2026-06-12T19:30:40Z https://www.fdr.uni-hamburg.de/oai2d

oai:fdr.uni-hamburg.de:12692 2023-07-10T07:19:36Z user-sfb936 user-uke user-uhh

Haaf, Moritz 2023-07-10 The dataset consists of single trial EEG data that was recorded from 24 participants during the performance of an auditory choice reaction task. Each participant completed the recording on separate days during the infusion of placebo (0-0) or sub-anesthetic ketamine (0-1). Type of data: EEG single trial ASCII data (64 channels, extended 10-20 system) 1000 Hz sampling rate What is the question/hypothesis behind the dataset? To test whether ketamine reduces the auditory evoked gamma response Which paradigm has been used? Cognitively demanding auditory choice reaction task (3 tones, 2 answers) S1 (800 Hz) and S3 (1200 Hz) markers code for target tone presentation S2 (1000 Hz) is the marker coding for the non-target tone S101 (for S1) and S103 (for S 3) are the response markers Which methods have been applied so far to analyse the dataset? Time-frequency analysis (focus on 40 Hz), phase locking factor, sLORETA source localization The dataset is described in more detail in the following publication: https://doi.org/10.1016/j.neuroimage.2022.119004 https://www.fdr.uni-hamburg.de/record/12692 10.25592/uhhfdm.12692 oai:fdr.uni-hamburg.de:12692 eng doi:10.25592/uhhfdm.12691 info:eu-repo/semantics/restrictedAccess The ketamine model of schizophrenia: EEG single trial data during an auditory choice reaction task info:eu-repo/semantics/other dataset

oai:fdr.uni-hamburg.de:14631 2024-08-26T09:38:55Z user-uke user-uhh

Lübbert, Annika Sengelmann, Malte Heimann, Katrin Schneider, Till R. Engel, Andreas K. Göschl, Florian 2024-07-08 To investigate the embodied, distributed and hence dynamically unfolding nature of social cognitive capacities, we present a novel laboratory-based coordination task: the BallGame. Our paradigm requires continuous sensing and acting between two players who jointly steer a virtual ball around obstacles towards as many targets as possible. Scripts and preprocessed behavioural data to conduct the main analyses (MANOVA and regression) published in: Lübbert A, Sengelmann M, Heimann K, Schneider TR, Engel AK, Göschl F. (2024) Predicting social experience from dyadic interaction dynamics: the BallGame, a novel paradigm to study social engagement. Scientific Reports 14, 19666. DOI: https://doi.org/10.1038/s41598-024-69678-9. Published open access: https://rdcu.be/dRWQV Data was collected at the Institute of Neurophysiology and Pathophysiology, University Medical Center Hamburg-Eppendorf, Germany, in 2019. The experiment involved twenty-three pairs of participants who played 60 one-minute trials of the ‘BallGame’, an interpersonal coordination task in which two players steer a virtual ball on a 2D surface around obstacles towards as many targets as possible by bending and flexing their index fingers. Participants played this game under three different conditions: (1) individual play: participants see the same six of nine active obstacles but play on separate landscapes (each steering their own ball), (2) joint play SAME: participants steer a shared ball, both of them see the same six of the nine active obstacles, and three obstacles remain invisible to both; and (3) joint play DIFF: participants steer a shared ball, three obstacles are visible to both players, three only to the first and three only to the second player. We used a blocked experimental design: first 10 trials of individual play, then 10 trials of either joint play SAME or DIFF (counter-balanced across pairs), followed by 10 trials of the other joint play condition. After a break, participants again completed 20 trials of joint play and 10 trials of individual play. During the trial, we measured finger movement, ball position, target collection and obstacle collision events (as well as eye movement, EEG). After every 3-4 trials, we asked participants to rate their level of engagement, agreement and predictability. After the game we conducted individual interviews with participants. https://www.fdr.uni-hamburg.de/record/14631 10.25592/uhhfdm.14631 oai:fdr.uni-hamburg.de:14631 eng info:eu-repo/grantAgreement/EC/H2020/641321/ doi:10.25592/uhhfdm.14630 info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/legalcode Scientific Reports 14 19666 social cognition dyadic interaction embodiment sensory motor contingencies Predicting social experience from dyadic interaction dynamics: the BallGame, a novel paradigm to study social engagement info:eu-repo/semantics/other dataset

oai:fdr.uni-hamburg.de:17620 2025-06-18T11:59:11Z user-uke user-uhh

Maack, Marike Christiane Ostrowski, Jan Rose, Michael 2025-06-16 The state of neural dynamics prior to the presentation of an external stimulus significantly influences its subsequent processing. The integration of stimuli across different sensory modalities is a fundamental mechanism underlying the formation of episodic memories. However, the causal role of pre-stimulus neural activity in this process remains largely unclear. In this preregistered study, we investigate the direct relationship between transient brain states induced by sensory entrainment and crossmodal memory encoding. Participants (n = 105) received rhythmic visual stimuli at theta (5 Hz) or alpha (9 Hz) frequencies to evoke specific brain states. EEG recordings confirmed successful entrainment, with sustained increases in neural activity within the stimulated frequency bands persisting until stimulus onset. Notably, induced alpha oscillatory activity enhanced recognition memory performance reflected by increased sensitivity, and suggesting that alpha oscillations prepare the brain for optimal multisensory integration. These findings highlight the functional significance of distinct oscillatory brain states in facilitating memory encoding by increasing cortical excitability before stimulus presentation. Overall, our results emphasize the importance of pre-stimulus brain states in shaping the efficiency of memory formation across sensory modalities and shed light on how dynamic neural preparations support learning. https://www.fdr.uni-hamburg.de/record/17620 10.25592/uhhfdm.17620 oai:fdr.uni-hamburg.de:17620 eng doi:10.25592/uhhfdm.17619 info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/legalcode Pre-Stimulus Entrainment, Visual Sensory Stimulation, Crossmodal Learning, Associative Memory Formation Disentangling the Functional Roles of Pre-Stimulus Oscillations in Crossmodal Associative Memory Formation via Sensory Entrainment info:eu-repo/semantics/preprint publication-preprint

