Showing papers by "Boise State University published in 2011"

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

Abstract: The mission of the Encyclopedia of DNA Elements (ENCODE) Project is to enable the scientific and medical communities to interpret the human genome sequence and apply it to understand human biology and improve health. The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns. In the process, standards to ensure high-quality data have been implemented, and novel algorithms have been developed to facilitate analysis. Data and derived results are made available through a freely accessible database. Here we provide an overview of the project and the resources it is generating and illustrate the application of ENCODE data to interpret the human genome.

Calibrating the End-Permian Mass Extinction

Abstract: The end-Permian mass extinction was the most severe biodiversity crisis in Earth history. To better constrain the timing, and ultimately the causes of this event, we collected a suite of geochronologic, isotopic, and biostratigraphic data on several well-preserved sedimentary sections in South China. High-precision U-Pb dating reveals that the extinction peak occurred just before 252.28 ± 0.08 million years ago, after a decline of 2 per mil (‰) in δ13C over 90,000 years, and coincided with a δ13C excursion of −5‰ that is estimated to have lasted ≤20,000 years. The extinction interval was less than 200,000 years and synchronous in marine and terrestrial realms; associated charcoal-rich and soot-bearing layers indicate widespread wildfires on land. A massive release of thermogenic carbon dioxide and/or methane may have caused the catastrophic extinction.

Constraining Dark Matter Models from a Combined Analysis of Milky Way Satellites with the Fermi Large Area Telescope

Abstract: Satellite galaxies of the Milky Way are among the most promising targets for dark matter searches in gamma rays. We present a search for dark matter consisting of weakly interacting massive particl ...

Passive Immunization Reduces Behavioral and Neuropathological Deficits in an Alpha-Synuclein Transgenic Model of Lewy Body Disease

Abstract: Dementia with Lewy bodies (DLB) and Parkinson's Disease (PD) are common causes of motor and cognitive deficits and are associated with the abnormal accumulation of alpha-synuclein (α-syn). This study investigated whether passive immunization with a novel monoclonal α-syn antibody (9E4) against the C-terminus (CT) of α-syn was able to cross into the CNS and ameliorate the deficits associated with α-syn accumulation. In this study we demonstrate that 9E4 was effective at reducing behavioral deficits in the water maze, moreover, immunization with 9E4 reduced the accumulation of calpain-cleaved α-syn in axons and synapses and the associated neurodegenerative deficits. In vivo studies demonstrated that 9E4 traffics into the CNS, binds to cells that display α-syn accumulation and promotes α-syn clearance via the lysosomal pathway. These results suggest that passive immunization with monoclonal antibodies against the CT of α-syn may be of therapeutic relevance in patients with PD and DLB.

Size Effects on Magnetic Actuation in Ni-Mn-Ga Shape-Memory Alloys

Abstract: The off-stoichiometric Ni2MnGa Heusler alloy is a magnetic shape-memory alloy capable of reversible magnetic-field-induced strains (MFIS). These are generated by twin boundaries moving under the influence of an internal stress produced by a magnetic field through the magnetocrystalline anisotropy. While MFIS are very large (up to 10%) for monocrystalline Ni-Mn-Ga, they are near zero (<0.01%) in fine-grained polycrystals due to incompatibilities during twinning of neighboring grains and the resulting internal geometrical constraints. By growing the grains and/or shrinking the sample, the grain size becomes comparable to one or more characteristic sample sizes (film thickness, wire or strut diameter, ribbon width, particle diameter, etc), and the grains become surrounded by free space. This reduces the incompatibilities between neighboring grains and can favor twinning and thus increase the MFIS. This approach was validated recently with very large MFIS (0.2-8%) measured in Ni-Mn-Ga fibers and foams with bamboo grains with dimensions similar to the fiber or strut diameters and in thin plates where grain diameters are comparable to plate thickness. Here, we review processing, micro- and macrostructure, and magneto-mechanical properties of (i) Ni-Mn-Ga powders, fibers, ribbons and films with one or more small dimension, which are amenable to the growth of bamboo grains leading to large MFIS, and (ii) “constructs” from these structural elements (e.g., mats, laminates, textiles, foams and composites). Various strategies are proposed to accentuate this geometric effect which enables large MFIS in polycrystalline Ni-Mn-Ga by matching grain and sample sizes.

