Long range forces between polar alkali diatoms aligned by external electric fields

Long range electrostatic, induction and dispersion coefficients including terms of order $R^{-8}$ have been calculated by the sum over states method using time dependent density functional theory. We also computed electrostatic moments and static polarizabilities of the individual diatoms up to the octopole order using coupled cluster and density functional theory. The laboratory-frame transformed electrostatic moments and van der Waals coefficients corresponding to the alignment of the diatomic molecules were found. We use this transformation to obtain the coupling induced by an external DC electric field, and present values for all XY combinations of like polar alkali diatomic molecules with atoms from Li to Cs. Analytic solutions to the dressed-state laboratory-frame electrostatic moments and long range intermolecular potentials are also given for the DC low-field limit

Genetic and structural elucidation of capsular polysaccharides from Streptococcus pneumoniae serotype 23A and 23B, and comparison to serotype 23F

Streptococcus pneumoniae is a globally important encapsulated human pathogen with approximately 100 different serotypes recognized. Serogroup 23 consists of serotype 23F, present in licensed vaccines, and emerging serotypes 23A and 23B. Here, we report the previously unknown structures of the pneumococcal capsular polysaccharides serotype 23A and 23B determined using genetic analysis, NMR spectroscopy, composition and linkage analysis and Smith degradation (of polysaccharide 23A). The structure of the serotype 23A capsular polysaccharide is: \u21924)-\u3b2-D-Glcp-(1\u21923)-[[\u3b1-L-Rhap-(1\u21922)]-[Gro-(2\u2192P\u21923)]-\u3b2-D-Galp-(1\u21924)]-\u3b2-L-Rhap-(1\u2192. This structure differs from polysaccharide 23F as it features a disaccharide backbone and the di-substituted \u3b2-Gal is linked to \u3b2-Rha as a side chain. This is due to the different polymerization position catalysed by the unusually divergent repeat unit polymerase Wzy in the 23A cps biosynthesis locus. Steric crowding in 23A, confirmed by molecular models, causes the NMR signal for H-1 of the di-substituted 2,3-\u3b2-Gal to resonate in the \u3b1-anomeric region. The structure of the serotype 23B capsular polysaccharide is the same as 23F, but without the terminal \u3b1-Rha: \u21924)-\u3b2-D-Glcp-(1\u21924)-[Gro-(2\u2192P\u21923)]-\u3b2-D-Galp-(1\u21924)-\u3b2-L-Rhap-(1\u2192. The immunodominant terminal \u3b1-Rha of 23F is more sterically crowded in 23A and absent in 23B. This may explain the reported typing cross reactions for serotype 23F: slight with 23A and none with 23B

Chandra X-Ray Observatory Observations of the Globular Cluster M71

We observed the nearby, low-density globular cluster M71 (NGC 6838) with the Chandra X-ray Observatory to study its faint X-ray populations. Five X-ray sources were found inside the cluster core radius, including the known eclipsing binary millisecond pulsar (MSP) PSR J1953+1846A. The X-ray light curve of the source coincident with this MSP shows marginal evidence for periodicity at the binary period of 4.2 h. Its hard X-ray spectrum and luminosity resemble those of other eclipsing binary MSPs in 47 Tuc, suggesting a similar shock origin of the X-ray emission. A further 24 X-ray sources were found within the half-mass radius, reaching to a limiting luminosity of 1.5 10^30 erg/s (0.3-8 keV). From a radial distribution analysis, we find that 18+/-6 of these 29 sources are associated with M71, somewhat more than predicted, and that 11+/-6 are background sources, both galactic and extragalactic. M71 appears to have more X-ray sources between L_X=10^30--10^31 erg/s than expected by extrapolating from other studied clusters using either mass or collision frequency. We explore the spectra and variability of these sources, and describe the results of ground-based optical counterpart searches.Comment: 36 pages including 7 figures and 8 tables, accepted by The Astrophysical Journa

Tracing a toad invasion: lack of mitochondrial DNA variation, haplotype origins, and potential distribution of introduced Duttaphrynus melanostictus in Madagascar

