cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24574432.v2
title: SEM Analysis metadata

description: This was a cross-sectional, descriptive, and analytical study of 865 Beninese and 813 Senegalese aged 18 years and older. Marginal quota sampling by age, gender and region was adopted. Data collection, using a survey instrument based on the Random Digit Dialing method, was conducted from December 24, 2020, to January 16, 2021, in Senegal and from March 29 to May 14, 2021, in Benin. The questionnaire used the Theory of Planned Behavior and the Health Belief Model. The influence of factors was assessed using a structural equation model based on a diagonally weighted least squares estimator to account for ordered categorical data (Likert scales).
DOI: 10.6084/m9.figshare.12376829.v4
title: Drivers of Human Migration: A Review of Scientific Evidence - Supplementary material

description: Supplementary data for the manuscript: "Drivers of Human Migration: A Review of Scientific Evidence".
DOI: 10.6084/m9.figshare.22573759.v1
title: Supplementary Material for: High Inner Centromere Protein (INCENP) expression correlates with aggressive features and predicts poor prognosis in patients with invasive breast cancer

description: Background: Inner centromere protein (INCENP) is a member of the chromosomal passenger complex (CPC) and plays a key role in mitosis and cell proliferation. This study aims to evaluate the clinical and prognostic significance of INCENP in invasive breast cancer (BC). Material and Methods: INCENP protein expression was evaluated on a tissue microarray of a large BC cohort (n=1295) using immunohistochemistry. At the mRNA level, INCENP expression was assessed using the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) (n=1980) and Cancer Genome Atlas (TCGA) BC cohorts (n=854). The correlations between INCENP expression, clinicopathological parameters and patient outcome were investigated. Results: INCENP protein expression was detected in the nucleus and cytoplasm of the tumour cells. Its expression was significantly associated with features characteristic of aggressive BC behaviour including high tumour grade, larger tumour size and high Nottingham Prognostic Index scores. High INCENP nuclear expression was a predictor of shorter BC-specific survival (BCSS) in the whole cohort, as well as in the luminal subtype (p&lt;0.001). High INCENP nuclear expression was predictive of poor prognosis in BC patients who received hormone treatment or chemotherapy. Conclusion: High INCENP expression is a poor prognostic biomarker in BC with potential therapeutic benefits.
DOI: 10.6084/m9.figshare.27939765.v1
title: Proteomics analysis comparing dsProsβ1- and dsmGFP-fed cabbage stem flea beetle adults.

description: Whole bodies of four CSFB adults receiving RNAi treatment were sampled on days 5, 15, and 30 post-emergence, frozen in liquid nitrogen, and homogenized by grinding. Proteins were extracted with a urea denaturation buffer (6 M urea, 2 M thiourea, 10 mM HEPES) at a ratio of 1 mL per 100 mg sample. Supernatants were recovered by centrifugation (12,000 g, 5 min), and protein concentrations were measured using a Bicinchoninic Acid (BCA) assay. Proteins were precipitated using a chloroform/methanol method, digested with RapiGest SF solution, treated with TFA (1:10), and incubated at 37°C for 45 minutes before drying in a speed vac. Samples were purified using a standard C18 stage tip protocol and analyzed by LC/MS at the Göttingen Center for Molecular Biosciences (Service Unit LCMS Protein Analytics). The proteomics experiments were repeated five times. The proteomics experiments included five biological replicates. Label-free quantification (LFQ) values were obtained by mapping peptides to the CSFB adult proteome. Proteins with fewer than three peptide counts were discarded. Statistical significance was set at adjusted P &lt; 0.05, with significantly altered proteins defined by LogFold2 &gt; 1 (increased) or LogFold2 &lt; -1 (decreased). Proteins showing significant differential abundance were subjected to Gene Ontology (GO) enrichment analysis using the R package clusterProfiler (v3.17). The functional annotations of the proteins were retrieved from our previous work where Trinotate (v4.0, https://github.com/griffithlab/rnaseq_tutorial/wiki/Trinotate-Functional-Annotation) was used.
DOI: 10.6084/m9.figshare.28498430.v1
title: Heritability of host traits in response to parasites in marine and coastal communities

