Showing papers by "Louisiana State University published in 2013"

Astropy: A community Python package for astronomy

Abstract: We present the first public version (v02) of the open-source and community-developed Python package, Astropy This package provides core astronomy-related functionality to the community, including support for domain-specific file formats such as flexible image transport system (FITS) files, Virtual Observatory (VO) tables, and common ASCII table formats, unit and physical quantity conversions, physical constants specific to astronomy, celestial coordinate and time transformations, world coordinate system (WCS) support, generalized containers for representing gridded as well as tabular data, and a framework for cosmological transformations and conversions Significant functionality is under activedevelopment, such as a model fitting framework, VO client and server tools, and aperture and point spread function (PSF) photometry tools The core development team is actively making additions and enhancements to the current code base, and we encourage anyone interested to participate in the development of future Astropy versions

Astropy: A Community Python Package for Astronomy

Abstract: We present the first public version (v0.2) of the open-source and community-developed Python package, Astropy. This package provides core astronomy-related functionality to the community, including support for domain-specific file formats such as Flexible Image Transport System (FITS) files, Virtual Observatory (VO) tables, and common ASCII table formats, unit and physical quantity conversions, physical constants specific to astronomy, celestial coordinate and time transformations, world coordinate system (WCS) support, generalized containers for representing gridded as well as tabular data, and a framework for cosmological transformations and conversions. Significant functionality is under active development, such as a model fitting framework, VO client and server tools, and aperture and point spread function (PSF) photometry tools. The core development team is actively making additions and enhancements to the current code base, and we encourage anyone interested to participate in the development of future Astropy versions.

Frontiers, Opportunities, and Challenges in Biochemical and Chemical Catalysis of CO2 Fixation

Abstract: Two major energy-related problems confront the world in the next 50 years. First, increased worldwide competition for gradually depleting fossil fuel reserves (derived from past photosynthesis) will lead to higher costs, both monetarily and politically. Second, atmospheric CO_2 levels are at their highest recorded level since records began. Further increases are predicted to produce large and uncontrollable impacts on the world climate. These projected impacts extend beyond climate to ocean acidification, because the ocean is a major sink for atmospheric CO2.1 Providing a future energy supply that is secure and CO_2-neutral will require switching to nonfossil energy sources such as wind, solar, nuclear, and geothermal energy and developing methods for transforming the energy produced by these new sources into forms that can be stored, transported, and used upon demand.

How to fail at species delimitation.

Abstract: Species delimitation is the act of identifying species-level biological diversity. In recent years, the field has witnessed a dramatic increase in the number of methods available for delimiting species. However, most recent investigations only utilize a handful (i.e. 2–3) of the available methods, often for unstated reasons. Because the parameter space that is potentially relevant to species delimitation far exceeds the parameterization of any existing method, a given method necessarily makes a number of simplifying assumptions, any one of which could be violated in a particular system. We suggest that researchers should apply a wide range of species delimitation analyses to their data and place their trust in delimitations that are congruent across methods. Incongruence across the results from different methods is evidence of either a difference in the power to detect cryptic lineages across one or more of the approaches used to delimit species and could indicate that assumptions of one or more of the methods have been violated. In either case, the inferences drawn from species delimitation studies should be conservative, for in most contexts it is better to fail to delimit species than it is to falsely delimit entities that do not represent actual evolutionary lineages.

Enhanced sensitivity of the LIGO gravitational wave detector by using squeezed states of light

Abstract: Nearly a century after Einstein first predicted the existence of gravitational waves, a global network of Earth-based gravitational wave observatories1, 2, 3, 4 is seeking to directly detect this faint radiation using precision laser interferometry. Photon shot noise, due to the quantum nature of light, imposes a fundamental limit on the attometre-level sensitivity of the kilometre-scale Michelson interferometers deployed for this task. Here, we inject squeezed states to improve the performance of one of the detectors of the Laser Interferometer Gravitational-Wave Observatory (LIGO) beyond the quantum noise limit, most notably in the frequency region down to 150 Hz, critically important for several astrophysical sources, with no deterioration of performance observed at any frequency. With the injection of squeezed states, this LIGO detector demonstrated the best broadband sensitivity to gravitational waves ever achieved, with important implications for observing the gravitational-wave Universe with unprecedented sensitivity.

