| 1. |
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| 2. |
- Jakosky, B. M., et al.
(author)
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MAVEN observations of the response of Mars to an interplanetary coronal mass ejection
- 2015
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In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 350:6261
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Journal article (peer-reviewed)abstract
- Coupling between the lower and upper atmosphere, combined with loss of gas from the upper atmosphere to space, likely contributed to the thin, cold, dry atmosphere of modern Mars. To help understand ongoing ion loss to space, the Mars Atmosphere and Volatile Evolution (MAVEN) spacecraft made comprehensive measurements of the Mars upper atmosphere, ionosphere, and interactions with the Sun and solar wind during an interplanetary coronal mass ejection impact in March 2015. Responses include changes in the bow shock and magnetosheath, formation of widespread diffuse aurora, and enhancement of pick-up ions. Observations and models both show an enhancement in escape rate of ions to space during the event. Ion loss during solar events early in Mars history may have been a major contributor to the long-term evolution of the Mars atmosphere.
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| 3. |
- Chaillou, Thomas, 1985-, et al.
(author)
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Identification of a conserved set of upregulated genes in mouse skeletal muscle hypertrophy and regrowth
- 2015
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In: Journal of applied physiology. - Bethesda, USA : American Physiological Society. - 8750-7587 .- 1522-1601. ; 118, s. 86-97
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Journal article (peer-reviewed)abstract
- The purpose of this study was to compare the gene expression profile of mouse skeletal muscle undergoing two forms of growth (hypertrophy and regrowth) with the goal of identifying a conserved set of differentially expressed genes. Expression profiling by microarray was performed on the plantaris muscle subjected to 1, 3, 5, 7, 10, and 14 days of hypertrophy or regrowth following 2 wk of hind-limb suspension. We identified 97 differentially expressed genes (≥2-fold increase or ≥50% decrease compared with control muscle) that were conserved during the two forms of muscle growth. The vast majority (∼90%) of the differentially expressed genes was upregulated and occurred at a single time point (64 out of 86 genes), which most often was on the first day of the time course. Microarray analysis from the conserved upregulated genes showed a set of genes related to contractile apparatus and stress response at day 1, including three genes involved in mechanotransduction and four genes encoding heat shock proteins. Our analysis further identified three cell cycle-related genes at day and several genes associated with extracellular matrix (ECM) at both days 3 and 10. In conclusion, we have identified a core set of genes commonly upregulated in two forms of muscle growth that could play a role in the maintenance of sarcomere stability, ECM remodeling, cell proliferation, fast-to-slow fiber type transition, and the regulation of skeletal muscle growth. These findings suggest conserved regulatory mechanisms involved in the adaptation of skeletal muscle to increased mechanical loading.
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| 4. |
- Kirby, T.J., et al.
(author)
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Blunted hypertrophic response in aged skeletal muscle is associated with decreased ribosome biogenesis
- 2015
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In: Journal of applied physiology. - Bethesda, USA : American Physiological Society. - 8750-7587 .- 1522-1601. ; 119:4, s. 321-327
-
Journal article (peer-reviewed)abstract
- The ability of skeletal muscle to hypertrophy in response to a growth stimulus is known to be compromised in older individuals. We hypothesized that a change in the expression of protein-encoding genes in response to a hypertrophic stimulus contributes to the blunted hypertrophy observed with aging. To test this hypothesis, we determined gene expression by microarray analysis of plantaris muscle from 5- and 25-mo-old mice subjected to 1, 3, 5, 7, 10, and 14 days of synergist ablation to induce hypertrophy. Overall, 1,607 genes were identified as being differentially expressed across the time course between young and old groups; however, the difference in gene expression was modest, with cluster analysis showing a similar pattern of expression between the two groups. Despite ribosome protein gene expression being higher in the aged group, ribosome biogenesis was significantly blunted in the skeletal muscle of aged mice compared with mice young in response to the hypertrophic stimulus (50% vs. 2.5-fold, respectively). The failure to upregulate pre-47S ribosomal RNA (rRNA) expression in muscle undergoing hypertrophy of old mice indicated that rDNA transcription by RNA polymerase I was impaired. Contrary to our hypothesis, the findings of the study suggest that impaired ribosome biogenesis was a primary factor underlying the blunted hypertrophic response observed in skeletal muscle of old mice rather than dramatic differences in the expression of protein-encoding genes. The diminished increase in total RNA, pre-47S rRNA, and 28S rRNA expression in aged muscle suggest that the primary dysfunction in ribosome biogenesis occurs at the level of rRNA transcription and processing.
