cssi/SciSciGPT-SciSciNet huggingface dataset:
Vavien: an algorithm for prioritizing candidate disease genes based on topological similarity of proteins in interaction networks.

Abstract Genome-wide linkage and association studies have demonstrated promise in identifying genetic factors that influence health and disease. An important challenge is to narrow down the set of candidate genes that are implicated by these analyses. Protein-protein interaction (PPI) networks are useful in extracting the functional relationships between known disease and candidate genes, based on the principle that products of genes implicated in similar diseases are likely to exhibit significant connectivity/proximity. Information flow–based methods are shown to be very effective in prioritizing candidate disease genes. In this article, we utilize the topology of PPI networks to infer functional information in the context of disease association. Our approach is based on the assumption that PPI networks are organized into recurrent schemes that underlie the mechanisms of cooperation among different proteins. We hypothesize that proteins associated with similar diseases would exhibit similar topological c...
An interactive optimization component for solving parameter estimation and policy decision problems in complex simulations

The increased use of large, nonlinear and dynamic models to represent real world phenomena has resulted in complex parameter estimation and policy decision problems. This paper describes an interactive optimization component, an integrated set of minimization techniques, to assist in the efficient solution of these problems. The component was developed with particular consideration given to computer execution requirements, interaction flexibility, problem solution accuracy, and component/computer compatibility. A pattern recognition sub-component used for examining model behavior and an optimization sub-component used for multi-level numerical searches combine to provide good problem solutions for broad classes of problems. Test results of component application for a Nigerian beef industry model and a single-commodity market model are discussed and analyzed. Finally general conclusions and further extensions of the research are presented.
Experimental determination of U and Th partitioning between clinopyroxene and natural and synthetic basaltic liquid

Clinopyroxene-silicate liquid partition coefficients for U and Th have been determined by particle track radiography from 1 atm crystallization experiments at controlled fO_2. Two natural basaltic and one synthetic composition were studied at fO_2 values from the Ni—NiO oxygen buffer to 1 log unit more oxidizing than Fe—FeO (IW+ 1). Over the range of fO_2 values and compositions studied, D_U^(cpx/liq) = 0.0034–0.015,D_(Th)^(cpx/liq) = 0.008–0.036, and D_(Th)/D_U= 3.4–1.1. With decreasing fO_2, D_(Th)/D_U can decrease by up to a factor of 3 for a given composition, primarily from an increase in D_U^(cpx/liq), which we interpret as resulting from an increase in the proportion of tetravalent U in the system with decreasing fO_2. This demonstrates that crystal-liquid U—Th fractionation is fO_2 dependent and that U in terrestrial magmas is not entirely tetravalent. D_(Th)^(cpx/liq) appears to decrease in the two basalts at the lowest fO_2, possibly as a result of changes in composition with fO_2. Our data show the sense of U—Th fractionation by clinopyroxene-liquid partitioning is consistent with previous experimental determinations, in that D_(Th)^(cpx)/D_U^(cpx)> 1 in all cases. This indicates that, during partial melting, the liquid will have a Th/U ratio less than the clinopyroxene in the source. The observed ^(238)—U^(230)Th disequilibrium in MORB requires that the partial melt should have a Th/U ratio greater than the bulk source, and, therefore, cannot result from clinopyroxene-liquid partitioning. Further, the magnitudes of the measured partition coefficients are too small to generate significant U—Th fractionation in either direction. Assuming that clinopyroxene contains the bulk of the U and Th in MORB source, our results indicate that ^(238)U—^(230)Th disequilibrium in MORB may not be caused by partial melting at all.
An immunological basis of hyperphagia driven by GABAergic dysfunction in Prader–Willi Syndrome

Impaired immune function is increasingly seen as a core element of various neurological, psychiatric, and developmental disorders but has not yet been investigated in subjects with Prader–Willi Syndrome. We hypothesize that the emergence and the progression of PWS may be regulated by immune dysfunction involving auto-antibodies and miRNA driven by GABAergic dysfunction. Future research testing this hypothesis is discussed.
Inactivation of intracellular proteolysis and cathepsin B enzyme activity by dehydroascorbic acid and reactivation by dithiothreitol in perfused rat heart

