| 1. |
- Baumeister, Hannah, et al.
(författare)
-
A generalizable data-driven model of atrophy heterogeneity and progression in memory clinic settings
-
Ingår i: Brain : a journal of neurology. - 1460-2156. ; 147:7, s. 2400-2413
-
Tidskriftsartikel (refereegranskat)abstract
- Memory clinic patients are a heterogeneous population representing various aetiologies of pathological aging. It is unknown if divergent spatiotemporal progression patterns of brain atrophy, as previously described in Alzheimer's disease (AD) patients, are prevalent and clinically meaningful in this group of older adults. To uncover distinct atrophy subtypes, we applied the Subtype and Stage Inference (SuStaIn) algorithm to baseline structural MRI data from 813 participants enrolled in the DELCODE cohort (mean ± SD age = 70.67 ± 6.07 years, 52% females). Participants were cognitively unimpaired (CU; n = 285) or fulfilled diagnostic criteria for subjective cognitive decline (SCD; n = 342), mild cognitive impairment (MCI; n = 118), or dementia of the Alzheimer's type (n = 68). Atrophy subtypes were compared in baseline demographics, fluid AD biomarker levels, the Preclinical Alzheimer Cognitive Composite (PACC-5), as well as episodic memory and executive functioning. PACC-5 trajectories over up to 240 weeks were examined. To test if baseline atrophy subtype and stage predicted clinical trajectories before manifest cognitive impairment, we analysed PACC-5 trajectories and MCI conversion rates of CU and SCD participants. Limbic-predominant and hippocampal-sparing atrophy subtypes were identified. Limbic-predominant atrophy first affected the medial temporal lobes, followed by further temporal and, finally, the remaining cortical regions. At baseline, this subtype was related to older age, more pathological AD biomarker levels, APOE ε4 carriership, and an amnestic cognitive impairment. Hippocampal-sparing atrophy initially occurred outside the temporal lobe with the medial temporal lobe spared up to advanced atrophy stages. This atrophy pattern also affected individuals with positive AD biomarkers and was associated with more generalised cognitive impairment. Limbic-predominant atrophy, in all and in only unimpaired participants, was linked to more negative longitudinal PACC-5 slopes than observed in participants without or with hippocampal-sparing atrophy and increased the risk of MCI conversion. SuStaIn modelling was repeated in a sample from the Swedish BioFINDER-2 cohort. Highly similar atrophy progression patterns and associated cognitive profiles were identified. Cross-cohort model generalizability, both on the subject and group level, were excellent, indicating reliable performance in previously unseen data. The proposed model is a promising tool for capturing heterogeneity among older adults at early at-risk states for AD in applied settings. The implementation of atrophy subtype- and stage-specific end-points may increase the statistical power of pharmacological trials targeting early AD.
|
|
| 2. |
- Hendriksen, Rene S., et al.
(författare)
-
Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage
- 2019
-
Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 10:1
-
Tidskriftsartikel (refereegranskat)abstract
- © 2019, The Author(s). Antimicrobial resistance (AMR) is a serious threat to global public health, but obtaining representative data on AMR for healthy human populations is difficult. Here, we use metagenomic analysis of untreated sewage to characterize the bacterial resistome from 79 sites in 60 countries. We find systematic differences in abundance and diversity of AMR genes between Europe/North-America/Oceania and Africa/Asia/South-America. Antimicrobial use data and bacterial taxonomy only explains a minor part of the AMR variation that we observe. We find no evidence for cross-selection between antimicrobial classes, or for effect of air travel between sites. However, AMR gene abundance strongly correlates with socio-economic, health and environmental factors, which we use to predict AMR gene abundances in all countries in the world. Our findings suggest that global AMR gene diversity and abundance vary by region, and that improving sanitation and health could potentially limit the global burden of AMR. We propose metagenomic analysis of sewage as an ethically acceptable and economically feasible approach for continuous global surveillance and prediction of AMR.
|
|
| 3. |
- Marouli, Eirini, et al.