oai:fdr.uni-hamburg.de:11943 2023-10-04T08:33:25Z user-uke

Louis Bellmann Alexander Johannes Wiederhold Leona Trübe Frank Ückert Karl Gottfried 2023-03-30 This dataset capures statistical analysis of the HCHS cohort study with knowledge graphs and dashboards. Properties of 10,000 participants were analyzed for their association with cardiovascular and cancer disease as well as for their relationships among each other. The data is presented in the form of Neo4J database dumps and can be explored following the given user guide. https://www.fdr.uni-hamburg.de/record/11943 10.25592/uhhfdm.11943 oai:fdr.uni-hamburg.de:11943 eng doi:10.25592/uhhfdm.11942 info:eu-repo/semantics/closedAccess Knowledge Graphs Cohort Studies Data Visualization Big Data HCHSGraphXplore: Visualizing Complex Medical Data with Knowledge Graphs info:eu-repo/semantics/other dataset

oai:fdr.uni-hamburg.de:14226 2024-08-22T06:25:24Z user-uke user-uhh

Nicola Wanner Nastassia Liaukouskaya Sydney E. Gies Geoffroy Andrieux Tobias B. Huber 2027-01-01 Low nephron endowment constitutes a risk factor for hypertension and renal disease. Epigenetic regulation is crucial for nephron progenitor cell differentiation, impacting nephron number and renal function. The role of many epigenetic modulators, such as Lysine-specific histone demethylase 1a (LSD1), remains unclear. We used Lsd1 knockout mice to demonstrate that Lsd1 depletion in nephron progenitor cells results in reduced kidney size in neonates and leads to glomerulosclerosis, proteinuria, and renal cysts in adults. Notably, LSD1 deletion in podocytes or tubular cells did not replicate these effects. CRISPR/Cas9-mediated LSD1 deletion in human kidney organoids caused cyst formation and altered gene expression, with snRNA-seq revealing downregulation of podocyte genes and upregulation of metabolic genes. The presence of non-coding RNAs indicates roles in cell proliferation. Our study reveals the critical role of LSD1 function in nephron development and highlights its impact on transcriptional programming for long-term renal function and susceptibility to cyst formation. https://www.fdr.uni-hamburg.de/record/14226 10.25592/uhhfdm.14226 oai:fdr.uni-hamburg.de:14226 doi:10.25592/uhhfdm.14225 info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/legalcode Lysine-specific histone demethylase 1a regulates nephron development and long-term transcriptional programming info:eu-repo/semantics/other dataset

oai:fdr.uni-hamburg.de:17691 2025-07-08T11:52:11Z user-uke user-uhh

Wimmert, Lukas Madesta, Frederic Gauer, Tobias Werner, Rene 2024-03-27 This SQLite-based database contains 2,510 respiratory signals from 419 patients (total acquisition time > 90 hours) with thoracic lesions treated between February 2013 and May 2022 at the Clinic of Radiotherapy and Radiation Oncology of the University Medical Center Hamburg-Eppendorf. We believe this comprehensive dataset is of high value to the radiotherapy community as well as to researchers working on time-series analysis tasks such as forecasting and classification. Open access to these retrospectively collected and anonymized respiratory signals was approved by the local ethics board, with the need for written informed consent waived [2023-300334-WF]. Usage Please refer to the corresponding GitHub repository for data reading and preprocessing functionalities. Additionally, review the provided README to understand the database structure. We recommend using DB Browser for SQLite as a convenient tool for browsing the database. Data All respiratory signals were recorded in the course of radiotherapy treatment. Signals were acquired using the Varian RPM System during: - 4D CT imaging (sampling rate: 25 Hz) - 4D CBCT imaging (66 Hz) - Dose delivery (66 Hz) The Varian RPM System monitors an external marker block placed on the patient’s chest wall with an infrared camera. From the obtained marker block signal, only the one-dimensional signal component representing the vertical displacement (anterior-posterior) of the chest wall is considered, resulting in univariate time series. All patients breathed freely during acquisition without visual guidance or coaching. Please also refer to the provided acquisition and example images for additional context. Citation If you use this database, please also cite the underlying publication: @article{wimmert2024benchmarking, doi={10.1002/mp.17038} title={Benchmarking machine learning-based real-time respiratory signal predictors in 4D SBRT}, author={Wimmert, Lukas and Nielsen, Maximilian and Madesta, Frederic and Gauer, Tobias and Hofmann, Christian and Werner, Rene}, journal={Medical Physics}, year={2024}, publisher={Wiley Online Library} } https://www.fdr.uni-hamburg.de/record/17691 10.25592/uhhfdm.17691 oai:fdr.uni-hamburg.de:17691 doi:10.1002/mp.17038 doi:10.25592/uhhfdm.17690 info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/legalcode Medical Physics 51(5) 3173-3183 univariate time-series, radiotherapy, free-breathing RespDB - A Respiratory Signal Database info:eu-repo/semantics/other dataset