The selective inhibition of some subcomponents of intracellular protein degradation was characterized under exposure to the cyclic multiketone thiol oxidizing agents dehydroascorbic acid (DHA) and alloxan. Proteins of the isolated perfused rat heart were labeled in vitro with a 10-min infusion of [3H] leucine, and subsequent release of radiolabeled amino acid from cell proteins was measured. As determined previously, four subcomponents of total proteolysis can be distinguished; the first three subcomponents are reversibly inhibited by the thiol-reactive agent diamide: (a) The rapid turnover proteins comprise most of the [3H] leucine release from 20 min to 3 hr after labeling. (b) Following 3 hr of degradation, the lysosomal (insulin-responsive) subcomponent comprises 35-40% of [3H] leucine release. (c) A third nonlysosomal (adrenergic-responsive) subcomponent comprises 35%. (d) A fourth nonlysosomal subcomponent consisting of 25% of [3H] leucine release is uninhibited by diamide. Infusion of supraphysiologic DHA (1 mM) or alloxan (1.5 mM) promptly mimicked the proteolytic inhibitory action of diamide on the first three subcomponents, but did not inhibit the diamide-resistant subcomponent. Infusion of a physiologic extracellular DHA concentration of 5 microM caused little or no change in proteolysis. The proteolytic inhibitory action of DHA (1 mM) could be reversed by concurrent infusion of dithiothreitol (DTT, 1.5 mM) simultaneously with continued DHA. DHA (1 mM) caused direct inhibition of the purified sulfhydryl proteinase cathepsin B (EC 3.4.22.1), which was reversible by subsequent excess DTT (5 mM). Results indicate that a nontoxic endogenous multiketone thiol oxidant can reversibly inhibit some proteolytic processes in viable tissue; however, approximately 25% of the observed proteolysis is uninhibited. Reversible inactivation of sulfhydryl proteinases, including cathepsin B, is among the possible multiple mechanisms of this DHA action.
Mitigating Resistance to Teaching Science Through Inquiry: Studying Self

This is the report of a qualitative emergent-design study of 2 different Web-enhanced science methods courses for preservice elementary teachers in which an experiential learning strategy, labeled “using yourself as a learning laboratory,” was implemented. Emergent grounded theory indicated this strategy, when embedded in a course organized as an inquiry with specified action foci, contributed to mitigating participants’ resistance to learning and teaching through inquiry. Enroute to embracing inquiry, learners experienced stages resembling the stages of grief one experiences after a major loss. Data sources included participant observation, electronic artifacts in WebCT, and interviews. Findings are reported in 3 major sections: “Action Foci Common to Both Courses,” “Participants’ Growth and Change,” and “Challenges and Tradeoffs.”
Organization of records with unequal multiple-valued attributes and combinatorial queries of order 2

Abstract This paper develops theories for constructing filing schemes for formatted files with unequal-valued attributes when the query set contains all queries which specify two values from two attributes. These filing schemes provide a set of buckets for storing accession numbers of records. The retrieval rule is based on identifying a bucket from a query by solving algebraic equations over finite fields. The theories underlying these filing schemes are based on properties of deleted finite geometries. Expressions for retrieval time and storage redundancy are also given.
Len Kleinrock: The First Two Packets on the Internet

Len Kleinrock describes the Internet's humble beginnings. The first Web extra at http://youtu.be/uY7dUJT7OsU is a video interview in which author Charles Severance speaks with Len Kleinrock about the Internet's humble beginnings. The second Web extra at http://youtu.be/r6nCrbitq0U is an audio recording of author Charles Severance reading his Computing Conversations column, in which he discusses his interview with Len Kleinrock about the Internet's humble beginnings.
A sequence-based identification of the genes detected by probesets on the Affymetrix U133 plus 2.0 array

One of the biggest problems facing microarray experiments is the difficulty of translating results into other microarray formats or comparing microarray results to other biochemical methods. We believe that this is largely the result of poor gene identification. We re-identified the probesets on the Affymetrix U133 plus 2.0 GeneChip array. This identification was based on the sequence of the probes and the sequence of the human genome. Using the BLAST program, we matched probes with documented and postulated human transcripts. This resulted in the redefinition of approximately 37% of the probes on the U133 plus 2.0 array. This updated identification specifically points out where the identification is complicated by cross-hybridization from splice variants or closely related genes. More than 5000 probesets detect multiple transcripts and therefore the exact protein affected cannot be readily concluded from the performance of one probeset alone. This makes naming difficult and impacts any downstream analysis such as associating gene ontologies, mapping affected pathways or simply validating expression changes. We have now automated the sequence-based identification and can more appropriately annotate any array where the sequence on each spot is known.
Experiences in Improving Flight Software Development Processes

In 2001, the Jet Propulsion Laboratory (JPL) initiated a software process improvement effort. In 2004, JPL began the Multimission System Architecture Platform (MSAP) project and designated it as part of this effort. In 2007, JPL's Engineering and Science Directorate, which controls the MSAP project's technical development, achieved CMMI Staged Maturity Level 3.1 This article describes the impacts of the CMMI rating and the JPL process improvement effort on the MSAP project's software engineering and assurance organizations.
Do Large Residential Subdivisions Induce Further Development?: A Spatially Explicit Hazard Analysis of Land Use Change in Charlotte

Problem: Most previous research on land use change has been conducted at coarse scales with aggregated data, and there are relatively few studies that attempt to establish and examine these linkages at a disaggregate level. In addition, the cumulative effects of large residential developments have been little investigated as potential drivers of land use change. Purpose: We hypothesize that residential subdivisions of 10 acres or more exert detectable priming effects and influence the rate of subsequent development in the vicinity. We use parcel-level data to test whether unilateral development decisions have spillover effects across both space and time. Methods: We analyze parcel changes and then conduct a spatially explicit hazard analysis of land use change in Mecklenburg County, NC, to identify a set of factors that predict which vacant land parcels are most likely to experience a subdivision event (be subdivided) during a given one-year time period. We also perform a sensitivity analysis to assess ho...
Survey of signal processing techniques for interference suppression in communication

