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Article ; Online: InParanoiDB 9: Ortholog Groups for Protein Domains and Full-Length Proteins.

Persson, Emma / Sonnhammer, Erik L L

2023 Volume 435, Issue 14, Page(s) 168001

Abstract: Prediction of orthologs is an important bioinformatics pursuit that is frequently used for inferring protein function and evolutionary analyses. The InParanoid database is a well known resource of ortholog predictions between a wide variety of organisms. ...

Abstract	Prediction of orthologs is an important bioinformatics pursuit that is frequently used for inferring protein function and evolutionary analyses. The InParanoid database is a well known resource of ortholog predictions between a wide variety of organisms. Although orthologs have historically been inferred at the level of full-length protein sequences, many proteins consist of several independent protein domains that may be orthologous to domains in other proteins in a way that differs from the full-length protein case. To be able to capture all types of orthologous relations, conventional full-length protein orthologs can be complemented with orthologs inferred at the domain level. We here present InParanoiDB 9, covering 640 species and providing orthologs for both protein domains and full-length proteins. InParanoiDB 9 was built using the faster InParanoid-DIAMOND algorithm for orthology analysis, as well as Domainoid and Pfam to infer orthologous domains. InParanoiDB 9 is based on proteomes from 447 eukaryotes, 158 bacteria and 35 archaea, and includes over one billion predicted ortholog groups. A new website has been built for the database, providing multiple search options as well as visualization of groups of orthologs and orthologous domains. This release constitutes a major upgrade of the InParanoid database in terms of the number of species as well as the new capability to operate on the domain level. InParanoiDB 9 is available at https://inparanoidb.sbc.su.se/.
MeSH term(s)	Algorithms ; Computational Biology ; Protein Domains ; Proteome
Chemical Substances	Proteome
Language	English
Publishing date	2023-02-09
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2023.168001
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: InParanoid-DIAMOND: faster orthology analysis with the InParanoid algorithm.

Persson, Emma / Sonnhammer, Erik L L

Bioinformatics (Oxford, England)

2022 Volume 38, Issue 10, Page(s) 2918–2919

Abstract: Summary: Predicting orthologs, genes in different species having shared ancestry, is an important task in bioinformatics. Orthology prediction tools are required to make accurate and fast predictions, in order to analyze large amounts of data within a ... ...

Abstract	Summary: Predicting orthologs, genes in different species having shared ancestry, is an important task in bioinformatics. Orthology prediction tools are required to make accurate and fast predictions, in order to analyze large amounts of data within a feasible time frame. InParanoid is a well-known algorithm for orthology analysis, shown to perform well in benchmarks, but having the major limitation of long runtimes on large datasets. Here, we present an update to the InParanoid algorithm that can use the faster tool DIAMOND instead of BLAST for the homolog search step. We show that it reduces the runtime by 94%, while still obtaining similar performance in the Quest for Orthologs benchmark. Availability and implementation: The source code is available at (https://bitbucket.org/sonnhammergroup/inparanoid). Supplementary information: Supplementary data are available at Bioinformatics online.
MeSH term(s)	Algorithms ; Software
Language	English
Publishing date	2022-05-12
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btac194
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Article ; Online: Spinal surgery and the risk of reoperation after total hip arthroplasty: a cohort study based on Swedish spine and hip arthroplasty registers.

Eneqvist, Ted / Persson, Louise / Kojer, Emma / Gunnarsson, Linus / Gerdhem, Paul

Acta orthopaedica

2024 Volume 95, Page(s) 25–31

Abstract: Background and purpose: Studies suggest increased revision risk of total hip arthroplasty (THA) in individuals with lumbar spinal fusion, but studies including non-fused individuals are lacking. We aimed to investigate whether individuals undergoing ... ...

