cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24125313
title: Supplementary Material for: Radiomics Correlation to CD68+ Tumor-Associated Macrophages in Clear Cell Renal Cell Carcinoma

description: Introduction: Renal cell carcinoma (RCC) is the ninth most common cancers worldwide, with clear cell RCC (ccRCC) being the most frequent histological subtype. The tumor immune microenvironment (TIME) of ccRCC is an important factor to guide treatment, but current assessments are tissue-based, which can be time-consuming and resource-intensive. In this study, we used radiomics extracted from clinically performed computed tomography (CT) as a non-invasive surrogate for CD68 tumor-associated macrophages (TAMs), a significant component of ccRCC TIME. Methods: TAM population was measured by CD68+/PanCK+ ratio and tumor-TAM clustering was measured by normalized K function was calculated from multiplex immunofluorescence (mIF). A total of 1,076 regions on mIF slides from 78 patients were included. Radiomic features were extracted from multiphase CT of the ccRCC tumor. Statistical machine learning models, including Random Forest, AdaBoost, and ElasticNet, were used to predicted TAM population and tumor-TAM clustering. Results: The best models achieved an AUROC of 0.81 (95% CI: [0.69, 0.92]) for TAM population and 0.77 (95% CI: [0.66, 0.88]) for tumor-TAM clustering, respectively. Conclusion: Our study demonstrates the potential of using CT radiomics derived imaging markers as a surrogate for assessment of TAM in ccRCC for real time treatment response monitoring and patient selection for targeted therapies and immunotherapies.
DOI: 10.6084/m9.figshare.24145422
title: Supplementary Material for: Use of Sotrovimab for COVID-19 in a patient with IGCCC Poor Prognosis testicular germ cell tumor

description: A 35-year-old man was diagnosed with stage IIIC non-seminoma with paralysis of the lower half of his body by 8th thoracic spine metastasis. The patient received bleomycin, etoposide, and cisplatin (BEP) therapy. On day 4 of the second course of BEP, the patient developed a fever and was diagnosed with coronavirus disease (COVID-19). COVID-19 was suspected to worsen because of cancer and chemotherapy-induced immunosuppression. However, the benefits of continuing BEP therapy outweighed these risks. After obtaining fully informed consent, BEP therapy was continued from day 5, while sotrovimab (anti-COVID-19 drug) was administered. The second course of BEP was completed without worsening severe COVID-19 or bleomycin-induced lung injury. The patient completed four courses of BEP, with normalization of tumor markers, partial response on imaging, and improvement in lower body paralysis. In this case, we successfully treated a patient with testicular germ cell tumor with chemotherapy while COVID-19 without treatment delay. During the COVID-19 pandemic, concomitant chemotherapy and COVID-19 treatment is warranted because delaying treatment will decrease the efficacy of highly curative diseases such as germ cell tumors.
DOI: 10.17189/1520327
title: MER 1 MARS NAVCAM 3 RADIOMETRIC RDR SCI V1.0
DOI: 10.17632/ntvxg7w28v.1
title: Simultaneous measurements of benthic oxygen fluxes by aquatic relaxed eddy accumulation and eddy covariance in different aquatic environments

description: This data set is relative to the article “Aquatic Relaxed Eddy Accumulation: a New Technique to Resolve Benthic Solute Fluxes”. 
The attached table (‘REA_EC_flux_results.xlsx’) contains the fluxes measured by relaxed eddy accumulation and eddy covariance as well as the characteristics of the measurements and calculated parameters during the campaigns. The flux values for accumulation periods 9 and 12 are the averages of two subperiods separated by boat passages which were excluded from the dataset.
The data used to compute the fluxes consist of two files for each measurement period: a time series of dissolved oxygen concentrations and a velocity file. Two types of oxygen concentration files are generated by a Firesting oximeter (Pyroscience): measurements with both upward and downward lines flowing in order to determine the bias between oxygen probes during preparation periods (‘DATE_Allopen.txt’), and measurements during accumulation periods (‘DATE_segment.txt’) of oxygen for each probe and water temperature and the calibration data of each oxygen probe. 
The velocity files are generated by the control system of the relaxed eddy accumulation. They consist of the following columns: 
1.	Date/time
2.	Valve activation on the upward line (0 closed/1 open);
3.	Cumulated activation time for upward line (ms); 
4.	Valve activation on the downward line (0 closed/1 open);
5.	Cumulated activation time for downward line (ms);
6.	Fluctuation of the vertical velocity (mm.s-1); 
7.	Running mean of the aligned vertical velocity for the past 30 s (mm.s-1); 
8.	Aligned velocity u (mm.s-1);
9.	Aligned velocity v (mm.s-1);
10.	Aligned velocity w (mm.s-1);
11.	Upward velocity threshold for relaxed eddy accumulation (mm.s-1);
12.	Downward velocity threshold for relaxed eddy accumulation (mm.s-1);
13.	Alignment angle around Z axis (rad);
14.	Alignment angle around X axis (rad); 
15.	Velocity u measured by the ADV (mm.s-1);
16.	Velocity v measured by the ADV (mm.s-1);
17.	Velocity w measured by the ADV (mm.s-1);
18.	Number of the measurement; 
19.	ADV signal correlation beam 1 (%);
20.	ADV signal correlation beam 2 (%);
21.	ADV signal correlation beam 3 (%); 
22.	test: 0 for adequate correlation (> 70%), else 1; 
23.	erroneous measurement
24.	erroneous measurement