The black-spined toad, Duttaphrynus melanostictus, is widespread in South and South-East (SE) Asia, although recent molecular analyses have revealed that it represents a species complex (here called the D. melanostictus complex). Invasive populations of this toad have been detected in Madagascar since, at least, 2014. We here trace the origin of this introduction based on mitochondrial DNA sequences of 340 samples. All 102 specimens from Madagascar have identical sequences pointing to a single introduction event. Their haplotype corresponds to a lineage occurring in Cambodia, China, Laos, Thailand, Vietnam, and some locations of eastern Myanmar and northern Malaysia, here named the SE Asian lineage. Within this lineage, specimens from one location in Cambodia and three locations in Vietnam have the same haplotype as found in Madagascar. This includes Ho Chi Minh City, which has a major seaport and might have been the source for the introduction. Species distribution models suggest that the current range of the Madagascan invasive population is within the bioclimatic space occupied by the SE Asian lineage in its native range. The potential invasion zone in Madagascar is narrower than suggested by models from localities representing the full range of the D. melanostictus complex. Thus, an accurate taxonomy is essential for such inferences, but it remains uncertain if the toad might be able to spread beyond the potential suitable range because (1) knowledge on species-delimitation of the complex is insufficient, and (2) the native range in SE Asia might be influenced by historical biogeography or competition

Distinct Roles of Non-Canonical Poly(A) Polymerases in RNA Metabolism

Trf4p and Trf5p are non-canonical poly(A) polymerases and are part of the heteromeric protein complexes TRAMP4 and TRAMP5 that promote the degradation of aberrant and short-lived RNA substrates by interacting with the nuclear exosome. To assess the level of functional redundancy between the paralogous Trf4 and Trf5 proteins and to investigate the role of the Trf4-dependent polyadenylation in vivo, we used DNA microarrays to compare gene expression of the wild-type yeast strain of S. cerevisiae with either that of trf4Δ or trf5Δ mutant strains or the trf4Δ mutant expressing the polyadenylation-defective Trf4(DADA) protein. We found little overlap between the sets of transcripts with altered expression in the trf4Δ or the trf5Δ mutants, suggesting that Trf4p and Trf5p target distinct groups of RNAs for degradation. Surprisingly, most RNAs the expression of which was altered by the trf4 deletion were restored to wild-type levels by overexpression of TRF4(DADA), showing that the polyadenylation activity of Trf4p is dispensable in vivo. Apart from previously reported Trf4p and Trf5p target RNAs, this analysis along with in vivo cross-linking and RNA immunopurification-chip experiments revealed that both the TRAMP4 and the TRAMP5 complexes stimulate the degradation of spliced-out introns via a mechanism that is independent of the polyadenylation activity of Trf4p. In addition, we show that disruption of trf4 causes severe shortening of telomeres suggesting that TRF4 functions in the maintenance of telomere length. Finally, our study demonstrates that TRF4, the exosome, and TRF5 participate in antisense RNA–mediated regulation of genes involved in phosphate metabolism. In conclusion, our results suggest that paralogous TRAMP complexes have distinct RNA selectivities with functional implications in RNA surveillance as well as other RNA–related processes. This indicates widespread and integrative functions of TRAMP complexes for the coordination of different gene expression regulatory processes

Melanesian mtDNA Complexity

Melanesian populations are known for their diversity, but it has been hard to grasp the pattern of the variation or its underlying dynamic. Using 1,223 mitochondrial DNA (mtDNA) sequences from hypervariable regions 1 and 2 (HVR1 and HVR2) from 32 populations, we found the among-group variation is structured by island, island size, and also by language affiliation. The more isolated inland Papuan-speaking groups on the largest islands have the greatest distinctions, while shore dwelling populations are considerably less diverse (at the same time, within-group haplotype diversity is less in the most isolated groups). Persistent differences between shore and inland groups in effective population sizes and marital migration rates probably cause these differences. We also add 16 whole sequences to the Melanesian mtDNA phylogenies. We identify the likely origins of a number of the haplogroups and ancient branches in specific islands, point to some ancient mtDNA connections between Near Oceania and Australia, and show additional Holocene connections between Island Southeast Asia/Taiwan and Island Melanesia with branches of haplogroup E. Coalescence estimates based on synonymous transitions in the coding region suggest an initial settlement and expansion in the region at ∼30–50,000 years before present (YBP), and a second important expansion from Island Southeast Asia/Taiwan during the interval ∼3,500–8,000 YBP. However, there are some important variance components in molecular dating that have been overlooked, and the specific nature of ancestral (maternal) Austronesian influence in this region remains unresolved

Chronic fatigue syndrome in an ethnically diverse population: the influence of psychosocial adversity and physical inactivity