Interferences of various kinds are of a major concern in communication system design and operation, since they could cause serious system performance deterioration. As the demand on communication resources, such as frequency spectrum, increases steadily, the desire for a more effective signal processing techniques for interference suppression resulting in efficient usage of resources becomes more important. This paper presents the results of a survey conducted on signal processing techniques and adaptive antenna arrays used for interference suppression applications. The interference types considered in this paper are jamming, adjacent channel interference (ACI), co-channel interference (CCI) and multi-access interference (MAI), and inter-symbol interference (ISI). A preliminary assessment of the impact of signal processing trends on the power spectral density, bandwidth, and spectrum packing efficiency is also presented in the paper.
Second 46,XX male with MLS syndrome

We report on a second 46,XX male with microphthalmia with linear skin defects (MLS) syndrome. In addition to microphthalmia and linear skin streaks, he had a secundum ASD, hypospadias with chordee, anal fistula, and agenesis of corpus callosum with colpocephaly. Biopsy of a linear streak showed smooth muscle hamartomata rather than the presumed dermal aplasia. Detailed ophthalmologic examination did not show retinal lacunae typical of Aicardi syndrome. DNA studies with distal Xp specific probes indicated a deletion in one X chromosome and fluorescence in situ hybridization (FISH) studies with X- and Y-specific probes demonstrated the presence of a derivative X chromosome from an X;Y translocation.
Computer‐generated global map of valley networks on Mars

[1] The presence of valley networks (VN) on Mars suggests that early Mars was warmer and wetter than present. However, detailed geomorphic analyses of individual networks have not led to a consensus regarding their origin. An additional line of evidence can be provided by the global pattern of dissection on Mars, but the currently available global map of VN, compiled from Viking images, is incomplete and outdated. We created an updated map of VN by using a computer algorithm that parses topographic data and recognizes valleys by their morphologic signature. This computer-generated map was visually inspected and edited to produce the final updated map of VN. The new map shows an increase in total VN length by a factor of 2.3. A global map of dissection density, D, derived from the new VN map, shows that the most highly dissected region forms a belt located between the equator and mid-southern latitudes. The most prominent regions of high values of D are the northern Terra Cimmeria and the Margaritifer Terra where D reaches the value of 0.12 km−1 over extended areas. The average value of D is 0.062 km−1, only 2.6 times lower than the terrestrial value of D as measured in the same fashion. These relatively high values of dissection density over extensive regions of the planet point toward precipitation-fed runoff erosion as the primary mechanism of valley formation. Assuming a warm and wet early Mars, peculiarity of the global pattern of dissection is interpreted in the terms of climate controlling factors influenced by the topographic dichotomy.
Should Violent Offenders Be Excluded From Drug Court Participation? An Examination of the Recidivism of Violent and Nonviolent Drug Court Participants

Policy often stipulates drug court funding cannot be used for offenders with violent criminal histories, although it has been argued that increasing funding to community programs for these individuals represents an important means for controlling crime. Because little research has examined whether a violent offense history is related to recidivism following drug court participation, predrug court criminal history and postdrug court arrest and charge data have been collected for 452 offenders in a postplea drug court program. Bivariate analyses show violent offenders have higher rates of recidivism following drug court discharge. However, multivariate analyses controlling for age, ethnicity, drug of choice, time at risk, and discharge status show the extent of criminal history, not violent history, is significantly related to recidivism. Results suggest that violent offenders should not be systematically excluded from the opportunity to participate in the unique combination of treatment and supervision offered in drug court programs.
Evidence for transposition of dispersed repetitive DNA families in yeast

Dispersed repetitive DNA sequences from yeast (Saccharomyces cerevisiae) nuclear DNA have been isolated as molecular hybrids in lambdagt. Related S. cerevisiae strains show marked alterations in the size of the restriction fragments containing these repetitive DNAs. "Ty1" is one such family of repeated sequences in yeast and consists of a 5.6 kilobase (kb) sequence including a noninverted 0.25 kb sequence of another repetitious family, "delta", on each end. There are about 35 copies of Ty1 and at least 100 copies of delta (not always associated with Ty1) in the haploid genome. A few Ty1 elements are tandem and/or circular, but most are disperse and show (along with delta) some sequence divergence between repeat units. Sequence alterations involving Ty1 elements have been found during the continual propagation of a single yeast clone over the course of a month. One region with a large number of delta sequences (SUP4) also shows a high frequency of sequence alterations when different strains are compared. One of the differences between two such strains involves the presence or absence of a Ty1 element. The novel joint is at one inverted pair of delta sequences.
Switching to Another SSRI or to Venlafaxine With or Without Cognitive Behavioral Therapy for Adolescents With SSRI-Resistant Depression: The TORDIA Randomized Controlled Trial

