| 1. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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| 2. |
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| 3. |
- Wang, Haidong, et al.
(författare)
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Global, regional, and national life expectancy, all-cause mortality, and cause-specific mortality for 249 causes of death, 1980-2015 : a systematic analysis for the Global Burden of Disease Study 2015
- 2016
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Ingår i: The Lancet. - 0140-6736 .- 1474-547X. ; 388:10053, s. 1459-1544
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Improving survival and extending the longevity of life for all populations requires timely, robust evidence on local mortality levels and trends. The Global Burden of Disease 2015 Study (GBD 2015) provides a comprehensive assessment of all-cause and cause-specific mortality for 249 causes in 195 countries and territories from 1980 to 2015. These results informed an in-depth investigation of observed and expected mortality patterns based on sociodemographic measures.METHODS: We estimated all-cause mortality by age, sex, geography, and year using an improved analytical approach originally developed for GBD 2013 and GBD 2010. Improvements included refinements to the estimation of child and adult mortality and corresponding uncertainty, parameter selection for under-5 mortality synthesis by spatiotemporal Gaussian process regression, and sibling history data processing. We also expanded the database of vital registration, survey, and census data to 14 294 geography-year datapoints. For GBD 2015, eight causes, including Ebola virus disease, were added to the previous GBD cause list for mortality. We used six modelling approaches to assess cause-specific mortality, with the Cause of Death Ensemble Model (CODEm) generating estimates for most causes. We used a series of novel analyses to systematically quantify the drivers of trends in mortality across geographies. First, we assessed observed and expected levels and trends of cause-specific mortality as they relate to the Socio-demographic Index (SDI), a summary indicator derived from measures of income per capita, educational attainment, and fertility. Second, we examined factors affecting total mortality patterns through a series of counterfactual scenarios, testing the magnitude by which population growth, population age structures, and epidemiological changes contributed to shifts in mortality. Finally, we attributed changes in life expectancy to changes in cause of death. We documented each step of the GBD 2015 estimation processes, as well as data sources, in accordance with Guidelines for Accurate and Transparent Health Estimates Reporting (GATHER).FINDINGS: Globally, life expectancy from birth increased from 61·7 years (95% uncertainty interval 61·4-61·9) in 1980 to 71·8 years (71·5-72·2) in 2015. Several countries in sub-Saharan Africa had very large gains in life expectancy from 2005 to 2015, rebounding from an era of exceedingly high loss of life due to HIV/AIDS. At the same time, many geographies saw life expectancy stagnate or decline, particularly for men and in countries with rising mortality from war or interpersonal violence. From 2005 to 2015, male life expectancy in Syria dropped by 11·3 years (3·7-17·4), to 62·6 years (56·5-70·2). Total deaths increased by 4·1% (2·6-5·6) from 2005 to 2015, rising to 55·8 million (54·9 million to 56·6 million) in 2015, but age-standardised death rates fell by 17·0% (15·8-18·1) during this time, underscoring changes in population growth and shifts in global age structures. The result was similar for non-communicable diseases (NCDs), with total deaths from these causes increasing by 14·1% (12·6-16·0) to 39·8 million (39·2 million to 40·5 million) in 2015, whereas age-standardised rates decreased by 13·1% (11·9-14·3). Globally, this mortality pattern emerged for several NCDs, including several types of cancer, ischaemic heart disease, cirrhosis, and Alzheimer's disease and other dementias. By contrast, both total deaths and age-standardised death rates due to communicable, maternal, neonatal, and nutritional conditions significantly declined from 2005 to 2015, gains largely attributable to decreases in mortality rates due to HIV/AIDS (42·1%, 39·1-44·6), malaria (43·1%, 34·7-51·8), neonatal preterm birth complications (29·8%, 24·8-34·9), and maternal disorders (29·1%, 19·3-37·1). Progress was slower for several causes, such as lower respiratory infections and nutritional deficiencies, whereas deaths increased for others, including dengue and drug use disorders. Age-standardised death rates due to injuries significantly declined from 2005 to 2015, yet interpersonal violence and war claimed increasingly more lives in some regions, particularly in the Middle East. In 2015, rotaviral enteritis (rotavirus) was the leading cause of under-5 deaths due to diarrhoea (146 000 deaths, 118 000-183 000) and pneumococcal pneumonia was the leading cause of under-5 deaths due to lower respiratory infections (393 000 deaths, 228 000-532 000), although pathogen-specific mortality varied by region. Globally, the effects of population growth, ageing, and changes in age-standardised death rates substantially differed by cause. Our analyses on the expected associations between cause-specific mortality and SDI show the regular shifts in cause of death composition and population age structure with rising SDI. Country patterns of premature mortality (measured as years of life lost [YLLs]) and how they differ from the level expected on the basis of SDI alone revealed distinct but highly heterogeneous patterns by region and country or territory. Ischaemic heart disease, stroke, and diabetes were among the leading causes of YLLs in most regions, but in many cases, intraregional results sharply diverged for ratios of observed and expected YLLs based on SDI. Communicable, maternal, neonatal, and nutritional diseases caused the most YLLs throughout sub-Saharan Africa, with observed YLLs far exceeding expected YLLs for countries in which malaria or HIV/AIDS remained the leading causes of early death.INTERPRETATION: At the global scale, age-specific mortality has steadily improved over the past 35 years; this pattern of general progress continued in the past decade. Progress has been faster in most countries than expected on the basis of development measured by the SDI. Against this background of progress, some countries have seen falls in life expectancy, and age-standardised death rates for some causes are increasing. Despite progress in reducing age-standardised death rates, population growth and ageing mean that the number of deaths from most non-communicable causes are increasing in most countries, putting increased demands on health systems.
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| 4. |
- Kassebaum, Nicholas J., et al.
(författare)
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Global, regional, and national disability-adjusted life-years (DALYs) for 315 diseases and injuries and healthy life expectancy (HALE), 1990-2015 : a systematic analysis for the Global Burden of Disease Study 2015
- 2016
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Ingår i: The Lancet. - 0140-6736 .- 1474-547X. ; 388:10053, s. 1603-1658
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Tidskriftsartikel (refereegranskat)abstract
- Background Healthy life expectancy (HALE) and disability-adjusted life-years (DALYs) provide summary measures of health across geographies and time that can inform assessments of epidemiological patterns and health system performance, help to prioritise investments in research and development, and monitor progress toward the Sustainable Development Goals (SDGs). We aimed to provide updated HALE and DALYs for geographies worldwide and evaluate how disease burden changes with development. Methods We used results from the Global Burden of Diseases, Injuries, and Risk Factors Study 2015 (GBD 2015) for all-cause mortality, cause-specific mortality, and non-fatal disease burden to derive HALE and DALYs by sex for 195 countries and territories from 1990 to 2015. We calculated DALYs by summing years of life lost (YLLs) and years of life lived with disability (YLDs) for each geography, age group, sex, and year. We estimated HALE using the Sullivan method, which draws from age-specific death rates and YLDs per capita. We then assessed how observed levels of DALYs and HALE differed from expected trends calculated with the Socio-demographic Index (SDI), a composite indicator constructed from measures of income per capita, average years of schooling, and total fertility rate. Findings Total global DALYs remained largely unchanged from 1990 to 2015, with decreases in communicable, neonatal, maternal, and nutritional (Group 1) disease DALYs off set by increased DALYs due to non-communicable diseases (NCDs). Much of this epidemiological transition was caused by changes in population growth and ageing, but it was accelerated by widespread improvements in SDI that also correlated strongly with the increasing importance of NCDs. Both total DALYs and age-standardised DALY rates due to most Group 1 causes significantly decreased by 2015, and although total burden climbed for the majority of NCDs, age-standardised DALY rates due to NCDs declined. Nonetheless, age-standardised DALY rates due to several high-burden NCDs (including osteoarthritis, drug use disorders, depression, diabetes, congenital birth defects, and skin, oral, and sense organ diseases) either increased or remained unchanged, leading to increases in their relative ranking in many geographies. From 2005 to 2015, HALE at birth increased by an average of 2.9 years (95% uncertainty interval 2.9-3.0) for men and 3.5 years (3.4-3.7) for women, while HALE at age 65 years improved by 0.85 years (0.78-0.92) and 1.2 years (1.1-1.3), respectively. Rising SDI was associated with consistently higher HALE and a somewhat smaller proportion of life spent with functional health loss; however, rising SDI was related to increases in total disability. Many countries and territories in central America and eastern sub-Saharan Africa had increasingly lower rates of disease burden than expected given their SDI. At the same time, a subset of geographies recorded a growing gap between observed and expected levels of DALYs, a trend driven mainly by rising burden due to war, interpersonal violence, and various NCDs. Interpretation Health is improving globally, but this means more populations are spending more time with functional health loss, an absolute expansion of morbidity. The proportion of life spent in ill health decreases somewhat with increasing SDI, a relative compression of morbidity, which supports continued efforts to elevate personal income, improve education, and limit fertility. Our analysis of DALYs and HALE and their relationship to SDI represents a robust framework on which to benchmark geography-specific health performance and SDG progress. Country-specific drivers of disease burden, particularly for causes with higher-than-expected DALYs, should inform financial and research investments, prevention efforts, health policies, and health system improvement initiatives for all countries along the development continuum.