American Cancer Society lung cancer screening guidelines

Abstract: Findings from the National Cancer Institute’s National Lung Screening Trial established that lung cancer mortality in specific high-risk groups can be reduced by annual screening with low-dose computed tomography. These findings indicate that the adoption of lung cancer screening could save many lives. Based on the results of the National Lung Screening Trial, the American Cancer Society is issuing an initial guideline for lung cancer screening. This guideline recommends that clinicians with access to high-volume, high-quality lung cancer screening and treatment centers should initiate a discussion about screening with apparently healthy patients aged 55 years to 74 years who have at least a 30–pack-year smoking history and who currently smoke or have quit within the past 15 years. A process of informed and shared decision-making with a clinician related to the potential benefits, limitations, and harms associated with screening for lung cancer with low-dose computed tomography should occur before any decision is made to initiate lung cancer screening. Smoking cessation counseling remains a high priority for clinical attention in discussions with current smokers, who should be informed of their continuing risk of lung cancer. Screening should not be viewed as an alternative to smoking cessation. CA Cancer J Clin 2013;000:000-000. V C 2013 American Cancer Society.

The CO-to-H2 Conversion Factor and Dust-to-gas Ratio on Kiloparsec Scales in Nearby Galaxies

Abstract: We present ~{}kiloparsec spatial resolution maps of the CO-to-H$_{2}$ conversion factor ({$α$}$_{CO}$) and dust-to-gas ratio (DGR) in 26 nearby, star-forming galaxies. We have simultaneously solved for {$α$}$_{CO}$ and the DGR by assuming that the DGR is approximately constant on kiloparsec scales. With this assumption, we can combine maps of dust mass surface density, CO-integrated intensity, and H I column density to solve for both {$α$}$_{CO}$ and the DGR with no assumptions about their value or dependence on metallicity or other parameters. Such a study has just become possible with the availability of high-resolution far-IR maps from the Herschel key program KINGFISH, $^{12}$CO J = (2-1) maps from the IRAM 30 m large program HERACLES, and H I 21 cm line maps from THINGS. We use a fixed ratio between the (2-1) and (1-0) lines to present our {$α$}$_{CO}$ results on the more typically used $^{12}$CO J = (1-0) scale and show using literature measurements that variations in the line ratio do not affect our results. In total, we derive 782 individual solutions for {$α$}$_{CO}$ and the DGR. On average, {$α$}$_{CO}$ = 3.1 M $_{☉}$ pc$^{–2}$ (K km s$^{–1}$)$^{–1}$ for our sample with a standard deviation of 0.3 dex. Within galaxies, we observe a generally flat profile of {$α$}$_{CO}$ as a function of galactocentric radius. However, most galaxies exhibit a lower {$α$}$_{CO}$ value in the central kiloparsec{mdash}a factor of ~{}2 below the galaxy mean, on average. In some cases, the central {$α$}$_{CO}$ value can be factors of 5-10 below the standard Milky Way (MW) value of {$α$}$_{CO, MW}$ = 4.4 M $_{☉}$ pc$^{–2}$ (K km s$^{–1}$)$^{–1}$. While for {$α$}$_{CO}$ we find only weak correlations with metallicity, the DGR is well-correlated with metallicity, with an approximately linear slope. Finally, we present several recommendations for choosing an appropriate {$α$}$_{CO}$ for studies of nearby galaxies.

