Spider Assemblages across Elevational and Latitudinal Gradients in the Yukon Territory, Canada

Arthropod assemblages in the Arctic are set for substantial changes in response to climate change, yet we know little about the ecological structure of many groups in the North. We tested the effects of elevation and latitude on northern spider assemblages by sampling along nine mountains across three latitudes in the Yukon Territory, Canada. Spiders were collected in 216 pitfall traps placed at four elevations along each of the nine mountains, representing 36 sites sampled across three latitudes (i.e., distinct mountain ranges). We collected 1954 individuals representing 89 species, 57 genera, and 12 families of spiders. Using nested ANOVAs, we found significant main effects of latitude, elevation, and an interaction of the two factors on species richness and abundance. Using MRPP and NMS ordination, we also found significant effects of latitude and mountain on species composition, but within each of the three latitudes, only elevation produced significant effects. Our study suggests that changes along spatial gradients associated with changes in habitat can have significant effects on the structure of spider assemblages, but responses vary among mountain ranges. We show that within a given mountain range, individual mountains may be used as spatial replicates for studies about northern arthropod assemblages.Les assemblages d’arthropodes de l’Arctique connaîtront des changements substantiels en raison du changement climatique mais malgré cela, nous en savons peu sur la structure écologique de nombreux groupes du Nord. Nous avons mis à l’épreuve les effets de l’élévation et de la latitude sur les assemblages d’araignées du Nord en prélevant des échantillons sur neuf montagnes réparties sur trois latitudes dans le territoire du Yukon, au Canada. Les araignées ont été recueillies à l’aide de 216 pièges placés à quatre élévations différentes le long de chacune des neuf montagnes, ce qui a représenté 36 emplacements échantillonnés sur trois latitudes (c’est-à-dire des chaînes de montagnes distinctes). Nous avons recueilli 1 954 individus représentant 89 espèces, 57 genres et 12 familles d’araignées. À l’aide d’analyses de variances (ANOVA), nous avons relevé d’importants effets découlant de la latitude, de l’élévation et de l’interaction de deux facteurs sur la richesse et l’abondance des espèces. Au moyen de l’ordination MRPP et NMS, nous avons également constaté que la latitude et la montagne ont des incidences considérables sur la composition des espèces, mais au sein de chacune des trois latitudes, seule l’élévation produisait des effets importants. Notre étude laisse entendre que les changements en matière de gradients spatiaux liés aux changements d’habitat peuvent avoir des effets considérables sur la structure d’assemblages d’araignées, mais les réactions varient d’une chaîne de montagne à l’autre. Nous montrons que dans une chaîne de montagne donnée, les montagnes individuelles peuvent servir de mesures spatiales en vue de l’étude d’assemblages d’arthropodes nordiques

Emission spectra and intrinsic optical bistability in a two-level medium

Scattering of resonant radiation in a dense two-level medium is studied theoretically with account for local field effects and renormalization of the resonance frequency. Intrinsic optical bistability is viewed as switching between different spectral patterns of fluorescent light controlled by the incident field strength. Response spectra are calculated analytically for the entire hysteresis loop of atomic excitation. The equations to describe the non-linear interaction of an atomic ensemble with light are derived from the Bogolubov-Born-Green-Kirkwood-Yvon hierarchy for reduced single particle density matrices of atoms and quantized field modes and their correlation operators. The spectral power of scattered light with separated coherent and incoherent constituents is obtained straightforwardly within the hierarchy. The formula obtained for emission spectra can be used to distinguish between possible mechanisms suggested to produce intrinsic bistability.Comment: 18 pages, 5 figure

Cross-Correlation Studies with CMB Polarization Maps

The free-electron population during the reionized epoch rescatters CMB temperature quadrupole and generates a now well-known polarization signal at large angular scales. While this contribution has been detected in the temperature-polarization cross power spectrum measured with WMAP data, due to the large cosmic variance associated with anisotropy measurements at tens of degree angular scales only limited information related to reionization, such as the optical depth to electron scattering, can be extracted. The inhomogeneities in the free-electron population lead to an additional secondary polarization anisotropy contribution at arcminute scales. While the fluctuation amplitude, relative to dominant primordial fluctuations, is small, we suggest that a cross-correlation between arcminute scale CMB polarization data and a tracer field of the high redshift universe, such as through fluctuations captured by the 21 cm neutral Hydrogen background or those in the infrared background related to first proto-galaxies, may allow one to study additional details related to reionization. For this purpose, we discuss an optimized higher order correlation measurement, in the form of a three-point function, including information from large angular scale CMB temperature anisotropies in addition to arcminute scale polarization signal related to inhomogeneous reionization. We suggest that the proposed bispectrum can be measured with a substantial signal-to-noise ratio and does not require all-sky maps of CMB polarization or that of the tracer field. A measurement such as the one proposed may allow one to establish the epoch when CMB polarization related to reionization is generated and to address if the universe was reionized once or twice.Comment: 13 pages, 7 figures; Version in press with Phys. Rev.

