| 1. |
- Hyde, K. D., et al.
(author)
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Global consortium for the classification of fungi and fungus-like taxa
- 2023
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In: MYCOSPHERE. - : Mushroom Research Foundation. - 2077-7000 .- 2077-7019. ; 14:1, s. 1960-2012
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Journal article (peer-reviewed)abstract
- The Global Consortium for the Classification of Fungi and fungus-like taxa is an international initiative of more than 550 mycologists to develop an electronic structure for the classification of these organisms. The members of the Consortium originate from 55 countries/regions worldwide, from a wide range of disciplines, and include senior, mid-career and early-career mycologists and plant pathologists. The Consortium will publish a biannual update of the Outline of Fungi and fungus-like taxa, to act as an international scheme for other scientists. Notes on all newly published taxa at or above the level of species will be prepared and published online on the Outline of Fungi website (https://www.outlineoffungi.org/), and these will be finally published in the biannual edition of the Outline of Fungi and fungus-like taxa. Comments on recent important taxonomic opinions on controversial topics will be included in the biannual outline. For example, 'to promote a more stable taxonomy in Fusarium given the divergences over its generic delimitation', or 'are there too many genera in the Boletales?' and even more importantly, 'what should be done with the tremendously diverse 'dark fungal taxa?' There are undeniable differences in mycologists' perceptions and opinions regarding species classification as well as the establishment of new species. Given the pluralistic nature of fungal taxonomy and its implications for species concepts and the nature of species, this consortium aims to provide a platform to better refine and stabilise fungal classification, taking into consideration views from different parties. In the future, a confidential voting system will be set up to gauge the opinions of all mycologists in the Consortium on important topics. The results of such surveys will be presented to the International Commission on the Taxonomy of Fungi (ICTF) and the Nomenclature Committee for Fungi (NCF) with opinions and percentages of votes for and against. Criticisms based on scientific evidence with regards to nomenclature, classifications, and taxonomic concepts will be welcomed, and any recommendations on specific taxonomic issues will also be encouraged; however, we will encourage professionally and ethically responsible criticisms of others' work. This biannual ongoing project will provide an outlet for advances in various topics of fungal classification, nomenclature, and taxonomic concepts and lead to a community-agreed classification scheme for the fungi and fungus-like taxa. Interested parties should contact the lead author if they would like to be involved in future outlines.
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| 2. |
- Campbell, PJ, et al.
(author)
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Pan-cancer analysis of whole genomes
- 2020
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In: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
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Journal article (peer-reviewed)abstract
- Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1–3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10–18.
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| 3. |
- Callaway, EM, et al.
(author)
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A multimodal cell census and atlas of the mammalian primary motor cortex
- 2021
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In: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 598:7879, s. 86-102
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Journal article (peer-reviewed)abstract
- Here we report the generation of a multimodal cell census and atlas of the mammalian primary motor cortex as the initial product of the BRAIN Initiative Cell Census Network (BICCN). This was achieved by coordinated large-scale analyses of single-cell transcriptomes, chromatin accessibility, DNA methylomes, spatially resolved single-cell transcriptomes, morphological and electrophysiological properties and cellular resolution input–output mapping, integrated through cross-modal computational analysis. Our results advance the collective knowledge and understanding of brain cell-type organization1–5. First, our study reveals a unified molecular genetic landscape of cortical cell types that integrates their transcriptome, open chromatin and DNA methylation maps. Second, cross-species analysis achieves a consensus taxonomy of transcriptomic types and their hierarchical organization that is conserved from mouse to marmoset and human. Third, in situ single-cell transcriptomics provides a spatially resolved cell-type atlas of the motor cortex. Fourth, cross-modal analysis provides compelling evidence for the transcriptomic, epigenomic and gene regulatory basis of neuronal phenotypes such as their physiological and anatomical properties, demonstrating the biological validity and genomic underpinning of neuron types. We further present an extensive genetic toolset for targeting glutamatergic neuron types towards linking their molecular and developmental identity to their circuit function. Together, our results establish a unifying and mechanistic framework of neuronal cell-type organization that integrates multi-layered molecular genetic and spatial information with multi-faceted phenotypic properties.
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| 4. |
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| 5. |
- Sadrizadeh, Sasan, et al.
(author)
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Indoor air quality and health in schools : A critical review for developing the roadmap for the future school environment
- 2022
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In: Journal of Building Engineering. - : Elsevier Ltd. - 2352-7102. ; 57
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Journal article (peer-reviewed)abstract
- Several research studies have ranked indoor pollution among the top environmental risks to public health in recent years. Good indoor air quality is an essential component of a healthy indoor environment and significantly affects human health and well-being. Poor air quality in such environments may cause respiratory disease for millions of pupils around the globe and, in the current pandemic-dominated era, require ever more urgent actions to tackle the burden of its impacts. The poor indoor quality in such environments could result from poor management, operation, maintenance, and cleaning. Pupils are a different segment of the population from adults in many ways, and they are more exposed to the poor indoor environment: They breathe in more air per unit weight and are more sensitive to heat/cold and moisture. Thus, their vulnerability is higher than adults, and poor conditions may affect proper development. However, a healthy learning environment can reduce the absence rate, improves test scores, and enhances pupil/teacher learning/teaching productivity. In this article, we analyzed recent literature on indoor air quality and health in schools, with the primary focus on ventilation, thermal comfort, productivity, and exposure risk. This study conducts a comprehensive review to summarizes the existing knowledge to highlight the latest research and solutions and proposes a roadmap for the future school environment. In conclusion, we summarize the critical limitations of the existing studies, reveal insights for future research directions, and propose a roadmap for further improvements in school air quality. More parameters and specific data should be obtained from in-site measurements to get a more in-depth understanding at contaminant characteristics. Meanwhile, site-specific strategies for different school locations, such as proximity to transportation routes and industrial areas, should be developed to suit the characteristics of schools in different regions. The socio-economic consequences of health and performance effects on children in classrooms should be considered. There is a great need for more comprehensive studies with larger sample sizes to study on environmental health exposure, student performance, and indoor satisfaction. More complex mitigation measures should be evaluated by considering energy efficiency, IAQ and health effects.
