cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4558015.v1
title: Supplementary Material for: Systemic Infection Generates a Local-Like Immune Response of the Bacteriome Organ in Insect Symbiosis

description: Endosymbiosis is common in insects thriving in nutritionally unbalanced habitats. The cereal weevil, <i>Sitophilus oryzae</i>, houses <i>Sodalis pierantonius</i>, a Gram-negative intracellular symbiotic bacterium (endosymbiont), within a dedicated organ called a bacteriome. Recent data have shown that the bacteriome expresses certain immune genes that result in local symbiont tolerance and control. Here, we address the question of whether and how the bacteriome responds to insect infections involving exogenous bacteria. We have established an infection model by challenging weevil larvae with the Gram-negative bacterium <i>Dickeya dadantii</i>. We showed that <i>D. dadantii</i> infects host tissues and triggers a systemic immune response. Gene transcript analysis indicated that the bacteriome is also immune responsive, but it expresses immune effector genes to a lesser extent than the systemic and intestinal responses. Most genes putatively involved in immune pathways remain weakly expressed in the bacteriome following <i>D. dadantii</i> infection. Moreover, quantitative PCR experiments showed that the endosymbiont load is not affected by insect infection or the resulting bacteriome immune activation. Thus, the contained immune effector gene expression in the bacteriome may prevent potentially harmful effects of the immune response on endosymbionts, whilst efficiently protecting them from bacterial intruders.
DOI: 10.26188/25868881.v1
title: Ryan et al., 2024: Data for One Tree Island Aerosol Measurement Paper

description: This dataset was used in the preparation of Ryan et al, 2024, a paper summarising aerosol extinction and optical depth made at One Tree Island in the Great Barrier Reef, during February and March 2023. The fieldwork was carried out under the auspices of the Reef Restoration and Adaptation Program's Cooling and Shading Subprogram.The data in this archive comes from:a mini-MPL LiDAR (MPL). The data in 'oti_mpl_nrb_NotCloudFilt_19Feb-31Mar_combinedpolar' is a netCDF file with normalised relative backscatter (NRB) profiles collected using the MPL. The MPL observes aerosol backscatter using a 532 nm laser. Aerosol extinction profiles were calculated from the NRB profiles using the methodology outlined in Ryan et al, 2024, but also following the methodologies outlined in Welton et al, 2001 (https://doi.org/10.1117/12.417040), Welton et al., 2000 (https://doi.org/10.1034/j.1600-0889.2000.00025.x) and Campbell et al., 2002 (https://doi.org/10.1175/1520-0426(2002)019&lt;0431:FTESCA&gt;2.0.CO;2).a Multi-axis Differential Optical Absorption Spectrometer (MAX-DOAS). The data in 'OTI_QD_AllBinSpec' are the differential slant column densities (dSCDs) obtained using the 'QDOAS' fitting algorithm (https://uv-vis.aeronomie.be/software/QDOAS/) and the settings outlined in Ryan et al, 2024. The profile retrieval algorithm 'RAPSODI' (see details in Tirpitz et al., 2022, https://doi.org/10.5194/amt-15-2077-2022) was used to convert the dSCDs to vertical aerosol extinction profiles. The dSCDs in this file are for a range of trace gases absorbing in the wavelength range 338-370nm. The relevant species for aerosol retrieval is O4, following the methodology in Wagner et al., 2004 (https://doi.org/10.1029/2004JD004904).a weather station; the file 'oti_weatherstation_data' includes text files with key meteorological variables such as temperature, relative humidity, wind speed and direction, all measured at 10 m altitude above One Tree Island.
DOI: 10.6084/m9.figshare.28218092.v1
title: Supplementary Material for: Hearing Loss as a Risk Factor for Dementia: A Nationwide 15-Year Follow-Up Cohort Study in Taiwan