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| 5. |
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| 6. |
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| 7. |
- Strandberg, B., et al.
(author)
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Near-threshold π-photoproduction on the deuteron
- 2020
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In: Physical Review C. - 2469-9985. ; 101:3
-
Journal article (peer-reviewed)abstract
- The first experimental investigation of the near-threshold cross section for incoherent π-photoproduction on the deuteron γd→π-pp is presented. The experimental technique involved detection of the ≈131 MeV γ ray resulting from the radiative capture of photoproduced π-in the target. The total cross section was measured using an unpolarized tagged-photon beam, a liquid-deuterium target, and three very large NaI(Tl) spectrometers. The data are compared to theoretical models that give insight into the elementary reaction γn→π-p and pion-nucleon and nucleon-nucleon final-state interactions.
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| 8. |
- Mansour, A., et al.
(author)
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Diarrhea Burden Due to Natural Infection with Enterotoxigenic Escherichia coli in a Birth Cohort in a Rural Egyptian Community
- 2014
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In: Journal of Clinical Microbiology. - : American Society for Microbiology. - 0095-1137 .- 1098-660X. ; 52:7, s. 2595-2603
-
Journal article (peer-reviewed)abstract
- Enterotoxigenic Escherichia coli (ETEC) is commonly associated with diarrhea in Egyptian children. Children less than 3 years old in Abu Homos, Egypt, had approximately five diarrheal episodes per child every year, and at least one of these episodes was due to ETEC. The epidemiology of ETEC diarrhea among children living in a rural Egyptian community was further evaluated in this study. Between January 2004 and April 2007, 348 neonates were enrolled and followed for 2 years. Children were visited twice weekly, and a stool sample was obtained every 2 weeks regardless of symptomatology. A stool sample was obtained whenever a child had diarrhea. From the routine stool culture, five E. coli-like colonies were selected and screened for heat-labile and heat-stable toxins by GM1 enzyme-linked immunosorbent assay (ELISA) and further typed for colonization factor antigens by dot blot assay. Incidence of ETEC infection was estimated among children with diarrhea (symptomatic) and without diarrhea (asymptomatic). Incidence of diarrhea and ETEC-associated diarrhea was 7.8 and 1.48 per child-year, respectively. High risk of repeated ETEC diarrhea was associated with being over 6 months of age, warm season, male gender, and crowded sleeping conditions. Exclusive breast-feeding was protective for repeated ETEC infection. ETEC-associated diarrhea remains common among children living in the Nile Delta. The protective role of breast-feeding demonstrates the importance of promoting exclusive breast-feeding during, at least, the first 6 months of life.
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| 9. |
- Rich, Rebecca L., et al.
(author)
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A global benchmark study using affinity-based biosensors
- 2009
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In: Analytical Biochemistry. - : Elsevier BV. - 0003-2697 .- 1096-0309. ; 386:2, s. 194-216
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Journal article (peer-reviewed)abstract
- To explore the variability in biosensor studies, 150 participants from 20 countries were given the same protein samples and asked to determine kinetic rate constants for the interaction. We chose a protein system that was amenable to analysis using different biosensor platforms as well as by users of different expertise levels. The two proteins (a 50-kDa Fab and a 60-kDa glutathione S-transferase [GST] antigen) form a relatively high-affinity complex, so participants needed to optimize several experimental parameters, including ligand immobilization and regeneration conditions as well as analyte concentrations and injection/dissociation times. Although most participants collected binding responses that could be fit to yield kinetic parameters, the quality of a few data sets could have been improved by optimizing the assay design. Once these outliers were removed, the average reported affinity across the remaining panel of participants was 620 pM with a standard deviation of 980 pM. These results demonstrate that when this biosensor assay was designed and executed appropriately, the reported rate constants were consistent, and independent of which protein was immobilized and which biosensor was used.