Abstract	Background and purpose: Studies suggest increased revision risk of total hip arthroplasty (THA) in individuals with lumbar spinal fusion, but studies including non-fused individuals are lacking. We aimed to investigate whether individuals undergoing lumbar spinal stenosis surgery with or without fusion are at an increased risk of reoperation before or after THA. Patients and methods: The Swedish Spine Register and the Swedish arthroplasty register were searched from 2000 through 2021. Chi-square, Kaplan-Meier and binary multivariate logistic regression were used to compare reoperation rates up to 10 years after THA surgery. Results: 7,908 individuals had undergone lumbar spinal stenosis surgery (LSSS) (fusion n = 1,281) and THA. LSSS before THA compared with THA-only controls was associated with a higher risk of THA reoperations: 87 (2%) out of 3,892 vs. 123 (1%) out of 11,662 (P < 0.001). LSSS after THA compared with THA-only controls was not associated with a higher risk of reoperation, confirmed by Kaplan- Meier analyses and binary multivariate logistic regression. Mortality was lower in individuals undergoing both LSSS and THA, regardless of procedure order. There was no difference in THA reoperations in individuals who had undergone LSSS before THA without fusion or with fusion. The individuals who had undergone LSSS after THA with fusion had an increased risk of THA reoperation compared with those without fusion. Conclusion: LSSS with or without fusion before THA is associated with an increased risk of THA reoperation. Spinal fusion increased the risk of reoperation of THA when performed after THA.
MeSH term(s)	Humans ; Arthroplasty, Replacement, Hip/adverse effects ; Arthroplasty, Replacement, Hip/methods ; Cohort Studies ; Reoperation ; Spinal Stenosis/surgery ; Sweden/epidemiology ; Lumbar Vertebrae/surgery ; Spinal Fusion/adverse effects ; Spinal Fusion/methods ; Retrospective Studies
Language	English
Publishing date	2024-01-18
Publishing country	Sweden
Document type	Journal Article
ZDB-ID	2180677-9
ISSN	1745-3682 ; 1745-3674
ISSN (online)	1745-3682
ISSN	1745-3674
DOI	10.2340/17453674.2024.35228
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Article ; Online: Impact of pre-pandemic sick leave diagnoses on the length of COVID-19-related sick leave: a nationwide registry-based study.

Abzhandadze, Tamar / Westerlind, Emma / Persson, Hanna C

BMC public health

2023 Volume 23, Issue 1, Page(s) 195

Abstract: Background: The COVID-19 pandemic has caused difficulties and changes in many aspects of people's health and lives. Although infection affected work capacity, during the first wave policies for sick leave due to COVID-19 were unclear. The aim of this ... ...

Abstract	Background: The COVID-19 pandemic has caused difficulties and changes in many aspects of people's health and lives. Although infection affected work capacity, during the first wave policies for sick leave due to COVID-19 were unclear. The aim of this study was to investigate the impact of sick leave diagnoses in the year before the COVID-19 diagnosis on sick leave duration due to COVID-19 in a nationwide non-hospitalised population. Methods: Data from three Swedish registries were analysed for sick leave commencing between 1 March and 31 August 2020, with a follow-up period of 4 months. Sick leave due to COVID-19 was considered the number of days that sickness benefits were used and included at least one registered COVID-19 diagnosis. Sick leave in the year before COVID-19 diagnosis were categorised into five diagnostic groups and one reference group (participants without prior sick leave). Results: The study comprised 8935 individuals who received sickness benefits due to COVID-19 in Sweden during the first pandemic wave (mean age 46.7 years, 67% females, and 24% had diagnoses for sick leave in the year before COVID-19 diagnosis). The duration of sick leave due to COVID-19 was significantly higher in the groups with prior sick leave owing to musculoskeletal system diseases (odds ratio [OR]: 1.08, 95% confidence interval [CI]: 1.01-1.15); respiratory system diseases (OR: 1.22, 95% CI: 1.14-1.31); all other isolated diagnoses (OR: 1.08, 95% CI: 1.03-1.14); and multiple diagnoses (OR: 1.32, 95% CI: 1.21-1.43). Conclusions: The results of this nationwide registry-based study indicate that individuals with premorbid conditions are more prone to longer sick leave durations due to COVID-19. Prediction of sick leave duration during the first wave of the COVID-19 pandemic is complex and several factors played a role.
MeSH term(s)	Female ; Humans ; Middle Aged ; Male ; Pandemics ; Sick Leave ; COVID-19 Testing ; COVID-19/epidemiology ; Registries ; Sweden/epidemiology
Language	English
Publishing date	2023-01-29
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2041338-5
ISSN	1471-2458 ; 1471-2458
ISSN (online)	1471-2458
ISSN	1471-2458
DOI	10.1186/s12889-023-15115-x
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: InParanoiDB 9: Ortholog Groups for Protein Domains and Full-Length Proteins

Persson, Emma / Sonnhammer, Erik L.L.