REA_pack contain all scripts of REA automation in LabVIEW (.vi).
DOI: 10.5281/zenodo.3685897
title: Biodiversidata: An Open-Access Biodiversity Database for Uruguay

description: We present a comprehensive database of tetrapod occurrence records native from Uruguay, with the latest taxonomic updates and geographic location accuracy. The dataset provides primary biodiversity data on extant Amphibia, Reptilia, Aves and Mammalia species recorded within the country area. The total number of records collated is 69,380, including 673 species. This is the largest and most geographically and taxonomically comprehensive database of Uruguayan tetrapod species available to date, and it represents the first open repository for the country.
DOI: 10.6084/m9.figshare.20407647
title: Effect of feed enriched by products formulated from coconut water, palm sap sugar, and mushroom on the chemical composition of feed and carcass, growth performance, body indices, and gut micromorphology of giant gourami, Osphronemus goramy (Lacepède, 1801), juveniles

description: <strong>Background:</strong> Giant gourami (Osphronemus goramy Lacepede, 1801) is a freshwater species of Indonesia's most important commercial fish, and most of the giant gourami is produced by aquaculture. The first purpose of this investigation is to determine the effect of various newly formulated products on the amino acid composition of the diet and whole-body carcass. The second aim is to analysed the impact of newly formulated products on the growth performance, body indices, and gut micromorphology. <strong>Methods:</strong> A total of 1.0 litres of palm sap sugar solution and 2.0 litres of mature coconut water were formulated. Each 1.0-litre product formulated was added to 2 g of Aspergillus niger (labeled CP2), 2 g of Rhizopus oligosporus (labeled CP3), and 2 g of Saccharomyces cerevisiae (labeled CP4). Commercial aquafeed to which freshwater was added was labeled CP1 (placebo). Aquafeed was added to CP1 and supplemented with CP2, CP3, and CP4 (labeled KP1, KP2, KP3, and KP4 diets). Their dosage was 150 ml/kg of feed. Juvenile giant gourami (initial weight 50 ± 0.25 g and length 13.2 ± 0.07 cm) were reared in triplicate net frames (2 m × 1 m × 1 m; water volume 1.5 m3/frame nets) in a freshwater concrete pond. The juveniles were randomly distributed at a stocking density of 30 juveniles/net. <strong>Results:</strong> Results support our hypothesis that different product formulations have a significant effect (P &lt; 0.05) on aquafeed nutrition and the whole-body carcass, growth indices, fish feed efficiency, and gut micromorphology of giant gourami juveniles. The KP3 diet contains a higher concentration of amino acids, which increased the growth rate, feed efficiency, and carcass quality more than the other diets that we tested. <strong>Conclusion:</strong> Diet KP3 contains higher total amino acids in diets and carcasses and gives the better growth of giant gourami.
DOI: 10.6084/m9.figshare.23807592
title: Supplementary Material for: CT-based and CTA-based posterior circulation ASPECTS in acute basilar artery occlusion: An Agreement Study

