cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7133075.v2
title: MH_heatmap_mask_re_upload

description: We want to use figshare for PeerJ.Title:Accuracy of deep learning, a machine-learning technology, using ultra-wideifield fundus ophthalmoscopy for detecting idiopathic macular holespaper No 26404
DOI: 10.6084/m9.figshare.11839191.v5
title: Viz Dump Data Simulations (Sine-wave model) Simulations 501-681

description: Visualization Dump Data for the Sine-wave model, simulations 501-681
DOI: 10.6084/m9.figshare.23118758.v1
title: SNGNN

description: An improved graph neural network (GNN) and a self and neighborhood merged graph neural network (SNGNN) were proposed.
DOI: 10.6084/m9.figshare.28281815.v1
title: Paleomagnetic data of the HSJ, ME, and MEW.

description: The South Shetland Islands paleomagnetic data used in the paper "Late Oligocene-early Miocene Evolution of the Scotia Sea: New Constraint From Paleomagnetic and 40Ar/39Ar Geochronological Results of the King George Island, West Antarctica"
DOI: 10.6084/m9.figshare.26893354.v1
title: Wet Pitfall trap data - 2020

description: Sampling was conducted in Kematen in Tirol, Austria, where spring barley (Hordeum vulgare L.) was grown in six fields that have had organic management for the past ten years, three in 2020 and 2021, respectively. Each field was split in half, one side being fertilized with manure and the other remaining unfertilized, as a negative control. The manure treatment was independently applied by each field’s respective owner, at a standard rate of 1.5 metric tons (1 500kg) per hectare, using manure spreaders, after tilling and pressing the soil. Four 5x5m plots per treatment were delimited, to carry out all sampling. These plots had no barriers or fences surrounding them that would impede or limit movement between the inside of the plots and the rest of the field area. Additionally, the plots were at least 5m from the field edge, to avoid edge effects. They were at least 10m way from each other along the field’s width, and between 15 to 20m along the length of the field. To avoid any spillover of treatment effects, plots were set at least 25m away from the border between the two treatments within the same field.Sampling was conducted every two weeks, with one week of sampling and one of rest. The sampling period started on the 21st of April and ended on the 14th of July in 2020, while it started on the 3rd of May and ended on the 16th of July in 2021, to encompass almost the entire crop season. This resulted in seven sampling time points for the first year and six for the second.Wet pitfall traps, with a teaspoon of salt (5-6g) and a drop of detergent (approx. 1ml) per litre of water, remained active for four days to sample the soil surface dwelling community. A total of 168 wet pitfall trap samples were obtained in 2020 (4 sampling plots x 2 treatments x 3 fields x 7 sampling sessions) and 144 for 2021 (4 x 2 x 3 x 6 sampling sessions), from which Shannon-Weaver’s diversity was calculated for the predator and prey communities.
DOI: 10.6084/m9.figshare.19091423.v5
title: Absence of enterotypes in the human gut microbiomes reanalyzed with non-linear dimensionality reduction methods

description: Here we provide data and software for the work "Absence of enterotypes in the human gut microbiomes reanalyzed with non-linear dimensionality reduction methods". <br> Enterotypes of the human gut microbiome have been proposed to be a powerful prognostic tool to evaluate the correlation between lifestyle, nutrition, and disease. However, the number of enterotypes suggested in the literature ranged from two to four. The growth of available metagenome data and the use of exact, non-linear methods of data analysis challenges the very concept of clusters in the multidimensional space of bacterial microbiomes. <br> We demonstrate the presence of a lower-dimensional structure in the microbiome space, with high-dimensional data concentrated near a low-dimensional non-linear submanifold, but the absence of distinct and stable clusters that could represent enterotypes. This observation is robust with regard to diverse combinations of dimensionality reduction techniques and clustering algorithms.<br> We used <strong>16S rRNA </strong>genotype data from the National Institutes of Health <strong>Human Microbiome Project (HMP)</strong> and <strong>American Gut Project (AGP) </strong>presented in <strong>Order, Family, and Genus taxonomic levels (O, F, and G, respectively)</strong>. These largest open-access available datasets provide a sufficient number of data points for correct estimation of the clustering partition and constructing a manifold. We used 4587 HMP samples from stool and rectum body sites downloaded from https://portal.hmpdacc.org/ and 9511 samples from AGP downloaded from https://figshare.com/ as abundance matrices. For comparison with the original research, we also analyzed Sanger, Illumina, and Pyroseq datasets from (http://www.bork.embl.de/Docu/Arumugam_et_al_2011/). <br> All datasets are provided in the `data.zip` and normalized by dividing the Operational Taxonomic Units (OTUs) values by the total sum of abundances for a given data sample.
DOI: 10.6084/m9.figshare.22262080.v1
title: Análisis de chi-cuadrado de la tabla de contingencias