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| 6. |
- Backis, A., et al.
(author)
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Time- and energy-resolved effects in the boron-10 based multi-grid and helium-3 based thermal neutron detectors
- 2021
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In: Measurement science and technology. - : IOP PUBLISHING LTD. - 0957-0233 .- 1361-6501. ; 32:3
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Journal article (peer-reviewed)abstract
- The boron-10 based multi-grid detector is being developed as an alternative to helium-3 based neutron detectors. At the European Spallation Source, the detector will be used for time-of-flight neutron spectroscopy at cold to thermal neutron energies. The objective of this work is to investigate fine time- and energy-resolved effects of the Multi-Grid detector, down to a few mu eV, while comparing it to the performance of a typical helium-3 tube. Furthermore, it is to characterize differences between the detector technologies in terms of internal scattering, as well as the time reconstruction of similar to mu s short neutron pulses. The data were taken at the Helmholtz Zentrum Berlin, where the Multi-Grid detector and a helium-3 tube were installed at the ESS test beamline, V20. Using a Fermi-chopper, the neutron beam of the reactor was chopped into a few tens of mu s wide pulses before reaching the detector, located a few tens of cm downstream. The data of the measurements show an agreement between the derived and calculated neutron detection efficiency curve. The data also provide fine details on the effect of internal scattering, and how it can be reduced. For the first time, the chopper resolution was comparable to the timing resolution of the Multi-Grid detector. This allowed a detailed study of time- and energy resolved effects, as well as a comparison with a typical helium-3 tube.
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| 7. |
- Beal, Jacob, et al.
(author)
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Robust estimation of bacterial cell count from optical density
- 2020
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In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Journal article (peer-reviewed)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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| 8. |
- Mao, W, et al.
(author)
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Bupi Yishen Formula Versus Losartan for Non-Diabetic Stage 4 Chronic Kidney Disease: A Randomized Controlled Trial
- 2021
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In: Frontiers in pharmacology. - : Frontiers Media SA. - 1663-9812. ; 11, s. 627185-
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Journal article (peer-reviewed)abstract
- Chinese herbal medicine (CHM) might have benefits in patients with non-diabetic chronic kidney disease (CKD), but there is a lack of high-quality evidence, especially in CKD4. This study aimed to assess the efficacy and safety of Bupi Yishen Formula (BYF) vs. losartan in patients with non-diabetic CKD4. This trial was a multicenter, double-blind, double-dummy, randomized controlled trial that was carried out from 11-08-2011 to 07-20-2015. Patients were assigned (1:1) to receive either BYF or losartan for 48 weeks. The primary outcome was the change in the slope of the estimated glomerular filtration rate (eGFR) over 48 weeks. The secondary outcomes were the composite of end-stage kidney disease, death, doubling of serum creatinine, stroke, and cardiovascular events. A total of 567 patients were randomized to BYF (n = 283) or losartan (n = 284); of these, 549 (97%) patients were included in the final analysis. The BYF group had a slower renal function decline particularly prior to 12 weeks over the 48-week duration (between-group mean difference of eGFR slopes: −2.25 ml/min/1.73 m2/year, 95% confidence interval [CI]: −4.03,−0.47), and a lower risk of composite outcome of death from any cause, doubling of serum creatinine level, end-stage kidney disease (ESKD), stroke, or cardiovascular events (adjusted hazard ratio = 0.61, 95%CI: 0.44,0.85). No significant between-group differences were observed in the incidence of adverse events. We conclude that BYF might have renoprotective effects among non-diabetic patients with CKD4 in the first 12 weeks and over 48 weeks, but longer follow-up is required to evaluate the long-term effects.Clinical Trial Registration:http://www.chictr.org.cn, identifier ChiCTR-TRC-10001518.
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| 9. |
- Sun, Jie, 1977, et al.
(author)
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Insights into the Mechanism for Vertical Graphene Growth by Plasma-Enhanced Chemical Vapor Deposition
- 2022
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In: Acs Applied Materials & Interfaces. - : American Chemical Society (ACS). - 1944-8244 .- 1944-8252. ; 14:5, s. 7152-7160
-
Journal article (peer-reviewed)abstract
- Vertically oriented graphene (VG) has attracted attention for years, but the growth mechanism is still not fully revealed. The electric field may play a role, but the direct evidence and exactly what role it plays remains unclear. Here, we conduct a systematic study and find that in plasma-enhanced chemical vapor deposition, the VG growth preferably occurs at spots where the local field is stronger, for example, at GaN nanowire tips. On almost round-shaped nanoparticles, instead of being perpendicular to the substrate, the VG grows along the field direction, that is, perpendicular to the particles' local surfaces. Even more convincingly, the sheath field is screened to different degrees, and a direct correlation between the field strength and the VG growth is observed. Numerical calculation suggests that during the growth, the field helps accumulate charges on graphene, which eventually changes the cohesive graphene layers into separate three-dimensional VG flakes. Furthermore, the field helps attract charged precursors to places sticking out from the substrate and makes them even sharper and turn into VG. Finally, we demonstrate that the VG-covered nanoparticles are benign to human blood leukocytes and could be considered for drug delivery. Our research may serve as a starting point for further vertical two-dimensional material growth mechanism studies.