oai:fdr.uni-hamburg.de:14189 2025-07-18T11:52:54Z user-uhh user-uke

Alexander Johannes Wiederhold Qi Rui Zhu Sören Spiegel Adrin Dadkhah Monika Pötter-Nerger Claudia Langebrake Frank Ückert Christopher Gundler 2024-04-11 Code for replication of our achieved results reported in the manuscript "Opportunities and limitations of wrist-worn devices for dyskinesia detection in Parkinson’s disease". https://www.fdr.uni-hamburg.de/record/14189 10.25592/uhhfdm.14189 oai:fdr.uni-hamburg.de:14189 doi:10.25592/uhhfdm.14188 info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/legalcode Parkinson's disease Dyskinesia Wearable devices Semantic movement features tsfresh Opportunities and limitations of wrist-worn devices for dyskinesia detection in Parkinson's disease info:eu-repo/semantics/other software

oai:fdr.uni-hamburg.de:11224 2023-04-13T06:57:30Z user-uke user-uhh

Kylies, Dominik Zimmermann, Marina Haas, Fabian Schwerk, Maria Kuehl, Malte Brehler, Michael Czogalla, Jan Hernandez, Lola C. Konczalla, Leonie Okabayashi, Yusuke Menzel, Julia Edenhofer, Ilka Mezher, Sam Aypek, Hande Dumoulin, Bernhard Wu, Hui Hofmann, Smilla Kretz, Oliver Wanner, Nicola Tomas, Nicola M. Krasemann, Susanne Glatzel, Markus Kuppe, Christoph Kramann, Rafael Banjanin, Bella Schneider, Rebekka K. Urbschat, Christopher Arck, Petra Gagliani, Nicola van Zandvoort, Marc Wiech, Thorsten Grahammer, Florian Sáez, Pablo J. Wong, Milagros N. Bonn, Stefan Huber, Tobias B, Puelles, Victor G. 2023-04-10 Expansion microscopy physically enlarges biological specimens to achieve nanoscale resolution using diffraction-limited microscopy systems. However, optimal performance is usually reached using laser-based systems (for example, confocal microscopy), restricting its broad applicability in clinical pathology, as most centres have access only to light-emitting diode (LED)-based widefield systems. As a possible alternative, a computational method for image resolution enhancement, namely, super-resolution radial fluctuations (SRRF), has recently been developed. However, this method has not been explored in pathology specimens to date, because on its own, it does not achieve sufficient resolution for routine clinical use. Here, we report expansion-enhanced super-resolution radial fluctuations (ExSRRF), a simple, robust, scalable and accessible workflow that provides a resolution of up to 25 nm using LED-based widefield microscopy. ExSRRF enables molecular profiling of subcellular structures from archival formalin-fixed paraffin-embedded tissues in complex clinical and experimental specimens, including ischaemic, degenerative, neoplastic, genetic and immune-mediated disorders. Furthermore, as examples of its potential application to experimental and clinical pathology, we show that ExSRRF can be used to identify and quantify classical features of endoplasmic reticulum stress in the murine ischaemic kidney and diagnostic ultrastructural features in human kidney biopsies. https://www.fdr.uni-hamburg.de/record/11224 10.25592/uhhfdm.11224 oai:fdr.uni-hamburg.de:11224 eng doi:10.25592/uhhfdm.11223 info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/legalcode Expansion-enhanced super-resolution radial fluctuations enable nanoscale molecular profiling of pathology specimens info:eu-repo/semantics/other dataset

oai:fdr.uni-hamburg.de:12136 2023-10-04T08:33:25Z user-uke

Louis Bellmann Alexander Johannes Wiederhold Leona Trübe Raphael Twerenbold Frank Ückert Karl Gottfried 2023-05-04 This dataset capures statistical analysis of the HCHS cohort study using a knowledge graph and dashboard. Properties of 10,000 participants were analyzed for their association with cardiovascular disease as well as for their relationships among each other. The data is presented in the form of Neo4J database dumps and can be explored following the given user guide. https://www.fdr.uni-hamburg.de/record/12136 10.25592/uhhfdm.12136 oai:fdr.uni-hamburg.de:12136 eng doi:10.25592/uhhfdm.11942 info:eu-repo/semantics/closedAccess Knowledge Graphs Cohort Studies Data Visualization Big Data HCHSGraphXplore: Visualizing Complex Medical Data with Knowledge Graphs info:eu-repo/semantics/other dataset

oai:fdr.uni-hamburg.de:13783 2023-11-28T21:00:49Z user-uke user-uhh

Krenz, Valentina Alink, Arjen Roozendaal, Benno Sommer, Tobias Schwabe, Lars 2023-11-23 This repository includes fmri and behavioral data for the manuscript "Memory boost for recurring emotional events is driven by initial amygdala response and stable neocortical patterns across encoding repetitions" behav.7z includes all behavioral data fmri_raw-sj-*.7z includes all raw images of the corresponding subject (note that for technical reasons, all subject folders were uploaded individually; the content of each subject's folder includes raw fmri data in BIDS format) fmri_processed-sj-*.7z includes the processed fmri images for the corresponding subject fmri_paramExtr.7z includes extracted univariate and multivariate fmri data All custom code to model and analyze the data is available at https://github.com/valentinakrenz/recurrentEmotionalMemoryEncoding https://www.fdr.uni-hamburg.de/record/13783 10.25592/uhhfdm.13783 oai:fdr.uni-hamburg.de:13783 doi:10.25592/uhhfdm.13782 info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/legalcode Memory boost for recurring emotional events is driven by initial amygdala response and stable neocortical patterns across encoding repetitions info:eu-repo/semantics/other dataset