description: Análisis de chi-cuadrado de la tabla de contingencias
DOI: 10.6084/m9.figshare.13317128.v2
title: Tarakihi alignement

description: Alignment of hypervariable region one (HVR1) of the mitochondrial control region of 370 New Zealand tarakihi (<i>Nemadactylus macropterus</i>)
DOI: 10.21954/ou.rd.14812587.v1
title: PASHI-framework User Experience Evaluation Study Interview Transcripts

description: This study evaluated the user experience of adaptive user interfaces when used in mitigating interpersonal privacy violating scenarios. This study used video prototypes as the stimulant to elicit user responses where each video prototype demonstrated how different variations of adaptive user interfaces can be used to mitigate different variations of interpersonal privacy violating scenarios. Here interpersonal privacy violations refer to privacy violations that happens between smart home users due to sharing smart home devices among themselves. There are two main variations of interpersonal privacy violations explored in this study: • Interpersonal information privacy: Privacy related to information disclosures caused by shared smart home devices,• Interpersonal physical privacy: Privacy related to disturbances caused by shared smart home devices.<br><b>9</b> scenarios were developed covering different adaptive user interface variations, interpersonal privacy variations, smart home contexts, and different user preferences. The study recruited <b>23</b> participants and they were inquired about the user experience of the video prototypes based on adaptive user interfaces. This document includes the transcriptions of those interviews.<br>This study was approved by the Open University’s Human Research Ethics Committee (<b>HREC/3588/Wijesundara</b>).<br>
DOI: 10.6084/m9.figshare.25163684.v5
title: BTR dataset

description: This spreadsheet contains a portion of the PRECISE and MAS datasets utilized in our article "Exploring the Link between Brain Topological Resilience and Cognitive Performance in the Context of Aging and Vascular Risk Factors: A Cross-Ethnicity Population-Based Study." The data include the sample IDs used and the BTR values after our processing. Data of models are also included here. Due to data ethical restrictions, the full datasets can only be accessed via the following link:PRECISE dataset: http://paper.ncrcnd.ttctrc.com/default/project-detail?id=297&lang=enMAS dataset: https://cheba.unsw.edu.au/research-projects/sydney-memory-and-ageing-study
DOI: 10.6084/m9.figshare.13651058.v1
title: SPRING 2020 survey: peer review of grant proposals

description: This survey is part of a larger study of grant peer review, and studies the perception of the grant peer review process by the reviewers of two funding programmes at a national research funding agency.
DOI: 10.6084/m9.figshare.3839715.v1
title: PowerPoint Slides for: Early Changes in Monocyte Adhesion Molecule Expression and Tumor Necrosis Factor-α Levels in Chronic Kidney Disease - A 5-Year Prospective Study

description: <i>Background:</i> Despite the absence of clinical symptoms, patients with chronic kidney disease (CKD) exhibit elevated levels of pro-inflammatory markers. To investigate whether it is possible to detect inflammatory activity and altered monocyte function at an early stage of renal disease, we studied patients with CKD stages 2-3 over 5 years. <i>Methods:</i> The expression of adhesion molecules on monocytes at resting state and after stimulation with formyl-methionyl-leucyl-phenylalanine (fMLP), as well as oxidative metabolism capacity was measured with flow cytometry in 108 CKD patients and healthy controls. Soluble markers of inflammation, such as cytokines, were analyzed using the Milliplex technique. <i>Results:</i> Patients showed significantly lower CD11b expression after stimulation during the 3rd (p = 0.002) and the 5th year (p &lt; 0.001), together with a lower oxidative burst in response to fMLP over time (p = 0.02). The expression of CD62L on resting monocytes was lower during the 3rd (p = 0.001) and the 5th (p = 0.001) year in patients. Levels of tumor necrosis factor-α and RANTES were significantly increased (p = 0.001, p = 0.006) and interleukin-12 levels were also higher in CKD patients during the 5th year (p = 0.007). <i>Conclusion:</i>Monocytes in CKD stages 2-3 show emerging functional abrasions, with altered adhesion molecule expression and impaired fMLP response. These findings suggest that a transformation of monocyte function occurs at an early phase of renal impairment and may together with increased plasma levels of pro-inflammatory cytokines contribute to the higher vulnerability of CKD patients to comorbidities, such as infections and cardiovascular disease.
DOI: 10.6084/m9.figshare.8313530.v4
title: ChinaCropPhen1km: A high-resolution crop phenological dataset for three staple crops in China during 2000-2015 based on LAI products