Context Only about 60% of adolescents with depression will show an adequate clinical response to an initial treatment trial with a selective serotonin reuptake inhibitor (SSRI). There are no data to guide clinicians on subsequent treatment strategy. Objective To evaluate the relative efficacy of 4 treatment strategies in adolescents who continued to have depression despite adequate initial treatment with an SSRI. Design, Setting, and Participants Randomized controlled trial of a clinical sample of 334 patients aged 12 to 18 years with a primary diagnosis of major depressive disorder that had not responded to a 2-month initial treatment with an SSRI, conducted at 6 US academic and community clinics from 2000-2006. Interventions Twelve weeks of: (1) switch to a second, different SSRI (paroxetine, citalopram, or fluoxetine, 20-40 mg); (2) switch to a different SSRI plus cognitive behavioral therapy; (3) switch to venlafaxine (150-225 mg); or (4) switch to venlafaxine plus cognitive behavioral therapy. Main Outcome Measures Clinical Global Impressions-Improvement score of 2 or less (much or very much improved) and a decrease of at least 50% in the Children's Depression Rating Scale-Revised (CDRS-R); and change in CDRS-R over time. Results Cognitive behavioral therapy plus a switch to either medication regimen showed a higher response rate (54.8%; 95% confidence interval [CI], 47%-62%) than a medication switch alone (40.5%; 95% CI, 33%-48%;P = .009), but there was no difference in response rate between venlafaxine and a second SSRI (48.2%; 95% CI, 41%-56% vs 47.0%; 95% CI, 40%-55%;P = .83). There were no differential treatment effects on change in the CDRS-R, self-rated depressive symptoms, suicidal ideation, or on the rate of harm-related or any other adverse events. There was a greater increase in diastolic blood pressure and pulse and more frequent occurrence of skin problems during venlafaxine than SSRI treatment. Conclusions For adolescents with depression not responding to an adequate initial treatment with an SSRI, the combination of cognitive behavioral therapy and a switch to another antidepressant resulted in a higher rate of clinical response than did a medication switch alone. However, a switch to another SSRI was just as efficacious as a switch to venlafaxine and resulted in fewer adverse effects. Trial Registration clinicaltrials.gov Identifier:NCT00018902
Molecular models for WH6 under pressure

At atmospheric pressure, some tungsten hydrides exist as discrete molecular complexes in low temperature matrices, but are very reactive and cannot be isolated in bulk at room temperature. Under pressure, one observes WH in experiment at room temperature, and calculations indicate several other stoichiometries are stable, all extended and not molecular. This work aims at constructing a bridge between discrete molecules and the pressurized extended structures, with the emblematic example of WH6. The equilibrium structure, known as a distorted trigonal prismatic molecule, is likely to be a good acceptor. In numerical experiments, discrete WH6 molecular complexes are allowed to interact with each other in their ground states at T = 0 K and P = 1 atm. They spontaneously rearrange to form 1D-chains, with the W centers adopting a tricapped trigonal prismatic environment. The electronic structure of these chains is examined and related to that of the monomer and extended solids.
Grade level differences in teacher perceptions of students by race and sex

Both research and theory point out differences in teacher attitudes or behavior toward students of varying race or sex. For example, teacher behavior toward black children may be qualitatively different from their instructional styles with white children (Washington, 1980). Similarly, decades of educational theory suggest that teachers expect boys and girls to exhibit dissimilar talents and skills (see Ayers, 1909; St. John, 1932; Sadker & Sadker 1980). Yet, it is empirically unclear how the race of the male, or the sex of the black, pupil may affect the pattern of teacher expectations in desegregated school settings across grade levels. Nonetheless, research does indicate that grade level may be a variable important to the delineation of teacher perceptions (e.g. Rosenthal & Jacobson, 1968; Rist, 1970; Ryan, 1971). For example, in her review of research on desegregated schools, St. John (1975) concluded that the gains of black children are more evident in earlier than in later grades. Role theory suggests that teacher perceptions are assigned to individuals on the basis of their location in the social system (Gross, Mason, & McEachern, 1958). Consistent with role theory, this study investigated grade level differences in first and fourth grade black and white teachers' perceptions of black boys, black girls, white boys and white girls in desegregated classrooms. Three school systems in the Southeastern USA participated in the study. The subjects were 64 teachers of first or fourth grades who had at least 15 % AfroAmerican enrollment in their classrooms. Teachers were asked, during individual interviews, to designate two children from their classrooms to each of 12 traits. The six positive and six negative traits, identified as important in a school context (see Washington, 1980), were:
HARTREE-FOCK STUDIES OF ATOMS IN STRONG MAGNETIC FIELDS

We present comprehensive calculations of the electronic structure of selected first-row atoms in uniform magnetic fields of strength \ensuremath{\le}${10}^{10}$ G, within a flexible implementation of the Hartree-Fock formalism. Ground-state and low-lying excited state properties are presented for first-row atoms He, Li, C, and ion ${\mathrm{H}}^{\mathrm{\ensuremath{-}}}$. We predict and describe a series of ground-state quantum transitions as a function of magnetic field strength. Due to its astrophysical importance, highly excited states of neutral He are also computed. Comparisons are made with previous works, where available. \textcopyright{} 1996 The American Physical Society.
Relationship of weight status and cardiometabolic outcomes for adolescents in the TEAMS study.

