| 1. |
- Älgenäs, Cajsa, et al.
(författare)
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Antibody performance in western blot applications is context- dependent
- 2014
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Ingår i: Biotechnology Journal. - : Wiley. - 1860-6768 .- 1860-7314. ; 9:3, s. 435-445
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Tidskriftsartikel (refereegranskat)abstract
- An important concern for the use of antibodies in various applications, such as western blot (WB) or immunohistochemistry (IHC), is specificity. This calls for systematic validations using well-designed conditions. Here, we have analyzed 13000 antibodies using western blot with lysates from human cell lines, tissues, and plasma. Standardized stratification showed that 45% of the antibodies yielded supportive staining, and the rest either no staining (12%) or protein bands of wrong size (43%). A comparative study of WB and IHC showed that the performance of antibodies is application-specific, although a correlation between no WB staining and weak IHC staining could be seen. To investigate the influence of protein abundance on the apparent specificity of the antibody, new WB analyses were performed for 1369 genes that gave unsupportive WBs in the initial screening using cell lysates with overexpressed full-length proteins. Then, more than 82% of the antibodies yielded a specific band corresponding to the full-length protein. Hence, the vast majority of the antibodies (90%) used in this study specifically recognize the target protein when present at sufficiently high levels. This demonstrates the context- and application-dependence of antibody validation and emphasizes that caution is needed when annotating binding reagents as specific or cross-reactive. WB is one of the most commonly used methods for validation of antibodies. Our data implicate that solely using one platform for antibody validation might give misleading information and therefore at least one additional method should be used to verify the achieved data.
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| 2. |
- Berglund, Lisa, et al.
(författare)
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A genecentric Human Protein Atlas for expression profiles based on antibodies
- 2008
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Ingår i: Molecular & Cellular Proteomics. - 1535-9476 .- 1535-9484. ; 7:10, s. 2019-2027
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Forskningsöversikt (refereegranskat)abstract
- An attractive path forward in proteomics is to experimentally annotate the human protein complement of the genome in a genecentric manner. Using antibodies, it might be possible to design protein-specific probes for a representative protein from every protein-coding gene and to subsequently use the antibodies for systematical analysis of cellular distribution and subcellular localization of proteins in normal and disease tissues. A new version (4.0) of the Human Protein Atlas has been developed in a genecentric manner with the inclusion of all human genes and splice variants predicted from genome efforts together with a visualization of each protein with characteristics such as predicted membrane regions, signal peptide, and protein domains and new plots showing the uniqueness (sequence similarity) of every fraction of each protein toward all other human proteins. The new version is based on tissue profiles generated from 6120 antibodies with more than five million immunohistochemistry-based images covering 5067 human genes, corresponding to approximately 25% of the human genome. Version 4.0 includes a putative list of members in various protein classes, both functional classes, such as kinases, transcription factors, G-protein-coupled receptors, etc., and project-related classes, such as candidate genes for cancer or cardiovascular diseases. The exact antigen sequence for the internally generated antibodies has also been released together with a visualization of the application-specific validation performed for each antibody, including a protein array assay, Western blot analysis, immunohistochemistry, and, for a large fraction, immunofluorescence-based confocal microscopy. New search functionalities have been added to allow complex queries regarding protein expression profiles, protein classes, and chromosome location. The new version of the protein atlas thus is a resource for many areas of biomedical research, including protein science and biomarker discovery.
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| 3. |
- Berglund, Lisa, et al.
(författare)
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A whole-genome bioinformatics approach to selection of antigens for systematic antibody generation
- 2008
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Ingår i: Proteomics. - : Wiley. - 1615-9853 .- 1615-9861. ; 8:14, s. 2832-2839
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Tidskriftsartikel (refereegranskat)abstract
- Here, we present an antigen selection strategy based on a whole-genome bioinformatics approach, which is facilitated by an interactive visualization tool displaying protein features from both public resources and in-house generated data. The web-based bioinformatics platform has been designed for selection of multiple, non-overlapping recombinant protein epitope signature tags by display of predicted information relevant for antigens, including domain- and epitope sized sequence similarities to other proteins, transmembrane regions and signal peptides. The visualization tool also displays shared and exclusive protein regions for genes with multiple splice variants. A genome-wide analysis demonstrates that antigens for approximately 80% of the human protein-coding genes can be selected with this strategy.
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| 4. |
- Berglund, Lisa, et al.
(författare)
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Generation of validated antibodies towards the human proteome
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Here we show the results from a large effort to generate antibodies towards the human proteome. A high-throughput strategy was developed based on cloning and expression of antigens as recombitant protein epitope signature tags (PrESTs) Affinity purified polyclonal antibodies were generated, followed by validation by protein microarrays, Western blotting and microarray-based immunohistochemistry. PrESTs were selected based on sequence uniqueness relative the proteome and a bioinformatics analysis showed that unique antigens can be found for at least 85% of the proteome using this general strategy. The success rate from antigen selection to validated antibodies was 31%, and from protein to antibody 55%. Interestingly, membrane-bound and soluble proteins performed equally and PrEST lengths between 75 and 125 amino acids were found to give the highest yield of validated antibodies. Multiple antigens were selected for many genes and the results suggest that specific antibodies can be systematically generated to most human proteibs.