description: <b>ChinaCropPhen1km: A high-resolution crop phenological dataset for three staple crops in China during 2000-2015 based on LAI products </b><b></b><b><br></b><b>The data file is in tif format, and the file name is named "crop type"+"doy"+"key phenological stages"+".tif". </b><b>Among them, the crop type takes values 1, 2, and 3, representing maize, wheat, and rice, respectively. </b><b>The key phenological stage has a value of 1, 2, and 3. The specific meaning is different for different crops. </b><b>For wheat, the key growth period is followed by green-up (emergence), heading and maturity date, while for maize, the key growth period is followed by three-leaf (V3) stage, heading and maturity date. </b><b>For rice, the key growth period is followed by transplanting stage, heading and maturity date. </b><b></b><b>The data with a spatial resolution of 1 km.</b>
DOI: 10.6084/m9.figshare.21936399.v2
title: Supplemental Data Sets — A genome-scale atlas reveals complex interplay of transcription and translation in an archaeon

description: Supplemental Data Sets S1-S8. This is part of the supplemental material for the study entitled: "A genome-scale atlas reveals complex interplay of transcription and translation in an archaeon" by Alan P. R. Lorenzetti, Ulrike Kusebauch, Lívia S. Zaramela, Wei-Ju Wu, João P. P. de Almeida, Serdar Turkarslan, Adrián L. G. de Lomana, José V. Gomes-Filho, Ricardo Z. N. Vêncio, Robert L. Moritz, Tie Koide, and Nitin S. Baliga. Data Set S1 | Atlas data. The non-redundant transcriptome locus tag dictionary, the normalized atlas data, and the non-normalized atlas data. Data Set S2 | Differentially expressed genes in the absence of RNase_2099C. Data Set S3 | Putative post-transcriptionally regulated genes (absolute abundance-based approach). Genes with patterns compatible with the post-transcriptional regulation hypothesis found by the abundance-based approach. Data Set S4 | Gene set enrichment analysis and comparison of features. Comparison of quantitative variables and enrichment tests for putative post-transcriptionally regulated gene sets found by the absolute abundance- and by the relative abundance-based approaches. Data Set S5 | Differential expression analysis of transcripts and proteins across the growth curve. Data Set S6 | Putative post-transcriptionally regulated genes (relative abundance-based approach). Genes with patterns compatible with the post-transcriptional regulation hypothesis found by the relative abundance -based approach. Data Set S7 | Atlas heatmap (expanded version). This file brings an expanded version of Figure 3. Data Set S8 | Insertion sequence mobilization events detected by the long-read DNA-Seq experiment.
DOI: 10.6084/m9.figshare.13614263.v1
title: Supplementary Material for: Observed and Modeled Positive Predictive Values Using Cell-free DNA Testing for Fetal Trisomy in a Clinical Laboratory Population

description: <b><i>Introduction:</i></b> The objective of this study was to explore different approaches to communicating the positive predictive value (PPV) of cell-free DNA screening for fetal trisomy. <b><i>Methods:</i></b> PPV was established for 4 maternal age-groups (&lt;30, 30–34, 35–39, and &gt;39 years) from clinical laboratory data and compared to the modeled PPV from an online calculator. In women under 35, PPV was compared between 2 subsets, high risk and low risk, classified based on the diagnosis codes that were provided to the laboratory. <b><i>Results:</i></b> In 503 high-probability trisomy 21 results, the observed PPVs in the 4 age-groups were 97.0% (&lt;30), 98.9% (30–34), 99.5% (35–39), and 96.3% (&gt;39), all higher than those from the calculator, which ranged from 53 to 95%. Likewise, PPVs were 77.4–97.0% observed versus 16–78% modeled in 131 trisomy 18 cases and 30.4–80.0% observed versus 6–61% modeled in 80 trisomy 13 cases. In women under 35, PPV for the trisomies combined was 90.4% in the higher-risk group compared to 79.7% in the lower-risk group. <b><i>Conclusion:</i></b> Modeling PPV based on maternal age will provide an underestimate in a clinical population. Although the PPV is higher for the samples with higher-risk diagnosis codes, the information that accompanies clinical samples is too general to model PPV for a specific patient.
DOI: 10.6084/m9.figshare.23585304.v1
title: Supplementary Material for: Expression profile of microenvironmental factors in the interface zone of colorectal cancer: histological-stromal biomarkers and cancer cell-CAF-related proteins combined for the assessment of tumor progression