The increase in the prevalence of obesity among youth is alarming. Relationships exist between excess weight and adverse cardiometabolic markers. The aims of this study among adolescents in the Tee...
Fuzzy Relation Equations (II): The Branch-point-solutions and the Categorized Minimal Solutions

This paper presents some novel theoretical results as well as practical algorithms and computational procedures on fuzzy relation equations (FRE). These results refine and improve what has already been reported in a significant manner. In the previous paper, the authors have already proved that the problem of solving the system of fuzzy relation equations is an NP-hard problem. Therefore, it is practically impossible to determine all minimal solutions for a large system if P ≠ NP. In this paper, an existence theorem is proven: there exists a special branch-point-solution that is greater than all minimal solutions and less than the maximum solution. Such branch-point-solution can be calculated based on the solution-base-matrix. Furthermore, a procedure for determining all branch-point-solutions is designed. We also provide efficient algorithms which is capable of determining as well as searching for certain types of minimal solutions. We have thus obtained: (1) a fast algorithm to determine whether a solution is a minimal solution, (2) the algorithm to search for the minimal solutions that has at least a minimum value at a component in the solution vector, and (3) the procedure of determining if a system of fuzzy relation equations has the unique minimal solution. Other properties are also investigated.
Cytoskeletal dynamics in rabbit synovial fibroblasts: II. Reformation of stress fibers in cells rounded by treatment with collagenase-inducing agents.

Modulation of the synthesis and secretion of extracellular matrix proteins and matrix-degrading metalloproteases by rabbit synovial fibroblasts in an important model system for studying the control of tissue-specific gene expression. Induction of collagenase expression is correlated with changes in cell shape and actin filament distribution, but the role of the cellular cytoskeleton in the sustained synthesis and secretion of metalloproteases has not been closely examined. When cells were allowed to respread after rounding by trypsin or cytochalasin, two known metalloprotease inducers, reformation of stress fibers was observed within 2 h in the presence of serum. In the absence of serum, trypsin-treated cells did not respread substantially, even after 24 h in culture. In contrast, cytochalasin-treated cells recovered almost as rapidly in the absence as in the presence of serum, showing reformation of well-formed microfilament bundles within 30 min of drug removal, especially at the spreading cell edges. High resolution electron-microscopic views of detergent-extracted cytoskeletons confirmed the rapid rebundling of peripheral microfilaments. Acrylamide-treated cells fell between these two extremes, spreading slowly in the absence of serum, but almost as rapidly as cytochalasin-treated cells in its presence. Reestablishment of normal intermediate filament distribution generally lagged slightly behind actin for all treatments, and intermediate filaments always appeared to spread back into the cellular cytoplasm within the confines of the reforming peripheral microfilament bundles. No obvious interaction between these two cytoskeletal elements was observed after any treatment, and no specific role for intermediate filaments in modulating gene expression in these cells is suggested by these results. The serum dependence displayed after trypsin or acrylamide treatment may be due to the disturbances in fibronectin synthesis observed in these cells and is consistent with evidence that both induction and sustained expression of matrix-degrading metalloprotease may involve signals transduced through plasma membrane matrix receptors (integrins).
A high-performance single-phase Phase-Locked-Loop with fast line-voltage amplitude tracking

This paper presents a single-phase Phase-Locked-Loop (PLL) system to reject the impact of input voltage amplitude variation. The proposed PLL is based on the unbalanced DQ transformation which doesn't require the generation of orthogonal. Aside from the input phaseangle tracking feedback loop, another peak-voltage detection loop is enclosed to fast track the input signal amplitude, thereby reducing the output second-order harmonic frequency ripple by as much as 80% in most cases. The proposed PLL also allows for the rejection of the dc offset of the input signal, which is thus deemed advantageous due to the ease of implementation, ideal zero steady-state error output, and the offset rejection. Analytical simulation and experimental results are presented for verification purposes.
Men, masculinity, and manhood acts.

In the 1980s research on men shifted from studying the “male sex role” and masculinity as a singular trait to studying how men enact diverse masculinities. This research has examined men's behavior as gendered beings in many contexts, from intimate relationships to the workplace to global politics. We consider the strengths and weaknesses of the multiple masculinities approach, proposing that further insights into the social construction of gender and the dynamics of male domination can be gained by focusing analytic attention on manhood acts and how they elicit deference from others. We interpret the literature in terms of what it tells us about how males learn to perform manhood acts, about how and why such acts vary, and about how manhood acts reproduce gender inequality. We end with suggestions for further research on the practices and processes through which males construct the category “men” and themselves as its members.
Yersinia pseudotuberculosis uses Ail and YadA to circumvent neutrophils by directing Yop translocation during lung infection.