Journal of Molecular Biology. 2023 July, v. 435, no. 14 p.168001-

2023

Abstract	Prediction of orthologs is an important bioinformatics pursuit that is frequently used for inferring protein function and evolutionary analyses. The InParanoid database is a well known resource of ortholog predictions between a wide variety of organisms. Although orthologs have historically been inferred at the level of full-length protein sequences, many proteins consist of several independent protein domains that may be orthologous to domains in other proteins in a way that differs from the full-length protein case. To be able to capture all types of orthologous relations, conventional full-length protein orthologs can be complemented with orthologs inferred at the domain level. We here present InParanoiDB 9, covering 640 species and providing orthologs for both protein domains and full-length proteins. InParanoiDB 9 was built using the faster InParanoid-DIAMOND algorithm for orthology analysis, as well as Domainoid and Pfam to infer orthologous domains. InParanoiDB 9 is based on proteomes from 447 eukaryotes, 158 bacteria and 35 archaea, and includes over one billion predicted ortholog groups. A new website has been built for the database, providing multiple search options as well as visualization of groups of orthologs and orthologous domains. This release constitutes a major upgrade of the InParanoid database in terms of the number of species as well as the new capability to operate on the domain level. InParanoiDB 9 is available at https://inparanoidb.sbc.su.se/.
Keywords	Archaea ; Internet ; algorithms ; bioinformatics ; databases ; eukaryotic cells ; molecular biology ; prediction ; proteome ; ortholog ; InParanoid ; orthologous domain ; protein domain ; ortholog database
Language	English
Dates of publication	2023-07
Publishing place	Elsevier Ltd
Document type	Article ; Online
Note	Pre-press version ; Use and reproduction
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2023.168001
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Impact of pre-pandemic sick leave diagnoses on the length of COVID-19-related sick leave

Tamar Abzhandadze / Emma Westerlind / Hanna C. Persson

BMC Public Health, Vol 23, Iss 1, Pp 1-

a nationwide registry-based study

2023 Volume 11

Abstract: Abstract Background The COVID-19 pandemic has caused difficulties and changes in many aspects of people’s health and lives. Although infection affected work capacity, during the first wave policies for sick leave due to COVID-19 were unclear. The aim of ... ...

Abstract	Abstract Background The COVID-19 pandemic has caused difficulties and changes in many aspects of people’s health and lives. Although infection affected work capacity, during the first wave policies for sick leave due to COVID-19 were unclear. The aim of this study was to investigate the impact of sick leave diagnoses in the year before the COVID-19 diagnosis on sick leave duration due to COVID-19 in a nationwide non-hospitalised population. Methods Data from three Swedish registries were analysed for sick leave commencing between 1 March and 31 August 2020, with a follow-up period of 4 months. Sick leave due to COVID-19 was considered the number of days that sickness benefits were used and included at least one registered COVID-19 diagnosis. Sick leave in the year before COVID-19 diagnosis were categorised into five diagnostic groups and one reference group (participants without prior sick leave). Results The study comprised 8935 individuals who received sickness benefits due to COVID-19 in Sweden during the first pandemic wave (mean age 46.7 years, 67% females, and 24% had diagnoses for sick leave in the year before COVID-19 diagnosis). The duration of sick leave due to COVID-19 was significantly higher in the groups with prior sick leave owing to musculoskeletal system diseases (odds ratio [OR]: 1.08, 95% confidence interval [CI]: 1.01–1.15); respiratory system diseases (OR: 1.22, 95% CI: 1.14–1.31); all other isolated diagnoses (OR: 1.08, 95% CI: 1.03–1.14); and multiple diagnoses (OR: 1.32, 95% CI: 1.21–1.43). Conclusions The results of this nationwide registry-based study indicate that individuals with premorbid conditions are more prone to longer sick leave durations due to COVID-19. Prediction of sick leave duration during the first wave of the COVID-19 pandemic is complex and several factors played a role.
Keywords	Epidemiology ; Return to work ; Sick leave ; Registry-based study ; SARS-CoV-2 infection ; Public aspects of medicine ; RA1-1270
Language	English
Publishing date	2023-01-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Sick leave one year after COVID-19 infection: a nationwide cohort study during the first wave in Sweden.

