cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3557712.v1
title: Supplement 2. R scripts for simulating and testing functional-diversity–area relationships of communities with known levels of biotic sorting and abiotic filtering.

description: File List R scripts for simulating communities with known levels of sorting or filtering.r (MD5: ba675c8f1030d23a5309ad532d646d26)Description R scripts for simulating communities with known levels of sorting or filtering.r contains an R script for simulating communities with user-specified levels of biotic sorting and/or environmental filtering and testing the output with the trait-level (TLM) and species-trail–level (STLM) models. The script is useful for determining the power of the null model tests. Comment lines specify input and its format . The code can be copied and pasted into the R command line interface or called using the source() function. Results are plotted and output as CSV files. The format of the CSV files is explained in the comments.
DOI: 10.6084/m9.figshare.5639305.v1
title: Conserved lands data used in linear regression models.

description: The file contains photo user days, survey user days and landscape attributes for conserved lands in Vermont, USA.
DOI: 10.6084/m9.figshare.5125990.v1
title: Supplementary Material for: MicroRNA Expression and Functional Profiles of Osteosarcoma

description: <b><i>Objective:</i></b> Osteosarcoma (OS) is the most frequent primary malignant bone tumor in children and young adults. Although the introduction of combined neoadjuvant chemotherapy has significantly prolonged survival, the outcome for OS patients showing a poor response to chemotherapy is still unfavorable. In order to develop new therapeutic approaches, elucidation of the entire molecular pathway regulating OS cell proliferation would be desirable. <b><i>Methods:</i></b> MicroRNA (miRNA) are highly conserved noncoding RNA that play important roles in the development and progression of various other cancers. Using miRNA microarrays capable of detecting a known number of 933 miRNA, 108 miRNA were found to be commonly expressed in 24 samples of OS tissue and subjected to a cell proliferation assay. <b><i>Results:</i></b> We found that inhibition of 5 let-7 family miRNA (hsa-let-7a, b, f, g and i) significantly suppressed the proliferation of OS cells. Using a quantitative shotgun proteomics approach, we also found that the let-7 family miRNA regulated the expression of vimentin and serpin H1 proteins. <b><i>Conclusions:</i></b> Our present results indicate the involvement of let-7 family miRNA in regulation of the cell proliferation as well as epithelial-mesenchymal transition of OS. Thus, let-7 family miRNA may potentially provide novel targets for the development of therapeutic strategies against OS.
DOI: 10.6084/m9.figshare.21427947.v1
title: Supplementary Material for: Comparison of Different Anti-<b><i>Demodex</i></b> Strategies: A Systematic Review and Meta-Analysis

description: <b><i>Background:</i></b> <i>Demodex</i> mites are related to some inflammatory diseases such as rosacea and blepharitis and could be harmful in patients with immunodeficiency or immunosuppression, especially notable in patients using biologic like dupilumab. In order to have an objective observation of different anti-<i>Demodex</i> strategies, we conducted this study, based on interventional clinical evidence with quantified <i>Demodex</i> mite data. <b><i>Methods:</i></b> We used the PubMed, Embase, ClinicalTrials.gov, Medline, and International Clinical Trials Registry Platform (ICTRP) as databases. To assess the risk of bias, the RoB2 and ROBINS-I tools were used. The certainty of evidence was assessed following the GRADE guideline. Furthermore, the effect sizes (ESs) of different strategies were compared in different time periods (0–1, 1–2, 2–3, &gt;3 months), as well as <i>Demodex</i> decrease rates. <b><i>Results:</i></b> 1,618 studies were identified in the databases, with 21 of which included in the final quantitative synthesis. Interventions in these studies included ivermectin, tea tree oil (TTO), permethrin, crotamiton, metronidazole, light therapies, combined therapies, and other therapies. During 0–1 month, the ES varied from 0.07 (cleanser) to 1.95 (systemic ivermectin-metronidazole). During 1–2 months, the ES varied from 0.88 (topical permethrin) to 4.40 (topical ivermectin). During 2–3 months, the ES varied from 0.79 (topical permethrin) to 8.37 (topical ivermectin). During the time of 3 months, the ES varied from 0.59 (topical permethrin) to 2.25 (intense pulsed light [IPL]). In terms of <i>Demodex</i> decrease rates, topical ivermectin, TTO, permethrin, IPL, and baby shampoo had achieved a nearly 100% decrease. The reported adverse events were mostly mild, without severe adverse events reported in any of the studies. <b><i>Conclusions:</i></b> We found ivermectin (topical and systemic), ivermectin-metronidazole (topical), and TTO (topical) are promising anti-<i>Demodex</i> interventions. In addition to traditional pharmacotherapy, light therapies, especially IPL and skin cleansing, could also be considered as effective methods to control <i>Demodex</i> mite infestation.
DOI: 10.6084/m9.figshare.24156375.v1
title: t2.nii.gz