Summary A Yersinia pseudotuberculosis (Yptb) murine model of lung infection was previously developed using the serotype III IP2666NdeI strain, which robustly colonized lungs but only sporadically dis- seminated to the spleen and liver. We demonstrate here that a serotype Ib Yptb strain, IP32953, colo- nizes the lungs at higher levels and disseminates more efficiently to the spleen and liver compared with IP2666NdeI. The role of adhesins was investi- gated during IP32953 lung infection by construct- ing isogenic Δail, Δinv, ΔpsaE and ΔyadA mutants. An IP32953ΔailΔyadA mutant initially colonized but failed to persist in the lungs and disseminate to the spleen and liver. Yptb expressing these adhesins selectively bound to and targeted neutrophils for translocation of Yops. This selective targeting was critical for virulence because persistence of the ΔailΔyadA mutant was restored following intrana- sal infection of neutropenic mice. Furthermore, Ail and YadA prevented killing by complement- mediated mechanisms during dissemination to and/or growth in the spleen and liver, but not in the lungs. Combined, these results demonstrate that Ail and YadA are critical, redundant virulence factors during lung infection, because they thwart neutrophils by directing Yop-translocation specifi- cally into these cells.
Photophysics and spectroscopy of metal particles

This paper describes our recent work using ultrafast laser spectroscopy to examine the fundamental properties of metal particles. Two studies are presented. First, the characteristic time scale for electron-phonon coupling in Au particles with sizes between 2 and 120 nm has been examined by bleach recovery measurements. These experiments show that the coupling between the electrons and phonons is independent of particle size, to within the signal-to- noise of our experiments. We have also used transient absorption spectroscopy to examine the low-frequency "breathing" modes of the Au particles. These modes are impulsively excited by the rapid lattice heating that accompanies electron-phonon coupling. The breathing motion contributes to the transient absorption signal because the position of the plasmon band depends on the free electron density and, thus, the particle volume. The measured frequencies are inversely proportional to the radius, and almost exactly match the predictions of classical mechanics calculations for Au.
Identification of the Molecular Mechanisms by Which the Diterpenoid Salvinorin A Binds to κ-Opioid Receptors†

Salvinorin A is a naturally occurring hallucinogenic diterpenoid from the plant Salvia divinorum that selectively and potently activates κ-opioid receptors (KORs). Salvinorin A is unique in that it is the only known lipid-like molecule that selectively and potently activates a G-protein coupled receptor (GPCR), which has as its endogenous agonist a peptide; salvinorin A is also the only known non-nitrogenous opioid receptor agonist. In this paper, we identify key residues in KORs responsible for the high binding affinity and agonist efficacy of salvinorin A. Surprisingly, we discovered that salvinorin A was stabilized in the binding pocket by interactions with tyrosine residues in helix 7 (Tyr313 and Tyr320) and helix 2 (Tyr119). Intriguingly, activation of KORs by salvinorin A required interactions with the helix 7 tyrosines Tyr312, Tyr313, and Tyr320 and with Tyr139 in helix 3. In contrast, the prototypical nitrogenous KOR agonist U69593 and the endogenous peptidergic agonist dynorphin A (1−13) showed d...
Human legacies differentially organize functional and phylogenetic diversity of urban herbaceous plant communities at multiple spatial scales

Questions Patterns of functional and phylogenetic homogenization of plant diversity at the scale of entire cities are well established. However, fewer studies have investigated how shifts in the composition of urban species pools may alter spatial variation in community assembly across patches within a city. We compared plant diversity both within and between vacant lots in a single urban neighborhood and asked: (1) how do heterogeneous human legacies of land use within vacant lots structure plant community diversity and composition and (2) what is the importance of human legacies for structuring community composition, relative to spatial and environmental variation? Location Urban residential neighbourhood in Baltimore, MD, US (39°17′ N, 76°38′ W). Methods We surveyed herbaceous plant species identity and abundance in 24 unmanaged vacant lots. We constructed functional and phylogenetic diversity metrics from databases and the literature and compared taxonomic, functional and phylogenetic diversity between sections of the lot where a residential building was once located (building footprint), and the area that was originally the garden or backyard (remnant garden). We term these different ‘human legacy’ groups. We partitioned variation in plant community composition between human legacy groups as well as across measured environmental and spatial gradients. Results We report significant plant community compositional divergence between human legacy groups. Beta-diversity, in particular, was significantly higher in remnant garden sections compared to building footprint sections for all metrics of biodiversity. Plant community compositional variation was primarily explained by differences in human legacies. We found no measurable effects of selected metrics of local environmental variation (abiotic soil characteristics) or environmental context (lot area, proximity to other vacant lots and tree canopy) on compositional variation. Geographic distance between sites, however, did interact with human legacy variation to structure phylogenetic composition. Conclusions Our findings suggest that human land-use legacies have complex but measurable effects on both the patterns and the processes by which species co-existence is maintained across the urban landscape. Within a single habitat type (here, residential vacant lots), variation in legacies of land use may have a stronger plant community structuring effect than contemporary environmental variation.
Discrimination of sedimentary lithologies using Hyperion and Landsat Thematic Mapper data: a case study at Melville Island, Canadian High Arctic