Abzhandadze, Tamar / Westerlind, Emma / Palstam, Annie / Sunnerhagen, Katharina S / Persson, Hanna C

Scientific reports

2024 Volume 14, Issue 1, Page(s) 572

Abstract: This study aimed to investigate the patterns of sick leave, as well as factors associated with sick leave due to COVID-19 during one year after the COVID-19 diagnosis, and sex-related aspects on sick leave. This nationwide study involved 11,902 ... ...

Abstract	This study aimed to investigate the patterns of sick leave, as well as factors associated with sick leave due to COVID-19 during one year after the COVID-19 diagnosis, and sex-related aspects on sick leave. This nationwide study involved 11,902 individuals who received sickness benefits for COVID-19 during the first wave of the pandemic. Data from three Swedish registries were analyzed for sick leave that commenced between March 1 and August 31, 2020, with a follow-up period of 12 months. Sick leave due to COVID-19 was counted as the number of days with sickness benefits and required to include at least one registered COVID-19 diagnosis. The median duration of sick leave was 35 days, and 347 (2.9%) individuals continued their sick leave during the entire follow-up period. Furthermore, 1 year later, the cumulative incidence of sick leave was slightly higher in males (3.5%) compared to females (2.7%). Older age, being single with no children, diagnosed with the virus, medium income level, history of sick leave, and need for inpatient care were significantly associated with a higher duration of sick leave due to COVID-19, both in the total population and when stratified by sex. These results indicated that three out of 100 (3%) patients were still on sick leave 1 year after their COVID-19 diagnosis. Aspects regarding the importance of sick leave duration differed between males and females and comprised sociodemographic characteristics and need for inpatient care. The results indicated the complexity of sick leave due to COVID-19.
MeSH term(s)	Male ; Female ; Humans ; Cohort Studies ; Sweden/epidemiology ; Sick Leave ; COVID-19 Testing ; COVID-19/epidemiology ; Registries
Language	English
Publishing date	2024-01-05
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-50413-9
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Article ; Online: Sick leave one year after COVID-19 infection

Tamar Abzhandadze / Emma Westerlind / Annie Palstam / Katharina S. Sunnerhagen / Hanna C. Persson

Scientific Reports, Vol 14, Iss 1, Pp 1-

a nationwide cohort study during the first wave in Sweden

2024 Volume 10

Abstract: Abstract This study aimed to investigate the patterns of sick leave, as well as factors associated with sick leave due to COVID-19 during one year after the COVID-19 diagnosis, and sex-related aspects on sick leave. This nationwide study involved 11,902 ... ...

Abstract	Abstract This study aimed to investigate the patterns of sick leave, as well as factors associated with sick leave due to COVID-19 during one year after the COVID-19 diagnosis, and sex-related aspects on sick leave. This nationwide study involved 11,902 individuals who received sickness benefits for COVID-19 during the first wave of the pandemic. Data from three Swedish registries were analyzed for sick leave that commenced between March 1 and August 31, 2020, with a follow-up period of 12 months. Sick leave due to COVID-19 was counted as the number of days with sickness benefits and required to include at least one registered COVID-19 diagnosis. The median duration of sick leave was 35 days, and 347 (2.9%) individuals continued their sick leave during the entire follow-up period. Furthermore, 1 year later, the cumulative incidence of sick leave was slightly higher in males (3.5%) compared to females (2.7%). Older age, being single with no children, diagnosed with the virus, medium income level, history of sick leave, and need for inpatient care were significantly associated with a higher duration of sick leave due to COVID-19, both in the total population and when stratified by sex. These results indicated that three out of 100 (3%) patients were still on sick leave 1 year after their COVID-19 diagnosis. Aspects regarding the importance of sick leave duration differed between males and females and comprised sociodemographic characteristics and need for inpatient care. The results indicated the complexity of sick leave due to COVID-19.
Keywords	Medicine ; R ; Science ; Q
Subject code	590
Language	English
Publishing date	2024-01-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Interleukin-6 Induces Stem Cell Propagation through Liaison with the Sortilin-Progranulin Axis in Breast Cancer.