description: Introduction: Although hearing loss is associated with dementia, the exact causal relationship between hearing loss and dementia remains unclear. Early detection and prevention of hearing loss are essential. In this study, data from the National Health Insurance Research Database (NHIRD) of Taiwan were used to monitor patients with hearing loss for 15 years to determine whether hearing loss leads to dementia.
Methods: This retrospective matched-cohort study involved 208,570 individuals, divided into 41,714 patients with hearing loss and 166,856 controls matched by sex, age, and chronic diseases. Cox regression analysis was conducted on data obtained from the NHIRD for the period 2000–2015 to determine the hazard ratio (HR) associated with dementia.
Results: The percentage of patients with hearing loss who developed dementia was higher than that of the control group (18.67% vs. 14.10%). The onset age of dementia was younger in the hearing loss group (69.95 vs. 70.31 years, p = 0.001). Middle-aged individuals (45–65 years) with hearing loss were more likely to develop dementia compared with those without hearing loss (48.53% vs. 47.94%, p = 0.03). Compared with the controls, the patients with hearing loss were more likely to develop hyperlipidemia and stroke. In the patients with hearing loss, the adjusted HRs for Alzheimer’s disease (AD), vascular dementia, and other types of dementia were significant. The patients were followed up for an average of 7.82 years. Compared with the controls, the patients with hearing loss exhibited a shorter mean time to dementia onset (5.21 vs. 5.49 years, p &lt; 0.001).
Conclusion: Hearing loss may increase the risks of AD, dementia, hyperlipidemia, and stroke. Therefore, health-care providers should closely monitor cardiovascular complications in patients with hearing loss.
DOI: 10.6084/m9.figshare.7938428.v1
title: gVCF_NA20515

description: 1000 Genomes gVCF mapped to hs37d5 for NA20515. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.12980840.v1
title: The effect of chronotype and time of assessment on cognitive performance

description: Standard cognitive measures are often applied at various times of the day to assess cognitive deficits in patients with neuropsychiatric and neurodegenerative disorders, irrespective of their chronotype. In this study, we aimed to determine whether the subjectively nonpreferred time of an assessment might be a crucial factor in persons with extreme chronotypes. We compared morning (08:00) and evening (20:00) cognitive performance in extreme morning, extreme evening, and intermediate chronotypes determined by the Morningness-Eveningness Questionnaire, supported by actigraphy and peripheral temperature measurement. The assessment sessions were performed in pseudorandom order over two consecutive weekend days. We administered the commonly used test battery for neurocognitive assessment comprised of tasks aimed mainly at attention, processing speed, working memory, and declarative memory. The time of assessment influenced the declarative memory measures, whereas the chronotype-specific differences occurred only in the Stroop colour-naming subtest aimed at processing speed. The observed effects should be considered in routine clinical practice because they might cause misrepresentation of the results obtained during improperly timed cognitive assessment. Our results also point towards similarity of doves and owls in contrast to larks in cognitive performance, suggesting that early morning assessments should also be considered in cases of intermediate chronotypes.
DOI: 10.6084/m9.figshare.21678884.v1
title: Supplementary Material for: Clinical Outcomes of Prolonged Antiplatelet Therapy after Percutaneous Coronary Intervention in Chronic Kidney Disease Patients: A Systematic Review and Meta-Analysis

description: <b><i>Background:</i></b> The optimal duration of dual antiplatelet therapy (DAPT) after percutaneous coronary intervention (PCI) is not established in chronic kidney disease (CKD) patients. <b><i>Objective:</i></b> In this meta-analysis, we evaluated the efficacy and safety of long duration DAPT compared with short duration DAPT in CKD patients after PCI. <b><i>Methods:</i></b> We searched PubMed<b>,</b> Cochrane, and Embase to identify studies assessing the effect of DAPT duration in CKD patients with PCI. Endpoints included all-cause mortality, major adverse cardiovascular events (MACE), death or myocardial infarction (MI), revascularization, and bleeding. Event rates were compared with a random-effects model expressed by odds ratio (OR) and 95% confidence interval (CI). <b><i>Results:</i></b> Six studies were included. CKD patients with extended DAPT duration were at a lower risk of mortality (OR 1.40, 95% CI: 1.11–1.77), MACE (OR 1.33, 95% CI: 1.17–1.51), mortality or MI (OR 1.24, 95% CI: 1.10–1.40), and stroke (OR 1.28, 95% CI: 1.05–1.56). However, there was no significant difference in revascularization and bleeding events between the two groups. Mortality was higher in patients with dialysis or drug-eluting stent comparing short- to long-term DAPT. <b><i>Conclusions:</i></b> Prolonged DAPT might decrease the risk of mortality, MACE, and stroke in patients with CKD without any significant difference in bleeding or revascularization. Additional studies are required to determine whether long-term DAPT could be considered for most CKD patients after PCI.
DOI: 10.6084/m9.figshare.26503255.v1
title: OSA

description: Class I polysomnography data set of subjects with obstructive sleep apnea syndrome
DOI: 10.6084/m9.figshare.5127598.v1
title: Supplementary Material for: Detection of Small Changes in Psoriasis Intensity with PrecisePASI