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| 10. |
- Strandberg, B., et al.
(author)
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Compton scattering from the deuteron above pion-production threshold
- 2018
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In: Physical Review C. - 2469-9985. ; 98:1
-
Journal article (peer-reviewed)abstract
- The electromagnetic polarizabilities of the nucleon are fundamental nucleon-structure observables that characterize its response to external electromagnetic fields. The neutron polarizabilities can be accessed from Compton-scattering data on light nuclear targets. Recent measurements of the differential cross section for Compton scattering on the deuteron below the pion-production threshold have decreased the uncertainties in the neutron polarizabilities, yet the proton polarizabilities remain known substantially more accurately. As the sensitivity of the cross section to the polarizabilities increases with incident photon energy, measurements above the pion threshold may offer a way for an improved determination of the neutron polarizabilities. In this Rapid Communiciation, the first measurement of the cross section for coherent Compton scattering on the deuteron above the pion-production threshold is presented.
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| 11. |
- Citron, I., et al.
(author)
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Surgical quality indicators in low-resource settings: A new evidence-based tool
- 2018
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In: Surgery. - : Elsevier BV. - 0039-6060. ; 164:5, s. 946-952
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Journal article (peer-reviewed)abstract
- Background: Worldwide efforts to improve access to surgical care must be accompanied by improvements in the quality of surgical care; however, these efforts are contingent on the ability to measure quality. This report describes a novel, evidence-based tool to measure quality of surgical care in low-resource settings. Methods: We defined a widely applicable, multidimensional conceptual framework for quality. The suitability of currently available quality metrics to low-resource settings was evaluated. Then we developed new indicators with sufficient supportive evidence to complete the framework. The complete set of metrics was condensed into four collection sources and tools. Results: The following 15 final evidence-based indicators were defined: (1) Safe structure: morbidity and mortality conference; (2) safe process: use of the safe surgery checklist; (3) (4) safe outcomes: perioperative mortality rate and proportion of cases with complications graded >2 on the Clavien-Dindo scale; (5) effective structure: provider density; (6) effective process: procedure rate; (7) effective outcome: rate of caesarean sections; (8) patient-centered process: use of informed consent; (9) patient-centered outcome: patient hospital satisfaction questionnaire; (10) timely structure: travel time to hospital; (11) timely process: time from emergency department presentation to non-elective abdominal surgery; (12) timely outcome: patient follow-up plan; (13) efficient process: daily operating room usage; (14) equitable outcome: comparative income of patients compared with population; and (15) proportion of patients facing catastrophic expenditure because of surgical care. Conclusion: This tool provides an evidence-based conceptual tool to assess the quality of surgical care in diverse low-resource settings.
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| 12. |
- Lillis, Robert J., et al.
(author)
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MOSAIC: A satellite constellation to enable groundbreaking mars climate system science and prepare for human exploration
- 2021
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In: Planetary Science Journal. - : Institute of Physics (IOP). - 2632-3338. ; 2:5
-
Journal article (peer-reviewed)abstract
- The Martian climate system has been revealed to rival the complexity of Earth's. Over the last 20 yr, a fragmented and incomplete picture has emerged of its structure and variability; we remain largely ignorant of many of the physical processes driving matter and energy flow between and within Mars' diverse climate domains. Mars Orbiters for Surface, Atmosphere, and Ionosphere Connections (MOSAIC) is a constellation of ten platforms focused on understanding these climate connections, with orbits and instruments tailored to observe the Martian climate system from three complementary perspectives. First, low-circular near-polar Sun-synchronous orbits (a large mothership and three smallsats spaced in local time) enable vertical profiling of wind, aerosols, water, and temperature, as well as mapping of surface and subsurface ice. Second, elliptical orbits sampling all of Mars' plasma regions enable multipoint measurements necessary to understand mass/energy transport and ion-driven escape, also enabling, with the polar orbiters, dense radio occultation coverage. Last, longitudinally spaced areostationary orbits enable synoptic views of the lower atmosphere necessary to understand global and mesoscale dynamics, global views of the hydrogen and oxygen exospheres, and upstream measurements of space weather conditions. MOSAIC will characterize climate system variability diurnally and seasonally, on meso-, regional, and global scales, targeting the shallow subsurface all the way out to the solar wind, making many first-of-their-kind measurements. Importantly, these measurements will also prepare for human exploration and habitation of Mars by providing water resource prospecting, operational forecasting of dust and radiation hazards, and ionospheric communication/positioning disruptions.
