cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5125000.v1
title: Supplementary Material for: Are Transrectal Prostate Biopsies Routinely Indicated in Patients with Incidentally Diagnosed Prostate Cancer following Transurethral Resection of the Prostate for Benign Disease?

description: <b><i>Objective:</i></b> To determine the indication of routine transrectal ultrasound-guided needle biopsy (TRUSBx) of the prostate gland following incidental cancer diagnosis after transurethral resection of the prostate (TURP) for benign prostatic hyperplasia. <b><i>Materials and Methods:</i></b> A multi-institutional search identified 63 patients with incidental TURP-diagnosed prostate cancer from 2001 to 2010, who underwent subsequent TRUSBx or radical prostatectomy (RP). The Gleason scores from TURP were compared to those from TRUSBx or RP. Whole mount maps from RP were analysed to provide an anatomical basis for the correlation observed. To determine the clinical impact of this problem, the incidence of TURP-diagnosed prostate cancer in the population was also determined. <b><i>Results:</i></b> Of 22 patients who underwent TRUSBx, the rates of Gleason score concordance, upgrading and downgrading were 32, 14 and 54% respectively (Spearman correlation coefficient 0.20). Most cases of pathological downgrading consisted of benign cores at biopsy. Therefore, TRUSBx did not give additional Gleason score (GS) information in 86% of patients. Of 41 RP patients, the respective rates were 61, 22 and 17% (Spearman correlation coefficient 0.15). The majority of them retained a similar or lower GS between TURP and RP. Of 13 whole mount maps analysed, 6 (46%) were found with anterior/transitional zone (AZ/TZ) tumours, 6 (46%) with multifocal tumours and 1 (8%) with a large peripheral zone (PZ) tumour extending into the TZ. Regional population data show that despite a gradual reduction in the proportion of TURP-diagnosed cases over the past decade, they still account for 8.5-13% of all new cases. <b><i>Conclusion:</i></b> TURP-diagnosed prostate cancers represent predominantly AZ tumours. A TRUSBx does not give additional GS information in a majority of cases, and therefore is not routinely indicated. It may be selectively useful prior to active surveillance, but not in all pursuing radical treatment. These findings may help reduce unnecessary TRUSBx in the population.
DOI: 10.6084/m9.figshare.7855592.v1
title: Knowledge and attitudes among life scientists towards reproducibility within journal articles_survey_datafile_raw_data

description: Raw datafile of the survey data collected from the survey distributed to collect knowledge and attitudes among life scientists towards reproducibility within journal articles.
DOI: 10.17632/vrk3p99fcs
title: Favelas of São Paulo

description: Dataset containing polygons and data for all favelas of São Paulo, all public lighting points, all bus stations points, declivity and administrative districts. We also provide here a code for working with the data and obtain some insights.
DOI: 10.6084/m9.figshare.155790.v1
title: Data collection sheets (baseline and follow up)

description: Data collection sheets that repeats the modified questions from the International Consultation on Incontinence Questionnaire (ICI-Q), completed at baseline and follow up
DOI: 10.6084/m9.figshare.16651723.v1
title: Supplementary Material for: Immune Checkpoint Inhibitors: The Emerging Cornerstone in Cholangiocarcinoma Therapy?

description: <b><i>Background:</i></b> Cholangiocarcinoma (CCA) encompasses a heterogeneous group of malignant tumors with dismal prognosis and increasing incidence worldwide. Both late diagnosis due to the lack of early symptoms and the refractory nature of these tumors seriously compromise patients’ welfare and outcomes. <b><i>Summary:</i></b> During the last decade, immunotherapy and, more specifically, modulation of immune checkpoints-mediated signaling pathways have been under the spotlight in the field of oncology, emerging as a potential therapeutic approach for the treatment of several cancers, including CCA. Generally, high expression levels of immune checkpoints in patients with CCA have been associated with worse clinical outcomes, particularly with shorter overall survival and relapse-free survival. Thus, immune checkpoint inhibitors (ICIs), which mainly constitute different monoclonal antibodies, have been developed in order to hamper the immune checkpoint-mediated pathways. Interestingly, chemotherapy may increase the expression of immune checkpoints, while other therapeutic approaches such as ablative and targeted therapies may enhance their antitumor activity. In this sense, several clinical trials evaluated the safety and efficacy of ICIs for CCA, both as a monotherapy and in combination with other ICIs or loco-regional and systemic therapies. Additionally, many other clinical trials are currently ongoing and results are eagerly awaited. Here, we summarize the key aspects of immune checkpoint molecules as prognostic factors and therapeutic targets in CCA, highlighting the most recent advances in the field and future research directions. <b><i>Key Messages:</i></b> (1) Effective therapeutic approaches for CCA are urgently needed. (2) Expression levels of immune checkpoints in patients with CCA have been proposed to be related with clinical outcomes. (3) Combination of different ICIs may outperform the efficacy of ICI monotherapy for CCA treatment. (4) Recent studies point toward the combination of ICIs and other common therapies, especially chemotherapy, as a promising strategy for treatment of CCA patients.
DOI: 10.6084/m9.figshare.25263748.v2
title: YKFData_ChaoGao2022.mat

