cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25824/redu/qmx1e8
title: Dados fontes primárias "Almanaques de Campinas" (1872, 1873, 1878, 1879, 1886 e 1888)

description: Dados de atividades econômica urbana em Campinas ao final do século XIX conforme conjunto de documentos históricos (edições para 1872, 1873, 1878, 1879, 1886 e 1888 dos Almanaques de Campinas). Contém categorias para identificação do ano de referência do documento ao qual o dado se refere, categoria do exercício produtivo ou comercial, tipo de atividade/ofício/profissão, nome do(s) proprietário(s) do estabelecimento ou sujeito que exercia a atividade, razão social do estabelecimento (quando há), endereço do estabelecimento ou de onde o sujeito exercia a atividade, e nome fantasia do estabelecimento (quando há). Os dados minerados foram organizados segundo as categorias originais, identificadas nas fontes primárias. A grafia de nomes proprios, nomes de estabelecimentos e razões sociais segundo referido nas fontes primárias mineradas também foi mantida.
DOI: 10.25824/redu/xymhuz
title: Symmetry-based build-up com frequency-based search em PDGDM de proteínas

description: Os códigos disponibilizados pelos autores no GitHub geram progressivamente todos os arquivos e pastas utilizados na parte da pesquisa de doutorado referente ao SBBU (Symmetry-Based Build-Up) dotado da busca FBS (Frequency-Based Search). Contudo, como algumas dessas pastas ocupam uma quantidade significativa de memória — como a pasta que contém os arquivos baixados do PDB (Protein Data Bank), cujo tamanho totaliza 25 gigabytes — os autores decidiram disponibilizar no repositório do GitHub apenas a pasta que contém os dados dos segmentos proteicos, que constitui a informação necessária para efetivamente reproduzir o experimento. Além disso, no mesmo repositório, os autores fornecem um arquivo ".csv" que lista os IDs do PDB de todas as estruturas 3D de proteínas baixadas. Esse projeto no GitHub também disponibiliza a implementação em C++ do algoritmo SBBU, com buscas do tipo DFS e FBS, bem como os códigos em Python utilizados para gerar os gráficos da tese referentes ao SBBU-FBS.
DOI: 10.25824/redu/gitu4g
title: Explorando o potencial de poda dos átomos de hidrogênio no problema do loop fechado

description: Os códigos disponibilizados pelos autores no GitHub contemplam os arquivos das instâncias de estruturas tridimensionais de proteínas baixados do PDB (Protein Data Bank) e na adaptação, em Python, do resolvedor Intervalar Branch-and-Prune (iBP) para os casos de loops de proteínas acrescidos de átomos de hidrogênios. Os resultados computacionais completos utilizados neste artigo também estão disponíveis nas pastas cujos nomes iniciam com "tests_".
DOI: 10.5281/zenodo.17518882
title: Soil health improvement buffers climate risks to global cropland protein production
DOI: 10.5281/zenodo.17518883
title: Soil health improvement buffers climate risks to global cropland protein production
DOI: 10.60534/esr6h-hjx96
title: The effect of FLOWERING LOCUS T1 (FT1) on the barley transcriptome

description: An RNA-sequencing experiment was performed to test how the central flowering time gene FLOWERING LOCUS T1 (FT1) affects gene expression in barley (Hordeum vulgare).
Spring cultivar Golden Promise (GP, carrying a mutated ppd-H1 allele) and its derived introgression line GP fast (wild-type Ppd H1 introgressed into GP from Igri, Gol et al., 2021) were transformed with a CRISPR-Cas9 construct to create plants with a nonfunctional FT1 (HORVU.MOREX.r3.7HG0653910) gene. The wildtypes and the three resulting ft1 KO mutants (ft1.1 and ft1.2 in GP-fast background and ft1.3 in GP background) were cultivated in controlled, flowering-inducing (long-day, 16h of light) growth conditions. Plants were sampled at three developmental stages (onset of spikelet initiation, W2.0; onset of floral development, W3.5; stop of spikelet induction, W5.0; Waddington et al., 1983). Leaf and developing shoot apex (MSA) tissue was sampled to detect changes in gene expression in vegetative and reproductive tissues.
DOI: 10.60534/zdm2e-8zy95
title: The effect of FLOWERING LOCUS T1 (FT1) on the barley transcriptome

