| 1. |
- Ademuyiwa, Adesoji O., et al.
(author)
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Determinants of morbidity and mortality following emergency abdominal surgery in children in low-income and middle-income countries
- 2016
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In: BMJ Global Health. - : BMJ Publishing Group Ltd. - 2059-7908. ; 1:4
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Journal article (peer-reviewed)abstract
- Background: Child health is a key priority on the global health agenda, yet the provision of essential and emergency surgery in children is patchy in resource-poor regions. This study was aimed to determine the mortality risk for emergency abdominal paediatric surgery in low-income countries globally.Methods: Multicentre, international, prospective, cohort study. Self-selected surgical units performing emergency abdominal surgery submitted prespecified data for consecutive children aged <16 years during a 2-week period between July and December 2014. The United Nation's Human Development Index (HDI) was used to stratify countries. The main outcome measure was 30-day postoperative mortality, analysed by multilevel logistic regression.Results: This study included 1409 patients from 253 centres in 43 countries; 282 children were under 2 years of age. Among them, 265 (18.8%) were from low-HDI, 450 (31.9%) from middle-HDI and 694 (49.3%) from high-HDI countries. The most common operations performed were appendectomy, small bowel resection, pyloromyotomy and correction of intussusception. After adjustment for patient and hospital risk factors, child mortality at 30 days was significantly higher in low-HDI (adjusted OR 7.14 (95% CI 2.52 to 20.23), p<0.001) and middle-HDI (4.42 (1.44 to 13.56), p=0.009) countries compared with high-HDI countries, translating to 40 excess deaths per 1000 procedures performed.Conclusions: Adjusted mortality in children following emergency abdominal surgery may be as high as 7 times greater in low-HDI and middle-HDI countries compared with high-HDI countries. Effective provision of emergency essential surgery should be a key priority for global child health agendas.
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| 2. |
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| 3. |
- Hudson, Lawrence N, et al.
(author)
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The database of the PREDICTS (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems) project
- 2017
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In: Ecology and Evolution. - : John Wiley & Sons. - 2045-7758. ; 7:1, s. 145-188
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Journal article (peer-reviewed)abstract
- The PREDICTS project-Projecting Responses of Ecological Diversity In Changing Terrestrial Systems (www.predicts.org.uk)-has collated from published studies a large, reasonably representative database of comparable samples of biodiversity from multiple sites that differ in the nature or intensity of human impacts relating to land use. We have used this evidence base to develop global and regional statistical models of how local biodiversity responds to these measures. We describe and make freely available this 2016 release of the database, containing more than 3.2 million records sampled at over 26,000 locations and representing over 47,000 species. We outline how the database can help in answering a range of questions in ecology and conservation biology. To our knowledge, this is the largest and most geographically and taxonomically representative database of spatial comparisons of biodiversity that has been collated to date; it will be useful to researchers and international efforts wishing to model and understand the global status of biodiversity.
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| 4. |
- Thomas, HS, et al.
(author)
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- 2019
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swepub:Mat__t
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| 5. |
- Foote, Andrew D., et al.
(author)
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Killer whale genomes reveal a complex history of recurrent admixture and vicariance
- 2019
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In: Molecular Ecology. - : WILEY. - 0962-1083 .- 1365-294X. ; 28:14, s. 3427-3444
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Journal article (peer-reviewed)abstract
- Reconstruction of the demographic and evolutionary history of populations assuming a consensus tree-like relationship can mask more complex scenarios, which are prevalent in nature. An emerging genomic toolset, which has been most comprehensively harnessed in the reconstruction of human evolutionary history, enables molecular ecologists to elucidate complex population histories. Killer whales have limited extrinsic barriers to dispersal and have radiated globally, and are therefore a good candidate model for the application of such tools. Here, we analyse a global data set of killer whale genomes in a rare attempt to elucidate global population structure in a nonhuman species. We identify a pattern of genetic homogenisation at lower latitudes and the greatest differentiation at high latitudes, even between currently sympatric lineages. The processes underlying the major axis of structure include high drift at the edge of species' range, likely associated with founder effects and allelic surfing during postglacial range expansion. Divergence between Antarctic and non-Antarctic lineages is further driven by ancestry segments with up to fourfold older coalescence time than the genome-wide average; relicts of a previous vicariance during an earlier glacial cycle. Our study further underpins that episodic gene flow is ubiquitous in natural populations, and can occur across great distances and after substantial periods of isolation between populations. Thus, understanding the evolutionary history of a species requires comprehensive geographic sampling and genome-wide data to sample the variation in ancestry within individuals.