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| 5. |
- 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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| 6. |
- Wang, Anqi, et al.
(författare)
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Characterizing prostate cancer risk through multi-ancestry genome-wide discovery of 187 novel risk variants
- 2023
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Ingår i: Nature Genetics. - : Springer Nature. - 1061-4036 .- 1546-1718. ; 55:12, s. 2065-2074
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Tidskriftsartikel (refereegranskat)abstract
- The transferability and clinical value of genetic risk scores (GRSs) across populations remain limited due to an imbalance in genetic studies across ancestrally diverse populations. Here we conducted a multi-ancestry genome-wide association study of 156,319 prostate cancer cases and 788,443 controls of European, African, Asian and Hispanic men, reflecting a 57% increase in the number of non-European cases over previous prostate cancer genome-wide association studies. We identified 187 novel risk variants for prostate cancer, increasing the total number of risk variants to 451. An externally replicated multi-ancestry GRS was associated with risk that ranged from 1.8 (per standard deviation) in African ancestry men to 2.2 in European ancestry men. The GRS was associated with a greater risk of aggressive versus non-aggressive disease in men of African ancestry (P = 0.03). Our study presents novel prostate cancer susceptibility loci and a GRS with effective risk stratification across ancestry groups.
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| 7. |
- Anney, Richard, et al.
(författare)
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A genome-wide scan for common alleles affecting risk for autism.
- 2010
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Ingår i: Human Molecular Genetics. - : Oxford University Press (OUP). - 0964-6906 .- 1460-2083. ; 19:20, s. 4072-4082
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Tidskriftsartikel (refereegranskat)abstract
- Although autism spectrum disorders (ASDs) have a substantial genetic basis, most of the known genetic risk has been traced to rare variants, principally copy number variants (CNVs). To identify common risk variation, the Autism Genome Project (AGP) Consortium genotyped 1558 rigorously defined ASD families for 1 million single-nucleotide polymorphisms (SNPs) and analyzed these SNP genotypes for association with ASD. In one of four primary association analyses, the association signal for marker rs4141463, located within MACROD2, crossed the genome-wide association significance threshold of P < 5 × 10(-8). When a smaller replication sample was analyzed, the risk allele at rs4141463 was again over-transmitted; yet, consistent with the winner's curse, its effect size in the replication sample was much smaller; and, for the combined samples, the association signal barely fell below the P < 5 × 10(-8) threshold. Exploratory analyses of phenotypic subtypes yielded no significant associations after correction for multiple testing. They did, however, yield strong signals within several genes, KIAA0564, PLD5, POU6F2, ST8SIA2 and TAF1C.
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| 8. |
- Block, Keith I., et al.
(författare)
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Designing a broad-spectrum integrative approach for cancer prevention and treatment
- 2015
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Ingår i: Seminars in Cancer Biology. - : Academic Press. - 1044-579X .- 1096-3650. ; 35, s. S276-S304
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Forskningsöversikt (refereegranskat)abstract
- Targeted therapies and the consequent adoption of "personalized" oncology have achieved notable successes in some cancers; however, significant problems remain with this approach. Many targeted therapies are highly toxic, costs are extremely high, and most patients experience relapse after a few disease-free months. Relapses arise from genetic heterogeneity in tumors, which harbor therapy-resistant immortalized cells that have adopted alternate and compensatory pathways (i.e., pathways that are not reliant upon the same mechanisms as those which have been targeted). To address these limitations, an international task force of 180 scientists was assembled to explore the concept of a low-toxicity "broadspectrum" therapeutic approach that could simultaneously target many key pathways and mechanisms. Using cancer hallmark phenotypes and the tumor microenvironment to account for the various aspects of relevant cancer biology, interdisciplinary teams reviewed each hallmark area and nominated a wide range of high-priority targets (74 in total) that could be modified to improve patient outcomes. For these targets, corresponding low-toxicity therapeutic approaches were then suggested, many of which were phytochemicals. Proposed actions on each target and all of the approaches were further reviewed for known effects on other hallmark areas and the tumor microenvironment Potential contrary or procarcinogenic effects were found for 3.9% of the relationships between targets and hallmarks, and mixed evidence of complementary and contrary relationships was found for 7.1%. Approximately 67% of the relationships revealed potentially complementary effects, and the remainder had no known relationship. Among the approaches, 1.1% had contrary, 2.8% had mixed and 62.1% had complementary relationships. These results suggest that a broad-spectrum approach should be feasible from a safety standpoint. This novel approach has potential to be relatively inexpensive, it should help us address stages and types of cancer that lack conventional treatment, and it may reduce relapse risks. A proposed agenda for future research is offered. (C) 2015 The Authors. Published by Elsevier Ltd.
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| 9. |
- Conti, David, V, et al.
(författare)
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Trans-ancestry genome-wide association meta-analysis of prostate cancer identifies new susceptibility loci and informs genetic risk prediction
- 2021
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Ingår i: Nature Genetics. - : Springer Nature. - 1061-4036 .- 1546-1718. ; 53:1, s. 65-75
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Tidskriftsartikel (refereegranskat)abstract
- Prostate cancer is a highly heritable disease with large disparities in incidence rates across ancestry populations. We conducted a multiancestry meta-analysis of prostate cancer genome-wide association studies (107,247 cases and 127,006 controls) and identified 86 new genetic risk variants independently associated with prostate cancer risk, bringing the total to 269 known risk variants. The top genetic risk score (GRS) decile was associated with odds ratios that ranged from 5.06 (95% confidence interval (CI), 4.84-5.29) for men of European ancestry to 3.74 (95% CI, 3.36-4.17) for men of African ancestry. Men of African ancestry were estimated to have a mean GRS that was 2.18-times higher (95% CI, 2.14-2.22), and men of East Asian ancestry 0.73-times lower (95% CI, 0.71-0.76), than men of European ancestry. These findings support the role of germline variation contributing to population differences in prostate cancer risk, with the GRS offering an approach for personalized risk prediction. A meta-analysis of genome-wide association studies across different populations highlights new risk loci and provides a genetic risk score that can stratify prostate cancer risk across ancestries.
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| 10. |
- Machiela, Mitchell J, et al.
(författare)
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Female chromosome X mosaicism is age-related and preferentially affects the inactivated X chromosome
- 2016
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Ingår i: Nature Communications. - : Nature Publishing Group. - 2041-1723. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- To investigate large structural clonal mosaicism of chromosome X, we analysed the SNP microarray intensity data of 38,303 women from cancer genome-wide association studies (20,878 cases and 17,425 controls) and detected 124 mosaic X events >2 Mb in 97 (0.25%) women. Here we show rates for X-chromosome mosaicism are four times higher than mean autosomal rates; X mosaic events more often include the entire chromosome and participants with X events more likely harbour autosomal mosaic events. X mosaicism frequency increases with age (0.11% in 50-year olds; 0.45% in 75-year olds), as reported for Y and autosomes. Methylation array analyses of 33 women with X mosaicism indicate events preferentially involve the inactive X chromosome. Our results provide further evidence that the sex chromosomes undergo mosaic events more frequently than autosomes, which could have implications for understanding the underlying mechanisms of mosaic events and their possible contribution to risk for chronic diseases.
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| 11. |
- Pinto, Dalila, et al.
(författare)
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Functional impact of global rare copy number variation in autism spectrum disorders.