description: An RNA-sequencing experiment was performed to test how the central flowering time gene FLOWERING LOCUS T1 (FT1) affects gene expression in barley (Hordeum vulgare).
Spring cultivar Golden Promise (GP, carrying a mutated ppd-H1 allele) and its derived introgression line GP fast (wild-type Ppd H1 introgressed into GP from Igri, Gol et al., 2021) were transformed with a CRISPR-Cas9 construct to create plants with a nonfunctional FT1 (HORVU.MOREX.r3.7HG0653910) gene. The wildtypes and the three resulting ft1 KO mutants (ft1.1 and ft1.2 in GP-fast background and ft1.3 in GP background) were cultivated in controlled, flowering-inducing (long-day, 16h of light) growth conditions. Plants were sampled at three developmental stages (onset of spikelet initiation, W2.0; onset of floral development, W3.5; stop of spikelet induction, W5.0; Waddington et al., 1983). Leaf and developing shoot apex (MSA) tissue was sampled to detect changes in gene expression in vegetative and reproductive tissues.
DOI: 10.34973/edwv-zc88
title: Expert stakeholder perspectives on CCUS deployment enablers and barriers in Europe – Interviews and Group Model Building data

description: This dataset was generated within Task 6.3 of the Horizon 2020 CaLby2030 project (grant number 101075416), which examines the enablers and barriers to carbon capture, utilisation and storage (CCUS) deployment in Europe. The data includes pseudonymised transcripts from ten semi-structured interviews and two Group Model Building workshops involving European experts working on CCUS. Participants represented a range of professional backgrounds across industry, policy, research and civil society.

The dataset also contains the system dynamics models developed during the workshops using Vensim software, together with outputs from exercises conducted with the XLeap facilitation platform. These materials capture how participants collectively mapped key enablers and barriers to CCUS deployment in Europe and how they reasoned about the interactions between technological, policy and societal factors.

The study aimed to provide a better understanding of the enablers and barriers to CCUS deployment and how these factors interact within the wider system. 

All participants provided informed consent to take part in the study and for their pseudonymised interview and workshop transcripts to be shared for future research purposes. Identifiable information has been removed and replaced with codes to protect confidentiality. The dataset does not include any raw audio files or personal data beyond the pseudonymised material described above.

The research was funded by the European Union under the Horizon 2020 Framework Programme. The views expressed are those of the authors and do not necessarily represent those of the European Union, CINEA, or UK Research and Innovation, which also supported the project.
DOI: 10.34973/sjtj-bb39
title: Early prediction of systemic treatment response in advanced non-small cell lung cancer by electronic nose analysis of exhaled breath: a multi-center prospective external validation study

description: The data was collected in the context of a multi-center prospective external validation study that primarily aimed to assess the predictive performance of four previously published electronic nose (eNose) models for predicting treatment response at three months after initiation of immunotherapy monotherapy. The secondary aim of the study was to explore the utility of the four previously published eNose models for predicting treatment response at three months after treatment initiation in patients receiving chemo-immunotherapy or targeted therapy. Patients were recruited at thoracic oncology outpatient clinics of four different treatment centers across the Netherlands between August 2018 and January 2025. Baseline characteristics of the patients are included in the files: "Baseline characteristics immunotherapy monotherapy", "Baseline characteristics chemo-immunotherapy", and "Baseline characteristics targeted therapy". ENose data and survival data of all patients are included in the file "eNose data and survival data of all patients".
DOI: 10.34973/52t4-mg44
title: Losmapimod fase 2 open label study FSHD1

description: This collection contains the full printout of the completed EDC belonging to the paper "An open-label pilot study of losmapimod to evaluate the safety, tolerability, and changes in biomarker and clinical outcome assessments in participants with facioscapulohumeral muscular dystrophy type 1", published in 2024 in the Journal of the neurological sciences by Joost Kools et al.
DOI: 10.34973/vmyf-xr17
title: Galectin-9 regulates dendritic cell polarity and uropod contraction by modulating RhoA activity

