| 1. |
- Klionsky, Daniel J., et al.
(författare)
-
Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 2. |
- Thompson, Paul M., et al.
(författare)
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The ENIGMA Consortium : large-scale collaborative analyses of neuroimaging and genetic data
- 2014
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Ingår i: BRAIN IMAGING BEHAV. - : Springer Science and Business Media LLC. - 1931-7557 .- 1931-7565. ; 8:2, s. 153-182
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Tidskriftsartikel (refereegranskat)abstract
- The Enhancing NeuroImaging Genetics through Meta-Analysis (ENIGMA) Consortium is a collaborative network of researchers working together on a range of large-scale studies that integrate data from 70 institutions worldwide. Organized into Working Groups that tackle questions in neuroscience, genetics, and medicine, ENIGMA studies have analyzed neuroimaging data from over 12,826 subjects. In addition, data from 12,171 individuals were provided by the CHARGE consortium for replication of findings, in a total of 24,997 subjects. By meta-analyzing results from many sites, ENIGMA has detected factors that affect the brain that no individual site could detect on its own, and that require larger numbers of subjects than any individual neuroimaging study has currently collected. ENIGMA's first project was a genome-wide association study identifying common variants in the genome associated with hippocampal volume or intracranial volume. Continuing work is exploring genetic associations with subcortical volumes (ENIGMA2) and white matter microstructure (ENIGMA-DTI). Working groups also focus on understanding how schizophrenia, bipolar illness, major depression and attention deficit/hyperactivity disorder (ADHD) affect the brain. We review the current progress of the ENIGMA Consortium, along with challenges and unexpected discoveries made on the way.
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| 3. |
- Amare, Azmeraw, et al.
(författare)
-
Association of Polygenic Score and the involvement of Cholinergic and Glutamatergic Pathways with Lithium Treatment Response in Patients with Bipolar Disorder.
- 2023
-
Ingår i: Research square. - : Research Square Platform LLC.
-
Tidskriftsartikel (refereegranskat)abstract
- Lithium is regarded as the first-line treatment for bipolar disorder (BD), a severe and disabling mental disorder that affects about 1% of the population worldwide. Nevertheless, lithium is not consistently effective, with only 30% of patients showing a favorable response to treatment. To provide personalized treatment options for bipolar patients, it is essential to identify prediction biomarkers such as polygenic scores. In this study, we developed a polygenic score for lithium treatment response (Li+PGS) in patients with BD. To gain further insights into lithium's possible molecular mechanism of action, we performed a genome-wide gene-based analysis. Using polygenic score modeling, via methods incorporating Bayesian regression and continuous shrinkage priors, Li+PGS was developed in the International Consortium of Lithium Genetics cohort (ConLi+Gen: N=2,367) and replicated in the combined PsyCourse (N=89) and BipoLife (N=102) studies. The associations of Li+PGS and lithium treatment response - defined in a continuous ALDA scale and a categorical outcome (good response vs. poor response) were tested using regression models, each adjusted for the covariates: age, sex, and the first four genetic principal components. Statistical significance was determined at P<����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������.
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| 4. |
- Amare, Azmeraw T, et al.
(författare)
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Association of polygenic score and the involvement of cholinergic and glutamatergic pathways with lithium treatment response in patients with bipolar disorder.
- 2023
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Ingår i: Molecular psychiatry. - 1476-5578. ; 28, s. 5251-5261
-
Tidskriftsartikel (refereegranskat)abstract
- Lithium is regarded as the first-line treatment for bipolar disorder (BD), a severe and disabling mental healthdisorder that affects about 1% of the population worldwide. Nevertheless, lithium is not consistently effective, with only 30% of patients showing a favorable response to treatment. To provide personalized treatment options for bipolar patients, it is essential to identify prediction biomarkers such as polygenic scores. In this study, we developed a polygenic score for lithium treatment response (Li+PGS) in patients with BD. To gain further insights into lithium's possible molecular mechanism of action, we performed a genome-wide gene-based analysis. Using polygenic score modeling, via methods incorporating Bayesian regression and continuous shrinkage priors, Li+PGS was developed in the International Consortium of Lithium Genetics cohort (ConLi+Gen: N=2367) and replicated in the combined PsyCourse (N=89) and BipoLife (N=102) studies. The associations of Li+PGS and lithium treatment response - defined in a continuous ALDA scale and a categorical outcome (good response vs. poor response) were tested using regression models, each adjusted for the covariates: age, sex, and the first four genetic principal components. Statistical significance was determined at P<0.05. Li+PGS was positively associated with lithium treatment response in the ConLi+Gen cohort, in both the categorical (P=9.8×10-12, R2=1.9%) and continuous (P=6.4×10-9, R2=2.6%) outcomes. Compared to bipolar patients in the 1st decile of the risk distribution, individuals in the 10th decile had 3.47-fold (95%CI: 2.22-5.47) higher odds of responding favorably to lithium. The results were replicated in the independent cohorts for the categorical treatment outcome (P=3.9×10-4, R2=0.9%), but not for the continuous outcome (P=0.13). Gene-based analyses revealed 36 candidate genes that are enriched in biological pathways controlled by glutamate and acetylcholine. Li+PGS may be useful in the development of pharmacogenomic testing strategies by enabling a classification of bipolar patients according to their response to treatment.
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| 5. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 6. |
- Clark, Andrew G., et al.
(författare)
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Evolution of genes and genomes on the Drosophila phylogeny
- 2007
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 450:7167, s. 203-218
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Tidskriftsartikel (refereegranskat)abstract
- Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.
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| 7. |
- Herrera-Rivero, Marisol, et al.
(författare)
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Exploring the genetics of lithium response in bipolar disorders.
- 2023
-
Ingår i: Research square.