oai:fdr.uni-hamburg.de:16914 2026-06-10T09:20:41Z user-uke user-uhh user-sfb1328

Lohr, David Werner, René 2025-02-27 The dataset contains the second of two processed open-source datasets used in the Github repository: https://github.com/IPMI-ICNS-UKE/AIMD.AI-for-microscopy-denoising The AIMD Github repository is demonstrating the use of open-source microscopy data for deep learning based image denoising and transfer learning as showcased in: Lohr, D., Meyer, L., Woelk, LM., Kovacevic, D., Diercks, BP., Werner, R. (2025). Deep Learning-Based Image Restoration and Super-Resolution for Fluorescence Microscopy: Overview and Resources. In: Diercks, BP. (eds) T Cell Activation. Methods in Molecular Biology, vol 2904. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-4414-0_3 The original open-source data is from "Fluorescence Microscopy Datasets for Training Deep Neural Networks" - CC0 license • http://gigadb.org/dataset/view/id/100888 • 16 bit image data, filetype: tif https://www.fdr.uni-hamburg.de/record/16914 10.25592/uhhfdm.16914 oai:fdr.uni-hamburg.de:16914 eng Humana doi:10.25592/uhhfdm.16913 info:eu-repo/semantics/openAccess https://creativecommons.org/publicdomain/zero/1.0/legalcode Microscopy, Denoising, Artificial Intelligence, Deep learning AIMD. AI for microscopy denoising - dataset 2 info:eu-repo/semantics/other dataset

oai:fdr.uni-hamburg.de:12762 2023-07-11T12:09:40Z user-uhh user-uke user-sfb936

Martin A. Horn Alessandro Gulberti Ute Hidding Christian Gerloff Wolfgang Hamel Christian K. E. Moll Monika Pötter-Nerger 2023-07-11 Background: The Parkinsonian [i.e., Parkinson's disease (PD)] gait disorder represents a therapeutical challenge with residual symptoms despite the use of deep brain stimulation of the subthalamic nucleus (STN DBS) and medical and rehabilitative strategies. The aim of this study was to assess the effect of different DBS modes as combined stimulation of the STN and substantia nigra (STN+SN DBS) and environmental rehabilitative factors as footwear on gait kinematics. Methods: This single-center, randomized, double-blind, crossover clinical trial assessed shod and unshod gait in patients with PD with medication in different DBS conditions (i.e., STIM OFF, STN DBS, and STN+SN DBS) during different gait tasks (i.e., normal gait, fast gait, and gait during dual task) and compared gait characteristics to healthy controls. Notably, 15 patients participated in the study, and 11 patients were analyzed after a dropout of four patients due to DBS-induced side effects. Results: Gait was modulated by both factors, namely, footwear and DBS mode, in patients with PD. Footwear impacted gait characteristics in patients with PD similarly to controls with longer step length, lower cadence, and shorter single-support time. Interestingly, DBS exerted specific effects depending on gait tasks with increased cognitive load. STN+SN DBS was the most efficient DBS mode compared to STIM OFF and STN DBS with intense effects as step length increment during dual task. Conclusion: The PD gait disorder is a multifactorial symptom, impacted by environmental factors as footwear and modulated by DBS. DBS effects on gait were specific depending on the gait task, with the most obvious effects with STN+SN DBS during gait with increased cognitive load. https://www.fdr.uni-hamburg.de/record/12762 10.25592/uhhfdm.12762 oai:fdr.uni-hamburg.de:12762 eng url:https://www.frontiersin.org/articles/10.3389/fnhum.2021.751242/full doi:10.25592/uhhfdm.12761 info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/legalcode Frontiers in Human Neuroscience 15 barefoot, shoes, gait, deep brain stimulation, subthalamic nucleus, substantia nigra, Parkinson's disease Comparison of Shod and Unshod Gait in Patients With Parkinson's Disease With Subthalamic and Nigral Stimulation info:eu-repo/semantics/other dataset

oai:fdr.uni-hamburg.de:13720 2024-04-22T06:22:52Z user-uhh user-uke

Christopher Lukas Gundler 2023-11-16 The individual error scores for different pupil detection algorithms as reported in the manuscript "Improving eye-tracking data quality: A framework for reproducible evaluations of detection algorithms" https://www.fdr.uni-hamburg.de/record/13720 10.25592/uhhfdm.13720 oai:fdr.uni-hamburg.de:13720 doi:10.25592/uhhfdm.13719 info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/legalcode Improving eye-tracking data quality: A framework for reproducible evaluations of detection algorithms info:eu-repo/semantics/article publication-article

oai:fdr.uni-hamburg.de:17120 2025-03-25T14:30:11Z user-uke user-uhh

Maack, Marike Christiane Ostrowski, Jan Rose, Michael 2025-03-24 The ability of the human brain to encode and recognize sequential information from different sensory modalities is key to memory formation. The sequence in which these modalities are presented during encoding critically affects recognition. This study investigates the encoding of sensory modality sequences and its neural impact on recognition using multivariate pattern analysis (MVPA) of oscillatory EEG activity. We examined the reinstatement of multisensory episode-specific sequences in n = 32 participants who encoded sound-image associations (e.g., the image of a ship with the sound of a frog). Images and sounds were natural scenes and 2-second real-life sounds, presented sequentially during encoding. During recognition, stimulus pairs were presented simultaneously, and classification was used to test whether the modality sequence order could be decoded as a contextual feature in memory. Oscillatory results identified a distinct neural signature during successful retrieval, associated with the original modality sequence. Furthermore, MVPA successfully decoded neural patterns of different modality sequences, hinting at specific memory traces. These findings suggest that the sequence in which sensory modalities are encoded forms a neural signature, affecting later recognition. This study provides novel insights into the relationship between modality encoding and recognition, with broad implications for cognitive neuroscience and memory research. https://www.fdr.uni-hamburg.de/record/17120 10.25592/uhhfdm.17120 oai:fdr.uni-hamburg.de:17120 doi:10.25592/uhhfdm.17119 info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/legalcode The order of multisensory associative sequences is reinstated as context feature during successful recognition info:eu-repo/semantics/article publication-article

