An Extinction Study of the Taurus Dark Cloud Complex

We present a study of the detailed distribution of extinction in a region of the Taurus dark cloud complex. Our study uses new BVR images of the region, spectral classification data for 95 stars, and IRAS Sky Survey Atlas (ISSA) 60 and 100 micron images. We study the extinction of the region in four different ways, and we present the first inter-comparison of all these methods, which are: 1) using the color excess of background stars for which spectral types are known; 2) using the ISSA 60 and 100 micron images; 3) using star counts; and 4) using an optical (V and R) version of the average color excess method used by Lada et al. (1994). We find that all four methods give generally similar results, with important exceptions. To study the structure in the dust distribution, we compare the ISSA extinction and the extinction measured for individual stars. From the comparison, we conclude that in the relatively low extinction regions studied, with 0.9 < A_V < 3.0 mag (away from filamentary dark clouds and IRAS cores), there are no fluctuations in the dust column density greater than 45% (at the 99.7% confidence level), on scales smaller than 0.2 pc. We also report the discovery of a previously unknown stellar cluster behind the Taurus dark cloud near R.A 4h19m00s, Dec. 27:30:00 (B1950)Comment: 49 pages (which include 6 pages of tables and 6 pages of figures

Gallus GBrowse: a unified genomic database for the chicken

Gallus GBrowse (http://birdbase.net/cgi-bin/gbrowse/gallus/) provides online access to genomic and other information about the chicken, Gallus gallus. The information provided by this resource includes predicted genes and Gene Ontology (GO) terms, links to Gallus In Situ Hybridization Analysis (GEISHA), Unigene and Reactome, the genomic positions of chicken genetic markers, SNPs and microarray probes, and mappings from turkey, condor and zebra finch DNA and EST sequences to the chicken genome. We also provide a BLAT server (http://birdbase.net/cgi-bin/webBlat) for matching user-provided sequences to the chicken genome. These tools make the Gallus GBrowse server a valuable resource for researchers seeking genomic information regarding the chicken and other avian species

Quantum algorithms for connectivity and related problems

An important family of span programs, st-connectivity span programs, have been used to design quantum algorithms in various contexts, including a number of graph problems and formula evaluation problems. The complexity of the resulting algorithms depends on the largest positive witness size of any 1-input, and the largest negative witness size of any 0-input. Belovs and Reichardt first showed that the positive witness size is exactly characterized by the effective resistance of the input graph, but only rough upper bounds were known previously on the negative witness size. We show that the negative witness size in an st-connectivity span program is exactly characterized by the capacitance of the input graph. This gives a tight analysis for algorithms based on st-connectivity span programs on any set of inputs. We use this analysis to give a new quantum algorithm for estimating the capacitance of a graph. We also describe a new quantum algorithm for deciding if a graph is connected, which improves the previous best quantum algorithm for this problem if we're promised that either the graph has at least k > 1 components, or the graph is connected and has small average resistance, which is upper bounded by the diameter. We also give an alternative algorithm for deciding if a graph is connected that can be better than our first algorithm when the maximum degree is small. Finally, using ideas from our second connectivity algorithm, we give an algorithm for estimating the algebraic connectivity of a graph, the second largest eigenvalue of the Laplacian

The Conway-Kochen argument and relativistic GRW models

In a recent paper, Conway and Kochen proposed what is now known as the "Free Will theorem" which, among other things, should prove the impossibility of combining GRW models with special relativity, i.e., of formulating relativistically invariant models of spontaneous wavefunction collapse. Since their argument basically amounts to a non-locality proof for any theory aiming at reproducing quantum correlations, and since it was clear since very a long time that any relativistic collapse model must be non-local in some way, we discuss why the theorem of Conway and Kochen does not affect the program of formulating relativistic GRW models.Comment: 16 pages, RevTe

"Better Safe than Sorry" - Individual Risk-free Pension Schemes in the European Union - Macroeconomic Benefits, the Mobile Working Citizen's Perspective and Why Nots

Variations between the diverse pension systems in the member states of the European Union hamper labour market mobility, across country borders but also within the countries of the European Union. From a macroeconomic perspective, and in the light of demographic pressure, this paper argues that allowing individual instead of collective pension building would greatly improve labour market flexibility and thus enhance the functioning of the monetary union. I argue that working citizens would benefit, for three reasons, from pension saving in a risk-free savings account. First, citizens would have a clear picture of the accumulation of their own pension savings throughout their working life. Second, they would pay hardly any extra costs and, third, once retired they would not be subject to the whims of government or other pension fund managers. This paper investigates the feasibility of individual pension building under various parameter settings by calculating the pension saved during a working life and the pension dis-saved after retirement. The findings show that there are no reasons why the European Union and individual member states should not allow individual risk-free pension savings accounts. This would have macroeconomic benefits and provide a solid pension provision that can enhance mobility, instead of engaging workers in different mandatory collective pension schemes that exist around in the European Union