description: Background and purpose: The purpose of the present study was to evaluate the agreement on pc-ASPECTS (posterior circulation Acute Stroke Prognosis Early Computed Tomography Scores) based on non-contrast CT (NCCT) and CT angiography (CTA) source images in patients with acute basilar artery occlusion (BAO). Methods: We prospectively enrolled consecutive patients with acute BAO from January 2022 to August 2022 at The First Affiliated Hospital of University of Science and Technology of China. The NCCT and CTA were scored independently by 15 raters during 2 different reading sessions at least 3 weeks apart. The pc-ASPECTS based on NCCT and CTA were analyzed on the full scale or were dichotomized (0-6 versus 7-10, 0-7 versus 8-10 and 0-8 versus 9-10). The level of agreement was measured using Fleiss κ Statistics. Results: The median (IQR) CT-based pc-ASPECTS was 8 (6.75-9). The interrater agreement for CT-based pc-ASPECTS (κ=0.133 [0.132-0.133]) and CTA-based pc-ASPECTS (κ=0.204 [0.203-0.204]) was slight for all raters. Dichotomizations obtaining the highest concordance for the CT-based pc-ASPECTS (0-6 versus 7-10) and the CTA-based pc-ASPECTS (0-8 versus 9-10) failed to increase the interrater agreement to a substantial level (κ=0.350 [0.348-0.351] and 0.396 [0.395-0.398], respectively). Intrarater agreement for global CT-based pc-ASPECTS was less than substantial for the 14/15 raters and reached the level of substantial for the 3/15 raters with dichotomization. Conclusions: Agreement between clinicians assessing CT-based and CTA-based pc-ASPECTS cannot be sufficient to make reproducible clinical decisions and assessments. The dichotomization failed to improve interrater and intrarater agreement to the level of substantial.
DOI: 10.6084/m9.figshare.23931180
title: Supplementary Material for: Effects of Decoction of Dihuang Yinzi on Alzheimer's disease: a systematic review and meta-analysis

description: OBJECTIVE: This study aims to systematically evaluate the therapeutic effects of Decoction of Dihuang Yinzi on Alzheimer's disease and provide evidence-based medical evidence for the clinical application of traditional Chinese medicine. METHODS: A comprehensive search was conducted across multiple databases, including PubMed, Embase, Cochrane Library, CNKI, VIP, Wan Fang database, and SinoMed database, to collect clinical randomized controlled trials of Decoction of Dihuang Yinzi in the treatment of Alzheimer's disease. Strict literature screening was performed based on predefined inclusion and exclusion criteria. The quality of the included studies was assessed using the Cochrane Collaboration risk of bias assessment tool and the GRADE system recommendation level method. Data synthesis and processing were performed using Review Manager 5.4 and Stata 17 software, while the quality of evidence for outcome indicators (RR, SMD, and WMD) was evaluated using GRADE Profiler 3.6 software. RESULTS: A total of 11 studies involving 798 patients met the inclusion criteria. Decoction of Dihuang Yinzi, whether used alone or in combination with conventional western medicine, demonstrated superior efficacy compared to conventional western medicine alone in improving the total clinical effective rate, TCM syndrome score, ADL score, MMSE, and HDS score in the treatment of Alzheimer's disease. Furthermore, it exhibited a favorable safety profile. However, the GRADE evidence quality rating for the included studies was determined to be low. CONCLUSIONS: Decoction of Dihuang Yinzi, either used alone or in combination with conventional western medicine, shows promising results in enhancing cognitive and memory functions as well as the self-care ability of patients with Alzheimer's disease. However, the low GRADE evidence quality rating underscores the need for targeted improvements in the design and implementation of clinical randomized controlled trials during future research endeavors.
DOI: 10.6084/m9.figshare.24151692
title: Supplementary Material for: Transcription factor Sox9 exacerbates kidney injury through inhibition of microRNA-96-5p and activation of the Trib3/IL-6 axis

description: Introduction: Our study investigated the possible mechanisms of the role of the transcription factor Sox9 in the development and progression of kidney injury through regulation of the miR-96-5p/Trib3/IL-6 axis. Methods: Bioinformatics analysis was performed to identify differentially expressed genes in kidney injury and normal tissues. An in vivo animal model of kidney injury and an in vitro cellular model of kidney injury were constructed using LPS induction in 8-week-old female C57BL/6 mice and human normal renal tubular epithelial cells HK-2 for studying the possible roles of Sox9, miR-96-5p, Trib3, and IL-6 in kidney injury. Results: Sox9 was highly expressed in both mouse and cellular models of kidney injury. Sox9 was significantly enriched in the promoter region of miR-96-5p and repressed miR-96-5p expression. Trib3 was highly expressed in both mouse and cellular models of kidney injury and promoted inflammatory responses and kidney injury. In addition, Trib3 promoted IL-6 expression, which was highly expressed in kidney injury and promoted the inflammatory response and extent of injury in kidney tissue. In vivo and in vitro experiments confirmed that the knockdown of Sox9 improved the inflammatory response and fibrosis of mouse kidney tissues and HK-2 cells, while the ameliorative effect of silencing Sox9 was inhibited by overexpression of IL-6. Conclusion: Collectively, Sox9 up-regulates miR-96-5p-mediated Trib3 and activates the IL-6 signaling pathway to exacerbate the inflammatory response, ultimately promoting the development and progression of kidney injury.
DOI: 10.26300/vpdb-v266
title: Data for Comparison of the coastal and regional ocean community model (CROCO) and NCAR-LES in non-hydrostatic simulations
DOI: 10.5281/zenodo.3531555
title: A complete time-calibrated multi-gene phylogeny of the European butterflies - data