-
Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Lithium (Li) remains the treatment of choice for bipolar disorders (BP). Its mood-stabilizing effects help reduce the long-term burden of mania, depression and suicide risk in patients with BP. It also has been shown to have beneficial effects on disease-associated conditions, including sleep and cardiovascular disorders. However, the individual responses to Li treatment vary within and between diagnostic subtypes of BP (e.g. BP-I and BP-II) according to the clinical presentation. Moreover, long-term Li treatment has been linked to adverse side-effects that are a cause of concern and non-adherence, including the risk of developing chronic medical conditions such as thyroid and renal disease. In recent years, studies by the Consortium on Lithium Genetics (ConLiGen) have uncovered a number of genetic factors that contribute to the variability in Li treatment response in patients with BP. Here, we leveraged the ConLiGen cohort (N=2,064) to investigate the genetic basis of Li effects in BP. For this, we studied how Li response and linked genes associate with the psychiatric symptoms and polygenic load for medical comorbidities, placing particular emphasis on identifying differences between BP-I and BP-II.We found that clinical response to Li treatment, measured with the Alda scale, was associated with a diminished burden of mania, depression, substance and alcohol abuse, psychosis and suicidal ideation in patients with BP-I and, in patients with BP-II, of depression only. Our genetic analyses showed that a stronger clinical response to Li was modestly related to lower polygenic load for diabetes and hypertension in BP-I but not BP-II. Moreover, our results suggested that a number of genes that have been previously linked to Li response variability in BP differentially relate to the psychiatric symptomatology, particularly to the numbers of manic and depressive episodes, and to the polygenic load for comorbid conditions, including diabetes, hypertension and hypothyroidism.Taken together, our findings suggest that the effects of Li on symptomatology and comorbidity in BP are partially modulated by common genetic factors, with differential effects between BP-I and BP-II.
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| 8. |
- Herrera-Rivero, Marisol, et al.
(författare)
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Immunogenetics of lithium response and psychiatric phenotypes in patients with bipolar disorder.
- 2023
-
Ingår i: Research square.
-
Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The link between bipolar disorder (BP) and immune dysfunction remains controversial. While epidemiological studies have long suggested an association, recent research has found only limited evidence of such a relationship. To clarify this, we investigated the contributions of immune-relevant genetic factors to the response to lithium (Li) treatment and the clinical presentation of BP. First, we assessed the association of a large collection of immune-related genes (4,925) with Li response, defined by the Retrospective Assessment of the Lithium Response Phenotype Scale (Alda scale), and clinical characteristics in patients with BP from the International Consortium on Lithium Genetics (ConLi+Gen, N = 2,374). Second, we calculated here previously published polygenic scores (PGSs) for immune-related traits and evaluated their associations with Li response and clinical features. We found several genes associated with Li response at p < 1×10- 4 values, including HAS3, CNTNAP5 and NFIB. Network and functional enrichment analyses uncovered an overrepresentation of pathways involved in cell adhesion and intercellular communication, which appear to converge on the well-known Li-induced inhibition of GSK-3β. We also found various genes associated with BP's age-at-onset, number of mood episodes, and presence of psychosis, substance abuse and/or suicidal ideation at the exploratory threshold. These included RTN4, XKR4, NRXN1, NRG1/3 and GRK5. Additionally, PGS analyses suggested serum FAS, ECP, TRANCE and cytokine ligands, amongst others, might represent potential circulating biomarkers of Li response and clinical presentation. Taken together, our results support the notion of a relatively weak association between immunity and clinically relevant features of BP at the genetic level.
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| 9. |
- Kalman, Janos L, et al.
(författare)
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Investigating polygenic burden in age at disease onset in bipolar disorder: Findings from an international multicentric study.
- 2019
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Ingår i: Bipolar disorders. - : Wiley. - 1399-5618 .- 1398-5647. ; 21:1, s. 68-75
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Tidskriftsartikel (refereegranskat)abstract
- Bipolar disorder (BD) with early disease onset is associated with an unfavorable clinical outcome and constitutes a clinically and biologically homogenous subgroup within the heterogeneous BD spectrum. Previous studies have found an accumulation of early age at onset (AAO) in BD families and have therefore hypothesized that there is a larger genetic contribution to the early-onset cases than to late onset BD. To investigate the genetic background of this subphenotype, we evaluated whether an increased polygenic burden of BD- and schizophrenia (SCZ)-associated risk variants is associated with an earlier AAO in BD patients.A total of 1995 BD type 1 patients from the Consortium of Lithium Genetics (ConLiGen), PsyCourse and Bonn-Mannheim samples were genotyped and their BD and SCZ polygenic risk scores (PRSs) were calculated using the summary statistics of the Psychiatric Genomics Consortium as a training data set. AAO was either separated into onset groups of clinical interest (childhood and adolescence [≤18years] vs adulthood [>18years]) or considered as a continuous measure. The associations between BD- and SCZ-PRSs and AAO were evaluated with regression models.BD- and SCZ-PRSs were not significantly associated with age at disease onset. Results remained the same when analyses were stratified by site of recruitment.The current study is the largest conducted so far to investigate the association between the cumulative BD and SCZ polygenic risk and AAO in BD patients. The reported negative results suggest that such a polygenic influence, if there is any, is not large, and highlight the importance of conducting further, larger scale studies to obtain more information on the genetic architecture of this clinically relevant phenotype.
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| 10. |
- Klionsky, Daniel J., et al.