(författare)
-
Rare and low-frequency coding variants alter human adult height
- 2017
-
Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 542:7640, s. 186-190
-
Tidskriftsartikel (refereegranskat)abstract
- Height is a highly heritable, classic polygenic trait with approximately 700 common associated variants identified through genome-wide association studies so far. Here, we report 83 height-associated coding variants with lower minor-allele frequencies (in the range of 0.1-4.8%) and effects of up to 2 centimetres per allele (such as those in IHH, STC2, AR and CRISPLD2), greater than ten times the average effect of common variants. In functional follow-up studies, rare height increasing alleles of STC2 (giving an increase of 1-2 centimetres per allele) compromised proteolytic inhibition of PAPP-A and increased cleavage of IGFBP-4 in vitro, resulting in higher bioavailability of insulin-like growth factors. These 83 height-associated variants overlap genes that are mutated in monogenic growth disorders and highlight new biological candidates (such as ADAMTS3, IL11RA and NOX4) and pathways (such as proteoglycan and glycosaminoglycan synthesis) involved in growth. Our results demonstrate that sufficiently large sample sizes can uncover rare and low-frequency variants of moderate-to-large effect associated with polygenic human phenotypes, and that these variants implicate relevant genes and pathways.
|
|
| 4. |
- Turcot, Valerie, et al.
(författare)
-
Protein-altering variants associated with body mass index implicate pathways that control energy intake and expenditure in obesity
- 2018
-
Ingår i: Nature Genetics. - : Nature Publishing Group. - 1061-4036 .- 1546-1718. ; 50:1, s. 26-41
-
Tidskriftsartikel (refereegranskat)abstract
- Genome-wide association studies (GWAS) have identified >250 loci for body mass index (BMI), implicating pathways related to neuronal biology. Most GWAS loci represent clusters of common, noncoding variants from which pinpointing causal genes remains challenging. Here we combined data from 718,734 individuals to discover rare and low-frequency (minor allele frequency (MAF) < 5%) coding variants associated with BMI. We identified 14 coding variants in 13 genes, of which 8 variants were in genes (ZBTB7B, ACHE, RAPGEF3, RAB21, ZFHX3, ENTPD6, ZFR2 and ZNF169) newly implicated in human obesity, 2 variants were in genes (MC4R and KSR2) previously observed to be mutated in extreme obesity and 2 variants were in GIPR. The effect sizes of rare variants are similar to 10 times larger than those of common variants, with the largest effect observed in carriers of an MC4R mutation introducing a stop codon (p.Tyr35Ter, MAF = 0.01%), who weighed similar to 7 kg more than non-carriers. Pathway analyses based on the variants associated with BMI confirm enrichment of neuronal genes and provide new evidence for adipocyte and energy expenditure biology, widening the potential of genetically supported therapeutic targets in obesity.
|
|
| 5. |
- Andrew, Churchill, et al.
(författare)
-
Vision of the hand and environmental context in human prehension
- 2000
-
Ingår i: Experimental Brain Research. - : Springer Science and Business Media LLC. - 0014-4819 .- 1432-1106. ; 134:1, s. 81-89
-
Tidskriftsartikel (refereegranskat)abstract
- Previous findings on the role of visual contact with the hand in the control of reaching and grasping have been contradictory. Some studies have shown that such contact is largely irrelevant, while more recent ones have emphasised its importance. In contrast, information arising from the surrounding environment has received relatively little attention in the study of prehensile actions. In order to identify the roles of both sources of information, we made kinematic comparisons between three conditions. In the first, reaching was performed in a dimly lit room and compared with a second condition in which reaches in the dark, but with the thumb and first finger illuminated, were made to a luminous object. This contrast allows the effects of environmental context to be identified. A comparison between the second and a third condition, in which both vision of the hand and the environment was removed, but the object was still visually available, enabled the assessment of how and when vision of the hand plays a role. Removing environmental cues had effects both early and late in the reach, while vision of the hand was only crucial in the period after peak deceleration. In addition, removal of both sources of information resulted in larger grip apertures. Differences and similarities between our findings and those of other studies are discussed, as is the ongoing debate about the relative importance of visual feedback of the hand in the control and co-ordination of prehensile actions. We conclude with suggestions for further research based on the set-up used in the present study.
|
|
| 6. |
- Aranda-Guillén, Maribel, et al.
