cssi/SciSciGPT-SciSciNet huggingface dataset:
Expansive arterial remodeling is associated with increased neointimal macrophage foam cell content: the murine model of macrophage-rich carotid artery lesions.

Background— Recent observations associate plaque instability with expansive arterial remodeling, suggesting a common driving mechanism. Methods and Results— To demonstrate that macrophages, a characteristic of vulnerable plaques, also assist in expansive remodeling, we compared carotid artery remodeling due to formation of experimental macrophage-rich and macrophage-poor lesions in the flow cessation model in hypercholesterolemic apolipoprotein E knockout (ApoE KO) and wild type (WT) mice. After ligation, macrophages started to rapidly accumulate in ApoE KO but not in WT carotid artery lesions. Macrophage-rich ApoE KO intimal lesions grew fast, typically occluding within 14 days, despite a tripling of the vessel area. Outward remodeling of macrophage-rich ApoE KO arteries positively correlated with macrophage area (r2=0.600, P<0.001). To investigate potential mechanisms of macrophage-enabled expansive remodeling, we compared levels of matrix metalloproteinases in homogenates of macrophage-rich and macroph...
Deep-Focus Earthquakes.

MR. F. J. SCRASE1 has recently found confirmation of the great depth assigned to certain earthquakes by the late Prof. H. H. Turner by recognising, in the data of the International Seismological Summary, the two separate branches of PR1 and SR1 that are to be expected if the focus be deep, and by observing the substantial agreement of their travel-times with the expected times calculated on the basis of the Zoeppritz-Turner tables. It may be of value to note in this connexion that we may, by the use of these reflected pulses, arrive at what is certainly a minimum value of the depth of focus, and this independently of any previous travel-time tables and even of any error in the assumed time of origin. This would eliminate any objection that might possibly be made to the use of the Zoeppritz-Turner tables.
The effect of the Transcendental Meditation technique on anxiety level.

Two weeks of twice-daily practice of the Transcendental Meditation (TM) technique was compared with 2 weeks of twice-daily practice of passive relaxation as a means of reduction of anxiety, as measured by the Trait scale of the State-Trait Anxiety Inventory. Thirty-three graduate and undergraduate students were assigned randomly to a relaxation group and a TM group. After a 2-week experimental interval, the relaxation Ss began TM. As hypothesized, in the comparison between the relaxation and meditation Ss, as well as between conditions of the relaxation-meditation group, TM was significantly more effective in reducing anxiety level. Thus, the anxiety-reducing effect of the practice of TM cannot be attributed merely to sitting quietly twice daily, although additional research must determine the extent to which S expectations for change contributed to this effect.
Beyond self-interest

A dramatic transformation has begun in the way scholars think about human nature. Political scientists, psychologists, economists, and evolutionary biologists are beginning to reject the view that human affairs are shaped almost exclusively by self-interest-a view that came to dominate social science in the last three decades. In "Beyond Self-Interest," leading social scientists argue for a view of individuals behavior and social organization that takes into account the powerful motivations of duty, love, and malevolence. Economists who go beyond "economic man," psychologists who go beyond stimulus-response, evolutionary biologists who go beyond the "selfish gene," and political scientists who go beyond the quest for power come together in this provocative and important manifesto. The essays trace, from the ancient Greeks to the present, the use of self-interest to explain political life. They investigate the differences between self-interest and the motivations of duty and love, showing how these motivations affect behavior in "prisoners' dilemma" interactions. They generate evolutionary models that explain how altruistic motivations escape extinction. They suggest ways to model within one individual the separate motivations of public spirit and self-interest, investigate public spirit and self-interest, investigate public spirit in citizen and legislative behavior, and demonstrate that the view of democracy in existing Constitutional interpretations is not based on self-interest. They advance both human evil and mothering as alternatives to self-interest, this last in a penetrating feminist critique of the "contract" model of human interaction.
Vacuolar Protein in Apical and Flower-Petal Cells*

Vegetative apices, floral apices and flower petals of five Solanaceae (potato, tomato, tobacco, petunia and nightshade) and of corn and Nigella were examined with an electron microscope for the presence of protein bodies in the cell vacuoles. Electron-dense bodies were found in vacuoles of all plants investigated but not in every tissue examined. The bodies observed in the apices are similar to the protein bodies previously found in tomato leaves where they appear to be related to the presence of chymotrypsin inhibitor I protein (Shumway et al., 1970). The bodies appeared in very young cells in small vacuoles, disappearing as the cell matured. They are apparently related to the growth and development of the new cells. The results suggest that plants may regulate specific proteins within the apical region through selective synthesis and degradation of proteins accompanied by compartmentalization in the vacuole.
Relationship of incident glaucoma versus physical activity and fitness in male runners.

Purpose To assess the dose–response relationship of vigorous physical activity (running distance, km/d) or cardiorespiratory fitness (meters-per-second pace during a 10-km footrace) to the risk for incident glaucoma.
Whatever happened to the Kuznets curve? Is it really upside down?