(författare)
-
Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes
- 2008
-
Ingår i: Autophagy. - : Landes Bioscience. - 1554-8627 .- 1554-8635. ; 4:2, s. 151-175
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Forskningsöversikt (refereegranskat)abstract
- Research in autophagy continues to accelerate,1 and as a result many new scientists are entering the field. Accordingly, it is important to establish a standard set of criteria for monitoring macroautophagy in different organisms. Recent reviews have described the range of assays that have been used for this purpose.2,3 There are many useful and convenient methods that can be used to monitor macroautophagy in yeast, but relatively few in other model systems, and there is much confusion regarding acceptable methods to measure macroautophagy in higher eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers of autophagosomes versus those that measure flux through the autophagy pathway; thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from fully functional autophagy that includes delivery to, and degradation within, lysosomes (in most higher eukaryotes) or the vacuole (in plants and fungi). Here, we present a set of guidelines for the selection and interpretation of the methods that can be used by investigators who are attempting to examine macroautophagy and related processes, as well as by reviewers who need to provide realistic and reasonable critiques of papers that investigate these processes. This set of guidelines is not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to verify an autophagic response.
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| 11. |
- Nijs, Jo, et al.
(författare)
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Nociceptive, neuropathic, or nociplastic low back pain? : The low back pain phenotyping (BACPAP) consortium's international and multidisciplinary consensus recommendations
- 2024
-
Ingår i: The Lancet Rheumatology. - : Elsevier. - 2665-9913. ; 6:3, s. e178-e188
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Tidskriftsartikel (refereegranskat)abstract
- The potential to classify low back pain as being characterised by dominant nociceptive, neuropathic, or nociplastic mechanisms is a clinically relevant issue. Preliminary evidence suggests that these low back pain phenotypes might respond differently to treatments; however, more research must be done before making specific recommendations. Accordingly, the low back pain phenotyping (BACPAP) consortium was established as a group of 36 clinicians and researchers from 13 countries (five continents) and 29 institutions, to apply a modified Nominal Group Technique methodology to develop international and multidisciplinary consensus recommendations to provide guidance for identifying the dominant pain phenotype in patients with low back pain, and potentially adapt pain management strategies. The BACPAP consortium's recommendations are also intended to provide direction for future clinical research by building on the established clinical criteria for neuropathic and nociplastic pain. The BACPAP consortium's consensus recommendations are a necessary early step in the process to determine if personalised pain medicine based on pain phenotypes is feasible for low back pain management. Therefore, these recommendations are not ready to be implemented in clinical practice until additional evidence is generated that is specific to these low back pain phenotypes.
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| 12. |
- Aartsen, M. G., et al.
(författare)
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Development of a general analysis and unfolding scheme and its application to measure the energy spectrum of atmospheric neutrinos with IceCube
- 2015
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Ingår i: European Physical Journal C. - : Springer Science and Business Media LLC. - 1434-6044 .- 1434-6052. ; 75:3
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Tidskriftsartikel (refereegranskat)abstract
- We present the development and application of a generic analysis scheme for the measurement of neutrino spectra with the IceCube detector. This scheme is based on regularized unfolding, preceded by an event selection which uses a Minimum Redundancy Maximum Relevance algorithm to select the relevant variables and a random forest for the classification of events. The analysis has been developed using IceCube data from the 59-string configuration of the detector. 27,771 neutrino candidates were detected in 346 days of livetime. A rejection of 99.9999 % of the atmospheric muon background is achieved. The energy spectrum of the atmospheric neutrino flux is obtained using the TRUEE unfolding program. The unfolded spectrum of atmospheric muon neutrinos covers an energy range from 100 GeV to 1 PeV. Compared to the previous measurement using the detector in the 40-string configuration, the analysis presented here, extends the upper end of the atmospheric neutrino spectrum by more than a factor of two, reaching an energy region that has not been previously accessed by spectral measurements.
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| 13. |
- Aartsen, M. G., et al.
(författare)
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Search for Prompt Neutrino Emission from Gamma-Ray Bursts with IceCube
- 2015
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Ingår i: Astrophysical Journal Letters. - 2041-8205 .- 2041-8213. ; 805:1
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Tidskriftsartikel (refereegranskat)abstract
- We present constraints derived from a search of four years of IceCube data for a prompt neutrino flux from gammaray bursts (GRBs). A single low-significance neutrino, compatible with the atmospheric neutrino background, was found in coincidence with one of the 506 observed bursts. Although GRBs have been proposed as candidate sources for ultra-high-energy cosmic rays, our limits on the neutrino flux disfavor much of the parameter space for the latest models. We also find that no more than similar to 1% of the recently observed astrophysical neutrino flux consists of prompt emission from GRBs that are potentially observable by existing satellites.
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| 14. |
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| 15. |
- Amare, Azmeraw T, et al.
(författare)
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Association of Polygenic Score for Schizophrenia and HLA Antigen and Inflammation Genes With Response to Lithium in Bipolar Affective Disorder: A Genome-Wide Association Study.