description: The datasets used for the article on phylogenetic relationships of European butterflies, including the treefile for all European species, as well as the posterior distributions of ages of each node.
DOI: 10.5281/zenodo.7511257
title: PQG Numerical Tests Data

description: Files contain a collection of PQG data (*.mat) with different evaporation rates in the paper "Combining Stochastic Parameterized Reduced-Order Models with Machine Learning for Data Assimilation and Uncertainty Quantification with Partial Observations". Three data sets includes E=0.0.2, E=0.2, E=0.35.
DOI: 10.5281/zenodo.8086284
title: Duarte_et_al_Dataset_GeoHealth.csv

description: This database refers to burned area, particulate matter with a diameter of 10 or 2.5 micrometers (μm) or less (PM<sub>10</sub>, PM<sub>2.5</sub>), carbon monoxide (CO), nitrogen dioxide (NO<sub>2</sub>), ozone (O<sub>3</sub>), temperature, relative humidity, wind speed, aerosol optical depth (AOD) and mortality rates of Circulatory System Disease (CSD), Respiratory System Disease (RSD), Pneumonia (PNEU), Chronic Obstructive Pulmonary Disease (COPD), and Asthma (ASMA) used on the article <strong>Fire-Pollutant-Atmosphere Components and Its Impact on Mortality in Portugal During Wildfire Seasons</strong> published at AGU GeoHealth in 2023. The full methodology is described in the article. The national monthly mean concentrations of PM<sub>10</sub>, PM<sub>2.5</sub>, CO, O<sub>3</sub>, and NO<sub>2</sub> were used as five variables named PM10_Obs, PM25_Obs, CO_Obs, O3_Obs, and NO2_Obs for multivariate statistical analysis. Daily exceedances of the WHO guidelines for PM<sub>10</sub>, PM<sub>2.5</sub>, and NO<sub>2</sub> were counted monthly and included as three variables named WHO_PM10, WHO_PM25, and WHO_NO2 for multivariate statistical analysis. Meteorological data of air temperature at 2 meters above the surface (TEMP_Obs) and relative humidity (RH_Obs), and 10 m wind speed (WS_Obs) from 43 meteorological stations in mainland Portugal. The CAMS global reanalysis monthly averaged fields of the Total aerosol optical depth at 550 nm (AOD_CAMs), Black carbon aerosol optical depth at 550 nm (BC_AOD_CAMs) and Dust aerosol optical depth at 550 nm (Dust_AOD_CAMs) were used. Standardized mortality rates (per 100 000 inhabitants - all ages) were selected according to the International Classification of Diseases, version 11 (ICD-11; https://icd.who.int/browse11/l-m/en): Circulatory System Diseases (CSD) (ICD-11: 1B40 - BE2Z); Respiratory System Diseases (RSD) (ICD-11: CA00 - CB40); Pneumonia (PNEU) (ICD-11: CA40 - CA40.Z); Chronic Obstructive Pulmonary Disease (COPD) (ICD-11: CA20.Z - CA22.Z); and Asthma (ASMA) (ICD-11: CA23 - CA23.3). Monthly national mortality data for Portugal were provided by the National Institute of Statistics (INE) (INE; https://www.ine.pt/).
DOI: 10.6084/m9.figshare.22188859
title: Supplementary Material for: Acute Late-Onset Cirrhosis in Zellweger Spectrum Disorder

