| 1. |
- Uhlén, Mathias, et al.
(author)
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A human protein atlas for normal and cancer tissues based on antibody proteomics
- 2005
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In: Molecular & Cellular Proteomics. - 1535-9476 .- 1535-9484. ; 4:12, s. 1920-1932
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Journal article (peer-reviewed)abstract
- Antibody-based proteomics provides a powerful approach for the functional study of the human proteome involving the systematic generation of protein-specific affinity reagents. We used this strategy to construct a comprehensive, antibody-based protein atlas for expression and localization profiles in 48 normal human tissues and 20 different cancers. Here we report a new publicly available database containing, in the first version, similar to 400,000 high resolution images corresponding to more than 700 antibodies toward human proteins. Each image has been annotated by a certified pathologist to provide a knowledge base for functional studies and to allow queries about protein profiles in normal and disease tissues. Our results suggest it should be possible to extend this analysis to the majority of all human proteins thus providing a valuable tool for medical and biological research.
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| 2. |
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| 3. |
- Agelfors, Eva, et al.
(author)
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Synthetic visual speech driven from auditory speech
- 1999
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In: Proceedings of Audio-Visual Speech Processing (AVSP'99)).
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Conference paper (peer-reviewed)abstract
- We have developed two different methods for using auditory, telephone speech to drive the movements of a synthetic face. In the first method, Hidden Markov Models (HMMs) were trained on a phonetically transcribed telephone speech database. The output of the HMMs was then fed into a rulebased visual speech synthesizer as a string of phonemes together with time labels. In the second method, Artificial Neural Networks (ANNs) were trained on the same database to map acoustic parameters directly to facial control parameters. These target parameter trajectories were generated by using phoneme strings from a database as input to the visual speech synthesis The two methods were evaluated through audiovisual intelligibility tests with ten hearing impaired persons, and compared to “ideal” articulations (where no recognition was involved), a natural face, and to the intelligibility of the audio alone. It was found that the HMM method performs considerably better than the audio alone condition (54% and 34% keywords correct respectively), but not as well as the “ideal” articulating artificial face (64%). The intelligibility for the ANN method was 34% keywords correct.
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| 4. |
- Ahmadian, Afshin, et al.
(author)
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Method for amplification
- 2005
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Patent (pop. science, debate, etc.)abstract
- The invention refers to a method for multiplex amplification of at least one specific nucleic acid locus, comprising the steps of: providing at least one oligonucleotide probe pair that is designed so that the first and second probe of the pair anneal to a specific nucleic acid locus on a target molecule, in which pair the first probe has an extendable 3'-end, and a second probe has a 5'-end that is directly or indirectly labelled with a phosphate group; providing a target molecule comprising at least one specific nucleic acid locus; allowing the probe pair to anneal to the target molecule; allowing the 3'-end of the first probe to extend by influence of polymerase by adding a set of three different dNTPs; ligating the 3'-end of the extended first probe to the 5'-end of the second probe. Hereby, a method is provided which allows a high specificity for simultaneous amplification of several loci. Further, the invention involves a kit for use in the method of the invention.
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| 5. |
- Alm, Fredrik, 1983-, et al.
(author)
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Adherence to Swedish Guidelines for Pain Treatment in Tonsil Surgery in Pediatric Patients
- 2016
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Conference paper (peer-reviewed)abstract
- Objective: As shown by data from the National Tonsil Surgery Register in Sweden, tonsil surgery often causes severe pain that lasts for many days. The register data demonstrate the necessity for better evidence-based pain treatment guidelines for tonsil surgery. The guidelines, introduced in 2013, consist of both pharmacological and non-pharmacological recommendations. In the guidelines, a multimodal analgesic approach and combination of analgesics are recommended to provide effective pain treatment with limited side effects. Two national multi-professional education days on pain, pharmacology and the guidelines were offered. Web-based information about pharmacological treatment (www.tonsililloperation.se) was designed for patients and next-of-kin. The current aims were to describe adherence to the Swedish guidelines for pain treatment in tonsil surgery in pediatric patients < 18 yearsMethod: An inter-professional questionnaire was developed, including questions linked to the relevant guidelines. The questions came from a national mapping before the guidelines were designed. The items were discussed by an expert group, and content validity was evaluated using the content validity index.ENT-and anesthesia physicians and nurses from all 50 ENT clinics in Sweden were enrolled.Results: Most clinics had received the guidelines, but there was a discrepancy between the professions. More than half had perused the literature review performed before the guidelines were designed, and attended themulti-professional education day. Pre- and perioperative treatment usually included paracetamol, clonidine and betamethasone. A multimodal pain approach after discharge from hospital (tonsillectomy and tonsillotomy) was used, combining paracetamol with cox-inhibitors. Most clinics used paracetamol, with a higher dose for the first 3 days (healthy children and acceptable nutrition), and a reduced dose from day 4.In case of inadequate analgesia after tonsillectomy, oral clonidine or opioids were used. Several clinics followed the recommendation to use clonidine as first choice and secondly an opioid. No respondents prescribed codeine compared to 80% at the mapping before the guidelines were designed. The guidelines were experienced as clear, safe and sufficient. The web-based information was used by most of the clinics to improve quality of care and provide facilitating tools for patients, relatives and caregivers.Conclusion: Swedish guidelines for tonsil surgery provide practical evidence-based pain treatment recommendations. To achieve a change, multi-professional education is necessary. This needs to be repeated for a wider spread.Future research should include evaluation through pain diaries and questionnaires to next-of-kin and children. There should be matching of data from the quality registers at each clinic, with pain variables such as unplanned health care contacts due to pain, number of days with analgesics, and return to normal diet
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| 7. |
- Asp, Michaela, et al.