oai:fdr.uni-hamburg.de:13995 2025-09-04T09:35:17Z user-uke user-uhh

Christopher Gundler Alexander Wiederhold Monika Pötter-Nerger 2025-09-04 Trained weights and scores for replicating our manuscript "Learning from Healthy Subjects for Clinical Routine? Assessing the Generalizability of Foundation Models for the Recognition of Motor Examinations in Parkinson’s Disease" https://www.fdr.uni-hamburg.de/record/13995 10.25592/uhhfdm.13995 oai:fdr.uni-hamburg.de:13995 doi:10.25592/uhhfdm.13994 info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/legalcode Assessing the Generalizability of Foundation Models for the Recognition of Motor Examinations in Parkinson's Disease info:eu-repo/semantics/other dataset

oai:fdr.uni-hamburg.de:17971 2025-12-01T17:15:59Z user-uke user-uhh

Mayer, Leonie 2025-11-24 Abstract MVA-MERS-S, a vaccine candidate against Middle East respiratory syndrome (MERS), was recently evaluated in a randomized, placebo-controlled, double-blind phase 1b clinical trial to assess its safety, immunogenicity, and optimal dosing in healthy adults in Hamburg and Rotterdam. A three-dose regimen was safe and elicited robust spike-specific antibody responses. We extended this trial to assess the two-year durability of MERS-CoV-specific antibody and T cell responses in 48 study participants of the Hamburg cohort. Our findings show that immune responses remain detectable for at least 24 months after the third vaccination. Antibodies persisted at levels comparable to the peak response observed after the second vaccination and were able to cross-neutralize MERS-CoV spike mutants. Although the immune correlates of protection against MERS remain unknown, the observed durability of humoral and cellular immune responses supports the potential of MVA-MERS-S as a promising MERS vaccine candidate and highlights the importance of a booster dose in sustaining long-term immunity. https://www.fdr.uni-hamburg.de/record/17971 10.25592/uhhfdm.17971 oai:fdr.uni-hamburg.de:17971 doi:10.25592/uhhfdm.17970 info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/legalcode Nature Communications vaccine Modified Vaccinia virus Ankara Middle East respiratory sydrome coronavirus immunogenicity Two-year persistence of MERS-CoV-specific antibody and T cell responses after MVA-MERS-S vaccination in healthy adults info:eu-repo/semantics/other dataset

oai:fdr.uni-hamburg.de:137 2019-07-08T14:44:04Z user-uke

Frye, Maike 2018-04-17 Global transcriptome analysis showed that human lymphatic endothelial cells (LECs) grown on a soft matrix exhibit increased GATA2 expression, concomitant with a GATA2-dependent upregulation of genes involved in cell migration and lymphangiogenesis, including the key lymphangiogenic growth factor receptor VEGFR3. Affymetrix GeneChip analysis revealed regulation of 2771 transcripts above or below a 1.4-fold change (log2 fold change >0.5 or <-0.5) threshold on soft versus stiff matrices. Moreover, 406 (27%) of the 1485 transcripts that were increased and 207 (16 %) of the 1286 transcripts that were decreased on soft matrix were regulated in a GATA2 dependent manner. Overall design: In total 18 samples were analyzed (first biological replicate is uploaded here). To identify differentially expressed genes between the ctrl stiff and ctrl soft groups, a stepwise analysis with 6 biological replicates was performed. First, exon set ID’s with an average expression lower than 5 were considered as not significantly expressed and excluded from the analysis. A threshold of 40% increase (>0.5 log2 fold change) or decrease (<-0.5 log2 fold change) of gene expression on the soft matrix (vs. stiff matrix) was considered for further analysis. For all genes with 3 or more exon probe set ID’s regulated above the defined thresholds, the average log2 fold change of the regulated exon probe ID’s was calculated and used to generate the final list of genes regulated by matrix stiffness. To determine which of the genes are regulated in a GATA2 dependent manner, a stepwise analysis with 2 biological replicates ctrl siRNA soft vs GATA2 siRNA soft groups was performed. The previously identified exon probe ID’s for genes differentially regulated between the ctrl stiff and ctrl soft groups were extracted and their average log2 fold change was calculated for the new data set. A threshold of 40% increase (>0.5 log2 fold change) or decrease (<-0.5 log2 fold change) of gene expression in the absence of the GATA2 was used to generate the final list of genes. https://www.fdr.uni-hamburg.de/record/137 10.25592/uhhfdm.137 oai:fdr.uni-hamburg.de:137 akh handle:10.1038/s41467-018-03959-6 doi:10.25592/uhhfdm.136 info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/legalcode Gata2 matrix stiffness lymphangiogenesis UKE (University Medical Center) Hamburg Eppendorf Expression profile of human lymphatic endothelial cells cultured on stiff (25 kPa) or soft (0.2 kPa) matrix conditions in the presence or absence of GATA2 info:eu-repo/semantics/other dataset

oai:fdr.uni-hamburg.de:12576 2023-06-23T13:22:03Z user-uhh user-sfb936 user-uke

Cheng, Bastian 2023-06-21 Longitudinal, structural brain connectome dataset derived by DWI and probabilistic tractography. Details provided in the methods file. Patients with first ever supratentorial stroke and upper extremity deficits were included. Timepoints of examinations: 3-5 days after stroke, 1 month, 3 month and 1 year. Related Publications: https://doi.org/10.1093/braincomms/fcz020 10.1177/0271678X19831583 https://www.fdr.uni-hamburg.de/record/12576 10.25592/uhhfdm.12576 oai:fdr.uni-hamburg.de:12576 doi:10.25592/uhhfdm.12575 info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/legalcode Longititudinal acute stroke study: structural brain connectomes info:eu-repo/semantics/other dataset

