cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13663298.v1
title: Supplementary Material for: Active Surveillance for Incidental (cT1a/b) Prostate Cancer: Long-Term Outcomes of the Prospective Noninterventional HAROW Study

description: <b><i>Introduction:</i></b> Optimal treatment for incidental prostate cancer (IPC) after surgical treatment for benign prostate obstruction is still debatable. We report on long-term outcomes of IPC patients managed with active surveillance (AS) in a German multicenter study. <b><i>Methods:</i></b> HAROW (2008–2013) was designed as a noninterventional, prospective, health-service research study for patients with localized prostate cancer (≤cT2), including patients with IPC (cT1a/b). A follow-up examination of all patients treated with AS was carried out. Overall, cancer-specific, and metastasis-free survival and discontinuation rates were determined. <b><i>Results:</i></b> Of 210 IPC patients, 68 opted for AS and were available for evaluation. Fifty-four patients had cT1a category and 14 cT1b category. Median follow-up was 7.7 years (IQR: 5.7–9.1). Eight patients died of which 6 were still under AS or watchful waiting (WW). No PCa-specific death could be observed. One patient developed metastasis. Twenty-three patients (33.8%) discontinued AS changing to invasive treatment: 12 chose radical prostatectomy, 7 radiotherapy, and 4 hormonal treatment. Another 19 patients switched to WW. The Kaplan-Meier estimated 10-year overall, cancer-specific, metastasis-free, and intervention-free survival was 83.8% (95% CI: 72.2–95.3), 100%, 98.4% (95% CI: 95.3–99.9), and 61.0% (95% CI: 47.7–74.3), respectively. In multivariable analysis, age (RR: 0.97; <i>p</i> &lt; 0.001), PSA density ≥0.2 ng/mL<sup>2</sup> (RR: 13.23; <i>p</i> &lt; 0.001), and PSA ≥1.0 ng/mL after surgery (RR: 5.19; <i>p</i> = 0.016) were significantly predictive for receiving an invasive treatment. <b><i>Conclusion:</i></b> In comparison with other AS series with a general low-risk prostate cancer population, our study confirmed the promising survival outcomes for IPC patients, whereas discontinuation rates seem to be lower for IPC. Thus, IPC patients at low risk of progression may be good candidates for AS.
DOI: 10.6084/m9.figshare.16652227.v1
title: Neobroker_Dataset.sav

description: This dataset was collected via an online survey in Germany and is the basis of the respective research article.<br>
DOI: 10.6084/m9.figshare.24539413.v1
title: The data for "Comparing behaviours induced by natural memory retrieval and optogenetic reactivation of an engram ensemble in mice"

description: we compared two defensive behaviors (freezing and the syllable structure of ultrasonic vocalizations, USVs) induced by training cues (natural memory retrieval) and optogenetic engram ensemble reactivation (artificial memory retrieval) in a threat conditioning paradigm in the same mice. During natural memory recall, we observed a strong positive correlation between freezing levels and USV syllable characteristics (characterized by an unsupervised algorithm, MUPET, Mouse Ultrasonic Profile ExTraction). Furthermore, strikingly similar behavioural profiles were observed in the same mice when engram ensemble neurons were optogenetically reactivated. Although our analysis focused on two behavioral measures of threat memory (freezing and USV characteristics), these results underscore the similarities between threat memory recall triggered naturally and through optogenetic engram reactivation.
DOI: 10.6084/m9.figshare.28551605.v1
title: Latin American Global Competitiveness - Data

description: The analysis considered variables such as trade openness, infrastructure investment, educational quality, inflation and institutional stability. The results of the study indicated that both trade openness and investment in education are key factors for strengthening regional competitiveness, while variables such as inflation and foreign direct investment did not show statistically significant impacts. It was also noted that investment in infrastructure and institutional strengthening play a fundamental role in the creation of a competitive environment. On the other hand, marked differences were identified in the levels of competitiveness among the countries analyzed, attributed to variations in their macroeconomic policies and development strategies.
DOI: 10.6084/m9.figshare.13079366.v1
title: Genbank accession numbers of sequences used to infer the host phylogeny.xlsx

description: List of species and sequence IDs for genes used for building host phylogeny
DOI: 10.6084/m9.figshare.14832258.v1
title: The acceptability and side effects of Covid-19 vaccine among health care workers in Nigeria