- 2010
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 466:7304, s. 368-372
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Tidskriftsartikel (refereegranskat)abstract
- The autism spectrum disorders (ASDs) are a group of conditions characterized by impairments in reciprocal social interaction and communication, and the presence of restricted and repetitive behaviours. Individuals with an ASD vary greatly in cognitive development, which can range from above average to intellectual disability. Although ASDs are known to be highly heritable ( approximately 90%), the underlying genetic determinants are still largely unknown. Here we analysed the genome-wide characteristics of rare (<1% frequency) copy number variation in ASD using dense genotyping arrays. When comparing 996 ASD individuals of European ancestry to 1,287 matched controls, cases were found to carry a higher global burden of rare, genic copy number variants (CNVs) (1.19 fold, P = 0.012), especially so for loci previously implicated in either ASD and/or intellectual disability (1.69 fold, P = 3.4 x 10(-4)). Among the CNVs there were numerous de novo and inherited events, sometimes in combination in a given family, implicating many novel ASD genes such as SHANK2, SYNGAP1, DLGAP2 and the X-linked DDX53-PTCHD1 locus. We also discovered an enrichment of CNVs disrupting functional gene sets involved in cellular proliferation, projection and motility, and GTPase/Ras signalling. Our results reveal many new genetic and functional targets in ASD that may lead to final connected pathways.
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| 12. |
- Abolfathi, Bela, et al.
(författare)
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The Fourteenth Data Release of the Sloan Digital Sky Survey : First Spectroscopic Data from the Extended Baryon Oscillation Spectroscopic Survey and from the Second Phase of the Apache Point Observatory Galactic Evolution Experiment
- 2018
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Ingår i: Astrophysical Journal Supplement Series. - : IOP Publishing Ltd. - 0067-0049 .- 1538-4365. ; 235:2
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Tidskriftsartikel (refereegranskat)abstract
- The fourth generation of the Sloan Digital Sky Survey (SDSS-IV) has been in operation since 2014 July. This paper describes the second data release from this phase, and the 14th from SDSS overall (making this Data Release Fourteen or DR14). This release makes the data taken by SDSS-IV in its first two years of operation (2014-2016 July) public. Like all previous SDSS releases, DR14 is cumulative, including the most recent reductions and calibrations of all data taken by SDSS since the first phase began operations in 2000. New in DR14 is the first public release of data from the extended Baryon Oscillation Spectroscopic Survey; the first data from the second phase of the Apache Point Observatory (APO) Galactic Evolution Experiment (APOGEE-2), including stellar parameter estimates from an innovative data-driven machine-learning algorithm known as "The Cannon"; and almost twice as many data cubes from the Mapping Nearby Galaxies at APO (MaNGA) survey as were in the previous release (N = 2812 in total). This paper describes the location and format of the publicly available data from the SDSS-IV surveys. We provide references to the important technical papers describing how these data have been taken (both targeting and observation details) and processed for scientific use. The SDSS web site (www.sdss.org) has been updated for this release and provides links to data downloads, as well as tutorials and examples of data use. SDSS-IV is planning to continue to collect astronomical data until 2020 and will be followed by SDSS-V.
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| 13. |
- Anney, Richard, et al.
(författare)
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Individual common variants exert weak effects on the risk for autism spectrum disorders.
- 2012
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Ingår i: Human Molecular Genetics. - : Oxford University Press (OUP). - 0964-6906 .- 1460-2083. ; 21:21, s. 4781-92
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Tidskriftsartikel (refereegranskat)abstract
- While it is apparent that rare variation can play an important role in the genetic architecture of autism spectrum disorders (ASD), the contribution of common variation to ASD risk is less clear. To produce a more comprehensive picture, we report Stage 2 of the Autism Genome Project genome-wide association study, adding 1301 ASD families and bringing the total to 2705 families analysed (Stages 1 and 2). In addition to evaluating association of individual SNPs, we also sought evidence that common variants, en masse, might affect risk. Despite genotyping over a million SNPs covering the genome, no single SNP shows significant association with ASD or selected phenotypes at a genome-wide level. The SNP that achieves the smallest p-value from secondary analyses is rs1718101. It falls in CNTNAP2, a gene previously implicated in susceptibility for ASD. This SNP also shows modest association with age of word/phrase acquisition in ASD subjects, of interest because features of language development are also associated with other variation in CNTNAP2. By contrast, allele-scores derived from the transmission of common alleles to Stage 1 cases significantly predict case-status in the independent Stage 2 sample. Despite being significant, the variance explained by these allele scores was small (Vm< 1%). Based on results from individual SNPs and their en masse effect on risk, as inferred from the allele-score results, it is reasonable to conclude that common variants affect ASD risk but their individual effects are modest.
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| 14. |
- Casey, Jillian P, et al.
(författare)
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A novel approach of homozygous haplotype sharing identifies candidate genes in autism spectrum disorder.
- 2012
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Ingår i: Human Genetics. - : Springer Science and Business Media LLC. - 0340-6717 .- 1432-1203. ; 131:4, s. 565-579
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Tidskriftsartikel (refereegranskat)abstract
- Autism spectrum disorder (ASD) is a highly heritable disorder of complex and heterogeneous aetiology. It is primarily characterized by altered cognitive ability including impaired language and communication skills and fundamental deficits in social reciprocity. Despite some notable successes in neuropsychiatric genetics, overall, the high heritability of ASD (~90%) remains poorly explained by common genetic risk variants. However, recent studies suggest that rare genomic variation, in particular copy number variation, may account for a significant proportion of the genetic basis of ASD. We present a large scale analysis to identify candidate genes which may contain low-frequency recessive variation contributing to ASD while taking into account the potential contribution of population differences to the genetic heterogeneity of ASD. Our strategy, homozygous haplotype (HH) mapping, aims to detect homozygous segments of identical haplotype structure that are shared at a higher frequency amongst ASD patients compared to parental controls. The analysis was performed on 1,402 Autism Genome Project trios genotyped for 1 million single nucleotide polymorphisms (SNPs). We identified 25 known and 1,218 novel ASD candidate genes in the discovery analysis including CADM2, ABHD14A, CHRFAM7A, GRIK2, GRM3, EPHA3, FGF10, KCND2, PDZK1, IMMP2L and FOXP2. Furthermore, 10 of the previously reported ASD genes and 300 of the novel candidates identified in the discovery analysis were replicated in an independent sample of 1,182 trios. Our results demonstrate that regions of HH are significantly enriched for previously reported ASD candidate genes and the observed association is independent of gene size (odds ratio 2.10). Our findings highlight the applicability of HH mapping in complex disorders such as ASD and offer an alternative approach to the analysis of genome-wide association data.
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| 15. |
- Elsik, Christine G., et al.
(författare)
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The Genome Sequence of Taurine Cattle : A Window to Ruminant Biology and Evolution
- 2009
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 324:5926, s. 522-528
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Tidskriftsartikel (refereegranskat)abstract
- To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.
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| 16. |
- Huyghe, Jeroen R., et al.
(författare)
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Discovery of common and rare genetic risk variants for colorectal cancer
- 2019
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Ingår i: Nature Genetics. - : Nature Publishing Group. - 1061-4036 .- 1546-1718. ; 51:1, s. 76-
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Tidskriftsartikel (refereegranskat)abstract
- To further dissect the genetic architecture of colorectal cancer (CRC), we performed whole-genome sequencing of 1,439 cases and 720 controls, imputed discovered sequence variants and Haplotype Reference Consortium panel variants into genome-wide association study data, and tested for association in 34,869 cases and 29,051 controls. Findings were followed up in an additional 23,262 cases and 38,296 controls. We discovered a strongly protective 0.3% frequency variant signal at CHD1. In a combined meta-analysis of 125,478 individuals, we identified 40 new independent signals at P < 5 x 10(-8), bringing the number of known independent signals for CRC to similar to 100. New signals implicate lower-frequency variants, Kruppel-like factors, Hedgehog signaling, Hippo-YAP signaling, long noncoding RNAs and somatic drivers, and support a role for immune function. Heritability analyses suggest that CRC risk is highly polygenic, and larger, more comprehensive studies enabling rare variant analysis will improve understanding of biology underlying this risk and influence personalized screening strategies and drug development.
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| 17. |
- Ong, Kwok Leung, et al.