Circular RNA (circRNA) in Alzheimer’s disease (AD)

Abstract: Circular RNAs (circRNAs) are a naturally occurring family of noncoding RNAs (ncRNAs) highly represented in the eukaryotic transcriptome. Recently characterized, traditional methods of RNA detection and analysis requiring a free 5′ or 3′ ribonucleotide terminus may have significantly underestimated circRNA abundance and significance in eukaryotic cells (Salzman et al., 2012; Wilusz and Sharp, 2013; unpublished observations). Intrinsically resistant to exonucleolytic RNA decay, circRNAs appear to be enriched in mammalian brain tissues (Hansen et al., 2013; Memczak et al., 2013). Interestingly, specific ncRNAs such as the evolutionary ancient microRNA-7 (miRNA-7; chr 9q21.32; an important post-transcriptional regulator of human brain gene expression), are not only highly abundant in human brain, but are also associated with a circRNA for miRNA-7 (ciRS-7), in the same tissues; ciRS-7 contains multiple, tandem anti-miRNA-7 sequences (Burmistrova et al., 2007; Hansen et al., 2013; Lukiw et al., 2013). ciRS-7 thereby acts as a kind of endogenous, competing, anti-complementary miRNA “sponge” to adsorb, and hence quench, normal miRNA-7 functions. Using Northern blot hybridization techniques and the circularity-sensitive circRNA probe RNaseR we here provide initial evidence of a mis-regulated miRNA-7-circRNA system in the sporadic Alzheimer's disease (AD) hippocampal CA1 region (Figure ​(Figure1).1). Deficits in ciRS-7, and ciRS-7 “sponging activities” might be expected to increase ambient miRNA-7 levels in AD-affected brain cells, as is observed, to ultimately contribute to the down-regulation of selective miRNA-7-sensitive messenger RNA (mRNA) targets (Cogswell et al., 2008; unpublished observations). The presence of up-regulated miRNA-7, due to a deficiency in ciRS-7 “sponging” effects, has high probability to down-regulate AD-relevant targets, such as, for example, the ubiquitin protein ligase A (UBE2A; miRNA-7-UBE2A mRNA energy of association, EA = −22.86 kcal/mol). UBE2A, an autophagic, phagocytic protein essential in the clearance of amyloid peptides in AD and other progressive inflammatory degenerations of the human CNS, is depleted in AD brain (Bingol and Sheng, 2011; Lonskaya et al., 2013). Such miRNA-mRNA regulatory systems mediated by a family of cell- and/or tissue-enriched circRNAs may represent another important layer of epigenetic control over gene expression in health and disease. Indeed, technological advancement and recent discoveries in the field of ncRNAs continue to challenge our basic doctrines of nucleic acid biochemistry and evolutionary biology. Deficits in other circRNA-mediated “miRNA sponging systems” and ambient up-regulation of specific inducible miRNAs may help explain the widely observed, generalized and progressive down-regulation of gene expression that is characteristic of the sporadic AD brain (Loring et al., 2001; Colangelo et al., 2002; Ginsberg et al., 2012; Lukiw, 2013). Figure 1 (A) Detection of circRNA for miRNA-7 (ciRS-7) in sporadic Alzheimer's disease (AD) and age-matched control hippocampal CA1 [control (C) N = 4; AD (A) N = 6]; the single upper ciRS-7 (~1400 nt) band contains ~70 selectively conserved miRNA-7 binding sites ...

Synthesis and characterization of red mud and rice husk ash-based geopolymer composites

Abstract: A new type of geopolymer composite was synthesized from two industrial wastes, red mud (RM) and rice husk ash (RHA), at varying mixing ratios of raw materials and the resulting products characterized by mechanical compression testing, X-ray diffraction, and scanning electron microscopy to assess their mechanical properties, microstructure, and geopolymerization reactions. Prolonged curing significantly increases the compressive strength and Young’s modulus, but reduces the ductility. Higher RHA/RM ratios generally lead to higher strength, stiffness, and ductility, but excessive RHA may cause the opposite effect. The compressive strength ranges from 3.2 to 20.5 MPa for the synthesized geopolymers with nominal Si/Al ratios of 1.68–3.35. Microstructural and compositional analyses showed that the final products are mainly composed of amorphous geopolymer binder with both inherited and neoformed crystalline phases as fillers, rendering the composites very complex composition and highly variable mechanical properties. Uncertainties in the composition, microstructure, the extent of RHA dissolution, and side reactions may be potential barriers for the practical application of the RM–RHA based geopolymers as a construction material.