Berger, Karoline / Persson, Emma / Gregersson, Pernilla / Ruiz-Martínez, Santiago / Jonasson, Emma / Ståhlberg, Anders / Rhost, Sara / Landberg, Göran

Cancers

2023 Volume 15, Issue 24

Abstract: Unraveling the complex network between cancer cells and their tumor microenvironment is of clinical importance, as it might allow for the identification of new targets for cancer treatment. Cytokines and growth factors secreted by various cell types ... ...

Abstract	Unraveling the complex network between cancer cells and their tumor microenvironment is of clinical importance, as it might allow for the identification of new targets for cancer treatment. Cytokines and growth factors secreted by various cell types present in the tumor microenvironment have the potential to affect the challenging subpopulation of cancer stem cells showing treatment-resistant properties as well as aggressive features. By using various model systems, we investigated how the breast cancer stem cell-initiating growth factor progranulin influenced the secretion of cancer-associated proteins. In monolayer cultures, progranulin induced secretion of several inflammatory-related cytokines, such as interleukin (IL)-6 and -8, in a sortilin-dependent manner. Further, IL-6 increased the cancer stem fraction similarly to progranulin in the breast cancer cell lines MCF7 and MDA-MB-231 monitored by the surrogate mammosphere-forming assay. In a cohort of 63 patient-derived scaffold cultures cultured with breast cancer cells, we observed significant correlations between IL-6 and progranulin secretion, clearly validating the association between IL-6 and progranulin also in human-based microenvironments. In conclusion, the interplay between progranulin and IL-6 highlights a dual breast cancer stem cell-promoting function via sortilin, further supporting sortilin as a highly relevant therapeutic target for aggressive breast cancer.
Language	English
Publishing date	2023-12-08
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2527080-1
ISSN	2072-6694
ISSN	2072-6694
DOI	10.3390/cancers15245757
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Article ; Online: PathBIX-a web server for network-based pathway annotation with adaptive null models.

Castresana-Aguirre, Miguel / Persson, Emma / Sonnhammer, Erik L L

Bioinformatics advances

2021 Volume 1, Issue 1, Page(s) vbab010

Abstract: Motivation: Pathway annotation is a vital tool for interpreting and giving meaning to experimental data in life sciences. Numerous tools exist for this task, where the most recent generation of pathway enrichment analysis tools, network-based methods, ... ...

Abstract	Motivation: Pathway annotation is a vital tool for interpreting and giving meaning to experimental data in life sciences. Numerous tools exist for this task, where the most recent generation of pathway enrichment analysis tools, network-based methods, utilize biological networks to gain a richer source of information as a basis of the analysis than merely the gene content. Network-based methods use the network crosstalk between the query gene set and the genes in known pathways, and compare this to a null model of random expectation. Results: We developed PathBIX, a novel web application for network-based pathway analysis, based on the recently published ANUBIX algorithm which has been shown to be more accurate than previous network-based methods. The PathBIX website performs pathway annotation for 21 species, and utilizes prefetched and preprocessed network data from FunCoup 5.0 networks and pathway data from three databases: KEGG, Reactome, and WikiPathways. Availability: https://pathbix.sbc.su.se/. Contact: erik.sonnhammer@scilifelab.se. Supplementary information: Supplementary data are available at
Language	English
Publishing date	2021-07-01
Publishing country	England
Document type	Journal Article
ISSN	2635-0041
ISSN (online)	2635-0041
DOI	10.1093/bioadv/vbab010
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