oai:fdr.uni-hamburg.de:12545 2023-10-04T08:33:25Z user-uke

Louis Bellmann Alexander Johannes Wiederhold Leona Trübe Raphael Twerenbold Frank Ückert Karl Gottfried 2023-06-12 This dataset capures statistical analysis of the HCHS cohort study using a knowledge graph and dashboard. Properties of 10,000 participants were analyzed for their association with cardiovascular disease as well as for their relationships among each other. The data is presented in the form of Neo4J database dumps and can be explored following the given user guide. https://www.fdr.uni-hamburg.de/record/12545 10.25592/uhhfdm.12545 oai:fdr.uni-hamburg.de:12545 eng doi:10.25592/uhhfdm.11942 info:eu-repo/semantics/restrictedAccess Knowledge Graphs Cohort Studies Data Visualization Big Data Introducing Attribute Association Graphs to Facilitate Medical Data Exploration: Development and Evaluation Using Epidemiological Study Data info:eu-repo/semantics/other dataset

oai:fdr.uni-hamburg.de:13421 2024-07-17T14:11:22Z user-uke

Louis Bellmann Alexander Johannes Wiederhold Leona Trübe Raphael Twerenbold Frank Ückert Karl Gottfried 2023-06-12 This dataset capures statistical analysis of the HCHS cohort study using an attribute association graph and dashboard. This graph structure considers and visualizes subject attributes, their association with disease and control cohorts, and conditional relationships between attributes. Properties of 10,000 participants were analyzed for their association with cardiovascular disease. The data is presented in the form of Neo4J database dumps and can be installed and explored following the given user guide. https://www.fdr.uni-hamburg.de/record/13421 10.25592/uhhfdm.13421 oai:fdr.uni-hamburg.de:13421 eng doi:10.25592/uhhfdm.11942 info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/legalcode Data Exploration Cohort Studies Data Visualization Big Data Introducing Attribute Association Graphs to Facilitate Medical Data Exploration: Development and Evaluation Using Epidemiological Study Data info:eu-repo/semantics/other dataset

oai:fdr.uni-hamburg.de:14759 2024-08-07T11:08:11Z user-uke user-uhh user-ru5389

Peter Murphy Katarina Krkovic Gina Monov Natalia Kudlek Tania Lincoln Tobias Donner 2024-08-01 This dataset contains data for: Murphy PR, Krkovic K, Monov G, Kudlek N, Lincoln, T & Donner TH (2024). Individual differences in belief updating and phasic arousal are related to psychosis proneness. The dataset is composed of four .zip files (‘behaviourDM’, ‘eye-trackingDM’, ‘behaviourWM’ ‘questionnaire’ and ‘figures’) and one .csv file (‘questionnaire.csv’). behaviourDM: Contains behavioural and task data from the decision-making task described in the paper. It consists of subfolders containing all data for a single participant, organised by task session (S1, S2), and containing the following: The Sample_seqs folder for each participant/session contains Matlab .mat files (labelled ID_SESS_BLOCK.mat, where ID is the participant ID, SESS is the experimental session and BLOCK is the block number within that session) with information about stimulus sequences presented to the participant on each trial of the decision-making task. The variables in each of these files are: gen – structure containing the generative statistics of the task stim – structure containing details about the physical presentation of the stimuli (see task script on Github for explanation of these) timing – structure containing details about the timing of stimulus presentation (see task script on Github for explanation of these) pshort – proportion of trials with stimulus sequences that were shorter than the full sequence length stimIn – trials*samples matrix of stimulus locations (in polar angle with horizontal midline = 0 degrees; NaN marks trials sequences that were shorter than the full sequence length) distseqs – trials*samples matrix of which generative distribution was used to draw each sample location pswitch – trials*samples matrix of binary flags marking when a switch in generative distribution occurred The Behaviour folder for each participant/session contains Matlab .mat files (same naming scheme as above) with information about the behaviour produced by the participant on each trial of the task. The main variable in each file is a matrix called Behav for which each row is a trial and columns are the following: column 1 – the generative distribution used to draw the final sample location on each trial (and thus, the correct response) column 2 – the response given by the participant column 3 – the accuracy of the participant’s response column 4 – response time relative to Go cue column 5 – trial onset according to psychtoolbox clock Each .mat file also contains a trials*samples matrix (tRefresh) of the timings of monitor flips corresponding to the onsets of each sample (and made relative to trial onset), as provided by psychtoolbox. eye-trackingDM: Contains raw data from a SMI RED 500 eye-tracker, recorded natively as .idf files (proprietary SMI format) and converted here to .txt files using the manufacturer’s IDF Converter utility. The folder contains data for all participants and experimental sessions, named according to the same scheme described above. For stimulus and response trigger information, see task scripts on Github. behaviourWM: Contains Matlab .mat files (one per participant) with information about the stimulus and participant behaviour on each trial of the working memory task. Each file contains a single variable (allbehav) containing the concatenated data across all blocks of the task performed by that participant. Each row is a trial and key columns are the following: column 1 – polar angle of the sample stimulus (i.e. the memorandum) column 2 – polar angle of the test stimulus column 3 – working memory delay duration (1, 3 or 9 seconds) column 4 – categorical trial type (1=match trial, 2=’near’ non-match, 3=’far’ non-match) column 5 – the response given by the participant (1=”same”, -1=”different”) column 6 – response accuracy column 7 – response time relative to go cue column 10 – trial number (usually 63 per trial; blocks of trials ordered consecutively) questionnaire: Contains anonymised participant IDs, age, sex, and prior psychosis diagnosis information for each participant, along with CAPE questionnaire data. Participants are rows in the spreadsheet, columns are different variables. figures: Contains data for generating all figures in the published manuscript, one (or in some cases, two/three) .mat file per figure. Preprocessing and analysis code to accompany this dataset are available at https://github.com/murphyp7/2024_Murphy_Belief-updating-psychosis-proneness. https://www.fdr.uni-hamburg.de/record/14759 10.25592/uhhfdm.14759 oai:fdr.uni-hamburg.de:14759 eng url:https://www.biorxiv.org/content/10.1101/2024.01.14.575567 doi:10.25592/uhhfdm.14758 info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/legalcode psychosis proneness arousal decision-making cognitive bias Behavioral and Eye-tracking Data for "Individual differences in belief updating and phasic arousal are related to psychosis proneness" info:eu-repo/semantics/other dataset