<p>Abstract</p> <p>Background</p> <p>Chronic fatigue syndrome (CFS) is a complex multifactorial disorder. This paper reports the prevalence of chronic fatigue (CF) and CFS in an ethnically diverse population sample and tests whether prevalence varies by social adversity, social support, physical inactivity, anxiety and depression.</p> <p>Methods</p> <p>Analysis of survey data linking the Health Survey for England (1998 and 1999) and the Ethnic Minority Psychiatric Illness Rates in the Community (EMPIRIC) study undertaken in 2000. The study population comprised a national population sample of 4,281 people ages 16 to 74 years. CF and CFS were operationally defined on the basis of an interview in the EMPIRIC study, alongside questions about psychosocial risk factors. Previous illnesses were reported in the Health Survey for England during 1998 and 1999, as was physical inactivity.</p> <p>Results</p> <p>All ethnic minority groups had a higher prevalence of CFS than the White group. The lowest prevalence was 0.8% in the White group, and it was highest at 3.5% in the Pakistani group (odds ratio (OR), 4.1; 95% confidence interval (95% CI), 1.6 to 10.4). Anxiety (OR, 1.8; 95% CI, 1.4 to 2.2), depression (OR, 1.4; 95% CI, 1.1 to 1.8), physical inactivity (OR, 2.0; 95% CI, 1.1 to 3.8), social strain (OR, 1.24; 95% CI, 1.04 to 1.48) and negative aspects of social support (OR, 2.12; 95% CI, 1.4 to 3.3) were independent risk factors for CFS in the overall sample. Together these risk factors explained ethnic differences in the prevalence of CFS, but no single risk factor could explain a higher prevalence in all ethnic groups.</p> <p>Conclusions</p> <p>The prevalence of CFS, but not CF, varies by ethnic group. Anxiety, depression, physical inactivity, social strain and negative aspects of social support together accounted for prevalence differences of CFS in the overall sample.</p

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Quantitative Analysis of Effects of UV Exposure and Spore Cluster Size on Deposition and Inhalation Hazards of <i>Bacillus</i> Spores

<div><p>Reviews of the effects of solar UV radiation on the survival rate of aerosolized biological material found that the current understanding of environmental viability degradation in response scenarios is insufficient to inform appropriate emergency response measures. We evaluated the effects of UV degradation, in terms of the number of viable, culture forming units as a function of spore cluster size on the downwind hazard presented by a release of a biological organism such as <i>Bacillus anthracis</i> into the environment. We used experimentally derived survival rates for <i>B. atrophaeus</i> var. <i>globigii</i> (BG) spores and BG spore clusters (as a surrogate for <i>Bacillus anthracis</i>) of various sizes exposed to UVC fluences to derive predicted survival rates for single spores and spore clusters of up to 10 µm. For the range of weather conditions encountered in hazard estimates, as characterized by Pasquill-Gifford-Turner classes, we calculated and compared the downwind inhalation and deposition hazards for single spores versus spore clusters up to 10 μm diameter based on standard plume dispersion and particle deposition models. These models can be used to predict survival rates for solar exposure taking into account differences in plume depletion due to deposition, and differences in dose–response due to particle size. The combined effects of solar degradation and size-dependent deposition resulted in clusters presenting from a few to up to 10 orders of magnitude greater hazards than single spores depending on meteorological conditions and downwind distance.</p><p>Copyright 2015 American Association for Aerosol Research</p></div

Corneal biomechanics in iatrogenic ectasia and keratoconus: A review of the literature

The Ocular Response Analyzer (ORA) (Reichert Ophthalmic Instruments, Buffalo, NY) allows direct measurement of corneal biomechanical properties. Since its introduction, many studies have sought to elucidate the clinical applications of corneal hysteresis (CH) and corneal resistance factor (CRF). More recently, detailed corneal deformation signal waveform analysis (WA) has potentially expanded the diagnostic capabilities of the ORA. In this review, the role of CH, CRF, and WA are examined in keratoconus (KC) and iatrogenic ectasia (IE). The PubMed database was searched electronically for peer-reviewed literature in July 2012 and August 2012 without date restrictions. The search strategy included medical subject heading (MeSH) and natural language terms to retrieve references on corneal biomechanics, CH, CRF, corneal deformation signal WA, IE, and KC. The evidence suggests that while CH and CRF are poor screening tools when used alone, increased sensitivity and specificity of KC and IE screening result when these parameters are combined with tomography and topography. Recent advances in WA are promising, but little is currently understood about its biomechanical and clinical relevance. Future studies should seek to refine the screening protocols for KC and IE as well as define the clinical applicability of WA parameters