description: Introduction The characterization of tumor microenvironment (TME) related-factors and their impact on tumor progression have attracted much interest. We investigated cancer cells and CAFs to evaluate biomarkers that are associated with neoplastic progression, observing them in different interface zones of colorectal cancer. Methods On 357 CRC tissue microarrays, using immunohistochemistry, we examined the associations of podoplanin and α-SMA expressed in cancer cells and CAFs and evaluated them in different areas: tumor core, invasive front, tumor budding, tumor-stroma ratio (TSR) scoring, and desmoplastic stroma. Results CAFs expressing α-SMA were found in more than 90% of the cases. Podoplanin+ was detected in cancer cells and CAFs, with positivities of 38.6% and 70%, respectively. Higher α-SMA+ CAFs and podoplanin+ cancer cells were observed predominantly at the TSR score area: 94.3% and 64.3% of cases, respectively. The status of podoplanin in CAFs+ was higher in the desmoplastic area (71.6%). Stroma-high tumors showed increased expression of α-SMA and podoplanin in comparison with stroma-low tumors. The status of podoplanin in cancer cells was observed in association with lymphatic invasion and distant metastasis. Conclusion The substance of the CRC was composed predominantly of the surrounding stroma-α-SMA+ CAF. Podoplanin expressed in the prognosticator zones was associated with unfavorable pathological features. The combination of histologic and protein-related biomarkers can result in a tool for the stratification of patients with CRC.
DOI: 10.6084/m9.figshare.26246150.v1
title: Supplementary Material for: THE ROLE OF IMMUNOMODULATORY THERAPY WITH OXIRIS IN COVID 19 WITH RENAL FAILURE AND IMMUNE DYSFUNCTION.

description: INTRODUCTION: The main objective of this study is to evaluate the impact of hemoadsorption on the elimination of inflammatory mediators.
METHODS: A prospective, bicenter, observational cohort study was conducted between March 2020 and February 2022 to explore the immunomodulatory response, demographic and clinical characteristics of individuals with COVID-19 admitted to the ICU with severe acute respiratory failure and in need of CRRT with Oxiris® with or without AKI.
RESULTS: 64 patients were analyzed. Statistically significant differences were observed between exposed and unexposed groups, regarding levels of D-dimer -15614 (24848.9) vs -4136.5(9913.47) (p .031, d:1.59, 95% CI -21830, -1126). An increase in PCT was observed 0.47(2.08) vs -0.75(2.3) (p .044 95% CI 0.03,2.44). No differences were found in a decrease in CRP -4.21(7.29) vs -1.6(9.02) (p .22) nor in the rest of inflammatory parameters fibrinogen, IL-6, ferritin, lymphocytes, and neutrophils. Subgroup analysis in patients exposed to therapy also showed a significant decrease in D-Dimer of 55% from baseline; 6000 (1984.5-277750) pre-therapy vs 2700 (2119.5-6145) (95% CI -23000, -2489) post-therapy with a strong effect size (p .001, d:0.65). 
CONCLUSION: The hemoadsorptive therapy in COVID 19 was associated with a significant decrease in D-dimer parameters without showing decreases in the rest of the clinical, inflammatory parameters and severity scales analyzed.
DOI: 10.6084/m9.figshare.26488216.v3
title: Pre-VFall: Vision Sensor Simulated Early Signs of Fall Dataset

description: The Pre-VFall dataset is a multimodal dataset. It includes images, keygradient vector magnitude features, and keygradient vector direction features available to researchers for advancing the robustness of fall detection systems. The dataset is intended for use by the machine learning community to identify pattern cues that signal the onset of falls. The dataset provides new insights into how frailty states in older adults may serve as precursors to fall incidents. This will help improve the robustness of fall detection systems, ensuring they can effectively account for irregularities in movement and behavior that indicate early signs of fall. The dataset consists of around 22K images selected from recorded videos of nine healthy young adult participants. Each participant's videos and corresponding images are organized in folders named after each video session as follows: confusion_delirium, confusion_nph, dizzy_fall_forward, dizzy_fall_side, weakness_fall_forward, and weakness_fall_side. It should be noted that weakness and dizziness sessions were succeeded by falls and so included fall in their labels. The terms “forward” and “side” in some labels indicate the direction of fall. Each folder contains videos recorded with RGB cameras positioned at 90° and 45° with forward-view and side-view cameras included to identify the angle of the camera. The frames of the videos were manually selected and sorted into their respective categories. For example, the pre-fall activities such as weakness, dizziness, delirium-confusion, and NPH-confusion were categorized as “Abnormal,” while states of falling and actual falls were categorized as “Fall.” Therefore, this dataset encompasses three activity classes: normal, abnormal, and fall.
DOI: 10.6084/m9.figshare.11394696.v1
title: Supplementary Material for: Association between Dialysis Modality and Cardiovascular Diseases: A Comparison between Peritoneal Dialysis and Hemodialysis