- 2018
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Ingår i: JAMA psychiatry. - : American Medical Association (AMA). - 2168-6238 .- 2168-622X. ; 75:1, s. 65-74
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Tidskriftsartikel (refereegranskat)abstract
- Lithium is a first-line mood stabilizer for the treatment of bipolar affective disorder (BPAD). However, the efficacy of lithium varies widely, with a nonresponse rate of up to 30%. Biological response markers are lacking. Genetic factors are thought to mediate treatment response to lithium, and there is a previously reported genetic overlap between BPAD and schizophrenia (SCZ).To test whether a polygenic score for SCZ is associated with treatment response to lithium in BPAD and to explore the potential molecular underpinnings of this association.A total of 2586 patients with BPAD who had undergone lithium treatment were genotyped and assessed for long-term response to treatment between 2008 and 2013. Weighted SCZ polygenic scores were computed at different P value thresholds using summary statistics from an international multicenter genome-wide association study (GWAS) of 36989 individuals with SCZ and genotype data from patients with BPAD from the Consortium on Lithium Genetics. For functional exploration, a cross-trait meta-GWAS and pathway analysis was performed, combining GWAS summary statistics on SCZ and response to treatment with lithium. Data analysis was performed from September 2016 to February 2017.Treatment response to lithium was defined on both the categorical and continuous scales using the Retrospective Criteria of Long-Term Treatment Response in Research Subjects with Bipolar Disorder score. The effect measures include odds ratios and the proportion of variance explained.Of the 2586 patients in the study (mean [SD] age, 47.2 [13.9] years), 1478 were women and 1108 were men. The polygenic score for SCZ was inversely associated with lithium treatment response in the categorical outcome, at a threshold P<5×10-2. Patients with BPAD who had a low polygenic load for SCZ responded better to lithium, with odds ratios for lithium response ranging from 3.46 (95% CI, 1.42-8.41) at the first decile to 2.03 (95% CI, 0.86-4.81) at the ninth decile, compared with the patients in the 10th decile of SCZ risk. In the cross-trait meta-GWAS, 15 genetic loci that may have overlapping effects on lithium treatment response and susceptibility to SCZ were identified. Functional pathway and network analysis of these loci point to the HLA antigen complex and inflammatory cytokines.This study provides evidence for a negative association between high genetic loading for SCZ and poor response to lithium in patients with BPAD. These results suggest the potential for translational research aimed at personalized prescribing of lithium.
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| 16. |
- Andersson, Eva K., et al.
(författare)
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Neighbourhood context and young adult mobility : A life course approach
- 2021
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Ingår i: Population, Space and Place. - : Wiley. - 1544-8444 .- 1544-8452. ; 27:3
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Tidskriftsartikel (refereegranskat)abstract
- This paper finds convincing evidence of upward progress out of poor Swedish neighbourhoods for individuals with a Swedish background, individuals with a European background, and those with a non-European background. We use the 1986 cohort of the Swedish population and follow them from age 15 when they are living at home to age 30. We find that by age 30, they live in a neighbourhood that in terms of the poverty level is relatively distant from the initial neighbourhood where they grew up. Mobility into less poor neighbourhoods is clearly linked to higher income, but interestingly, initial context is even more important. Mobility to less poor neighbourhoods is found for those starting in high-poverty neighbourhoods and vice versa for those starting in low-poverty neighbourhoods. Moreover, large-scale context and regional context strongly influence neighbourhood mobility along the poverty gradient. The analysis shows that a large proportion of individuals with a non-European background improve their neighbourhood status from where they were living as teenagers, to where they live after leaving home. Individuals who stay in the poorest neighbourhoods come from less favourable backgrounds, from large-scale poverty contexts, have low school grades, tend to have children early, and have low incomes and lower educational attainment. Individuals with a non-European background are overrepresented in this group. Thus, despite the overall gains in neighbourhood quality, the process of spatial sorting still contributes to an increased spatial concentration of vulnerable populations.
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| 17. |
- Beck, Silke, et al.
(författare)
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Towards a reflexive turn in the governance of global environmental expertise : The cases of the IPCC and the IPBES
- 2014
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Ingår i: GAIA. - : oekom verlag. - 0940-5550 .- 2625-5413. ; 23:2, s. 80-87
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Tidskriftsartikel (refereegranskat)abstract
- The role and design of global expert organizations such as the Intergovernmental Panel on Climate Change (IPCC) or the Intergovernmental Platform on Biodiversity and Ecosystem Services (IPBES) needs rethinking. Acknowledging that a one-size-fits-all model does not exist, we suggest a reflexive turn that implies treating the governance of expertise as a matter of political contestation.
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| 18. |
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| 19. |
- Clark, Leigh, et al.
(författare)
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Mapping Theoretical and Methodological Perspectives for Understanding Speech Interface Interactions
- 2019
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Ingår i: CHI EA '19 EXTENDED ABSTRACTS. - New York, NY, USA : ASSOC COMPUTING MACHINERY.
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Konferensbidrag (refereegranskat)abstract
- The use of speech as an interaction modality has grown considerably through the integration of Intelligent Personal Assistants (IPAs- e.g. Siri, Google Assistant) into smartphones and voice based devices (e.g. Amazon Echo). However, there remain significant gaps in using theoretical frameworks to understand user behaviours and choices and how they may applied to specific speech interface interactions. This part-day multidisciplinary workshop aims to critically map out and evaluate theoretical frameworks and methodological approaches across a number of disciplines and establish directions for new paradigms in understanding speech interface user behaviour. In doing so, we will bring together participants from HCI and other speech related domains to establish a cohesive, diverse and collaborative community of researchers from academia and industry with interest in exploring theoretical and methodological issues in the field.
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| 20. |
- Clark, William A. V., et al.
(författare)
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A Multiscalar Analysis of Neighborhood Composition in Los Angeles, 2000-2010 : A Location-Based Approach to Segregation and Diversity
- 2015
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Ingår i: Annals of the Association of American Geographers. - : Informa UK Limited. - 0004-5608 .- 1467-8306. ; 105:6, s. 1260-1284
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Tidskriftsartikel (refereegranskat)abstract
- There continues to be cross-disciplinary interest in the patterns, extent, and changing contexts of segregation and spatial inequality more generally. The changes are clearly context dependent but at the same time there are broad generalizations that arise from the processes of residential sorting and selection. A major question in U.S. segregation research is how the growth of Asian and Hispanic populations is influencing patterns of segregation and diversity at the neighborhood level. In this article we use a variant of a nearest neighbor approach to map, graph, and evaluate patterns of race and ethnicity at varying scales. We show that using a multiscalar approach to segregation can provide a detailed and more complete picture of segregation. The research confirms work from other studies that segregation is decreasing between some groups and increasing between others, and the patterns, and processes can be described as dynamic diversity. In a series of maps of ethnic clusters and population homogeneity we show how metropolitan areas, represented in this case by Los Angeles, now display patterns of complex living arrangements with multiple groups inhabiting both local neighborhoods and wider community spheres.