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| 10. |
- Auchtung, Thomas A, et al.
(author)
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Temporal changes in gastrointestinal fungi and the risk of autoimmunity during early childhood : the TEDDY study
- 2022
-
In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 13
-
Journal article (peer-reviewed)abstract
- Fungal infections are a major health problem that often begin in the gastrointestinal tract. Gut microbe interactions in early childhood are critical for proper immune responses, yet there is little known about the development of the fungal population from infancy into childhood. Here, as part of the TEDDY (The Environmental Determinants of Diabetes in the Young) study, we examine stool samples of 888 children from 3 to 48 months and find considerable differences between fungi and bacteria. The metagenomic relative abundance of fungi was extremely low but increased while weaning from milk and formula. Overall fungal diversity remained constant over time, in contrast with the increase in bacterial diversity. Fungal profiles had high temporal variation, but there was less variation from month-to-month in an individual than among different children of the same age. Fungal composition varied with geography, diet, and the use of probiotics. Multiple Candida spp. were at higher relative abundance in children than adults, while Malassezia and certain food-associated fungi were lower in children. There were only subtle fungal differences associated with the subset of children that developed islet autoimmunity or type 1 diabetes. Having proper fungal exposures may be crucial for children to establish appropriate responses to fungi and limit the risk of infection: the data here suggests those gastrointestinal exposures are limited and variable.
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| 11. |
- Bell, E., et al.
(author)
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Active sulfur cycling in the terrestrial deep subsurface
- 2020
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In: The ISME Journal. - : Springer Nature. - 1751-7362 .- 1751-7370. ; 14:5, s. 1260-1272
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Journal article (peer-reviewed)abstract
- The deep terrestrial subsurface remains an environment where there is limited understanding of the extant microbial metabolisms. At Olkiluoto, Finland, a deep geological repository is under construction for the final storage of spent nuclear fuel. It is therefore critical to evaluate the potential impact microbial metabolism, including sulfide generation, could have upon the safety of the repository. We investigated a deep groundwater where sulfate is present, but groundwater geochemistry suggests limited microbial sulfate-reducing activity. Examination of the microbial community at the genome-level revealed microorganisms with the metabolic capacity for both oxidative and reductive sulfur transformations. Deltaproteobacteria are shown to have the genetic capacity for sulfate reduction and possibly sulfur disproportionation, while Rhizobiaceae, Rhodocyclaceae, Sideroxydans, and Sulfurimonas oxidize reduced sulfur compounds. Further examination of the proteome confirmed an active sulfur cycle, serving for microbial energy generation and growth. Our results reveal that this sulfide-poor groundwater harbors an active microbial community of sulfate-reducing and sulfide-oxidizing bacteria, together mediating a sulfur cycle that remained undetected by geochemical monitoring alone. The ability of sulfide-oxidizing bacteria to limit the accumulation of sulfide was further demonstrated in groundwater incubations and highlights a potential sink for sulfide that could be beneficial for geological repository safety.
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| 12. |
- de Winter, J M, et al.
(author)
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KBTBD13 is an actin-binding protein that modulates muscle kinetics
- 2020
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In: Journal of Clinical Investigation. - : Stanford University Press. - 0021-9738 .- 1558-8238. ; 130:2, s. 754-767
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Journal article (peer-reviewed)abstract
- The mechanisms that modulate the kinetics of muscle relaxation are critically important for muscle function. A prime example of the impact of impaired relaxation kinetics is nemaline myopathy caused by mutations in KBTBD13 (NEM6). In addition to weakness, NEM6 patients have slow muscle relaxation, compromising contractility and daily life activities. The role of KBTBD13 in muscle is unknown, and the pathomechanism underlying NEM6 is undetermined. A combination of transcranial magnetic stimulation-induced muscle relaxation, muscle fiber- and sarcomere-contractility assays, low-angle x-ray diffraction, and superresolution microscopy revealed that the impaired muscle-relaxation kinetics in NEM6 patients are caused by structural changes in the thin filament, a sarcomeric microstructure. Using homology modeling and binding and contractility assays with recombinant KBTBD13, Kbtbd13-knockout and Kbtbd13(R408c)-knockin mouse models, and a GFP-labeled Kbtbd13-transgenic zebrafish model, we discovered that KBTBD13 binds to actin - a major constituent of the thin filament - and that mutations in KBTBD13 cause structural changes impairing muscle-relaxation kinetics. We propose that this actin-based impaired relaxation is central to NEM6 pathology.
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| 13. |
- Dust, Lukas, et al.
(author)
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Federated Fuzzy Learning with Imbalanced Data
- 2021
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In: Proceedings - 20th IEEE International Conference on Machine Learning and Applications, ICMLA 2021. - : Institute of Electrical and Electronics Engineers Inc.. - 9781665443371 ; , s. 1130-1137
-
Conference paper (peer-reviewed)abstract
- Federated learning (FL) is an emerging and privacy-preserving machine learning technique that is shown to be increasingly important in the digital age. The two challenging issues for FL are: (1) communication overhead between clients and the server, and (2) volatile distribution of training data such as class imbalance. The paper aims to tackle these two challenges with the proposal of a federated fuzzy learning algorithm (FFLA) that can be used for data-based construction of fuzzy classification models in a distributed setting. The proposed learning algorithm is fast and highly cheap in communication by requiring only two rounds of interplay between the server and clients. Moreover, FFLA is empowered with an an imbalance adaptation mechanism so that it remains robust against heterogeneous distributions of data and class imbalance. The efficacy of the proposed learning method has been verified by the simulation tests made on a set of balanced and imbalanced benchmark data sets.
