On the fourth-order accurate compact ADI scheme for solving the unsteady Nonlinear Coupled Burgers' Equations

The two-dimensional unsteady coupled Burgers' equations with moderate to severe gradients, are solved numerically using higher-order accurate finite difference schemes; namely the fourth-order accurate compact ADI scheme, and the fourth-order accurate Du Fort Frankel scheme. The question of numerical stability and convergence are presented. Comparisons are made between the present schemes in terms of accuracy and computational efficiency for solving problems with severe internal and boundary gradients. The present study shows that the fourth-order compact ADI scheme is stable and efficient

Epidemiological situation of bovine brucellosis in the State of São Paulo, Brazil

Realizou-se um estudo para caracterizar a situação epidemiológica da brucelose bovina no Estado de São Paulo. O Estado foi estratificado em sete circuitos produtores de bovinos, e 150 rebanhos com atividade reprodutiva foram aleatoriamente selecionados em cada um deles. No total, foram amostrados 1.073 rebanhos. Foram aletoriamente coletadas amostras de soro de 10 ou 15 fêmeas bovinas com idade ³24 meses, totalizando 8.761 animais. Os soros foram submetidos a um protocolo de testes em série, tendo o teste do antígeno acidificado tamponado como método de triagem e o da fixação de complemento como confirmatório. A prevalência estimada de rebanhos com pelo menos um animal soropositivo foi de 9,7% [7,8-11,6%], enquanto a prevalência estimada de animais soropositivos foi de 3,8% [0,7-6,9%], no Estado. Em cada rebanho foi aplicado um questionário epidemiológico para avaliar o grau de associação de possíveis fatores de risco (odds ratio, OR) com a doença. Propriedades com 87 ou mais bovinos (OR= 2,25) e compra de reprodutores (OR= 1,56) foram as variáveis mais associadas à condição de foco de brucelose. ____________________________________________________________________________________________________________ ARQUIVOA study to characterize the epidemiological situation of bovine brucellosis in the State of São Paulo was carried out. The state was stratified in seven cattle production regions and 150 herds with reproductive activity were randomly selected within each one. A total of 1,073 herds were sampled. In a second stage, 10 or 15 cows older than 24 month age (in herds with <100 cows and herds ≥100 cows, respectively) were bled at random. A total of 8,761 animals were bled. Sera were tested using a serial testing procedure with the Rose Bengal test as the screening method and the Complement Fixation as the confirmatory method. The estimated prevalence of herds with at least one positive animal was 9.7% [7.8-11.6%], whereas the estimated prevalence of positive cattle was 3.8% [0.7-6.9%] in São Paulo State. An epidemiological questionnaire was applied in each farm, allowing the evaluation of the association of selected risk factors with the disease. The characteristics associated with the brucellosis infected herds were farms with more than 87 bovines (OR= 2.25) and introduction of breeding cattle (OR= 1.56)

FGF receptor genes and breast cancer susceptibility: results from the Breast Cancer Association Consortium

Background:Breast cancer is one of the most common malignancies in women. Genome-wide association studies have identified FGFR2 as a breast cancer susceptibility gene. Common variation in other fibroblast growth factor (FGF) receptors might also modify risk. We tested this hypothesis by studying genotyped single-nucleotide polymorphisms (SNPs) and imputed SNPs in FGFR1, FGFR3, FGFR4 and FGFRL1 in the Breast Cancer Association Consortium. Methods:Data were combined from 49 studies, including 53 835 cases and 50 156 controls, of which 89 050 (46 450 cases and 42 600 controls) were of European ancestry, 12 893 (6269 cases and 6624 controls) of Asian and 2048 (1116 cases and 932 controls) of African ancestry. Associations with risk of breast cancer, overall and by disease sub-type, were assessed using unconditional logistic regression. Results:Little evidence of association with breast cancer risk was observed for SNPs in the FGF receptor genes. The strongest evidence in European women was for rs743682 in FGFR3; the estimated per-allele odds ratio was 1.05 (95 confidence interval=1.02-1.09, P=0.0020), which is substantially lower than that observed for SNPs in FGFR2. Conclusion:Our results suggest that common variants in the other FGF receptors are not associated with risk of breast cancer to the degree observed for FGFR2. © 2014 Cancer Research UK

Exceptional skull of huayqueriana (mammalia, litopterna, macraucheniidae) from the late miocene of Argentina: Anatomy, systematics, and peleobiological implications