A cocoon of freshly accelerated cosmic rays detected by Fermi in the Cygnus superbubble

Abstract: The origin of Galactic cosmic rays is a century-long puzzle. Indirect evidence points to their acceleration by supernova shockwaves, but we know little of their escape from the shock and their evolution through the turbulent medium surrounding massive stars. Gamma rays can probe their spreading through the ambient gas and radiation fields. The Fermi Large Area Telescope (LAT) has observed the star-forming region of Cygnus X. The 1- to 100-gigaelectronvolt images reveal a 50-parsec-wide cocoon of freshly accelerated cosmic rays that flood the cavities carved by the stellar winds and ionization fronts from young stellar clusters. It provides an example to study the youth of cosmic rays in a superbubble environment before they merge into the older Galactic population.

A Physical Model of the Temperature Dependence of the Current Through $\hbox{SiO}_{2}\hbox{/}\hbox{HfO}_{2}$ Stacks

Abstract: In this paper, we investigate the characteristics of the defects responsible for the leakage current in the SiO2 and SiO2/HfO2 gate dielectric stacks in a wide temperature range (6 K-400 K). We simulated the temperature dependence of the I -V characteristics both at positive and negative gate voltages by applying the multiphonon trap-assisted tunneling model describing the charge transport through the dielectric. In the depletion/weak inversion regime, the current is limited by the supply of carriers available for tunneling. In strong inversion, the temperature dependence is governed by the charge transport mechanisms through the stacks; in particular, in SiO2/HfO2 dielectric stacks, the coupling of the injected carriers with the dielectric phonons at the trap sites is the dominant mechanism. Matching the simulation results to the measurement data allows extracting important trap parameters, e.g., the trap relaxation and ionization energies, which identify the atomic structure of the electrically active defects in the gate dielectric.

Methylthioadenosine/S-adenosylhomocysteine nucleosidase, a critical enzyme for bacterial metabolism

Abstract: The importance of methylthioadenosine/S-adenosylhomocysteine (MTA/SAH) nucleosidase in bacteria has started to be appreciated only in the past decade. A comprehensive analysis of its various roles here demonstrates that it is an integral component of the activated methyl cycle, which recycles adenine and methionine through S-adenosylmethionine (SAM)-mediated methylation reactions, and also produces the universal quorum-sensing signal, autoinducer-2 (AI-2). SAM is also essential for synthesis of polyamines, N-acylhomoserine lactone (autoinducer-1), and production of vitamins and other biomolecules formed by SAM radical reactions. MTA, SAH and 5'-deoxyadenosine (5'dADO) are product inhibitors of these reactions, and are substrates of MTA/SAH nucleosidase, underscoring its importance in a wide array of metabolic reactions. Inhibition of this enzyme by certain substrate analogues also limits synthesis of autoinducers and hence causes reduction in biofilm formation and may attenuate virulence. Interestingly, the inhibitors of MTA/SAH nucleosidase are very effective against the Lyme disease causing spirochaete, Borrelia burgdorferi, which uniquely expresses three homologous functional enzymes. These results indicate that inhibition of this enzyme can affect growth of different bacteria by affecting different mechanisms. Therefore, new inhibitors are currently being explored for development of potential novel broad-spectrum antimicrobials.

Associations Between Young Adults' Use of Sexually Explicit Materials and Their Sexual Preferences, Behaviors, and Satisfaction

Abstract: This study examined how levels of sexually explicit material (SEM) use during adolescence and young adulthood were associated with sexual preferences, sexual behaviors, and sexual and relationship satisfaction. Participants included 782 heterosexual college students (326 men and 456 women; Mage = 19.9) who completed a questionnaire online. Results revealed high frequencies and multiple types and contexts of SEM use, with men's usage rates systematically higher than women's. Regression analyses revealed that both the frequency of SEM use and number of SEM types viewed were uniquely associated with more sexual experience (a higher number of overall and casual sexual intercourse partners, as well as a lower age at first intercourse). Higher frequencies of SEM use were associated with less sexual and relationship satisfaction. The frequency of SEM use and number of SEM types viewed were both associated with higher sexual preferences for the types of sexual practices typically presented in SEM. These findings ...