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| 13. |
- Reardon, Anthony J. F., et al.
(author)
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Maternal co-exposure to mercury and perfluoroalkyl acid isomers and their associations with child neurodevelopment in a Canadian birth cohort
- 2023
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In: Environment International. - 0160-4120 .- 1873-6750. ; 178
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Journal article (peer-reviewed)abstract
- Background: Perfluoroalkyl acids (PFAAs) within the broader class of per- and polyfluoroalkyl substances (PFAS) are present in human serum as isomer mixtures, but epidemiological studies have yet to address isomer-specific associations with child development and behavior. Objectives: To examine associations between prenatal exposure to 25 PFAAs, including perfluorooctane sulfonate (PFOS) and perfluorooctanoate (PFOA) isomers, and child neurodevelopment among 490 mother-child pairs in a prospective Canadian birth cohort, the Alberta Pregnancy Outcomes and Nutrition (APrON) study. To consider the influence of a classic neurotoxicant, total mercury (THg), based on its likelihood of co-exposure with PFAAs from common dietary sources. Methods: Maternal blood samples were collected in the second trimester and child neurodevelopment was assessed at 2 years of age using the Bayley Scales of Infant and Toddler Development, 3rd Edition (Bayley-III). Linear or curvilinear multiple regression models were used to examine associations between exposures and neurodevelopment outcomes. Results: Select PFAAs were associated with lower Cognitive composite scores, including perfluoroheptanoate (PFHpA) (& beta; = -0.88, 95% confidence interval (CI): -1.7, -0.06) and perfluorododecanoate (PFDoA) (& beta; = -2.0, 95% CI: -3.9, -0.01). Non-linear relationships revealed associations of total PFOS (& beta; = -4.4, 95% CI: -8.3, -0.43), and linear-PFOS (& beta; = -4.0, 95% CI: -7.5, -0.57) and 1m-PFOS (& beta; = -1.8, 95% CI: -3.3, -0.24) isomers with lower Language composite scores. Although there was no effect modification, including THg interaction terms in PFAA models revealed negative associations between perfluorononanoate (PFNA) and Motor (& beta; = -3.3, 95% CI: -6.2, -0.33) and Social-Emotional (& beta; = -3.0, 95% CI: -5.6, -0.40) composite scores. Discussion: These findings reinforce previous reports of adverse effects of maternal PFAA exposure during pregnancy on child neurodevelopment. The unique hazards posed from isomers of PFOS justify isomer-specific analysis in future studies. To control for possible confounding, mercury co-exposure may be considered in studies of PFAAs.
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| 14. |
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| 15. |
- Abramovitz, T, et al.
(author)
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MONA LISA : Deep seismic investigations of the lithosphere in the southeastern North Sea
- 1997
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In: TECTONOPHYSICS. - : ELSEVIER SCIENCE BV. - 0040-1951. ; 269:1-2, s. 1-19
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Journal article (other academic/artistic)abstract
- The MONA LISA collaborative project has collected 1112 km of seismic normal-incidence reflection data (recorded to 26 s) and wide-angle data from 26 onshore and 2 offshore locations along 4 profiles in the southeastern North Sea. The seismic data clearly
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| 16. |
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| 17. |
- Chafik, L., et al.