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| 14. |
- Gehrmann, Sebastian, et al.
(author)
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GEMv2: Multilingual NLG Benchmarking in a Single Line of Code
- 2022
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In: Proceedings of the 2022 Conference on Empirical Methods in Natural Language Processing: System Demonstrations. - : Association for Computational Linguistics (ACL). ; , s. 266-281
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Conference paper (peer-reviewed)abstract
- Evaluations in machine learning rarely use the latest metrics, datasets, or human evaluation in favor of remaining compatible with prior work. The compatibility, often facilitated through leaderboards, thus leads to outdated but standardized evaluation practices. We pose that the standardization is taking place in the wrong spot. Evaluation infrastructure should enable researchers to use the latest methods and what should be standardized instead is how to incorporate these new evaluation advances.We introduce GEMv2, the new version of the Generation, Evaluation, and Metrics Benchmark which uses a modular infrastructure for dataset, model, and metric developers to benefit from each other’s work. GEMv2 supports 40 documented datasets in 51 languages, ongoing online evaluation for all datasets, and our interactive tools make it easier to add new datasets to the living benchmark.
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| 15. |
- Guintivano, Jerry, et al.
(author)
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Meta-Analyses of Genome-Wide Association Studies for Postpartum Depression
- 2023
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In: American Journal of Psychiatry. - : American Psychiatric Association Publishing. - 0002-953X .- 1535-7228. ; 180:12, s. 884-895
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Journal article (peer-reviewed)abstract
- OBJECTIVE: Postpartum depression (PPD) is a common subtype of major depressive disorder (MDD) that is more heritable, yet is understudied in psychiatric genetics. The authors conducted meta-analyses of genome-wide association studies (GWASs) to investigate the genetic architecture of PPD.METHOD: Meta-analyses were conducted on 18 cohorts of European ancestry (17,339 PPD cases and 53,426 controls), one cohort of East Asian ancestry (975 cases and 3,780 controls), and one cohort of African ancestry (456 cases and 1,255 controls), totaling 18,770 PPD cases and 58,461 controls. Post-GWAS analyses included 1) single-nucleotide polymorphism (SNP)-based heritability ([Formula: see text]), 2) genetic correlations between PPD and other phenotypes, and 3) enrichment of the PPD GWAS findings in 27 human tissues and 265 cell types from the mouse central and peripheral nervous system.RESULTS: No SNP achieved genome-wide significance in the European or the trans-ancestry meta-analyses. The [Formula: see text] of PPD was 0.14 (SE=0.02). Significant genetic correlations were estimated for PPD with MDD, bipolar disorder, anxiety disorders, posttraumatic stress disorder, insomnia, age at menarche, and polycystic ovary syndrome. Cell-type enrichment analyses implicate inhibitory neurons in the thalamus and cholinergic neurons within septal nuclei of the hypothalamus, a pattern that differs from MDD.CONCLUSIONS: While more samples are needed to reach genome-wide levels of significance, the results presented confirm PPD as a polygenic and heritable phenotype. There is also evidence that despite a high correlation with MDD, PPD may have unique genetic components. Cell enrichment results suggest GABAergic neurons, which converge on a common mechanism with the only medication approved by the U.S. Food and Drug Administration for PPD (brexanolone).
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| 16. |
- Harder, Constantin, et al.
(author)
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Optical Properties of Slot‐Die Coated Hybrid Colloid/Cellulose‐Nanofibril Thin Films
- 2023
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In: Advanced Optical Materials. - : Wiley. - 2162-7568 .- 2195-1071. ; 11:13
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Journal article (peer-reviewed)abstract
- Correlating nanostructure and optical properties of thin hybrid films is the crucial ingredient for designing sustainable applications ranging from structural colors in anticounterfeiting to sensors. Here, the tailoring of the refractive index of hybrid cellulose nanofibril/water-dispersed colloidal ink thin films is presented. The authors apply scalable, layer-by-layer slot-die coating for preparing the cellulose nanofibril and hybrid thin films. Making use of the mobility of the polymer chains in the colloids upon annealing, the influence of the different colloid sizes and their glass transition temperature on the refractive index of the hybrid material is shown. The complex refractive indices of the thin films are characterized by spectroscopic ellipsometry and correlated to the different nanostructures of the thin films. The authors find that post-deposition annealing changes the colloidal nanostructure from particulate to agglomerates. Depending on the size of the colloids, imbibition of the colloids into the cellulose nanofibril template is observed. This scalable approach offers new avenues in structural color functional biomaterial hybrid layers.
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| 17. |
- Johnson, Suzanne Bennett, et al.