Navigating the Terrain of Third Space: Tensions With/In Relationships in School-University Partnerships

Abstract: Using theoretical conceptions of third space and hybrid teacher education, the authors engaged in a collaborative self-study of their practices as university-based teacher educators working in student teaching partnership settings. The authors sought to understand ways in which hybrid teacher educators foster and mediate relationships to work toward a collective third space. In this article, the authors describe the nature of relationships in their work, the tensions wrought by complexities of these relationships, and ways they negotiated tensions to foster relationships that productively mediated processes of teacher education. The authors also propose a framework for moving beyond traditional notions of oppositional triadic relationships of student teacher, mentor teacher, and supervisor in recognition of complex social interactions in the third space.

Anthropogenic Noise Exposure in Protected Natural Areas: Estimating the Scale of Ecological Consequences

Abstract: The extensive literature documenting the ecological effects of roads has repeatedly implicated noise as one of the causal factors. Recent studies of wildlife responses to noise have decisively identified changes in animal behaviors and spatial distributions that are caused by noise. Collectively, this research suggests that spatial extent and intensity of potential noise impacts to wildlife can be studied by mapping noise sources and modeling the propagation of noise across landscapes. Here we present models of energy extraction, aircraft overflight and roadway noise as examples of spatially extensive sources and to present tools available for landscape scale investigations. We focus these efforts in US National Parks (Mesa Verde, Grand Teton and Glacier) to highlight that ecological noise pollution is not a threat restricted to developed areas and that many protected natural areas experi- ence significant noise loads. As a heuristic tool for understanding past and future noise pollution we forecast community noise utilizing a spatially-explicit land-use change model that depicts the intensity of human development at sub-county resolution. For road noise, we transform effect distances from two studies into sound levels to begin a discussion of noise thresholds for wildlife. The spatial scale of noise exposure is far larger than any protected area, and no site in the continental US is free form noise. The design of observational and experimental studies of noise effects should be informed by knowledge of regional noise exposure patterns.

Storage as a Metric of Catchment Comparison

Abstract: The volume of water stored within a catchment, and its partitioning among groundwater, soil moisture, snowpack, vegetation, and surface water are the variables that ultimately characterize the state of the hydrologic system. Accordingly, storage may provide useful metrics for catchment comparison. Unfortunately, measuring and predicting the amount of water present in a catchment is seldom done; tracking the dynamics of these stores is even rarer. Storage moderates fluxes and exerts critical controls on a wide range of hydrologic and biologic functions of a catchment. While understanding runoff generation and other processes by which catchments release water will always be central to hydrologic science, it is equally essential to understand how catchments retain water. We have initiated a catchment comparison exercise to begin assessing the value of viewing catchments from the storage perspective. The exercise is based on existing data from five watersheds, no common experimental design, and no integrated modelling efforts. Rather, storage was estimated independently for each site. This briefing presents some initial results of the exercise, poses questions about the definitions and importance of storage and the storage perspective, and suggests future directions for ongoing activities. Copyright. (C) 2011 John Wiley & Sons, Ltd.