The use of remote-sensing techniques in the discrimination of rock and soil classes in northern regions can support a diverse range of activities, such as environmental characterization, mineral exploration and the study of Quaternary paleoenvironments. Although images with low spectral resolution can commonly be used in the mapping of classes possessing distinct spectral properties, hyperspectral images offer greater potential for discrimination of materials characterized by more subtle reflectance properties. In an effort to better constrain the utility of broadband and hyperspectral datasets in high-latitude research, this study investigated the effectiveness of Landsat Thematic Mapper (TM) and EO-1 Hyperion data for discrimination of lithological classes at eastern Melville Island, Nunavut, Canada. TM data were classified using a standard neural-network algorithm, and both TM and Hyperion data were linearly unmixed using ground-truth spectra. TM classification results successfully discriminate between classes over much of the study area, although with incomplete separation between clastic and carbonate materials. TM unmixing results are poor, with useful class separation restricted to vegetation and red-weathered sandstone classes. Hyperion results effectively depict the fractional cover of end members, although the abundance images of several classes contain background abundance values that overestimate surface exposure in some areas. For the study area and surface classes involved, noisy hyperspectral data were found to be of greater utility than higher-fidelity broadband multispectral data in the generation of fractional abundance images for an inclusive set of surface-cover classes.
Sterol Intermediates from Cholesterol Biosynthetic Pathway as Liver X Receptor Ligands

The liver X receptors (LXRs) are ligand-activated transcription factors that regulate the expression of genes controlling lipid metabolism. Oxysterols bind LXRs with high affinity in vitro and are implicated as ligands for the receptor. We showed previously that accumulation of selected dietary sterols, in particular stigmasterol, is associated with activation of LXR in vivo. In the course of the defining of structural features of stigmasterol that confer LXR agonist activity, we determined that the presence of an unsaturated bond in the side chain of the sterol was necessary and sufficient for activity, with the C-24 unsaturated cholesterol precursor sterols desmosterol and zymosterol exerting the largest effects. Desmosterol failed to increase expression of the LXR target gene, ABCA1, in LXRalpha/beta-deficient mouse fibroblasts, but was fully active in cells lacking cholesterol 24-, 25-, and 27-hydroxylase; thus, the effect of desmosterol was LXR-dependent and did not require conversion to a side chain oxysterol. Desmosterol bound to purified LXRalpha and LXRbeta in vitro and supported the recruitment of steroid receptor coactivator 1. Desmosterol also inhibited processing of the sterol response element-binding protein-2 and reduced expression of hydroxymethylglutaryl-CoA reductase. These observations are consistent with specific intermediates in the cholesterol biosynthetic pathway regulating lipid homeostasis through both the LXR and sterol response element-binding protein pathways.
The Impacts of Undergraduate Service-Learning on Post-Graduation Employment Outcomes

This article highlights the results of a study assessing service-learning’s impact on post-graduation employment for students from a large, public land-grant university who had completed their undergraduate degree. Survey data collected three years after graduation yielded 44 unique pairs matched for undergraduate major, graduation date, gender, and academic performance, but with only a single member of each pair having taken service-learning coursework. The study investigated employment outcomes including time needed to find a first job, starting salary, timing of promotions and raises, and type of employment. Paired t-tests found significantly higher starting salaries and significantly shorter time to receive a first raise for graduates with service-learning experience. No significant differences were found regarding (a) whether either set received a raise or promotion, (b) whether the job was in their desired field, (c) the overall time to find an initial job, or (d) the length of time from hiring to first promotion. These results represent the first empirical data assessing service-learning’s potential influence on economic aspects of post-university employment.
Increasing Latina/o Student Success: Examining Culturally Responsive College Readiness in the Rio Grande Valley of South Texas

Drawing upon Franquiz & Salazar's (2004) humanizing pedagogy, this qualitative case study explored the perspectives of 22 school and community leaders in the Rio Grande Valley of South Texas. Focus...
Optical Materials, Adhesive and Encapsulant, III-V, and Optical Characterization Evaluation: Cooperative Research and Development Final Report, CRADA Number CRD-07-216

SolFocus is currently developing solar technology for utility scale application using Winston collector based concentrating photovoltaics (CPV). Part of that technology development includes small mirror dishes and front surface reflectors, and bonding the separate parts to the assembly. Mirror panels must meet rigid optical specifications in terms of radius of curvature, slope errors and specularity. The reflective surfaces must demonstrate long term durability and maintain high reflectivity. Some bonded surfaces must maintain adhesion and transparency under high concentrations and high temperatures. Others will experience moderate temperatures and do not require transparency. NREL researchers have developed methods and tools that address these related areas.
Kinetics and Mechanism of Molybdenum-Mediated Acrylate Formation from Carbon Dioxide and Ethylene