The Huayquerías Formation (Late Miocene, Huayquerian SALMA) is broadly exposed in westcentral Argentina (Mendoza). The target of several major paleontological expeditions in the first half of the 20th century, the Mendozan Huayquerías (badlands) have recently yielded a significant number of new fossil finds. In this contribution we describe a complete skull (IANIGLA-PV 29) and place it systematically as Huayqueriana cf. H. cristata (Rovereto, 1914) (Litopterna, Macraucheniidae). The specimen shares some nonexclusive features with H. cristata (similar size, rostral border of the orbit almost level with distal border of M3, convergence of maxillary bones at the level of the P3/P4 embrasure, flat snout, very protruding orbits, round outline of premaxillary area in palatal view, and small diastemata between I3/C and C/P1). Other differences (e.g., lack of sagittal crest) may or may not represent intraspecific variation. In addition to other features described here, endocast reconstruction utilizing computer tomography (CT) revealed the presence of a derived position of the orbitotemporal canal running below the rhinal fissure along the lateroventral aspect of the piriform lobe. CT scanning also established that the maxillary nerve (CN V2) leaves the skull through the sphenoorbital fissure, as in all other litopterns, a point previously contested for macraucheniids. The angle between the lateral semicircular canal and the plane of the base of the skull is about 26°, indicating that in life the head was oriented much as in modern horses. Depending on the variables used, estimates of the body mass of IANIGLA-PV 29 produced somewhat conflicting results. Our preferred body mass estimate is 250 kg, based on the centroid size of 36 3D cranial landmarks and accompanying low prediction error. The advanced degree of tooth wear in IANIGLA-PV 29 implies that the individual died well into old age. However, a count of cementum lines on the sectioned left M2 is consistent with an age at death of 10 or 11 years, younger than expected given its body mass. This suggests that the animal had a very abrasive diet. Phylogenetic analysis failed to resolve the position of IANIGLA-PV 29 satisfactorily, a result possibly influenced by intraspecific variation. There is no decisive evidence for the proposition that Huayqueriana, or any other litoptern, were foregut fermenters.Fil: Forasiepi, Analia Marta. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales. Provincia de Mendoza. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales. Universidad Nacional de Cuyo. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales; ArgentinaFil: MacPhee, Ross D. E.. American Museum Of Natural History; Estados UnidosFil: Hernández del Pino, Santiago Ezequiel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales. Provincia de Mendoza. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales. Universidad Nacional de Cuyo. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales; ArgentinaFil: Schmidt, Gabriela Ines. Provincia de Entre Ríos. Centro de Investigaciones Científicas y Transferencia de Tecnología a la Producción. Universidad Autónoma de Entre Ríos. Centro de Investigaciones Científicas y Transferencia de Tecnología a la Producción. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Centro de Investigaciones Científicas y Transferencia de Tecnología a la Producción; ArgentinaFil: Amson, Eli. Universitat Zurich; SuizaFil: Grohé, Camille. American Museum Of Natural History; Estados Unido

A new flowering time gene on wheat chromosome 3B characterization and genetic mapping

Genes that alter disease risk only in combination with certain environmental exposures may not be detected in genetic association analysis. By using methods accounting for gene-environment (G x E) interaction, we aimed to identify novel genetic loci associated with breast cancer risk. Up to 34,475 cases and 34,786 controls of European ancestry from up to 23 studies in the Breast Cancer Association Consortium were included. Overall, 71,527 single nucleotide polymorphisms (SNPs), enriched for association with breast cancer, were tested for interaction with 10 environmental risk factors using three recently proposed hybrid methods and a joint test of association and interaction. Analyses were adjusted for age, study, population stratification, and confounding factors as applicable. Three SNPs in two independent loci showed statistically significant association: SNPs rs10483028 and rs2242714 in perfect linkage disequilibrium on chromosome 21 and rs12197388 in ARID1B on chromosome 6. While rs12197388 was identified using the joint test with parity and with age at menarche (P-values = 3 x 10(-07)), the variants on chromosome 21 q22.12, which showed interaction with adult body mass index (BMI) in 8,891 postmenopausal women, were identified by all methods applied. SNP rs10483028 was associated with breast cancer in women with a BMI below 25 kg/m(2) (OR = 1.26, 95% CI 1.15-1.38) but not in women with a BMI of 30 kg/m(2) or higher (OR = 0.89, 95% CI 0.72-1.11, P for interaction = 3.2 x 10(-05)). Our findings confirm comparable power of the recent methods for detecting G x E interaction and the utility of using G x E interaction analyses to identify new susceptibility loci

Association of genetic susceptibility variants for type 2 diabetes with breast cancer risk in women of European ancestry.

Purpose: Type 2 diabetes (T2D) has been reported to be associated with an elevated risk of breast cancer. It is unclear, however, whether this association is due to shared genetic factors. Methods: We constructed a genetic risk score (GRS) using risk variants from 33 known independent T2D susceptibility loci and evaluated its relation to breast cancer risk using the data from two consortia, including 62,328 breast cancer patients and 83,817 controls of European ancestry. Unconditional logistic regression models were used to derive adjusted odds ratios (ORs) and 95 % confidence intervals (CIs) to measure the association of breast cancer risk with T2D GRS or T2D-associated genetic risk variants. Meta-analyses were conducted to obtain summary ORs across all studies. Results: The T2D GRS was not found to be associated with breast cancer risk, overall, by menopausal status, or for estrogen receptor positive or negative breast cancer. Three T2D associated risk variants were individually associated with breast cancer risk after adjustment for multiple comparisons using the Bonferroni method (at p < 0.001), rs9939609 (FTO) (OR 0.94, 95 % CI = 0.92–0.95, p = 4.13E−13), rs7903146 (TCF7L2) (OR 1.04, 95 % CI = 1.02–1.06, p = 1.26E−05), and rs8042680 (PRC1) (OR 0.97, 95 % CI = 0.95–0.99, p = 8.05E−04). Conclusions: We have shown that several genetic risk variants were associated with the risk of both T2D and breast cancer. However, overall genetic susceptibility to T2D may not be related to breast cancer risk