(författare)
-
A polygenic risk score to help discriminate primary adrenal insufficiency of different etiologies.
- 2023
-
Ingår i: Journal of internal medicine. - : John Wiley & Sons. - 0954-6820 .- 1365-2796. ; 294:1, s. 96-109
-
Tidskriftsartikel (refereegranskat)abstract
- Autoimmune Addison's disease (AAD) is the most common cause of primary adrenal insufficiency (PAI). Despite its exceptionally high heritability, tools to estimate disease susceptibility in individual patients are lacking. We hypothesized that polygenic risk score (PRS) for AAD could help investigate PAI pathogenesis in pediatric patients.We here constructed and evaluated a PRS for AAD in 1223 seropositive cases and 4097 controls. To test its clinical utility, we reevaluated 18 pediatric patients, whose whole genome we also sequenced. We next explored the individual PRS in more than 120 seronegative patients with idiopathic PAI.The genetic susceptibility to AAD-quantified using PRS-was on average 1.5 standard deviations (SD) higher in patients compared with healthy controls (p<2e-16), and 1.2 SD higher in the young patients compared with the old (p=3e-4). Using the novel PRS, we searched for pediatric patients with strikingly low AAD susceptibility and identified cases of monogenic PAI, previously misdiagnosed as AAD. By stratifying seronegative adult patients by autoimmune comorbidities and disease duration we could delineate subgroups of PRS suggesting various disease etiologies.The PRS performed well for case-control differentiation and susceptibility estimation in individual patients. Remarkably, a PRS for AAD holds promise as a means to detect disease etiologies other than autoimmunity.
|
|
| 7. |
- Deans, Andrew R, et al.
(författare)
-
Finding Our Way through Phenotypes.
- 2015
-
Ingår i: PLoS Biology. - : Public Library of Science (PLoS). - 1545-7885. ; 13:1
-
Tidskriftsartikel (refereegranskat)abstract
- Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility.
|
|
| 8. |
- Dumas, Patrice, et al.
(författare)
-
Options to achieve net-zero emissions from agriculture and land use changes in Latin America and the Caribbean
- 2022
-
Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Eleven countries in Latin America and the Caribbean have pledged to reach net-zero emissions by around 2050. Changes in the food system are key to reach these carbon neutrality goals, as agriculture and resulting land-use changes are responsible for almost half of greenhouse gas emissions in the region. We quantify the effect of supply-side (e.g., yield improvements, silvopasture, agroforestry) and demand-side (e.g., reduction of waste and losses, changing diets) options to reduce emissions and transform the land use system in a net carbon sink by 2050 while improving nutrition for the growing population. We consider both direct agriculture emissions and the pressure that food production puts on land use changes, and track separately emissions that happen in the region and emissions linked to trade. Our findings confirm that cattle plays a preponderant role, emitting nearly 60% of greenhouse gas emissions from agriculture and land-use change. Reaching a net-negative emissions food system able to balance emissions from the rest of the economy will require ambitious and sustained improvements in yields and changes in diets to moderate the increasing demand for beef, continuously decrease the share of land dedicated to agriculture, and increase instead land dedicated to carbon sequestration and biodiversity preservation.
|
|
| 9. |
- Gaches, Brandt A. L., et al.
