cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.25907917
title: Supplementary Material for: Age-related Variations in Patterns of Patent Foramen Ovale-Stroke versus Other Cryptogenic Stroke

description: Introduction: Patent Foramen Ovale (PFO)-stroke, a form of cryptogenic stroke, has certain identifying clinical and imaging features. However, data describing this stroke type remains inconsistent. This study examined the potential variations in PFO-stroke features, depending on age.

Methods: From a hospital registry, cryptogenic stroke patients were retrospectively selected, and PFO-strokes identified by the presence of &gt;10 microembolic signals (MES) on transcranial doppler (TCD) saline agitation test. Cryptogenic strokes were grouped according to age (&lt;70 as young, &gt;70 as elderly). Clinical and imaging variables of PFO-strokes and non-PFO strokes were compared, with and without age considered. 

Results: Of the 462 cryptogenic patients, 30.5% (141/462) were PFO-strokes, while majority (321/462) had no PFO. When cryptogenic strokes were analyzed by age, the significant difference was noted in the lesion number, pattern, and side. A single (72.8% vs 57.9%, p=0.020) and a small single lesion (51.1% vs 35.5%, p=0.039) were frequently seen in the younger PFO-strokes than the non-PFO counterpart, while mixed territory lesions identified the elderly PFO-strokes (30.6% vs 8.9%, p=0.001). A multivariate logistic regression analysis of PFO-strokes further showed that age was independently associated with lesion side (OR 1.12 (1.05-1.20), p&lt;0.001) and lesion number (OR 1.06 (1.02-1.10), p=0.005). 

Conclusions: Incorporating age-specific imaging criteria in the identification of PFO-strokes may be of additional value. Further, PFO may remain contributory to the stroke risk in the elderly, in association with vascular risk factors.
DOI: 10.6084/m9.figshare.25907917.v1
title: Supplementary Material for: Age-related Variations in Patterns of Patent Foramen Ovale-Stroke versus Other Cryptogenic Stroke

description: Introduction: Patent Foramen Ovale (PFO)-stroke, a form of cryptogenic stroke, has certain identifying clinical and imaging features. However, data describing this stroke type remains inconsistent. This study examined the potential variations in PFO-stroke features, depending on age.

Methods: From a hospital registry, cryptogenic stroke patients were retrospectively selected, and PFO-strokes identified by the presence of &gt;10 microembolic signals (MES) on transcranial doppler (TCD) saline agitation test. Cryptogenic strokes were grouped according to age (&lt;70 as young, &gt;70 as elderly). Clinical and imaging variables of PFO-strokes and non-PFO strokes were compared, with and without age considered. 

Results: Of the 462 cryptogenic patients, 30.5% (141/462) were PFO-strokes, while majority (321/462) had no PFO. When cryptogenic strokes were analyzed by age, the significant difference was noted in the lesion number, pattern, and side. A single (72.8% vs 57.9%, p=0.020) and a small single lesion (51.1% vs 35.5%, p=0.039) were frequently seen in the younger PFO-strokes than the non-PFO counterpart, while mixed territory lesions identified the elderly PFO-strokes (30.6% vs 8.9%, p=0.001). A multivariate logistic regression analysis of PFO-strokes further showed that age was independently associated with lesion side (OR 1.12 (1.05-1.20), p&lt;0.001) and lesion number (OR 1.06 (1.02-1.10), p=0.005). 

Conclusions: Incorporating age-specific imaging criteria in the identification of PFO-strokes may be of additional value. Further, PFO may remain contributory to the stroke risk in the elderly, in association with vascular risk factors.
DOI: 10.15468/dl.e6u86f
title: Occurrence Download

description: A dataset listing the 3295512 species recorded in GBIF matching the query:
{ }