Abstract Kuznets (1955) embarked on a research program whose goal was to find the determinants of the long run levels and trends in income inequality and the relationship between income inequality and economic growth. Recently a small body of theoretical work has developed which tries to obtain the inverted U hypothesis as an equilibrium outcome in dynamic general equilibrium model. One of the types of general equilibrium models which can deliver a Kuznets curve is a model which allows for persistent migration out of one sector, e.g. agriculture, into another—e.g., manufacturing. Most industrialized countries have not only experienced shifts from agriculture to manufacturing, but also into services, especially associated with information technologies. This is responsible for the rise in inequality. If such a model of the arrival of new opportunities is correct, we would not expect to find a Kuznets curve, right side up or up-side down. Here we review the empirical evidence regarding the Kuzuets curve.
The synthesis and reactions of Mn and Re formyl complexes, fac-(PP)M(CO)3CHO. The X-ray structure of fac-(dppp)Mn(CO)3CH2OCH3

Abstract Treatment of the salts fac -[(PP)M(CO) 4 ][BF 4 ] (M = Mn, Re; PP = dppe, dppp) with NaBH 4 gives the corresponding formyl complexes, fac -(PP)M(CO) 3 CHO in excellent yield. Solutions of these formyls undergo spontaneous loss of CO to give the corresponding hydrides, fac -(PP)M(CO) 3 H. On treatment with methyl triflate or protic acids the formyls undergo expected disproportionation reactions; the X-ray crystal structure determination of one of the products, fac -(dppp)Mn(CO) 3 CH 2 OCH 3 , is reported.
Optical lifetime measurements using a positive ion van de graaff accelerator.

A system for direct observation of excited state optical mean lives using the delayed coincidence counting technique is described. The system uses a pulsed proton beam for excitation, a high speed time-to-amplitude converter and an on-line digital computer for data reduction. Mean lives longer than 1 nsec can be measured. Preliminary measurements on the 31P, 43S, and 41D levels of helium and several vibrational bands of N2 are presented to illustrate the capabilities of the system.
Ischemic arm pain and nonnarcotic analgesics

Abstract A modification of the ischemic muscle technique has been developed and utilized for comparative studies of nonnarcotic analgesics and several combinations of these agents. These studies may be summarized as follows: 1. 1. Of the agents or combinations tested, acetylsalicylic acid is the most potent both in individual subjects and in the group as a whole. 2. 2. Acetophenetidine alone, while effective in some individuals, is not effective in the group, i.e., in the average individual. 3. 3. Caffeine added to a mixture of analgesic agents lessens their pain threshold-raising ability. 4. 4. A minority group of the subjects (4 of 18) studied showed some degree of just the opposite effects, i.e., a significant lowering of threshold.
Longitudinal measures of perfluoroalkyl substances (PFAS) in serum of Gullah African Americans in South Carolina: 2003-2013

Abstract Background Charleston Harbor has elevated concentrations of PFAS in dolphins, but local human exposure data are limited. Objectives We sought to describe PFAS serum concentrations’ temporal trends among Gullah African American residents of coastal South Carolina. Methods Longitudinal measures of PFAS in blood serum from a Gullah clinical sample, without lupus, were examined using spaghetti plots and visit-to-visit change scores (e.g., differences in concentrations between visits) among the 68 participants with repeated measures available. We also modeled population-level trends among the 71 participants with any data using proportionate percentile models, accounting for clustering through robust standard errors. In a post-hoc analysis we examined heterogeneity of temporal trends by age through mixed-effects models for the log-transformed PFAS compounds. Results Population concentrations of PFOS dropped approximately 9 (95% CI: 8, 10) percent each year over 2003–2013. This was concordant with individual PFOS trajectories (median PFOS change score −21.7 ng/g wet weight, interquartile range of PFOS change scores: −32.8, −14.9) and reports for other populations over this time period. Several other compounds including PFOA, PFHxS, and PFuNDA also showed a population-level decrease. However, examination of individual trajectories suggested substantial heterogeneity. Post-hoc analyses indicated that PFAS trajectories were heterogeneous by age. Conclusions Many PFAS compounds are decreasing in a sample of Gullah African Americans from coastal South Carolina. There may be age differences in the elimination kinetics of PFASs. The possible role of age as a modifier of PFAS serum trends merits further research.
Quantization of Poisson SU(2)

In this paper, we describe and compare two different C*-algebraic deformation quantizations (in Rieffel’s sense [Rl, R2, R3]) of the ‘multiplicative’ Poisson structure on the Lie group SU(2), which are ‘compatible’ with Woronowicz’s C*-algebraic quantization [Wol, Wo2] of the group structure of SU(2) by pseudogroups (or quantum groups). Due to the space limitation, in this paper we only describe the results and leave their proof to a separate paper [Sh3].
Rooms in Common: Where Teaching and Learning Matter

The chapter details the creation of a new administrative space to coordinate a number of the fundamental practices of undergraduate education. The new Office of Undergraduate Education at the City University of New York (CUNY) brought together both faculty and administrators from the system’s 17 campuses to find ways to improve the quality of our undergraduate experience for its quarter of a million students. Under one organizational umbrella, called the Coordinated Undergraduate Education (CUE) Initiative, I was able to combine a number of discrete long-standing system-wide initiatives and new projects. The goal of the CUE Initiative, as expressed on the University Web site, is “to provide students with a coherent and meaningful college experience, from the moment of admission through to graduation.
The Three Errors: Pathways to False Confession and Wrongful Conviction

