Zooarcheology and bone technology from Arenosa shelter (41VV99), lower Pecos region, Texas

textResearch into the zooarchaeology and bone technology of the Lower Pecos cultural region provided in insight into extraction of faunal resources from the arid canyon lands of the region by its prehistoric inhabitants and how they incorporated those resources into human subsistence and technological systems. Using samples from the National Park Service held-in-trust faunal and bone artifact collections obtained from Arenosa Shelter during excavations at 1960s, the current research detailed the extensive use of faunal resources in the site and use of diverse econiches in subsistence pursuits by prehistoric inhabitants of the region. In particular, heavy reliance on resources from the rivers themselves was documented. The current research discovered specific processing methods for the many medium to large fish caught by prehistoric inhabitants. Filleting was used prehistorically in preparing fish for consumption and raises the possibility of both long-term storage and transport of food products away from the rivers and canyons themselves. Also encountered in the faunal study was a specific skinning method used prehistorically to remove whole pelts, preserving the distinctive features of the head. Presence of this method, termed caping, raises the possibility of pelt use for shamanistic purposes and may have implications for connections to the region’s prominent rock art. More typical was the documentation of fauna-related subsistence pursuits with a heavy reliance on rabbits, artiodactyls, and certain other terrestrial animals from late Pleistocene to Historic times. Detailed butchering sequences were determined from the analysis. From those pursuits, subsistence byproducts entered the technological system as input for bone technology subsystem operating in parallel to and in support of subsystems based on other raw materials. Detailed analysis of manufacturing and use wear characteristics was conducted using a large sample of the bone artifacts from Arenosa Shelter. The analysis enabled the prehistoric manufacturing process for bone implements and ornaments to be defined. The use wear component was the first of its kind in this region and documented use of implements in support of subsistence, textile, lithic, and other segments of the technological system over a significant time period.Anthropolog

Minkowski Sum Construction and other Applications of Arrangements of Geodesic Arcs on the Sphere

We present two exact implementations of efficient output-sensitive algorithms that compute Minkowski sums of two convex polyhedra in 3D. We do not assume general position. Namely, we handle degenerate input, and produce exact results. We provide a tight bound on the exact maximum complexity of Minkowski sums of polytopes in 3D in terms of the number of facets of the summand polytopes. The algorithms employ variants of a data structure that represents arrangements embedded on two-dimensional parametric surfaces in 3D, and they make use of many operations applied to arrangements in these representations. We have developed software components that support the arrangement data-structure variants and the operations applied to them. These software components are generic, as they can be instantiated with any number type. However, our algorithms require only (exact) rational arithmetic. These software components together with exact rational-arithmetic enable a robust, efficient, and elegant implementation of the Minkowski-sum constructions and the related applications. These software components are provided through a package of the Computational Geometry Algorithm Library (CGAL) called Arrangement_on_surface_2. We also present exact implementations of other applications that exploit arrangements of arcs of great circles embedded on the sphere. We use them as basic blocks in an exact implementation of an efficient algorithm that partitions an assembly of polyhedra in 3D with two hands using infinite translations. This application distinctly shows the importance of exact computation, as imprecise computation might result with dismissal of valid partitioning-motions.Comment: A Ph.D. thesis carried out at the Tel-Aviv university. 134 pages long. The advisor was Prof. Dan Halperi

Autophagy gene haploinsufficiency drives chromosome instability, increases migration, and promotes early ovarian tumors.

Autophagy, particularly with BECN1, has paradoxically been highlighted as tumor promoting in Ras-driven cancers, but potentially tumor suppressing in breast and ovarian cancers. However, studying the specific role of BECN1 at the genetic level is complicated due to its genomic proximity to BRCA1 on both human (chromosome 17) and murine (chromosome 11) genomes. In human breast and ovarian cancers, the monoallelic deletion of these genes is often co-occurring. To investigate the potential tumor suppressor roles of two of the most commonly deleted autophagy genes in ovarian cancer, BECN1 and MAP1LC3B were knocked-down in atypical (BECN1+/+ and MAP1LC3B+/+) ovarian cancer cells. Ultra-performance liquid chromatography mass-spectrometry metabolomics revealed reduced levels of acetyl-CoA which corresponded with elevated levels of glycerophospholipids and sphingolipids. Migration rates of ovarian cancer cells were increased upon autophagy gene knockdown. Genomic instability was increased, resulting in copy-number alteration patterns which mimicked high grade serous ovarian cancer. We further investigated the causal role of Becn1 haploinsufficiency for oncogenesis in a MISIIR SV40 large T antigen driven spontaneous ovarian cancer mouse model. Tumors were evident earlier among the Becn1+/- mice, and this correlated with an increase in copy-number alterations per chromosome in the Becn1+/- tumors. The results support monoallelic loss of BECN1 as permissive for tumor initiation and potentiating for genomic instability in ovarian cancer

An Open Access Database of Genome-wide Association Results

<p>Abstract</p> <p>Background</p> <p>The number of genome-wide association studies (GWAS) is growing rapidly leading to the discovery and replication of many new disease loci. Combining results from multiple GWAS datasets may potentially strengthen previous conclusions and suggest new disease loci, pathways or pleiotropic genes. However, no database or centralized resource currently exists that contains anywhere near the full scope of GWAS results.</p> <p>Methods</p> <p>We collected available results from 118 GWAS articles into a database of 56,411 significant SNP-phenotype associations and accompanying information, making this database freely available here. In doing so, we met and describe here a number of challenges to creating an open access database of GWAS results. Through preliminary analyses and characterization of available GWAS, we demonstrate the potential to gain new insights by querying a database across GWAS.</p> <p>Results</p> <p>Using a genomic bin-based density analysis to search for highly associated regions of the genome, positive control loci (e.g., MHC loci) were detected with high sensitivity. Likewise, an analysis of highly repeated SNPs across GWAS identified replicated loci (e.g., <it>APOE</it>, <it>LPL</it>). At the same time we identified novel, highly suggestive loci for a variety of traits that did not meet genome-wide significant thresholds in prior analyses, in some cases with strong support from the primary medical genetics literature (<it>SLC16A7, CSMD1, OAS1</it>), suggesting these genes merit further study. Additional adjustment for linkage disequilibrium within most regions with a high density of GWAS associations did not materially alter our findings. Having a centralized database with standardized gene annotation also allowed us to examine the representation of functional gene categories (gene ontologies) containing one or more associations among top GWAS results. Genes relating to cell adhesion functions were highly over-represented among significant associations (p < 4.6 × 10^-14), a finding which was not perturbed by a sensitivity analysis.</p> <p>Conclusion</p> <p>We provide access to a full gene-annotated GWAS database which could be used for further querying, analyses or integration with other genomic information. We make a number of general observations. Of reported associated SNPs, 40% lie within the boundaries of a RefSeq gene and 68% are within 60 kb of one, indicating a bias toward gene-centricity in the findings. We found considerable heterogeneity in information available from GWAS suggesting the wider community could benefit from standardization and centralization of results reporting.</p