(author)
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Global linkages originating from decadal oceanic variability in the subpolar North Atlantic
- 2016
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In: Geophysical Research Letters. - 0094-8276 .- 1944-8007. ; 43:20, s. 10909-10919
-
Journal article (peer-reviewed)abstract
- The anomalous decadal warming of the subpolar North Atlantic Ocean (SPNA), and the northward spreading of this warm water, has been linked to rapid Arctic sea ice loss and more frequent cold European winters. Recently, variations in this heat transport have also been reported to covary with global warming slowdown/acceleration periods via a Pacific climate response. We here examine the role of SPNA temperature variability in this Atlantic-Pacific climate connectivity. We find that the evolution of ocean heat content anomalies from the subtropics to the subpolar region, likely due to ocean circulation changes, coincides with a basin-wide Atlantic warming/cooling. This induces an Atlantic-Pacific sea surface temperature seesaw, which in turn, strengthens/weakens the Walker circulation and amplifies the Pacific decadal variability that triggers pronounced global-scale atmospheric circulation anomalies. We conclude that the decadal oceanic variability in the SPNA is an essential component of the tropical interactions between the Atlantic and Pacific Oceans.
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| 18. |
- Dewey, Deborah, et al.
(author)
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Sex-specific associations between maternal phthalate exposure and neurodevelopmental outcomes in children at 2 years of age in the APrON cohort
- 2023
-
In: Neurotoxicology. - 0161-813X .- 1872-9711. ; 98, s. 48-60
-
Journal article (peer-reviewed)abstract
- Background: There is inconsistent evidence regarding the sex-specific associations between prenatal phthalate exposure and children's neurodevelopment. This could be due to differences in the phthalate exposures inves-tigated and the neurodevelopmental domains assessed.Objective: To evaluate the associations between prenatal phthalate exposure and sex-specific outcomes on measures of cognition, language, motor, executive function, and behaviour in children 2 years of age in the Alberta Pregnancy Outcomes and Nutrition (APrON) cohort.Methods: We evaluated the associations between prenatal phthalate exposure and sex-specific neuro-developmental outcomes in children at 2 years of age using data from 448 mothers and their children (222 girls, 226 boys). Nine phthalate metabolites were measured in maternal urine collected in the second trimester of pregnancy. Children's cognitive, language, and motor outcomes were assessed using the Bayley Scales of Infant Development - Third Edition (Bayley-III). Parents completed questionnaires on children's executive function and behavior, the Behavior Rating Inventory of Executive Function-Preschool Version (BRIEF-P) and Child Behavior Checklist (CBCL), respectively. Sex-stratified robust multivariate regressions were performed.Results: Higher maternal concentrations of & sigma;DEHP and its metabolites were associated with lower scores on the Bayley-III Cognitive (& beta;'s from-11.8 to-0.07 95% CI's from-21.3 to-0.01), Language (& beta;'s from-11.7 to-0. 09, 95% CI's from-22.3 to-0.02) and Motor (& beta;'s from-10.9 to-0.07, 95% CI from-20.4 to-0.01) composites in boys. The patterns of association in girls were in the opposite direction on the Cognitive and Language composites; on the Motor composite they were in the same direction as boys, but of reduced strength. Higher concentrations of & sigma;DEHP and its metabolites were associated with higher scores (i.e., more difficulties) on all measures of executive function in girls: inhibitory self-control (B's from 0.05 to 0.11, 95% CI s from-0.01 to 0.15), flexibility (B's from 0.04 to 0.11, 95% CI s from 0.01 to 0.21) and emergent metacognition (B's from-0.01 to 0.06, 95% CIs from-0.01 to 0.20). Similar patterns of attenuated associations were seen in boys. Higher concentrations of & sigma;DEHP and its metabolites were associated with more Externalizing Problems in girls and boys (B's from 0.03 to 6.82, 95% CIs from-0.08 to 12.0). Two phthalates, MMP and MBP, had sex-specific adverse associations on measures of executive function and behaviour, respectively, while MEP was positively associated with boys' cognitive, language, and motor performance. Limited associations were observed between mixtures of maternal phthalates and sex-specific neurodevelopmental outcomes.Conclusions: Maternal prenatal concentrations of DEHP phthalates were associated with sex specific difference on measures of cognition and language at 2 years of age, specifically, poorer outcomes in boys. Higher exposure to DEHP was associated with poorer motor, executive function, and behavioural outcomes in girls and boys but the strength of these associations differed by sex. Limited associations were noted between phthalate mixtures and child neurodevelopment.