Improved Search for $\bar \nu_\mu \rightarrow \bar \nu_e$ Oscillations in the MiniBooNE Experiment

Abstract: The MiniBooNE experiment at Fermilab reports results from an analysis of ν¯e appearance data from 11.27×10²⁰ protons on target in the antineutrino mode, an increase of approximately a factor of 2 over the previously reported results. An event excess of 78.4±28.5 events (2.8σ) is observed in the energy range 200QEν<1250 MeV. If interpreted in a two-neutrino oscillation model, ν¯μ→ν¯e, the best oscillation fit to the excess has a probability of 66% while the background-only fit has a χ² probability of 0.5% relative to the best fit. The data are consistent with antineutrino oscillations in the 0.01<Δm²<1.0 eV² range and have some overlap with the evidence for antineutrino oscillations from the Liquid Scintillator Neutrino Detector. All of the major backgrounds are constrained by in situ event measurements so nonoscillation explanations would need to invoke new anomalous background processes. The neutrino mode running also shows an excess at low energy of 162.0±47.8 events (3.4σ) but the energy distribution of the excess is marginally compatible with a simple two neutrino oscillation formalism. Expanded models with several sterile neutrinos can reduce the incompatibility by allowing for CP violating effects between neutrino and antineutrino oscillations.

Combined analysis of all three phases of solar neutrino data from the Sudbury Neutrino Observatory

Abstract: We report results from a combined analysis of solar neutrino data from all phases of the Sudbury Neutrino Observatory. By exploiting particle identification information obtained from the proportional counters installed during the third phase, this analysis improved background rejection in that phase of the experiment. The combined analysis resulted in a total flux of active neutrino flavors from 8B decays in the Sun of (5.25 \pm 0.16(stat.)+0.11-0.13(syst.))\times10^6 cm^{-2}s^{-1}. A two-flavor neutrino oscillation analysis yielded \Deltam^2_{21} = (5.6^{+1.9}_{-1.4})\times10^{-5} eV^2 and tan^2{\theta}_{12}= 0.427^{+0.033}_{-0.029}. A three-flavor neutrino oscillation analysis combining this result with results of all other solar neutrino experiments and the KamLAND experiment yielded \Deltam^2_{21} = (7.41^{+0.21}_{-0.19})\times10^{-5} eV^2, tan^2{\theta}_{12} = 0.446^{+0.030}_{-0.029}, and sin^2{\theta}_{13} =(2.5^{+1.8}_{-1.5})\times10^{-2}. This implied an upper bound of sin^2{\theta}_{13} < 0.053 at the 95% confidence level (C.L.).

A comprehensive review of climate adaptation in the United States: more than before, but less than needed

Abstract: We reviewed existing and planned adaptation activities of federal, tribal, state, and local governments and the private sector in the United States (U.S.) to understand what types of adaptation activities are underway across different sectors and scales throughout the country. Primary sources of review included material officially submitted for consideration in the upcoming 2013 U.S. National Climate Assessment and supplemental peer-reviewed and grey literature. Although substantial adaptation planning is occurring in various sectors, levels of government, and the private sector, few measures have been implemented and even fewer have been evaluated. Most adaptation actions to date appear to be incremental changes, not the transformational changes that may be needed in certain cases to adapt to significant changes in climate. While there appear to be no one-size-fits-all adaptations, there are similarities in approaches across scales and sectors, including mainstreaming climate considerations into existing policies and plans, and pursuing no- and low-regrets strategies. Despite the positive momentum in recent years, barriers to implementation still impede action in all sectors and across scales. The most significant barriers include lack of funding, policy and institutional constraints, and difficulty in anticipating climate change given the current state of information on change. However, the practice of adaptation can advance through learning by doing, stakeholder engagements (including “listening sessions”), and sharing of best practices. Efforts to advance adaptation across the U.S. and globally will necessitate the reduction or elimination of barriers, the enhancement of information and best practice sharing mechanisms, and the creation of comprehensive adaptation evaluation metrics.