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| 21. |
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| 22. |
- Clark, William A V, et al.
(författare)
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Segregation and De-segregation in Metropolitan Contexts : Los Angeles as a Paradigm for a Changing Ethnic World
- 2014
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- The residential changes in the Los Angeles metropolitan area can be seen as a metaphor for the kinds of changes which are occurring and will continue to accelerate in the large metropolitan areas of the United States and global cities more generally. New immigrants are changing the ethnic patterns of neighborhoods and communities, and the old patterns of black white segregation are increasingly a picture of the past. In this paper we use a variant of a nearest neighbor approach to map, graph and evaluate the likelihood of individuals meeting other similar race individuals or of meeting individuals of a different race or ethnicity. The research provides evidence that segregation is decreasing between some groups, increasing between others and that the distribution of mixed race individuals is a growing part of the story about residential ethnic patterns. In a series of maps of both homogeneity and heterogeneity the research shows how the metropolitan areas, represented in this case by Los Angeles, are now patterns of complex living arrangements with multiple groups inhabiting both local neighborhoods and wider community spheres. In this study we identify emerging mixed neighborhoods of different types. Some neighborhoods are disadvantaged in terms of income and employment others are among the most advantaged in the Los Angeles area. Overall the picture is one of growing complexity in the patterns of racial and ethnic groups.
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| 23. |
- Clark, William A. V., et al.
(författare)
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What can we learn about changing ethnic diversity from the distributions of mixed-race individuals?
- 2018
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Ingår i: Urban geography. - : Informa UK Limited. - 0272-3638 .- 1938-2847. ; 39:2, s. 263-281
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Tidskriftsartikel (refereegranskat)abstract
- It is hypothesized that self-defined mixed-race persons live in residentially mixed areas in the largest metropolitan areas in California. The hypothesis is tested by examining the distribution of mixed-race persons among ethnically and racially diverse and nondiverse neighborhoods in the San Francisco and Los Angeles Metropolitan Areas. The research confirmed that mixed-race individuals are more likely to live in areas with ethnic diversity and that the tendency is greater for the mixed-race population in the San Francisco–Oakland Metropolitan Areas than in the Los Angeles Metropolitan Area. Mixed-race individuals live in neighborhoods which are diverse with mixes of all four major ethnic and racial groups, and in “well-off” (but not the most affluent) neighborhoods. The study also shows that the mixed-race population is youthful. The association of mixed-race individuals and racially integrated neighborhoods will have important implications for the evolving nature of spatial integration in California specifically, and the United States more generally.
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| 24. |
- Coombes, Brandon J, et al.
(författare)
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Association of Attention-Deficit/Hyperactivity Disorder and Depression Polygenic Scores with Lithium Response: A Consortium for Lithium Genetics Study.
- 2021
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Ingår i: Complex psychiatry. - : S. Karger AG. - 2673-3005 .- 2673-298X. ; 7:3-4, s. 80-89
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Tidskriftsartikel (refereegranskat)abstract
- Response to lithium varies widely between individuals with bipolar disorder (BD). Polygenic risk scores (PRSs) can uncover pharmacogenomics effects and may help predict drug response. Patients (N = 2,510) with BD were assessed for long-term lithium response in the Consortium on Lithium Genetics using the Retrospective Criteria of Long-Term Treatment Response in Research Subjects with Bipolar Disorder score. PRSs for attention-deficit/hyperactivity disorder (ADHD), major depressive disorder (MDD), and schizophrenia (SCZ) were computed using lassosum and in a model including all three PRSs and other covariates, and the PRS of ADHD (β = -0.14; 95% confidence interval [CI]: -0.24 to -0.03; p value = 0.010) and MDD (β = -0.16; 95% CI: -0.27 to -0.04; p value = 0.005) predicted worse quantitative lithium response. A higher SCZ PRS was associated with higher rates of medication nonadherence (OR = 1.61; 95% CI: 1.34-1.93; p value = 2e-7). This study indicates that genetic risk for ADHD and depression may influence lithium treatment response. Interestingly, a higher SCZ PRS was associated with poor adherence, which can negatively impact treatment response. Incorporating genetic risk of ADHD, depression, and SCZ in combination with clinical risk may lead to better clinical care for patients with BD.
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| 25. |
- Culvenor, Adam G, et al.
(författare)
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Dynamic Single-Leg Postural Control is Impaired Bilaterally Following ACL Reconstruction : Implications for Reinjury Risk
- 2016
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Ingår i: Journal of Orthopaedic and Sports Physical Therapy. - : Journal of Orthopaedic & Sports Physical Therapy (JOSPT). - 0190-6011 .- 1938-1344. ; 46:5, s. 357-364
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Tidskriftsartikel (refereegranskat)abstract
- Study Design Controlled laboratory study; cross-sectional. Background Postural control following anterior cruciate ligament reconstruction (ACLR) primarily has been investigated during static single-leg balance tasks. Little is known about dynamic postural control deficits post-ACLR. Objectives To compare dynamic postural control (bilaterally) in persons who have undergone ACLR and healthy controls, and to evaluate the relationship between dynamic postural control and self-reported and objective function. Methods 97 participants (66 males, median age 28 years) 12 months post-ACLR and 48 healthy controls (20 males, median age 30 years) underwent balance assessment using a Nintendo Wii Balance Board during a single-leg squat. Center of pressure (CoP) path velocity, as well as CoP amplitude and standard deviation (SD) in both mediolateral (ML) and anteroposterior (AP) directions, were recorded. Self-reported function was assessed with the International Knee Documentation Committee Subjective form (IKDC), while hop-for-distance was used to evaluate functional status. Results Compared to healthy controls, the ACLR group had greater mean CoP path velocity (16% higher, p=0.004), ML range (23%, p<0.001), ML SD (28%, p<0.001), AP range (14%, p=0.009) and AP SD (15%, p=0.013) indicating worse dynamic balance post-ACLR. Dynamic balance performance was similar between the ACLR limb and the uninjured contralateral limb. AP SD was weakly associated with hop performance (β -0.2, p=0.046); no balance measures were associated with the IKDC score. Conclusion Individuals who have undergone ACLR demonstrate impaired dynamic balance bilaterally when performing a single-leg squat which may have implications for physical function and future injury risk. Routine dynamic balance assessment may help identify patients who could benefit from targeted neuromuscular training programs to improve objective function and potentially lower re-injury risk. J Orthop Sports Phys Ther, Epub 21 Mar 2016. doi:10.2519/jospt.2016.6305.