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| 19. |
- England, RW, et al.
(author)
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Closure of the Tornquist sea: Constraints from MONA LISA deep seismic reflection data
- 1997
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In: GEOLOGY. - : GEOLOGICAL SOC AMERICA. - 0091-7613. ; 25:12, s. 1071-1074
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Journal article (other academic/artistic)abstract
- Deep seismic reflection profiles west of Denmark across the suture between Baltica and Eastern Avalonia reveal weak, southward-dipping reflectors within the crystalline basement. These reflectors are interpreted as thrusts resulting from emplacement of Ea
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| 20. |
- Grover, A, et al.
(author)
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A novel tau mutation in exon 9 (1260V) causes a four-repeat tauopathy
- 2003
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In: Experimental Neurology. - 0014-4886. ; 184:1, s. 131-140
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Journal article (peer-reviewed)abstract
- A novel mutation in exon 9 of tau, I260V, is associated with a clinical syndrome consistent with frontotemporal dementia with extensive tau pathology; however, neurofibrillary tangles and Pick bodies are absent. Significantly, Sarkosyl- insoluble tau extracted from affected brain tissue consisted almost exclusively of four-repeat isoforms. Consistent with these findings, in vitro biochemical assays demonstrated that the I260V mutation causes a selective increase in tau aggregation and a decrease in tau-induced microtubule assembly with four-repeat isoforms only. The contrasting pathology and biochemical effects of this mutation suggest a different disease mechanism from the other exon 9 mutations and demonstrates the critical role for the first microtubule-binding domain in tau-promoted microtubule assembly and the pathogenic aggregation of tau.
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| 21. |
- Irvine, Nathalie, et al.
(author)
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Associations between maternal folate status and choline intake during pregnancy and neurodevelopment at 3–4 years of age in the Alberta Pregnancy Outcomes and Nutrition (APrON) study
- 2023
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In: Journal of Developmental Origins of Health and Disease. - 2040-1744 .- 2040-1752. ; 14:3, s. 402-414
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Journal article (peer-reviewed)abstract
- Folate and choline are methyl donor nutrients that may play a role in fetal brain development. Animal studies have reported that prenatal folate and choline supplementation are associated with better cognitive outcomes in offspring and that these nutrients may interact and affect brain development. Human studies that have investigated associations between maternal prenatal folate or choline levels and neurodevelopmental outcomes have reported contradictory findings and no human studies have examined the potential interactive effect of folate and choline on children’s neurodevelopment. During the second trimester of pregnancy, maternal red blood cell folate was measured from blood samples and choline intake was estimated using a 24-h dietary recall in 309 women in the APrON cohort. At 3–5 years of age, their children’s neurodevelopment was assessed using the Wechsler Preschool and Primary Scales of Intelligence – Fourth EditionCND, NEPSY-II language and memory subtests, four behavioral executive function tasks, and the Movement Assessment Battery for Children – Second Edition. Adjusted regressions revealed no associations between maternal folate and choline levels during pregnancy and most of the child outcomes. On the Dimensional Change Card Sort, an executive function task, there was an interaction effect; at high levels of choline intake (i.e., 1 SD above the mean; 223.03 mg/day), higher maternal folate status was associated with decreased odds of receiving a passing score (β = −0.44; 95%CI −0.81, −0.06). In conclusion, maternal folate status and choline intake during the second trimester of pregnancy were not associated with children’s intelligence, language, memory, or motor outcomes at 3–4 years of age; however, their interaction may have an influence children’s executive functions.
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| 22. |
- Koratkar, A, et al.
