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- Ramilowski, JA, et al.
(författare)
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Functional annotation of human long noncoding RNAs via molecular phenotyping
- 2020
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Ingår i: Genome research. - : Cold Spring Harbor Laboratory. - 1549-5469 .- 1088-9051. ; 30:7, s. 1060-1072
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Tidskriftsartikel (refereegranskat)abstract
- Long noncoding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian genomes, and yet, their functions remain largely unknown. As part of the FANTOM6 project, we systematically knocked down the expression of 285 lncRNAs in human dermal fibroblasts and quantified cellular growth, morphological changes, and transcriptomic responses using Capped Analysis of Gene Expression (CAGE). Antisense oligonucleotides targeting the same lncRNAs exhibited global concordance, and the molecular phenotype, measured by CAGE, recapitulated the observed cellular phenotypes while providing additional insights on the affected genes and pathways. Here, we disseminate the largest-to-date lncRNA knockdown data set with molecular phenotyping (over 1000 CAGE deep-sequencing libraries) for further exploration and highlight functional roles for ZNF213-AS1 and lnc-KHDC3L-2.
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| 3. |
- Baranasic, D, et al.
(författare)
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Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements
- 2022
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Ingår i: Nature genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 54:87, s. 1037-
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Tidskriftsartikel (refereegranskat)abstract
- Zebrafish, a popular organism for studying embryonic development and for modeling human diseases, has so far lacked a systematic functional annotation program akin to those in other animal models. To address this, we formed the international DANIO-CODE consortium and created a central repository to store and process zebrafish developmental functional genomic data. Our data coordination center (https://danio-code.zfin.org) combines a total of 1,802 sets of unpublished and re-analyzed published genomic data, which we used to improve existing annotations and show its utility in experimental design. We identified over 140,000 cis-regulatory elements throughout development, including classes with distinct features dependent on their activity in time and space. We delineated the distinct distance topology and chromatin features between regulatory elements active during zygotic genome activation and those active during organogenesis. Finally, we matched regulatory elements and epigenomic landscapes between zebrafish and mouse and predicted functional relationships between them beyond sequence similarity, thus extending the utility of zebrafish developmental genomics to mammals.
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| 7. |
- Aspvall, K., et al.
(författare)
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Cost-effectiveness of Internet-Delivered vs In-Person Cognitive Behavioral Therapy for Children and Adolescents With Obsessive-Compulsive Disorder
- 2021
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Ingår i: JAMA network open. - : American Medical Association (AMA). - 2574-3805. ; 4:7
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Tidskriftsartikel (refereegranskat)abstract
- IMPORTANCE Therapist-guided, internet-delivered cognitive behavioral therapy is an effective treatment option for children and adolescents with obsessive-compulsive disorder, but to our knowledge, its cost-effectiveness compared with traditional in-person treatment has not been established. OBJECTIVE To evaluate the cost-effectiveness of guided internet-delivered cognitive behavioral therapy implemented within a stepped-care model compared with in-person cognitive behavioral therapy for young people with obsessive-compulsive disorder. DESIGN, SETTING, AND PARTICIPANTS This economic evaluation of a randomized noninferiority trial conducted at 2 specialist obsessive-compulsive disorder clinics in Sweden enrolled 152 children and adolescents aged 8 to 17 years with obsessive-compulsive disorder, mainly through clinician referrals (110 [72%]). Recruitment began October 6, 2017, and ended May 24, 2019. Follow-up ended April 14, 2020. INTERVENTIONS Participants were randomly assigned to receive either guided internet-delivered cognitive behavioral therapy or in-person cognitive behavioral therapy during a 16-week period. At the 3-month follow-up, nonresponders in both groups were offered additional in-person cognitive behavior therapy sessions. MAIN OUTCOMES AND MEASURES Health outcomes were treatment response rates (primary outcome), remission rates, and quality-adjusted life-years. Cost data were collected before treatment, after treatment, at 3-month follow-up, and at 6-month follow-up (primary end point) and are presented in 2020 US dollars. The differences in incremental costs and health outcomes were compared between the groups and presented from the health care professional, health care sector, and societal perspectives. RESULTS A total of 152 participants (94 girls [62%]; mean [SD] age, 13.4 [2.5] years) were randomized; 151 (99%) completed the trial. At the 6-month follow-up, 50 of 74 participants (68%) in the stepped-care group and 52 of 77 participants (68%) in the in-person cognitive behavioral therapy groupwere classified as treatment responders (odds ratio, 1.00 [95% CI, 0.51-1.98]; P=.99). Health economic analyses showed that the stepped-care group used fewer therapist resources than the in-person cognitive behavioral therapy group, resulting in a mean cost savings of $2104 (95% CI, $1202-$3006) per participant for the full study period of 10 months, corresponding to a relative savings of 39%. The cost savings remained largely comparable when taking wider health care sector and societal perspectives. CONCLUSIONS AND RELEVANCE This study suggests that, for young people with obsessive-compulsive disorder, a low-cost digital intervention followed by in-person treatment for nonresponders was cost-effective compared with in-person cognitive behavior therapy alone.
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| 8. |
- Aspvall, K., et al.