Research has demonstrated that false confessors whose cases are not dismissed before trial are often convicted despite their innocence. In order to prevent such wrongful convictions, criminal justice officials must better understand the role that false confessions play in creating and perpetuating miscarriages of justice. This chapter examines police-induced false confessions and analyzes three sequential errors that occur in the social production of every false confession: investigators first misclassify an innocent person as guilty; they next subject him to a guilt-presumptive, accusatory interrogation that invariably involves lies about evidence and often the repeated use of implicit and/or explicit promises and threats as well; and once they have elicited a false admission, they pressure the suspect to provide a post-admission narrative that they jointly shape, often supplying the innocent suspect with the (public and nonpublic) facts of the crime. We refer to these as the misclassification error, the coercion error, and the contamination error. Additionally, at least three other processes – "misleading specialized knowledge," "tunnel vision," and "confirmation bias" – usually pave the way to a wrongful conviction by convincing all of the criminal justice actors to ignore the possibility that the confession is false. We analyze these processes in this chapter and conclude with recommendations designed to reduce false confessions and prevent false confessions from leading to wrongful convictions.
Fast Varying Loads

The operation of Fast Varying Loads (FVLs) in distribution systems is associated with high variation in the active power and bursts of distortion. FVLs affect surrounding loads sensitive to voltage rms variation and distortion. Thus they affect quality of the supply. This paper presents an overview of some electric loads that behave as FVLs. FVLs are characterized in this paper in terms of the main two properties that distinguish them from other electrical loads, namely, the active power variation and the contribution to the distortion. When a FVL is the major load in a distribution system, the power variation and the burst of waveform distortion could reach unacceptable levels. Thus, compensation could be necessary. The requirements for this compensation are also presented in this paper.
Comparison of Inhaled Corticosteroids

OBJECTIVE:To review the comparative studies evaluating both efficacy and safety of inhaled corticosteroids in the management of asthma. Specifically, comparative clinical trials are evaluated that allow clinicians to determine relative potencies of the various inhaled corticosteroids.METHODS:A critical review was performed of the published clinical trials, either as articles or abstracts, comparing the clinical efficacy or systemic activity of inhaled corticosteroids. No a priori criteria were applied, as this was not a meta-analysis.FINDINGS:In vitro measures of antiinflammatory activity of corticosteroids consistently demonstrate potency differences among the various corticosteroids. Traditionally, these in vitro measures have been used to develop new corticosteroids with greater topical activity. While no accepted direct measure of antiasthmatic antiinflammatory activity exists, clinical trials using surrogate measures (e.g., forced expiratory volume in 1 second, peak expiratory flow, bronchial hyperre...
Correlations of xanthophylls in catfish fillets, plankton, shad and snails in catfish production ponds in west Alabama

article i nfo Yellow coloration of catfish fillets has always been a problem. Recently increased consumer scrutiny has brought this to the forefront as a major industry concern. As catfish cannot synthesize xanthophyll, commer- cial feeds and natural prey items are the initial sources of the yellow color. To better understand the contri- bution of natural foods, a field study was conducted to identify if there were correlations of yellow fillet and natural productivity under commercial pond conditions. Upon notification from a west Alabama fish proces- sor, yellow catfish fillets and natural organism samples (plankton, shad and snails) were collected from dif- ferent farm ponds in west Alabama. "Clean" catfish fillets (no unacceptable yellow coloration) and natural organisms were also collected at multiple farms where problematic yellow fillets were not present. In addi- tion to large food items, microorganism samples from the ponds were collected by pumping pond water through two filters (sizes 20 μm and 75 μm) for a period of 10 min. The fillet and field samples were analyzed quantitatively for xanthophyll levels through High-Pressure Liquid Chromatography (HPLC). Results revealed a correlation between xanthophyll level in catfish fillets and in microorganisms (>75 μm). Results indicate that natural productivity consumed by gizzard shad and other filter feeders appears to contribute to the xan- thophyll levels in catfish fillets. Published by Elsevier B.V.
A Transcriptional Regulatory Role of the THAP11–HCF-1 Complex in Colon Cancer Cell Function

The recently identified Thanatos-associated protein (THAP) domain is an atypical zinc finger motif with sequence-specific DNA-binding activity. Emerging data suggest that THAP proteins may function in chromatin-dependent processes, including transcriptional regulation, but the roles of most THAP proteins in normal and aberrant cellular processes remain largely unknown. In this work, we identify THAP11 as a transcriptional regulator differentially expressed in human colon cancer. Immunohistochemical analysis of human colon cancers revealed increased THAP11 expression in both primary tumors and metastases. Knockdown of THAP11 in SW620 colon cancer cells resulted in a significant decrease in cell proliferation, and profiling of gene expression in these cells identified a novel gene set composed of 80 differentially expressed genes, 70% of which were derepressed by THAP11 knockdown. THAP11 was found to associate physically with the transcriptional coregulator HCF-1 (host cell factor 1) and recruit HCF-1 to target promoters. Importantly, THAP11-mediated gene regulation and its chromatin association require HCF-1, while HCF-1 recruitment at these genes requires THAP11. Collectively, these data provide the first characterization of THAP11-dependent gene expression in human colon cancer cells and suggest that the THAP11–HCF-1 complex may be an important transcriptional and cell growth regulator in human colon cancer.
Weaving Interventions into the Fabric of Everyday Life An Approach to Family Assessment