description: This data is belong to Dr Chao Gao, which cannot be used by others unless the author has given the permission.
DOI: 10.6084/m9.figshare.7054199.v1
title: Observer ckf

description: The instructions how to use this data set are available in a text file titled 'The relative contribution of color and material in object selection.txt' which can be found at https://github.com/BrainardLab/ColorMaterial .
DOI: 10.17632/b6zh5mjd5p
title: Data on Physical Education Teachers’ Burnout during Pandemic: Structural Equation Modelling 

description: The dataset elaborates the correlations between Physical Education (PE) teachers’ self-concept and teacher efficacy as the predictors of burnout variables of Maslach Burnout Inventory (emotional exhaustion, depersonalization, and reduced personal accomplishment) during distance learning due to the Corona Virus Disease 2019 (COVID-19).
DOI: 10.17632/xj3x7vmsdg
title: Implementation of ['YOLO-OB: An improved anchor-free real-time multi-scale colon polyp detector in colonoscopy']

description: This repo is the implementation of
['YOLO-OB: An improved anchor-free real-time multi-scale colon polyp detector in colonoscopy']

The deep learning-based object detection algorithm is currently one of the most effective methods for improving polyp detection during colonoscopy. This repository proposes a new model called YOLO-OB based on YOLOv3. It improves network's feature fusion capacity by adopting the Spatial Pyramid Pooling (SPP) and the Bi-directional Feature Pyramid Network (BiFPN) modules. It also employs the ObjectBox detection head, which uses a center-based anchor-free box regression strategy that can detect polyps of different sizes on feature maps of any scale.
DOI: 10.6084/m9.figshare.19092761.v1
title: Oscilloscope data for SPAD quenched by 100 kohm

description: Oscilloscope data for SPAD quenched by 100 kohm . 1photon/pulse.<br>Oscilloscope data of SPAD quenched by 100 kohm for "Dynamic-quenching of a single-photon avalanche photodetector using an adaptive resistive switch"<br>
DOI: 10.6084/m9.figshare.24886239.v1
title: <b><i>Sanguinoderma infundibulare</i></b>

description: Genomic annotation of <i>Sanguinoderma infundibulare</i>
DOI: 10.6084/m9.figshare.25106123.v3
title: Oceanic Anoxic Event 2 triggered by Kerguelen volcanismOceanic Anoxic Event 2 triggered by Kerguelen Plateau volcanism - datasetshttps://doi.org/10.1038/s41467-024-49032-3

description: Large Igneous Provinces (LIPs) are associated with global warming and carbon cycle perturbations during Oceanic Anoxic Event 2 (OAE2, ~94 Ma) and the Mid-Cenomanian Event (MCE, ~96.5 Ma). However, there is still no consensus on the role volcanism played as a trigger, or its source – previously ascribed to the Caribbean LIP or High Arctic LIP. Here, we use Mentelle Basin sedimentary mercury (Hg) concentrations to determine the timing of volcanism, and neodymium (Nd) and strontium (Sr) isotopes for sedimentary provenance. High Hg concentrations compared to Northern Hemisphere records, and a shift to radiogenic Nd isotopes, indicates Kerguelen volcanic activity and plateau uplift occurred in the lead up to and within OAE2. Whilst we find limited evidence that a volcanic event caused the MCE, pulsed Hg spikes before and during OAE2 imply volcanic emissions were key in driving climate and carbon cycle changes and triggering OAE2.  The data here are from the following paper: Oceanic Anoxic Event 2 triggered by Kerguelen Plateau volcanism
DOI: 10.6084/m9.figshare.7722062.v4
title: Drugs, Active Ingredients and Diseases database in Spanish. Augmenting the resources for analysis on drugs-illness interaction