(författare)
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Effect of an Internet-Delivered Stepped-Care Program vs In-Person Cognitive Behavioral Therapy on Obsessive-Compulsive Disorder Symptoms in Children and Adolescents: A Randomized Clinical Trial
- 2021
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Ingår i: Jama-Journal of the American Medical Association. - : American Medical Association (AMA). - 0098-7484 .- 1538-3598. ; 325:18, s. 1863-1873
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Tidskriftsartikel (refereegranskat)abstract
- Key PointsQuestionIs internet-delivered cognitive behavioral therapy (CBT) implemented in a stepped-care model noninferior to in-person CBT for children and adolescents with obsessive-compulsive disorder? FindingsIn this randomized, noninferiority clinical trial, 152 children and adolescents with obsessive-compulsive disorder were treated with an internet-delivered CBT program followed by traditional in-person CBT if necessary vs in-person CBT alone. After 6 months, the mean Children's Yale-Brown Obsessive-Compulsive Scale score was 11.57 in those treated with internet-delivered CBT vs 10.57 in those treated with in-person CBT, a difference that met the noninferiority criterion of 4 points. MeaningTreating children and adolescents with obsessive-compulsive disorder with an internet intervention followed by traditional face-to-face therapy if necessary was noninferior to in-person therapy alone. ImportanceIn most countries, young people with obsessive-compulsive disorder have limited access to specialist cognitive behavioral therapy (CBT), a first-line treatment. ObjectiveTo investigate whether internet-delivered CBT implemented in a stepped-care model is noninferior to in-person CBT for pediatric obsessive-compulsive disorder. Design, Setting and ParticipantsA randomized clinical noninferiority trial conducted at 2 specialist child and adolescent mental health clinics in Sweden. Participants included 152 individuals aged 8 to 17 years with obsessive-compulsive disorder. Enrollment began in October 2017 and ended in May 2019. Follow-up ended in April 2020. InterventionsParticipants randomized to the stepped-care group (n=74) received internet-delivered CBT for 16 weeks. Nonresponders at the 3-month follow-up were then offered a course of traditional face-to-face treatment. Participants randomized to the control group (n=78) immediately received in-person CBT for 16 weeks. Nonresponders at the 3-month follow-up received additional face-to-face treatment. Main Outcomes and MeasuresThe primary outcome was the masked assessor-rated Children's Yale-Brown Obsessive-Compulsive Scale (CY-BOCS) score at the 6-month follow-up. The scale includes 10 items rated from 0(no symptoms) to 4(extreme symptoms), yielding a total score range of 0 to 40, with higher scores indicating greater severity. Assessors were masked to treatment allocation at pretreatment, posttreatment, 3-month follow-up, and 6-month follow-up assessments. The predefined noninferiority margin was 4 points on the CY-BOCS. ResultsAmong the 152 randomized participants (mean age, 13.4 years; 94 [62%] females), 151 (99%) completed the trial. At the 3-month follow-up, 34 participants (46%) in the stepped-care group and 23 (30%) in the in-person CBT group were nonresponders. At the 6-month follow-up, the CY-BOCS score was 11.57 points in the stepped-care group vs 10.57 points in the face-to-face treatment group, corresponding to an estimated mean difference of 0.91 points ([1-sided 97.5% CI, -infinity to 3.28]; P for noninferiority=.02). Increased anxiety (30%-36%) and depressive symptoms (20%-28%) were the most frequently reported adverse events in both groups. There were 2 unrelated serious adverse events (1 in each group). Conclusions and RelevanceAmong children and adolescents with obsessive-compulsive disorder, treatment with an internet-delivered CBT program followed by in-person CBT if necessary compared with in-person CBT alone resulted in a noninferior difference in symptoms at the 6-month follow-up. Further research is needed to understand the durability and generalizability of these findings. Trial RegistrationClinicalTrials.gov Identifier: NCT03263546 This noninferiority trial compares the effects of an internet-delivered cognitive behavioral therapy (CBT) program followed by traditional in-person CBT if necessary vs in-person CBT alone on symptoms of obsessive compulsive disorder (OCD) in children and adolescents.
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| 9. |
- Aspvall, K., et al.
(författare)
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Implementation of internet-delivered cognitive behaviour therapy for pediatric obsessive-compulsive disorder: Lessons from clinics in Sweden, United Kingdom and Australia
- 2020
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Ingår i: Internet Interventions. - : Elsevier BV. - 2214-7829. ; 20
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Tidskriftsartikel (refereegranskat)abstract
- Obsessive-compulsive disorder (OCD) can be successfully treated with cognitive behaviour therapy (CBT). However, as few patients have access to CBT, there is a strong push to develop and evaluate scalable and cost-effective internet-delivered interventions. BIP OCD is a therapist-guided online CBT intervention for pediatric OCD that has shown promise in trials conducted at a single site in Stockholm, Sweden. In this study, we evaluated if BIP OCD is an acceptable, feasible, and effective treatment in other countries and clinical contexts. Thirty-one patients were recruited at three different sites; a specialist OCD clinic in Gothenburg (Sweden), a specialist OCD clinic in London (United Kingdom), and a university-based clinic in Brisbane (Australia). Acceptability and feasibility measures included treatment adherence and feedback from therapists. Clinician assessments were conducted at baseline, post-treatment, and 3-month follow-up. The average module completion for the participants was 8.1/12 (SD = 3.2) and the majority of patients completed the BIP OCD treatment (100% in Gothenburg, and 55.6% in both London and Brisbane). Pooling data from the three sites, the within-group effect sizes from baseline to post-treatment on the Children's Yale-Brown Obsessive-Compulsive Scale were in the expected range (bootstrapped Cohen's d = 1.78; 95% CI 1.18–2.39), with an additional symptom reduction to the 3-month follow-up (bootstrapped Cohen's d = 0.27; 95% CI 0.02–0.51). Participating therapists identified both advantages and difficulties supporting patients in this digital format. The results of this study suggest that the treatment effects obtained in the original BIP OCD trials can be generalized to other clinical contexts nationally and internationally. Lessons learned provide important information for successful implementation of BIP OCD in regular healthcare contexts. © 2020 The Authors
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