https://researchdata.se/en/catalogue Search results en Breast Ultrasound (BUS) imaging plays an important role in the early detection and diagnosis of breast cancer. The rapid advancement of deep learning-based Computer-Aided Diagnosis (CAD) systems has demonstrated remarkable potential. However, the clinical applicability of CAD is constrained by the scarcity of large-scale, diverse, and well-annotated datasets. Existing public BUS datasets are highly fragmented. To address these gaps, we present BUS-Large, a large-scale curated BUS dataset for method development and evaluation, comprising more than 21,00 images from 21 publicly available datasets across multiple countries and clinical institutions. The dataset integrates all the public available static image datasets. All cohorts have been harmonized with unified diagnostic labels, pixel-level segmentation mask, and standardized BI-RADS clinical information. To the best of our knowledge, this is one of the most extensive datasets providing lesion segmentation masks annotated from publicly available BUS datasets.  This work was supported by grants from Marie Skłodowska-Curie Doctoral Networks Actions (HORIZON-MSCA-2021-DN-01-01;  101073222), Cancerfonden (22-2389 Pj). In addition to the MAIA platform at KTH, the computations were enabled by the Berzelius resource provided by the Knut and Alice Wallenberg Foundation at the National Academic Infrastructure for Supercomputing in Sweden.  We also acknowledge the public dataset owners for making the imaging and clinical data used in this study publicly available. Wed, 15 Jul 2026 00:00:00 GMT https://researchdata.se/en/catalogue/dataset/oai-datarepository-kth-se-frfd6-ymw69 https://researchdata.se/en/catalogue/dataset/oai-datarepository-kth-se-frfd6-ymw69 Royal Institute of Technology Yang, Zhikai Affinity proteomics data for Venous thromboembolism biomarker study (VEBIOS) rescreening This dataset contain two documents with log-transformed and normalised MFI values from an affinity proteomics screenings in citrate plasma from individuals with venous thromboembolism. The dataset 1 contains plasma profile data for the individual with suspected acute venous thrombosis. Dataset 2 includes the plasma profile data for the individuals analyzed after a frist-time venous thrombosis along with the corresponding control subjects. Wed, 18 Feb 2026 00:00:00 GMT https://researchdata.se/en/catalogue/dataset/doi-10-17044-scilifelab-31047682 https://researchdata.se/en/catalogue/dataset/doi-10-17044-scilifelab-31047682 Royal Institute of Technology Philip Smith David Kotol Maria Farm Jochen Schwenk Mathias Uhlén Maria Magnusson Pierre Emmanuel Morange David Alexandre Trégouët, Jovan Antovic Lynn Marie Butler Fredrik Edfors Arfwidsson Maria Jesus Iglesias Mareque Jacob Odeberg ANCA-associated vasculitides (AAV) are rare but severe disorders. Little is known about the pathophysiology of AAV. In this study, we analyzed the relative levels of 181 proteins using proximity extension assay (Olink) in plasma samples from patients with active AAV (n=66), matched population controls (n=138) and disease controls with rheumatoid arthritis (n=31) and systemic lupus erythematosus n=14), respectively. Distinct sets of upregulated proteins were identified in subgroups of patients with AAV defined by ANCA (PR3-ANCA and MPO-ANCA, respectively) compared with controls. Fri, 13 Jun 2025 00:00:00 GMT https://researchdata.se/en/catalogue/dataset/doi-10-17044-scilifelab-29291642 https://researchdata.se/en/catalogue/dataset/doi-10-17044-scilifelab-29291642 Region Uppsala Johanna Dahlqvist Erik Hellbacher This dataset contains the count matrices required to reproduce the web application for interactive visualization of single-cell RNA-seq (scRNA-seq) data from equine bronchoalveolar lavage (BAL) cells. The Shiny app is available at: https://equbal-explorer.serve.scilifelab.se/app/equbal-explorer hosted by SciLifeLab serve. The web application can be recreated using the scripts provided in the associated GitHub repository: https://github.com/Molmed/EquBAL_explorer. The scRNA-seq data were generated from 21 clinical equine asthma cases and 8 healthy controls using the HIVE and Drop-seq platforms. Details of the laboratory procedures and the generation of the count matrices are described in the original publications: https://doi.org/10.1038/s41598-023-43368-4 and https://doi.org/10.1371/journal.pone.0317343. Raw sequencing data is available at SRA as described in these papers. A phenotype file is also provided, containing BAL cytology and other phenotypic information for the samples included in the web application. Thu, 15 May 2025 00:00:00 GMT https://researchdata.se/en/catalogue/dataset/doi-10-17044-scilifelab-28869398 https://researchdata.se/en/catalogue/dataset/doi-10-17044-scilifelab-28869398 Uppsala University Julia Sulayeva Kim Fegraeus Miia Riihimäki Jessica Nordlund Amanda Raine Abstract Increased knowledge of the evolution of molecular changes in neurodegenerative disorders such as Alzheimer’s disease (AD) is important for the understanding of disease pathophysiology and also