description: Adaptive immunity relies on dendritic cell (DC) migration to transport antigens from tissues to lymph nodes. Galectins, a family of β-galactoside–binding proteins, control cell membrane organization, exerting crucial roles in multiple physiological processes. Here, we report a novel mechanism underlying cell polarity and uropod retraction by demonstrating that galectin-9 regulates basal and chemokine-driven DC migration in humans and mice. Galectin-9 depletion caused a defect in RhoA signaling that resulted in impaired cell rear contractility. Mechanistically, galectin-9 interacts with and organizes CD44 at the cell surface, in turn modulating RhoA binding to GEF-H1 and the initiation of downstream signaling. Analysis of DC motility in the 3D tumor microenvironment revealed galectin-9 is also required for DC recruitment and infiltration. Exogenous galectin-9 rescued the motility of tumor-immunocompromised human blood DCs, validating the physiological relevance of galectin-9 in DC migration. Our results identify galectin-9 as a necessary mechanistic component for DC motility by regulating cell polarity and contractility, and underscore its implications for DC-based immunotherapies.

For the data collection, I have included all datasets presented in the manuscript. The files are organized into folders corresponding to each main figure and supplementary figure. Each folder contains a README text file, which explains the contents of the folder, details the types of files included, and provides instructions on how to open them.
DOI: 10.34973/m781-tw13
title: Cell surface interactome analysis identifies TSPAN4 as a negative regulator of PD-L1 in melanoma

description: PD-L1 is a key immune checkpoint ligand that suppresses anti-tumor immunity by engaging PD-1 on T cells. While therapeutic blockade of PD-L1/PD-1 interactions has shown clinical benefit, many patients fail to respond, indicating modulation by other factors. Here, we identified a novel regulatory axis in which the membrane-organizing protein Tetraspanin-4 (TSPAN4) modulates PD-L1 in melanoma cells. Using cell surface proximity biotinylation coupled with mass spectrometry, we discovered that TSPAN4 physically associates with PD-L1, with both proteins colocalizing on migrasomes and retraction fibers. Mechanistically, we show that TSPAN4 negatively regulates PD-L1 protein levels by enhancing its degradation and restricting its lateral mobility at the plasma membrane. Loss of TSPAN4 stabilized PD-L1, promoted its interaction with CMTM6, and increased PD-L1 surface availability for PD-1 binding. Functionally, TSPAN4 knockdown in melanoma cells led to more efficient immune checkpoint blockade through PD-1 on T cells. This study identifies TSPAN4 as a negative regulator of PD-L1 at the cell surface of melanoma cells suggesting that targeting TSPAN4 may offer a new therapeutic strategy to enhance immune checkpoint blockade in melanoma and other cancers. For the data collection, I have included all datasets presented in the manuscript. The files are organized into folders corresponding to each main figure and supplementary figure. Each folder contains a README text file, which explains the contents of the folder, details the types of files included, and provides instructions on how to open them.
DOI: 10.34973/nh8z-e483
title: Oral health-related quality of life and dental treatment need 5 to 10 years after hematopoietic cell transplantation

description: This study investigates patient-reported oral health-related quality of life 5 to 10 years after hematopoietic cell transplantation (HCT), and its association with type of HCT and dental treatment needs. All adult post- autologous or allogeneic HCT survivors treated at the Radboud university medical center, Nijmegen, The Netherlands between 2012 and 2017 were invited for this research. Patients who were already enrolled in the prospective ORASTEM/HOME-(2) study were excluded. Eligible patients were contacted by telephone to obtain informed consent and to confirm their current address. Patients who not gave informed consent or were unattainable after multiple calls were excluded. 
Oral health-related quality of life was determined using the OHIP-14, Summated XI, OES and the first nine questions of the MFIQ questionnaires. These questionnaires were sent on paper to all patients between June 2023 and October 2023. No reminders were sent. With the questionnaires, all patients were also sent a form where they could fill in their current dentist and give consent to obtain dental records of their dentist. After consent, the dental records were asked from their treating dentist. In case of no response from the dental office, a reminder was sent after a few weeks. 
From the dental records the number of natural teeth, excluding third molars, around the date of answering the questionnaires were determined. Counting from the HCT date, the number of years with dental visits was determined from the dental records. A year was included only if entries for routine check-ups or oral hygiene sessions were present; otherwise, that year was not counted as visited the dentist. The number of restorations and extractions were noted in the period from 7 years before HCT (excluding the year before HCT) to 10 years after HCT. For restorations the billing-codes V15, V71, V72, V73, V74, V81, V82, V83, V84, V91, V92, V93 and V94 were counted. For extractions the billing-codes H11, H16 and H35 were counted and the files were searched for mentions of referrals to an oral surgeon, to include also the more complicated extractions performed by the oral surgeon. Extractions or restorations performed in third molars were excluded.
DOI: 10.34973/vx39-8972
title: Radboudumc datasets concerning computer-aided detection in colonoscopy