(author)
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First-appearing islet autoantibodies for type 1 diabetes in young children : maternal life events during pregnancy and the child's genetic risk
- 2021
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In: Diabetologia. - : Springer Science and Business Media LLC. - 1432-0428 .- 0012-186X. ; 64:3, s. 591-602
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Journal article (peer-reviewed)abstract
- AIMS/HYPOTHESIS: Psychological stress has long been considered a possible trigger of type 1 diabetes, although prospective studies examining the link between psychological stress or life events during pregnancy and the child's type 1 diabetes risk are rare. The objective of this study was to examine the association between life events during pregnancy and first-appearing islet autoantibodies (IA) in young children, conditioned by the child's type 1 diabetes-related genetic risk.METHODS: The IA status of 7317 genetically at-risk The Environmental Determinants of Diabetes in the Young (TEDDY) participants was assessed every 3 months from 3 months to 4 years, and bi-annually thereafter. Reports of major life events during pregnancy were collected at study inception when the child was 3 months of age and placed into one of six categories. Life events during pregnancy were examined for association with first-appearing insulin (IAA) (N = 222) or GAD (GADA) (N = 209) autoantibodies in the child until 6 years of age using proportional hazard models. Relative excess risk due to interaction (RERI) by the child's HLA-DR and SNP profile was estimated.RESULTS: Overall, 65% of mothers reported a life event during pregnancy; disease/injury (25%), serious interpersonal (28%) and job-related (25%) life events were most common. The association of life events during pregnancy differed between IAA and GADA as the first-appearing autoantibody. Serious interpersonal life events correlated with increased risk of GADA-first only in HLA-DR3 children with the BACH2-T allele (HR 2.28, p < 0.0001), an additive interaction (RERI 1.87, p = 0.0004). Job-related life events were also associated with increased risk of GADA-first among HLA-DR3/4 children (HR 1.53, p = 0.04) independent of serious interpersonal life events (HR 1.90, p = 0.002), an additive interaction (RERI 1.19, p = 0.004). Job-related life events correlated with reduced risk of IAA-first (HR 0.55, p = 0.004), particularly in children with the BTNL2-GG allele (HR 0.48; 95% CI 0.31, 0.76).CONCLUSIONS/INTERPRETATION: Specific life events during pregnancy are differentially related to IAA vs GADA as first-appearing IA and interact with different HLA and non-HLA genetic factors, supporting the concept of different endotypes underlying type 1 diabetes. However, the mechanisms underlying these associations remain to be discovered. Life events may be markers for other yet-to-be-identified factors important to the development of first-appearing IA.
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| 18. |
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| 19. |
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| 20. |
- Lin, Jake, et al.
(author)
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Distinct transcriptomic profiles in children prior to the appearance of type 1 diabetes-linked islet autoantibodies and following enterovirus infection
- 2023
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In: Nature Communications. - 2041-1723. ; 14, s. 1-13
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Journal article (peer-reviewed)abstract
- Although the genetic basis and pathogenesis of type 1 diabetes have been studied extensively, how host responses to environmental factors might contribute to autoantibody development remains largely unknown. Here, we use longitudinal blood transcriptome sequencing data to characterize host responses in children within 12 months prior to the appearance of type 1 diabetes-linked islet autoantibodies, as well as matched control children. We report that children who present with insulin-specific autoantibodies first have distinct transcriptional profiles from those who develop GADA autoantibodies first. In particular, gene dosage-driven expression of GSTM1 is associated with GADA autoantibody positivity. Moreover, compared with controls, we observe increased monocyte and decreased B cell proportions 9-12 months prior to autoantibody positivity, especially in children who developed antibodies against insulin first. Lastly, we show that control children present transcriptional signatures consistent with robust immune responses to enterovirus infection, whereas children who later developed islet autoimmunity do not. These findings highlight distinct immune-related transcriptomic differences between case and control children prior to case progression to islet autoimmunity and uncover deficient antiviral response in children who later develop islet autoimmunity.
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| 21. |
- López, D., et al.
(author)
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BELIEF : A distance-based redundancy-proof feature selection method for Big Data
- 2021
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In: Information Sciences. - : Elsevier Inc.. - 0020-0255 .- 1872-6291. ; 558, s. 124-139
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Journal article (peer-reviewed)abstract
- With the advent of Big Data era, data reduction methods are in highly demand given their ability to simplify huge data, and ease complex learning processes. Concretely, algorithms able to select relevant dimensions from a set of millions are of huge importance. Although effective, these techniques also suffer from the “scalability” curse when they are brought into tackle large-scale problems. In this paper, we propose a distributed feature weighting algorithm which precisely estimates feature importance in large datasets using the well-know algorithm RELIEF in small problems. Our solution, called BELIEF, incorporates a novel redundancy elimination measure that generates similar schemes to those based on entropy, but at a much lower time cost. Furthermore, BELIEF provides a smooth scale-up when more instances are required to increase precision in estimations. Empirical tests performed on our method illustrate the estimation ability of BELIEF in manifold huge sets – both in number of features and instances, as well as its reduced runtime cost as compared to other state-of-the-art methods.
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| 22. |
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| 23. |
- Pasman, Joëlle A., et al.
(author)
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Epidemiological overview of major depressive disorder in Scandinavia using nationwide registers
- 2023
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In: The Lancet Regional Health. - : Elsevier. - 2666-7762. ; 29
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Journal article (peer-reviewed)abstract
- BACKGROUND: Major depressive disorder (MDD) is a common psychiatric disorder associated with a high disease burden. This study gives a comprehensive overview of the prevalence, outcomes, treatment, and genetic epidemiology of MDD within and across the Scandinavian countries.METHODS: This study has aimed to assess and compare across Norway, Denmark, and Sweden 1) the prevalence and trajectories of MDD and comorbidity, 2) outcomes and treatment, and 3) heritability (Denmark and Sweden only). The analyses leveraged data on 272,944 MDD cases (and 6.2 million non-cases) from Norway, Sweden, and Denmark in specialist care in national longitudinal health registers covering 1975-2013. Relying on harmonized public data global comparisons of socioeconomic and health metrics were performed to assess to what extent findings are generalizable.FINDINGS: MDD ranked among the most prevalent psychiatric disorders. For many cases, the disorder trajectory was severe, with varying proportions experiencing recurrence, developing comorbid disorders, requiring inpatient treatment, or dying of suicide. Important country differences in specialist care prevalence and treatment were observed. Heritability estimates were moderate (35-48%). In terms of socioeconomic and health indices, the Scandinavian nations were comparable to one another and grouped with other Western nations.INTERPRETATION: The Scandinavian countries were similar with regards to MDD epidemiological measures, but we show that differences in health care organization need to be taken into consideration when comparing countries. This study demonstrates the utility of using comprehensive population-wide registry data, outlining possibilities for other applications. The findings will be of use to policy makers for developing better prevention and intervention strategies.