Aspect influences on soil water retention and storage

Abstract: : Many catchment hydrologic and ecologic processes are impacted by the storage capacity of soil water, which is dictated by the profile thickness and water retention properties of soil. Soil water retention properties are primarily controlled by soil texture, which in turn varies spatially in response to microclimate-induced differences in insolation, wetness, and temperature. All of these variables can be strongly differentiated by slope aspect. In this study, we compare quantitative measures of soil water retention capacity for two opposing slopes in a semi-arid catchment in southwest Idaho, USA. Undisturbed soil cores from north and south aspects were subjected to a progressive drainage experiment to estimate the soil water retention curve for each sample location. The relatively large sample size (35) supported statistical analysis of slope scale differences in soil water retention between opposing aspects. Soils on the north aspect retain as much as 25% more water at any given soil water pressure than samples from the south aspect slope. Soil porosity, soil organic matter, and silt content were all greater on the north aspect, and each contributed to greater soil water retention. These results, along with the observation that soils on north aspect slopes tend to be deeper indicate that north aspect slopes can store more water from the wet winter months into the dry summer in this region, an observation with potential implications for ecological function and landscape evolution.

Phylogenetic reconstruction of Chirita and allies (Gesneriaceae) with taxonomic treatments

Abstract: Chirita D Don, a large genus in the subfamily Cyrtandroideae of Gesneriaceae, has been the subject of much debate whether it is a natural group or not In addition, the highly heterogeneous Chirita has also been very problematic with regard to delimitation and subdivision Here we used the nrDNA internal transcribed spacer and cpDNA trnL-F for molecular phylogenetic analaysis, combined with morphological data Our results suggest that Chirita is an artificial, polyphyletic genus The most important character that defines Chirita, the dorso-ventrally oblique and bilamellar stigma, has evolved convergently in different clades of diandrous Cyrtandroideae Chirita sensu stricto only includes the species of Chirita sect Chirita, whereas Chirita sect Microchirita is an independent clade located at the basal node of the phylogenetic tree Chirita sect Liebigia is closely related to Didymocarpus with an entire stigma unlike other species of Chirita The species of Chirita sect Gibbosaccus, Chiritopsis, Primulina, and Wentsaiboea form a monophyletic group that is sister to a strongly supported clade comprising four monotypic genera Paralagarosolen, Calcareoboea, Petrocodon, and Tengia We further analyzed the morphological evolution of Chirita and identified a series of morphological synapomorphies for the monophyletic groups revealed herein, and thereby provide a taxonomic treatment in this study

Effects of Changes in Arctic Lake and River Ice

Abstract: Climatic changes to freshwater ice in the Arctic are projected to produce a variety of effects on hydrologic, ecological, and socio-economic systems. Key hydrologic impacts include changes to low flows, lake evaporation regimes and water levels, and river-ice break-up severity and timing. The latter are of particular concern because of their effect on river geomorphology, vegetation, sediment and nutrient fluxes, and sustainment of riparian aquatic habitats. Changes in ice phenology will affect a wide range of related biological aspects of seasonality. Some changes are likely to be gradual, but others could be more abrupt as systems cross critical ecological thresholds. Transportation and hydroelectric production are two of the socio-economic sectors most vulnerable to change in freshwater-ice regimes. Ice roads will require expensive on-land replacements while hydroelectric operations will both benefit and be challenged. The ability to undertake some traditional harvesting methods will also be affected.

γ-RAY AND PARSEC-SCALE JET PROPERTIES OF A COMPLETE SAMPLE OF BLAZARS FROM THE MOJAVE PROGRAM

Abstract: We investigate the Fermi LAT gamma-ray and 15 GHz VLBA radio properties of a joint gamma-ray- and radio-selected sample of AGNs obtained during the first 11 months of the Fermi mission (2008 Aug 4 - 2009 Jul 5). Our sample contains the brightest 173 AGNs in these bands above declination -30 deg. during this period, and thus probes the full range of gamma-ray loudness (gamma-ray to radio band luminosity ratio) in the bright blazar population. The latter quantity spans at least four orders of magnitude, reflecting a wide range of spectral energy distribution (SED) parameters in the bright blazar population. The BL Lac objects, however, display a linear correlation of increasing gamma-ray loudness with synchrotron SED peak frequency, suggesting a universal SED shape for objects of this class. The synchrotron self-Compton model is favored for the gamma-ray emission in these BL Lacs over external seed photon models, since the latter predict a dependence of Compton dominance on Doppler factor that would destroy any observed synchrotron SED peak - gamma-ray loudness correlation. The high-synchrotron peaked (HSP) BL Lac objects are distinguished by lower than average radio core brightness temperatures, and none display large radio modulation indices or high linear core polarization levels. No equivalent trends are seen for the flat-spectrum radio quasars (FSRQ) in our sample. Given the association of such properties with relativistic beaming, we suggest that the HSP BL Lacs have generally lower Doppler factors than the lower-synchrotron peaked BL Lacs or FSRQs in our sample.