description: <b><i>Background:</i></b> The Psoriasis Area and Severity Index (PASI) is the score of choice to grade psoriasis severity and detect clinical changes. Due to low resolution based on the calculation of the score by fixed area classes, PASI scores &lt;10 have little value. <b><i>Methods:</i></b> At 756 patient examinations, psoriasis activity was measured with both PASI and PrecisePASI. <b><i>Results:</i></b> PrecisePASI has a linear increase while PASI has a staircase pattern. Both scores meet at the endpoint-relevant values of body surface area (BSA) 10, 30, 50, 70 and 90%. PASI and PrecisePASI correlate significantly over the whole range of BSA. In the region of BSA &lt;5%, PrecisePASI shows a significantly higher resolution (p &lt; 0.0001). <b><i>Conclusion:</i></b> The calculation of PrecisePASI corrects the undesired inaccuracies of PASI in the lower BSA ranges and is a tool to use as an endpoint in trials aiming to detect differences in the lower ranges of BSA.
DOI: 10.6084/m9.figshare.5995408.v1
title: MC-dataset-binary

description: Binary and labeled dataset containing 11480 samples of cleanwares and malwares with 5740 samples of each class. Files with a maximum size of approximately 3.2 MB. All files were named with their md5 hashes, hiding their original names. The cleanwares were extracted from several different versions of Windows systems and the malwares obtained from the VirusShare repository.
DOI: 10.6084/m9.figshare.7102766.v1
title: Methylene blue-related corneal edema and iris discoloration

description: ABSTRACT We report the case of a 70-year-old female patient who developed corneal edema and iris discoloration following the inadvertent use of 1% methylene blue instead of 0.025% trypan blue to stain the anterior capsule during cataract phacoemulsification surgery. Copious irrigation was performed upon realization of incorrect dye use. Corneal edema and iris discoloration developed during the early postoperative period and persisted at 24-months follow-up. However, keratoplasty was not required. The intracameral use of 1% methylene blue has a cytotoxic effect on the corneal endothelium and iris epithelium. Copious irrigation for at least 30 min using an anterior chamber maintainer may improve outcomes.
DOI: 10.6084/m9.figshare.22650610.v1
title: GTEx v8 metadata

description: The GTEx dataset is a public resource that has generated a broad collection of gene expression data collected from a diverse set of human tissues. Here we share the processed GTEx data used in <em>Hypergraph factorisation for multi-tissue gene expression imputation</em> (Vinas Torne et al., 2023). We processed the data following the GTEx eQTL discovery pipeline. <br> If you use this data for your research, please cite the GTEx consortium paper: <em>GTEx Consortium. The GTEx Consortium atlas of genetic regulatory effects across human tissues. DOI: </em>10.1126/science.aaz1776
DOI: 10.6084/m9.figshare.16644973.v1
title: Supplementary Material for: Evolutionary Learning-Derived Clinical-Radiomic Models for Predicting Early Recurrence of Hepatocellular Carcinoma after Resection

description: <b><i>Background and Aims:</i></b> Current prediction models for early recurrence of hepatocellular carcinoma (HCC) after surgical resection remain unsatisfactory. The aim of this study was to develop evolutionary learning-derived prediction models with interpretability using both clinical and radiomic features to predict early recurrence of HCC after surgical resection. <b><i>Methods:</i></b> Consecutive 517 HCC patients receiving surgical resection with available contrast-enhanced computed tomography (CECT) images before resection were retrospectively enrolled. Patients were randomly assigned to a training set (<i>n</i> = 362) and a test set (<i>n</i> = 155) in a ratio of 7:3. Tumor segmentation of all CECT images including noncontrast phase, arterial phase, and portal venous phase was manually performed for radiomic feature extraction. A novel evolutionary learning-derived method called genetic algorithm for predicting recurrence after surgery of liver cancer (GARSL) was proposed to design prediction models for early recurrence of HCC within 2 years after surgery. <b><i>Results:</i></b> A total of 143 features, including 26 preoperative clinical features, 5 postoperative pathological features, and 112 radiomic features were used to develop GARSL preoperative and postoperative models. The area under the receiver operating characteristic curves (AUCs) for early recurrence of HCC within 2 years were 0.781 and 0.767, respectively, in the training set, and 0.739 and 0.741, respectively, in the test set. The accuracy of GARSL models derived from the evolutionary learning method was significantly better than models derived from other well-known machine learning methods or the early recurrence after surgery for liver tumor (ERASL) preoperative (AUC = 0.687, <i>p</i> &lt; 0.001 vs. GARSL preoperative) and ERASL postoperative (AUC = 0.688, <i>p</i> &lt; 0.001 vs. GARSL postoperative) models using clinical features only. <b><i>Conclusion:</i></b> The GARSL models using both clinical and radiomic features significantly improved the accuracy to predict early recurrence of HCC after surgical resection, which was significantly better than other well-known machine learning-derived models and currently available clinical models.
DOI: 10.6084/m9.figshare.19403648.v1
title: Supplementary Material for: A Community-Based Education Program for Overactive Bladder in a Predominantly Minority Older Female Population: A Pilot Study