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| 5. |
- Björling, Gunilla, Docent, et al.
(författare)
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Tracheostomy inner cannula care : a randomized crossover study of two decontamination procedures
- 2007
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Ingår i: American Journal of Infection Control. - : Elsevier BV. - 0196-6553 .- 1527-3296. ; 35:9, s. 600-5
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Today several methods for decontaminating inner cannulae exist. These methods are not based on scientific data, but often on local clinical tradition. This study compares two different decontamination methods. The aim was to find a practical and safe decontamination method. It is a randomized, single-blinded, comparative crossover study. METHODS: Fifty outpatients with long-term tracheostomy with an inner cannula were consecutively included and randomly allocated to begin with one of two different treatment sequences: detergent and chlorhexidine-alcohol (A) or detergent (B). Samples for bacterial culture were taken before and after decontamination, and the number of bacteria colonies was counted. RESULTS: Before decontamination, the inner cannulae grew high numbers of bacteria, which were parts of the normal flora of the upper respiratory tract and did not differ significantly between the two sequences (AB; BA). The primary variable was the culture count value after chlorhexidine-alcohol/detergent (A) and detergent (B). The effects of both methods were larger than expected, and the results showed a nearly total elimination of organisms. The equivalence criterion, ratio of mean colony counts (A/B) >0.8, was met at a significance level of P<0.001. CONCLUSIONS: Cleaning the tracheostomy inner cannula with detergent and water is sufficient to achieve decontamination.
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| 6. |
- Fagerberg, Linn, et al.
(författare)
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Contribution of antibody-based protein profiling to the human chromosome-centric proteome project (C-HPP)
- 2013
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Ingår i: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 12:6, s. 2439-2448
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Tidskriftsartikel (refereegranskat)abstract
- A gene-centric Human Proteome Project has been proposed to characterize the human protein-coding genes in a chromosome-centered manner to understand human biology and disease. Here, we report on the protein evidence for all genes predicted from the genome sequence based on manual annotation from literature (UniProt), antibody-based profiling in cells, tissues and organs and analysis of the transcript profiles using next generation sequencing in human cell lines of different origins. We estimate that there is good evidence for protein existence for 69% (n = 13985) of the human protein-coding genes, while 23% have only evidence on the RNA level and 7% still lack experimental evidence. Analysis of the expression patterns shows few tissue-specific proteins and approximately half of the genes expressed in all the analyzed cells. The status for each gene with regards to protein evidence is visualized in a chromosome-centric manner as part of a new version of the Human Protein Atlas (www.proteinatlas.org).
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| 7. |
- George-Svahn, Lisa, et al.
(författare)
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Barriers to HIV testing as reported by individuals newly diagnosed with HIV infection in Sweden
- 2021
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Ingår i: AIDS Care. - : Taylor & Francis. - 0954-0121 .- 1360-0451. ; 33:10, s. 1286-1295
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Tidskriftsartikel (refereegranskat)abstract
- Despite the availability of free and anonymous HIV testing almost 60% of Swedish patients are diagnosed late. Identifying predictors of different types of barriers could inform policy makers and health care of interventions to increase testing where needed. This cross-sectional study aimed to describe and analyze barriers to HIV testing as reported by Swedish patients newly diagnosed with HIV infection. N = 285 patients completed the 18-item Barriers to HIV Testing Scale - Karolinska Version. Descriptive analysis and logistic regressions were performed to assess the prevalence of barriers and to identify predictors for the different investigated barriers. Barriers to testing were reported by 60%. Approximately 67% of patients originating from Sweden, 50% from Sub-Saharan Africa and 75% from Eastern European/East Asian countries reported barriers. Patients who were younger and patients who self-initiated HIV testing, had greater odds of reporting a barrier than older individuals and those who were offered a test through screening or by a healthcare professional. To counteract barriers that still exist on an individual level, healthcare-initiated HIV testing could be offered more broadly and information about risks for transmission and effectiveness of HIV treatment still needs to be disseminated among both people born in Sweden and different migrant groups.
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| 8. |
- Manhica, Hélio, et al.
(författare)
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Promoting sustainable health and wellbeing for pregnant adolescents in Uganda – A qualitative case study among health workers
- 2021
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Ingår i: International Journal of Africa Nursing Sciences. - : Elsevier. - 2214-1391. ; 14, s. 1-7
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Tidskriftsartikel (refereegranskat)abstract
- Background: Adolescent pregnancy is a global health problem. In Uganda, the rate of teenage pregnancies is approximately 25% and these are associated with both poor maternal- and perinatal health outcome.Objective: This qualitative case study aimed to examine health workers’ experiences of promoting sustainable health and well-being for pregnant adolescent girls in Uganda.Method: A qualitative study design was used. Data was collected through semi-structured interviews of four health workers working for a Non-Government Organization (NGO) based in Uganda. Data was inductively analyzed by content analysis.Result: Three categories emerged: social structure, organization’s work – rehabilitation and therapy, and outcome. Healthcare workers worked with health promotion using a person-centered approach, emphasizing therapies and empowerment strategies and an overall faith-based approach. Furthermore, the result showed that girls were abandoned by their families when entering the center, but with help from the NGO they increased their understanding of the girls situation, due to resettlement of plan and follow up made by the health workers.Conclusion: Health workers can promote health and well-being among pregnant adolescent by applying person-centered care, including therapies and empowerment strategies by a faith-based approach. Social structures and families should be encouraged to provide support to pregnant adolescent girls.