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| 6. |
- Jones, Lesley, et al.
(author)
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Convergent genetic and expression data implicate immunity in Alzheimer's disease
- 2015
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In: Alzheimer's & Dementia. - : Wiley. - 1552-5260 .- 1552-5279. ; 11:6, s. 658-671
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Journal article (peer-reviewed)abstract
- Background: Late-onset Alzheimer's disease (AD) is heritable with 20 genes showing genome-wide association in the International Genomics of Alzheimer's Project (IGAP). To identify the biology underlying the disease, we extended these genetic data in a pathway analysis. Methods: The ALIGATOR and GSEA algorithms were used in the IGAP data to identify associated functional pathways and correlated gene expression networks in human brain. Results: ALIGATOR identified an excess of curated biological pathways showing enrichment of association. Enriched areas of biology included the immune response (P = 3.27 X 10(-12) after multiple testing correction for pathways), regulation of endocytosis (P = 1.31 X 10(-11)), cholesterol transport (P = 2.96 X 10(-9)), and proteasome-ubiquitin activity (P = 1.34 X 10(-6)). Correlated gene expression analysis identified four significant network modules, all related to the immune response (corrected P = .002-.05). Conclusions: The immime response, regulation of endocytosis, cholesterol transport, and protein ubiquitination represent prime targets for AD therapeutics.
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| 7. |
- Key, Timothy J., et al.
(author)
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Carotenoids, retinol, tocopherols, and prostate cancer risk : pooled analysis of 15 studies
- 2015
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In: American Journal of Clinical Nutrition. - : Elsevier BV. - 0002-9165 .- 1938-3207. ; 102:5, s. 1142-1157
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Journal article (peer-reviewed)abstract
- Background: Individual studies have suggested that circulating carotenoids, retinol, or tocopherols may be associated with prostate cancer risk, but the studies have not been large enough to provide precise estimates of associations, particularly by stage and grade of disease. Objective: The objective of this study was to conduct a pooled analysis of the associations of the concentrations of 7 carotenoids, retinol, alpha-tocopherol, and gamma-tocopherol with risk of prostate cancer and to describe whether any associations differ by stage or grade of the disease or other factors. Design: Principal investigators of prospective studies provided individual participant data for prostate cancer cases and controls. Risk by study-specific fifths of each biomarker was estimated by using multivariable-adjusted conditional logistic regression in matched case-control sets. Results: Data were available for up to 11,239 cases (including 1654 advanced stage and 1741 aggressive) and 18,541 controls from 15 studies. Lycopene was not associated with overall risk of prostate cancer, but there was statistically significant heterogeneity by stage of disease, and the OR for aggressive disease for the highest compared with the lowest fifth of lycopene was 0.65 (95% CI: 0.46, 0.91; P-trend = 0.032). No other carotenoid was significantly associated with overall risk of prostate cancer or with risk of advanced-stage or aggressive disease. For retinol, the OR for the highest compared with the lowest fifth was 1.13 (95% CI: 1.04, 1.22; P-trend = 0.015). For alpha-tocopherol, the OR for the highest compared with the lowest fifth was 0.86 (95% CI: 0.78, 0.94; P-trend < 0.001), with significant heterogeneity by stage of disease; the OR for aggressive prostate cancer was 0.74 (95% CI: 0.59, 0.92; P-trend = 0.001). gamma-Tocopherol was not associated with risk. Conclusions: Overall prostate cancer risk was positively associated with retinol and inversely associated with alpha-tocopherol, and risk of aggressive prostate cancer was inversely associated with lycopene and alpha-tocopherol. Whether these associations reflect causal relations is unclear.
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| 8. |
- Wang, Li-San, et al.
(author)
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Rarity of the Alzheimer Disease-Protective APP A673T Variant in the United States.