Clinical significance of interleukin (IL)-6 in cancer metastasis to bone: potential of anti-IL-6 therapies.

Abstract: Metastatic events to the bone occur frequently in numerous cancer types such as breast, prostate, lung, and renal carcinomas, melanoma, neuroblastoma, and multiple myeloma. Accumulating evidence suggests that the inflammatory cytokine interleukin (IL)-6 is frequently upregulated and is implicated in the ability of cancer cells to metastasize to bone. IL-6 is able to activate various cell signaling cascades that include the STAT (signal transducer and activator of transcription) pathway, the PI3K (phosphatidylinositol-3 kinase) pathway, and the MAPK (mitogen-activated protein kinase) pathway. Activation of these pathways may explain the ability of IL-6 to mediate various aspects of normal and pathogenic bone remodeling, inflammation, cell survival, proliferation, and pro-tumorigenic effects. This review article will discuss the role of IL-6: 1) in bone metabolism, 2) in cancer metastasis to bone, 3) in cancer prognosis, and 4) as potential therapies for metastatic bone cancer.

Metamorphic history of the central Himalaya, Annapurna region, Nepal, and implications for tectonic models

Abstract: Pressure-temperature-time (P-T-t) conditions of metamorphism have been determined in the Annapurna region of central Nepal that place new constraints on the structural and tectonic evolution of the Himalayan orogenic wedge. Peak P-T conditions increase structurally upward: ∼525 °C and 8 kbar in the Lesser Himalayan sequence, 650 °C and 12 kbar at the base of the Greater Himalayan sequence across the Main Central thrust, 750 °C and 12 kbar in the middle of the Greater Himalayan sequence, and 775 °C and 13 kbar near the top of the Greater Himalayan sequence. Metamorphic monazite ages in the Greater Himalayan sequence also increase structurally upward: 16–21 Ma for subsolidus growth at the base of the Greater Himalayan sequence to ∼25 Ma for peak-T metamorphism and anatexis near the top of the Greater Himalayan sequence. These ages are several million years older than at equivalent structural levels at Langtang, ∼200 km to the east. The P-T-t data recommend reinterpretation of the Bhanuwa fault within the Greater Himalayan sequence as a thrust, and the presence of a different thrust structurally above the Bhanuwa thrust, here named the Sinuwa thrust. The new data are consistent with progressive stacking of tectonic slices, with calculated overthrust rates that are consistent with some (but not all) models that presume ∼2 cm/yr convergence across the Himalaya since 25 Ma. Despite differences in absolute ages, similarities among the chemical systematics of monazite, peak P-T conditions, and overthrust rates calculated for Annapurna when compared to Langtang imply that the broad geodynamics in one part of an orogen can be realistically extrapolated within a few hundred kilometers, although the timing and duration of movement on discrete thrust surfaces may differ.

YouTube across the Disciplines: A Review of the Literature

Abstract: YouTube has grown to become the largest and most highly visited online video-sharing service, and interest in the educational use of YouTube has become apparent. Paralleling the rise of academic interest in YouTube is the emergence of YouTube scholarship. This article presents the results of a review of 188 peer reviewed journal articles and conference papers with “YouTube” in the title that were published between 2006 and 2009. Four questions were answered through the review of YouTube literature: (1) What is the overall distribution of publication activity for refereed journal articles and conference papers with "YouTube" in the title? (2) How are publications with "YouTube" in the title distributed across academic disciplines? (3) What have scholars written about instructional methodologies involving YouTube in a sample of literature containing "YouTube" in the title? (4) What have scholars reported about the results of studies involving YouTube in a sample of literature containing "YouTube" in the title? An analysis of the publications revealed that the literature emerged from multiple academic disciplines. The sample of literature included 39 articles and papers describing methods for teaching with YouTube. A total of 99 articles and papers containing the results of research studies were identified and categorized. This literature review is particularly relevant to those online educators who are interested in learning what scholars from their own academic disciplines are writing about YouTube. An emphasis is placed on trends in teaching and research discussed in the sampled literature.