Evacuation transportation modeling: An overview of research, development, and practice

Abstract: This paper presents a review of highway-based evacuation modeling and simulation and its evolution over the past decade. The review includes the major components of roadway transportation planning and operations, including the current state of modeling in the forecasting of evacuation travel demand, distribution and assignment of evacuation demand to regional road networks to reach destinations, assignment of evacuees to various modes of transportation, and evaluation and testing of alternative management strategies to increase capacity of evacuation networks or manage demand. Although this discussion does not cover recent work in other modes used in evacuation such as air, rail, and pedestrian, this paper does highlight recent interdisciplinary modeling work in evacuation to help bridge the gap between the behavioral sciences and engineering and the application of emerging techniques for the verification, validation, and calibration of models. The manuscript also calls attention to special considerations and logistical difficulties, which have received limited attention to date. In addition to these concerns, the following future directions are discussed: further interdisciplinary efforts, including incorporating the medical community; using new technologies for communication of warnings and traffic condition information, data collection, and increased modeling resolution and confidence; using real-time information; and further model refinements and validation.

Conducting Polyaniline Nanowire and Its Applications in Chemiresistive Sensing

Abstract: One dimensional polyaniline nanowire is an electrically conducting polymer that can be used as an active layer for sensors whose conductivity change can be used to detect chemical or biological species. In this review, the basic properties of polyaniline nanowires including chemical structures, redox chemistry, and method of synthesis are discussed. A comprehensive literature survey on chemiresistive/conductometric sensors based on polyaniline nanowires is presented and recent developments in polyaniline nanowire-based sensors are summarized. Finally, the current limitations and the future prospect of polyaniline nanowires are discussed.

Role Stress, Work-Family Conflict and Emotional Exhaustion: Inter-Relationships and Effects on Some Work-Related Consequences

Abstract: Recent research demonstrates that attitudes toward the workplace are influenced by both work and non-work domains. This study examines the inter-relationships of role conflict, role ambiguity, work-family conflict, emotional exhaustion, job satisfaction and propensity to leave in a sales environment. Results indicate that: role conflict is significantly related to emotional exhaustion; work-family conflict is significantly related to both emotional exhaustion and job satisfaction; and, that emotional exhaustion and job satisfaction are related to salesperson propensity to leave. These results support other research indicating the conflict between the work and home domains is highly related to important workplace attitudes and perceptions and suggests that work-family conflict should be included in models examining employee response to the effects of stress.

The Importance of Dissimilatory Nitrate Reduction to Ammonium (DNRA) in the Nitrogen Cycle of Coastal Ecosystems

Abstract: Author Posting. © The Oceanography Society, 2013. This article is posted here by permission of The Oceanography Society for personal use, not for redistribution. The definitive version was published in Oceanography 26, no. 3 (2013): 124–131, doi:10.5670/oceanog.2013.54.

Role of Inflammation and Its Mediators in Acute Ischemic Stroke

Abstract: Inflammation plays an important role in the pathogenesis of ischemic stroke and other forms of ischemic brain injury. Increasing evidence suggests that inflammatory response is a double-edged sword, as it not only exacerbates secondary brain injury in the acute stage of stroke but also beneficially contributes to brain recovery after stroke. In this article, we provide an overview on the role of inflammation and its mediators in acute ischemic stroke. We discuss various pro-inflammatory and anti-inflammatory responses in different phases after ischemic stroke and the possible reasons for their failures in clinical trials. Undoubtedly, there is still much to be done in order to translate promising pre-clinical findings into clinical practice. A better understanding of the dynamic balance between pro- and anti-inflammatory responses and identifying the discrepancies between pre-clinical studies and clinical trials may serve as a basis for designing effective therapies.

