| 1. |
- Robinson, Jonathan, 1986, et al.
(författare)
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An atlas of human metabolism
- 2020
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Ingår i: Science Signaling. - : American Association for the Advancement of Science (AAAS). - 1945-0877 .- 1937-9145. ; 13:624
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Tidskriftsartikel (refereegranskat)abstract
- Genome-scale metabolic models (GEMs) are valuable tools to study metabolism and provide a scaffold for the integrative analysis of omics data. Researchers have developed increasingly comprehensive human GEMs, but the disconnect among different model sources and versions impedes further progress. We therefore integrated and extensively curated the most recent human metabolic models to construct a consensus GEM, Human1. We demonstrated the versatility of Human1 through the generation and analysis of cell- and tissue-specific models using transcriptomic, proteomic, and kinetic data. We also present an accompanying web portal, Metabolic Atlas (https://www.metabolicatlas.org/), which facilitates further exploration and visualization of Human1 content. Human1 was created using a version-controlled, open-source model development framework to enable community-driven curation and refinement. This framework allows Human1 to be an evolving shared resource for future studies of human health and disease.
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| 2. |
- Björnsson, Bergthor, et al.
(författare)
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Digital twins to personalize medicine
- 2020
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Ingår i: Genome Medicine. - : Springer Science and Business Media LLC. - 1756-994X. ; 12:1
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Forskningsöversikt (refereegranskat)abstract
- Personalized medicine requires the integration and processing of vast amounts of data. Here, we propose a solution to this challenge that is based on constructing Digital Twins. These are high-resolution models of individual patients that are computationally treated with thousands of drugs to find the drug that is optimal for the patient.
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| 3. |
- Agirre, Jon, et al.
(författare)
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The CCP4 suite: integrative software for macromolecular crystallography
- 2023
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Ingår i: Acta Crystallographica Section D. - : INT UNION CRYSTALLOGRAPHY. - 2059-7983. ; 79, s. 449-461
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Tidskriftsartikel (refereegranskat)abstract
- The Collaborative Computational Project No. 4 (CCP4) is a UK-led international collective with a mission to develop, test, distribute and promote software for macromolecular crystallography. The CCP4 suite is a multiplatform collection of programs brought together by familiar execution routines, a set of common libraries and graphical interfaces. The CCP4 suite has experienced several considerable changes since its last reference article, involving new infrastructure, original programs and graphical interfaces. This article, which is intended as a general literature citation for the use of the CCP4 software suite in structure determination, will guide the reader through such transformations, offering a general overview of the new features and outlining future developments. As such, it aims to highlight the individual programs that comprise the suite and to provide the latest references to them for perusal by crystallographers around the world.
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| 4. |
- Dai, Bitao, et al.
(författare)
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Identifying influential nodes by leveraging redundant ties
- 2023
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Ingår i: Journal of Computational Science. - 1877-7503 .- 1877-7511. ; 69
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Tidskriftsartikel (refereegranskat)abstract
- Structure-based influential nodes identification is a long-term challenge in the study of complex networks. While global centrality-based approaches are generally considered to be more accurate and reliable, the requirements of complete network information and high computational complexity are hard to meet, limiting their applications in many practical scenarios. In addition, recent studies have highlighted the effect of cyclic structures introducing redundant paths in network connectivity and exaggerating the importance of traditional centrality measures. In this work, we develop a new centrality metric, called Multi-Spanning Tree-based Degree Centrality (MSTDC), to quantify node importance with linear complexity by leveraging redundant ties. MSTDC is calculated using the aggregation of degrees of a small number of spanning trees constructed with a few randomly selected root nodes. Experiments on synthetic and empirical networks reveal that MSTDC obtains superior performance than other benchmark network centralities in identifying influential nodes from the perspective of both maintaining network connectivity and maximizing spreading capacity. In addition, we find that MSTDC is extraordinarily effective in networks with high clustering coefficients. Our study provides novel insights into the role of redundant ties in network structural and functional analyses.
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| 5. |
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| 6. |
- Eimontas, Jonas, et al.
(författare)
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A tailored Internet-delivered modular intervention based on cognitive behavioral therapy for depressed older adults : a study protocol for a randomized controlled trial
- 2021
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Ingår i: Trials. - : BMC. - 1745-6215. ; 22:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: Depression is most common among the elderly and is associated with major impairment With limited accessible treatments available, remotely provided interventions are needed. Internet-based interventions have been proven effective for a number of mental and somatic health problems. However, the elderly population has received relatively limited attention in previous studies. This study aims to address this gap by investigating the effectiveness of a tailored Internet-delivered modular intervention based on cognitive behavioral therapy (CBT). Methods: A minimum of 60 participants will be recruited and randomly assigned to groups in a two-armed parallel controlled trial with a waiting list. The intervention group will have access to an 8-week therapist-supported modular intervention. The waiting list group will be instructed to wait for 8 weeks and then granted access to the intervention for 8 weeks. Pre, post, and 3-, 12-, and 24-month follow-up assessments are planned for measuring changes in depression symptoms, anxiety symptoms, and psychological well-being using PHQ-9, GDS, GAD-7, and WHO-5. Primary outcomes of all the participants will be analyzed using the intention-to-treat principle, and withinand between-group effect sizes will be calculated. Discussion: Internet-based interventions could help address the existing treatment gap for depressed older adults. However, to date, the effectiveness of Internet-based CBT (ICBT) for depressed older adults has only been tested in a few studies. This trial will demonstrate if Internet-based CBT is effective for this population when compared to a waiting list control. Further analysis of secondary outcomes and participant behavior in the intervention will potentially reveal effectiveness moderating factors.