oai:fdr.uni-hamburg.de:15921 2025-09-18T09:51:04Z user-uhh user-uke

Cortesi, Filippo Konzcalla, Leonie Kumar, Yogesh Wahib, Ramez Sturmheit, Tabea Steglich, Babett Huber, Samuel Gagliani, Nicola 2025-01-08 Dataset of IL-17A-producing CD4+T cells in human colorectal cancer. https://www.fdr.uni-hamburg.de/record/15921 10.25592/uhhfdm.15921 oai:fdr.uni-hamburg.de:15921 eng doi:10.25592/uhhfdm.15920 info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/legalcode IL-17A+ CD4+ T in colorectal cancer info:eu-repo/semantics/other dataset

oai:fdr.uni-hamburg.de:18262 2026-02-02T09:01:26Z user-uke user-uhh

Christoph Kilian Lorenz Adlung 2026-01-28 To investigate the differential effects of extracellular vesicles (EVs) derived from live versus apoptotic cells on macrophage function, we performed bulk RNA sequencing on murine bone marrow-derived macrophages (BMDMs) treated with EVs isolated from live thymocytes (liveT-EVs) or apoptotic thymocytes (aT-EVs). BMDMs were generated from C57BL/6J mice and differentiated over seven days. On day 7, cells were treated for 24 hours with either liveT-EVs or aT-EVs. Apoptosis in donor thymocytes was induced by 24-hour culture following initial harvest, and EVs were isolated via differential ultracentrifugation. RNA was extracted using QIAshredder columns and the RNeasy mini Kit (Qiagen), with three biological replicates per condition. Library preparation and transcriptome sequencing were performed by BGI using 100 bp paired-end reads on the DNBSEQ platform. Reads were aligned to the mouse reference genome GRCm39 using STAR aligner (version 2.7.10b). Differential gene expression analysis was performed using DESeq2 (version 1.40.2), and pathway analysis was conducted using clusterProfiler (version 4.8.3) and enrichR (version 3.4). This dataset reveals distinct transcriptomic signatures induced by EVs depending on the viability status of their donor cells, with apoptotic cell-derived EVs notably activating nitric oxide-related pathways in target macrophages. https://www.fdr.uni-hamburg.de/record/18262 10.25592/uhhfdm.18262 oai:fdr.uni-hamburg.de:18262 eng doi:10.25592/uhhfdm.18261 info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/legalcode Extracellular vesicles Apoptosis Macrophages RNA-seq Nitric oxide Bulk RNA-sequencing of murine bone marrow-derived macrophages upon treatment with live or apoptotic thymocyte-derived extracellular vesicles info:eu-repo/semantics/other dataset

oai:fdr.uni-hamburg.de:18248 2026-02-02T09:01:30Z user-uke user-uhh

Behrens, Janina Adlung, Lorenz 2025-09-11 This Seurat object (v5.1) contains single-nucleus RNA-sequencing data from murine interscapular brown adipose tissue (BAT). The dataset comprises 36,611 nuclei from six samples representing two genotypes (ChREBP^flox/flox^ Ucp1-Cre negative [Cre-] and Ucp1-Cre positive [Cre+]) across three housing conditions: room temperature (22°C, RT), acute cold exposure (24 hours at 6°C, AC), and chronic cold exposure (10 days at 6°C, CC). BAT from 3-4 male mice (12-20 weeks old) was pooled per sample. Libraries were prepared using the 10X Genomics Chromium Single Cell V3.1 reagent kit and sequenced on an Illumina NovaSeq platform with paired-end 150 bp reads, targeting approximately 50,000 read pairs per nucleus. Raw sequencing data were processed using Cell Ranger (v7.1.0) with alignment to the GRCm38 (mm10) reference genome. Quality control filtering excluded nuclei with >15% mitochondrial reads, >25,000 UMI counts, or >5,000 detected genes, as well as genes detected in fewer than 3 cells. The six samples were integrated using the Harmony algorithm (v1.2.3). Clustering was performed using the top 30 principal components at resolution 0.8, yielding 21 annotated cell populations: seven adipocyte subtypes (basal brown, OXPHOS-high brown, white-like, lipogenic brown, endothelium-derived brown, stroma-derived brown, and contractile brown adipocytes), three stromal cell types, three endothelial cell types (capillary, arterial, venous), two muscle fiber types (fast and slow), myeloid cells (MonDC), smooth muscle cells, pericytes, lymphocytes, satellite glia cells, and Schwann cells. Key metadata columns include sample identifier (orig.ident), genotype, housing condition, cluster assignments (seurat_clusters), annotated cell type names (cell_type), and DoubletFinder classifications. https://www.fdr.uni-hamburg.de/record/18248 10.25592/uhhfdm.18248 oai:fdr.uni-hamburg.de:18248 eng doi:10.1016/j.molmet.2025.102252 doi:10.25592/uhhfdm.18247 info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/legalcode Molecular Metabolism 101 102252 Brown adipose tissue Carbohydrate response element-binding protein Single nucleus RNA-sequencing De-novo lipogenesis Cold exposure Energy metabolism Integrated Seurat data object from single-nucleus mRNA-sequencing of brown adipose tissue of mice in response to cold exposure info:eu-repo/semantics/other dataset