description: We did a search on ISI’s Web-of-Science (December 31 2024) using the following search terms: “heritab*” and “disease or parasit* or pathogen* or infectio*” and “marine or estuarine or coastal.” We also gathered articles cited in several review papers. We kept papers that estimated heritability of a species’ fitness-related trait when exposed to a parasite population. Estimates were made in the field or in a more manipulated environment (sea pen, production pond, mesocosm, laboratory tanks). We included heritability of fitness-related traits: survivorship (days to death, binomial survival curve, etc..), a growth (body length or weight), and parasite load (density, presence/absence). Estimates were generated using a traditional structured breeding strategy (half-sibs, full-sibs), unstructured breeding strategy (i.e., Pedigree “animal” models) and Genomic relationship matrix (or GRM "animal" models; sensu (Richards et al. 2023). The methods used were largely via structure breeding of families, until 2000 when microsatellite- and SNP-based approaches were being incorporated (Figure 1A). We found 130 estimates of heritability in host response traits (survivorship, growth and parasite load) to micro- and macro-parasites for 24 species of hosts. We could find no estimate of heritability within any parasite, nor in any seaweed nor vascular plant; these are clear gaps in the literature.
DOI: 10.6084/m9.figshare.3544262.v1
title: Appendix C. Seasonal variation in soil biota abundances and functional groups.

description: Seasonal variation in soil biota abundances and functional groups.
DOI: 10.6084/m9.figshare.28792436.v1
title: Supplementary Data SCMA - AM

description: Images used for manual test and 3D video reconstructions.
DOI: 10.6084/m9.figshare.89805.v1
title: [05INTRINSIC].pdf

description: financial liquidity
DOI: 10.6084/m9.figshare.25857301.v1
title: Rcode_KorCOPDGene.R

description:  
<strong>Rcode_KorCOPDGene.R</strong>
DOI: 10.6084/m9.figshare.5127643.v1
title: Supplementary Material for: Extracorporeal Virus Elimination for the Treatment of Severe Ebola Virus Disease - First Experience with Lectin Affinity Plasmapheresis

description: Therapeutic options for Ebola virus disease (EVD) are currently limited to (1) best supportive care, and (2) evolving virus-specific therapies, resulting from decades of analyzing one of the world's deadliest diseases. Supportive care ranges from oral or intravenous rehydration therapy and anti-emetics in developing countries to much more extensive life-support interventions in resource-rich countries. Current EVD-specific therapies attempt to either interfere with the earliest steps of viral replication or to elicit a strong immune response against the virus. An entirely new approach is the extracorporeal elimination of viruses and viral glycoproteins by lectin affinity plasmapheresis. Herein, we report for the first time the successful and safe use of lectin affinity plasmapheresis in a patient with severe Ebola virus disease.
DOI: 10.6084/m9.figshare.28554230.v1
title: Supplementary Material for: Endoscopic ultrasound-guided fine needle aspiration of suspected locoregional rectal cancer localizations: a valuable tool.

description: Introduction: 
Organ-preserving treatment for rectal cancer using local excision and/or chemoradiotherapy (CRT) is increasingly used. Locoregional metastasis precludes local excision (LE), and locoregional regrowth, recurrence, or persistence after LE or chemoradiation (CRT) may prompt total mesorectal excision (TME). We believe that the time has passed to make such life-changing treatment decisions without pathological confirmation, and investigated the use of linear endoscopic ultrasound with fine-needle aspiration (EUS-FNA).
Methods:
We report eight cases of suspected locoregional tumor growth (LRTG) on MRI: adjacent or in the rectal wall, within the mesorectal fascia, high presacral region, and obturator foramen. MRI images were studied thoroughly before and during EUS to identify the target lesion using rectal EUS-FNA. Patients were prepared using an enema. The procedure was performed on an outpatient basis without conscious sedation. FNA was performed using a 25 G needle. The patient received a three-day course of ciprofloxacin after the procedure to prevent infection of the perirectal space.
Results:
Identification of the target was the most difficult part of EUS but was successful in all cases. FNA revealed adenocarcinoma in seven cases. Five cases were confirmed by TME results: one patient died before the operation, and one patient was treated with CRT. One patient with a suspected node in the obturator foramen was free of tumors on FNA. The TME resection specimen contained 31 lymph nodes without metastasis. All procedures were well tolerated, and no complications were observed.
Conclusion:
Suspected locoregional tumor growth on MRI can be confirmed using EUS-FNA. In the era of organ-preserving treatment for rectal cancer, EUS-FNA may play a supportive role when considering TME or CRT.
DOI: 10.6084/m9.figshare.26395093.v1
title: Foliage's Opensource Dataset

description: The public dataset of Foliage's bug clustering
DOI: 10.6084/m9.figshare.7373876.v1
title: Analysis_high-speed-footage

