The Fluctuating Intergalactic Radiation Field at Redshifts z = 2.3-2.9 from He II and H I Absorption towards HE 2347-4342

We provide an in-depth analysis of the He II and H I absorption in the intergalactic medium (IGM) at redshifts z = 2.3-2.9 toward HE 2347-4342, using spectra from the Far Ultraviolet Spectroscopic Explorer (FUSE) and the Ultraviolet-Visual Echelle Spectrograph (UVES) on the VLT telescope. Following up on our earlier study (Kriss et al. 2001, Science, 293, 1112), we focus here on two major topics: (1) small-scale variability (Delta z = 10^-3) in the ratio eta = N(He II)/N(H I); and (2) an observed correlation of high-eta absorbers (soft radiation fields) with voids in the (H I) Ly-alpha distribution. These effects may reflect fluctuations in the ionizing sources on scales of 1 Mpc, together with radiative transfer through a filamentary IGM whose opacity variations control the penetration of 1-5 ryd radiation over 30-40 Mpc distances. Owing to photon statistics and backgrounds, we can measure optical depths over the ranges 0.1 < tau(HeII) < 2.3 and 0.02 < tau(HI) < 3.9, and reliably determine values of eta = 4 tau(HeII)/tau(HI) over the range 0.1 to 460. Values of eta = 20-200 are consistent with models of photoionization by quasars with observed spectral indices alpha_s = 0-3. Values of eta > 200 may require additional contributions from starburst galaxies, heavily filtered quasar radiation, or density variations. Regions with eta < 30 may indicate the presence of local hard sources. We find that eta is higher in "void" regions, where H I is weak or undetected and 80% of the path length has eta > 100. These voids may be ionized by soft sources (dwarf starbursts) or by QSO radiation softened by escape from the AGN cores or transfer through the "cosmic web". The apparent differences in ionizing spectra may help to explain the 1.45 Gyr lag between the reionization epochs, z(HI) = 6.2 +/-0.2 and z(HeII) = 2.8 +/-0.2.Comment: 27 pages, 7 figures, to appear in Ap

RCMAT: a regularized covariance matrix approach to testing gene sets

<p>Abstract</p> <p>Background</p> <p>Gene sets are widely used to interpret genome-scale data. Analysis techniques that make better use of the correlation structure of microarray data while addressing practical "n<p" concerns could provide a real increase in power. However correlation structure is hard to estimate with typical genomics sample sizes. In this paper we present an extension of a classical multivariate procedure that confronts this challenge by the use of a regularized covariance matrix.</p> <p>Results</p> <p>We evaluated our testing procedure using both simulated data and a widely analyzed diabetes data set. We compared our approach to another popular multivariate test for both sets of data. Our results suggest an increase in power for detecting gene set differences can be obtained using our approach relative to the popular multivariate test with no increase in the false positive rate.</p> <p>Conclusion</p> <p>Our regularized covariance matrix multivariate approach to gene set testing showed promise in both real and simulated data comparisons. Our findings are consistent with the recent literature in gene set methodology.</p

A dynamic model for delta rhythm fit to high-frequency cortical activity data shows discrete functional connectivity in mouse cortex

Spontaneous activity as recorded by fMRI has often been used to infer active connections (\u27functional connectivity\u27) in the human brain through correlations of activity measures. Some serious questions have been raised about the interpretation of these correlations, which are often apparent only on time scales of tens of seconds. Confirmation of correlations in measures of activity on shorter time-scales closer to those of neural activity would be very desirable. Numerous mechanisms have been proposed for various rhythms but in the past half-century little consensus has been reached on the mechanism of any major rhythm. The recent development of high-throughput imaging methods enable us for the first time to rigorously and quantitatively test ideas about the dynamics of brain rhythms. We have generated high-resolution data on neural activity over most of one hemisphere of mouse cortex by voltage-sensitive dyes, in both anesthetized and awake animals. In previous work [1] we have analyzed relations between activity measures at different locations in terms of correlations. Here we fit these data to a predictive model, in which we attempt to predict the next change in activity at every point on cortex from the current pattern of activity over cortex. We fit both linear and non-linear models, whose parameters represent the intrinsic dynamics of local cortical regions and the inputs from distal regions. We find that all regions of mouse cortex appear to have virtually identical patterns of intrinsic dynamics (Figure 1A). We find that even a simple linear fit gives surprisingly sparse patterns of inferred connectivity. Where we have clear anatomical information, these fitted patterns appear to match known anatomy. Furthermore this fit can be used to identify the most prominent functional inputs into anatomically diffusely-connected areas such as the parietal association area (Figure 1B). Poster presentation from the Twenty Third Annual Computational Neuroscience Meeting: CNS*201