The Long-Baseline Neutrino Experiment: Exploring Fundamental Symmetries of the Universe

Abstract: The preponderance of matter over antimatter in the early Universe, the dynamics of the supernova bursts that produced the heavy elements necessary for life and whether protons eventually decay --- these mysteries at the forefront of particle physics and astrophysics are key to understanding the early evolution of our Universe, its current state and its eventual fate. The Long-Baseline Neutrino Experiment (LBNE) represents an extensively developed plan for a world-class experiment dedicated to addressing these questions. LBNE is conceived around three central components: (1) a new, high-intensity neutrino source generated from a megawatt-class proton accelerator at Fermi National Accelerator Laboratory, (2) a near neutrino detector just downstream of the source, and (3) a massive liquid argon time-projection chamber deployed as a far detector deep underground at the Sanford Underground Research Facility. This facility, located at the site of the former Homestake Mine in Lead, South Dakota, is approximately 1,300 km from the neutrino source at Fermilab -- a distance (baseline) that delivers optimal sensitivity to neutrino charge-parity symmetry violation and mass ordering effects. This ambitious yet cost-effective design incorporates scalability and flexibility and can accommodate a variety of upgrades and contributions. With its exceptional combination of experimental configuration, technical capabilities, and potential for transformative discoveries, LBNE promises to be a vital facility for the field of particle physics worldwide, providing physicists from around the globe with opportunities to collaborate in a twenty to thirty year program of exciting science. In this document we provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess.

A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing.

Abstract: Evolutionary relationships among birds in Neoaves, the clade comprising the vast majority of avian diversity, have vexed systematists due to the ancient, rapid radiation of numerous lineages. We applied a new phylogenomic approach to resolve relationships in Neoaves using target enrichment (sequence capture) and high-throughput sequencing of ultraconserved elements (UCEs) in avian genomes. We collected sequence data from UCE loci for 32 members of Neoaves and one outgroup (chicken) and analyzed data sets that differed in their amount of missing data. An alignment of 1,541 loci that allowed missing data was 87% complete and resulted in a highly resolved phylogeny with broad agreement between the Bayesian and maximum-likelihood (ML) trees. Although results from the 100% complete matrix of 416 UCE loci were similar, the Bayesian and ML trees differed to a greater extent in this analysis, suggesting that increasing from 416 to 1,541 loci led to increased stability and resolution of the tree. Novel results of our study include surprisingly close relationships between phenotypically divergent bird families, such as tropicbirds (Phaethontidae) and the sunbittern (Eurypygidae) as well as between bustards (Otididae) and turacos (Musophagidae). This phylogeny bolsters support for monophyletic waterbird and landbird clades and also strongly supports controversial results from previous studies, including the sister relationship between passerines and parrots and the non-monophyly of raptorial birds in the hawk and falcon families. Although significant challenges remain to fully resolving some of the deep relationships in Neoaves, especially among lineages outside the waterbirds and landbirds, this study suggests that increased data will yield an increasingly resolved avian phylogeny.

Clinical Practice Guideline: Bell's Palsy

Abstract: ObjectiveBell’s palsy, named after the Scottish anatomist, Sir Charles Bell, is the most common acute mono-neuropathy, or disorder affecting a single nerve, and is the most common diagnosis associa...

Definitions of terms relating to mass spectrometry (IUPAC Recommendations 2013)

Abstract: This document contains recommendations for terminology in mass spectrometry. Development of standard terms dates back to 1974 when the IUPAC Commission on Analytical Nomenclature issued recommendations on mass spectrometry terms and defini- tions. In 1978, the IUPAC Commission on Molecular Structure and Spectroscopy updated and extended the recommendations and made further recommendations regarding symbols, acronyms, and abbreviations. The IUPAC Physical Chemistry Division Commission on Molecular Structure and Spectroscopy's Subcommittee on Mass Spectroscopy revised the recommended terms in 1991 and appended terms relating to vacuum technology. Some addi- tional terms related to tandem mass spectrometry were added in 1993 and accelerator mass spectrometry in 1994. Owing to the rapid expansion of the field in the intervening years, par- ticularly in mass spectrometry of biomolecules, a further revision of the recommendations has become necessary. This document contains a comprehensive revision of mass spectrom- etry terminology that represents the current consensus of the mass spectrometry community.