthamii ), Clone 2 (E. dunni), Clone 3 (E. benthamii) and Clone 4 (E. urophylla x E. globulus). Scale of classes was used for calculations of Disease Index (DI) and Final Incidence (I). Temporal analysis was performed using the Logistic and Gompertz models. The molecular identification confirmed the identity of the isolates approximate to Podosphaera pannosa (teleomorphic phase of Oidium eucalypti). The Gompertz model obtained a better adjustment to the severity and incidence data, and clones 1 and 2 showed greater susceptibility to eucalyptus powdery mildew.
DOI: 10.6084/m9.figshare.c.3697897_d1.v1
title: MOESM1 of Estimation and monitoring of city-to-city travel times using call detail records

description: Supporting web-site: Travel time estimates and inter-observation time distributions (zip)
DOI: 10.6084/m9.figshare.20038814.v1
title: CAV1 Western blot

description: CAV1 western blot in gracilis artery, normoxic and 49hr chronic hypoxia
DOI: 10.25403/upresearchdata.24559282.v1
title: Literacy instruction for learners with autism spectrum disorder (ASD)

description: Dataset for a Masters study titled 'Teacher perceptions of literacy instruction for their learners with autism spectrum disorder' where a descriptive, cross-sectional paper-based survey design was used to investigate teacher perceptions of literacy instruction for their learners with autism spectrum disorder (ASD). The study focused on seven public schools for learners with special education needs in the broader Johannesburg metro, with a sample size of 67 teachers. Teachers provided their own definitions of literacy, and digital literacy, which provided information on how they view literacy for their learners with ASD. Teachers then identified factors that negatively and positively impacted literacy instruction. They also shared their positive and negative perceptions of their learners with ASD. They described the nature of literacy instruction provided, and the context in which they teach. It was found that most teachers did not believe that their learners with ASD could develop conventional literacy skills, and that their learners should not be exposed to digital literacy as they are not ready. Teachers also reported that they faced various barriers to literacy instruction. Additionally, many teachers used their knowledge of ASD teaching practices to guide how they taught literacy to their learners with ASD. The implications of this studies’ results indicate a need for teacher training regarding literacy development and approached to literacy instruction for learners with ASD.
DOI: 10.6084/m9.figshare.15121110.v1
title: Scripts and resulting files from the analysis of positive selection in Clupeiformes

description: Scripts and datasets to obtain positively selected genes in Clupeiformes<br>
DOI: 10.6084/m9.figshare.24084255.v1
title: The first highly contiguous genome assembly of Japanese lady bell (<i>Adenophora triphylla</i>)

description: Supplementary files for the genome analysis of Japanese lady bell (<i>Adenophora triphylla</i>)
DOI: 10.6084/m9.figshare.5765967.v1
title: Weekly Large Wildfire Probability in Western US Forests andWoodlands, 2005-2017

description: This dataset is a weekly time-series of images from 2005-2017 that depict the probability of large fire across western US forests and woodlands. Specifically, the images depict the probability that an area on the landscape will burn in a large (i.e., &gt; 405 ha) fire following an ignition event, on the given date. Each product in the dataset is a three-band GeoTIFF image (250-m resolution) in the WGS84 geographic coordinate reference system (EPSG:4326). Names of each product correspond to the image prediction date. Band 1 values are the output of a Random Forest classification algorithm, trained on 10 independent, random samples of small and large wildfires that occurred from 2005-2014, and represent the mean predicted probability of an individual pixel burning in a large fire. Band 1 values range from 0-100 (probability scaled by 100). Band 2 values represent the standard deviation of predicted probability of an individual pixel burning in a large fire, and values also range from 0-100 (standard deviation scaled by 100). Band 3 values indicate the quality of MODIS predictor variables. Multiple MODIS products were used as predictor variables to describe the vegetation and land surface immediately preceding a fire event. Only good quality pixels were retained for model training, but all pixels were retained when creating spatial predictions. Therefore, Band 3 indicates if one of these MODIS predictors had unreliable quality, where0 = All MODIS pixels were processed and good quality and 1 = At least one MODIS pixel was not processed or had bad quality. No Data values in each image are set to 255.<br>
DOI: 10.6084/m9.figshare.7302515.v1
title: CRISPR-Cas9 screening data for MUG-Chor1 and UM-Chor1 cell lines

description: Read-count data for genome-scale CRISPR-Cas9 screens performed in MUG-Chor1 and UM-Chor1 chordoma cell lines. Data for three biological replicates per cell line are provided. Each file corresponds to a sequencing technical replicate for the three biological samples. <br>The reference pDNA batch for these screens is batch 2. Read counts for batch 2 pDNA can be found in the raw_readcounts file in avana_public_18Q4 at https://doi.org/10.6084/m9.figshare.7270880.v1.<br>
DOI: 10.6084/m9.figshare.20337603.v2
title: PCR assay for rapid taxonomic differentiation of virulent Staphylococcus aureus and Klebsiella pneumoniae bacteriophages

description: Phage therapy is now seen as a promising way to overcome the current global crisis in the spread of multidrug-resistant bacteria. However, phages are highly strain specific and, in most cases, one will have to isolate a new phage, or search for a suitable for therapeutic application phage in existing libraries. At an early stage of the isolation process, rapid screening techniques are needed to identify and type potential virulent phage. Here, we proposed a simple PCR approach to differentiate between two families of virulent <em>Staphylococci</em> phages (<em>Herelleviridae</em> and <em>Rountreeviridae</em>) and eleven genera of virulent <em>Klebsiella</em> phages (<em>Przondovirus, Taipeivirus, Drulisvirus, Webervirus, Jiaodavirus, Sugarlandvirus, Slopekvirus, Jedunavirus, Marfavirus, Mydovirus</em>, and <em>Yonseivirus</em>). This assay included a thorough search for specific genes, that are highly conserved at the taxonomic group level, on a dataset comprising <em>S. aureus</em> (<em>n</em> = 269) and <em>K. pneumoniae</em> (<em>n</em> = 480) phage genomes available in the NCBI RefSeq/GenBank database. The selected primers showed high sensitivity and specificity for both isolated DNA and crude phage lysates, which allows circumventing the DNA purification protocols. Our approach can be extended and applied to any group of phages, given the large number of available genomes in the databases.