- 2015
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In: JAMA neurology. - : American Medical Association (AMA). - 2168-6157 .- 2168-6149. ; 72:2
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Journal article (peer-reviewed)abstract
- Recently, a rare variant in the amyloid precursor protein gene (APP) was described in a population from Iceland. This variant, in which alanine is replaced by threonine at position 673 (A673T), appears to protect against late-onset Alzheimer disease (AD). We evaluated the frequency of this variant in AD cases and cognitively normal controls to determine whether this variant will significantly contribute to risk assessment in individuals in the United States.
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| 9. |
- Foote, Andrew D., et al.
(author)
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Genome-culture coevolution promotes rapid divergence of killer whale ecotypes
- 2016
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In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 7
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Journal article (peer-reviewed)abstract
- Analysing population genomic data from killer whale ecotypes, which we estimate have globally radiated within less than 250,000 years, we show that genetic structuring including the segregation of potentially functional alleles is associated with socially inherited ecological niche. Reconstruction of ancestral demographic history revealed bottlenecks during founder events, likely promoting ecological divergence and genetic drift resulting in a wide range of genome-wide differentiation between pairs of allopatric and sympatric ecotypes. Functional enrichment analyses provided evidence for regional genomic divergence associated with habitat, dietary preferences and post-zygotic reproductive isolation. Our findings are consistent with expansion of small founder groups into novel niches by an initial plastic behavioural response, perpetuated by social learning imposing an altered natural selection regime. The study constitutes an important step towards an understanding of the complex interaction between demographic history, culture, ecological adaptation and evolution at the genomic level.
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| 10. |
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| 11. |
- Hooper, Rebecca, et al.
(author)
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Host-derived population genomics data provides insights into bacterial and diatom composition of the killer whale skin
- 2019
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In: Molecular Ecology. - : John Wiley & Sons. - 0962-1083 .- 1365-294X. ; 28:2, s. 484-502
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Journal article (peer-reviewed)abstract
- Recent exploration into the interactions and relationship between hosts and their microbiota has revealed a connection between many aspects of the host's biology, health and associated micro-organisms. Whereas amplicon sequencing has traditionally been used to characterize the microbiome, the increasing number of published population genomics data sets offers an underexploited opportunity to study microbial profiles from the host shotgun sequencing data. Here, we use sequence data originally generated from killer whale Orcinus orca skin biopsies for population genomics, to characterize the skin microbiome and investigate how host social and geographical factors influence the microbial community composition. Having identified 845 microbial taxa from 2.4 million reads that did not map to the killer whale reference genome, we found that both ecotypic and geographical factors influence community composition of killer whale skin microbiomes. Furthermore, we uncovered key taxa that drive the microbiome community composition and showed that they are embedded in unique networks, one of which is tentatively linked to diatom presence and poor skin condition. Community composition differed between Antarctic killer whales with and without diatom coverage, suggesting that the previously reported episodic migrations of Antarctic killer whales to warmer waters associated with skin turnover may control the effects of potentially pathogenic bacteria such as Tenacibaculum dicentrarchi. Our work demonstrates the feasibility of microbiome studies from host shotgun sequencing data and highlights the importance of metagenomics in understanding the relationship between host and microbial ecology.
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| 12. |
- Kampmann, Tobias Christoph, 1987-, et al.