description: image mai
DOI: 10.6084/m9.figshare.7399235.v1
title: Supplementary Material for: The Role of Intestinal Fatty Acid Binding Proteins in Protecting Cells from Fatty Acid Induced Impairment of Mitochondrial Dynamics and Apoptosis

description: <b><i>Background/Aims:</i></b> The conformation, folding and lipid binding properties of the intestinal fatty acid binding proteins (IFABP) have been extensively investigated. In contrast, the functional aspects of these proteins are not understood and matter of debates. In this study, we aim to address the deleterious effects of FA overload on cellular components, particularly mitochondria; and how IFABP helps in combating this stress by restoring the mitochondrial dynamics. <b><i>Methods:</i></b> In the present study the functional aspect of IFABP under conditions of lipid stress was studied by a string of extensive in-cell studies; flow cytometry by fluorescence-activated cell sorting (FACS), confocal imaging, western blotting and quantitative real time PCR. We deployed ectopic expression of IFABP in rescuing cells under the condition of lipid stress. Again in order to unveil the mechanistic insights of functional traits, we arrayed extensive computational approaches by means of studying centrality calculations along with protein-protein association and ligand induced cluster dissociation. While addressing its functional importance, we used FCS and in-silico computational analyses, to show the structural distribution and the underlying mechanism of IFABP’s action. <b><i>Results:</i></b> Ectopic expression of IFABP in HeLa cells has been found to rescue mitochondrial morphological dynamics and restore membrane potential, partially preventing apoptotic damage induced by the increased FAs. These findings have been further validated in the functionally relevant intestinal Caco-2 cells, where the native expression of IFABP protects mitochondrial morphology from abrogation induced by FA overload. However, this native level expression is insufficient to protect against apoptotic cell death, which is rescued, at least partially in cells overexpressing IFABP. In addition, shRNA mediated IFABP knockdown in Caco-2 cells compromises mitochondrial dynamics and switches on intrinsic apoptotic pathways under FA-induced metabolic stress. <b><i>Conclusion:</i></b> To summarize, the present study implicates functional significance of IFABP in controlling ligand-induced damage in mitochondrial dynamics and apoptosis.
DOI: 10.6084/m9.figshare.17012411.v2
title: Gut microbiota in mucosa and feces of newly diagnosed, treatment-naïve adult inflammatory bowel disease and irritable bowel syndrome patients

description: <br> For more details see DOI: 10.1080/19490976.2022.2083419 <br> 16S rRNA gene amplicon V3-V4 sequencing performed on Illumina Mi-Seq with Nextera XT kit, processed with QIIME pipeline. Gut mucosa samples at 6 positions along the gut of adult, treatment-naive IBD and IBS patients.<br>
DOI: 10.6084/m9.figshare.25020743.v1
title: DATASETS

description: This study proposes a hybrid model: LSHS integrating Long Short-Term Memory (LSTM) and the Harmony Search optimization method to enhance the accuracy of software effort estimation. To evaluate its effectiveness, we evaluate our proposed model on four diverse datasets — China, Finnish, Desharnais, and Albrecht — with the number of records of 499, 407, 81, and 24, respectively. Our model is systematically benchmarked against eight existing machine learning models, employing 3 evaluation metrics.
DOI: 10.6084/m9.figshare.5125345.v1
title: Supplementary Material for: Imaging Findings Associated with Cognitive Performance in Primary Lateral Sclerosis and Amyotrophic Lateral Sclerosis