 The dataset's 3295512 records were derived from 36508 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0299022-200613084148143/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.16928624.v1
title: Additional file 8 of A simplified synthetic community rescues Astragalus mongholicus from root rot disease by activating plant-induced systemic resistance

description: Additional file 7: Table S6. Effects of different inoculation and treatment time on Astragalus JA content and ISR-related enzyme activities.
DOI: 10.6084/m9.figshare.7492100.v1
title: Co-occurrence of 3 different resistance plasmids in a multi-drug resistant <i>Cronobacter sakazakii</i> isolate causing neonatal infections

description: <i>Cronobacter sakazakii</i> 505108 was isolated from a sputum specimen of a neonate with severe pneumonia. <i>C. sakazakii</i> 505108 co-harbors 3 resistance plasmids of the IncHI2, IncX3, and IncFIB incomparability groups, respectively. These 3 plasmids have acquired several accessory modules, which carry an extremely large number of resistance genes, especially including those involved in resistance to carbapenems, aminoglycoside, tetracyclines, and phenicols and sulphonamide/trimethoprim. These plasmid-borne antibiotic resistance genes were associated with insertion sequences, integrons, and transposons, indicating that the assembly and mobilization of the corresponding accessory modules with complex chimera structures are facilitated by transposition and/or homologous recombination. This is the first report of fully sequence plasmids in clinical <i>Cronobacter</i>, which provides a deeper insight into plasmid-mediated multi-drug resistance in <i>Cronobacter</i> from hospital settings.
DOI: 10.6084/m9.figshare.16928796.v1
title: Additional file 7 of Genome-wide investigation of the GRAS transcription factor family in foxtail millet (Setaria italica L.)

description: Additional file 7 : Table S7. One-to-one orthologous relationships between S. italica and other plants.
DOI: 10.6084/m9.figshare.16928775.v1
title: Additional file 1 of Genome-wide investigation of the GRAS transcription factor family in foxtail millet (Setaria italica L.)

description: Additional file 1 : Table S1. List of the 57 S. italica GRAS genes identified in this study.
DOI: 10.6084/m9.figshare.16928778.v1
title: Additional file 2 of Genome-wide investigation of the GRAS transcription factor family in foxtail millet (Setaria italica L.)

description: Additional file 2 : Table S2. Subfamilies and protein sequences of Arabidopsis and rice.
DOI: 10.6084/m9.figshare.16928787.v1
title: Additional file 5 of Genome-wide investigation of the GRAS transcription factor family in foxtail millet (Setaria italica L.)

description: Additional file 5 : Table S5. Tandem duplication events of S. italica GRAS genes.
DOI: 10.6084/m9.figshare.16928784.v1
title: Additional file 4 of Genome-wide investigation of the GRAS transcription factor family in foxtail millet (Setaria italica L.)

description: Additional file 4 : Table S4. Cis-regulatory elements in the promoter region of GRAS genes.
DOI: 10.6084/m9.figshare.16928802
title: Additional file 8 of Genome-wide investigation of the GRAS transcription factor family in foxtail millet (Setaria italica L.)

description: Additional file 8 : Table S8. Results of Tajima's D neutrality test.
DOI: 10.6084/m9.figshare.7491911.v1
title: Graphical representation of survival curves in the presence of time-dependent categorical covariates with application to liver transplantation

description: Graphical representation of survival curves is often used to illustrate associations between exposures and time-to-event outcomes. However, when exposures are time-dependent, calculation of survival probabilities is not straightforward. Our aim was to develop a method to estimate time-dependent survival probabilities and represent them graphically. Cox models with time-dependent indicators to represent state changes were fitted, and survival probabilities were plotted using pre-specified times of state changes. Time-varying hazard ratios for the state change were also explored. The method was applied to data from the Adult-to-Adult Living Donor Liver Transplantation Cohort Study (A2ALL). Survival curves showing a ‘split’ at a pre-specified time <i>t</i> allow for the qualitative comparison of survival probabilities between patients with similar baseline covariates who do and do not experience a state change at time <i>t</i>. Time since state change interactions can be visually represented to reflect changing hazard ratios over time. A2ALL study results showed differences in survival probabilities among those who did not receive a transplant, received a living donor transplant, and received a deceased donor transplant. These graphical representations of survival curves with time-dependent indicators improve upon previous methods and allow for clinically meaningful interpretation.
DOI: 10.6084/m9.figshare.12210683.v1
title: Evaluation of the cytotoxic and genotoxic effects by melamine and cyanuric acid co-exposure in human embryonic kidney 293 cells