description: The dataset is on the understanding the attitude, the side effect experienced and the willingness to get vaccinated with the overtly newly introduced COVID 19 vaccine in the country
DOI: 10.6084/m9.figshare.1609804.v3
title: The role of spatial boundaries in shaping long-term event representations: computational model

description: MATLAB code for model presented in paper.
DOI: 10.6084/m9.figshare.22621784.v1
title: Additional file 1 of Belowground microbiota analysis indicates that Fusarium spp. exacerbate grapevine trunk disease

description: Additional file 1: Table S1. The environmental temperature conditions during the seasons of 2019 and 2020. Table S2. The physical and chemical characteristics of the soil in the sampling vineyard. Table S3. The records of chemical agents and fertilizers in the sampling vineyard. Table S4. The reads numbers used to analyze in this study. Table S5. Alpha diversity index values for fungal communities in different soil–plant compartments. PE: rhizoPlane and Endophyte; R: rhizosphere; and B: bulk soils. Samples were collected from grapevine trunk disease (GTD) asymptomatic (As) and symptomatic (S) grapevines in 2019 (0.19) and 2020 (0.20). Table S6. Operational taxonomic units (OTUs) specific to asymptomatic or symptomatic samples. Table S7. The relative abundances of grapevine trunk disease (GTD)-associated fungi annotated at the species and genus levels detected with ITS amplicon sequencing data. Table S8. Grapevine trunk disease (GTD)-associated fungi exhibiting significant differences in relative abundance between comparison groups based on ITS amplicon sequencing. Statistical differences were evaluated with Wilcoxon tests. Table S9. Disease index values for grapevines inoculated with isolates in this study.
DOI: 10.6084/m9.figshare.25883863.v3
title: Code and Supporting Files for reproducing quantitative analyses and figures in Levy et al., Increased bird abundances over 30 years in an extensive commercial forest landscape

description: Habitat loss and degradation are considered the primary drivers of continental bird declines. We replicated an extensive study of forest bird populations and forest structure and composition that we conducted 30 years ago in a 238,000-ha commercial forest landscape in northern Maine. The two study periods (1992-93 and 2021-22) marked either side of a landscape-scale transition in forest ownership and management. Code and supporting data files are provided for reproducing quantitative analyses and their associated figures: bootstrapping-derived 83.4% C.I.'s for per-forest-type densities across species, Delta-method-derived 83.4% C.I.'s for landscape abundances across species, Shannon's Diversity indices and associated statistical tests, generalized linear models of functional guild vs. abundance trend, and analyses of vegetation metrics collected at each bird survey site. See associated Figs under this Project heading.
DOI: 10.6084/m9.figshare.14957658.v1
title: Supplementary Material for: The Efficacy and Short- and Long-Term Side Effects of Radioactive Iodine Treatment in Pediatric Graves’ Disease: A Systematic Review

description: <b><i>Background:</i></b> Graves’s disease (GD) is the most common cause of hyperthyroidism. Maximal 30% of pediatric GD patients achieve remission with antithyroid drugs. The majority of patients therefore require definitive treatment. Both thyroidectomy and radioactive iodine (RAI) are often used as definitive treatment for GD. However, data on efficacy and short- and long-term side effects of RAI treatment for pediatric GD are relatively scarce. <b><i>Methods:</i></b> A systematic review of the literature (PubMed and Embase) was performed to identify studies reporting the efficacy or short- and long-term side effects of RAI treatment in pediatric GD. <b><i>Results:</i></b> Twenty-three studies evaluating 1,283 children and adolescents treated with RAI for GD were included. The treatment goal of RAI treatment changed over time, from trying to achieve euthyroidism in the past to aiming at complete thyroid destruction and subsequent hypothyroidism in the last 3 decades. The reported efficacy of a first RAI treatment when aiming at hypothyroidism ranged from 42.8 to 97.5%, depending on the activity administered. The efficacy seems to increase with higher RAI activities. When aiming at hypothyroidism, both short- and long-term side effects of treatment are very rare. Long-term side effects were mainly seen in patients in whom treatment aimed at achieving euthyroidism. <b><i>Conclusion:</i></b> RAI is a safe definitive treatment option for pediatric GD when aiming at complete thyroid destruction. When aiming at hypothyroidism, the efficacy of treatment seems to increase with a higher RAI activity. Prospective studies are needed to determine the optimal RAI dosing regimen in pediatric GD.
DOI: 10.6084/m9.figshare.25092971.v1
title: Supplementary Material for: Prognostic value of pathological response for patients with unresectable hepatocellular carcinoma undergoing conversion surgery