Weak Lensing of the CMB: Sampling Errors on B-Modes

The B modes generated by the lensing of CMB polarization are a primary target for the upcoming generation of experiments and can potentially constrain quantities such as the neutrino mass and dark energy equation of state. The net sample variance on the small scale B modes out to l=2000 exceeds Gaussian expectations by a factor of 10 reflecting the variance of the larger scale lenses that generate them. It manifests itself as highly correlated band powers with correlation coefficients approaching 70% for wide bands of Delta l/l \~0.25. It will double the total variance for experiments that achieve a sensitivity of approximately 4 uK-arcmin and a beam of several arcminutes or better. This non-Gaussianity must be taken into account in the analysis of experiments that go beyond first detection.Comment: 6 pages, 4 figures, submitted to PRD; small problem with detector noise calc fixed (5uK'->4uK') main conclusions unchange

Bacterial 16S rRNA/rDNA Profiling in the Liquid Phase of Human Saliva

Human saliva can be separated by centrifugation into cell pellet and cell-free supernatant, which are called cellular phase and liquid phase in this study. While it is well documented that the cellular phase of saliva contains hundreds of oral bacteria species, little is known whether the liquid phase of saliva contains any information related to oral microbiota. In this study, we analyzed the bacterial nucleic acid contents of the liquid phase of saliva. Using primers universal to most eubacterial 16S rDNA, we detected large amounts of bacterial 16S rRNA and rDNA in the cell-free phase of saliva. Random sequencing analysis of forty PCR amplicons from the cell-free phase of saliva led to 15 operational taxonomic unit (OTU) groups. Furthermore, using denaturing gradient gel electrophoresis (DGGE), we compared 16S rRNA/rDNA profiles derived from liquid phases and cellular phases of saliva samples, and found positive correlations (Pearson Correlation=0.822, P<0.001) between these sample groups. These findings indicate that the liquid phase of saliva contains numerous bacterial 16S rRNA/rDNA molecules that have correlations with bacteria existing in the cellular phase

A new strategy for enhancing imputation quality of rare variants from next-generation sequencing data via combining SNP and exome chip data

Background: Rare variants have gathered increasing attention as a possible alternative source of missing heritability. Since next generation sequencing technology is not yet cost-effective for large-scale genomic studies, a widely used alternative approach is imputation. However, the imputation approach may be limited by the low accuracy of the imputed rare variants. To improve imputation accuracy of rare variants, various approaches have been suggested, including increasing the sample size of the reference panel, using sequencing data from study-specific samples (i.e., specific populations), and using local reference panels by genotyping or sequencing a subset of study samples. While these approaches mainly utilize reference panels, imputation accuracy of rare variants can also be increased by using exome chips containing rare variants. The exome chip contains 250 K rare variants selected from the discovered variants of about 12,000 sequenced samples. If exome chip data are available for previously genotyped samples, the combined approach using a genotype panel of merged data, including exome chips and SNP chips, should increase the imputation accuracy of rare variants. Results: In this study, we describe a combined imputation which uses both exome chip and SNP chip data simultaneously as a genotype panel. The effectiveness and performance of the combined approach was demonstrated using a reference panel of 848 samples constructed using exome sequencing data from the T2D-GENES consortium and 5,349 sample genotype panels consisting of an exome chip and SNP chip. As a result, the combined approach increased imputation quality up to 11 %, and genomic coverage for rare variants up to 117.7 % (MAF < 1 %), compared to imputation using the SNP chip alone. Also, we investigated the systematic effect of reference panels on imputation quality using five reference panels and three genotype panels. The best performing approach was the combination of the study specific reference panel and the genotype panel of combined data. Conclusions: Our study demonstrates that combined datasets, including SNP chips and exome chips, enhances both the imputation quality and genomic coverage of rare variants

Meta-analysis of type 2 Diabetes in African Americans Consortium

Type 2 diabetes (T2D) is more prevalent in African Americans than in Europeans. However, little is known about the genetic risk in African Americans despite the recent identification of more than 70 T2D loci primarily by genome-wide association studies (GWAS) in individuals of European ancestry. In order to investigate the genetic architecture of T2D in African Americans, the MEta-analysis of type 2 DIabetes in African Americans (MEDIA) Consortium examined 17 GWAS on T2D comprising 8,284 cases and 15,543 controls in African Americans in stage 1 analysis. Single nucleotide polymorphisms (SNPs) association analysis was conducted in each study under the additive model after adjustment for age, sex, study site, and principal components. Meta-analysis of approximately 2.6 million genotyped and imputed SNPs in all studies was conducted using an inverse variance-weighted fixed effect model. Replications were performed to follow up 21 loci in up to 6,061 cases and 5,483 controls in African Americans, and 8,130 cases and 38,987 controls of European ancestry. We identified three known loci (TCF7L2, HMGA2 and KCNQ1) and two novel loci (HLA-B and INS-IGF2) at genome-wide significance (4.15 × 10(-94)<P<5 × 10(-8), odds ratio (OR)  = 1.09 to 1.36). Fine-mapping revealed that 88 of 158 previously identified T2D or glucose homeostasis loci demonstrated nominal to highly significant association (2.2 × 10(-23) < locus-wide P<0.05). These novel and previously identified loci yielded a sibling relative risk of 1.19, explaining 17.5% of the phenotypic variance of T2D on the liability scale in African Americans. Overall, this study identified two novel susceptibility loci for T2D in African Americans. A substantial number of previously reported loci are transferable to African Americans after accounting for linkage disequilibrium, enabling fine mapping of causal variants in trans-ethnic meta-analysis studies.Peer reviewe