(författare)
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Association of omega 3 polyunsaturated fatty acids with incident chronic kidney disease : pooled analysis of 19 cohorts
- 2023
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Ingår i: BMJ. British Medical Journal. - : BMJ Publishing Group Ltd. - 0959-8146 .- 0959-535X. ; 380
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Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVE: To assess the prospective associations of circulating levels of omega 3 polyunsaturated fatty acid (n-3 PUFA) biomarkers (including plant derived a linolenic acid and seafood derived eicosapentaenoic acid, docosapentaenoic acid, and docosahexaenoic acid) with incident chronic kidney disease (CKD).DESIGN: Pooled analysis.DATA SOURCES: A consortium of 19 studies from 12 countries identified up to May 2020.STUDY SELECTION: Prospective studies with measured n-3 PUFA biomarker data and incident CKD based on estimated glomerular filtration rate.DATA EXTRACTION AND SYNTHESIS: Each participating cohort conducted de novo analysis with prespecified and consistent exposures, outcomes, covariates, and models. The results were pooled across cohorts using inverse variance weighted meta-analysis.MAIN OUTCOME MEASURES: Primary outcome of incident CKD was defined as new onset estimated glomerular filtration rate <60 mL/ min/1.73 m(2). In a sensitivity analysis, incident CKD was defined as new onset estimated glomerular filtration rate <60 mL/min/1.73 m(2) and <75% of baseline rate.RESULTS: 25 570 participants were included in the primary outcome analysis and 4944 (19.3%) developed incident CKD during follow-up (weighted median 11.3 years). In multivariable adjusted models, higher levels of total seafood n-3 PUFAs were associated with a lower incident CKD risk (relative risk per interquintile range 0.92, 95% confidence interval 0.86 to 0.98; P=0.009, I-2=9.9%). In categorical analyses, participants with total seafood n-3 PUFA level in the highest fifth had 13% lower risk of incident CKD compared with those in the lowest fifth (0.87, 0.80 to 0.96; P=0.005, I-2=0.0%). Plant derived a linolenic acid levels were not associated with incident CKD (1.00, 0.94 to 1.06; P=0.94, I-2=5.8%). Similar results were obtained in the sensitivity analysis. The association appeared consistent across subgroups by age (=60 v <60 years), estimated glomerular filtration rate (60-89 v =90 mL/min/1.73 m(2)), hypertension, diabetes, and coronary heart disease at baseline.CONCLUSIONS: Higher seafood derived n-3 PUFA levels were associated with lower risk of incident CKD, although this association was not found for plant derived n-3 PUFAs. These results support a favourable role for seafood derived n-3 PUFAs in preventing CKD.
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| 18. |
- Pautler, Brent G., et al.
(författare)
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A High-Pressure NMR Probe for Aqueous Geochemistry
- 2014
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Ingår i: Angewandte Chemie International Edition. - : Wiley. - 1433-7851 .- 1521-3773. ; 53:37, s. 9788-9791
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Tidskriftsartikel (refereegranskat)abstract
- A non-magnetic piston-cylinder pressure cell is presented for solution-state NMR spectroscopy at geochemical pressures. The probe has been calibrated up to 20kbar using insitu ruby fluorescence and allows for the measurement of pressure dependencies of a wide variety of NMR-active nuclei with as little as 10L of sample in a microcoil. Initial (BNMR)-B-11 spectroscopy of the H3BO3-catechol equilibria reveals a large pressure-driven exchange rate and a negative pressure-dependent activation volume, reflecting increased solvation and electrostriction upon boron-catecholate formation. The inexpensive probe design doubles the current pressure range available for solution NMR spectroscopy and is particularly important to advance the field of aqueous geochemistry.
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| 19. |
- Schweinsberg, Martin, et al.
(författare)
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Same data, different conclusions : Radical dispersion in empirical results when independent analysts operationalize and test the same hypothesis
- 2021
-
Ingår i: Organizational Behavior and Human Decision Processes. - : Elsevier BV. - 0749-5978 .- 1095-9920. ; 165, s. 228-249
-
Tidskriftsartikel (refereegranskat)abstract
- In this crowdsourced initiative, independent analysts used the same dataset to test two hypotheses regarding the effects of scientists' gender and professional status on verbosity during group meetings. Not only the analytic approach but also the operationalizations of key variables were left unconstrained and up to individual analysts. For instance, analysts could choose to operationalize status as job title, institutional ranking, citation counts, or some combination. To maximize transparency regarding the process by which analytic choices are made, the analysts used a platform we developed called DataExplained to justify both preferred and rejected analytic paths in real time. Analyses lacking sufficient detail, reproducible code, or with statistical errors were excluded, resulting in 29 analyses in the final sample. Researchers reported radically different analyses and dispersed empirical outcomes, in a number of cases obtaining significant effects in opposite directions for the same research question. A Boba multiverse analysis demonstrates that decisions about how to operationalize variables explain variability in outcomes above and beyond statistical choices (e.g., covariates). Subjective researcher decisions play a critical role in driving the reported empirical results, underscoring the need for open data, systematic robustness checks, and transparency regarding both analytic paths taken and not taken. Implications for orga-nizations and leaders, whose decision making relies in part on scientific findings, consulting reports, and internal analyses by data scientists, are discussed.
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| 20. |
- Segal, Eran, et al.
(författare)
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Building an international consortium for tracking coronavirus health status
- 2020
-
Ingår i: Nature Medicine. - : Springer Science and Business Media LLC. - 1078-8956 .- 1546-170X. ; 26:8, s. 1161-1165
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- We call upon the research community to standardize efforts to use daily self-reported data about COVID-19 symptoms in the response to the pandemic and to form a collaborative consortium to maximize global gain while protecting participant privacy.
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| 21. |
- 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
-
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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| 22. |
- Aureliano, Manuel, et al.
(författare)
-
Characterization of decavanadate and decaniobate solutions by Raman spectroscopy
- 2016
-
Ingår i: Dalton Transactions. - : Royal Society of Chemistry (RSC). - 1477-9226 .- 1477-9234. ; 45:17, s. 7391-7399
-
Tidskriftsartikel (refereegranskat)abstract
- The decaniobate ion, (Nb-10 = [Nb10O28](6-)) being isoelectronic and isostructural with the decavanadate ion (V-10 = [V10O28](6-)), but chemically and electrochemically more inert, has been useful in advancing the understanding of V-10 toxicology and pharmacological activities. In the present study, the solution chemistry of Nb-10 and V-10 between pH 4 and 12 is studied by Raman spectroscopy. The Raman spectra of V-10 show that this vanadate species dominates up to pH 6.45 whereas it remains detectable until pH 8.59, which is an important range for biochemistry. Similarly, Nb-10 is present between pH 5.49 and 9.90 and this species remains detectable in solution up to pH 10.80. V-10 dissociates at most pH values into smaller tetrahedral vanadate oligomers such as V-1 and V-2, whereas Nb-10 dissociates into Nb-6 under mildly (10 > pH > 7.6) or highly alkaline conditions. Solutions of V-10 and Nb-10 are both kinetically stable under basic pH conditions for at least two weeks and at moderate temperature. The Raman method provides a means of establishing speciation in the difficult niobate system and these findings have important consequences for toxicology activities and pharmacological applications of vanadate and niobate polyoxometalates.
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| 23. |
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| 24. |
- Colla, Christopher A., et al.
(författare)
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Computational prediction of Mg-isotope fractionation between aqueous [Mg(OH2)6]2+ and brucite
- 2018
-
Ingår i: Geochimica et Cosmochimica Acta. - : Elsevier. - 0016-7037 .- 1872-9533. ; 227, s. 64-74
-
Tidskriftsartikel (refereegranskat)abstract
- The fractionation factor in the magnesium-isotope fractionation between aqueous solutions of magnesium and brucite changes sign with increasing temperature, as uncovered by recent experiments. To understand this behavior, the Reduced Partition Function Ratios and isotopic fractionation factors (Δ26/24Mgbrucite-Mg(aq)) are calculated using molecular models of aqueous [Mg(OH2)6]2+ and the mineral brucite at increasing levels of density functional theory. The calculations were carried out on the [Mg(OH2)6]2+·12H2O cluster, along with different Pauling-bond-strength-conserving models of the mineral lattice of brucite. Three conclusions were reached: (i) all levels of theory overestimate 〈Mg‒O〉 bond distances in the aqua ion complex relative to Tutton’s salts; (ii) the calculations predict that brucite at 298.15 K is always enriched in the heavy isotope, in contrast with experimental observations; (iii) the temperature dependencies of Wimpenny et al. (2014) and Li et al. (2014) could only be achieved by fixing the 〈Mg‒O〉 bond distances in the [Mg(OH2)6]2+·12H2O cluster to values close to those observed in crystals that trap the hydrated ion.
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| 25. |
- Dunn, Casey W, et al.
(författare)
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Broad phylogenomic sampling improves resolution of the animal tree of life.