In response to legislative mandates, the focus in early childhood special education has shifted from the child to the child in the context of the family. This shift has major implications for assessment as well as for intervention. In this article we describe an ecocultural approach for assessing families of young children with developmental problems. It is an approach that has grown out of empirical work and that we believe has clinical utility in designing interventions for young children and their families.
Dealing with Uncertainty in Agent-Based Simulation: Farm-Level Modeling of Adaptation to Climate Change in Southwest Germany

Climate change will most likely confront agricultural producers with natural, economic, and political conditions that have not previously been observed and are largely uncertain. As a consequence, extrapolation from past data reaches its limits, and a process-based analysis of farmer adaptation is required. Simulation of changes in crop yields using crop growth models is a first step in that direction. However, changes in crop yields are only one pathway through which climate change affects agricultural production. A meaningful process-based analysis of farmer adaptation requires a whole-farm analysis at the farm level. We use a highly disaggregated mathematical programming model to analyze farm-level climate change adaptation for a mountainous area in southwest Germany. Regional-level results are obtained by simulating each full-time farm holding in the study area. We address parameter uncertainty and model underdetermination using a cautious calibration approach and a comprehensive uncertainty analysis. We deal with the resulting computational burden using efficient experimental designs and high-performance computing. We show that in our study area, shifted crop management time slots can have potentially significant effects on agricultural supply, incomes, and various policy objectives promoted under German and European environmental policy schemes. The simulated effects are robust against model uncertainty and underline the importance of a comprehensive assessment of climate change impacts beyond merely looking at crop yield changes. Our simulations demonstrate how farm-level models can contribute to a process-based analysis of climate change adaptation if they are embedded into a systematic framework for treating inherent model uncertainty.
Research in the Ranks: Vulnerable Subjects, Coercible Collaboration, and the Hepatitis E Vaccine Trial in Nepal

Concern over the diminished autonomy of members of the armed forces has resulted in the classification of these groups as "vulnerable" in many international codes of research ethics, a designation that places the onus on researchers to provide special justification for the inclusion of these persons in research. This paper examines the application of these ethical requirements to a recent trial carried out by U.S. Army researchers among soldiers of the Royal Nepal Army (RNA) and concludes that the requirements to justify conducting research in this population were not met. Furthermore, noting the human rights abuses rampant in the RNA, it is appropriate to question the choice of this institution as both a partner and a subject pool for U.S. state-sponsored research. This case study raises another important ethical question about the vulnerability to coerced collaboration of groups or institutions. In response, I propose the idea of "institutional vulnerability" as an extension of the idea of individual "juridic vulnerability." The recent military and financial assistance that the RNA received from the U.S. Army, in light of their partnership in this biomedical research trial, constitutes an appropriate and revealing context in which to ground this discussion.
Applying Model Management to Classical Meta Data Problems

Model management is a new approach to meta data management that offers a higher level programming interface than current techniques. The main abstractions are models (e.g., schemas, interface definitions) and mappings between models. It treats these
Age-associated memory impairment is associated with greater rate of longitudinal brain atrophy

N 105 203 159 98 63 116 85 Age in years 75.7 (5.2) 75.4 (7.3) 74.5 (7.0) 71.1 (7.3) 76.8 (5.7) 75.1 (6.6) 78.0 (7.1) <0.0001 Gender % male 51% 66% 60% 58% 83% 54% 69% <0.0001 Converters % 38% 48% 36% 59% 0.01 ApoE4 carrier % 20% 45% 69% 59% 46% 53% 61% 0.2 MMSE 29.1 (1.0) 27.2 (1.8) 26.7 (1.7) 27.2 (1.8) 26.9 (1.8) 27.1 (1.9) 26.6 (1.6) 0.2 CSF biomarkers Tau (baseline) y 69 (28) 93 (54) 114 (53) 92 (46) 80 (38) 110 (57) 119 (63) 0.01 P-tau (baseline) y 24 (13) 31 (17) 41 (17) 34 (18) 29 (13) 39 (18) 38 (18) 0.02 Abeta1-42 (baseline) y 209 (54) 175 (59) 145 (40) 166 (61) 156 (49) 166 (53) 154 (50) 0.6
Why can insulin resistance be a natural consequence of thyroid dysfunction

Evidence for a relationship between T4 and T3 and glucose metabolism appeared over 100 years ago when the influence of thyroid hormone excess in the deterioration of glucose metabolism was first noticed. Since then, it has been known that hyperthyroidism is associated with insulin resistance. More recently, hypothyroidism has also been linked to decreased insulin sensitivity. The explanation to this apparent paradox may lie in the differential effects of thyroid hormones at the liver and peripheral tissues level. The purpose of this paper is to explore the effects of thyroid hormones in glucose metabolism and analyze the mechanisms whereby alterations of thyroid hormones lead to insulin resistance.
Nonlinear wave equations for numerical relativity: towards the computation of gravitational wave forms of black hole binaries

The prime candidate of LIGO/VIRGO sources of gravitational waves is the spiral in of black holes and neutron stars in compact binaries. While the early stages of the evolution of compact binaries is computable from post-Newtonian calculations, prediction of their late stages requires large scale numerical simulation. A fully covariant and strictly hyperbolic formulation for numerical relativity is described, and illustrated in a one-dimensional computation of a Gowdy-wave on the three-torus. This formulation allows foliations in full generality, in particular it poses no restriction on the lapse function.
Paleoshoreline patterns in the transgressive-regressive sequences of Pennsylvanian rocks in the northern Appalachian Basin, U.S.A.