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| 24. |
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| 25. |
- Singh, Harishchandra, et al.
(author)
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Unveiling nano-scaled chemical inhomogeneity impacts on corrosion of Ce-modified 2507 super-duplex stainless steels
- 2022
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In: npj Materials Degradation. - : Springer Science and Business Media LLC. - 2397-2106. ; 6:1
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Journal article (peer-reviewed)abstract
- The widely used stainless steels and their deformed variants are anticorrosive in ambient conditions due to passivation layers composed of chromium oxides. Conventionally, corrosion and erosion of the steels are attributed to the breakdown of such layers but seldomly to the origin that depends on surface heterogeneity at the microscopic level. In this work, the nanometer-scaled chemical heterogeneity at the surface unveiled via spectro-microscopy and chemometric analysis unexpectedly dominates the breakdown and corrosion behavior of the cold-rolled Ce-modified 2507 super-duplex stainless steels (SDSS) over its hot-deformed counterpart. Though relatively uniformly covered by a native Cr2O3 layer revealed by X-ray photoemission electron microscopy, the cold-rolled SDSS behaved poorly in passivity because of locally distributed Fe3+ rich nano-islands over the Fe/Cr oxide layer. This atomic-level knowledge provides a deep understanding of corrosion of stainless steel and is expected to benefit corrosion controls of similar high-alloyed metals.
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| 26. |
- Sun, H., et al.
(author)
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Effect of early prophylactic low-dose recombinant human erythropoietin on retinopathy of prematurity in very preterm infants
- 2020
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In: Journal of Translational Medicine. - : Springer Science and Business Media LLC. - 1479-5876. ; 18:1
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Journal article (peer-reviewed)abstract
- Background: Very preterm infants are at risk of developing retinopathy of prematurity (ROP). Recombinant human erythropoietin (rhEPO) is routinely used to prevent anemia in preterm infants; however, the effect of rhEPO on ROP development is still controversial. The purpose of this study was to evaluate the effect of early prophylactic low-dose rhEPO administration on ROP development in very preterm infants. Methods: A total of 1898 preterm infants born before 32weeks of gestation were included. Preterm infants received rhEPO (n = 950; 500 U/kg, rhEPO group) or saline (n = 948, control group) intravenously within 72h of birth and then once every other day for 2weeks. Results: The total incidence of ROP was not significantly different between the two groups (10.2% vs. 13.2%, p = 0.055). Further analysis showed that rhEPO group had lower rates of type 2 ROP than the control group (2.2% vs. 4.1%, RR 0.98; 95% CI 0.96–1.00; p = 0.021). Subgroup analysis found that rhEPO treatment significantly decreased the incidence of type 2 ROP in infant boys (1.8% vs. 4.3%, p = 0.021) and in those with a gestational age of 28–296/7weeks (1.1% vs. 4.9%, p = 0.002) and birth weight of 1000–1499g (1.2% vs. 4.2%, p = 0.002). There was a small increasing tendency for the incidence of ROP in infants with a gestational age of < 28weeks after rhEPO treatment. Conclusions: Repeated low-dose rhEPO administration has no significant influence on the development of ROP; however, it may be effective for type 2 ROP in infant boys or in infants with gestational age > 28weeks and birth weight > 1500g. Trial registration The data of this study were retrieved from two clinical studies registered ClinicalTrials.gov (NCT 02036073) on January 14, 2014, https://clinicaltrials.gov/ct2/show/NCT02036073; and (NCT03919500) on April 18, 2019. https://clinicaltrials.gov/ct2/show/NCT03919500. © 2020, The Author(s).
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| 27. |
- Sun, Y., et al.
(author)
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Battery degradation evaluation based on impedance spectra using a limited number of voltage-capacity curves
- 2024
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In: eTransporation. - : Elsevier. - 2590-1168. ; 22
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Journal article (peer-reviewed)abstract
- Degradation prediction is crucial for ensuring safe and reliable operation of batteries. However, relying solely on capacity to characterize aging cannot comprehensively represent the health status of the battery. This work explores the potential of using a limited number of partial voltage-capacity curves to evaluate battery degradation with the aid of deep learning approaches, which can be used for onboard applications. A sequence-to-sequence model is proposed to predict the electrochemical impedance spectra during battery degradation. It only uses capacity sequences within a specific voltage range at fixed voltage increments from a limited number of cycles, which can be flexibly adapted to different life stages in an end-to-end manner. The proposed method has been validated based on the developed degradation dataset. The root mean square errors for the prediction of impedance spectra are less than 1.48 mΩ. Capacities and resistances associated with electrochemical processes can be further extracted from the obtained impedance spectra, facilitating a comprehensive evaluation of battery degradation. As a limited number of measured data are needed, the proposed method can reduce data storage requirements and computational demands, which enables fast and comprehensive aging diagnosis.