Defending false data injection attack on smart grid network using adaptive CUSUM test

Abstract: In modern smart grid networks, the traditional power grid is enabled by the technological advances in sensing, measurement, and control devices with two-way communications between the suppliers and customers. The smart grid integration helps the power grid networks to be smarter, but it also increases the risk of adversaries because of the currently obsoleted cyber-infrastructure. Adversaries can easily paralyzes the power facility by misleading the energy management system with injecting false data. In this paper, we proposes a defense strategy to the malicious data injection attack for smart grid state estimation at the control center. The proposed “adaptive CUSUM algorithm”, is recursive in nature, and each recursion comprises two inter-leaved stages: Stage 1 introduces the linear unknown parameter solver technique, and Stage 2 applies the multi-thread CUSUM algorithm for quickest change detection. The proposed scheme is able to determine the possible existence of adversary at the control center as quickly as possible without violating the given constraints such as a certain level of detection accuracy and false alarm. The performance of the proposed algorithm is evaluated by both mathematic analysis and numerical simulation.

3-D Transient Hydraulic Tomography in Unconfined Aquifers with Fast Drainage Response

Abstract: We investigate, through numerical experiments, the viability of three-dimensional transient hydraulic tomography (3DTHT) for identifying the spatial distribution of groundwater flow parameters (primarily, hydraulic conductivity K) in permeable, unconfined aquifers. To invert the large amount of transient data collected from 3DTHT surveys, we utilize an iterative geostatistical inversion strategy in which outer iterations progressively increase the number of data points fitted and inner iterations solve the quasilinear geostatistical formulas of Kitanidis. In order to base our numerical experiments around realistic scenarios, we utilize pumping rates, geometries, and test lengths similar to those attainable during 3DTHT field campaigns performed at the Boise Hydrogeophysical Research Site (BHRS). We also utilize hydrologic parameters that are similar to those observed at the BHRS and in other unconsolidated, unconfined fluvial aquifers. In addition to estimating K, we test the ability of 3DTHT to estimate both average storage values (specific storage Ss and specific yield Sy) as well as spatial variability in storage coefficients. The effects of model conceptualization errors during unconfined 3DTHT are investigated including: (1) assuming constant storage coefficients during inversion and (2) assuming stationary geostatistical parameter variability. Overall, our findings indicate that estimation of K is slightly degraded if storage parameters must bemore » jointly estimated, but that this effect is quite small compared with the degradation of estimates due to violation of ‘‘structural’’ geostatistical assumptions. Practically, we find for our scenarios that assuming constant storage values during inversion does not appear to have a significant effect on K estimates or uncertainty bounds.« less

Past and Future Changes in Arctic Lake and River Ice

Abstract: Paleolimnological evidence from some Arctic lakes suggests that longer ice-free seasons have been experienced since the beginning of the nineteenth century. It has been inferred from some additional records that many Arctic lakes may have crossed an important ecological threshold as a result of recent warming. In the instrumental record, long-term trends exhibit increasingly later freeze-ups and earlier break-ups, closely corresponding to increasing air temperature trends, but with greater sensitivity at the more temperate latitudes. Broad spatial patterns in these trends are also related to major atmospheric circulation patterns. Future projections of lake ice indicate increasingly later freeze-ups and earlier break-ups, decreasing ice thickness, and changes in cover composition, particularly white-ice. For rivers, projected future decreases in south to north air-temperature gradients suggest that the severity of ice-jam flooding may be reduced but this could be mitigated by changes in the magnitude of spring snowmelt.