description: <b><i>Introduction:</i></b> Knowledge gaps regarding available treatment and social stigmatization are barriers to care in patients with overactive bladder (OAB). We assessed the feasibility of an OAB education program targeting older community-dwelling females. <b><i>Methods:</i></b> Community-dwelling women over 55 years old were recruited. Eligible participants underwent an education program covering continence-promotion strategies. The Overactive Bladder Questionnaire-Short Form and Short Form-12 were completed at baseline, 1 week, 3 months, and 6 months post-intervention to measure symptom bother and condition-specific and general quality of life (QoL). Data were analyzed using a linear mixed-effects model for repeated measures. <b><i>Results:</i></b> Thirty-seven female patients with OAB symptoms at baseline were assessed with the majority from Latino/Hispanic or Black/African American ethnic/racial backgrounds. For our youngest subgroup (≤68 years old), significant improvements were observed at 3 and 6 months compared to 1 week post-intervention for symptom bother (3 months, −22.75, <i>p</i> = 0.006; 6 months, −25.76; <i>p</i> = 0.001) and condition-specific and health-related QoL subscale scores for concern (3 months, +23.76, <i>p</i> = 0.006; 6 months, +22.15, <i>p</i> = 0.011) and social interaction (3 months, +21.11, <i>p</i> = 0.017; 6 months, +20.51; <i>p</i> = 0.021). For all age subgroups, improvements in general QoL measures for mental health were seen at 3 and 6 months compared to baseline (3 months, +7.57, <i>p</i> = 0.02; 6 months, +6.70; <i>p</i> = 0.048). <b><i>Conclusions:</i></b> Statistically significant improvements in symptom bother, condition-specific, and general QoL measures were observed following an OAB education program pilot study in a predominantly minority female population. Further studies are needed to support efficacy and optimize program design.
DOI: 10.4121/uuid:d8920243-eda0-4ef4-a985-9198924afce8
title: Numerical Simulation of Hydrodynamic Forces on Bridge Decks

description: This study presents numerical simulations performed to quantify the hydrodynamic forces on a bridge deck with a rectangular cross section. Numerical inputs for one of the simulations is provided here which can be used for further research.
DOI: 10.6084/m9.figshare.11704491.v1
title: Raw data and metadata

description: Data from elevated CO2 experiments on the effect of elevated CO2 on soil carbon storage and plant biomass<br>
DOI: 10.6084/m9.figshare.15104916.v1
title: GPP,GPPsun,GPPshade 1992-2019

description: Here we produced three global-scale products GPP, GPP<sub>shade</sub>, and GPP<sub>sun</sub> at a spatial resolution of 0.05°for three temporal scales (8-day, monthly and annual) from 1992 to 2019 using an improved two-leaf light use efficiency model with an added CO<sub>2</sub> concentration regular scalar and the modified temperature scalar.These products are driven by the GLOBMAP leaf area index, Climatic Research Unit and Japanese reanalysis (CRUJRA) meteorological data, and Climate Change Initiative Land Cover (CCI-LC) data.
DOI: 10.6084/m9.figshare.28836638.v1
title: Raw image files of tissue stretching experiments, endoderm and mesoderm

description: A simple approach is devised to quantitatively apply tension to epithelia in vivo, and used to study endoderm mechanics in the developing chick embryo
DOI: 10.6084/m9.figshare.7844822.v1
title: SupplementaryDataset_MetastaticNetwork_Castilloetal

description: Data set used in the analyses of the metastatic network under a metapopulation view.<br><b>data01_dataIncidence.csv</b>Data with the metastatic incidence, i.e. number of cases for each pair source-acceptor over the total number of cases.<br><b>data02_summarydata.csv</b>This dataset contains data used for correlations. Origin of the estimated values are included in supplementary methods, values corresponding to network connectivity and metastatic incidence are from this study.<b><br></b><b>data03_con_art.csv</b><br>This dataset corresponds to a incidence matrix for organs sharing supply vessels.<br><b>data04_con_vei.csv</b><br>This dataset corresponds to a incidence matrix for organs sharing drainage vessels.<br>
DOI: 10.6084/m9.figshare.7694615.v1
title: Supplementary Material for: Molecular Network Analysis of the Urinary Proteome of Alzheimer’s Disease Patients