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| 28. |
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| 29. |
- Wood, Madeline E., et al.
(author)
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Sex differences in associations between APOE ε2 and longitudinal cognitive decline
- 2023
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In: Alzheimer's and Dementia. - : Wiley. - 1552-5260 .- 1552-5279. ; 19:10, s. 4651-4661
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Journal article (peer-reviewed)abstract
- INTRODUCTION: We examined whether sex modifies the association between APOE ε2 and cognitive decline in two independent samples. METHODS: We used observational data from cognitively unimpaired non-Hispanic White (NHW) and non-Hispanic Black (NHB) adults. Linear mixed models examined interactive associations of APOE genotype (ε2 or ε4 carrier vs. ε3/ε3) and sex on cognitive decline in NHW and NHB participants separately. RESULTS: In both Sample 1 (N = 9766) and Sample 2 (N = 915), sex modified the association between APOE ε2 and cognitive decline in NHW participants. Specifically, relative to APOE ε3/ε3, APOE ε2 protected against cognitive decline in men but not women. Among APOE ε2 carriers, men had slower decline than women. Among APOE ε3/ε3 carriers, cognitive trajectories did not differ between sexes. There were no sex-specific associations of APOE ε2 with cognition in NHB participants (N = 2010). DISCUSSION: In NHW adults, APOE ε2 may protect men but not women against cognitive decline. Highlights: We studied sex-specific apolipoprotein E (APOE) ε2 effects on cognitive decline. In non-Hispanic White (NHW) adults, APOE ε2 selectively protects men against decline. Among men, APOE ε2 was more protective than APOE ε3/ε3. In women, APOE ε2 was no more protective than APOE ε3/ε3. Among APOE ε2 carriers, men had slower decline than women. There were no sex-specific APOE ε2 effects in non-Hispanic Black (NHB) adults.
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| 30. |
- Wu, Jingnan, et al.
(author)
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Carboxylate substituted pyrazine: A simple and low-cost building block for novel wide bandgap polymer donor enables 15.3% efficiency in organic solar cells
- 2021
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In: Nano Energy. - : Elsevier BV. - 2211-2855. ; 82
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Journal article (peer-reviewed)abstract
- In addition to high power conversion efficiency (PCE) and good stability, the low-cost of photovoltaic materials is also very important for the practical application of organic solar cells (OSCs). Herein, we synthesized a carboxylate substituted pyrazine-based electron-deficient building block (DTCPz) with a simple structure and low synthetic cost, and then developed a novel wide bandgap polymer donor PFBCPZ. Due to the synergistic electron-withdrawing effects of the fluorination in donor unit (BDT-TF) and esterification and C=N double-bond in DTCPz unit, PFBCPZ shows a deeper HOMO level of −5.60 eV, a strong intermolecular π-π interaction, good crystallinity and stacking, and high hole-mobility of 2.11 × 10−3 cm2 V−1 s−1. Matched with a low bandgap acceptor IT-4F, excellent charge transfer, weak recombination, and small non-radiative energy loss in OSCs was achieved, resulting in an impressive fill factor of 0.785 and a high open-circuit voltage of 0.92 V. As a result, a PCE of up to 15.3% is obtained in OSCs, which is the highest value in the IT-4F-based binary OSCs so far and indicates that low-cost DTCPz with a simple structure is a promising building block to construct high-performance polymer donors for application in efficient OSCs.
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| 31. |
- Xhonneux, Louis-Pascal, et al.
(author)
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Transcriptional networks in at-risk individuals identify signatures of type 1 diabetes progression
- 2021
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In: Science Translational Medicine. - : American Association for the Advancement of Science (AAAS). - 1946-6242 .- 1946-6234. ; 13:587
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Journal article (peer-reviewed)abstract
- Type 1 diabetes (T1D) is a disease of insulin deficiency that results from autoimmune destruction of pancreatic islet β cells. The exact cause of T1D remains unknown, although asymptomatic islet autoimmunity lasting from weeks to years before diagnosis raises the possibility of intervention before the onset of clinical disease. The number, type, and titer of islet autoantibodies are associated with long-term disease risk but do not cause disease, and robust early predictors of individual progression to T1D onset remain elusive. The Environmental Determinants of Diabetes in the Young (TEDDY) consortium is a prospective cohort study aiming to determine genetic and environmental interactions causing T1D. Here, we analyzed longitudinal blood transcriptomes of 2013 samples from 400 individuals in the TEDDY study before both T1D and islet autoimmunity. We identified and interpreted age-associated gene expression changes in healthy infancy and age-independent changes tracking with progression to both T1D and islet autoimmunity, beginning before other evidence of islet autoimmunity was present. We combined multivariate longitudinal data in a Bayesian joint model to predict individual risk of T1D onset and validated the association of a natural killer cell signature with progression and the model's predictive performance on an additional 356 samples from 56 individuals in the independent Type 1 Diabetes Prediction and Prevention study. Together, our results indicate that T1D is characterized by early and longitudinal changes in gene expression, informing the immunopathology of disease progression and facilitating prediction of its course.
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| 32. |
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| 33. |
- Xiong, R., et al.