Genomic sequence analysis and characterization of Sneathia amnii sp. nov

Background Bacteria of the genus Sneathia are emerging as potential pathogens of the female reproductive tract. Species of Sneathia, which were formerly grouped with Leptotrichia, can be part of the normal microbiota of the genitourinary tracts of men and women, but they are also associated with a variety of clinical conditions including bacterial vaginosis, preeclampsia, preterm labor, spontaneous abortion, post-partum bacteremia and other invasive infections. Sneathia species also exhibit a significant correlation with sexually transmitted diseases and cervical cancer. BecauseSneathia species are fastidious and rarely cultured successfully in vitro; and the genomes of members of the genus had until now not been characterized, very little is known about the physiology or the virulence of these organisms. Results Here, we describe a novel species, Sneathia amnii sp. nov, which closely resembles bacteria previously designated Leptotrichia amnionii . As part of the Vaginal Human Microbiome Project at VCU, a vaginal isolate of S. amnii sp. nov. was identified, successfully cultured and bacteriologically cloned. The biochemical characteristics and virulence properties of the organism were examined in vitro, and the genome of the organism was sequenced, annotated and analyzed. The analysis revealed a reduced circular genome of ~1.34 Mbp, containing ~1,282 protein-coding genes. Metabolic reconstruction of the bacterium reflected its biochemical phenotype, and several genes potentially associated with pathogenicity were identified. Conclusions Bacteria with complex growth requirements frequently remain poorly characterized and, as a consequence, their roles in health and disease are unclear. Elucidation of the physiology and identification of genes putatively involved in the metabolism and virulence of S. amnii may lead to a better understanding of the role of this potential pathogen in bacterial vaginosis, preterm birth, and other issues associated with vaginal and reproductive health

Two Rare Magnetic Cataclysmic Variables with Extreme Cyclotron Features Identified in the Sloan Digital Sky Survey

Two newly identified magnetic cataclysmic variables discovered in the Sloan Digital Sky Survey (SDSS), SDSSJ155331.12+551614.5 and SDSSJ132411.57+032050.5, have spectra showing highly prominent, narrow, strongly polarized cyclotron humps with amplitudes that vary on orbital periods of 4.39 and 2.6 hrs, respectively. In the former, the spacing of the humps indicates the 3rd and 4th harmonics in a magnetic field of ~60 MG. The narrowness of the cyclotron features and the lack of strong emission lines imply very low temperature plasmas and very low accretion rates, so that the accreting area is heated by particle collisions rather than accretion shocks. The detection of rare systems like these exemplifies the ability of the SDSS to find the lowest accretion rate close binaries.Comment: Accepted for publication in the Astrophysical Journal, vol. 583, February 1, 2003; slight revisions and additions in response to referee's comments; 17 pages, 6 figures, AASTeX v4.

Heating and Ionization of the Intergalactic Medium by an Early X-Ray Background

Observational studies indicate that the intergalactic medium (IGM) is highly ionized up to redshifts just over 6. A number of models have been developed to describe the process of reionization and the effects of the ionizing photons from the first luminous objects. In this paper, we study the impact of an X-ray background, such as high-energy photons from early quasars, on the temperature and ionization of the IGM prior to reionization, before the fully ionized bubbles associated with individual sources have overlapped. X-rays, which have large mean free paths relative to EUV photons, and their photoelectrons can have significant effects on the thermal and ionization balance. We find that hydrogen ionization is dominated by the X-ray photoionization of neutral helium and the resulting secondary electrons. Thus, the IGM may have been warm and weakly ionized prior to full reionization. We examine several related consequences, including the filtering of the baryonic Jeans mass scale, signatures in the cosmic microwave background, and the H$^{-}$-catalyzed production of molecular hydrogen.Comment: 9 emulateapj pages with 5 embedded postscript figures; accepted for publication in Ap.J. (Dec. 10, 2001 issue

The long run relationship between private consumption and wealth : common and idiosyncratic effects

We investigate the long run relationship between private consump- tion, disposable income and wealth approximated by equity and house price indices for a panel of 15 industrialized countries. Consumption, income and wealth are cointegrated in their common components. The impact of house prices exceeds the effect arising from equity wealth. The long run vector is broadly in line with the life cycle permanent income hypothesis, if house prices are allowed to enter the relationship. At the idiosyncratic level, a long run equilibrium is detected between consumption and income, i.e. the wealth variable can be excluded. The income elasticity in the idiosyncratic relationship is significantly less than unity. Hence, the presence of wealth effects in consumption equations arises from the international integration of asset markets and points to the relevance of risk sharing activities of agents. Without sufficient opportunities, an increase in national saving rates would be expected, leading to a lower path of private consumption expenditures.info:eu-repo/semantics/publishedVersio

