Gene loss and lineage specific restriction-modification systems associated with niche differentiation in the Campylobacter jejuni Sequence Type 403 clonal complex

Campylobacter jejuni is a highly diverse species of bacteria commonly associated with infectious intestinal disease of humans and zoonotic carriage in poultry, cattle, pigs, and other animals. The species contains a large number of distinct clonal complexes that vary from host generalist lineages commonly found in poultry, livestock, and human disease cases to host-adapted specialized lineages primarily associated with livestock or poultry. Here, we present novel data on the ST403 clonal complex of C. jejuni, a lineage that has not been reported in avian hosts. Our data show that the lineage exhibits a distinctive pattern of intralineage recombination that is accompanied by the presence of lineage-specific restriction-modification systems. Furthermore, we show that the ST403 complex has undergone gene decay at a number of loci. Our data provide a putative link between the lack of association with avian hosts of C. jejuni ST403 and both gene gain and gene loss through nonsense mutations in coding sequences of genes, resulting in pseudogene formation

Searching for Extra Dimensions in the Early Universe

We investigate extra spatial dimensions ($D = 3+\epsilon$) in the early universe using very high resolution molecular rotational spectroscopic data derived from a large molecular cloud containing moderately cold carbon monoxide gas at Z $\approx 6.42$. It turns out that the $\epsilon$-dependent quantum mechanical wavelength transitions are solvable for a linear molecule and we present the solution here. The CO microwave data allows a very precise determination of $= -0.00000657 \pm .10003032$. The probability that $\neq 0$ is one in 7794, only 850 million years (using the standard cosmology) after the Big Bang.Comment: 17 pages, 2 figure

Graph theory in higher order topological analysis of urban scenes

Interpretation and analysis of spatial phenomena is a highly time-consuming and laborious task in several fields of the Geomatics world. That is why the automation of these tasks is especially needed in areas such as GISc. Carrying out those tasks in the context of an urban scene is particularly challenging given the complex spatial pattern of its elements. The aim of retrieving structured information from an initial unstructured data set translated into more meaningful homogeneous regions can be achieved by identifying meaningful structures within the initial collection of objects, and by understanding their topological relationships and spatial arrangement. This task is being accomplished by applying graph theory and by performing urban scene topology analysis. For this purpose, a graph-based system is being developed, and LiDAR data are currently being used as an example scenario. A particular emphasis is being given to the visualisation aspects of graph analysis, as visual inspections can often reveal patterns not discernable by current automated analysis techniques. This paper focuses primarily on the role of graph theory in the design of such a tool for the analysis of urban scene topology.http://www.sciencedirect.com/science/article/B6V9K-4P6MPBP-2/1/e1b4066db2881db3de31085d779a27c

Improved simulation of aerosol, cloud, and density measurements by shuttle lidar

Data retrievals are simulated for a Nd:YAG lidar suitable for early flight on the space shuttle. Maximum assumed vertical and horizontal resolutions are 0.1 and 100 km, respectively, in the boundary layer, increasing to 2 and 2000 km in the mesosphere. Aerosol and cloud retrievals are simulated using 1.06 and 0.53 microns wavelengths independently. Error sources include signal measurement, conventional density information, atmospheric transmission, and lidar calibration. By day, tenuous clouds and Saharan and boundary layer aerosols are retrieved at both wavelengths. By night, these constituents are retrieved, plus upper tropospheric, stratospheric, and mesospheric aerosols and noctilucent clouds. Density, temperature, and improved aerosol and cloud retrievals are simulated by combining signals at 0.35, 1.06, and 0.53 microns. Particlate contamination limits the technique to the cloud free upper troposphere and above. Error bars automatically show effect of this contamination, as well as errors in absolute density nonmalization, reference temperature or pressure, and the sources listed above. For nonvolcanic conditions, relative density profiles have rms errors of 0.54 to 2% in the upper troposphere and stratosphere. Temperature profiles have rms errors of 1.2 to 2.5 K and can define the tropopause to 0.5 km and higher wave structures to 1 or 2 km

Cross-cultural comparison of genetic and cultural transmission of smoking initiation using an extended twin kinship model