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| 26. |
- Fresard, Laure, et al.
(författare)
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Identification of rare-disease genes using blood transcriptome sequencing and large control cohorts
- 2019
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Ingår i: Nature Medicine. - : NATURE PUBLISHING GROUP. - 1078-8956 .- 1546-170X. ; 25:6, s. 911-919
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Tidskriftsartikel (refereegranskat)abstract
- It is estimated that 350 million individuals worldwide suffer from rare diseases, which are predominantly caused by mutation in a single gene(1). The current molecular diagnostic rate is estimated at 50%, with whole-exome sequencing (WES) among the most successful approaches(2-5). For patients in whom WES is uninformative, RNA sequencing (RNA-seq) has shown diagnostic utility in specific tissues and diseases(6-8). This includes muscle biopsies from patients with undiagnosed rare muscle disorders(6,9), and cultured fibroblasts from patients with mitochondrial disorders(7). However, for many individuals, biopsies are not performed for clinical care, and tissues are difficult to access. We sought to assess the utility of RNA-seq from blood as a diagnostic tool for rare diseases of different pathophysiologies. We generated whole-blood RNA-seq from 94 individuals with undiagnosed rare diseases spanning 16 diverse disease categories. We developed a robust approach to compare data from these individuals with large sets of RNA-seq data for controls (n = 1,594 unrelated controls and n = 49 family members) and demonstrated the impacts of expression, splicing, gene and variant filtering strategies on disease gene identification. Across our cohort, we observed that RNA-seq yields a 7.5% diagnostic rate, and an additional 16.7% with improved candidate gene resolution.
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| 27. |
- Guerreiro, Rita, et al.
(författare)
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Genome-wide analysis of genetic correlation in dementia with Lewy bodies, Parkinson's and Alzheimer's diseases.
- 2016
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Ingår i: Neurobiology of Aging. - : Elsevier BV. - 1558-1497 .- 0197-4580. ; 38, s. 7-214
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Tidskriftsartikel (refereegranskat)abstract
- The similarities between dementia with Lewy bodies (DLB) and both Parkinson's disease (PD) and Alzheimer's disease (AD) are many and range from clinical presentation, to neuropathological characteristics, to more recently identified, genetic determinants of risk. Because of these overlapping features, diagnosing DLB is challenging and has clinical implications since some therapeutic agents that are applicable in other diseases have adverse effects in DLB. Having shown that DLB shares some genetic risk with PD and AD, we have now quantified the amount of sharing through the application of genetic correlation estimates, and show that, from a purely genetic perspective, and excluding the strong association at the APOE locus, DLB is equally correlated to AD and PD.
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| 28. |
- Holder, Peter E., et al.
(författare)
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Preparing for a changing future in recreational fisheries : 100 research questions for global consideration emerging from a horizon scan
- 2020
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Ingår i: Reviews in Fish Biology and Fisheries. - : Springer Science and Business Media LLC. - 0960-3166 .- 1573-5184. ; 30:1, s. 137-151
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Forskningsöversikt (refereegranskat)abstract
- Recreational fisheries hold immense ecological, social, and economic value. The management of these fisheries is increasingly important as we move forward in the Anthropocene. Recreational fisheries managers face several challenges as fisheries often involve diverse social and ecological systems comprised of complex feedback and stakeholder motivations and needs. Here, we used a horizon scanning exercise to yield 100 research questions related to recreational fisheries science and management in the Anthropocene. Initial research questions (n = 205) were collected from recreational fisheries experts (i.e., stakeholders, managers, researchers) from various sectors (i.e., industry, government, NGOs) and geographic locations (14 countries: Australia, Brazil, Canada, Czech Republic, Germany, Italy, New Zealand, Norway, South Africa, Spain, Sweden, Switzerland, United Kingdom, USA). These questions were subsequently categorized, thematized, and refined by our authorship team, eventually yielding what we considered to be the top 100 research questions of relevance to management of recreational fisheries. The key themes include: human dimensions; bioeconomics; resource monitoring and data acquisition; governance; management-regulatory actions; management-stock and habitat enhancement; catch-and-release; impacts of recreational fisheries on populations, communities and ecosystems; threats and sustainability; and angler outreach, education and engagement. It is our intention that this comprehensive and forward-looking list will create a framework to guide future research within this field, and contribute to evidence-based recreational fisheries management and policy.
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| 29. |
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| 30. |
- Jerneck, Anne, et al.