- 2008
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 452:7188, s. 745-9
-
Tidskriftsartikel (refereegranskat)abstract
- Long-held ideas regarding the evolutionary relationships among animals have recently been upended by sometimes controversial hypotheses based largely on insights from molecular data. These new hypotheses include a clade of moulting animals (Ecdysozoa) and the close relationship of the lophophorates to molluscs and annelids (Lophotrochozoa). Many relationships remain disputed, including those that are required to polarize key features of character evolution, and support for deep nodes is often low. Phylogenomic approaches, which use data from many genes, have shown promise for resolving deep animal relationships, but are hindered by a lack of data from many important groups. Here we report a total of 39.9 Mb of expressed sequence tags from 29 animals belonging to 21 phyla, including 11 phyla previously lacking genomic or expressed-sequence-tag data. Analysed in combination with existing sequences, our data reinforce several previously identified clades that split deeply in the animal tree (including Protostomia, Ecdysozoa and Lophotrochozoa), unambiguously resolve multiple long-standing issues for which there was strong conflicting support in earlier studies with less data (such as velvet worms rather than tardigrades as the sister group of arthropods), and provide molecular support for the monophyly of molluscs, a group long recognized by morphologists. In addition, we find strong support for several new hypotheses. These include a clade that unites annelids (including sipunculans and echiurans) with nemerteans, phoronids and brachiopods, molluscs as sister to that assemblage, and the placement of ctenophores as the earliest diverging extant multicellular animals. A single origin of spiral cleavage (with subsequent losses) is inferred from well-supported nodes. Many relationships between a stable subset of taxa find strong support, and a diminishing number of lineages remain recalcitrant to placement on the tree.
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| 26. |
- Fraqueza, Gil, et al.
(författare)
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Decavanadate, decaniobate, tungstate and molybdate interactions with sarcoplasmic reticulum Ca2+-ATPase : quercetin prevents cysteine oxidation by vanadate but does not reverse ATPase inhibition
- 2012
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Ingår i: Dalton Transactions. - : Royal Society of Chemistry (RSC). - 1477-9226 .- 1477-9234. ; 41:41, s. 12749-12758
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Tidskriftsartikel (refereegranskat)abstract
- Recently we demonstrated that the decavanadate (V-10) ion is a stronger Ca2+-ATPase inhibitor than other oxometalates, such as the isoelectronic and isostructural decaniobate ion, and the tungstate and molybdate monomer ions, and that it binds to this protein with a 1 : 1 stoichiometry. The V-10 interaction is not affected by any of the protein conformations that occur during the process of calcium translocation (i.e. E1, E1P, E2 and E2P) (Fraqueza et al., J. Inorg. Biochem., 2012). In the present study, we further explore this subject, and we can now show that the decaniobate ion, [Nb-10 = Nb10O28](6-), is a useful tool in deducing the interaction and the non-competitive Ca2+-ATPase inhibition by the decavanadate ion [V-10 = V10O28](6-). Moreover, decavanadate and vanadate induce protein cysteine oxidation whereas no effects were detected for the decaniobate, tungstate or molybdate ions. The presence of the antioxidant quercetin prevents cysteine oxidation, but not ATPase inhibition, by vanadate or decavanadate. Definitive V(IV) EPR spectra were observed for decavanadate in the presence of sarcoplasmic reticulum Ca2+-ATPase, indicating a vanadate reduction at some stage of the protein interaction. Raman spectroscopy clearly shows that the protein conformation changes that are induced by V-10, Nb-10 and vanadate are different from the ones induced by molybdate and tungstate monomer ions. Here, Mo and W cause changes similar to those by phosphate, yielding changes similar to the E1P protein conformation. The putative reduction of vanadium(V) to vanadium(IV) and the non-competitive binding of the V-10 and Nb-10 decametalates may explain the differences in the Raman spectra compared to those seen in the presence of molybdate or tungstate. Putting it all together, we suggest that the ability of V-10 to inhibit the Ca2+-ATPase may be at least in part due to the process of vanadate reduction and associated protein cysteine oxidation. These results contribute to the understanding and application of these families of mono-and polyoxometalates as effective modulators of many biological processes, particularly those associated with calcium homeostasis.
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| 27. |
- Fraqueza, Gil, et al.
(författare)
-
Sarcoplasmic reticulum calcium ATPase interactions with decaniobate, decavanadate, vanadate, tungstate and molybdate
- 2012
-
Ingår i: Journal of Inorganic Biochemistry. - : Elsevier BV. - 0162-0134 .- 1873-3344. ; 107:1, s. 82-89
-
Tidskriftsartikel (refereegranskat)abstract
- Over the last few decades there has been increasing interest in oxometalate and polyoxometalate applications to medicine and pharmacology. This interest arose, at least in part, due to the properties of these classes of compounds as anti-cancer, anti-diabetic agents, and also for treatment of neurodegenerative diseases, among others. However, our understanding of the mechanism of action would be improved if biological models could be used to clarify potential toxicological effects in main cellular processes. Sarcoplasmic reticulum (SR) vesicles, containing a large amount of Ca(2+)-ATPase, an enzyme that accumulates calcium by active transport using ATP, have been suggested as a useful model to study the effects of oxometalates on calcium homeostasis. In the present article, it is shown that decavanadate, decaniobate, vanadate, tungstate and molybdate, all inhibited SR Ca(2+)-ATPase, with the following IC(50) values: 15, 35, 50, 400 mu M and 45 mM, respectively. Decaniobate (Nb(10)), is the strongest P-type enzyme inhibitor, after decavanadate (V(10)). Atomic-absorption spectroscopy (AAS) analysis, indicates that decavanadate binds to the protein with a 1:1 decavanadate:Ca(2+)-ATPase stoichiometry. Furthermore, V10 binds with similar extension to all the protein conformations, which occur during calcium translocation by active transport, namely El, El P, E2 and E2P, as analysed by MS. In contrast, it was confirmed that the binding of monomeric vanadate (H(2)VO(4)(2-):V(1)) to the calcium pump is favoured only for the E2 and E2P conformations of the ATPase, whereas no significant amount of vanadate is bound to the E1 and E1P conformations. Scatchard plot analysis, confirmed a 1:1 ratio for decavanadate-Ca(2+)-ATPase, with a dissociation constant, k(d) of 1 mu M(-1). The interaction of decavanadate V(10)O(28)(6-) (V(10)) with Ca(2+)-ATPase is prevented by the isostructural and isoelectronic decaniobate Nb(10)O(28)(6-) (Nb(10)), whereas no significant effects were detected with ATP or with heparin, a known competitive ATP binding molecule, suggesting that V(10) binds non-competitively, with respect to ATP, to the protein. Finally, it was shown that decaniobate inhibits SR Ca(2+)-ATPase activity in a non competitive type of inhibition, with respect to ATP. Taken together, these data demonstrate that decameric niobate and vanadate species are stronger inhibitors of the SR calcium ATPase than simple monomeric vanadate, tungstate and molybdate oxometalates, thus affecting calcium homeostasis, cell signalling and cell bioenergetics, as well many other cellular processes. The ability of these oxometalates to act either as phosphate analogues, as a transition-state analogue in enzyme-catalysed phosphoryl group transfer processes and as potentially nucleotide-dependent enzymes modulators or inhibitors, suggests that different oxometalates may reveal different mechanistic preferences in these classes of enzymes. (C) 2011 Elsevier Inc. All rights reserved.
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| 28. |
- Frid, Casey J., et al.