crucial to be able to identify and validate disease biomarkers. While several biological changes that occur early in the disease development have already been recognised, the need for further characterization of the pathophysiological mechanisms behind AD still remains. In this study, we investigated cerebrospinal fluid (CSF) levels of 104 proteins in 307 asymptomatic 70-year-olds from the H70 Gothenburg Birth Cohort Studies using a multiplexed antibody-based technology. The protein levels were first correlated with the core AD CSF biomarker concentrations of total tau, phospho-tau and Aβ42 in all individuals. Sixty-three proteins showed significant correlations with either total tau, phospho-tau or Aβ42. Thereafter, individuals were divided based on CSF Aβ42/Aβ40 ratio and Clinical Dementia Rating (CDR) score to determine if early changes in pathology and cognition had an effect on the correlations. We compared the associations of the analysed proteins to CSF markers between groups and found 33 proteins displaying significantly different associations for amyloid-positive individuals and amyloid negative individuals, as defined by the CSF Aβ42/Aβ40 ratio. No differences in the associations could be seen for individuals divided by CDR score. We identified a series of transmembrane proteins, proteins associated to or anchored to the plasma membrane, and proteins involved in or connected to synaptic vesicle transport that were associated with CSF biomarkers of amyloid and tau pathology in AD. Further studies are needed to explore their role in AD pathophysiology. Data Access Statement The dataset contains relative protein levels as well as CSF concentrations of amyloid beta and tau which constitutes sensitive personal information that fall under GDPR. Therefore, access to data and related code is restricted. The data can be made available upon reasonable request, in accordance with GDPR and other regulations regarding data sharing. A reasonable request should contain: 1) Name of PI and host organisation 2) Contact details 3) Scientific purpose of data access request 4) Commitment to inform when the data has been used in a publication 5) Commitment not to host or share the data outside the requesting organisation 6) Statement of non-commercial use of data Tue, 04 Apr 2023 00:00:00 GMT https://researchdata.se/en/catalogue/dataset/doi-10-17044-scilifelab-13280867 https://researchdata.se/en/catalogue/dataset/doi-10-17044-scilifelab-13280867 Royal Institute of Technology Anna Månberg Affinity proteomics data for Venous thromboembolism biomarker study (VEBIOS) This dataset contain normalised MFI values from an affinity proteomics screenings in Citrate plasma and EDTA plasma from 96 individuals with suspected acute venous thrombosis.  The data is disaggregated on individual level with information about sex. Data linked to other phenotype information has been deposited separately with restricted access available upon request. Thu, 23 Mar 2023 00:00:00 GMT https://researchdata.se/en/catalogue/dataset/doi-10-17044-scilifelab-22225942 https://researchdata.se/en/catalogue/dataset/doi-10-17044-scilifelab-22225942 Royal Institute of Technology Maria Jesus Iglesias Mareque Jacob Odeberg Lynn Marie Butler Laura Sanchez-Rivera David Alexandre Trégouët, Pierre Emmanuel Morange Mun-Gwan Hong Jochen Schwenk Philip Smith Maria Magnusson Angela Silveira Mathias Uhlen Jose Soria Fernandez Joan Carles Souto The study is based on 6 different cohorts and case control studies of patients with venous thromboembolism (VTE). The six cohorts are briefly as described below:  VEBIOS ER, Swedish acute VTE cohort including 48 cases and 48 controls.  DFW. Swedish acute VTE cohort with 54 cases/146 controls. FARIVE: French cohort including 582 patients recruited druing initiation of treatment for VTE and 576 hospital-based controls. VEBIOS Coagulation, Swedish cohort, with 144 cases followed after ending treatment of VTE and 140 controls population-based recluted. RETROVE, Spanish cohort of 308 cases and 360 controls. Cases were recruted after ending VTE treatment. MARTHA, French cohort, Patiens with prior VTE. n=774. The datasets include anonymized participant-level data generated from analyses of plasma samples from the included cohort and case-control studies, including plasma affinity proteomics data, absolute protein quantifications, Thrombin Generation Potential (TGP) measurements, together with clinical chemistry data and clinical information used in the analyses described in the paper. The data can be made available for validation purposes upon reasonable request (jacob.odeberg@scilifelab.se) A reasonable request should contain: 1) Name of PI and host organisation 2) Contact details 3) Scientific purpose of data access request 4) Commitment to inform when the data has been used in a publication 5) Commitment not to host or share the data outside the requesting organisation 6) Statement of non-commercial use of data Thu, 23 Mar 2023 00:00:00 GMT https://researchdata.se/en/catalogue/dataset/doi-10-17044-scilifelab-22226350 https://researchdata.se/en/catalogue/dataset/doi-10-17044-scilifelab-22226350 