description: <b><i>Introduction:</i></b> Executive dysfunction occurs in many patients with amyotrophic lateral sclerosis (ALS), but it has not been well studied in primary lateral sclerosis (PLS). The aims of this study were to (1) compare cognitive function in PLS to that in ALS patients, (2) explore the relationship between performance on specific cognitive tests and diffusion tensor imaging (DTI) metrics of white matter tracts and gray matter volumes, and (3) compare DTI metrics in patients with and without cognitive and behavioral changes. <b><i>Methods:</i></b> The Delis-Kaplan Executive Function System (D-KEFS), the Mattis Dementia Rating Scale (DRS-2), and other behavior and mood scales were administered to 25 ALS patients and 25 PLS patients. Seventeen of the PLS patients, 13 of the ALS patients, and 17 healthy controls underwent structural magnetic resonance imaging (MRI) and DTI. Atlas-based analysis using MRI Studio software was used to measure fractional anisotropy, and axial and radial diffusivity of selected white matter tracts. Voxel-based morphometry was used to assess gray matter volumes. The relationship between diffusion properties of selected association and commissural white matter and performance on executive function and memory tests was explored using a linear regression model. <b><i>Results:</i></b> More ALS than PLS patients had abnormal scores on the DRS-2. DRS-2 and D-KEFS scores were related to DTI metrics in several long association tracts and the callosum. Reduced gray matter volumes in motor and perirolandic areas were not associated with cognitive scores. <b><i>Conclusion:</i></b> The changes in diffusion metrics of white matter long association tracts suggest that the loss of integrity of the networks connecting fronto-temporal areas to parietal and occipital areas contributes to cognitive impairment.
DOI: 10.6084/m9.figshare.15377112.v2
title: Supplemental Information S12: Effect of two successive stimulation experiment LabChart data file

description: LabChart data file of effect of two successive stimulation experiment. The file can be opened using LabChart reader software provided freely by ADInstruments, Australia at https://www.adinstruments.com/products/labchart-reader.
DOI: 10.6084/m9.figshare.24153420.v1
title: Sev REE Project 2023

description: This study investigated aeolian sediment transport and spatial distribution of sediment in the surface soil for seven years following a prescribed fire using a multiple rare earth element tracer-based approach in a shrub-encroached desert grassland in the northern Chihuahuan desert. The data sets include data on: rare earth element tracer (REE tracers: holmium (Ho), Ytterbium (Yb), and Europium (Eu) on shrub, bare, and grass microsites, respectively) concentrations in sediment from aeolian sediment collectors and from soil, aeolian erosion rates (horizontal mass flux) and meteorological parameters.<br>
DOI: 10.6084/m9.figshare.3563745.v1
title: Supplement 1. Data containing a list of studies used in the meta-analysis, including type of CO2 treatment, dominant vegetation, and values for mean ambient and mean elevated activity for the various enzyme groups.

description: File List data.txt -- (MD5: f6ba0153fbb3db8e543a20ee1f948437) Description The data.txt file is a tab-delimited file. It contains a list of studies used in the meta-analysis, including type of CO<sub>2</sub> treatment, dominant vegetation, and values for mean ambient and mean elevated activity for the various enzyme groups. Column definitions 1. Study citation 2. Type of CO<sub>2</sub> treatment 3. Length of CO<sub>2</sub> treatment 4. Dominant Vegetation 5. Treatment (Elevated or Ambient) 6. Simple Sugar Degradation 7. Starch Degradation 8. b-glucan Degradation 9. Cellulose Degradation 10. Xylan/Hemicellulose Degradation 11. Lignin Degradation 12. Chitin Degradation 13. Protein Degradation 14. Organic P Degradation 15. Organic S Degradation Missing values are represented as “-9999”. Checksum values are (calculations do not include “-9999” for missing values): Column 6 (Simple Sugar Degradation): SUM= 35031.1; 126 missing values (rows with data: 32) Column 8 (b-glucan Degradation): SUM= 24891.97; 102 missing values (rows with data: 56) Column 11 (Lignin Degradation): SUM= 29411.038; 120 missing values (rows with data: 38) Column 15 (Organic S Degradation): SUM= 1053.8; 130 missing values (rows with data: 28)
DOI: 10.6084/m9.figshare.4545784.v1
title: RespiratoryPathogenDetectionData.xlsx

description: Detection histories of respiratory pathogens for individual bighorn sheep that were sampled using several specified diagnostic protocols.
DOI: 10.6084/m9.figshare.24249574.v1
title: Supplementary Material for: The Fatty Liver Index, the Strongest Risk Factor for Low Testosterone Level