Background: Considerable evidence from twin and adoption studies indicates that genetic and shared environmental factors play a role in the initiation of smoking behavior. Although twin and adoption designs are powerful to detect genetic and environmental influences, they do not provide information on the processes of assortative mating and parent–offspring transmission and their contribution to the variability explained by genetic and/or environmental factors. Methods: We examined the role of genetic and environmental factors in individual differences for smoking initiation (SI) using an extended kinship design. This design allows the simultaneous testing of additive and non-additive genetic, shared and individual-specific environmental factors, as well as sex differences in the expression of genes and environment in the presence of assortative mating and combined genetic and cultural transmission, while also estimating the regression of the prevalence of SI on age. A dichotomous lifetime ‘ever’ smoking measure was obtained from twins and relatives in the ‘Virginia 30,000’ sample and the ‘Australian 25,000’. Results: Results demonstrate that both genetic and environmental factors play a significant role in the liability to SI. Major influences on individual differences appeared to be additive genetic and unique environmental effects, with smaller contributions from assortative mating, shared sibling environment, twin environment, cultural transmission, and resulting genotype-environment covariance. Age regression of the prevalence of SI was significant. The finding of negative cultural transmission without dominance led us to investigate more closely two possible mechanisms for the lower parent–offspring correlations compared to the sibling and DZ twin correlations in subsets of the data: (1) age × gene interaction, and (2) social homogamy. Neither of the mechanism provided a significantly better explanation of the data. Conclusions: This study showed significant heritability, partly due to assortment, and significant effects of primarily non-parental shared environment on liability to SI

Developmental Contexts and Features of Elite Academy Footoall Players: Coach and Player Perspectives

Player profiling can reap many benefits; through reflective coach-athlete dialogue that produces a profile the athlete has a raised awareness of their own development, while the coach has an opportunity to understand the athlete's viewpoint. In this study, we explored how coaches and players perceived the development features of an elite academy footballer and the contexts in which these features are revealed, in order to develop a player profile to be used for mentoring players. Using a Delphi polling technique, coaches and players experienced a number of ‘rounds’ of expressing their opinions regarding player development contexts and features, ultimately reduced into a consensus. Players and coaches had differing priorities on the key contexts of player development. These contexts, when they reflect the consensus between players and coaches were heavily dominated by ability within the game and training. Personal, social, school, and lifestyle contexts featured less prominently. Although ‘discipline’ was frequently mentioned as an important player development feature, coaches and players disagreed on the importance of ‘training’

Cannabis and depression: A twin model approach to co-morbidity

Cannabis use disorder (CUD) co-occurs with major depressive disorder (MDD) more frequently than would be expected by chance. However, studies to date have not produced a clear understanding of the mechanisms underlying this co-morbidity. Genetically informative studies can add valuable insight to this problem, as they allow the evaluation of competing models of co-morbidity. This study uses data from the Australian Twin Registry to compare 13 co-morbidity twin models initially proposed by Neale and Kendler (Am J Hum Genet 57:935–953, 1995). The analysis sample comprised 2410 male and female monozygotic and dizygotic twins (average age 32) who were assessed on CUD and MDD using the SSAGA-OZ interview. Data were analyzed in OpenMx. Of the 13 different co-morbidity models, two fit equally well: CUD causes MDD and Random Multiformity of CUD. Both fit substantially better than the Correlated Liabilities model. Although the current study cannot differentiate between them statistically, these models, in combination, suggest that CUD risk factors may causally influence the risk to develop MDD, but only when risk for CUD is high

An L Band Spectrum of the Coldest Brown Dwarf

The coldest brown dwarf, WISE 0855, is the closest known planetary-mass, free-floating object and has a temperature nearly as cold as the solar system gas giants. Like Jupiter, it is predicted to have an atmosphere rich in methane, water, and ammonia, with clouds of volatile ices. WISE 0855 is faint at near-infrared wavelengths and emits almost all its energy in the mid-infrared. Skemer et al. 2016 presented a spectrum of WISE 0855 from 4.5-5.1 micron (M band), revealing water vapor features. Here, we present a spectrum of WISE 0855 in L band, from 3.4-4.14 micron. We present a set of atmosphere models that include a range of compositions (metallicities and C/O ratios) and water ice clouds. Methane absorption is clearly present in the spectrum. The mid-infrared color can be better matched with a methane abundance that is depleted relative to solar abundance. We find that there is evidence for water ice clouds in the M band spectrum, and we find a lack of phosphine spectral features in both the L and M band spectra. We suggest that a deep continuum opacity source may be obscuring the near-infrared flux, possibly a deep phosphorous-bearing cloud, ammonium dihyrogen phosphate. Observations of WISE 0855 provide critical constraints for cold planetary atmospheres, bridging the temperature range between the long-studied solar system planets and accessible exoplanets. JWST will soon revolutionize our understanding of cold brown dwarfs with high-precision spectroscopy across the infrared, allowing us to study their compositions and cloud properties, and to infer their atmospheric dynamics and formation processes.Comment: 19 pages, 21 figures. Accepted for publication in Ap