New insights on final Epigravettian funerary behavior at Arene Candide cave (Western Liguria, Italy)

We gained new insights on Epigravettian funerary behavior at the Arene Candide cave through the osteological and spatial analysis of the burials and human bone accumulations found in the cave during past excavations. Archaeothanathological information on the human skeletal remains was recovered from diaries, field pictures and notes, and data from recent excavations was integrated. The secondary deposits have traditionally been interpreted as older burials that were disturbed to make space for new inhumations. Our results suggest that those disturbances were not casual: older burials were intentionally displaced to bury younger inhumations. Subsequently, some skeletal elements, especially crania, were arranged around the new burial; these were often placed within stone niches. Based on the composition of some clusters, which contain the bones of two individuals displaced together, it is possible that a double burial composed of two adults was originally present at the site. This would be a burial type that had not been recognized at Arene Candide until now. Strikingly, this potential double burial contained an individual showing pathological bowing of the limbs, a finding which is not infrequent in skeletons from Gravettian and Epigravettian multiple burials. In addition, the crania and other skeletal elements derived from this burial were intentionally placed around a new inhumation, whose skeleton possibly shows a milder form of the same disease (possibly hereditary rickets). This and other observations suggest that the five individuals belonging to the second phase of this “cemetery” (AMS dates spanning 12,030 – 11,180 cal BP) might have been buried over a relatively brief time span. Our study demonstrated similar behaviors in the first phase of mortuary use of the cave (12,820 – 12,420 cal BP), indicating a remarkable persistence in Final Epigravettian funerary models despite their archaeologically apparent rarity and intermittent nature

Classification using distance nearest neighbours

This paper proposes a new probabilistic classification algorithm using a Markov random field approach. The joint distribution of class labels is explicitly modelled using the distances between feature vectors. Intuitively, a class label should depend more on class labels which are closer in the feature space, than those which are further away. Our approach builds on previous work by Holmes and Adams (2002, 2003) and Cucala et al. (2008). Our work shares many of the advantages of these approaches in providing a probabilistic basis for the statistical inference. In comparison to previous work, we present a more efficient computational algorithm to overcome the intractability of the Markov random field model. The results of our algorithm are encouraging in comparison to the k-nearest neighbour algorithm.Comment: 12 pages, 2 figures. To appear in Statistics and Computin

A Novel Genome-Wide Association Study Approach Using Genotyping by Exome Sequencing Leads to the Identification of a Primary Open Angle Glaucoma Associated Inversion Disrupting ADAMTS17

Closed breeding populations in the dog in conjunction with advances in gene mapping and sequencing techniques facilitate mapping of autosomal recessive diseases and identification of novel disease-causing variants, often using unorthodox experimental designs. In our investigation we demonstrate successful mapping of the locus for primary open angle glaucoma in the Petit Basset Griffon Vendéen dog breed with 12 cases and 12 controls, using a novel genotyping by exome sequencing approach. The resulting genome-wide association signal was followed up by genome sequencing of an individual case, leading to the identification of an inversion with a breakpoint disrupting the ADAMTS17 gene. Genotyping of additional controls and expression analysis provide strong evidence that the inversion is disease causing. Evidence of cryptic splicing resulting in novel exon transcription as a consequence of the inversion in ADAMTS17 is identified through RNAseq experiments. This investigation demonstrates how a novel genotyping by exome sequencing approach can be used to map an autosomal recessive disorder in the dog, with the use of genome sequencing to facilitate identification of a disease-associated variant

Clinical brca1/2 reversion analysis identifies hotspot mutations and predicted neoantigens associated with therapy resistance

Reversion mutations in BRCA1 or BRCA2 are associated with resistance to PARP inhibitors and platinum. To better understand the nature of these mutations, we collated, codified, and analyzed more than 300 reversions. This identified reversion “hotspots” and “deserts” in regions encoding the N and C terminus, respectively, of BRCA2, suggesting that pathogenic mutations in these regions may be at higher or lower risk of reversion. Missense and splice-site pathogenic mutations in BRCA1/2 also appeared less likely to revert than truncating mutations. Most rever-sions were <100 bp deletions. Although many deletions exhibited microhomology, this was not universal, suggesting that multiple DNA-repair processes cause reversion. Finally, we found that many reversions were predicted to encode immunogenic neopeptides, suggesting a route to the treatment of reverted disease. As well as providing a freely available database for the collation of future reversion cases, these observations have implications for how drug resistance might be managed in BRCA-mutant cancers. SIGNIFICANCE: Reversion mutations in BRCA genes are a major cause of clinical platinum and PARP inhibitor resistance. This analysis of all reported clinical reversions suggests that the position of BRCA2 mutations affects the risk of reversion. Many reversions are also predicted to encode tumor neoantigens, providing a potential route to targeting resistance