A zerovalent molybdenum complex, [(Ph2PCH2CH2)2PPh]Mo(C2H4)(N2)2, was found to promote coupling of CO2 and ethylene to afford a molybdenum(II) acrylate hydride complex. The identity of the molybdenum(II) acrylate hydride complex was established by spectroscopy and reactivity studies. The mechanism of carbon dioxide functionalization with ethylene has been investigated by a series of kinetic and isotopic labeling studies, in addition to the observation of a formally molybdenum(0) carbon dioxide−ethylene intermediate along the reaction pathway. Acrylate formation from the molybdenum(0) intermediate proceeds with a rate constant of 3.8(3) × 10−5 s−1 and an isotope effect of 1.2(2) for C2H4 vs C2D4 at 23 °C. Measuring rate constants of the CO2 reduction over a 40 °C temperature range established activation parameters for acrylate formation of ΔS‡ = 1(7) eu and ΔH‡ = 24(3) kcal/mol. The mechanism of CO2−ethylene coupling is proposed to proceed from a molybdenum(0) carbon dioxide−ethylene adduct via rate-limiti...
Abstract 2648: Gene-asbestos interaction and lung cancer risk from a genome-wide association study

Occupational asbestos exposure has been found to increase lung cancer risk based on epidemiologic studies. In order to clarify the respective roles of genetic factors and asbestos exposure on lung cancer risk, we conducted the asbestos exposure-gene interaction analyses. The first discovery stage included 745 Caucasian cases and 839 Caucasian controls using Illumina Human 610-Quad BeadChips. Several independent populations were included in the second replication stage. Cumulative lifetime asbestos exposure score (AES), which was previously developed and validated in our study population, was calculated from self-reported duration and intensity of occupational and nonoccupational exposures. We have found several suggested interesting / significant regions that might be associated with lung cancer risk in our SNP-asbestos exposure interaction tests, especially on 2p25.3, which has been replicated in another independent population. Further replication is still in process. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2648. doi:1538-7445.AM2012-2648
AB0740 Comparative Study of Patients with Peripheral Psoriatic Arthritis, Axial Psoriatic Arthritis and Axial Spondyloarthritis without Psoriasis

Background Axial involvement in Psoriatic Arthritis (PsA) is reported to be between 40 -70% 1 . We aimed to compare the disease characteristics and quality of life (QoL) in patients with PsA with axial involvement (PsAax), PsA with only peripheral disease without axial involvement (PsApr), and axial spondyloarthritis patients without psoriasis (axSpA). Objectives To compare the disease characteristics and quality of life (QoL) in patients with PsAax, PsApr, and axSpA Methods Patients seen at Oregon Health & Sciences University with new diagnosis of PsAax between 2007 and 2012 were identified by searching electronic medical records. Age and sex matched patients with PsApr (polyarticular arthritis) and axSpA without psoriasis were identified. Demographic and clinical data was collected retrospectively. Disease activity and QoL was measured using validated measures like RAPID 3 and BASDAI. Statistical significance was estimated using Mann-Whitney, Chi square and Fisher9s exact tests as applicable. Results Twenty eight patients with PsAax were compared to age and sex matched patients with PsApr (n=26) and axSpA without psoriasis (n=29) respectively. Mean age, disease duration, BMI, BASDAI and RAPID 3 scores were similar among three groups (see Table). Smokers were more prevalent in axSpA than PsAPr patients (p=0.05). PsAax patients had more peripheral arthritis compared to axSpA patients (p=0.01 for both). Uveitis was significantly more prevalent in axSpA than the other 2 groups. Prevalence of depression was more in patients with psoriasis (PsAax and PsApr (about 40%)) compared to axSpA (24%) but did not reach statistical significance. Prevalence of fibromyalgia, inflammatory bowel disease, mean ESR and CRP were similar in all three groups. More patients in axSpA group used NSAIDs compared to PsAax group (p=0.05). DMARDs were used more often in patients with PsAax (p=0.01) and PsApr (p=0.01) than in axSpA. TNF blockers were used more often in PsAax than in axSpA group (p=0.03). Conclusions In this comparative study between PsA patients with axial and peripheral disease and axSpA patients without psoriasis, PsAax patients had higher prevalence of peripheral arthritis compared to those with axSpA alone. Uveitis was less prevalent in PsAax and PsApr compared to axSpA patients. Depression was more prevalent in patients with psoriasis suggesting an important impact on QoL related to skin disease. References Hanly JG, Russell ML, Gladman DD (1988) Psoriatic spondyloarthropathy: a long term prospective study. Ann Rheum Dis 47:386–393 Disclosure of Interest None declared DOI 10.1136/annrheumdis-2014-eular.1322
Hardware-Based Malware Detection Using Low-Level Architectural Features

Security exploits and ensuant malware pose an increasing challenge to computing systems as the variety and complexity of attacks continue to increase. In response, software-based malware detection tools have grown in complexity, thus making it computationally difficult to use them to protect systems in real-time. Therefore, software detectors are applied selectively and at a low frequency, creating opportunities for malware to remain undetected. In this paper, we propose Malware-Aware Processors (MAP)—processors augmented with a hardware-based online malware detector to serve as the first line of defense to differentiate malware from legitimate programs. The output of this detector helps the system prioritize how to apply more expensive software-based solutions. The always-on nature of MAP detector helps protect against intermittently operating malware. We explore the use of different features for classification and study both logistic regression and neural networks. We show that the detectors can achieve excellent performance, with little hardware overhead. We integrate the MAP implementation with an open-source x86-compatible core, synthesizing the resulting design to run on an FPGA.