(author)
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The disappearing broad absorption lines and variable emission lines in NGC 3516
- 1996
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In: ASTROPHYSICAL JOURNAL. - : UNIV CHICAGO PRESS. - 0004-637X. ; 470:1, s. 378-393
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Journal article (other academic/artistic)abstract
- The Seyfert 1 galaxy NGC 3516 was monitored during 1993 February 16-May 13 by IUE every 4 days for the first month, and then every 2 days for 2 months giving a total of 40 observations. This paper gives the initial results from this campaign, (1) The broa
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| 23. |
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| 24. |
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| 25. |
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| 26. |
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| 27. |
- Singer-Berk, Moriel, et al.
(author)
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Advanced variant classification framework reduces the false positive rate of predicted loss-of-function variants in population sequencing data
- 2023
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In: American Journal of Human Genetics. - : Elsevier BV. - 0002-9297 .- 1537-6605. ; 110:9, s. 1496-1508
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Journal article (peer-reviewed)abstract
- Predicted loss of function (pLoF) variants are often highly deleterious and play an important role in disease biology, but many pLoF variants may not result in loss of function (LoF). Here we present a framework that advances interpretation of pLoF variants in research and clinical settings by considering three categories of LoF evasion: (1) predicted rescue by secondary sequence properties, (2) uncertain biological relevance, and (3) potential technical artifacts. We also provide recommendations on adjustments to ACMG/AMP guidelines’ PVS1 criterion. Applying this framework to all high-confidence pLoF variants in 22 genes associated with autosomal-recessive disease from the Genome Aggregation Database (gnomAD v.2.1.1) revealed predicted LoF evasion or potential artifacts in 27.3% (304/1,113) of variants. The major reasons were location in the last exon, in a homopolymer repeat, in a low proportion expressed across transcripts (pext) scored region, or the presence of cryptic in-frame splice rescues. Variants predicted to evade LoF or to be potential artifacts were enriched for ClinVar benign variants. PVS1 was downgraded in 99.4% (162/163) of pLoF variants predicted as likely not LoF/not LoF, with 17.2% (28/163) downgraded as a result of our framework, adding to previous guidelines. Variant pathogenicity was affected (mostly from likely pathogenic to VUS) in 20 (71.4%) of these 28 variants. This framework guides assessment of pLoF variants beyond standard annotation pipelines and substantially reduces false positive rates, which is key to ensure accurate LoF variant prediction in both a research and clinical setting.
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| 28. |
- Soomro, Munawar Hussain, et al.
(author)
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Associations between the chemical exposome and pregnancy induced hypertension
- 2023
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In: Environmental Research. - 0013-9351 .- 1096-0953. ; 237
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Journal article (peer-reviewed)abstract
- Exposure to environmental chemicals has been linked to an increased risk of pregnancy-induced hypertension (PIH). This prospective cohort study examined the associations between PIH and maternal chemical exposure to four classes of chemicals (i.e., phthalates, bisphenols, perfluoroalkyl acids, non-essential metals and trace minerals). Participants included 420 pregnant women from the Alberta Pregnancy Outcomes and Nutrition (APrON) cohort who had data available on diagnosed PIH and environmental chemical exposure. Twelve phthalate metabolites, two bisphenols, eight perfluoroalkyl acids and eleven non-essential metals or trace minerals were quantified in maternal urine or blood samples collected in the second trimester of pregnancy. Associations between the urinary and blood concentrations of these chemicals and PIH were assessed using multiple logistic and LASSO regression analyses in single- and multi-chemical exposure models, respectively. Thirty-five (8.3%) participants were diagnosed with PIH. In single chemical exposure models, two phthalate metabolites, mono-methyl phthalate (MMP) and monoethyl phthalate (MEP), three perfluoroalkyl acids, perfluoroheptanoic acid (PFHpA), perfluorononanoic acid (PFNA), and perfluorodecanoic acid (PFDA), and one metal, manganese, were associated with increased odds of PIH. The metabolites of di (2-ethylhexyl) phthalate (DEHP) and the molar sum of these metabolites, as well as antimony, displayed trend associations (p < 0.10). In multi-chemical exposure models using LASSO penalized regressions and double-LASSO regressions, MEP (AOR: 1.43, 95% CI: 1.09–1.88, p = 0.009) and PFNA (AOR: 2.03, 95% CI: 1.01–4.07, p = 0.04) were selected as the chemicals most highly associated with PIH. These findings suggest that maternal levels of phthalates and perfluoroalkyl acids may be associated with the diagnosis on PIH. Future research should consider both individual and multi-chemical exposures when examining predictors of PIH and other maternal cardiometabolic health disorders, such as preeclampsia, eclampsia, HELLP syndrome, and gestational diabetes.