(författare)
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Structuring Sustainability Science
- 2011
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Ingår i: Sustainability Science. - : Springer Science and Business Media LLC. - 1862-4057 .- 1862-4065. ; 6:1, s. 69-82
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Tidskriftsartikel (refereegranskat)abstract
- It is urgent in science and society to address climate change and other sustainability challenges such as biodiversity loss, deforestation, depletion of marine fish stocks, global ill-health, land degradation, land use change and water scarcity. Sustainability science (SS) is an attempt to bridge the natural and social sciences for seeking creative solutions to these complex challenges. In this article, we propose a research agenda that advances the methodological and theoretical understanding of what SS can be, how it can be pursued and what it can contribute. The key focus is on knowledge structuring. For that purpose, we designed a generic research platform organised as a three-dimensional matrix comprising three components: core themes (scientific understanding, sustainability goals, sustainability pathways); cross-cutting critical and problem- solving approaches; and any combination of the sustainability challenges above. As an example, we insert four sustainability challenges into the matrix (biodiversity loss, climate change, land use changes, water scarcity). Based on the matrix with the four challenges, we discuss three issues for advancing theory and methodology in SS: how new synergies across natural and social sciences can be created; how integrated theories for understanding and responding to complex sustainability issues can be developed; and how theories and concepts in economics, gender studies, geography, political science and sociology can be applied in SS. The generic research platform serves to structure and create new knowledge in SS and is a tool for exploring any set of sustainability challenges. The combined critical and problem- solving approach is essential.
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| 31. |
- Kehoe, Laura, et al.
(författare)
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Make EU trade with Brazil sustainable
- 2019
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 364:6438, s. 341-
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 32. |
- Kelsoe, John, et al.
(författare)
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Lithium Response in Bipolar Disorder is Associated with Focal Adhesion and PI3K-Akt Networks: A Multi-omics Replication Study.
- 2023
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Ingår i: Research square.
-
Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Lithium is the gold standard treatment for bipolar disorder (BD). However, its mechanism of action is incompletely understood, and prediction of treatment outcomes is limited. In our previous multi-omics study of the Pharmacogenomics of Bipolar Disorder (PGBD) sample combining transcriptomic and genomic data, we found that focal adhesion, the extracellular matrix (ECM), and PI3K-Akt signaling networks were associated with response to lithium. In this study, we replicated the results of our previous study using network propagation methods in a genome-wide association study of an independent sample of 2,039 patients from the International Consortium on Lithium Genetics (ConLiGen) study. We identified functional enrichment in focal adhesion and PI3K-Akt pathways, but we did not find an association with the ECM pathway. Our results suggest that deficits in the neuronal growth cone and PI3K-Akt signaling, but not in ECM proteins, may influence response to lithium in BD.
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| 33. |
- Kun-Rodrigues, Celia, et al.
(författare)
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Analysis of C9orf72 repeat expansions in a large international cohort of dementia with Lewy bodies
- 2017
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Ingår i: Neurobiology of Aging. - : Elsevier BV. - 0197-4580 .- 1558-1497. ; 49
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Tidskriftsartikel (refereegranskat)abstract
- . C9orf72 repeat expansions are a common cause of amyotrophic lateral sclerosis and frontotemporal dementia. To date, no large-scale study of dementia with Lewy bodies (DLB) has been undertaken to assess the role of . C9orf72 repeat expansions in the disease. Here, we investigated the prevalence of . C9orf72 repeat expansions in a large cohort of DLB cases and identified no pathogenic repeat expansions in neuropathologically or clinically defined cases, showing that . C9orf72 repeat expansions are not causally associated with DLB.
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| 34. |
- Ou, Anna H., et al.
(författare)
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Lithium response in bipolar disorder is associated with focal adhesion and PI3K-Akt networks: a multi-omics replication study
- 2024
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Ingår i: TRANSLATIONAL PSYCHIATRY. - 2158-3188. ; 14:1
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Tidskriftsartikel (refereegranskat)abstract
- Lithium is the gold standard treatment for bipolar disorder (BD). However, its mechanism of action is incompletely understood, and prediction of treatment outcomes is limited. In our previous multi-omics study of the Pharmacogenomics of Bipolar Disorder (PGBD) sample combining transcriptomic and genomic data, we found that focal adhesion, the extracellular matrix (ECM), and PI3K-Akt signaling networks were associated with response to lithium. In this study, we replicated the results of our previous study using network propagation methods in a genome-wide association study of an independent sample of 2039 patients from the International Consortium on Lithium Genetics (ConLiGen) study. We identified functional enrichment in focal adhesion and PI3K-Akt pathways, but we did not find an association with the ECM pathway. Our results suggest that deficits in the neuronal growth cone and PI3K-Akt signaling, but not in ECM proteins, may influence response to lithium in BD.
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| 35. |
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| 36. |
- Tang, Weiyi, et al.