(författare)
-
Low-wealth entrepreneurs and access to external financing
- 2016
-
Ingår i: International Journal of Entrepreneurial Behaviour & Research. - : Emerald Group Publishing Limited. - 1355-2554 .- 1758-6534. ; 22:4, s. 531-555
-
Tidskriftsartikel (refereegranskat)abstract
- Purpose– The purpose of this paper is to explore the relationship between low-wealth business founders in the USA and external startup funding. Specifically, the authors test whether a founders’ low personal net worth is correlated with a lower probability of acquiring funding from outside sources during the business creation process.Design/methodology/approach– The authors use a double-hurdle Cragg model to jointly estimate: first, the decision to acquire external financing; and second, the amount received. The sample is the US-based Panel Study of Entrepreneurial Dynamics II (PSED II). The PSED II tracks business founders attempting to start ventures from 2005 to 2012.Findings– Receipt of outside financing during business formation is largely determined by the business founder’s personal finances (controlling for human capital, venture type and industry, and whether money was sought in the first place). A higher household net worth results in larger amounts of external funding received. Low-wealth business founders, therefore, are less likely to get external funds, and they receive lower amounts when they do. The disparity between low-and high-wealth business founders is more pronounced for formal, monitored sources of external financing such as bank loans.Research limitations/implications– Because the study eliminates survivor bias by using a nationally representative sample of business founders who are in the venture creation process, the findings apply to both successful business founders and those who disengaged during the business creation process. The authors offer insights into the sources and amounts of external funds acquired by individuals across all levels of wealth. The authors accomplish this by disaggregating business founders into wealth quintiles. The study demonstrates the importance of personal wealth as a factor in acquiring external startup financing compared to human capital, industry, or personal characteristics.Social implications– If the ability to acquire external funding is significantly constrained, the quality of the opportunity and the skill of the business founder may be less a determinant of success at creating a new business as prior studies have suggested. Consequently, entrepreneurship (as measured by business formation) as a path toward upward, socioeconomic mobility will be afforded only to those individuals with sufficient financial endowments at the outset.Originality/value– Unlike prior studies, the data used are not subject to survivor bias or an underrepresentation of self-employment. The statistical model jointly estimates acquisition of financing and the amount received. This resolves selection and censoring problems. Finally, the dependent variables directly measure liquidity constraints in the context of business formation, that is, before a new venture is created. Prior research contexts have typically studied existing businesses, and are therefore not true examinations of conditions affecting business creation.
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| 29. |
- Harley, Steven J., et al.
(författare)
-
Geochemical kinetics via the Swift-Connick equations and solution NMR
- 2011
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Ingår i: Geochimica et Cosmochimica Acta. - : Elsevier BV. - 0016-7037 .- 1872-9533. ; 75:13, s. 3711-3725
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Tidskriftsartikel (refereegranskat)abstract
- Signal analysis in Nuclear Magnetic Resonance spectroscopy is among the most powerful methods to quantify reaction rates in aqueous solutions. To this end, the Swift-Connick approximations to the Bloch-McConnell equations have been used extensively to estimate rate parameters for elementary reactions. The method is primarily used for O-17 NMR in aqueous solutions, but the list of geochemically relevant nuclei that can be used is long, and includes Si-29, Al-27, F-19, C-13 and many others of particular interest to geochemists. Here we review the derivation of both the Swift-Connick and Bloch-McConnell equations and emphasize assumptions and quirks. For example, the equations were derived for CW-NMR, but are used with modern pulse FT-NMR and can be applied to systems that have exchange rates that are shorter than the lifetime of a typical pulse. The method requires a dilute solution where the minor reacting species contributes a negligible amount of total magnetization. We evaluate the sensitivity of results to this dilute-solution requirement and also highlight the need for chemically well-defined systems if reliable data are to be obtained. The limitations in using longitudinal relaxation to estimate reaction rate parameters are discussed. Finally, we provide examples of the application of the method, including ligand exchanges from aqua ions and hydrolysis complexes, that emphasize its flexibility. Once the basic requirements of the Swift-Connick method are met, it allows geochemists to establish rates of elementary reactions. Reactions at this scale lend themselves well to methods of computational simulation and could provide key tests of accuracy. (C) 2011 Elsevier Ltd. All rights reserved.
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| 30. |
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| 31. |
- Huyghe, Jeroen R, et al.
(författare)
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Genetic architectures of proximal and distal colorectal cancer are partly distinct
- 2021
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Ingår i: Gut. - : BMJ Publishing Group Ltd. - 0017-5749 .- 1468-3288. ; 70:7, s. 1325-1334
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Tidskriftsartikel (refereegranskat)abstract
- Objective: An understanding of the etiologic heterogeneity of colorectal cancer (CRC) is critical for improving precision prevention, including individualized screening recommendations and the discovery of novel drug targets and repurposable drug candidates for chemoprevention. Known differences in molecular characteristics and environmental risk factors among tumors arising in different locations of the colorectum suggest partly distinct mechanisms of carcinogenesis. The extent to which the contribution of inherited genetic risk factors for CRC differs by anatomical subsite of the primary tumor has not been examined.Design: To identify new anatomical subsite-specific risk loci, we performed genome-wide association study (GWAS) meta-analyses including data of 48 214 CRC cases and 64 159 controls of European ancestry. We characterised effect heterogeneity at CRC risk loci using multinomial modelling.Results: We identified 13 loci that reached genome-wide significance (p<5×10-8) and that were not reported by previous GWASs for overall CRC risk. Multiple lines of evidence support candidate genes at several of these loci. We detected substantial heterogeneity between anatomical subsites. Just over half (61) of 109 known and new risk variants showed no evidence for heterogeneity. In contrast, 22 variants showed association with distal CRC (including rectal cancer), but no evidence for association or an attenuated association with proximal CRC. For two loci, there was strong evidence for effects confined to proximal colon cancer.Conclusion: Genetic architectures of proximal and distal CRC are partly distinct. Studies of risk factors and mechanisms of carcinogenesis, and precision prevention strategies should take into consideration the anatomical subsite of the tumour.
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| 32. |
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| 33. |
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| 34. |
- Johnson, Rene L., et al.
(författare)
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O-17 NMR and Computational Study of a Tetrasiliconiobate Ion, [H2+xSi4Nb16O56]((14-x)-)
- 2011
-
Ingår i: Chemistry - A European Journal. - : Wiley. - 0947-6539 .- 1521-3765. ; 17:34, s. 9359-9367
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Tidskriftsartikel (refereegranskat)abstract
- Rates of oxygen-isotope exchange were measured in the tetrasiliconiobate ion [H2+xSi4Nb16O56]((14-x)-) to better understand how large oxide ions interact with water. The molecule has 19 nonequivalent oxygen sites and is sufficiently complex to evaluate hypotheses derived from our previous work on smaller clusters. We want to examine the extent to which individual oxygen atoms react independently with particular attention given to the order of protonation of the various oxygen sites as the pH decreases from 13 to 6. As in our previous work, we find that the set of oxygen sites reacts at rates that vary over approximately 104 across the molecule at 6 < pH < 13 but with similar pH dependencies. There is NMR evidence of an intra-or intermolecular reaction at pH similar to 7, where new peaks began to slowly form without losing the O-17 isotopic tag, and at pH <= 6 these new peaks formed rapidly. The oxygen atoms bonded to silicon atoms began to isotopically exchange at pH 9 and below. The 17O NMR peak positions also vary considerably with pH for some, but not all, nonequivalent oxygen sites. This variation could be only partly accounted by electronic calculations, which indicate that oxygen atoms should shift similarly upon protonation. Instead, we see that some sites change enormously with pH, whereas other, similarly coordinated oxygen atoms are less affected, suggesting that either some protons are exchanging so rapidly that the oxygen sites are seeing an averaged charge, or that counterions are modulating the effect of the coordinated protons.
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| 35. |
- McAlpin, J. Gregory, et al.
(författare)
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Electronic Structure Description of a [Co(III)(3)Co(IV)O-4] Cluster : A Model for the Paramagnetic Intermediate in Cobalt-Catalyzed Water Oxidation
- 2011
-
Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 133:39, s. 15444-15452
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Tidskriftsartikel (refereegranskat)abstract
- Multifrequency electron paramagnetic resonace (EPR) spectroscopy and electronic structure calculations were performed on [Co4O4(C5H5N)(4)(CH3CO2)(4)](+) (1(+)), a cobalt tetramer with total electron spin S = 1/2 and formal cobalt oxidation states III, III, III, and IV. The cuboidal arrangement of its cobalt and oxygen atoms is similar to that of proposed structures for the molecular cobaltate clusters of the cobalt-phosphate (Co-Pi) water-oxidizing catalyst. The Davies electron-nuclear double resonance (ENDOR) spectrum is well-modeled using a single class of hyperfine-coupled Co-59 nuclei with a modestly strong interaction (principal elements of the hyperfine tensor are equal to [-20(+/- 2), 77(+/- 1), -5(+/- 15)] MHz). Mims H-1 ENDOR spectra of 1(+) with selectively deuterated pyridine ligands confirm that the amount of unpaired spin on the cobalt-bonding partner is significantly reduced from unity. Multifrequency N-14 ESEEM spectra (acquired at 9.5 and 34.0 GHz) indicate that four nearly equivalent nitrogen nuclei are coupled to the electron spin. Cumulatively, our EPR spectroscopic findings indicate that the unpaired spin is delocalized almost equally across the eight core atoms, a finding corroborated by results from DFT calculations. Each octahedrally coordinated cobalt ion is forced into a low-spin electron configuration by the anionic oxo and carboxylato ligands, and a fractional electron hole is localized on each metal center in a Co 3d(xz,yz)-based molecular orbital for this essentially [Co4+3.125O4] system. Comparing the EPR spectrum of 1(+) with that of the catalyst film allows us to draw conclusions about the electronic structure of this water-oxidation catalyst.