description: Introduction: Transarterial chemoembolization combined with lenvatinib and PD-1 inhibitor (triple therapy) has displayed encouraging clinical outcomes for unresectable hepatocellular carcinoma (uHCC). We aim to explore the prognostic value of pathologic response (PR) in patients with initially uHCC who underwent conversion surgery following triple therapy, and identify predictors of major pathologic response (MPR).
Methods: A total of 76 patients with initially uHCC who underwent conversion surgery following triple therapy were retrospectively analyzed. PR was calculated as the proportion of non-viable tumor cell surface area of the whole tumor bed surface area. MPR was identified when PR was ≥ 90%. Pathological complete response (pCR) was defined as the absence of viable tumor cells.
Results: MPR and pCR were identified in 53 (69.7%) and 25 (32.9%) patients, respectively. The 1- and 2-year overall survival in patients with MPR was significantly higher than in those without MPR (100.0% and 91.3% vs. 67.7 % and 19.4%; p &lt;0.001). The corresponding recurrence-free survival was also improved in patients with MPR compared to those without (75.9% and 50.8% vs. 22.3 and 11.2%; p &lt; 0.001). Similar results were observed among patients with pCR and those without. Patients who achieved MPR without pCR exhibited survival rates comparable to those of patients who achieved pCR. Baseline neutrophil-to-lymphocyte ratio ≥ 2.6 (p = 0.016) and preoperative alpha-fetoprotein ≥ 400 ng/mL (p = 0.015) were independent predictors of MPR.
Conclusion: The presence of MPR or pCR could improve prognosis in patients with initially uHCC who underwent conversion surgery following triple therapy. The PR may become a surrogate marker for predicting the prognosis of these patients.
DOI: 10.15468/dl.fya28y
title: Occurrence Download

description: A dataset containing 209 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Observation, Human Observation, Machine Observation, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Melangyna quadrimaculata (Verrall, 1873)"
 ]
}

 The dataset includes 209 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009615-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.25877542.v1
title: How to detect a polytrauma patient at risk of complications: A validation and database analysis of four published scales

description: Early accurate assessment of the clinical status of severely injured patients is crucial for guiding the surgical treatment strategy. Several scales are available to differentiate between risk categories. They vary between expert recommendations and scores developed on the basis of patient data (level II). We compared four established scoring systems in regard to their predictive abilities for early (e.g., hemorrhage-induced mortality) versus late (Multiple Organ Failure (MOF), sepsis, late death) in-hospital complications.
DOI: 10.6084/m9.figshare.12562253.v1
title: JVASP-49983 to JVASP-50904

description: JARVIS-DFT
DOI: 10.6084/m9.figshare.4814740.v1
title: PRG GS Heading Date Data

description: Conditional modes (BLUPs) for heading date generated in lme4 from data collected over two years in a replicated field trial.Sequencing data from these genotypes are available on NCBI (PRJNA352789).
DOI: 10.6084/m9.figshare.4541236.v2
title: Is my research right? Surviving in a post-expert world

description: This is a talk motivating why all researchers should learn enough about research software to survive in a post-expert world, for the research software management, sharing and sustainability workshop series. #researchsoftware<br>This talk was given as a keynote at the workshops at the British Library (12th January 2017) and the University of Cambridge (16th January 2017).
DOI: 10.6084/m9.figshare.4551628.v1
title: Fig 1.- Flow diagram of the literature search.

description: Flow diagram<br>
DOI: 10.6084/m9.figshare.15090711.v1
title: Supplementary Material for: A Staged Operation as a Surgical Strategy for a Patient with Type VI Isolated Superior Mesenteric Artery Dissection