description: Introduction: The study aimed to determine if hepatic steatosis assessed by Fatty Liver Index (FLI) was an independent risk factor for male testosterone insufficiencylow testosterone level and whether the FLI was the strongest risk factor for testosterone insufficiencylow testosterone level in two different age groups. Methods: Two cross-sectional studies were performed. A total of 3443 male participants (aged 46-75) were recruited into study A (part of lONgitudinal study (REACTION)). Then a total of 267 male participants (aged 25-45) were recruited into study B. Serum TT and sex hormone-binding globulin (SHBG) levels, indicators for assessing hepatic steatosis were measured. The Pearson correlation and regression analysis were performed to investigate the risk factors for testosterone insufficiencylow testosterone level. Results: The FLI had the strongest negative correlation with serum testosterone in the study A (r=-0.436) and B (r=-0.542). Compared with patients with a FLI lower than 30, the risk for testosterone insufficiencylow testosterone level increased by 3.48–fold in subjects with a FLI higher than 60 adjusted for potential risk factors in study A. In study B, the OR of testosterone insufficiencylow testosterone level in patients with potential hepatic steatosis was 4.26 (1.57-11.60) after adjusted for age and HOMA-IR, and 0.59 (0.14-2.60) after adjusted for age, HOMA-IR, waist circumference, body mass index, and SHBG. Conclusions: FLI, was the strongest risk factor for male testosterone insufficiencylow testosterone level independent of insulin resistance in a male populations of different ages, however the association can be modulated by SHBG levels in the young.
DOI: 10.6084/m9.figshare.25624767.v1
title: 将单个情绪和情绪组合放入睡眠分期模型后的增长率和回忆率

description: 将 16 种单一情绪和 7 种情绪组合放入睡眠分期模型进行训练后的分类回忆率和准确率
DOI: 10.6084/m9.figshare.3492773.v1
title: Retinal thickness raw data.xlsx

description: Raw thickness data for intra-retinal layer segmentation by both the Iowa Reference Algorithms, and on-board commercial software. Both fixed-axial eye length and axial eye length-dependent scaling are used.
DOI: 10.6084/m9.figshare.7217729.v3
title: Socio-economic, built environment, and mobility conditions associated with crime: A study of multiple cities

description: Dataset to replicate the study in the paper<br>
DOI: 10.6084/m9.figshare.1210773.v2
title: Metadata: Fish Mercury Datalayer for Canada (FIDMAC)

description: Metadata: Fish Mercury Datalayer for Canada (FIDMAC). Excerpt: SUMMARY Until now, characterization of mercury (Hg) risks posed to piscivorous fish and wildlife through the consumption of prey fish has generally remained limited to local or regional surveys. Furthermore, spatiotemporal and sample characteristic effects in fish-mercury data can lead to difficulty comparing results from different studies. The Fish Mercury Datalayer for Canada (FIMDAC, Depew et al. 2013a) provides model-derived estimates of Hg in a common indicator species (12-cm whole-yellow perch), and represents a useful preliminary national-level standardized index of Hg exposure to piscivorous fish and wildlife. DESCRIPTION The FIMDAC represents a model-derived output of Hg concentrations in a common indicator species (12-cm whole-yellow perch), established from the application of the United States Geological Survey's (USGS) National Descriptive Model of Mercury in Fish (NDMMF, Wente 2004) to the Canadian Fish Mercury Database (CFMD, Depew et al. 2013b). The geographical distribution of yellow perch is wide-ranging, and they represent an important prey species for piscivorous fish, birds, and mammals. Parameters estimated by way of NDMMF were unbiased, and strong spatial biases in prediction error were not evident. The FIMDAC records represent the estimated Hg burden (ug.g, wet weight) for a standard length (12 cm) whole-yellow perch at 1936 unique freshwater sites across Canada, collected between 1990 and 2010. Further details regarding the development of the FIMDAC can be found in Depew et al. (2013a).
DOI: 10.6084/m9.figshare.19801684.v1
title: Supplementary Material for: Development and Validation of a Mortality Prediction Model in Extremely Low Gestational Age Neonates

description: <b><i>Introduction:</i></b> Understanding factors that associate with neonatal death may lead to strategies or interventions that can aid clinicians and inform families. <b><i>Objective:</i></b> The aim of the study was to develop an early prediction model of neonatal death in extremely low gestational age (ELGA, &lt;28 weeks) neonates. <b><i>Methods:</i></b> A predictive cohort study of ELGA neonates was derived from the Swedish Neonatal Quality Register between the years 2011 to May 2021. The goal was to use readily available clinical variables, collected within the first hour of birth, to predict in-hospital death. Data were split into a train cohort (80%) to build the model and tested in 20% of randomly selected neonates. Model performance was assessed via area under the receiver operating characteristic curve (AUC) and compared to validated mortality prediction models and an external cohort of neonates. <b><i>Results:</i></b> Among 3,752 live-born extremely preterm infants (46% girls), in-hospital mortality was 18% (<i>n</i> = 685). The median gestational age and birth weight were 25.0 weeks (interquartile range [IQR] 24.0, 27.0) and 780 g (IQR 620, 940), respectively. The proposed model consisted of three variables: birth weight (grams), <i>A</i>pgar score at 5 min of age, and <i>g</i>estational age (weeks). The <i>BAG</i> model had an AUC of 76.9% with a 95% confidence interval (CI) (72.6%, 81.3%), while birth weight and gestational age had an AUC of 73.1% (95% CI: 68.4%,77.9%) and 71.3% (66.3%, 76.2%). In the validation cohort, the BAG model had an AUC of 68.9%. <b><i>Conclusion:</i></b> The BAG model is a new mortality prediction model in ELGA neonates that was developed using readily available information.
DOI: 10.6084/m9.figshare.28111892.v1
title: <b>Corticothalamic Neurons in Motor Cortex Have a Permissive Role in Motor Execution</b>