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| 36. |
- Ohlin, C. André, et al.
(författare)
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17O NMR as a Tool in Discrete Metal Oxide Cluster Chemistry
- 2018
-
Ingår i: Annual Reports on NMR Spectroscopy. - : Elsevier. - 9780128152126 ; , s. 187-248
-
Bokkapitel (refereegranskat)abstract
- This chapter covers recent developments in 17O NMR spectroscopy as applied to discrete metal oxide clusters, particularly in the context of their use as models in geochemistry and catalysis. Dynamic 17O NMR methods based on the McConnell–Bloch equations are explored in depth, and recent advances are reviewed. High-pressure NMR methods are also discussed and reviewed, as are recent developments in the use of density functional theory in the computation of 17O NMR shifts in polyoxometalates. The emphasis of the chapter is on the new developments that promise to reinvigorate 17O NMR as a central tool in the study of aqueous chemical kinetics, with the most urgent challenges being understanding the rates of isotopic substitution into bridging oxygens in clusters.
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| 37. |
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| 38. |
- Ohlin, C. Andre, et al.
(författare)
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Dissolution of insulating oxide materials at the molecular scale
- 2010
-
Ingår i: Nature Materials. - 1476-1122 .- 1476-4660. ; 9:1, s. 11-19
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Forskningsöversikt (refereegranskat)abstract
- Our understanding of mineral and glass dissolution has advanced from simple thermodynamic treatments to models that emphasize adsorbate structures. This evolution was driven by the idea that the best understanding is built at the molecular level. Now, it is clear that the molecular questions cannot be answered uniquely with dissolution experiments. At the surface it is unclear which functional groups are present, how they are arranged, and how they interact with each other and with solutes as the key bonds are activated. An alternative approach has developed whereby reactions are studied with nanometre-sized aqueous oxide ions that serve as models for the more complicated oxide interface. For these ions, establishing the structure is not a research problem in itself, and bond ruptures and dissociations can be followed with much confidence. We review the field from bulk-dissolution kinetics to the new isotope-exchange experiments in large oxide ions.
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| 39. |
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| 40. |
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| 41. |
- Ohlin, C. Andre, et al.
(författare)
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Oxygen isotopic exchange in an (MnMn3IV)-Mn-III-oxo cubane
- 2009
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Ingår i: Dalton Transactions. - : Royal Society of Chemistry (RSC). - 1477-9226 .- 1477-9234. ; :27, s. 5278-5280
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Tidskriftsartikel (refereegranskat)abstract
- The rate and activation parameters for oxygen exchange of the mu(3)-oxo bridges in a manganese tetranuclear cluster with (H2O)-O-18 have been measured by ESI-MS; the observed Delta S double dagger of -146 +/- 22 J K-1 mol(-1) is consistent with the expected associative mechanism of substitution.
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| 42. |
- Ohlin, C. Andre, et al.
(författare)
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Rates of Water Exchange for Two Cobalt(II) Heteropolyoxotungstate Compounds in Aqueous Solution
- 2011
-
Ingår i: Chemistry - A European Journal. - : Wiley. - 0947-6539 .- 1521-3765. ; 17:16, s. 4408-4417
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Tidskriftsartikel (refereegranskat)abstract
- Polyoxometalate ions are used as ligands in water-oxidation processes related to solar energy production. An important step in these reactions is the association and dissociation of water from the catalytic sites, the rates of which are unknown. Here we report the exchange rates of water ligated to Co-II atoms in two polyoxotungstate sandwich molecules using the O-17-NMR-based Swift-Connick method. The compounds were the [Co-4(H2O)(2)(B-alpha-PW9O34)(2)](10-) and the larger alpha beta beta alpha-[Co-4(H2O)(2)(P2W15O56)(2)](16-) ions, each with two water molecules bound trans to one another in a Co-II sandwich between the tungstate ligands. The clusters, in both solid and solution state, were characterized by a range of methods, including NMR, EPR, FT-IR, UV-Vis, and EXAFS spectroscopy, ESI-MS, single-crystal Xray crystallography, and potentiometry. For [Co-4(H2O)(2)(B-alpha-PW9O34)(2)](10-) at pH 5.4, we estimate: k(298) = 1.5(5) +/- 0.3 x 10(6) s(-1), Delta H-not equal = 39.8 +/- 0.4 kJ mol(-1), Delta S-not equal = + 7.1 +/- 1.2 J mol(-1)K(-1) and Delta V-not equal = 5.6 +/- 1.6 cm(3)mol(-1). For the Wells-Dawson sandwich cluster (alpha beta beta alpha-[Co-4(H2O)(2)(P2W15O56)(2)](16-)) at pH 5.54, we find: k(298) = 1.6(2) +/- 0.3 x 10(6)s(-1), Delta H-not equal = 27.6 +/- 0.4 kJ mol(-1) Delta S-not equal = -33 +/- 1.3 J mol(-1)K(-1) and Delta V-not equal = 2.2 +/- 1.4 cm(3)mol(-1) at pH 5.2. The molecules are clearly stable and monospecific in slightly acidic solutions, but dissociate in strongly acidic solutions. This dissociation is detectable by EPR spectroscopy as S=3/2 Co-II species (such as the [Co(H2O)(6)](2+) monomer ion) and by the significant reduction of the Co-Co vector in the XAS spectra.
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| 43. |
- Ohlin, C. Andre, et al.
(författare)
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The energetics of isomerisation in Keggin-series aluminate cations
- 2014
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Ingår i: Dalton Transactions. - : Royal Society of Chemistry (RSC). - 1477-9226 .- 1477-9234. ; 43:39, s. 14533-14536
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Tidskriftsartikel (refereegranskat)abstract
- Electronic-structure calculations show that the e-isomer of the polyoxoaluminate ion in the Keggin structure [AlO4-(Al(OH)(2)-(H2O))(12)](7+) is the thermodynamically favoured one. Direct interconversion between the epsilon- and delta-isomers via cap rotation has a prohibitively high energy barrier in vacuo, suggesting that isomerisation in solution either proceeds via a dissolution-precipitation pathway, or that solvation and/or coordination to counterions reduces the barrier significantly. The implications for the formation of the [Al2O8Al28(OH)(56)(H2O)26](18+) ion are discussed.
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| 44. |
- Ohlin, C. Andre, et al.
(författare)
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The first peroxotitanoniobate cluster - [N(CH3)(4)](10)[Ti12Nb6O38(O-2(I))(6)]
- 2010
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Ingår i: Inorganica Chimica Acta. - : Elsevier BV. - 0020-1693 .- 1873-3255. ; 363:15, s. 4405-4407
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Tidskriftsartikel (refereegranskat)abstract
- The synthesis and structure of the first discrete peroxotitanoniobate cluster, [N(CH3)(4)](10)[Ti12Nb6O38(O-2(I))(6)], is described. (C) 2010 Elsevier B.V. All rights reserved.
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| 45. |
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| 46. |
- Panasci, Adele F., et al.
