Efficient identification of identical-by-descent status in pedigrees with many untyped individuals

Motivation: Inference of identical-by-descent (IBD) probabilities is the key in family-based linkage analysis. Using high-density single nucleotide polymorphism (SNP) markers, one can almost always infer haplotype configurations of each member in a family given all individuals being typed. Consequently, the IBD status can be obtained directly from haplotype configurations. However, in reality, many family members are not typed due to practical reasons. The problem of IBD/haplotype inference is much harder when treating untyped individuals as missing

Mesozoic–Tertiary exhumation history of the Altai Mountains, northern Xinjiang, China: New constraints from apatite fission track data

This study uses apatite fission track (FT) analysis to constrain the exhumation history of bedrock samples collected from the Altai Mountains in northern Xinjiang, China. Samples were collected as transects across the main structures related to Palaeozoic crustal accretion events. FT results and modeling identify three stages in sample cooling history spanning the Mesozoic and Tertiary. Stage one records rapid cooling to the low temperature part of the fission track partial annealing zone circa 70 ± 10 °C. Stage two, records a period of relative stability with little if any cooling taking place between 75 and 25–20 Ma suggesting the Altai region had been reduced to an area of low relief. Support for this can be found in the adjacent Junngar Basin that received little if any sediment during this interval. Final stage cooling took place in the Miocene at an accelerated rate bringing the sampled rocks to the Earth's surface. This last stage, linked to the far field effects of the Himalayan collision, most likely generated the surface uplift and relief that define the present-day Altai Mountains

QSpec: online control and data analysis system for single-cell Raman spectroscopy

Single-cell phenotyping is critical to the success of biological reductionism. Raman-activated cell sorting (RACS) has shown promise in resolving the dynamics of living cells at the individual level and to uncover population heterogeneities in comparison to established approaches such as fluorescence-activated cell sorting (FACS). Given that the number of single-cells would be massive in any experiment, the power of Raman profiling technique for single-cell analysis would be fully utilized only when coupled with a high-throughput and intelligent process control and data analysis system. In this work, we established QSpec, an automatic system that supports high-throughput Raman-based single-cell phenotyping. Additionally, a single-cell Raman profile database has been established upon which data-mining could be applied to discover the heterogeneity among single-cells under different conditions. To test the effectiveness of this control and data analysis system, a sub-system was also developed to simulate the phenotypes of single-cells as well as the device features

Intelligence in Williams Syndrome Is Related to STX1A, Which Encodes a Component of the Presynaptic SNARE Complex

Although genetics is the most significant known determinant of human intelligence, specific gene contributions remain largely unknown. To accelerate understanding in this area, we have taken a new approach by studying the relationship between quantitative gene expression and intelligence in a cohort of 65 patients with Williams Syndrome (WS), a neurodevelopmental disorder caused by a 1.5 Mb deletion on chromosome 7q11.23. We find that variation in the transcript levels of the brain gene STX1A correlates significantly with intelligence in WS patients measured by principal component analysis (PCA) of standardized WAIS-R subtests, r  = 0.40 (Pearson correlation, Bonferroni corrected p-value  = 0.007), accounting for 15.6% of the cognitive variation. These results suggest that syntaxin 1A, a neuronal regulator of presynaptic vesicle release, may play a role in WS and be a component of the cellular pathway determining human intelligence

Reactor Neutrinos

We review the status and the results of reactor neutrino experiments, that toe the cutting edge of neutrino research. Short baseline experiments have provided the measurement of the reactor neutrino spectrum, and are still searching for important phenomena such as the neutrino magnetic moment. They could open the door to the measurement of coherent neutrino scattering in a near future. Middle and long baseline oscillation experiments at Chooz and KamLAND have played a relevant role in neutrino oscillation physics in the last years. It is now widely accepted that a new middle baseline disappearance reactor neutrino experiment with multiple detectors could provide a clean measurement of the last undetermined neutrino mixing angle theta13. We conclude by opening on possible use of neutrinos for Society: NonProliferation of Nuclear materials and Geophysics

Constraining Deformation in the North Pamir and the Westernmost Tarim Basin

Abstract HKT-ISTP 2013 A

Frequent coexistence of anti-topoisomerase I and anti-U1RNP autoantibodies in African American patients associated with mild skin involvement: a retrospective clinical study

Introduction: The presence of anti-topoisomerase I (topo I) antibodies is a classic scleroderma (SSc) marker presumably associated with a unique clinical subset. Here the clinical association of anti-topo I was reevaluated in unselected patients seen in a rheumatology clinic setting.Methods: Sera from the initial visit in a cohort of unselected rheumatology clinic patients (n = 1,966, including 434 systemic lupus erythematosus (SLE), 119 SSc, 85 polymyositis/dermatomyositis (PM/DM)) were screened by radioimmunoprecipitation. Anti-topo I-positive sera were also tested with immunofluorescence and RNA immunoprecipitation.Results: Twenty-five (15 Caucasian, eight African American, two Latin) anti-topo I positive patients were identified, and all except one met the ACR SSc criteria. Coexistence of other SSc autoantibodies was not observed, except for anti-U1RNP in six cases. When anti-topo I alone versus anti-topo I + U1RNP groups were compared, African American (21% vs. 67%), overlap with SLE (0 vs. 50%; P = 0.009) or PM/DM (0 vs. 33%; P = 0.05) or elevated creatine phosphokinase (CPK) (P = 0.07) were more common in the latter group. In comparison of anti-topo I-positive Caucasians versus African Americans, the latter more frequently had anti-U1RNP (13% vs. 50%), mild/no skin changes (14% vs. 63%; P = 0.03) and overlap with SLE (0 vs. 38%; P = 0.03) and PM/DM (0 vs. 25%; P = 0.05).Conclusions: Anti-topo I detected by immunoprecipitation in unselected rheumatology patients is highly specific for SSc. Anti-topo I coexisting with anti-U1RNP in African American patients is associated with a subset of SLE overlapping with SSc and PM/DM but without apparent sclerodermatous changes. \ua9 2011 Satoh et al.; licensee BioMed Central Ltd

Efficient genome ancestry inference in complex pedigrees with inbreeding

Motivation: High-density SNP data of model animal resources provides opportunities for fine-resolution genetic variation studies. These genetic resources are generated through a variety of breeding schemes that involve multiple generations of matings derived from a set of founder animals. In this article, we investigate the problem of inferring the most probable ancestry of resulting genotypes, given a set of founder genotypes. Due to computational difficulty, existing methods either handle only small pedigree data or disregard the pedigree structure. However, large pedigrees of model animal resources often contain repetitive substructures that can be utilized in accelerating computation