Automatic Mapping and Characterisation of Linear Depositional Bedforms: Theory and Application Using Bathymetry from the North West Shelf of Australia

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Integration of gene ontology pathways with North American Rheumatoid Arthritis Consortium genome-wide association data via linear modeling

We describe an empirical Bayesian linear model for integration of functional gene annotation data with genome-wide association data. Using case-control study data from the North American Rheumatoid Arthritis Consortium and gene annotation data from the Gene Ontology, we illustrate how the method can be used to prioritize candidate genes for further investigation

Discovery of Holocene ooid shoals in a siliciclastic delta, De Grey River, North West Shelf, Australia

Onshore and offshore site investigations along the dryland tide-dominated De Grey River delta (northwestern Australia) led to the unexpected discovery of the largest yet-known marine ooid shoals in the Indo-Pacific region. Ooids exhibit up to 60 tangential aragonitic laminae that were formed around fluvial sediment grains during the late Holocene. Covering an area >1250 km2, their spatial extent rivals in size individual ooid shoals from the Bahamas. Shoals appear to be spatially linked with the De Grey River, suggesting that fluvial outputs, combined with a macrotidal range, facilitated the precipitation of the ooids. Following their formation, ooids were reworked through tidal and wave processes along the delta. As a result, the delta sedimentary features, including beach ridges, mouth bars, and distributary channels, are composed of ooids. This discovery broadens the range of depositional and climatic environments in which ooids can form and demonstrates that fluvial runoff may not inhibit aragonite precipitation. Such a configuration also provides a unique analogue for ancient ooids found in association with siliciclastic grains and further indicates that the interpretation of typical siliciclastic geomorphologies from geophysical data does not preclude the presence of carbonate grains.Discovery of Holocene ooid shoals in a siliciclastic delta, De Grey River, North West Shelf, AustraliapublishedVersio

Locally weighted transmission/disequilibrium test for genetic association analysis

The transmission/disequilibrium test statistic has been used for assessing genetic association in affected-parent trios. In the presence of multiple tightly linked marker loci where local dependency may exist, haplotypes are reconstructed statistically to estimate the joint effects of these markers. In this manuscript, we propose an alternative to the haplotype approach by taking a weighted average of multiple loci, where the weight is proportional to the product of (1-2X recombination fraction) and the linkage disequilibrium between markers. As an illustration, we applied the method to the simulated Aipotu data

Influence of genotyping error in linkage mapping for complex traits – an analytic study

<p>Abstract</p> <p>Background</p> <p>Despite the current trend towards large epidemiological studies of unrelated individuals, linkage studies in families are still thoroughly being utilized as tools for disease gene mapping. The use of the single-nucleotide-polymorphisms (SNP) array technology in genotyping of family data has the potential to provide more informative linkage data. Nevertheless, SNP array data are not immune to genotyping error which, as has been suggested in the past, could dramatically affect the evidence for linkage especially in selective designs such as affected sib pair (ASP) designs. The influence of genotyping error on selective designs for continuous traits has not been assessed yet.</p> <p>Results</p> <p>We use the identity-by-descent (IBD) regression-based paradigm for linkage testing to analytically quantify the effect of simple genotyping error models under specific selection schemes for sibling pairs. We show, for example, that in extremely concordant (EC) designs, genotyping error leads to decreased power whereas it leads to increased type I error in extremely discordant (ED) designs. Perhaps surprisingly, the effect of genotyping error on inference is most severe in designs where selection is least extreme. We suggest a genomic control for genotyping errors via a simple modification of the intercept in the regression for linkage.</p> <p>Conclusion</p> <p>This study extends earlier findings: genotyping error can substantially affect type I error and power in selective designs for continuous traits. Designs involving both EC and ED sib pairs are fairly immune to genotyping error. When those designs are not feasible the simple genomic control strategy that we suggest offers the potential to deliver more robust inference, especially if genotyping is carried out by SNP array technology.</p

Patterns and variability in ocean acidification conditions in Puget Sound and the Strait of Juan de Fuca

The Washington Ocean Acidification Center is working with NOAA and other partners to increase understanding of ocean acidification dynamics and spatial variability in the Salish Sea, and how these correlate with planktonic responses. These data are critical for assessing water quality, areas with higher or lower OA stress, and to understand effects on the food web. Two main strategies are employed; seasonal ship cruises provide spatial coverage and the ability to collect plankton, while mooring buoys provide information on mechanisms and the range of variation due to the high-resolution and constant coverage they provide. Results show a strong degree of depth, seasonal, and spatial variation in pH and aragonite saturation state. In general, the lowest pH and aragonite saturation state values are at depth, particularly in stratified areas, though this can shift during seasonal localized upwelling, e.g., Southern Hood Canal, and in mixed water columns, e.g., the Main Basin. Seasonal patterns are spatially diverse, with stratified areas exhibiting strong vertical gradients with depth during summer and more homogenous conditions during winter; well-mixed areas show less variation year-round. This implies that species encounter quite different OA conditions in various parts of the Salish Sea between the seasons. Mooring CO2 data reveal higher variation during late fall through early spring at sites within the Salish Sea, due to winter mixing of stratified waters, yet the reverse pattern off the Washington coast, due to summer upwelling. In both cases, these mechanisms (winter mixing and summer upwelling) operate across a gradient, bringing relatively deeper lower pH / aragonite saturation state waters in contact with surface waters with higher values. Such changes in the spatial and depth distribution of corrosive conditions have broad implications for sensitive marine life