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| 9. |
- Mattsson, Janet, Docent, Ph.D, 1967-, et al.
(författare)
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Nurses’ Experiences of Caring for Patients With Suspected or Confirmed COVID-19 in the Initial Stage of the Pandemic
- 2022
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Ingår i: Sage Open Nursing. - : Sage Publications. - 2377-9608. ; 8, s. 1-11
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Tidskriftsartikel (refereegranskat)abstract
- Introduction: Nursing staff have faced various challenges during the global pandemic of COVID-19 such as nursing shortages. The great number of COVID-19 patients requiring hospitalization placed heavy demands on healthcare staff to maintain patient safety and to work according to constantly changing guidelines to prevent the spread of infection.Objective: The objective was to describe nurses’ experiences of caring for patients with suspected or confirmed COVID-19 in the initial phase of the pandemic.Methods: The study has a qualitative design. Semi-structured interviews were conducted with seven nurses in primary care and hospital care during the initial stage of the pandemic. Qualitative content analysis with an inductive approach was used.Results: The nurses expressed that the working routines changed very quickly at the onset of the pandemic. A triage system was implemented to care for patients with symptoms of COVID-19 to prevent transmission between patients. A major change was the constant use of personal protective equipment in patient care. The nurses also experienced a sense of inadequacy regarding the care of the patients and became emotionally affected and exhausted.Conclusion: The nurses experienced that many patients worsened clinically, leading to exhausting and difficult nursing care situations. They also experienced increasing responsibility since new protective equipment and procedures needed to be quickly implemented according to frequently changing recommendations, causing the nurses to feel uncertain about how to maintain patient safety. Support from colleagues was crucial to cope throughout the initial stage of the pandemic.
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| 10. |
- Nilsson, Kenneth, Docent, 1953-, et al.
(författare)
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A comprehensive clinical and laboratory evaluation of 224 patients with persistent symptoms attributed to presumed tick-bite exposure
- 2021
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 16:3
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Tidskriftsartikel (refereegranskat)abstract
- Background Persistent symptoms attributed to presumed tick-bite exposure constitute an unresolved medical controversy. We evaluated whether Swedish adults who met the criteria for post-treatment Lyme disease syndrome (PTLDS) exhibited characteristics distinguishable from adults who did not, but who displayed similar symptoms and disease course after suspected previous tick-bite infection (TBI). Methods and findings During 2015-2018, 255 patients-referred to the Centre for Vector-borne Infections, Uppsala University Hospital, Sweden with symptoms lasting longer than six months-were recruited. Of this group, 224 completed the study. Each patient was examined by an infectious disease specialist and, besides a full medical history, underwent a panel of blood and cerebrospinal fluid laboratory tests including hematological, biochemical, microbiological and immunological analyses, and the RAND-36 scale to measure quality of life. For analysis purposes, patients were divided into five subgroups, of which one represented PTLDS. According to serological results indicating TBI and documented/ reported objective signs of Lyme disease, 85 (38%) patients fulfilled the criteria for PTLDS and were compared with the other 139 (62%) serologically classified patients. In the PTLDS group, erythema chronicum migrans (ECM) was documented/reported in 86% of patients, previous neuroborreliosis in 15%, and acrodermatitis chronica atroficans (ACA) in 3.5%. However, there were no significant differences regarding symptoms, laboratory results or disease course between patients with PTLDS and those without laboratory evidence of Borrelia exposition. Most reported symptoms were fatigue-related (70%), musculoskeletal (79%), neurological (82%) and neurocognitive (57%). Tick bites were recalled by 74%. The RAND-36 score was significantly below that of the general Swedish population. Signs of immunological/inflammatory reactivity with myositis antibodies were detected in 20% of patients, fibrinogen levels were moderately increased in 21% and elevated rheumatoid factor in 6%. Conclusions The PTLDS group did not differ exclusively in any respect from the other subgroups, which either lacked previously documented/reported evidence of borreliosis or even lacked detectable serological signs of exposure to Lyme disease. The results suggest that symptoms often categorized as Chronic-Lyme-Disease (CLD) in the general debate, cannot be uniquely linked to Lyme disease. However, approximately 20% of the total group of patients showed signs of autoimmunity. Further studies are needed to elucidate the underlying causes and mechanisms of PTLDS and there is reason to consider a multifactorial approach.
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