description: <b><i>Background/Aims:</i></b> The identification of predictive biomarkers for Alzheimer’s disease (AD) from urine would aid in screening for the disease, but information about biological and pathophysiological changes in the urine of AD patients is limited. This study aimed to explore the comprehensive profile and molecular network relations of urinary proteins in AD patients. <b><i>Methods:</i></b> Urine samples collected from 18 AD patients and 18 age- and sex-matched cognitively normal controls were analyzed by mass spectrometry and semiquantified with the normalized spectral index method. Bioinformatics analyses were performed on proteins which significantly increased by more than 2-fold or decreased by less than 0.5-fold compared to the control (<i>p</i> &lt; 0.05) using DAVID bioinformatics resources and KeyMolnet software. <b><i>Results:</i></b> The levels of 109 proteins significantly differed between AD patients and controls. Among these, annotation clusters related to lysosomes, complement activation, and gluconeogenesis were significantly enriched. The molecular relation networks derived from these proteins were mainly associated with pathways of lipoprotein metabolism, heat shock protein 90 signaling, matrix metalloproteinase signaling, and redox regulation by thioredoxin. <b><i>Conclusion:</i></b> Our findings suggest that changes in the urinary proteome of AD patients reflect systemic changes related to AD pathophysiology.
DOI: 10.6084/m9.figshare.3510233.v1
title: Postoperative pain treatment after vascular surgical procedures

description: This study was conducted at the Department of Surgery of the University Hospital Split, Croatia. The following data on 501 patients who underwent vascular surgical procedures during year 2013 were collected from patients’ medical records: age, gender, type and dosage of premedication, preoperative patient's physical status, type of procedure, duration of procedure – surgical and anesthesia time, type and dosage of anesthesia, the type and dosage of postoperative analgesia for each postoperative day, the need for intensive care. Departmental procedures were examined to assess adherence to guidelines for perioperative pain management.
DOI: 10.6084/m9.figshare.19583722.v1
title: nBOSS_3D_P_S

description: P-wave and S-wave tomographic models of the upper mantle beneath northern Borneo.
DOI: 10.6084/m9.figshare.19914973.v4
title: Beluga Social Games Qualitative Results

description: Supplementary qualitative results accompanying the paper "Social Games that Belugas (<em>Delphinapterus leucas</em>) Play" submmited to <em>The International Journal of Play</em>.
DOI: 10.6084/m9.figshare.9758894.v2
title: Whiskerman tutorial

description: 3D whisker tracking example. Folder contains:<br>1) Video of the Horizontal View (Horizontal_view.dat)2) Video of the Vertical View(vertical_vew\Vertical_view.dat)3) Tracked video (Horizontal_view.tr4)4) Calibration information to start tracking from scratch (Calibration_information.tr4)<br>Code availability:Whiskerman has been implemented in Matlab and is available at https://github.com/PetersenLab/WhiskerMan.<br>
DOI: 10.6084/m9.figshare.14280466.v1
title: Prognostic values of physical and hematological parameters of dogs naturally infected with parvovirus PVC-2: retrospective study of 103 cases

description: ABSTRACT Canine parvovirosis is a high mortality disease with acute clinical picture. However, there are few available resources to help stablish prognosis accurately. This study aimed to determine the prognostic threshold values for vital and hematological parameters of dogs naturally infected by the Carnivore protoparvovirus 1 (CPV). A retrospective study of 103 canine parvovirosis cases was carried out. Twenty seven percent of these (28/103) died, 96% (27/28) of which within the first four days of hospitalization. Deceased animals had significantly higher median values for heart (HR) and respiratory (f) rates, as well as significantly lower systolic blood pressure (SBP) than survivors. Severely leukopenic animals (&lt;1,000 cells/μL), had a significantly higher mortality rate (68%, n=13) compared to that of other patients (P&lt;0.0007). Animals with at least two of the following findings: severe hypotension (SBP&lt; 90mmHg), tachycardia (HR &gt; 150 bpm) and leukopenia, represented 34% (34/101) of the cases and had a survival rate of 29% (10/34), while animals with at most one of these parameters represented 66% (67/101) and had a survival rate of 94% (63/67). The presence of two or three abnormal parameters was significantly related to the higher death risk among dogs with parvovirosis (P&lt;0.0001).