description: Zellweger spectrum disorders (ZSD) is known to present with variable hepatic manifestations ranging from benign hepatosplenomegaly and elevated liver enzymes to advanced liver cirrhosis with hepatocellular carcinoma. However, the progression of liver disease in ZSD patients over time is poorly characterized due to scarcity of the disease. Herein we report a case of newly diagnosed liver cirrhosis in a ZSD patient with rapid progression and fatal outcome to demonstrate key clinical learning points.
DOI: 10.6084/m9.figshare.23641551
title: Supplementary Material for: Preoperative prediction of microvascular invasion with gadoxetic acid-enhanced magnetic resonance imaging in patients with single hepatocellular carcinoma: The implication of surgical decision on the extent of liver resection

description: Introduction: Microvascular invasion (MVI) is one of the most important prognostic factors for hepatocellular carcinoma (HCC) recurrence, but its application in preoperative clinical decisions is limited. This study aimed to identify preoperative predictive factors for MVI in HCC and further evaluate oncologic outcomes of different types and extents of hepatectomy according to stratified risk of MVI. Methods: Patients with surgically resected single HCC (≤5 cm) who underwent preoperative gadoxetic acid-enhanced magnetic resonance imaging (MRI) were included in a single-center retrospective study. Two radiologists reviewed the images with no clinical, pathological, or prognostic information. Significant predictive factors for MVI were identified using logistic regression analysis against pathologic MVI and used to stratify patients. In the subgroup analysis, long-term outcomes of the stratified patients were analyzed using the Kaplan-Meier method with log-rank test and compared between anatomical and non-anatomical or major and minor resection. Results: A total of 408 patients, 318 men and 90 women, with a mean age of 56.7 years were included. Elevated levels of tumor markers (α-FP ≥25 ng/mL and PIVKA-II ≥40 mAU/mL) and three MRI features (tumor size ≥ 3 cm, non-smooth tumor margin, and arterial peritumoral enhancement) were independent predictive factors for MVI. As the MVI risk increased from low (no predictive factor) and intermediate (1–2 factors) to high-risk (3–4 factors), recurrence-free and overall survival of each group significantly decreased (P= 0.001). In the high MVI risk group, 5-year cumulative recurrence rate was significantly lower in patients who underwent major compared to minor hepatectomy (26.6 vs 59.8%, P= 0.027). Conclusion: Tumor markers and MRI features can predict the risk of MVI and prognosis after hepatectomy. Patients with high MVI risk had the worst prognosis among the three groups, and major hepatectomy improved long-term outcomes in these high-risk patients.
DOI: 10.6084/m9.figshare.23676063
title: Supplementary Material for: Early counselling to improve oral health behavior in children with major congenital heart defects – a randomized controlled trial

description: Maintaining optimal oral health behavior in children with a congenital heart defect (CHD) is important in managing the risk for caries development and infective endocarditis. The aim of this study was to evaluate the impact of an early and repeat oral health promotion intervention (OHPI) among of children with major CHD. Randomized controlled trial including 72 out of 91 children born in Finland 1.4.2017-31.10.2020 with a) major CHD potentially included in the criteria of endocarditis prophylaxis or b) any CHD with surgical repair combined with a chromosomal syndrome. A parallel passive control (C) group of 87 healthy children were recruited at birth. CHD children were randomized 1:1 to intervention (CHD-I) and control (CHD-C) groups. The OHPI included counselling by motivational interviewing, home delivered toothpaste and toothbrushes, and written information, and was provided at baseline, 6, 12, and 18 months of age to CHD-I group. The primary outcome measure at 24 months was child’s oral health behavior (toothbrushing, sugar intake, and dental care contact). The secondary outcome measures were parents’ awareness of the importance of oral health behavior, and oral health behavior as a predictor for child behavior. At 24 months, toothbrushing was performed twice a day in 20/27 (74%) among CHD-I, in 13/30 (43 %) among CHD-C (CHD-I vs CHD-C p=0.031), and in 37/50 (74 %) among healthy comparisons (CHD-C vs C p=0.009). Electric toothbrush use was 12/27 (44 %) in CHD-I, 5/30 (17 %) in CHD-C (CHD-I vs CHD-C p=0.041), and 7/50 (14%) in healthy comparison (CHD-C vs C p=0.756) children. Among CHD-I, toothbrushing and use of electric toothbrush improved between 12 months and 24 months. Sugar drink intake was more common among CHD-C (CHD-C vs C p=0.015), but comparable to CHD-I children. Parental toothbrushing predicted child toothbrushing twice a day. There were no statistical group differences in dental care contact. Children with CHD are at risk for poor oral health behavior. This could be improved with early and repeat oral health promotion parental counselling.