(författare)
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Database of nitrification and nitrifiers in the global ocean
- 2023
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Ingår i: EARTH SYSTEM SCIENCE DATA. - 1866-3508 .- 1866-3516. ; 15:11, s. 5039-5077
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Tidskriftsartikel (refereegranskat)abstract
- As a key biogeochemical pathway in the marine nitrogen cycle, nitrification (ammonia oxidation and nitrite oxidation) converts the most reduced form of nitrogen - ammonium-ammonia (NH-NH3) - into the oxidized species nitrite (NO) and nitrate (NO). In the ocean, these processes are mainly performed by ammonia-oxidizing archaea (AOA) and bacteria (AOB) and nitrite-oxidizing bacteria (NOB). By transforming nitrogen speciation and providing substrates for nitrogen removal, nitrification affects microbial community structure; marine productivity (including chemoautotrophic carbon fixation); and the production of a powerful greenhouse gas, nitrous oxide (N2O). Nitrification is hypothesized to be regulated by temperature, oxygen, light, substrate concentration, substrate flux, pH and other environmental factors. Although the number of field observations from various oceanic regions has increased considerably over the last few decades, a global synthesis is lacking, and understanding how environmental factors control nitrification remains elusive. Therefore, we have compiled a database of nitrification rates and nitrifier abundance in the global ocean from published literature and unpublished datasets. This database includes 2393 and 1006 measurements of ammonia oxidation and nitrite oxidation rates and 2242 and 631 quantifications of ammonia oxidizers and nitrite oxidizers, respectively. This community effort confirms and enhances our understanding of the spatial distribution of nitrification and nitrifiers and their corresponding drivers such as the important role of substrate concentration in controlling nitrification rates and nitrifier abundance. Some conundrums are also revealed, including the inconsistent observations of light limitation and high rates of nitrite oxidation reported from anoxic waters. This database can be used to constrain the distribution of marine nitrification, to evaluate and improve biogeochemical models of nitrification, and to quantify the impact of nitrification on ecosystem functions like marine productivity and N2O production. This database additionally sets a baseline for comparison with future observations and guides future exploration (e.g., measurements in the poorly sampled regions such as the Indian Ocean and method comparison and/or standardization). The database is publicly available at the Zenodo repository: https://doi.org/10.5281/zenodo.8355912 (Tang et al., 2023).
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| 37. |
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| 38. |
- Wang, Shijun, et al.
(författare)
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Electrochemical and Electrogenerated Chemiluminescent Studies of a Trinuclear Complex, [((phen)2Ru(dpp))2RhCl2]5+, and Its Interactions with Calf Thymus DNA
- 2009
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Ingår i: Analytical Chemistry. - : American Chemical Society (ACS). - 0003-2700 .- 1520-6882. ; 81:10, s. 4068-4075
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Tidskriftsartikel (refereegranskat)abstract
- The electrochemical behavior of a trinuclear ruthenium(II)-containing complex, [((phen)2Ru(dpp))2RhCl2]5+ (where phen = 1,10-phenanthroline, dpp = 2,3-bis(2-pyridyl)pyrazine), was studied in acetonitrile (MeCN) and aqueous solutions. In MeCN containing 0.10 M tetra-n-butylammonium perchlorate (TBAP), the complex displayed a reversible, overlapping RuII/III redox process with E1/2 = +1.21 V vs Ag/Ag+ (10 mM), an irreversible reduction of RhIII/I at −0.73 V vs Ag/Ag+, and two quasi-reversible dpp/dpp− couples with E1/2 = −1.11 and −1.36 V vs Ag/Ag+ at a Pt electrode with a scan rate of 50 mV s−1. In 0.20 M Tris buffer solution (pH 7.4), an irreversible, overlapping RuII/III oxidation at +1.48 V vs Ag/AgCl (3 M KCl), and an irreversible reduction of RhIII/II at −0.78 V vs Ag/AgCl were observed at a glassy carbon electrode with a scan rate of 50 mV/s. Investigations on the electrogenerated chemiluminescence (ECL) of the complex revealed that 2-(dibutylamino) ethanol (DBAE) was superior to tri-n-propylamine (TPrA) as an ECL coreactant within their entire concentration range of 10−100 mM in MeCN, and in aqueous media, as low as 1.0 nM of the complex can be detected using TPrA coreactant ECL. A maximum ECL emission of 640 nm, which is about 55 nm blue shift to its fluorescence, was observed in MeCN with DBAE as a coreactant. Interactions of the complex with calf thymus DNA (ctDNA) were conducted with a flow-cell based quartz-crystal microbalance, and a binding constant of 2.5 × 105 M−1 was calculated on the basis of the Langmuir isotherm equation.
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| 39. |
- Wittenmyer, Robert A., et al.
(författare)
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The Pan-Pacific Planet Search. VII. the Most Eccentric Planet Orbiting a Giant Star
- 2017
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Ingår i: The Astronomical Journal. - : American Astronomical Society. - 0004-6256 .- 1538-3881. ; 154:6
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Tidskriftsartikel (refereegranskat)abstract
- Radial velocity observations from three instruments reveal the presence of a 4 M Jup planet candidate orbiting the K giant HD 76920. HD 76920b has an orbital eccentricity of 0.856 ±0.009, making it the most eccentric planet known to orbit an evolved star. There is no indication that HD 76920 has an unseen binary companion, suggesting a scattering event rather than Kozai oscillations as a probable culprit for the observed eccentricity. The candidate planet currently approaches to about four stellar radii from its host star, and is predicted to be engulfed on a ∼100 Myr timescale due to the combined effects of stellar evolution and tidal interactions.
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| 40. |
- Woll, Petter S, et al.
(författare)
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Myelodysplastic Syndromes Are Propagated by Rare and Distinct Human Cancer Stem Cells In Vivo.
- 2014
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Ingår i: Cancer Cell. - : Elsevier BV. - 1878-3686 .- 1535-6108. ; 25:6, s. 794-808
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Tidskriftsartikel (refereegranskat)abstract
- Evidence for distinct human cancer stem cells (CSCs) remains contentious and the degree to which different cancer cells contribute to propagating malignancies in patients remains unexplored. In low- to intermediate-risk myelodysplastic syndromes (MDS), we establish the existence of rare multipotent MDS stem cells (MDS-SCs), and their hierarchical relationship to lineage-restricted MDS progenitors. All identified somatically acquired genetic lesions were backtracked to distinct MDS-SCs, establishing their distinct MDS-propagating function in vivo. In isolated del(5q)-MDS, acquisition of del(5q) preceded diverse recurrent driver mutations. Sequential analysis in del(5q)-MDS revealed genetic evolution in MDS-SCs and MDS-progenitors prior to leukemic transformation. These findings provide definitive evidence for rare human MDS-SCs in vivo, with extensive implications for the targeting of the cells required and sufficient for MDS-propagation.
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