Multi-label classification using ensembles of pruned sets

This paper presents a Pruned Sets method (PS) for multi-label classification. It is centred on the concept of treating sets of labels as single labels. This allows the classification process to inherently take into account correlations between labels. By pruning these sets, PS focuses only on the most important correlations, which reduces complexity and improves accuracy. By combining pruned sets in an ensemble scheme (EPS), new label sets can be formed to adapt to irregular or complex data. The results from experimental evaluation on a variety of multi-label datasets show that [E]PS can achieve better performance and train much faster than other multi-label methods

Constraining a Historical Black Carbon Emission Inventory of the United States for 1960–2000

We present an observationally constrained United States black carbon emission inventory with explicit representation of activity and technology between 1960 and 2000. We compare measured coefficient of haze data in California and New Jersey between 1965 and 2000 with predicted concentration trends and attribute discrepancies between observations and predicted concentrations among several sources based on seasonal and weekly patterns in observations. Emission factors for sources with distinct fuel trends are then estimated by comparing fuel and concentration trends and further substantiated by in‐depth examination of emission measurements. We recommend (1) increasing emission factors for preregulation vehicles by 80–250%; (2) increasing emission factors for residential heating stoves and boilers by 70% to 200% for 1980s and before; (3) explicitly representing naturally aspired off‐road engines for 1980s and before; and (4) explicitly representing certified wood stoves after 1985. We also evaluate other possible sources for discrepancy between model and measurement, including bias in modeled meteorology, subgrid spatial heterogeneity of concentrations, and inconsistencies in reported fuel consumption. The updated U.S. emissions are higher than the a priori estimate by 80% between 1960 and 1980, totaling 690 Gg/year in 1960 and 620 Gg/year in 1970 (excluding open burning). The revised inventory shows a strongly decreasing trend that was present in the observations but missing in the a priori inventory.Key PointsSystematic evaluation of long‐term U.S. black carbon observations identifies a small number of poorly estimated emission sourcesUpdated black carbon emission is higher than the previous estimate by 80% for 1960–1980, showing a decreasing trend as found in observationEmission factors for preregulation vehicles, off‐road engines, and residential heating stoves in 1980 and before should be increasedPeer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/149266/1/jgrd55339_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/149266/2/jgrd55339.pd

The Caenorhabditis elegans vulva: A post-embryonic gene regulatory network controlling organogenesis

The Caenorhabditis elegans vulva is an elegant model for dissecting a gene regulatory network (GRN) that directs postembryonic organogenesis. The mature vulva comprises seven cell types (vulA, vulB1, vulB2, vulC, vulD, vulE, and vulF), each with its own unique pattern of spatial and temporal gene expression. The mechanisms that specify these cell types in a precise spatial pattern are not well understood. Using reverse genetic screens, we identified novel components of the vulval GRN, including nhr-113 in vulA. Several transcription factors (lin-11, lin-29, cog-1, egl-38, and nhr-67) interact with each other and act in concert to regulate target gene expression in the diverse vulval cell types. For example, egl-38 (Pax2/5/8) stabilizes the vulF fate by positively regulating vulF characteristics and by inhibiting characteristics associated with the neighboring vulE cells. nhr-67 and egl-38 regulate cog-1, helping restrict its expression to vulE. Computational approaches have been successfully used to identify functional cis-regulatory motifs in the zmp-1 (zinc metalloproteinase) promoter. These results provide an overview of the regulatory network architecture for each vulval cell type

Searching for New Physics Through AMO Precision Measurements

We briefly review recent experiments in atomic, molecular, and optical physics using precision measurements to search for physics beyond the Standard Model. We consider three main categories of experiments: searches for changes in fundamental constants, measurements of the anomalous magnetic moment of the electron, and searches for an electric dipole moment of the electron.Comment: Prepared for Comments on AMO Physics at Physica Script