(författare)
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Cooperation between bound waters and hydroxyls in controlling isotope-exchange rates
- 2012
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Ingår i: Geochimica et Cosmochimica Acta. - : Elsevier BV. - 0016-7037 .- 1872-9533. ; 78, s. 18-27
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Tidskriftsartikel (refereegranskat)abstract
- Mineral oxides differ from aqueous ions in that the bound water molecules are usually attached to different metal centers, or vicinal, and thus separated from one another. In contrast, for most monomeric ions used to establish kinetic reactivity trends, such as octahedral aquo ions (e.g., Al(H(2)O)(6)(3+)), the bound waters are closely packed, or geminal. Because of this structural difference, the existing literature about ligand substitution in monomer ions may be a poor guide to the reactions of geochemical interest. To understand how coordination of the reactive functional groups might affect the rates of simple water-exchange reactions, we synthesized two structurally similar Rh(III) complexes, [Rh(phen)(2)(H(2)O)(2)](3+) [1] and [Rh(phen)(2)(H(2)O)Cl](2+) [2] where (phen) = 1,10-phenanthroline. Complex [1] has two adjacent, geminal, bound waters in the inner-coordination sphere and [2] has a single bound water adjacent to a bound chloride ion. We employed Rh(III) as a trivalent metal rather than a more geochemically relevant metal like Fe(III) or Al(III) to slow the rate of reaction, which makes possible measurement of the rates of isotopic substitution by simple mass spectrometry. We prepared isotopically pure versions of the molecules, dissolved them into isotopically dissimilar water, and measured the rates of exchange from the extents of (18)O and (16)O exchange at the bound waters. The pH dependency of rates differ enormously between the two complexes. Pseudo-first-order rate coefficients at 298 K for water exchanges from the fully protonated molecules are close: k(0)(298) = 5 x 10(-8) (+/- 0.5 x 10(-8)) s(-1) for [1] and k(0)(298) = 2.5 x 10(-9)(+/- 1 x 10(-9)) for [2]. Enthalpy and entropy activation parameters (Delta H(double dagger) and Delta S(double dagger)) were measured to be 119(+/- 3) kJ mol(-1), and 14(+/- 1) J mol(-1) K(-1), respectively for [1]. The corresponding parameters for the mono-aquo complex, [2], are 132(+/- 3) kJ mol(-1) and 41.5(+/- 2) J mol(-1) K(-1). Rates increase by many orders of magnitude upon deprotonation of one of the bound waters in complex [1] because of the close proximity of a transferable proton that can convert the bound hydroxyl to a bound water. This interconversion allows the oxygen to exchange as a bound water, rather than as a bound hydroxyl, which is slow at near-neutral pH conditions. (C) 2011 Elsevier Ltd. All rights reserved.
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| 47. |
- Panasci, Adele F., et al.
(författare)
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Rates of Water Exchange on the [Fe-4(OH)(2)(hpdta)(2)(H2O)(4)](0) Molecule and Its Implications for Geochemistry
- 2012
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Ingår i: Inorganic Chemistry. - : American Chemical Society (ACS). - 0020-1669 .- 1520-510X. ; 51:12, s. 6731-6738
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Tidskriftsartikel (refereegranskat)abstract
- The ammonium salt of [Fe4O(OH)(hpdta)(2)(H2O)(4)](-) is soluble and makes a monospecific solution of [Fe-4(OH)(2)(hpdta)(2)(H2O)(4)](0)(aq) in acidic solutions (hpdta = 2-hydroxypropane-1,3-diamino-N,N,N’,W-tetraacetate). This tetramer is a diprotic acid with pK(a1) estimated at 5.7 +/- 0.2 and pK(a2) = 8.8(5) +/- 0.2. In the pH region below pK(a1), the molecule is stable in solution and O-17 NMR line widths can be interpreted using the Swift-Connick equations to acquire rates of ligand substitution at the four isolated bound water sites. Averaging five measurements at pH < 5, where contribution from the less-reactive conjugate base are minimal, we estimate: k(ex)(298) = 8.1 (+/- 2.6) X 10(5) s(-1), Delta H-double dagger = 46 (+/- 4.6) kJ mol(-1), Delta S-double dagger = 22 (+/- 18) J mol(-1) K-1, and Delta V-double dagger = +1.85 (+/- 0.2) cm(3) mol(-1) for waters bound to the fully protonated, neutral molecule. Regressing the experimental rate coefficients versus 1/[H+] to account for the small pH variation in rate yields a similar value of k(ex)(298) = 8.3 (+/- 0.8) X 10(5) s(-1). These rates are similar to 10(4) times faster than those of the [Fe(OH2)(6)](3+) ion (k(ex)(298) = 1.6 X 10(2) s(-1)) but are about an order of magnitude slower than other studied aminocarboxylate complexes, although these complexes have seven-coordinated Fe(III), not six as in the [Fe-4(OH)(2)(hpdta)(2)(H2O)(4)](0)(aq) molecule. As pH approaches pK(a1), the rates decrease and a compensatory relation is evident between the experimental Delta H-double dagger and Delta S-double dagger values. Such variation cannot be caused by enthalpy from the deprotonation reaction and is not well understood. A correlation between < Fe-III-OH2 > bond lengths and the logarithm of k(ex)(298) is geochemically important because it could be used to estimate rate coefficients for geochemical materials for which only DFT calculations are possible. This molecule is the only neutral, oxo-bridged Fe(III) multimer for which rate data are available.
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| 48. |
- Schmit, Stephanie L, et al.
(författare)
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Novel Common Genetic Susceptibility Loci for Colorectal Cancer.
- 2019
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Ingår i: Journal of the National Cancer Institute. - : Oxford University Press (OUP). - 0027-8874 .- 1460-2105. ; 111:2, s. 146-157
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Tidskriftsartikel (refereegranskat)abstract
- Background: Previous genome-wide association studies (GWAS) have identified 42 loci (P < 5 × 10-8) associated with risk of colorectal cancer (CRC). Expanded consortium efforts facilitating the discovery of additional susceptibility loci may capture unexplained familial risk.Methods: We conducted a GWAS in European descent CRC cases and control subjects using a discovery-replication design, followed by examination of novel findings in a multiethnic sample (cumulative n = 163 315). In the discovery stage (36 948 case subjects/30 864 control subjects), we identified genetic variants with a minor allele frequency of 1% or greater associated with risk of CRC using logistic regression followed by a fixed-effects inverse variance weighted meta-analysis. All novel independent variants reaching genome-wide statistical significance (two-sided P < 5 × 10-8) were tested for replication in separate European ancestry samples (12 952 case subjects/48 383 control subjects). Next, we examined the generalizability of discovered variants in East Asians, African Americans, and Hispanics (12 085 case subjects/22 083 control subjects). Finally, we examined the contributions of novel risk variants to familial relative risk and examined the prediction capabilities of a polygenic risk score. All statistical tests were two-sided.Results: The discovery GWAS identified 11 variants associated with CRC at P < 5 × 10-8, of which nine (at 4q22.2/5p15.33/5p13.1/6p21.31/6p12.1/10q11.23/12q24.21/16q24.1/20q13.13) independently replicated at a P value of less than .05. Multiethnic follow-up supported the generalizability of discovery findings. These results demonstrated a 14.7% increase in familial relative risk explained by common risk alleles from 10.3% (95% confidence interval [CI] = 7.9% to 13.7%; known variants) to 11.9% (95% CI = 9.2% to 15.5%; known and novel variants). A polygenic risk score identified 4.3% of the population at an odds ratio for developing CRC of at least 2.0.Conclusions: This study provides insight into the architecture of common genetic variation contributing to CRC etiology and improves risk prediction for individualized screening.
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| 49. |
- Son, Jung-Ho, et al.
(författare)
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A new class of soluble and stable transition-metal-substituted polyoxoniobate : [Cr-2(OH)(4)Nb10O30](8-)
- 2012
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Ingår i: Dalton Transactions. - : Royal Society of Chemistry (RSC). - 1477-9226 .- 1477-9234. ; 41:41, s. 12674-12677
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Tidskriftsartikel (refereegranskat)abstract
- Hydrothermal synthesis of [Cr-2(III)(OH)(4)Nb10O30](8-) in gram-scale quantities leads to a new polyoxometalate ion composed of two CrNb6O19 Lindqvist-type units that are fused via shared faces. The two Cr-III atoms are located in the centre of the molecule and are bridged by two mu(4)-O atoms. Electronic transitions are calculated using density functional theory and compare well with the measured UV-Vis spectra.
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| 50. |
- Son, Jung-Ho, et al.
(författare)
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A Soluble Phosphorus-Centered Keggin Polyoxoniobate with Bicapping Vanadyl Groups
- 2013
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Ingår i: Chemistry - A European Journal. - : Wiley. - 0947-6539 .- 1521-3765. ; 19:16, s. 5191-5197
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Tidskriftsartikel (refereegranskat)abstract
- A water-soluble tetramethylammonium (TMA) salt of a novel Keggin-type polyoxoniobate has been isolated as TMA9[PV2Nb12O42]19H2O (1). This species contains a central phosphorus site and two capping vanadyl sites. Previously only a single example of a phosphorus-containing polyoxoniobate, [(PO2)3PNb9O34]15, was known, which is a lacunary Keggin ion decorated with three PO2 units. However, that cluster was isolated as an insoluble structure consisting of chains linked by sodium counterions. In contrast, the [PV2Nb12O42]9 cluster in 1 is stable over a wide pH range, as evident by 31P and 51V NMR, UV/Vis spectroscopy, and ESI-MS spectrometry. The ease of substitution of phosphate into the central tetrahedral position suggests that other oxoanions can be similarly substituted, promising a richer set of structures in this class.
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