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| 7. |
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| 8. |
- Georgsson, Susanne, et al.
(författare)
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Readability of web-based sources about induced abortion : a cross-sectional study
- 2020
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Ingår i: BMC Medical Informatics and Decision Making. - : BioMed Central. - 1472-6947. ; 20:1
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: High-quality information is essential if clients who request an abortion are to reach informed decisions and feel prepared for the procedure, but little is known concerning the readability of web-based sources containing such material. The aim was to investigate the readability of web-based information about induced abortion.METHODS: The search engine Google was used to identify web pages about induced abortion, written in the English language. A total of 240 hits were screened and 236 web pages fulfilled the inclusion criteria. After correcting for duplicate hits, 185 web pages were included. The readability of the text-based content of each web page was determined with Flesch Kincaid Grade Level, Gunning Fog Index, Coleman-Liau Index, Simple Measure of Gobbledygook, and Flesch Reading Ease. Data were analyzed with descriptive statistics, Pearson's correlation coefficient and Kruskal-Wallis with Dunn's test as post hoc analysis.RESULTS: Across all grade level measures, a small minority of the web pages had a readability corresponding to elementary school (n < 3, 1%), while the majority had readability corresponding to senior high school or above (n > 153, 65%). The means of the grade level measures ranged between 10.5 and 13.1, and the mean Flesch Reading Ease score was 45.3 (SD 13.6). Only weak correlations (rho < 0.2) were found between the readability measures and search rank in the hit lists. Consistently, web pages affiliated with health care had the least difficult readability and those affiliated with scientific sources had the most difficult readability.CONCLUSIONS: Overall, web-based information about induced abortions has difficult readability. Incentives are needed to improve the readability of these texts and ensure that clients encounter understandable information so that they may reach informed decisions and feel adequately prepared when requesting an abortion.
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| 9. |
- Hall, CL, et al.
(författare)
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Investigating a therapist-guided, parent-assisted remote digital behavioural intervention for tics in children and adolescents-'Online Remote Behavioural Intervention for Tics' (ORBIT) trial: protocol of an internal pilot study and single-blind randomised controlled trial
- 2019
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Ingår i: BMJ open. - : BMJ. - 2044-6055. ; 9:1, s. e027583-
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Tidskriftsartikel (refereegranskat)abstract
- Tourette syndrome and chronic tic disorder are common, disabling childhood-onset conditions. Guidelines recommend that behavioural therapy should be offered as first-line treatment for children with tics. However, there are very few trained behaviour therapists for tics and many patients cannot access appropriate care. This trial investigates whether an internet-delivered intervention for tics can reduce severity of symptoms.Methods and analysisThis parallel-group, single-blind, randomised controlled superiority trial with an internal pilot will recruit children and young people (aged 9–17 years) with tic disorders. Participants will be randomised to receive 10 weeks of either online, remotely delivered, therapist-supported exposure response prevention behavioural therapy for tics, or online, remotely delivered, therapist-supported education about tics and co-occurring conditions. Participants will be followed up mid-treatment, and 3, 6, 12 and 18 months post randomisation.The primary outcome is reduction in tic severity as measured on the Yale Global Tic Severity Scale total tic severity score. Secondary outcomes include a cost-effectiveness analysis and estimate of the longer-term impact on patient outcomes and healthcare services. An integrated process evaluation will analyse quantitative and qualitative data in order to fully explore the implementation of the intervention and identify barriers and facilitators to implementation. The trial is funded by the National Institute of Health Research (NIHR), Health Technology Assessment (16/19/02).Ethics and disseminationThe findings from the study will inform clinicians, healthcare providers and policy makers about the clinical and cost-effectiveness of an internet delivered treatment for children and young people with tics. The results will be submitted for publication in peer-reviewed journals. The study has received ethical approval from North West Greater Manchester Research Ethics Committee (ref.: 18/NW/0079).Trial registration numbersISRCTN70758207andNCT03483493; Pre-results.
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| 10. |
- Jacobsson, Martin, 1976-, et al.
(författare)
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The role of compression in large scale data transfer and storage of typical biomedical signals at hospitals
- 2023
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Ingår i: Health Informatics Journal. - : Sage Publications. - 1460-4582 .- 1741-2811. ; 29:4
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Tidskriftsartikel (refereegranskat)abstract
- In modern hospitals, monitoring patients’ vital signs and other biomedical signals is standard practice. With the advent of data-driven healthcare, Internet of medical things, wearable technologies, and machine learning, we expect this to accelerate and to be used in new and promising ways, including early warning systems and precision diagnostics. Hence, we see an ever-increasing need for retrieving, storing, and managing the large amount of biomedical signal data generated. The popularity of standards, such as HL7 FHIR for interoperability and data transfer, have also resulted in their use as a data storage model, which is inefficient. This article raises concern about the inefficiency of using FHIR for storage of biomedical signals and instead highlights the possibility of a sustainable storage based on data compression. Most reported efforts have focused on ECG signals; however, many other typical biomedical signals are understudied. In this article, we are considering arterial blood pressure, photoplethysmography, and respiration. We focus on simple lossless compression with low implementation complexity, low compression delay, and good compression ratios suitable for wide adoption. Our results show that it is easy to obtain a compression ratio of 2.7:1 for arterial blood pressure, 2.9:1 for photoplethysmography, and 4.1:1 for respiration.
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