(author)
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Lithium-ion battery aging mechanisms and diagnosis method for automotive applications : Recent advances and perspectives
- 2020
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In: Renewable & sustainable energy reviews. - : Elsevier Ltd. - 1364-0321 .- 1879-0690. ; 131
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Journal article (peer-reviewed)abstract
- Lithium-ion batteries decay every time as it is used. Aging-induced degradation is unlikely to be eliminated. The aging mechanisms of lithium-ion batteries are manifold and complicated which are strongly linked to many interactive factors, such as battery types, electrochemical reaction stages, and operating conditions. In this paper, we systematically summarize mechanisms and diagnosis of lithium-ion battery aging. Regarding the aging mechanism, effects of different internal side reactions on lithium-ion battery degradation are discussed based on the anode, cathode, and other battery structures. The influence of different external factors on the aging mechanism is explained, in which temperature can exert the greatest impact compared to other external factors. As for aging diagnosis, three widely-used methods are discussed: disassembly-based post-mortem analysis, curve-based analysis, and model-based analysis. Generally, the post-mortem analysis is employed for cross-validation while the curve-based analysis and the model-based analysis provide quantitative analysis. The challenges in the use of quantitative diagnosis and on-board diagnosis on battery aging are also discussed, based on which insights are provided for developing online battery aging diagnosis and battery health management in the next generation of intelligent battery management systems (BMSs).
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| 34. |
- Xiong, R., et al.
(author)
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Toward a Safer Battery Management System : A Critical Review on Diagnosis and Prognosis of Battery Short Circuit
- 2020
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In: iScience. - CAMBRIDGE, MA USA : CELL PRESS. - 2589-0042. ; 23:4
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Journal article (peer-reviewed)abstract
- Lithium-ion batteries are commonly used as sources of power for electric vehicles (EVs). Battery safety is a major concern, due to a large number of accidents, for which short circuit has been considered as one of the main causes. Therefore, diagnosing and prognosticating short circuit are of great significance to improve EV safety. This work reviews the current state of the art about the diagnosis and prognosis of short circuit, covering the method and the key indicators. The findings provide important insights regarding how to improve the battery safety.
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| 35. |
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| 36. |
- Xiong, Y., et al.
(author)
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Polygenic risk scores of lithium response and treatment resistance in major depressive disorder
- 2023
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In: Translational Psychiatry. - 2158-3188. ; 13:1
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Journal article (peer-reviewed)abstract
- Treatment response and resistance in major depressive disorder (MDD) are suggested to be heritable. Due to significant challenges in defining treatment-related phenotypes, our understanding of their genetic bases is limited. This study aimed to derive a stringent definition of treatment resistance and to investigate the genetic overlap between treatment response and resistance in MDD. Using electronic medical records on the use of antidepressants and electroconvulsive therapy (ECT) from Swedish registers, we derived the phenotype of treatment-resistant depression (TRD) and non-TRD within similar to 4500 individuals with MDD in three Swedish cohorts. Considering antidepressants and lithium are first-line treatment and augmentation used for MDD, respectively, we generated polygenic risk scores (PRS) of antidepressants and lithium response for individuals with MDD and evaluated their associations with treatment resistance by comparing TRD with non-TRD. Among 1778 ECT-treated MDD cases, nearly all (94%) used antidepressants before their first ECT and the vast majority had at least one (84%) or two (61%) antidepressants of adequate duration, suggesting these MDD cases receiving ECT were resistant to antidepressants. We did not observe a significant difference in the mean PRS of antidepressant response between TRD and non-TRD; however, we found that TRD cases had a significantly higher PRS of lithium response compared to non-TRD cases (OR = 1.10-1.12 under various definitions). The results support the evidence of heritable components in treatment-related phenotypes and highlight the overall genetic profile of lithium-sensitivity in TRD. This finding further provides a genetic explanation for lithium efficacy in treating TRD.
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| 37. |
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| 38. |
- Yuan, Shuai, et al.
(author)
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Deciphering the genetic architecture of atrial fibrillation offers insights into disease prediction, pathophysiology and downstream sequelae.
- 2023
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In: medRxiv : the preprint server for health sciences.
-
Journal article (peer-reviewed)abstract
- AIMS: The study aimed to discover novel genetic loci for atrial fibrillation (AF), explore the shared genetic etiologies between AF and other cardiovascular and cardiometabolic traits, and uncover AF pathogenesis using Mendelian randomization analysis.METHODS AND RESULTS: We conducted a genome-wide association study meta-analysis including 109,787 AF cases and 1,165,920 controls of European ancestry and identified 215 loci, among which 91 were novel. We performed Genomic Structural Equation Modeling analysis between AF and four cardiovascular comorbidities (coronary artery disease, ischemic stroke, heart failure, and vneous thromboembolism) and found 189 loci shared across these diseases as well as a universal genetic locus shared by atherosclerotic outcomes (i.e., rs1537373 near CDKN2B). Three genetic loci (rs10740129 near JMJD1C, rs2370982 near NRXN3, and rs9931494 near FTO) were associated with AF and cardiometabolic traits. A polygenic risk score derived from this genome-wide meta-analysis was associated with AF risk (odds ratio 2.36, 95% confidence interval 2.31-2.41 per standard deviation increase) in the UK biobank. This score, combined with age, sex, and basic clinical features, predicted AF risk (AUC 0.784, 95% CI 0.781-0.787) in Europeans. Phenome-wide association analysis of the polygenic risk score identified many AF-related comorbidities of the circulatory, endocrine, and respiratory systems. Phenome-wide and multi-omic Mendelian randomization analyses identified associations of blood lipids and pressure, diabetes, insomnia, obesity, short sleep, and smoking, 27 blood proteins, one gut microbe (genus.Catenibacterium), and 11 blood metabolites with risk to AF.CONCLUSIONS: This genome-wide association study and trans-omic Mendelian randomization analysis provides insights into disease risk prediction, pathophysiology and downstream sequelae.
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| 39. |
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