Pentoxifylline Does Not Decrease Short-term Mortality but Does Reduce Complications in Patients With Advanced Cirrhosis

Background &amp; AimsPentoxifylline, an inhibitor of tumor necrosis factor-α, is given to patients with liver diseases, but its effects in patients with advanced cirrhosis are unknown. We performed a randomized, placebo-controlled, double-blind trial of its effects in patients with cirrhosis. Methods A total of 335 patients with cirrhosis (Child–Pugh class C) were assigned to groups given either pentoxifylline (400 mg, orally, 3 times daily; n = 164) or placebo (n = 171) for 6 months. The primary end point was mortality at 2 months. Secondary end points were mortality at 6 months and development of liver-related complications. Results By 2 months, 28 patients in the pentoxifylline group (16.5%) and 31 in the placebo group (18.2%) had died (P = .84). At 6 months, 50 patients in the pentoxifylline group (30.0%) and 54 in the placebo group (31.5%) had died (P = .75). The proportions of patients without complications (eg, bacterial infection, renal insufficiency, hepatic encephalopathy, or gastrointestinal hemorrhage) were higher in the pentoxifylline group than in the placebo group at 2 months (78.6% vs 63.4%; P = .006) and 6 months (66.8% vs 49.7%; P = .002). The probability of survival without complications was higher in the pentoxifylline group than in the placebo group at 2 and 6 months (P = .04). In multivariate analysis, the factors associated with death were age, the Model for End-Stage Liver Disease score, and presence of early-stage carcinoma. Treatment with pentoxifylline was the only factor associated with liver-related complications. Conclusions Although pentoxifylline does not decrease short-term mortality in patients with advanced cirrhosis, it does reduce the risk of complications

Effect of diabetes on caregiver burden in an observational study of individuals with Alzheimer’s disease

Background The burden on caregivers of patients with Alzheimer’s disease (AD) is associated with the patient’s functional status and may also be influenced by chronic comorbid medical conditions, such as diabetes. This post-hoc exploratory analysis assessed whether comorbid diabetes in patients with AD affects caregiver burden, and whether caregivers with diabetes experience greater burden than caregivers without diabetes. Caregiver and patient healthcare resource use (HCRU) were also assessed. Methods Baseline data from the GERAS observational study of patients with AD and their caregivers (both n = 1495) in France, Germany and the UK were analyzed. Caregiver burden was assessed using the Zarit Burden Interview (ZBI). Caregiver time on activities of daily living (ADL: basic ADL; instrumental ADL, iADL) and supervision (hours/month), and caregiver and patient HCRU (outpatient visits, emergency room visits, nights hospitalized) were assessed using the Resource Utilization in Dementia instrument for the month before the baseline visit. Regression analyses were adjusted for relevant covariates. Time on supervision and basic ADL was analyzed using zero-inflated negative binomial regression. Results Caregivers of patients with diabetes (n = 188) were younger and more likely to be female (both p < 0.05), compared with caregivers of patients without diabetes (n = 1307). Analyses showed caregivers of patients with diabetes spent significantly more time on iADL (+16 %; p = 0.03; increases were also observed for basic ADL and total caregiver time but did not reach statistical significance) and had a trend towards increased ZBI score. Patients with diabetes had a 63 % increase in the odds of requiring supervision versus those without diabetes (p = 0.01). Caregiver and patient HCRU did not differ according to patient diabetes. Caregivers with diabetes (n = 127) did not differ from those without diabetes (n = 1367) regarding burden/time, but caregivers with diabetes had a 91 % increase in the odds of having outpatient visits (p = 0.01). Conclusions This cross-sectional analysis found caregiver time on iADL and supervision was higher for caregivers of patients with AD and diabetes versus without diabetes, while HCRU was unaffected by patient diabetes. Longitudinal analyses assessing change in caregiver burden over time by patient diabetes status may help clarify the cumulative impact of diabetes and AD dementia on caregiver burden

Fulminant hepatitis: a clinical review of 11 years

24 cases of fulminant hepatitis (FH) hospitalized in the Clínica de Doenças Infecciosas e Parasitárias do Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo during the period from January 1976 to December 1986 were reviewed from their clinical, epidemiological and laboratorial aspects. 88% of the patients died; 20 patients (83%) presented hemorrhages and, of these, 19 died. Bacterial infections occurred in 14 patients (58%) all of whom died. Ascitis was noted in 3 cases; cerebral edema was present in 16 cases. Maximal ALT levels for each patient during hospitalization ranged widely from 81 to 4,460 UI/l. Thirteen patients presented high creatinine levels (54%). Prothrombin time activity ranged from 2.1% to 67%. Fever was present in 20 cases (83%). Encephalopathy occurred within the first 2 weeks of illness in 72% of the cases. In 7 cases other illnesses were present. The etiology could not be determined in 13 cases. In 3 cases it was due to yellow fever and 6 cases were caused by viruses other than yellow fever. In one case the cause was drug usage and in another case, possibly alcohol. The authors believe that the clinical definition of FH requires further discussion before it is established. In this study FH is a young person's disease. The mortality found was similar to that by other authors. Factors that contributed to death were: hemorrhages and bacterial infection. Factors that worsened the prognosis of hepatitis were: associated illnesses and surgical procedure. The levels of ALT during hospitalization did not correlate well with the severity of the hepatitis. The authors believe that yellow fever should be considered a cause of FH where the clinical picture meets the criteria for such, although its mechanisms of encephalopathy remain obscure. The clinical details of the 3 cases of yellow fever are presented