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| 29. |
- Souche, E. L., et al.
(author)
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Range-wide population structure of European sea bass Dicentrarchus labrax
- 2015
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In: Biological Journal of the Linnean Society. - : Oxford University Press (OUP). - 0024-4066. ; 116:1, s. 86-105
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Journal article (peer-reviewed)abstract
- The euryhaline European sea bass Dicentrarchus labrax L., inhabiting the coasts of the eastern Atlantic Ocean and Mediterranean Sea, has had many opportunities for differentiation throughout its large natural range. However, evidence for this has been incompletely documented geographically and with an insufficient number of markers. Therefore, its full range was sampled at 22 sites and individuals were genotyped with a suite of mapped markers, including 14 microsatellite loci (N=536) and 46 neutral or gene-linked single nucleotide polymorphisms (SNPs; N=644). We confirm that the Atlantic and Mediterranean basins harbour two distinct lineages. Within the Atlantic Ocean no pattern was obvious based on the microsatellite and SNP genotypes, except for a subtle difference between South-eastern and North-eastern Atlantic sea bass attributed to limited introgression of alleles of Mediterranean origin. SNP genotypes of the Mediterranean lineage differentiated into three groups, probably under the influence of geographical isolation. The Western Mediterranean group showed genetic homogeneity without evidence for outlier loci. The Adriatic group appeared as a distinct unit. The Eastern Mediterranean group showed a longitudinal gradient of genotypes and most interestingly an outlier locus linked to the somatolactin gene. Overall, the spatial pattern fits those observed with other taxa of between-basin segregation and within-basin connectivity, which concurs well with the swimming capabilities of European sea bass. Evidence from a few outlier loci in this and other studies encourages further exploration of its regional connectivity and adaptive evolution.
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| 30. |
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| 31. |
- Wilkes, Martin A., et al.
(author)
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Physical and biological controls on fine sediment transport and storage in rivers
- 2019
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In: WIREs Water. - : John Wiley & Sons. - 2049-1948. ; 6:2
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Research review (peer-reviewed)abstract
- Excess fine sediment, comprising particles <2 mm in diameter, is a major cause of ecological degradation in rivers. The erosion of fine sediment from terrestrial or aquatic sources, its delivery to the river, and its storage and transport in the fluvial environment are controlled by a complex interplay of physical, biological, and anthropogenic factors. While the physical controls exerted on fine sediment dynamics are relatively well‐documented, the role of biological processes and their interactions with hydraulic and physicochemical phenomena has been largely overlooked. The activities of biota, from primary producers to predators, exert strong controls on fine sediment deposition, infiltration, and resuspension. For example, extracellular polymeric substances associated with biofilms increase deposition and decrease resuspension. In lower energy rivers, aquatic macrophyte growth and senescence are intimately linked to sediment retention and loss, whereas riparian trees are dominant ecosystem engineers in high energy systems. Fish and invertebrates also have profound effects on fine sediment dynamics through activities that drive both particle deposition and erosion depending on species composition and abiotic conditions. The functional traits of species present will determine not only these biotic effects but also the responses of river ecosystems to excess fine sediment. We discuss which traits are involved and put them into context with spatial processes that occur throughout the river network. While strides towards better understanding of the impacts of excess fine sediment have been made, further progress to identify the most effective management approaches is urgently required through close communication between authorities and scientists.
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