description: This collection contains the pseudonymized datasets underlying two international multicenter studies evaluating computer-aided detection (CADe) in colonoscopy. The studies assessed the effect of CADe on polyp detection and colonoscopy quality indicators in patients undergoing diagnostic, screening, and surveillance colonoscopy.

The first study is a randomized controlled trial evaluating CADe-assisted colonoscopy compared to conventional colonoscopy in an everyday clinical setting (Discovery II). The second study evaluated the effect of combining a mucosal exposure device (MED) with CADe on detection outcomes in a multicenter cohort compared to the historical CADe controls (Discovery III).

The collection includes colonoscopy-level datasets for both studies, along with SPSS and R scripts used for data preparation and statistical analyses. Variables cover patient demographics, colonoscopy indication, procedural characteristics, polyp detection and histopathology outcomes, and CADe-related detection parameters. Detailed study design and methods are described in the associated publications.
DOI: 10.5281/zenodo.17950741
title: Spatial optimization of integrated crop management can increase relative global phosphorus use efficiency by 40%

description: This repository contains the data and code supporting the analyses presented in this study on global phosphorus use efficiency (PUE). The data component comprises a harmonized global field dataset of phosphorus inputs, crop outputs, and associated climate, soil and management variables collected across major cropping systems.
DOI: 10.5281/zenodo.17950742
title: Spatial optimization of integrated crop management can increase relative global phosphorus use efficiency by 40%

description: This repository contains the data and code supporting the analyses presented in this study on global phosphorus use efficiency (PUE). The data component comprises a harmonized global field dataset of phosphorus inputs, crop outputs, and associated climate, soil and management variables collected across major cropping systems.
DOI: 10.34973/0zfe-x827
title: More than just "Uh, was?": Strengthening communicative competence through plurilingual strategies in the school subject German: Study 1 + 2

description: During a school exchange, pupils from the Netherlands and from Germany prepared a presentation in plurilingual groups. There were 27 Dutch pupils (vwo5) and 20 German pupils (Gymnasium, Klasse 11) with B1 level in the neighbouring language. They made a linguistic landscape of the university building and had to show three interesting pictures. The conversations they had whilst preparing their presentations were recorded with Philips DVT3500 recording devices. The pupils didn't get any language instructions and so they used several languages from their language repertoire (for example Dutch, German, English, Spanish, Dutch dialect (Limburgs)). There are twelve conversations with an average length of 43,20 minutes. This amounts to a total of 518,43 minutes. The conversations were recorded on two separate occasions, one in 2018 (conversations 1-6, 16 Dutch and 11 German pupils) and one in 2023 (conversations 7-12, 11 Dutch and 11 German pupils). These conversations are transcribed according to a simplified version of HIAT. This dataset contains the transcripts of the conversations. Each conversation is transcribed in a separate .txt file. Due to privacy restrictions the audio files are not available.
DOI: 10.34973/pjxv-c602
title: Radboudumc dataset concerning recurrence after piecemeal endoscopic mucosal resection

description: This collection contains the pseudonymized datasets and analysis code underlying the associated publication. The study evaluated recurrence rates, post-EMR scar identification, and associated factors at early surveillance colonoscopy, as well as subsequent surveillance outcomes, following piecemeal endoscopic mucosal resection (pEMR) performed between 2014 and 2021 in five Dutch hospitals.

The collection includes two pseudonymized tabular datasets, along with SPSS and R scripts used for data preparation and statistical analyses. Variables cover patient demographics, lesion and procedural characteristics, early surveillance colonoscopy findings, and follow-up outcomes.