description: The melamine and cyanuric acid (CA) complex has been suggested to cause the toxic effects observed in melamine-contaminated food or milk. However, the cytotoxic and genotoxic effects of co-exposure to melamine and CA are not fully clear. Therefore, the cytotoxic effects of melamine and CA were first examined by co‐exposure in human kidney 293 cells using the MTT assay. During a 24-h period for the three concentrations tested (0.5, 1, and 5 mg/mL), neither melamine nor CA alone showed significant toxic effects on 293 cells at 0.5 mg/mL, while higher concentrations led to decreased in cell viability. However, co-exposure to several combinations of melamine and CA [100:1, 10:1, 1:10, and 1:100 (v:v), at a final concentration of 0.5 mg/mL] did cause cytotoxicity with higher levels of CA leading to higher cytotoxicity. By contrast, while neither melamine nor CA alone induced phosphorylated-H2AX (γH2AX) foci formation, melamine and CA at a 100:1 ratio induced γH2AX foci 24 h post-treatment. The alkaline comet assay also revealed the presence of DNA damage following melamine and CA co-exposure. In vivo assay also revealed the presence of melamine-CA complex in the kidney. These data indicated that the cytotoxic and genotoxic effects of melamine and CA co-exposure differ from those of melamine or CA alone.
DOI: 10.6084/m9.figshare.21647921
title: Feature Screening for Interval-Valued Response with Application to Study Association between Posted Salary and Required Skills

description: It is important to quantify the differences in returns to skills using the online job advertisements data, which have attracted great interest in both labor economics and statistics fields. In this article, we study the relationship between the posted salary and the job requirements in online labor markets. There are two challenges to deal with. First, the posted salary is always presented in an interval-valued form, for example, 5k–10k yuan per month. Simply taking the mid-point or the lower bound as the alternative for salary may result in biased estimators. Second, the number of the potential skill words as predictors generated from the job advertisements by word segmentation is very large and many of them may not contribute to the salary. To this end, we propose a new feature screening method, Absolute Distribution Difference Sure Independence Screening (ADD-SIS), to select important skill words for the interval-valued response. The marginal utility for feature screening is based on the difference of estimated distribution functions via nonparametric maximum likelihood estimation, which sufficiently uses the interval information. It is model-free and robust to outliers. Numerical simulations show that the new method using the interval information is more efficient to select important predictors than the methods only based on the single points of the intervals. In the real data application, we study the text data of job advertisements for data scientists and data analysts in a major China’s online job posting website, and explore the important skill words for the salary. We find that the skill words like optimization, long short-term memory (LSTM), convolutional neural networks (CNN), collaborative filtering, are positively correlated with the salary while the words like Excel, Office, data collection, may negatively contribute to the salary. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.16928778
title: Additional file 2 of Genome-wide investigation of the GRAS transcription factor family in foxtail millet (Setaria italica L.)

description: Additional file 2 : Table S2. Subfamilies and protein sequences of Arabidopsis and rice.
DOI: 10.6084/m9.figshare.8016437
title: Penalized Spline of Propensity Methods for Treatment Comparison

description: Valid causal inference from observational studies requires controlling for confounders. When time-dependent confounders are present that serve as mediators of treatment effects and affect future treatment assignment, standard regression methods for controlling for confounders fail. Similar issues also arise in trials with sequential randomization, when randomization at later time points is based on intermediate outcomes from earlier randomized assignments. We propose a robust multiple imputation-based approach to causal inference in this setting called penalized spline of propensity methods for treatment comparison (PENCOMP), which builds on the penalized spline of propensity prediction method for missing data problems. PENCOMP estimates causal effects by imputing missing potential outcomes with flexible spline models and draws inference based on imputed and observed outcomes. Under the SUTVA, positivity, and ignorability assumptions, PENCOMP has a double robustness property for causal effects. Simulations suggest that it tends to outperform doubly robust marginal structural modeling when the weights are variable. We apply our method to the multicenter AIDS cohort study to estimate the effect of antiretroviral treatment on CD4 counts in HIV-infected patients. Supplementary materials for this article are available online. Code submitted with this article was checked by an Associate Editor for Reproducibility and is available as an online supplement.
DOI: 10.6084/m9.figshare.6967814
title: Free tissue flaps in head and neck reconstruction: clinical application and analysis of 93 patients of a single institution