(author)
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Syn-tectonic sulphide remobilization and trace element redistribution at the Falun pyritic Zn-Pb-Cu-(Au-Ag) sulphide deposit, Bergslagen, Sweden
- 2018
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In: Ore Geology Reviews. - : Elsevier. - 0169-1368 .- 1872-7360. ; 96, s. 48-71
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Journal article (peer-reviewed)abstract
- Mineralization types at the Palaeoproterozoic Falun base metal sulphide deposit are predominantly pyritic Zn-Pb-Cu-rich massive sulphide mineralization, disseminated to semi-massive Cu-Au mineralization, auriferous quartz veins, and mineralized shear zones of talc-chlorite-dominated schist. The massive and disseminated to semi-massive sulphide mineralization types were subject to polyphase ductile deformation (D1 and D2) and metamorphism under low-P, lower-amphibolite facies conditions, which led to the development of ore textures and paragenetic relationships indicating both mechanical and chemical remobilization of sulphides. In the massive sulphide mineralization, rare inclusion-rich pyrite occurs as relic cores inside inclusion-poor metamorphosed pyrite. Imaging and spot analysis using multielement laser ablation inductively-coupled plasma mass spectrometry (LA-ICP-MS) reveal that inclusion-poor pyrite was depleted in trace elements, which were originally present as non-stoichiometric lattice substitutions or in mineral inclusions. The inclusion-rich pyrite was shielded from depletion and, at least partly, retained its initially higher trace element concentrations, including Au.Gold is also associated with chalcopyrite in the disseminated to semi-massive Cu-Au mineralization and in the system of auriferous quartz veins hosted therein, the latter being also affected by the D2 ductile strain. It is inferred that emplacement of the vein system took place after the peak of metamorphism, which occurred between D1 and D2, but prior to and possibly even shortly after completion of the D2 deformational event. Similarities in trace element signatures in chalcopyrite are compatible with the interpretation that the quartz veins formed by local chemical remobilization of components from the Cu-Au mineralization. Transport of liberated Au from pyrite during grain growth in the massive sulphide mineralization may have upgraded the Au endowment in the quartz veins, leading to the additional formation of native gold in the veins. A strong correspondence between elements liberated from pyrite (e.g. Pb, Bi, Se and Au) and those forming discrete and characteristic mineral phases in the quartz veins (Pb-Bi sulphosalts, native gold) supports this hypothesis.Trace element signatures for the main sulphide minerals pyrite, chalcopyrite, sphalerite and galena are similar to previously published data from other metamorphosed massive sulphide deposits. The association of the Falun mineralization with elevated Bi is reflected by its occurrence in sulphide minerals (e.g. galena) and in abundant mineral inclusions of Pb-Bi sulphosalts (e.g. weibullite), especially in the disseminated to semi-massive Cu-Au mineralization. Elevated Sn concentrations in the lattice and/or as cassiterite inclusions in chalcopyrite, sphalerite and galena are compatible with a hot, acidic and reducing fluid during formation of the syn-volcanic, base metal sulphide mineralization and associated host-rock alteration.
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| 13. |
- Morin, Phillip A., et al.
(author)
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Geographic and temporal dynamics of a global radiation and diversification in the killer whale
- 2015
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In: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 24:15, s. 3964-3979
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Journal article (peer-reviewed)abstract
- Global climate change during the Late Pleistocene periodically encroached and then released habitat during the glacial cycles, causing range expansions and contractions in some species. These dynamics have played a major role in geographic radiations, diversification and speciation. We investigate these dynamics in the most widely distributed of marine mammals, the killer whale (Orcinus orca), using a global data set of over 450 samples. This marine top predator inhabits coastal and pelagic ecosystems ranging from the ice edge to the tropics, often exhibiting ecological, behavioural and morphological variation suggestive of local adaptation accompanied by reproductive isolation. Results suggest a rapid global radiation occurred over the last 350000years. Based on habitat models, we estimated there was only a 15% global contraction of core suitable habitat during the last glacial maximum, and the resources appeared to sustain a constant global effective female population size throughout the Late Pleistocene. Reconstruction of the ancestral phylogeography highlighted the high mobility of this species, identifying 22 strongly supported long-range dispersal events including interoceanic and interhemispheric movement. Despite this propensity for geographic dispersal, the increased sampling of this study uncovered very few potential examples of ancestral dispersal among ecotypes. Concordance of nuclear and mitochondrial data further confirms genetic cohesiveness, with little or no current gene flow among sympatric ecotypes. Taken as a whole, our data suggest that the glacial cycles influenced local populations in different ways, with no clear global pattern, but with secondary contact among lineages following long-range dispersal as a potential mechanism driving ecological diversification.
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| 14. |
- Ongaya, Kizito, et al.