The Vaginal Microbiome: Disease, Genetics and the Environment

The vagina is an interactive interface between the host and the environment. Its surface is covered by a protective epithelium colonized by bacteria and other microorganisms. The ectocervix is nonsterile, whereas the endocervix and the upper genital tract are assumed to be sterile in healthy women. Therefore, the cervix serves a pivotal role as a gatekeeper to protect the upper genital tract from microbial invasion and subsequent reproductive pathology. Microorganisms that cross this barrier can cause preterm labor, pelvic inflammatory disease, and other gynecologic and reproductive disorders. Homeostasis of the microbiome in the vagina and ectocervix plays a paramount role in reproductive health. Depending on its composition, the microbiome may protect the vagina from infectious or non-infectious diseases, or it may enhance its susceptibility to them. Because of the nature of this organ, and the fact that it is continuously colonized by bacteria from birth to death, it is virtually certain that this rich environment evolved in concert with its microbial flora. Specific interactions dictated by the genetics of both the host and microbes are likely responsible for maintaining both the environment and the microbiome. However, the genetic basis of these interactions in both the host and the bacterial colonizers is currently unknown. _Lactobacillus_ species are associated with vaginal health, but the role of these species in the maintenance of health is not yet well defined. Similarly, other species, including those representing minor components of the overall flora, undoubtedly influence the ability of potential pathogens to thrive and cause disease. Gross alterations in the vaginal microbiome are frequently observed in women with bacterial vaginosis, but the exact etiology of this disorder is still unknown. There are also implications for vaginal flora in non-infectious conditions such as pregnancy, pre-term labor and birth, and possibly fertility and other aspects of women&#x2019;s health. Conversely, the role of environmental factors in the maintenance of a healthy vaginal microbiome is largely unknown. To explore these issues, we have proposed to address the following questions:&#xd;&#xa;&#xd;&#xa;*1.&#x9;Do the genes of the host contribute to the composition of the vaginal microbiome?* We hypothesize that genes of both host and bacteria have important impacts on the vaginal microbiome. We are addressing this question by examining the vaginal microbiomes of mono- and dizygotic twin pairs selected from the over 170,000 twin pairs in the Mid-Atlantic Twin Registry (MATR). Subsequent studies, beyond the scope of the current project, may investigate which host genes impact the microbial flora and how they do so.&#xd;&#xa;*2.&#x9;What changes in the microbiome are associated with common non-infectious pathological states of the host?* We hypothesize that altered physiological (e.g., pregnancy) and pathologic (e.g., immune suppression) conditions, or environmental exposures (e.g., antibiotics) predictably alter the vaginal microbiome. Conversely, certain vaginal microbiome characteristics are thought to contribute to a woman&#x2019;s risk for outcomes such as preterm delivery. We are addressing this question by recruiting study participants from the ~40,000 annual clinical visits to women&#x2019;s clinics of the VCU Health System.&#xd;&#xa;*3.&#x9;What changes in the vaginal microbiome are associated with relevant infectious diseases and conditions?* We hypothesize that susceptibility to infectious disease (e.g. HPV, _Chlamydia_ infection, vaginitis, vaginosis, etc.) is impacted by the vaginal microbiome. In turn, these infectious conditions clearly can affect the ability of other bacteria to colonize and cause pathology. Again, we are exploring these issues by recruiting participants from visitors to women&#x2019;s clinics in the VCU Health System.&#xd;&#xa;&#xd;&#xa;Three kinds of sequence data are generated in this project: i) rDNA sequences from vaginal microbes; ii) whole metagenome shotgun sequences from vaginal samples; and iii) whole genome shotgun sequences of bacterial clones selected from vaginal samples. The study includes samples from three vaginal sites: mid-vaginal, cervical, and introital. The data sets also include buccal and perianal samples from all twin participants. Samples from these additional sites are used to test the hypothesis of a per continuum spread of bacteria in relation to vaginal health. An extended set of clinical metadata associated with these sequences are deposited with dbGAP. We have currently collected over 4,400 samples from ~100 twins and over 450 clinical participants. We have analyzed and deposited data for 480 rDNA samples, eight whole metagenome shotgun samples, and over 50 complete bacterial genomes. These data are available to accredited investigators according to NIH and Human Microbiome Project (HMP) guidelines. The bacterial clones are deposited in the Biodefense and Emerging Infections Research Resources Repository (&#x22;http://www.beiresources.org/&#x22;:http://www.beiresources.org/). &#xd;&#xa;&#xd;&#xa;In addition to the extensive sequence data obtained in this study, we are collecting metadata associated with each of the study participants. Thus, participants are asked to complete an extensive health history questionnaire at the time samples are collected. Selected clinical data associated with the visit are also obtained, and relevant information is collected from the medical records when available. This data is maintained securely in a HIPAA-compliant data system as required by VCU&#x2019;s Institutional Review Board (IRB). The preponderance of these data (i.e., that judged appropriate by NIH staff and VCU&#x2019;s IRB are deposited at dbGAP (&#x22;http://www.ncbi.nlm.nih.gov/gap&#x22;:http://www.ncbi.nlm.nih.gov/gap). Selected fields of this data have been identified by NIH staff as &#x2018;too sensitive&#x2019; and are not available in dbGAP. Individuals requiring access to these data fields are asked to contact the PI of this project or NIH Program Staff. &#xd;&#xa

Making Informed Choices about Microarray Data Analysis

This article describes the typical stages in the analysis of microarray data for non-specialist researchers in systems biology and medicine. Particular attention is paid to significant data analysis issues that are commonly encountered among practitioners, some of which need wider airing. The issues addressed include experimental design, quality assessment, normalization, and summarization of multiple-probe data. This article is based on the ISMB 2008 tutorial on microarray data analysis. An expanded version of the material in this article and the slides from the tutorial can be found at http://www.people.vcu.edu/~mreimers/OGMDA/index.html