Royal Institute of Technology Maria Jesus Iglesias Mareque Jacob Odeberg Jochen Schwenk David Alexandre Trégouët, Lynn Marie Butler Pierre Emmanuel Morange Joan Carles Souto Jose Soria Fernandez Laura Sanchez-Rivera Manal Ibrahim-Kosta Clement Naudin Gaëlle Munsch Louisa Goumidi Maria Farm Philip Smith Julia Barbara Kral-Pointner Mun-Gwan Hong Pierre Suchon Marine Germain Philip Dusart Anne Boland David Kotol Fredrik Edfors David M Smadja Margareta Holmström Maria Magnusson Angela Silveira Mathias Uhlen Thomas Renné Angel Martinez-Perez Joseph Emmerich Jean-François Deleuze Jovan Antovic Alice Assinger It has long been thought that vision is the most essential factor in maintaining stable quiet standing compared to other sources (i.e., vestibular and somatosensory inputs) of information. Specifically, several vision studies on postural control have shown evidence for the importance of the visual system,particularly peripheral vision rather than central vision, and optical flow. Nevertheless, to date, no study has manipulated both visual field and optical flow concurrently. In the present study, we experimentally manipulated both the visual field (the central and peripheral visual fields) and the occurrence of optical flow during quiet standing, examining the effects of the visual field and optical flow on postural sway measured in terms of the center of pressure (CoP). Stationary random dot stimuli were presented exclusively in either the central or peripheral visual field, while the occurrence of optical flow was manipulated using a desktop (DTD) or a head-mounted (HMD) display. The optical flow that occurred while using the DTD was a function of the postural sway during quiet standing, while for the HMD, no optical flow occurred even when the body/head swayed during quiet standing. Our results show that the extent of postural sway (e.g., CoP area) was smaller when visual stimuli were presented in the peripheral visual field than that in the central visual field; this was the case while using the DTD alone, with noeffects of the peripheral vision on the extent of postural sway while using the HMD. It is therefore suggested that the optical flow occurring in the peripheral visual field is essential for stable quiet standing. The data contains five CoP variables (Envelopment area, rectangular area, rms area, total CoP trajectory and total CoP trajectory per area). Each set of variables is presented for two display conditions and four visual field conditions. See Horiuchi et al. (2017) for details. Mon, 18 Sep 2017 00:00:00 GMT https://researchdata.se/en/catalogue/dataset/snd1029-1 https://researchdata.se/en/catalogue/dataset/snd1029-1 Tokyo Metropolitan University Kentaro Horiuchi "That which we call a rose by any other name would smell as sweet.” Shakespeare has Juliet tell her Romeo that a name is just a convention without meaning, what counts is the reference, the 'thing itself', to which the property of smelling sweet pertains alone. Frege in his classical paper “Über Sinn und Bedeutung” was not so sure, he assumed names can be inherently meaningful, even without a known reference. And Wittgenstein later in Philosophical Investigations (PI) seems to deny the sheer arbitrariness of names and reject looking for meaning out of context, by pointing to our inability to just utter some random sounds and by that really implying e.g. the door. The word cannot simply be separated from its meaning, in the same way as the money from the cow that could be bought for them (PI 120). Scientific names of biota, in particular, are often descriptive of properties pertaining to the organism or species itself. On the other hand, in semantic web technology and Linked Open Data (LOD) there is an overall effort to replace names by their references, in the form of web links or Uniform Resource Identifiers (URIs). “Things, not strings” is the motto. But, even in view of the many "challenges with using names to link digital biodiversity information" that were extensively described in a recent paper, would it at all be possible or even desirable to replace scientific names of biota with URIs? Or would it be sufficient to just identify equivalence relationships between different variants of names of the same biota, having the same reference, and then just link them to the same “thing”, by means of a property sameAs(URI)? The Global Names Architecture (GNA) has a resolver of scientific names that is already doing that kind of work, linking names of biota such as Pinus thunbergii to global identifiers and URIs from other data sources, such as Encyclopedia of Life (EOL) and uBio Namebank. But there may be other challenges with going from a “natural language”, even from a not entirely coherent system of scientific names, to a semantic web ontology, a solution to some of which have been proposed recently by means of so called 'lexical bridges'. Sun, 01 Jan 2017 00:00:00 GMT https://researchdata.se/en/catalogue/dataset/doi-10-7910-dvn-bamcsi https://researchdata.se/en/catalogue/dataset/doi-10-7910-dvn-bamcsi Stockholm University Philipson, Joakim