description: Analysis of the high-speed video footag. CSV file counting attack success of <i>Chaoborus </i>larva in the high-speed footage.<br>1. column 'file': name of the corresponding avi-file <br>2. column 'Treatment': either 'Ctrl' or 'Ind'; referring to the morphotype of the used daphniid. That was undefended (Ctrl) or defended (Ind).<br>3. column 'attack successful': either 'Yes' or 'No'; outcome of the <i>Chaoborus </i>larva attack in the corresponding footage. Prey ingestion equals 'Yes', prey escape equals 'No'.<br>4. column 'attack succesful 1/0': either '1' or '0'; same information as 3. column, '1' equals 'Yes' in the 3. column, '0' equals 'No' in 3. column.<br>5. column 'Prey morph': either 'Undefended' or 'Defended'; Morphotype of the daphniid used in the corresponding footage.
DOI: 10.6084/m9.figshare.25422769.v1
title: Study on the impact of kinesiophobia after Total knee replacement on the rehabilitation of patients during hospitalization.xlsx

description: Kinesiophobia following knee replacement surgery significantly impacts patients' ability to engage in postoperative rehabilitation exercises. However, research on this topic is relatively new in China. Current efforts to identify and address kinesiophobia are not yet comprehensive. Our team focused on a subset of patients who had undergone unilateral knee replacement for our study. We first identified patients experiencing kinesiphobia and then compared the rehabilitation progress of patients with and without kinesiophobia during their hospital stay. This comparison included assessing pain levels, knee flexion at various postoperative time points, and milestones such as getting out of bed for the first time and completing the 2-minute walk test on the day of discharge. This pioneering research in China aims to bridge existing gaps in knowledge and may serve as a valuable foundation for future interventional studies.
DOI: 10.6084/m9.figshare.4225688.v1
title: Sigure S3C - LE

description: SIM image reconstruction and log files and overlay image for mSin1.2-GFP (enhanced by Atto488-conjugated anti-GFP scAb) and mCherry-tagged Rab7.<br>The reconstructed SIM image file was split into 2 fluorescence channels and the contrast was adjusted across the entire image using ImageJ (Fiji built). No non-linear adjustments were made. Contrast settings: 1000..10000 (Rab7); 1000..10000 (mSin1).
DOI: 10.6084/m9.figshare.5127301.v1
title: Supplementary Material for: Bronchopulmonary Dysplasia Is Associated with Delayed Structural Brain Maturation in Preterm Infants

description: <b><i>Background:</i></b> In recent years, cerebral magnetic resonance imaging (MRI) has been increasingly used to depict the wide spectrum of preterm brain injury. Furthermore, it has already been demonstrated by MRI at term-equivalent age (TEA) that preterm infants show delayed brain maturation as compared to term infants, and this delay has been related to neurobehavioral outcome. <b><i>Objectives:</i></b> The aim of the current study was to investigate the influence of prevalent neonatal risk factors for adverse outcome on structural brain maturation in very preterm infants at TEA. <b><i>Methods:</i></b> One hundred and thirty very preterm infants born at a mean gestational age of 29.7 weeks were included. MRI was performed at TEA and given a validated ‘total maturation score'. Brain maturation scores were compared with neonatal data. <b><i>Results:</i></b> In univariate analysis, bronchopulmonary dysplasia (BPD), late-onset sepsis and retinopathy of prematurity were significantly associated with delayed brain maturation. Furthermore, infants with delayed maturation had been ventilated significantly longer and more often suffered from severe arterial hypotension. In multivariate analysis, BPD remained significant as predictor of delayed brain maturation. <b><i>Conclusions:</i></b> This study is the first to show that delayed structural brain maturation as evaluated by MRI at TEA is preceded by BPD, which is known to be a predictor of adverse outcome in preterm infants. This finding adds further evidence to show that adverse outcome in preterm infants may have additional neural correlates that exceed common brain injury.
DOI: 10.6084/m9.figshare.5128465.v1
title: Supplementary Material for: Molecular Mechanisms of Renal Ischemic Conditioning Strategies

description: Ischemia-reperfusion injury is the leading cause of acute kidney injury in a variety of clinical settings such as renal transplantation and hypovolemic and/or septic shock. Strategies to reduce ischemia-reperfusion injury are obviously clinically relevant. Ischemic conditioning is an inherent part of the renal defense mechanism against ischemia and can be triggered by short periods of intermittent ischemia and reperfusion. Understanding the signaling transduction pathways of renal ischemic conditioning can promote further clinical translation and pharmacological advancements in this era. This review summarizes research on the molecular mechanisms underlying both local and remote ischemic pre-, per- and postconditioning of the kidney. The different types of conditioning strategies in the kidney recruit similar powerful pro-survival mechanisms. Likewise, renal ischemic conditioning mobilizes many of the same protective signaling pathways as in other organs, but differences are recognized.
DOI: 10.17632/vt8bf9pmf8.1
title: Colocalization analysis of high-resolution cortical structures from GV-oocytes injected with ZnT2mCherry + ZnT4TGFP and MII eggs immunostained with anti-ZnT2 + anti-ZnT4