(author)
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A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart
- 2019
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In: Cell. - : CELL PRESS. - 0092-8674 .- 1097-4172. ; 179:7, s. 1647-
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Journal article (peer-reviewed)abstract
- The process of cardiac morphogenesis in humans is incompletely understood. Its full characterization requires a deep exploration of the organ-wide orchestration of gene expression with a single-cell spatial resolution. Here, we present a molecular approach that reveals the comprehensive transcriptional landscape of cell types populating the embryonic heart at three developmental stages and that maps cell-type-specific gene expression to specific anatomical domains. Spatial transcriptomics identified unique gene profiles that correspond to distinct anatomical regions in each developmental stage. Human embryonic cardiac cell types identified by single-cell RNA sequencing confirmed and enriched the spatial annotation of embryonic cardiac gene expression. In situ sequencing was then used to refine these results and create a spatial subcellular map for the three developmental phases. Finally, we generated a publicly available web resource of the human developing heart to facilitate future studies on human cardiogenesis.
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| 8. |
- Asp, Michaela, et al.
(author)
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An organ‐wide gene expression atlas of the developing human heart
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Other publication (other academic/artistic)abstract
- The human developing heart holds a greater proportion of stem-cell-like cells than the adult heart. However, it is not completely understood how these stem cells differentiate into various cardiac cell types. We have performed an organ-wide transcriptional landscape analysis of the developing heart to advance our understanding of cardiac morphogenesis in humans. Comprehensive spatial gene expression analyses identified distinct profiles that correspond not only to individual chamber compartments, but also distinctive regions within the outflow tract. Furthermore, the generated spatial expression reference maps facilitated the assignment of 3,787 human embryonic cardiac cells obtained from single-cell RNA-sequencing to an in situlocation. Through this approach we reveal that the outflow tract contains a wider range of cell types than the chambers, and that the epicardium expression profile can be traced to several cell types that are activated at different stages of development. We also provide a 3D spatial model of human embryonic cardiac cells to enable further studies of the developing human heart.
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| 9. |
- Asp, Michaela, et al.
(author)
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Spatial Isoform Profiling within Individual Tissue Sections
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Other publication (other academic/artistic)abstract
- Spatial Transcriptomics has been shown to be a persuasive RNA sequencingtechnology for analyzing cellular heterogeneity within tissue sections. Thetechnology efficiently captures and barcodes 3’ tags of all polyadenylatedtranscripts from a tissue section, and thus provides a powerful platform whenperforming quantitative spatial gene expression studies. However, the currentprotocol does not recover the full-length information of transcripts, andconsequently lack information regarding alternative splice variants. Here, weintroduce a novel protocol for spatial isoform profiling, using SpatialTranscriptomics barcoded arrays.
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| 10. |
- Berglund, Emelie, et al.
(author)
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Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity
- 2018
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In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 9
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Journal article (peer-reviewed)abstract
- Intra-tumor heterogeneity is one of the biggest challenges in cancer treatment today. Here we investigate tissue-wide gene expression heterogeneity throughout a multifocal prostate cancer using the spatial transcriptomics (ST) technology. Utilizing a novel approach for deconvolution, we analyze the transcriptomes of nearly 6750 tissue regions and extract distinct expression profiles for the different tissue components, such as stroma, normal and PIN glands, immune cells and cancer. We distinguish healthy and diseased areas and thereby provide insight into gene expression changes during the progression of prostate cancer. Compared to pathologist annotations, we delineate the extent of cancer foci more accurately, interestingly without link to histological changes. We identify gene expression gradients in stroma adjacent to tumor regions that allow for re-stratification of the tumor microenvironment. The establishment of these profiles is the first step towards an unbiased view of prostate cancer and can serve as a dictionary for future studies.
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