description: An isolated superior mesenteric artery (SMA) dissection (ISMAD) is extremely rare among visceral artery dissections. Its diagnosis is made by abdominal contrast CT scan which shows SMA occlusion partially or completely. The ISMAD is classified into 6 types: type I–V has partial occlusion and treated medically using antiplatelets or anticoagulants. On the other hand, type VI has complete occlusion and must be treated by urgent surgical operation. We present a 67-year-old female who presented with sudden onset abdominal pain and melena. An urgent contrast CT revealed type VI ISMAD. She underwent 3 staged operations as follows: (1) first, as laparotomy showed pale color in almost the extensive length of the small intestine, arterial bypassing of SMA was undertaken using SMA to the right common iliac artery bypass; (2) as the second-look operation on the next day, the terminal ileum was resected, and the remaining small intestine was able to be preserved. However, when the abdomen was tried to be closed, systemic blood pressure decreased to pre-shock condition, so the abdominal wall was closed at skin level with silastic sheet. (3) As the third-look operation on the 7th day, ileostomy was created, and the abdominal wall was safely closed. The postoperative course was uneventful. This case study shows that SMA grafting and staged operations might be an option to preserve the length of the small intestine when ISMAD is diagnosed as type VI.
DOI: 10.6084/m9.figshare.17058272.v5
title: code_and_data_for_impacts_of_319_wind_farms

description: Codes and datasets for “Impacts of 319 wind farms on local surface temperature and vegetation in the United States” . Codes for processing and plotting can be downloaded from github ( https://github.com/qinqin66/1_us_wind_farms.git).Users should cite the original paper of (Qin et al. 2022 ERL) and cite or acknowledge this dataset (DOI: 10.6084/m9.figshare.17058272) when using it.<br>
DOI: 10.6084/m9.figshare.25246378.v1
title: Marchesi2023_Vertebral morphology in Dolphins: a qualitative analisis

description: For the first time, this work employs 3D geometric morphometrics to provide a detailed description of vertebral morphology along the vertebral column of 24 dolphin species in order relate particular morphologies with biomechanical requirements of the most specious odontocete family.
DOI: 10.6084/m9.figshare.13005305.v1
title: Social Accountability review - final combined search results

description: Social accountability for reproductive, maternal, newborn, child and adolescent health: a review of reviews: combined search results
DOI: 10.6084/m9.figshare.1348830_d1
title: TEX86 Surface Sediment Database

description: This file contains a database of modern sediment observations of the TEX86 temperature proxy, an index that describes the relative cyclization of marine archaeal glycerol dialkyl glycerol tetraethers. Please refer to the separate metadata file for a description of the variables. Note that missing values appear as -999. This is database version 1.0.
DOI: 10.6084/m9.figshare.26317915.v1
title: Tomato Data of Different Ripeness Stages

description: Data from Tomato Plantations of Different Ripeness Stages in Changping District, November 2023
DOI: 10.6084/m9.figshare.23909700.v1
title: Supplementary Material for: Driving Automation for Older Adults with Preclinical Alzheimer’s Disease

description: Background: Older adults with preclinical Alzheimer’s disease (AD) show changes in on-road driving performance. The impact of preclinical AD on using automated vehicle (AV) technology is unknown. The aim was to evaluate safety and cognitive workload while operating AV technology in drivers with preclinical AD. Methods: This cross-sectional study included 40 participants: 19 older adults (age 74.16 ± 4.78; MOCA scores 26.42 ± 2.52) with preclinical AD, evidenced by elevated cortical beta-amyloid; and 21 controls (age 73.81 ± 5.62; MOCA scores 28.24 ± 1.67). All participants completed two scenarios in a driving simulator. Scenario 1 included conditional automation with an emergency event that required a manual take-over maneuver. Scenario 2 was identical but with a cognitive distractor task. Emergency response time was the main safety outcome measure. Cognitive workload was calculated using moment-to-moment changes in pupillary size and converted into an Index of Cognitive Activity (ICA). Mann-Whitney U and independent t-tests were used to compare group differences. Results: Emergency response times were similar between drivers with preclinical AD and controls in scenario 1 (20.85s ± 1.08 vs 20.52s ± 3.18; p = 0.83) and scenario 2 (14.83s ± 7.37 vs 13.45s ± 10.43; p = 0.92). Likewise, no differences were found in ICA between drivers with preclinical AD and controls in scenario 1 (0.34 ± 0.08 vs 0.33 ± 0.17; p = 0.74) or scenario 2 (0.30 ± 0.07 vs 0.29 ± 0.17; p = 0.93). Conclusions: Older drivers with preclinical AD may safely operate AV technology, without increased response times or cognitive workload. Future on-road studies with AV technology should confirm these preliminary results in drivers with preclinical AD.
DOI: 10.6084/m9.figshare.21756212.v2
title: Lineages