Abstract Sheets of sponge spicule flint of Pennsylvanian age (Bashkirian, Moscovian, Kasimovian) that are present in the northern Appalachian Basin of Ohio and adjacent parts of Kentucky, Pennsylvania and West Virginia, are important indicators of paleoshorelines. This flint typically occurs with or occupies the position normally held by shallow-water limestone and contains a normal marine fauna. The flint was deposited above coal or underclay, representing the detritus-starved marine portion of a transgressive-regressive sequence and marking the eastern limit of transgression across a westward-spreading alluvial plain. Flint occurs at several stratigraphic positions in the upper Pottsville-lower Conemaugh interval. The most important are: Boggs, Upper Mercer and Kanawha flints of the upper Pottsville Group; Kilgore-Flint Ridge, Zaleski and Vanport flints of the lower Allegheny Group; and Brush Creek flint of the lower Conemaugh Group. Lithofacies maps of these beds were constructed to show the distribution of the flint. Limestone-hosted flint occurs in long discontinuous chains of sheetlike bodies, whereas shale-hosted flint occurs in single sheets with restricted geographic distribution. Chains of limestone-hosted flint attain maximum dimensions of a few meters in thickness, a few kilometers in width and several hundreds of kilometers in length. The Upper Mercer, Vanport and Brush Creek flints are particularly extensive, forming arcuate shoreline patterns that parallel the fronts of large delta systems. Beds of clay ironstone and/or coal above flint indicate that the lagoonal environment in which flint was deposited was followed closely by a change to stagnant waters. Cementation of flint with silica likely occurred under the lower pH conditions existing at that time and when depths of burial were shallow.
Optimizing collective communications on SMP clusters

We describe a generic programming model to design collective communications on SMP clusters. The programming model utilizes shared memory for collective communications and overlapping inter-node/intra-node communications, both of which are normally platform specific approaches. Several collective communications are designed based on this model and tested on three SMP clusters of different configurations. The results show that the developed collective communications can, with proper tuning, provide significant performance improvements over existing generic implementations. For example, when broadcasting an 8 MB message our implementations outperform the vendor's MPl/spl I.bar/Bcast by 35% on an IBM SP system, 51% on a G4 cluster, and 63% on an Intel cluster, the latter two using MPICH's MPl/spl I.bar/Bcast. With all-gather operations using 8 MB messages, our implementation outperform the vendor's MPI/spl I.bar/Allgather by 75% on the IBM SP, 60% on the Intel cluster, and 48% on the G4 cluster.
VaWiRAM: a variable width random access memory module

Presents the design of a variable width RAM (VaWiRAM) which will be extremely useful in building flexible memory systems. Principles of reconfigurability of programmable logic and programmable interconnect is incorporated into random access memories to achieve this flexibility. The chip can be reconfigured by setting a few configuration pins on the memory chip. A VaWiRAM reconfigurable between widths 1 and W/sub max/ can be constructed with the extra cost of W/sub max/-1 pass gates, W max/2- to -1 multiplexers, and [log/sub 2/[log/sub 2/(k)+1]] mode pins. The paper discusses the architecture of the proposed VaWiRAMs, and analyzes the trade-offs in their design.
Variability of Irradiation Creep and Swelling of HT9 Irradiated to High Neutron Fluence at 400–600°C

Sets of pressurized tubes constructed from a combination of three lots of HT9 and two heat-treatments were examined after irradiation in FFTF-MOTA at four different temperatures between 400 and 600 C. Diametral measurements indicated that small amounts of swelling occurred at 400 C, with the magnitude of the swelling varying from tube-set to tube-set. At 495, 550, and 600 C, no indications of swelling were observed. Over a limited stress range that decreased with increasing irradiation temperature, the irradiation creep was found to be proportional to the stress level and mirrored the swelling behavior, confirming the B{sub o} + D{dot S} creep model. The creep compliance, B{sub o}, appears to be about half of that observed in austenitic steels, whereas the creep-swelling coupling coefficient, D, appears to be comparable to that of austenitics. At the highest stress levels examined, the value of the stress exponent became much greater than 1.0. Higher irradiation temperatures resulted in creep behavior with pronounced thermal creep characteristics. A primary creep transient was observed at the three higher irradiation temperatures and increased in magnitude with increasing irradiation temperature, while a stress exponent between 1.0 and 2.0 was observed at 550 C.
Generalized random set framework for functional enrichment analysis using primary genomics datasets