(author)
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Towards a spatial-temporal model of prevalence of nodding syndrome and epilepsy
- 2019
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In: AFRICOMM 2018: e-Infrastructure and e-Services for Developing Countries. - Cham : Springer International Publishing. - 1867-8211. - 9783030160418 ; 275, s. 67-77
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Conference paper (peer-reviewed)abstract
- Nodding syndrome is an emerging disease which have unknown transmission patterns and no properly established mechanisms for diagnosis leading to numerous hypothetical postulations. It has affected thousands of children in Uganda with debilitating effect and serious economic consequences. Spatial-temporal analysis may provide a quick mechanism to establish comparative understanding of the various hypotheses ascribed to nodding syndrome and any other emerging diseases with similar clinical manifestation. There is considerable suspicion that “nodding syndrome is a form of epilepsy”, a hypothesis that has hardly been investigated in literature. The aim of the study described in this paper is to establish spatial-temporal relationships between ailments diagnosed as nodding syndrome and ailments diagnosed as epilepsy. An exploratory cross section survey in three districts of Northern Uganda was done. Spatial data of health centers were recorded and ArcGIS was used for display. The findings show significant spatial-temporal correlation of diagnosis reporting of nodding syndrome to epilepsy. The regression statistics overall, epilepsy significantly (p < 0.05) ex-plains about 58% of Nodding syndrome variability. The F-statistic shows a very highly significant value (p = 8.20481E-13; p < 0.05), meaning that the output of the regression is not by chance.
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| 15. |
- Sutherland, Dez-Ann A. T., et al.
(author)
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Glucose Tolerance and Plasma Non-Esterified Fatty Acid Levels in Chickens Selected for Low Body Weight, Red Junglefowl, and their Reciprocal Cross
- 2019
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In: The Journal of Poultry Science. - : JAPAN POULTRY SCIENCE ASSOC. - 1346-7395 .- 1349-0486. ; 56:4, s. 245-252
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Journal article (peer-reviewed)abstract
- Responses of an individual to food deprivation, such as a 16-h fast, are complex, and are influenced by environmental and genetic factors. Domestication is an ongoing process during which adaptations to changing environments occur over generations. Food deprivation by their caretakers is less for domestic chickens than for their junglefowl ancestors. Unlike domestic chicken, the junglefowl adapted over generations to periods of food deprivation, which may be reflected in differences in metabolic responses to brief periods without food. Here, we compared the blood glucose and plasma levels of non-esterified fatty acids (NEFA) among four populations when deprived of feed for 16 h. The four populations included a domestic White Rock experimental line (LWS) maintained for generations under ad libitum feeding, adult red junglefowl (RJF), and a reciprocal cross of the lines. Although there were significant differences in adult (31-week) body weight between the RJF (683 g) and LWS (1282 g), with the weight of F-1 crosses being intermediate, the amount of abdominal fat relative to body weight was similar for all populations. Patterns for blood glucose responses to a glucose bolus after a 16-h fast were similar for the initial and final points in the parental and cross populations. However, RJF reached their peak faster than LWS, with the reciprocal cross intermediate to the parental populations. Plasma NEFA concentrations were higher after the 16-h fast than in fed states, with no population differences for the fasting state. However, in the fed state, NEFA levels were lesser for LWS than for others, which was reflected further in percentage change from fed to fasted. This larger change in LWS suggests differences in mobilization of energy substrates and implies that during domestication or development of the LWS line, thresholds for responses to acute stressors may have increased.
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| 16. |
- van Rheenen, Wouter, et al.
(author)
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Genome-wide association analyses identify new risk variants and the genetic architecture of amyotrophic lateral sclerosis
- 2016
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In: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 48:9, s. 1043-1048
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Journal article (peer-reviewed)abstract
- To elucidate the genetic architecture of amyotrophic lateral sclerosis (ALS) and find associated loci, we assembled a custom imputation reference panel from whole-genome-sequenced patients with ALS and matched controls (n = 1,861). Through imputation and mixed-model association analysis in 12,577 cases and 23,475 controls, combined with 2,579 cases and 2,767 controls in an independent replication cohort, we fine-mapped a new risk locus on chromosome 21 and identified C21orf2 as a gene associated with ALS risk. In addition, we identified MOBP and SCFD1 as new associated risk loci. We established evidence of ALS being a complex genetic trait with a polygenic architecture. Furthermore, we estimated the SNP-based heritability at 8.5%, with a distinct and important role for low-frequency variants (frequency 1-10%). This study motivates the interrogation of larger samples with full genome coverage to identify rare causal variants that underpin ALS risk.
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