description: Each of the .zip files in this dataset correspond to one of the microcolonies in the cib.zip file of the data repository of van Vliet et al (2017): https://zenodo.org/record/268921. Files generally correspond to the standard FAST formats. However, to facilitate the benchmarking process, several copies of each type of file exist containing datasets processed in different ways. In general, these can be split into <em>ground truth datasets</em> (fully manually corrected), <em>Corrected vs. automated analyses </em>(differ in whether inputs to the modules were manually corrected or not) and <em>all features vs. centroids only </em>(differ in whether all features or just the centroids were used by the tracking module. Specifically, each module is associated with the following files/directories: <br> Segmentations Original_Segmentations: Segmentations as output directly by the FAST segmentation module. Corrected_Segmentations: Segmentations corrected by hand. Feature extraction CellFeatures_AutoSeg.mat: Features extracted based on Original_Segmentations. CellFeatures_ManualSeg.mat: Features extracted based on Corrected_Segmentations. Tracking Tracks_AutoSeg_Auto.mat: Automatically generated tracks output by the Tracking module with length, width, fluorescence and position as features and Original_Segmentations as the raw segmentations. Tracks_AutoSeg_Auto_CentroidsOnly.mat: Automatically generated tracks output by the Tracking module with only positional coordinates as features and Original_Segmentations as the raw segmentations. Tracks_AutoSeg_Corrected.mat: Manually corrected ground truth for the tracks associated with Original_Segmentations. Generated with the track correction GUI. Tracks_ManualSeg_Auto.mat: Automatically generated tracks output by the Tracking module with length, width, fluorescence and position as features and Corrected_Segmentations as the raw segmentations. Tracks_ManualSeg_Corrected.mat: Manually corrected ground truth for the tracks associated with Corrected_Segmentations. Generated with the track correction GUI. Divisions Tracks_GoldStandardDivisions.mat: Manually corrected ground truth for division assignment, based on Tracks_ManualSeg_Corrected.mat. Tracks_AutoStreamDivisions.mat: Automatically generated output of the division detection module using Tracks_AutoSeg_Auto.mat as input. Tracks_AutoStreamDivisions_CentroidsOnly.mat: Automatically generated output of the division detection module using Tracks_AutoSeg_Auto_CentroidsOnly.mat as input. Tracks_ManualStreamDivisions.mat: Automatically generated output of the division detection module using Tracks_ManualSeg_Corrected.mat as input. In general, to use any one of these as an input to a later module, just rename the corresponding file to the FAST standard (e.g. rename Tracks_AutoSeg_Auto.mat to Tracks.mat to view the associated tracks in the overlays module). In some cases, you will also need to make sure that the Segmentation directory is filled with the corresponding segmentations (either Original or Corrected, depending on whether you are looking at the auto or the manual streams).
DOI: 10.6084/m9.figshare.27309477.v1
title: Effects of vegetation restoration on soil carbon sequestration on the Loess Plateau, China using a combined remote sensing and process-based modeling approach

description: The input data for the CLS model.The CLS model code file is in https://github.com/fanlei21/LP_SOC_sequestration
DOI: 10.6084/m9.figshare.12309806.v1
title: Supplementary Material for: Alcohol Use and Cancer in the European Union

description: <b><i>Background:</i></b> Cancers constitute a major non-communicable disease category globally and in the European Union (EU). <b><i>Summary:</i></b> Alcohol use has been established as a major cause of cancer in humans. Principal cancer agencies agree that the following cancer sites are causally impacted by alcohol: lip and oral cavity, pharynx (excluding nasopharynx), oesophagus, colon and rectum, liver, (female) breast, and larynx. For all of these cancer sites, there is a dose-response relationship with no apparent threshold: the higher the average level of consumption, the higher the risk of cancer incidence. In the EU in 2016, about 80,000 people died of alcohol-attributable cancer, and about 1.9 million years of life were lost due to premature mortality or due to disability. <b><i>Key messages:</i></b> Given the above-described impact of alcohol on cancer, public awareness about the alcohol-cancer link needs to be increased. In addition, effective alcohol policy measures should be implemented. As a large part of alcohol-attributable cancers are in low and moderate alcohol users, in particular for females, general population measures such as increases in taxation, restrictions on availability, and bans on marketing and advertisement are best suited to reduce the alcohol-attributable cancer burden.