Pockets of Proterozoic hydrocarbons and implications for the Archaean

Precambrian biomarkers convey invaluable information about the early evolution of life, ancient ecosystems, redox conditions, climate and depositional environment and prospective petroleum systems. They are however thermally unstable, easily obliterated by contamination and thus extremely difficult to find. This is particularly true if conditions favourable for biomarker preservation had to prevail for more than 2.5 billion years – the prerequisite for finding Archaean biomarkers. Many organic geochemists abandoned this hope after original discoveries of Archaean biomarkers proved to be of younger origin [1,2] but our study of ca. 550-825 Ma old sediments from the Centralian Superbasin now shows that biomarkers can be preserved in distinctive pockets in seemingly barren areas, even if sections are metamorphosed in parts. Most Centralian sections seem empty. Yet, eventually we identified intervals with preserved biomarkers in three drill cores. A detailed investigation of 825 Ma sediments in drill core Mt Charlotte-1 revealed maturity variations that are most likely due to hydrothermal influence and in turn control the hydrocarbon preservation. Sediments might appear metamorphosed after localized, subtle alteration by hydrothermal fluids but protected intervals can still contain biomarkers. The same might be true for Archaean sediments and we might still find those protected intervals with indigenous biomarkers that allow us to glimpse the early life on earth

IFNL3 (IL28B) favorable genotype escapes hepatitis C virus-induced microRNAs and mRNA decay

The IFNL3 (IL28B) gene has received immense attention in the hepatitis C virus (HCV) field as multiple independent genome-wide association studies identified a strong association between polymorphisms near the IFNL3 gene and HCV clearance. However, the mechanism underlying this association has remained elusive. In this study, we report the identification of a functional polymorphism (rs4803217) located in the 3′ untranslated region (3′ UTR) of the IFNL3 mRNA that dictates transcript stability. This polymorphism influences AU-rich element-mediated decay as well as the binding of HCV-induced microRNAs during infection. Together, these pathways mediate robust repression of the unfavorable IFNL3 genotype. These data reveal a novel mechanism by which HCV attenuates the antiviral response and uncover new potential therapeutic targets for HCV treatment

A large microRNA cluster on chromosome 19 is a transcriptional hallmark of WHO type A and AB thymomas

BACKGROUND: Thymomas are one of the most rarely diagnosed malignancies. To better understand its biology and to identify therapeutic targets, we performed next-generation RNA sequencing. METHODS: The RNA was sequenced from 13 thymic malignancies and 3 normal thymus glands. Validation of microRNA expression was performed on a separate set of 35 thymic malignancies. For cell-based studies, a thymoma cell line was used. RESULTS: Hierarchical clustering revealed 100% concordance between gene expression clusters and WHO subtype. A substantial differentiator was a large microRNA cluster on chr19q13.42 that was significantly overexpressed in all A and AB tumours and whose expression was virtually absent in the other thymomas and normal tissues. Overexpression of this microRNA cluster activates the PI3K/AKT/mTOR pathway. Treatment of a thymoma AB cell line with a panel of PI3K/AKT/mTOR inhibitors resulted in marked reduction of cell viability. CONCLUSIONS: A large microRNA cluster on chr19q13.42 is a transcriptional hallmark of type A and AB thymomas. Furthermore, this cluster activates the PI3K pathway, suggesting the possible exploration of PI3K inhibitors in patients with these subtypes of tumour. This work has led to the initiation of a phase II clinical trial of PI3K inhibition in relapsed or refractory thymomas (http://clinicaltrials.gov/ct2/show/NCT02220855)

Distributions, conservation status, and abiotic stress tolerance potential of wild cucurbits (Cucurbita L.)

Societal Impact Statement Crop wild relatives—wild species closely related to cultivated plants—are valuable genetic resources for crop improvement, but gaps in knowledge constrain their conservation and limit their further use. We develop new information on the distributions, potential breeding value, and conservation status of the 16 known wild relatives of cultivated pumpkins, squashes, zucchini, and gourds (Cucurbita L.). The taxa occur from the central USA to Central America, plus two South American species, with the greatest richness in central Mexico and the western borderlands between Mexico and the USA. We determine the majority of species are of medium priority for conservation, both with regard to collecting for ex situ maintenance, and for enhanced habitat protection. Summary Crop wild relatives are valuable genetic resources for crop improvement. Knowledge gaps, including with regard to taxonomy, distributions, and characterization for traits of interest constrain their use in plant breeding. These deficiencies also affect conservation planning, both with regard to in situ habitat protection, and further collection of novel diversity for ex situ maintenance. Here we model the potential ranges of all 16 known wild cucurbit taxa (Cucurbita L.), use ecogeographic information to infer their potential adaptations to abiotic stresses, and assess their ex situ and in situ conservation status. The taxa occur from the central USA to Central America, plus two South American species. Predicted taxon richness was highest in central Mexico and in the western borderlands between Mexico and the USA. We find substantial ecogeographic variation both across taxa and among populations within taxa, with regard to low temperatures, high and low precipitation, and other adaptations of potential interest for crop breeding. We categorize 13 of the taxa medium priority for further conservation as a combination of the ex situ and in situ assessments, two low priority, and one sufficiently conserved. Further action across the distributions of the taxa, with emphasis on taxonomic richness hotspots, is needed to comprehensively conserve wild Cucurbita populations