description: Abstract Introduction Reconstruction with a free flap is routine in head and neck surgery because of better functional outcomes, improved esthetics, and generally higher success rates. Objective To evaluate the clinical outcomes in patients undergoing different microvascular free flap reconstructions. Methods This was a retrospective study of 93 patients undergoing reconstructions with free flaps from 2007 to 2015. Four types of free flap were performed: anterolateral thigh (76.3%), radial forearm (16.1%), fibula (4.3%) and jejunum (3.3%). Patients' demographic data were collected, and the outcomes measured included flap survival and complications. Postoperative functional and oncological outcome were also analyzed. Results The patients included 73 men and 20 women, with a mean age of 56.1 years. The most common tumor location was the tongue. Squamous cell carcinoma represented the vast majority of the diagnosed tumors (89.2%). The most common recipient vessels were the superior thyroid artery (77.4%) and the internal jugular vein (91.4%). Nine patients required emergency surgical re-exploration and the overall flap success rate was 90.3%. Venous thrombosis was the most common cause for re-exploration. Other complications included wound infection (5.4%), wound dehiscence (1.1%), partial flap necrosis (9.7%), fistula formation (10.8%), and 1 bleeding (1.1%). The majority of patients had satisfactory cosmetic and functional results of both donor site and recipient site after 46.7 months of mean follow-up. Conclusion Microsurgical free flap is shown to be a valuable and reliable method in head and neck surgery. It can be used safely and effectively with minimal morbidity in selected patients. The reconstruction can be performed by appropriately skilled surgeons with acceptable outcomes. Success rate appears to increase as clinical experience is gained.
DOI: 10.6084/m9.figshare.6443579.v1
title: Additional file 3: of Distinct sperm nucleus behaviors between genotypic and temperature-dependent sex determination males are associated with replication and expression-related pathways in a gynogenetic fish

description: Table S3. Up-regulated DEPs (males of TSD vs males of GSD). (XLS 235 kb)
DOI: 10.6084/m9.figshare.7491911
title: Graphical representation of survival curves in the presence of time-dependent categorical covariates with application to liver transplantation

description: Graphical representation of survival curves is often used to illustrate associations between exposures and time-to-event outcomes. However, when exposures are time-dependent, calculation of survival probabilities is not straightforward. Our aim was to develop a method to estimate time-dependent survival probabilities and represent them graphically. Cox models with time-dependent indicators to represent state changes were fitted, and survival probabilities were plotted using pre-specified times of state changes. Time-varying hazard ratios for the state change were also explored. The method was applied to data from the Adult-to-Adult Living Donor Liver Transplantation Cohort Study (A2ALL). Survival curves showing a ‘split’ at a pre-specified time <i>t</i> allow for the qualitative comparison of survival probabilities between patients with similar baseline covariates who do and do not experience a state change at time <i>t</i>. Time since state change interactions can be visually represented to reflect changing hazard ratios over time. A2ALL study results showed differences in survival probabilities among those who did not receive a transplant, received a living donor transplant, and received a deceased donor transplant. These graphical representations of survival curves with time-dependent indicators improve upon previous methods and allow for clinically meaningful interpretation.
DOI: 10.6084/m9.figshare.6443558.v1
title: Additional file 2: of Distinct sperm nucleus behaviors between genotypic and temperature-dependent sex determination males are associated with replication and expression-related pathways in a gynogenetic fish

description: Table S2. All proteins identified by iTRAQ approach and their annotation information in 6 databases. (XLS 4444 kb)
DOI: 10.6084/m9.figshare.24421762
title: Medium-quality Nitrososphaera MAGs from the GCEF project

description: Here, we present 85 medium-quality Nitrososphaera metagenome-assembled genomes (MAGs) from 180 soil samples. The soil samples were taken at the Global Change Experimental Facility (GCEF) of the Helmholtz-Center for Environmental Research (UFZ). More information related to sampling and metagenomic analysis can be found in our previous ISME paper. https://www.nature.com/articles/s41396-023-01470-5
DOI: 10.6084/m9.figshare.24421762.v1
title: Medium-quality Nitrososphaera MAGs

description: Here, we present 85 medium-quality Nitrososphaera metagenome-assembled genomes (MAGs) from 180 soil samples. The soil samples were taken at the Global Change Experimental Facility (GCEF) of the Helmholtz-Center for Environmental Research (UFZ). More information related to sampling and metagenomic analysis can be found in our previous ISME paper. https://www.nature.com/articles/s41396-023-01470-5
DOI: 10.6084/m9.figshare.6967652
title: NF-kB mediated CX3CL1 activation in the dorsal root ganglion contributes to the maintenance of neuropathic pain induced in adult male Sprague Dawley rats