description: <pre>Quantitative and qualitative data on active-ingredient drug composition are essential information for characterizing near-field exposure. Equally as important is the characterization of the relationship between one or many active ingredients in terms of the diseases they are prescribed for. Such evaluations however require quantitative and well-classified information at different anatomical levels. Here we present two datasets which contain details of 12,827 drugs, 40,164 diseases, 6,231 active pharmaceutical ingredients and 4,093 side effects. </pre> <pre>These datasets will allow researchers, physicians and pharmacists to evaluate the active substances at an anatomical level, enabling them to infer the range of different active substances and possible side effects on patients with comorbidities. These datasets also contains information about clinical and pharmacological classification, which may be useful for clinical researchers and physicians.</pre>
DOI: 10.6084/m9.figshare.1247641.v6
title: RNA shotgun metagenomic sequencing of northern California mosquitoes uncovers viruses, bacteria, and fungi

description: See the README file for details
DOI: 10.6084/m9.figshare.16863559.v1
title: "Optimal Experimental Design Based on Two-Dimensional Likelihood Profiles" - Matlab Data and Scripts

description: Data sets and analysis scripts used in the study "Optimal Experimental Design Based on Two-Dimensional Likelihood Profiles". The Data2Dynamics toolbox (https://github.com/Data2Dynamics/d2d) is needed to run the provided scripts.
DOI: 10.6084/m9.figshare.21435369.v1
title: Supplementary Material for: Reduction of missed diagnosis of G6PD deficiency in heterozygous females by G6PD/6PGD ratio assay combined with ARMS-PCR

description: Objective: Glucose-6-phosphate dehydrogenase (G6PD) deficiency is an X-linked genetic disorder that results in impaired enzyme activity. The G6PD/6PGD ratio assay was routinely used for G6PD deficiency screening in China, but there is an apparent defect of missed diagnosis in heterozygous females. The study aims to explore the means to improve its accuracy. Methods: A total of 4161 Chinese females of childbearing age were collected in this retrospective study. All samples were first subjected to G6PD/6PGD ratio assay and then screened by amplification refractory mutation system PCR (ARMS-PCR) for six hotspot mutants in Chinese population (c.1376G&gt;T, c.1388G&gt;A, c.95A&gt;G, c.1024C&gt;T, c.392G&gt;T, and c.871G&gt;A). For the samples with G6PD/6PGD ratio &lt;1.0 and no mutations were found by ARMS-PCR, next-generation sequencing (NGS) was performed. Sanger sequencing was finally used to verify all the variants. Results: The prevalence of G6PD deficiency in Shenzhen females of childbearing age was 7.31%. The proportion of the six hotspot mutations accounted for 98.03% of all 304 G6PD variants carriers. Taking the ARMS-PCR/NGS results as a reference, the missed diagnosis rate of the G6PD/6PGD ratio assay was 33.88%. Using ARMS-PCR to retest the samples with a G6PD/6PGD ratio between 1.00~1.10 or 1.00~1.15 could reduce the missed diagnosis rate from the original 33.88% to 18.09% or 12.05% separately. Conclusion: ARMS-PCR is an appropriate supplementary method for discovering most carriers missed by the G6PD/6PGD ratio assay.
DOI: 10.6084/m9.figshare.22691170.v2
title: Untitled Item

description: The MIDOG++ dataset represents an extension of the data set used in the MIDOG 2021 and 2022 challenges. We provide region of interest images from 503 histological specimens of seven different tumor types with variable morphology: breast carcinoma, lung carcinoma, lymphosarcoma, neuroendocrine tumor, cutaneous mast cell tumor, cutaneous melanoma, and (sub)cutaneous soft tissue sarcoma. The human and canine samples were processed and stained at different human and veterinary pathology laboratories with standard H&E dye and digitized with different digital whole slide image scanners. We provide labels for 11,937 mitotic figures that have been differentiated against 14,351 imposter cells in a blinded consensus by two pathologists and a final decision by a third pathologist for disagreed labels.
DOI: 10.6084/m9.figshare.28120544.v4
title: China's Provincial Level Expressions of Public Views Indices on Climate Risk and Government Responses on Climate Risk

description: A dataset on China's climate risk public opinion and government response indices in provincial Level, 2011-2023 (excluding data from Hong Kong, Macao, and Taiwan).
DOI: 10.6084/m9.figshare.28501778.v2
title: Datasets for training and testing Daphne, Emerald, Florence, Greece and Hilda Multi-Layer perceptron models

description: Training and testing datasets
DOI: 10.17632/2m2gw7cvs5
title: Prevalence of White Spot Syndrome Virus (WSSV) in wild-caught Indian white shrimp, Fenneropenaeus indicus in the Cuddalore coast, Tamilnadu.