description: Large datasets for the following publication:<b>Corticothalamic Neurons in Motor Cortex Have a Permissive Role in Motor Execution</b>Fig2E and G also contains data for S4F.<br>Fig2H also contains data for S5C and D.Fig 2K also contains data for 2L and S7C.<br>Fig5A also contains data for S14C.<br>
DOI: 10.6084/m9.figshare.24953343.v1
title: Supplementary Material for: Mac-2 Binding Protein Glycosylation Isomer to Albumin Ratio Predicts Bacterial Infections in Cirrhotic Patients

description: Introduction
Mac-2-binding protein glycosylation isomer (M2BPGi) is a novel biomarker for liver fibrosis, but little is known about its role in cirrhosis-associated clinical outcomes. This study aimed to investigate the predictive role of M2BPGi in cirrhosis-associated complications.
Methods
One hundred and forty-nine cirrhotic patients were retrospectively enrolled. Patients were followed up for one year and cirrhosis-associated clinical events were recorded. Receiver operating characteristic curve (ROC) analysis was used to establish the values of the predictive models for cirrhotic outcomes. and Cox proportional hazards regression models were used to identify predictors of clinical outcomes, 
Results 
Sixty (40.3%) patients experienced cirrhosis-associated clinical events and had higher M2BPGi levels compared to those without events (8.7 vs. 5.1 cut-off index, p &lt; 0.001). The most common cirrhosis-associated complications were bacterial infections (24.2%). On ROC analysis, M2BPGi to albumin ratio (M2BPGi/albumin) had comparable discriminant abilities for all cirrhosis-associated events [area under the ROC curve (AUC) = 0.74] compared with M2BPGi, Child-Pugh, Model for End-Stage Liver Disease, Albumin-Bilirubin scores, and neutrophil to lymphocyte ratio and was superior to M2BPGi alone for all bacterial infectious events (AUC = 0.80). Cox regression analysis revealed that the M2BPGi/albumin, but not M2BPGi alone, independently predicted all cirrhosis-associated events [Hazar ratio (HR) = 1.34, p = 0.038] and all bacterial infectious events (HR = 1.51, p = 0.011) within one year. However, M2BPGi/albumin did not predict other cirrhotic complications and transplant free survival.
Discussion/Conclusion 
M2BPGi/albumin might serve as a potential prognostic indicator for patients with cirrhosis, particularly for predicting bacterial infections.
DOI: 10.6084/m9.figshare.13570748.v1
title: Datasets for: Variational autoencoders learn universal representations of metabolomics data

description: <br> This file contains the type 2 diabetes (QMDiab), schizophrenia, and acute myeloid leukemia (AML) datasets necessary to replicate our findings in the paper <em>"Variational autoencoders learn universal representations of metabolomics data".</em><br> <strong>Paper Link: </strong>Gomari*, Schweickart* et al., https://www.nature.com/articles/s42003-022-03579-3 <br> <strong>Code Repository: </strong>https://github.com/krumsieklab/mtVAE <br> NOTE: This archive is for reviewing purposes only at this point. Please do not share the figshare URL with others.
DOI: 10.6084/m9.figshare.1400491.v1
title: Bird dropping masquerading of the nest by the potter wasp <i>Minixi suffusum</i> (Fox, 1899) (Hymenoptera: Vespidae: Eumeninae)

description: The nest of <i>Minixi suffusum</i> offers a rare form of mimicry: bird dropping masquerading of the nest by the potter wasp was recorded in mid-western Brazil, in the municipality of Dourados MS. Nesting biology of <i>M. suffusum</i> and the material involved in the action of the camouflage were observed. Eleven nests were sampled, with a total of 38 cells. Use of uric acid for staining the cell was evident in all nests. The way that the wasp stains the cells was observed. Substrate nest site, seasonality, larvae biology, sex ratio, prey and parasitoids of <i>M</i>. <i>suffusum</i> were reported. Nest camouflage may be related to defense against natural enemies.
DOI: 10.60893/figshare.apl.28263782.v1
title: Supplementary Material

description: Additional Experiments and more detailed description of experiments