Motivation: Functional enrichment analysis using primary genomics datasets is an emerging approach to complement established methods for functional enrichment based on predefined lists of functionally related genes. Currently used methods depend on creating lists of ‘significant’ and ‘non-significant’ genes based on ad hoc significance cutoffs. This can lead to loss of statistical power and can introduce biases affecting the interpretation of experimental results. Results: We developed and validated a new statistical framework, generalized random set (GRS) analysis, for comparing the genomic signatures in two datasets without the need for gene categorization. In our tests, GRS produced correct measures of statistical significance, and it showed dramatic improvement in the statistical power over other methods currently used in this setting. We also developed a procedure for identifying genes driving the concordance of the genomics profiles and demonstrated a dramatic improvement in functional coherence of genes identified in such analysis. Availability: GRS can be downloaded as part of the R package CLEAN from http://ClusterAnalysis.org/. An online implementation is available at http://GenomicsPortals.org/. Contact: mario.medvedovic@uc.edu Supplementary information:Supplementary data are available at Bioinformatics online.
Beta-catenin activation promotes liver regeneration after acetaminophen-induced injury.

Acute liver failure (ALF) remains a disease with poor patient outcome. Improved prognosis is associated with spontaneous liver regeneration, which supports the relevance of exploring ‘regenerative’ therapies. Therefore, the role of the Wnt/β-catenin pathway in liver regeneration following ALF was investigated. ALF was induced in mice by acetaminophen overdose, which is also a leading cause of liver failure in patients. β-catenin distribution was also studied in liver sections from acetaminophen-induced ALF patients. A nonlethal dose of acetaminophen, which induces liver regeneration, led to stabilization and activation of β-catenin for 1 to 12 hours. These data were also verified by increased expression of the β-catenin surrogate target glutamine synthetase. β-Catenin activation occurred secondary to the inactivation of glycogen synthase kinase-3β and an increase in levels of casein kinase 2α, and led to increased cyclin-D1, another known β-catenin target. These observations were next substantiated in β-catenin conditional-null mice (β-catenin-null), which show dampened regeneration after acetaminophen injury following induction of CYP2e1/1a2 expression. In light of decreased acetaminophen injury in β-catenin-null mice despite CYP induction, equitoxic studies in control mice were performed. Significant differences in regeneration persisted following comparable injury in β-catenin-null and control animals. Retrospective analysis of liver samples from acetaminophen-overdose patients demonstrated a positive correlation between nuclear β-catenin, proliferation, and spontaneous liver regeneration. Thus, our studies demonstrate early activation of β-catenin signaling during acetaminophen-induced injury, which contributes to hepatic regeneration.
A fast CRAM SEU error detection scheme for FPGAs

This paper proposes a scheme that can detect SEU errors occurring in an FPGA configuration SRAM cell (CRAM) in a time-efficient manner (>40X faster or &#60;2 ms). The concept and design implementation of the proposed scheme is described in detail. This is a low-cost solution as most of the implementation reuses existing circuits. In addition, the benefits of the proposed schemes are discussed.
Draft Genome Sequence of the Marine Pathogen Vibrio coralliilyticus RE22.

ABSTRACT Vibrio coralliilyticus RE22 is a causative agent of vibriosis in larval bivalves. We report here the draft genome sequence of V. coralliilyticus RE22 and describe additional virulence factors that may provide insight into its mechanism of pathogenicity.
Hydraulics of Psilophyton and evolutionary trends in plant water transport after terrestrialization

Mathematical models of fluid flow through and embolism resistance of extinct plant xylem provide insight into the ecology and physiology of individual fossil plants. Disparate lineages of vascular plants exhibit a variety of ecophysiological strategies: extreme adaptations for maximum flow and maximum safety have both been documented in living and extinct plants. Analysis of early-diverging vascular plants and early-diverging seed plants shows that a variety of hydraulic strategies were pursued early in the evolution of terrestrial plants, especially during the Devonian and Carboniferous Periods. Analysis of five species of the Lower and Middle Devonian trimerophyte genus Psilophyton indicates that some species possess low-resistance metaxylem tracheids with numerous, highly porous pits and relatively low embolism resistance, whereas other species contain xylem with higher embolism resistance and lower hydraulic conductivity. Despite a simple vegetative morphology, physiological analysis of several Psilophyton fossils suggests that species possessed distinct ecophysiological strategies and there may be cryptic functional diversity within other trimerophyte genera. When integrated with previous hydraulic analyses of extinct and extant plants, including the Lower Devonian stem group lycophyte Asteroxylon mackiei; a series of Carboniferous stem group seed plants, including Medullosa, Callistophyton, and Lyginopteris; eleven genera of extant conifers and cycads; two species of ginkgophytes, and others, the occupation of tracheid-based hydraulic ecospace can be mapped. Soon after the evolution of vascular tissue in land plants, the high-conductivity/low-safety-margin space was occupied; particularly by plants that grew in the tropical lowland swamps during the Carboniferous Period. Upon the disappearance of the coal swamp floras during the Permian Period, that portion of the ecospace may have remained unoccupied until the evolution of angiosperms with vessels in the Cretaceous Period. Taken as a whole, the evolution of vascular tissue during (and after) the terrestrialization process records several physiological adaptive radiations, occurring early in plant evolution, which likely had major effects on global environmental and biogeochemical processes.
Predictors of acute toxicities during definitive chemoradiation using intensity-modulated radiotherapy for anal squamous cell carcinoma