Detailed study design, methods and results are described in the associated publication.
DOI: 10.34973/xs2b-v018
title: Serological response patterns to assess treatment outcomes  in advanced non-small cell lung cancer

description: This data was collected in the context of our real-world exploratory multi-center cohort study that aimed to determine which STM dynamics recur during treatment in advanced non-small cell lung cancer (NSCLC) patients with disease control three months after start with immune checkpoint inhibitor (ICI)-containing treatment and to explore whether these dynamics retain information on treatment outcomes. Between March 2013 and January 2023, 256 patients were included at two thoracic oncology outpatient clinics in The Netherlands (e.g. the Radboudumc, Nijmegen, The Netherlands, and the Netherlands Cancer Institute, Amsterdam, The Netherlands). In the "Patient characteristics" file, clinincal and tumor characteristics, including survival data, of all included patients can be found. In the "Patient serum tumor marker data" file, serum tumor marker data of all included patients can be found.
DOI: 10.34973/t441-vw82
title: Transformative Landscape Governance

description: This data was gathered for the purpose of the project "Transformative landscape governance", in which we studied the role of landscape-oriented partnerships in transformative change for biodiversity worldwide and in two cases in the Netherlands. The data consists of a literature review, a q-methodology study, a discourse analysis and an amplification analysis of so-called 'seeds'. The data was gathered between 2021 and 2025 in the Netherlands. As most of the data contains qualitative data with personal details, this database mainly contains the policy documents that were analyzed, as well as the quantitative data of the q-methodology study.
DOI: 10.34973/t28y-ys13
title: Dynamic computed tomography assessment of patellofemoral and tibiofemoral kinematics before and after total knee arthroplasty: A pilot study

description: Description:
This dataset contains derived tibiofemoral (TF) and patellofemoral (PF) kinematic measurements from a prospective clinical study conducted at Radboud University Medical Center. The study investigated knee joint kinematics before and after total knee arthroplasty (TKA) using a dynamic computed tomography (CT) protocol capable of capturing continuous in vivo motion.

Study design:
Eleven patients with primary knee osteoarthritis scheduled for cemented TKA were enrolled. Each participant underwent both static and dynamic CT scanning preoperatively and one year postoperatively. Due to missing postoperative data for one participant, ten participants were included in the final analysis. During dynamic scans, participants performed a flexion–extension–flexion movement, enabling six degree of freedom analysis of knee joint motion.
                           

Content of this dataset:
This dataset contains derived patellofemoral (PF) and tibiofemoral (TF) kinematic values obtained during the extension phase of the dynamic CT scans.
Kinematics were computed using anatomical coordinate systems that were defined on the preoperative bone models. The same coordinate systems were used postoperatively. Rotations were calculated using an intrinsic Z–X–Y Euler sequence. Translations were computed relative to the femoral coordinate system.

Intended use:
This collection allows researchers to inspect and reuse the underlying kinematic values associated with the figures in the published article. The dataset is intended for readers who have consulted the accompanying manuscript and wish to explore the quantitative results in more detail.

Not included in this dataset:
•	Participant characteristics
•	CT scans
•	Segmentation masks
•	3D bone or implant surface meshes
•	Analysis scripts
These files are archived on the department server and are available upon request to the research team, provided the requests meet the conditions for sharing the data as described in the signed informed consent.
DOI: 10.34973/r1j1-2x76
title: Deep Learning Based Detection and Segmentation of Liver Trauma from Computed Tomography Images

description: This repository contains data for the study "Deep Learning Based Detection and Segmentation of Liver Trauma from Computed Tomography Images". This pilot study aimed to evaluate the performance of a deep learning model in the detection of liver injury as a first step in the development of an automated assessment system.

This collection stores the final model weights, code necessary to run said model and some imaging samples to verify its operation.
DOI: 10.25824/redu/da8qux
title: Replication data for: Dados relativos à sistematização de informações sobre conselhos de cinema no Brasil

description: Três conjuntos de dados, relativos à sistematização de informações da pesquisa. O primeiro sobre as características do GEICINE em comparação com o projeto do INC criado pelo GEICINE; o segundo com as funções comparativas dos conselhos deliberativo e consultivo do INC; e o terceiro com dados sobre o Conselho Superior de Cinema.