description: The prevalence of asymptomatic WSSV carriers and hosts in the wild. Experimental infectivity studies were used to investigate the infectivity potential of asymptomatic carriers in the transmission of infection of the widely cultured candidate F. indicus. This investigation requires gross observation, light microscopy, histopathology, and molecular diagnosis. Samples were taken from four locations in the Cuddalore district: Vellar estuary, Buckingham canal, Pichavaram mangrove forest, and Uppanar estuary. The white spots on the carapace have a melanized double membrane circular pattern.
DOI: 10.17632/y4vntp5nvx
title: Replication data for: Designing Optimal Macroeconomic Policy Rules under Parameter Uncertainty: A Stochastic Dominance Approach

description: Research data associated with the manuscript:
[1] Górajski, M., Kuchta, Z., 2022, Designing Optimal Macroeconomic Policy Rules under Parameter Uncertainty: A Stochastic Dominance Approach.

This work is supported by the National Science Centre in Poland under Grant No. 2017/26/D/HS4/00942.

It contains all user-defined MATLAB and R functions that implement our algorithms and replicate all results. We group them into seven folders: 
1. main_data
It performs the data preparation process.

2. main_estimation
It estimates 25 versions of the Erceg, Henderson, and Levine (2000) small-scale DSGE model (EHL model). They differ by the monetary policy rule. We consider eight Taylor-type rules (see Table 1) and one nominal GDP targeting rule (H.2) (see Appendix H).

3. main_measuring_uncertainty
It evaluates the MWL and OPFC distributions for all versions of the EHL model.

4. main_compare_losses
It contains the novel EP Bayesian tests for the SDk relations from Section 4.2. We use these tests to compare the MWLs.

5. main_robust_simple_rules
It replicates all Bayesian and min-max robust strategies.

6. main_simulations
It collects all codes that perform the simulations of the EHL model with SDk-optimal and estimated policy rules.

7. main_performance_BayesEP_SDk_tests
It assesses the performance of the EP Bayesian tests for SDk relations.



Abstract
In this paper, we offer a Bayesian decision-theoretic approach to policy evaluation in rational expectation models. First, we show how to correctly assess and rank simple policy rules under the welfare loss minimization criterion in the presence of uncertainty about the model's structural parameters. We consider a Bayesian policymaker that assesses the effectiveness of policy actions, by comparing the distributions of welfare losses using stochastic dominance orderings. Second, we propose a new Bayesian testing procedure to verify higher and infinite degrees of stochastic dominance. Third, we demonstrate a potential use of the suggested approach to a dynamic stochastic general equilibrium model, estimated for the U.S. economy. We show that using stochastic dominance to rank simple monetary policy rules yields different rankings than well-established robust approaches. The contemporaneous monetary policy rule that reacts to inflation and the output gap, with an interest rate smoothing mechanism, minimizes the welfare loss for all decision-makers who admit infinite degree stochastic dominance preferences.
DOI: 10.6084/m9.figshare.11634372.v2
title: Mainland China SSP Population Grids

description: Mainland China SSP Population Grids ~100m (Taiwan, Hong Kong and Macau are nodata regions). To reduce the size, the original population estimates have been formatted in integer type. The 2015 base-year population map has been adjusted using the national statistics of total population. <br> Please cite the following paper if using this dataset: Chen, Y., Li, X., Huang, K., Luo, M., & Gao, M. (2020). High‐resolution gridded population projections for China under the shared socioeconomic pathways. <em>Earth's Future</em>, <em>8</em>(6), e2020EF001491.
DOI: 10.6084/m9.figshare.12501455.v1
title: Sub counties of Kenya based on County Intergrated Development Plans(CIDPS)

description: A geospatial layer of 295 sub-counties in Kenya created by digitizing sub-county maps available for each county from the county integrated development plans (CIDPs)
DOI: 10.6084/m9.figshare.19710724.v1
title: Antimicrobial resistance surveillance report, Sunpasitthiprasong Hospital, Ubon Ratchathani, Thailand, 01 Jan 2020 to 27 Sep 2020 and 23 Jul 2020 to 31 Jan 2021

description: <br> The AMASSplus application is an extension of AMASS Version 1.1 that was released on 12 January 2021. AMASSplus has an additional report (page 38-40) on selected notifiable bacterial diseases.For implementation of AMASSplus at your hospitals in Thailand.The application can be downloaded from https://www.amass.website This is a repository of the files for Sunpasitthiprasong Hospital.The attached seven files are: 1) The two of AMR surveillance report automatically generated from AMASSplus using hospital admission and microbiology data of Sunpasitthiprasong Hospital in Thailand. 2) The two of Aggregated summary data in .csv format automatically generated from AMASSplus 3) The two of Data dictionary for microbiology data file of Sunpasitthiprasong Hospital (configured by the hospital to be used with the AMASSplus application).Export data from M-lab and ALLABIS. 4) Data dictionary for hospital admission data of Sunpasitthiprasong Hospital (configured by the hospital to be used with the AMASSplus application) Please note that the two data dictionary files can be re-used with the data files of the hospital in the future in cases when variables names and values in the raw data remained unchanged.
DOI: 10.6084/m9.figshare.29037140.v1
title: Raman-ChEMBL-part1-db