description: Abstract Purpose: To evaluate the role of CX3CL1 and NF-κB in the lumbar disc herniation induced neuropathic pain. Methods: After LDH induced by implantation of autologous nucleus pulposus (NP) on the left L5 nerve root was established, mechanical thresholds and thermal hyperalgesia were tested at relevant time points during an observation period of 28 days. Expression of CX3CL1 and NF-κBin the dorsal root ganglion (DRG) were performed by using Western blotting and RT-PCR. Results: Implantation of autologous nucleus pulposus (NP) induced neuropathic pain, associated with increased mRNA and protein expression of CX3CL1 in the DRG. Moreover, intrathecal injection of neutralizing antibody against CX3CL1 could attenuates LDH-induced persistent pain hypersensitivity. Interestingly, NF-κB activation in the DRGs were found in LDH-induced neuropathic pain. Furthermore, NF-κB downregulation by p65 inhibitor PDTC markedly alleviated LDH-induced mechanical allodynia and thermal hyperalgesia in rat. Importantly, CX3CL1 neutralizing antibody (10 μg/10 μl, i.t.) reduces p-p65 protein level in DRG Conclusions: CX3XL1 could regulate LDH-induced neuropathic pain through NF-κB pathway. Targeting CX3CL1 and NF-κB may represent a potential treatment for neuropathic pain caused by LDH.
DOI: 10.6084/m9.figshare.6443624.v1
title: Additional file 5: of Distinct sperm nucleus behaviors between genotypic and temperature-dependent sex determination males are associated with replication and expression-related pathways in a gynogenetic fish

description: Table S5. Detailed data of the top 20 enriched KEGG pathways, related to Fig. 6b (XLS 40 kb)
DOI: 10.6084/m9.figshare.6443603.v1
title: Additional file 4: of Distinct sperm nucleus behaviors between genotypic and temperature-dependent sex determination males are associated with replication and expression-related pathways in a gynogenetic fish

description: Table S4. Down-regulated DEPs (males of TSD vs males of GSD). (XLS 243 kb)
DOI: 10.6084/m9.figshare.6443645
title: Additional file 6: of Distinct sperm nucleus behaviors between genotypic and temperature-dependent sex determination males are associated with replication and expression-related pathways in a gynogenetic fish

description: Table S6. DEPs assigned to the process of â Replication and repairâ , related to Fig. 6c. (XLS 28 kb)
DOI: 10.6084/m9.figshare.6443663
title: Additional file 7: of Distinct sperm nucleus behaviors between genotypic and temperature-dependent sex determination males are associated with replication and expression-related pathways in a gynogenetic fish

description: Table S7. DEPs assigned to the process of â Translationâ , related to Fig. 6d. (XLS 29 kb)
DOI: 10.6084/m9.figshare.12210683
title: Evaluation of the cytotoxic and genotoxic effects by melamine and cyanuric acid co-exposure in human embryonic kidney 293 cells

description: The melamine and cyanuric acid (CA) complex has been suggested to cause the toxic effects observed in melamine-contaminated food or milk. However, the cytotoxic and genotoxic effects of co-exposure to melamine and CA are not fully clear. Therefore, the cytotoxic effects of melamine and CA were first examined by co‐exposure in human kidney 293 cells using the MTT assay. During a 24-h period for the three concentrations tested (0.5, 1, and 5 mg/mL), neither melamine nor CA alone showed significant toxic effects on 293 cells at 0.5 mg/mL, while higher concentrations led to decreased in cell viability. However, co-exposure to several combinations of melamine and CA [100:1, 10:1, 1:10, and 1:100 (v:v), at a final concentration of 0.5 mg/mL] did cause cytotoxicity with higher levels of CA leading to higher cytotoxicity. By contrast, while neither melamine nor CA alone induced phosphorylated-H2AX (γH2AX) foci formation, melamine and CA at a 100:1 ratio induced γH2AX foci 24 h post-treatment. The alkaline comet assay also revealed the presence of DNA damage following melamine and CA co-exposure. In vivo assay also revealed the presence of melamine-CA complex in the kidney. These data indicated that the cytotoxic and genotoxic effects of melamine and CA co-exposure differ from those of melamine or CA alone.
DOI: 10.6084/m9.figshare.16928865
title: Additional file 9 of Phosphoproteome analysis reveals the involvement of protein dephosphorylation in ethylene-induced corolla senescence in petunia

description: Additional file 9.