description: Colocalization analysis of high-resolution cortical structures from GV-oocytes injected with ZnT2mCherry + ZnT4TGFP and MII eggs immunostained with anti-ZnT2 + anti-ZnT4
DOI: 10.6084/m9.figshare.4956356.v1
title: Authorship dataset of scientific articles on eating disorders indexed in Web of Science Core Collection and Scopus (1980-2014)

description: Dataset in a xlsx file table used by Juan-Carlos Valderrama-Zurián & collaborators in the research “Productivity trends and collaboration patterns of the researchers: a diachronic study in the eating disorders field”. The signature variations from single authors were standardized throught a manual review of all signatures, checking institutional affiliations in case of doubt.
DOI: 10.6084/m9.figshare.5572663.v1
title: Dataset for "One Step at a Time: Representational Overlap Between Active-voice, Be-passive, and Get-passive in English"

description: This is the data corresponding to the submitted paper "<i>One Step at a Time: Representational Overlap Between Active-voice, Be-passive, and Get-passive in English</i>".<br>There are three experiments; one per sheet. These show raw ratings, presence or absence of a suggested rephrase, and the type of rephrase suggested.
DOI: 10.6084/m9.figshare.6152417.v1
title: Cognitive, functional and physical activity impairment in elderly with Alzheimer's disease

description: ABSTRACT Alzheimer's Disease (AD) is a progressive degenerative disorder that negatively affects quality of life of patients and family members. Objective: The aim of this study is to compare the cognition, level of physical activity and functioning of elderly individuals with mild AD and those without dementia. Methods: The study comprised 24 elderly with mild AD (mean age = 76.9 ± 5.3 years) and 30 elderly without dementia (mean age = 74.1 ± 5.6 years). The following instruments were applied to evaluate cognitive functions: MMSE; Frontal Assessment Battery; Clock Drawing Test; Corsi Blocks, and Verbal Paired Associates. Event-related potential P300 was used to evaluate cognitive processing. The Modified Baecke Questionnaire For Older Adults was applied to evaluate the level of physical activity together with use of a pedometer for 7 consecutive days. For the evaluation of the functioning, the Direct Assessment of Functional Status-Revised scale and functional tests were used. Results: There was a significant difference between the groups in level of physical activity and functioning, except on the test evaluating flexibility. Conclusion: Elderly with AD had cognitive, functional and physical activity deficits which can manifest even in the early stages of the disease.
DOI: 10.6084/m9.figshare.22302952.v1
title: SECAPR extraction file from the respective Thladiantha-specific references

description: This file was created using the reference file by the SECAPR extraction (*_selected_blast_hit.tsv from all the samples) step. Further, it was used for comparison with HybPiper and SECAPR. The python script was used to process this file to remove the overlaps in the blast output file.
DOI: 10.6084/m9.figshare.14661174.v2
title: 1000 random numbers in range of 0 to 100

description: This JSON file contais 1000 random numbers in a range of 0 to 100 stored in a python list format.
DOI: 10.6084/m9.figshare.3465233.v1
title: Supplementary Material for: Increased Levels of Copeptin, a Surrogate Marker of Arginine Vasopressin, Are Associated with an Increased Risk of Chronic Kidney Disease in a General Population