description: Raman-ChEMBL-part1-db
DOI: 10.6084/m9.figshare.6662999.v1
title: Delay adaptation in VR

description: This dataset includes the experimental data for investigating the effects of visuomotor delay-adaptation on the subjective experiences of virtual reality. The study was approved by the Ethics Committee of the Department of Psychology at the University of Essex prior to data collection. <br>
DOI: 10.6084/m9.figshare.7257179.v1
title: X-ray microtomography images of trabecular bone from the femoral head and condyle of 18 avian, 72 mammalian and one crocodilian species.

description: This is the complete set of X-ray microtomography images used for inter-species trabecular scaling analysis in Doube et al. (2011).<br>Images were produced by scanning whole femoral heads and condyles, or 1 cm cubes cut from femoral heads and condyles, on an X-tek HMX 225 (Tring, UK), with a maximum pixel spacing of 15 µm. MD and JRH collected the specimens; MD cut the cubes; MMK did the imaging with assistance from Richie Abel of NHM London. Full details are included in the paper.<br><br>Images are spatially-calibrated 16-bit tiff stacks that will open readily in ImageJ. They have been compressed with bzip2, so will require decompression prior to loading in image processing software.<br>If you use these data, please cite both this dataset (as required by the CC BY licence) and Doube et al. (2011):<br> Doube M, Kłosowski MM, Wiktorowicz-Conroy AM, Hutchinson JR, Shefelbine SJ. 2011 Trabecular bone scales allometrically in mammals and birds. <i>Proc. R. Soc. B</i> <b>278</b>, 3067–3073. (doi:10.1098/rspb.2011.0069) <br>Between the original study and archiving this set, a small number of images were lost. We have recreated the inner cubes by cropping from the original DICOM data following the study protocol, for:<br>IC deer1 <i>Cervus elaphus</i> red deer, head, condyleUMZC 429p <i>Geococcyx californianus</i> roadrunner head, condyleUMZC h15052 <i>Tragulus ravus</i> lesser mouse deer, head, condyleRVC kent_cheetah <i>Acinonyx jubatus</i> cheetah, head, condyleRVC Przewalski's horse, <i>Equus caballus przewalskii</i> head, condyle<br>File naming follows a convention of:Institution_accessionID_Genus_species_headORcondyle.tif.bz2<br>
DOI: 10.6084/m9.figshare.13359770.v1
title: Dataset Spiketimes and stimulations

description: Recorded neural action potentials and stimulation protocols.
DOI: 10.6084/m9.figshare.19859002.v3
title: High-Yield, Green, and Scalable Production Methods of MOF-303 for Water Harvesting from Desert Air

description: Water vapor sorption data and nitrogen sorption data for MOF-303 synthesized by solvothermal, reflux, vessel and microwave method.
DOI: 10.6084/m9.figshare.20146943.v1
title: G-SchNet for OE62

description: OE62 data set + molecues generated with G-SchNet trained on the OE62 data set.
DOI: 10.6084/m9.figshare.22266361.v1
title: Concatenated alignments

description: Concatenated alignment files.
DOI: 10.6084/m9.figshare.20311167.v1
title: unemployment_data.csv

description: This dataset comprises of unemployment rate and its attributes. It can be used to forecast unemployment rate predictions in various economies.
DOI: 10.6084/m9.figshare.22247161.v1
title: Copy of Mental Health Survey 2021_August 16, 2022_12.33.xlsx

description: Mental health survey data from medical students in all four class cohorts collected during the Spring of 2021. The survey is a modified version of the survey used by Gold et al., 2014 and Young Imposter Syndrome Quiz. The survey was composed of questions about demographics, stress and burnout, imposter syndrome, general and Mental Health/ Health Seeking Behaviors, academic Help Seeking Behaviors, Attitudes to Mental Health, and Personal Health and Coping Behaviors.
DOI: 10.6084/m9.figshare.9633038.v1
title: incident drug embeddings

description: This file contains the embeddings for new (incident) prescriptions of a drug, as described in the paper (Fig 1B)
DOI: 10.17632/5gy6s8trbm
title: Addressing the emergence of drones – a policy development framework for drone transportation systems

description: The articles included in the systematic literature review in this paper are made available.