The BRCA2 c.68-7T > A variant is not pathogenic : A model for clinical calibration of spliceogenicity

Although the spliceogenic nature of the BRCA2 c.68-7T > A variant has been demonstrated, its association with cancer risk remains controversial. In this study, we accurately quantified by real-time PCR and digital PCR (dPCR), the BRCA2 isoforms retaining or missing exon 3. In addition, the combined odds ratio for causality of the variant was estimated using genetic and clinical data, and its associated cancer risk was estimated by case-control analysis in 83,636 individuals. Co-occurrence in trans with pathogenic BRCA2 variants was assessed in 5,382 families. Exon 3 exclusion rate was 4.5-fold higher in variant carriers (13%) than controls (3%), indicating an exclusion rate for the c.68-7T > A allele of approximately 20%. The posterior probability of pathogenicity was 7.44x10(-115). There was neither evidence for increased risk of breast cancer (OR 1.03; 95% CI 0.86-1.24) nor for a deleterious effect of the variant when co-occurring with pathogenic variants. Our data provide for the first time robust evidence of the nonpathogenicity of the BRCA2 c.68-7T > A. Genetic and quantitative transcript analyses together inform the threshold for the ratio between functional and altered BRCA2 isoforms compatible with normal cell function. These findings might be exploited to assess the relevance for cancer risk of other BRCA2 spliceogenic variants.Peer reviewe

No evidence that protein truncating variants in BRIP1 are associated with breast cancer risk: implications for gene panel testing.

BACKGROUND: BRCA1 interacting protein C-terminal helicase 1 (BRIP1) is one of the Fanconi Anaemia Complementation (FANC) group family of DNA repair proteins. Biallelic mutations in BRIP1 are responsible for FANC group J, and previous studies have also suggested that rare protein truncating variants in BRIP1 are associated with an increased risk of breast cancer. These studies have led to inclusion of BRIP1 on targeted sequencing panels for breast cancer risk prediction. METHODS: We evaluated a truncating variant, p.Arg798Ter (rs137852986), and 10 missense variants of BRIP1, in 48 144 cases and 43 607 controls of European origin, drawn from 41 studies participating in the Breast Cancer Association Consortium (BCAC). Additionally, we sequenced the coding regions of BRIP1 in 13 213 cases and 5242 controls from the UK, 1313 cases and 1123 controls from three population-based studies as part of the Breast Cancer Family Registry, and 1853 familial cases and 2001 controls from Australia. RESULTS: The rare truncating allele of rs137852986 was observed in 23 cases and 18 controls in Europeans in BCAC (OR 1.09, 95% CI 0.58 to 2.03, p=0.79). Truncating variants were found in the sequencing studies in 34 cases (0.21%) and 19 controls (0.23%) (combined OR 0.90, 95% CI 0.48 to 1.70, p=0.75). CONCLUSIONS: These results suggest that truncating variants in BRIP1, and in particular p.Arg798Ter, are not associated with a substantial increase in breast cancer risk. Such observations have important implications for the reporting of results from breast cancer screening panels.The COGS project is funded through a European Commission's Seventh Framework Programme grant (agreement number 223175 - HEALTH-F2-2009-223175). BCAC is funded by Cancer Research UK [C1287/A10118, C1287/A12014] and by the European Community´s Seventh Framework Programme under grant agreement number 223175 (grant number HEALTH-F2-2009-223175) (COGS). Funding for the iCOGS infrastructure came from: the European Community's Seventh Framework Programme under grant agreement n° 223175 (HEALTH-F2-2009-223175) (COGS), Cancer Research UK (C1287/A10118, C1287/A 10710, C12292/A11174, C1281/A12014, C5047/A8384, C5047/A15007, C5047/A10692, C8197/A16565), the National Institutes of Health (CA128978) and Post-Cancer GWAS initiative (1U19 CA148537, 1U19 16 CA148065 and 1U19 CA148112 - the GAME-ON initiative), the Department of Defense (W81XWH-10-1- 0341), the Canadian Institutes of Health Research (CIHR) for the CIHR Team in Familial Risks of Breast Cancer, Komen Foundation for the Cure, the Breast Cancer Research Foundation, and the Ovarian Cancer Research Fund. This study made use of data generated by the Wellcome Trust Case Control consortium. Funding for the project was provided by the Wellcome Trust under award 076113. The results published here are in part based upon data generated by The Cancer Genome Atlas Project established by the National Cancer Institute and National Human Genome Research Institute.This is the author accepted manuscript. The final version is available from BMJ Group at http://dx.doi.org/10.1136/jmedgenet-2015-103529

Fine-Scale Mapping of the 5q11.2 Breast Cancer Locus Reveals at Least Three Independent Risk Variants Regulating MAP3K1

Peer reviewe