description: <i>Background:</i> Our aim was to test if plasma copeptin, a stable surrogate marker of arginine vasopressin, predicts decline of glomerular filtration rate (GFR) and risk of chronic kidney disease (CKD). <i>Methods:</i> We measured copeptin and renal function at the Malmö Diet and Cancer Cardiovascular Cohort baseline exam and reassessed renal function after a follow-up time of 16.6 ± 1.5 years (n = 3,186). Furthermore, we defined CKD based on an estimated GFR (eGFR) calculated by the Modification of Diet in Renal Disease (MDRD) &lt;60 (CKD_60MDRD), &lt;45 (CKD_45MDRD) and &lt;30 (CKD_30MDRD) ml/min/1.73 m2. <i>Results:</i> After multivariate adjustment (gender, age, baseline eGFR, smoking status, systolic blood pressure, antihypertensive treatment and follow-up time), copeptin (beta-coefficient per 1 SD increment of copeptin) was independently associated with significantly greater annual decline of eGFR (ml/min/1.73 m2) according to the MDRD formula (OR 0.057, 95% CI 0.022-0.093; p = 0.001) as well as according to the CKD Epidemiology Collaboration (CKD-EPI) formula (OR 0.050, 95% CI 0.022-0.077; p &lt; 0.001). Each SD increment of copeptin independently predicted incident CKD_60MDRD (OR 1.19, 95% CI 1.04-1.36; p = 0.010), CKD_45MDRD (OR 1.33, 95% CI 1.04-1.71; p = 0.026) and CKD_30MDRD (OR 3.69, 95% CI 1.41-9.66; p = 0.008). The relationship between copeptin and CKD defined by CKD-EPI gave similar results. <i>Conclusion:</i> Our data suggest that increased levels of copeptin independently predict decline in eGFR and greater risk of new-onset CKD.
DOI: 10.6084/m9.figshare.5121148.v1
title: Supplementary Material for: Association of <i>AHSG</i> Gene Polymorphisms and Aortic Stiffness in Peritoneal Dialysis Patients

description: <i>Background/Aims:</i> Fetuin-A is a negative acute-phase reactant and extraosseous calcification inhibitor. Decreased serum concentration of fetuin-A is independently related to all-cause and cardiovascular mortality in dialysis patients. Our aim is to investigate the association between the genetic polymorphism of α<sub>2</sub>-Heremans-Schmid-glycoprotein <i>(AHSG)</i> encoding fetuin-A and its serum concentration, vascular calcification, and aortic stiffness in peritoneal dialysis (PD) patients. <i>Method:</i> A total of six single nucleotide polymorphisms (SNPs) in the <i>AHSG</i> gene were genotyped and evaluated for association with serum fetuin-A level, quantitative measures of vascular calcification and aortic stiffness represented by heart-to-femoral pulse wave velocity (hfPWV). <i>Results:</i> Five SNPs in the <i>AHSG</i> gene were nominally associated with the serum fetuin-A level in our PD patients. In haplotype analyses, there were haplotypes positively (H1; AGCA, H2; CC) and inversely (H1; TTCG, H2; TT) related with the serum fetuin-A level. The serum fetuin-A level inversely and independently correlated with hfPWV. Moreover, the serum fetuin-A concentration was a determinant for the simple vascular calcification score (SVCS), which subsequently was associated with hfPWV. <i>Conclusions:</i> Our study showed an association between <i>AHSG</i> polymorphism and its serum concentration, and also revealed an association of the serum fetuin-A level with SVCS and aortic stiffness in PD patients.
DOI: 10.6084/m9.figshare.19499108.v1
title: patches and local annotations, slide 192, 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.21957449.v1
title: Phenotypic values of grain size traits of main crop and ratoon rice under two environments

description: All the 159 <em>indica</em> rice accessions were planted, with a randomized complete block design, in Wuhan in 2021. This experiment was replicated two times in different fields, namely environments 1 and 2. Each material was planted in one plot with 10 seedlings, row spacing was 16.7 cm × 20 cm, and one line empty between cells. At yellow ripening stage, grain width (GW) (mm), grain length (GL) (mm), and thousand grain weight (TGW) (g) for each accession in mian crop (MC) and ratoon rice (RR) were measured for three times. GL in MC is abbreviated as GL-MC, and it is true for other traits.
DOI: 10.6084/m9.figshare.7890917.v1
title: gVCF_HG03086

description: 1000 Genomes gVCF mapped to hs37d5 for HG03086. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.14959923.v1
title: Plant-pollinator Interaction Data for Nine Ponds with MANOVA and Pairwise Analysis

description: Cumulative interaction data between plants and pollinators at nine study ponds. Data collected between March-October during 2016 & 2017. The final two sheets show MANOVA and Pairwise t-test (Bonferroni correction) results for differences between management treatment. Management treatment codes: REST - recently restored ponds, LTM - long-term managed ponds, and TERR - overgrown ponds.
DOI: 10.6084/m9.figshare.3527339.v1
title: Appendix G. Instability in BLAST-based identifications at the genus and family levels for foliar endophytes from two focal tropical hosts (Heisteria concinna, Ouratea lucens).

description: Instability in BLAST-based identifications at the genus and family levels for foliar endophytes from two focal tropical hosts (Heisteria concinna, Ouratea lucens).