description: <b><i>Introduction:</i></b> In patients with end-stage kidney disease (ESKD), cardiovascular diseases (CVDs) are the most common causes of hospitalization and death. <b><i>Objective:</i></b> We aimed to determine the association between dialysis modality and CVDs. <b><i>Methods:</i></b> This retrospective observational cohort study compared the emergency hospitalization and mortality of patients with CVDs who underwent peritoneal dialysis (PD) versus hemodialysis (HD). After propensity score matching, the risk factors were evaluated using Cox proportional hazards regression models. <b><i>Results:</i></b> A total of 260 patients were matched: 130 of 135 PD (75 men; age, 65.4 years; dialysis vintage, 3.3 years) and 130 of 706 HD (70 men [<i>p</i> = 0.5]; 66.6 years [<i>p</i> = 0.4]; dialysis vintage, 3.1 years [<i>p</i> = 0.5]) patients. Emergency hospitalization rates (hospitalizations/person-years) for overall CVDs (0.138 vs. 0.066, <i>p</i> = 0.002) and pulmonary edema (0.048 vs. 0.019, <i>p</i> = 0.03) were significantly higher in patients who underwent PD than those who underwent HD. The log-rank test revealed that all-cause and CVD mortalities were significantly higher in PD (both <i>p</i> &lt; 0.001). Mortality rates (deaths/person-years) for overall CVDs (0.058 vs. 0.015, <i>p</i> &lt; 0.002), cerebrovascular disease (0.019 vs. 0.004, <i>p</i> = 0.03), and ischemic heart disease (0.010 vs. 0, <i>p</i> = 0.02) were significantly higher in PD. The Cox proportional hazards regression model showed that PD and age were significant predictors of emergency hospitalization (hazard ratio [HR] 2.70; 95% CI 1.53–4.77; <i>p</i> = 0.001) and mortality (HR 4.41; 95% CI 1.66–11.72; <i>p</i> = 0.003) for CVDs. <b><i>Conclusions:</i></b> PD is a risk factor for emergency hospitalization and mortality associated with CVDs in dialysis patients with ESKD. Strict control of body fluid balance may prevent cardiovascular events in patients undergoing PD.
DOI: 10.6084/m9.figshare.28472858.v1
title: Epigenetic age prediction using N6-methyladenine

description: Methylation matrix used for epigenetic clocks training and validation in 'Epigenetic age prediction based on N6-methyladenine'.
DOI: 10.6084/m9.figshare.28868906.v1
title: Systems_DNN_TFDN_OPF

description: We provide the descriptions and parameters of test systems that have been used in the submission titled "Advancing Performance Guarantees for DNN-based OPF in Topology-flexible Distribution Networks".
DOI: 10.6084/m9.figshare.22656430.v1
title: Supplementary Material for: Meta-Analysis of Electroencephalographic Correlates and Cognitive Performance for Acute Exercise-Induced Modulation

description: <b><i>Introduction:</i></b> Although abundant research delving into the acute exercise-induced modulation of cognitive performance and the P300-ERP component has been conducted, there is a lack of consensus regarding whether or not this type of intervention has a beneficial effect on cognition and how it relates to the P300-ERP. <b><i>Methods:</i></b> To examine the possible sources of this discrepancy, we conducted a meta-analysis of ERP results together with cognitive performance that were systemically stratified by relevant demographic and methodological moderators. <b><i>Results:</i></b> Our results indicate that while acute exercise exerted an overall stable effect on cognitive improvement, associated with enlarged P300 amplitudes, the effect size varied across factors of age, biological sex, exercise intensity, exercise type, control type, and experimental design. Future research taking into consideration modulating factors as to avoid misestimating the beneficial effects of acute exercise are encouraged. <b><i>Conclusion:</i></b> All in all, and to our knowledge, this is the first meta-analysis quantitatively summarizing the relevant literature on the associations between P300-ERP correlates, acute exercise, and its positive influence on attention and cognitive performance in healthy individuals.
DOI: 10.6084/m9.figshare.13264793.v2
title: BioSR

description: BioSR datasets for super-resolution microscopy, currently including linear SIM data and nonlinear SIM data.
DOI: 10.6084/m9.figshare.25621548.v1
title: 免疫检查点抑制剂在发生靶向治疗耐药后发生罕见突变的晚期NSCLC患者中的疗效和安全性

description: 我们回顾性地收集了携带罕见致癌驱动突变的NSCLC患者的统计数据。