Purpose. To identify clinical and dosimetric factors associated with acute hematologic and gastrointestinal (GI) toxicities during definitive therapy using intensity-modulated radiotherapy (IMRT) for anal squamous cell carcinoma (ASCC).Materials and methods. We retrospectively analyzed 108 ASCC patients treated with IMRT. Clinical information included age, gender, stage, concurrent chemotherapy, mitomycin (MMC) chemotherapy and weekly hematologic and GI toxicity during IMRT. From contours of the bony pelvis and bowel, dose-volume parameters were extracted. Logistic regression models were used to test associations between toxicities and clinical or dosimetric predictors.Results. The median age was 59 years, 81 patients were women and 84 patients received concurrent MMC and 5-fluorouracil (5FU). On multivariate analysis (MVA), the model most predictive of Grade 2 + anemia included the maximum bony pelvis dose (Dmax), female gender, and T stage [p = 0.035, cross validation area under the curve (cvAUC) = 0.66...
Long-Term Neurocognitive Functioning and Social Attainment in Adult Survivors of Pediatric CNS Tumors: Results From the St Jude Lifetime Cohort Study

PurposeTo assess the prevalence and severity of neurocognitive impairment in adult survivors of pediatric CNS tumors and to examine associated treatment exposures.Patients and MethodsParticipants included 224 survivors of CNS tumors who were treated at St Jude Children's Research Hospital (current median age [range], 26 years [19 to 53 years]; time from diagnosis, 18 years [11 to 42 years]) and completed neurocognitive testing. Information on cranial radiation therapy (CRT) doses and parameters of delivery were abstracted from medical records. The prevalence of severe impairment (ie, at least two standard deviations below normative mean) was compared across radiation treatment groups (no CRT, focal irradiation, craniospinal irradiation) using the χ2 test. Log-binomial models were used to estimate risk ratios (RRs) and corresponding 95% CIs for severe impairment.ResultsIn multivariable models, craniospinal irradiation was associated with a 1.5- to threefold increased risk of severe impairment compared with...
Oil-spill forensics using two-dimensional gas chromatography: Differentiating highly correlated petroleum sources using peak manifold clusters

Petroleum forensics for apportioning the environmental impact of oil spills necessitate quantitative differentiation between highly correlated biomarker distributions of neighboring oil sources. (GC × GC) generates high-resolution images that represent the complex hydrocarbon peak profiles of these petroleum biomarkers. As such, source differentiation reduces to the complex challenge of disambiguating the source-specific biomarker peak profile against strong regional commonalities, which are challenging to decorrelate using statistical techniques. We propose signal processing innovations that enhance recent methods in petroleum fingerprinting to achieve quantitative source differentiation. Specifically, we propose three related techniques: Peak topography maps; Peak Manifold clustering techniques; and Baseline interference mitigation.
Dependency of Indium Concentration on Structural Defects in MOVPE-grown InGaN/GaN Heterostructures

Indium Gallium Nitride (InxGa1-xN) alloys are currently playing an ever increasing role in optoelectronic devices as the bandgap of such alloys can theoretically be tuned between 0.7eV and 3.4eV—covering the entire visible spectrum. Although growth of high quality InxGa1-xN alloys with high indium mole fractions are difficult or presently unattainable, InGaN alloys are still a viable choice for light emitters and detectors over the visible (blue/green) to ultraviolet spectrum. However, many inherent problems during InGaN growth via Metal Organic Vapor Phase Epitaxy (MOVPE) arise due to the large lattice mismatch and low miscibility between GaN and InN-leading to the formation of Inverted Hexagonal Pyramid (IHP) defects at the termination of threading dislocations. Additionally, growth of InGaN at lower temperatures to promote increased indium incorporation results in poor surface morphology. Several methods such as strained layer superlattices and low mole fraction InGaN layers before the growth of the InGaN/GaN MQW structures have been shown to relive strain in the MQWs, thus reducing the density of IHP defects and/or improving the optical output characteristics. This work focuses on the application of GaN monolayer insertions during InGaN quantum well growth via Metal Organic Vapor Phase Epitaxy (MOVPE) as a means to reduce the IHP defect density and passivate effects on surface roughness while observing variations in indium concentration. Observations include the reduction of IHP defect density by nearly twofold as the number of GaN monolayer interruptions increase from zero to three while sustaining only slightly lower effective indium concentrations.
Bollworms and Tobacco Budworms: Mating of Adults at Three Locations in the Mississippi Delta

When adult bollworms, Heliothis zea (Boddie), and tobacco budworms, H. virescens (F.), were collected over a 2-year period in insect traps equipped with blacklight lamps at 3 locations (north, central, and south) in the Mississippi Delta, a high percentage of the bollworm catch at each location was males. A higher percentage of mated females occurred at the locations that had a higher percentage of males. An average of one or more spermatophores per female bollworm usually was found when the monthly collections consisted 55% or more males. Many of the females collected at each location were young unmated moths, but of those that had mated, the larger percentage had mated only and Similarly, the percentage of male tobacco budworm moths and the average number of spermatophores per mated female tobacco budworm moth were highest at the north location and decreased at the more southern locations.
BACULITIDS FROM THE SANTONIAN-MAESTRICHTIAN NANAIMO GROUP, BRITISH COLUMBIA, CANADA AND WASHINGTON STATE, USA