(författare)
-
The Astrochemistry Low-energy Electron Cross-Section (ALeCS) database
- 2024
-
Ingår i: ASTRONOMY & ASTROPHYSICS. - 0004-6361 .- 1432-0746. ; 684
-
Tidskriftsartikel (refereegranskat)abstract
- Context. Electron-molecule interaction is a fundamental process in radiation-driven chemistry in space, from the interstellar medium to comets. Therefore, knowledge of interaction cross sections is key. There have been a plethora of both theoretical and experimental studies of total ionization cross sections spanning from diatomics to complex organics. However, the data are often spread over many sources or are not public or readily available. Aims. We introduce the Astrochemistry Low-energy Electron cross-section (ALeCS) database. This is a public database for electron interaction cross sections and ionization rates for molecules of astrochemical interest. In particular, we present here the first data release, comprising total ionization cross sections and ionization rates for over 200 neutral molecules. Methods. We include optimized geometries and molecular orbital energies at various levels of quantum chemistry theory. Furthermore, for a subset of the molecules, we have calculated ionization potentials. We computed the total ionization cross sections using the binary-encounter Bethe model and screening-corrected additivity rule, and we computed ionization rates and reaction network coefficients for molecular cloud environments. Results. We present the cross sections and reaction rates for >200 neutral molecules ranging from diatomics to complex organics, with the largest being C14H10. We find that the screening-corrected additivity rule cross sections generally significantly overestimate experimental total ionization cross sections. We demonstrate that our binary-encounter Bethe cross sections agree well with experimental data. We show that the ionization rates scale roughly linearly with the number of constituent atoms in the molecule. Conclusions. We introduce and describe the public ALeCS database. For the initial release, we include total ionization cross sections for >200 neutral molecules and several cations and anions calculated with different levels of quantum chemistry theory, the chemical reaction rates for the ionization, and network files in the formats of the two most popular astrochemical networks: the Kinetic Database for Astrochemistry, and UMIST. The database will be continuously updated for more molecules and interactions.
|
|
| 10. |
- Gaches, Brandt, 1990, et al.
(författare)
-
The Astrochemistry Low-energy Electron Cross-Section (ALeCS) database I. Semi-empirical electron-impact ionization cross-section calculations and ionization rates
- 2024
-
Ingår i: Astronomy and Astrophysics. - 0004-6361 .- 1432-0746. ; 684
-
Tidskriftsartikel (refereegranskat)abstract
- Context. Electron–molecule interaction is a fundamental process in radiation-driven chemistry in space, from the interstellar medium to comets. Therefore, knowledge of interaction cross sections is key. There have been a plethora of both theoretical and experimental studies of total ionization cross sections spanning from diatomics to complex organics. However, the data are often spread over many sources or are not public or readily available. Aims. We introduce the Astrochemistry Low-energy Electron cross-section (ALeCS) database. This is a public database for electron interaction cross sections and ionization rates for molecules of astrochemical interest. In particular, we present here the first data release, comprising total ionization cross sections and ionization rates for over 200 neutral molecules. Methods. We include optimized geometries and molecular orbital energies at various levels of quantum chemistry theory. Furthermore, for a subset of the molecules, we have calculated ionization potentials. We computed the total ionization cross sections using the binary-encounter Bethe model and screening-corrected additivity rule, and we computed ionization rates and reaction network coefficients for molecular cloud environments. Results. We present the cross sections and reaction rates for >200 neutral molecules ranging from diatomics to complex organics, with the largest being C14H10. We find that the screening-corrected additivity rule cross sections generally significantly overestimate experimental total ionization cross sections. We demonstrate that our binary-encounter Bethe cross sections agree well with experimental data. We show that the ionization rates scale roughly linearly with the number of constituent atoms in the molecule. Conclusions. We introduce and describe the public ALeCS database. For the initial release, we include total ionization cross sections for >200 neutral molecules and several cations and anions calculated with different levels of quantum chemistry theory, the chemical reaction rates for the ionization, and network files in the formats of the two most popular astrochemical networks: the Kinetic Database for Astrochemistry, and UMIST. The database will be continuously updated for more molecules and interactions.
|
|
