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

Tests of the ratio rule in categorization

Many theories of learning and memory (e.g. connectionist, associative, rational, exemplar-based) produce psychological magnitude terms as output (i.e. numbers representing the momentary level of some subjective property). Many theories assume that these numbers may be translated into choice probabilities via the Ratio Rule, a.k.a. the Choice Axiom (Luce, 1959) or the Constant-Ratio Rule (Clarke, 1957). We present two categorization experiments employing artificial, visual, prototype-structured stimuli constructed from twelve symbols positioned on a grid. The Ratio Rule is shown to be incorrect for these experiments, given the assumption that the magnitude terms for each category are univariate functions of the number of category-appropriate symbols contained in the presented stimulus. A connectionist winner-take-all model of categorical decision (Wills & McLaren, 1997) is shown to account for our data given the same assumption. The central feature underlying the success of this model is the assumption that categorical decisions are based on a Thurstonian choice process (Thurstone, 1927, Case V) whose noise distribution is not double exponential in form

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

Imaging and spectroscopy of galaxies associated with two z~0.7 damped Lyman-alpha absorption systems

We have identified galaxies near two quasars which are at the redshift of damped Lyman-alpha (DLA) systems in the UV spectra of the quasars. Both galaxies are actively forming stars. One galaxy has a luminosity close to the break in the local galaxy luminosity function, L*, the other is significantly fainter than L* and appears to be interacting with a nearby companion. Despite the strong selection effects favoring spectroscopic identification of the most luminous DLA galaxies, many of the spectroscopically-identified DLA galaxies in the literature are sub-L*, suggesting that the majority of the DLA population is probably sub-L*, in contrast to MgII absorbers at similar redshifts whose mean luminosity is close to L*.Comment: 9 pages, to appear in AJ, November 2003 issu

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

GALEX and Optical Light Curves of WX LMi, SDSSJ103100.5+202832.2 and SDSSJ121209.31+013627.7

{\it GALEX} near ultraviolet (NUV) and far-ultraviolet (FUV) light curves of three extremely low accretion rate polars show distinct modulations in their UV light curves. While these three systems have a range of magnetic fields from 13 to 70 MG, and of late type secondaries (including a likely brown dwarf in SDSSJ121209.31+013627.7), the accretion rates are similar, and the UV observations imply some mechanism is operating to create enhanced emission zones on the white dwarf. The UV variations match in phase to the two magnetic poles viewed in the optical in WX LMi and to the single poles evident in the optical in SDSSJ1212109.31+013627.7 and SDSSJ103100.55+202832.2. Simple spot models of the UV light curves show that if hot spots are responsible for the UV variations, the temperatures are on the order of 10,000-14,000K. For the single pole systems, the size of the FUV spot must be smaller than the NUV and in all cases, the geometry is likely more complicated than a simple circular spot.Comment: 29 pages, 4 tables, 10 figures, Astrophysical Journal, accepte

Quality assessment of microarrays: Visualization of spatial artifacts and quantitation of regional biases

BACKGROUND: Quality-control is an important issue in the analysis of gene expression microarrays. One type of problem is regional bias, in which one region of a chip shows artifactually high or low intensities (or ratios in a two-channel array) relative to the majority of the chip. Current practice in quality assessment for microarrays does not address regional biases. RESULTS: We present methods implemented in R for visualizing regional biases and other spatial artifacts on spotted microarrays and Affymetrix chips. We also propose a statistical index to quantify regional bias and investigate its typical distribution on spotted and Affymetrix arrays. We demonstrate that notable regional biases occur on both Affymetrix and spotted arrays and that they can make a significant difference in the case of spotted microarray results. Although strong biases are also seen at the level of individual probes on Affymetrix chips, the gene expression measures are less affected, especially when the RMA method is used to summarize intensities for the probe sets. A web application program for visualization and quantitation of regional bias is provided at . CONCLUSION: Researchers should visualize and measure the regional biases and should estimate their impact on gene expression measurements obtained. Here, we (i) introduce pictorial visualizations of the spatial biases; (ii) present for Affymetrix chips a useful resolution of the biases into two components, one related to background, the other to intensity scale factor; (iii) introduce a single parameter to reflect the global bias present across an array. We also examine the pattern distribution of such biases and conclude that algorithms based on smoothing are unlikely to compensate adequately for them

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.

2016 Nebraska Water Leaders Academy - Final Report

The effective management of Nebraska’s water resources is evermore challenged by variations in weather, climate, technology, socioeconomic policies, and regulation. Anthropogenic climate change, declining water tables and stream flows, increasing demands on freshwater, aging water infrastructure, fiscal constraints, and impacts on aquatic organisms are particularly imminent challenges in Nebraska and around the world (Pahl-Wostl et al., 2013; Pittock et al., 2008; USACE, 2010). Sustaining freshwater ecosystem services in the face of emerging environmental threats presents an immense societal dilemma worldwide (Pittock et al., 2013; Rockström et al., 2009, Millenium Ecosystem Assessment, 2005). The rapidly changing conditions of water resources in Nebraska demands knowledgeable and skilled leaders (Burbach, et al., 2015; Lincklaen Arriëns & When de Montalvo, 2013; Morton & Brown, 2011). McIntosh and Taylor (2013) assert that in order to meet future water challenges, “leadership is needed to initiate and drive change, enable innovation (both incremental and radical), build shared visions for a more sustainable water future, and deliver these visions through aligning resources and building commitment to collective success” (p. 46). Building leadership capacity is required to drive the necessary change (Brasier et al., 2011; Morton et al., 2011; Pahl-Wostl et al., 2011; Redekop, 2010; Taylor et al., 2012). Recognizing this critical need for future leaders in water resources, the Nebraska State Irrigation Associatio