The ammonite fauna of the Upper Cretaceous (Santonian-Maestrichtian) Nanaimo Group of the Vancouver Island region includes six species of Baculites: B. bailyi Woods from the upper Santonian-lower Campanian Haslam Formation, B. chicoensis Trask from the lower Campanian Pender Formation, B. inornatus Meek from the middle Campanian part of the Cedar District For- mation, B. anceps pacificus Matsumoto and Obata and B. rex Anderson from the upper Campanian part of the Cedar District Formation, and B. occidentalis Meek from the upper Campanian part of the Cedar District Formation and upper Campanian to lower Maestrichtian Spray Formation. These species are assigned to two evolutionary lineages. One lineage, composed of B. bailyi, B. inornatus, B. anceps pacificus and B. occidentalis, is characterized by strongly phylloid septal sutures. The other, composed of B. chicoensis and B. rex, is characterized by normal lytoceratine septal sutures.
Two regulatory isozymes of glutamine synthetase from Bacillus caldolyticus, an extreme thermophile

Abstract Two glutamine synthetases (EC 6.3.1.2) have been purified to homogeneity from B. caldolyticus strain YTP, grown at 70° on a minimal, defined medium. The enzymes are virtually identical in size and molecular weight (12 sub-units of MW 50,000), but differ in their isoelectric points, electrophoretic mobility, net charge, inherent thermal stability, affinity for substrates, and activity responses to metal ions and pH. Of primary interest is the observation that the more acidic form (pI = 5.2), EI, is strongly feedback-regulated by certain amino acids derived from glutamine (Gly, L-Ala, L- and D-ser) but not by L-Glu or AMP, whereas the less acidic form (pI = 5.5), EII, is inhibited most strongly by L-Gln and AMP, but not by the above amino acids. Both enzymes are inhibited strongly by ADP, CTP, NAD, glucosamine-6-P, less strongly by nucleotide diphosphates and L-Trp, and are activated by nucleotide monophosphates other than AMP. These results suggest that overall regulation of glutamine synthetase by the full spectrum of end product metabolites derived from L-Gln is accomplished by regulatory isozymes in this extremely thermophilic organism.
Phylogenetic and taxonomic assessment of the endangered Cumberland bean, Villosa trabalis and purple bean, Villosa perpurpurea (Bivalvia: Unionidae)

Inadequate understanding of the phylogeography, taxonomy, and historical distribution of two critically imperiled freshwater mussels, Cumberland bean, Villosa trabalis, and purple bean, Villosa perpurpurea, has hindered management and recovery actions related to population restoration within their extant ranges. For more than 100 years, the purple-to-pink nacre of V. perpurpurea and white nacre of V. trabalis have been the only defining phenotypic characteristics used to distinguish each species. Genetic samples were analyzed from 140 individuals collected from 10 streams located in Virginia, Tennessee, and Kentucky, representing all known extant populations of each species. A 784-bp section of the mitochondrial DNA ND1 region was sequenced to assess the phylogeography and taxonomic validity of these taxa. Results of our phylogenetic analyses showed 100 % Bayesian posterior support for two distinct clades, one occurring in the Cumberland River basin and the other in the Tennessee River basin, separated by a mean genetic distance of 4 %. Mean genetic distances between haplotypes within each clade was <1 %. Among individuals from the Cumberland River basin, the nacre of shells was white to bluish-white, but in the Tennessee River basin, nacre graded from white to pink to dark purple; thus, nacre color is a variable and inconsistent character in nominal V. trabalis and V. perpurpurea occurring in the Tennessee River basin. Our data suggest that these morphologically similar species do not co-occur, as was previously believed. Instead, we conclude that the two species most likely share a common ancestor, but became isolated within each basin and experienced allopatric speciation. Updates to nomenclature, taxonomic placement, and recovery plans for the investigated species are needed.
In-Depth View of the Structure and Growth of SnO2 Nanowires and Nanobrushes

Strategic application of an array of complementary imaging and diffraction techniques is critical to determine accurate structural information on nanomaterials, especially when also seeking to elucidate structure–property relationships and their effects on gas sensors. In this work, SnO2 nanowires and nanobrushes grown via chemical vapor deposition (CVD) displayed the same tetragonal SnO2 structure as revealed via powder X-ray diffraction bulk crystallinity data. Additional characterization using a range of electron microscopy imaging and diffraction techniques, however, revealed important structure and morphology distinctions between the nanomaterials. Tailoring scanning transmission electron microscopy (STEM) modes combined with transmission electron backscatter diffraction (t-EBSD) techniques afforded a more detailed view of the SnO2 nanostructures. Indeed, upon deeper analysis of individual wires and brushes, we discovered that, despite a similar bulk structure, wires and brushes grew with different c...
HfO/sub 2/ and HfAlO for CMOS: thermal stability and current transport

This paper reports the thermal stability of HfO/sub 2/ with/without Al inclusion (based on XRD and leakage current data), and energy band diagrams for metal/HfO/sub 2//Si structures as well as associated current transport mechanisms (based on gate current characteristics at various temperatures).