oai:fdr.uni-hamburg.de:18135 2026-05-01T16:54:20Z user-uke user-uhh

Xu, Yang Weltzsch, Jan Philipp Kilian, Christoph Steglich, Babett Herkel, Johannes Adlung, Lorenz Schramm, Christoph Gagliani, Nicola Lohse, Ansgar Wilhelm 2026-08-13 Processed single cell sequencing data from Xu, Weltzsch, Kilian et al., J Hepat 2026 . This repository contains an anonymized set of Seurat objects of the human single cell sequencing data and spatial transcriptomics, as well as DEG lists. Human single cell count matrices and spatial transcriptomics data are available under restricted access due to the data privacy. Access can be obtained by contacting Prof. Ansgar Lohse (a.lohse@uke.de), and signing a data transfer agreement. https://www.fdr.uni-hamburg.de/record/18135 10.25592/uhhfdm.18135 oai:fdr.uni-hamburg.de:18135 eng doi:10.25592/uhhfdm.18134 info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/legalcode Integrative omics and phase IIa clinical trial identify TNF as key node in autoimmune hepatitis info:eu-repo/semantics/other dataset

oai:fdr.uni-hamburg.de:18513 2026-05-27T07:38:42Z user-uke user-uhh

Lorenz Adlung 2026-05-18 Here we provide the processed bulk mRNA-sequencing data of murine bone marrow-derived macrophages treated with bile acid-loaded apoptotic hepatocytes or DMSO-loaded apoptotic hepatocytes from two biological replicates. The two uploaded files are specified below: samples_aH.csv: Sample metadata table for the four bulk RNA-seq libraries included in this source data file. Each row corresponds to one sequencing library and contains the following columns: mouse (biological replicate identifier; WT1 and WT2 are two independent wild-type mice), treatment1 (primary treatment; "aH" denotes apoptotic hepatocytes), treatment2(secondary treatment applied on top of treatment1; either DMSO vehicle control or TLCA, taurolithocholic acid; which were loaded on the hepatocytes prior to inducing apoptosis), condition (combined treatment label used as the column header in the counts matrix), and batch (sequencing batch; all four libraries shown here were processed in batch1). counts_aH.txt: Raw gene-level read count matrix for the same four libraries, in tab-delimited format. Rows correspond to genes and columns correspond to samples. Column headers (WT1_aH_DMSO, WT2_aH_DMSO, WT1_aH_TLCA, WT2_aH_TLCA) match the mouse and condition fields in samples_aH.csv and follow the convention <mouse>_<treatment1>_<treatment2>. Values are unnormalized integer read counts obtained from HISAT2 alignment to the mouse reference genome GRCm38.p6 followed by gene-level quantification with featureCounts (Subread package) using the NCBI RefSeq annotation (assembly accession GCF_000001635.26), counted in paired-end mode on exon features summarized per gene_id, with multi-mapping and ambiguously assigned reads excluded. These raw counts are the direct input to the differential expression analysis (via DESeq2) reported in Figure 3B. https://www.fdr.uni-hamburg.de/record/18513 10.25592/uhhfdm.18513 oai:fdr.uni-hamburg.de:18513 eng doi:10.25592/uhhfdm.18512 info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/legalcode macrophages bulk mRNA-sequencing phagocytosis apoptosis hepatocytes bile acids Bulk mRNA-sequencing data of murine bone marrow-derived macrophages treated with bile acid-loaded apoptotic hepatocytes info:eu-repo/semantics/other dataset

oai:fdr.uni-hamburg.de:16868 2026-06-10T09:19:29Z user-uke user-uhh user-sfb1328

Lohr, David Werner, René 2025-02-27 The dataset contains the first of two processed open-source datasets used in the Github repository: https://github.com/IPMI-ICNS-UKE/AIMD.AI-for-microscopy-denoising The AIMD Github repository is demonstrating the use of open-source microscopy data for deep learning based image denoising and transfer learning as showcased in: Lohr, D., Meyer, L., Woelk, LM., Kovacevic, D., Diercks, BP., Werner, R. (2025). Deep Learning-Based Image Restoration and Super-Resolution for Fluorescence Microscopy: Overview and Resources. In: Diercks, BP. (eds) T Cell Activation. Methods in Molecular Biology, vol 2904. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-4414-0_3 The folder models contains pre-trained denoising models generated using the code of the AIMD repository. The original open-source data is the "Fluorescence Microscopy Denoising (FMD) dataset" - CC BY-SA 4.0 license https://curate.nd.edu/articles/dataset/Fluorescence_Microscopy_Denoising_FMD_dataset/24744648 8 bit image data, filetype: png https://www.fdr.uni-hamburg.de/record/16868 10.25592/uhhfdm.16868 oai:fdr.uni-hamburg.de:16868 eng Humana doi:10.25592/uhhfdm.16867 info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by-sa/4.0/legalcode Microscopy, Denoising, Artificial Intelligence, Deep learning AIMD. AI for microscopy denoising - dataset 1 info:eu-repo/semantics/other dataset