cssi/SciSciGPT-SciSciNet huggingface dataset:
Generalized n-colorings of links

The notion of an (n, r)-coloring for a link diagram generalizes the idea of an n-coloring introduced by R. H. Fox. For any positive integer n the various (n, r)-colorings of a diagram for an oriented link l correspond in a natural way to the periodic points of the representation shift ΦZ/n(l) of the link. The number of (n, r)-colorings of a diagram for a satellite knot is determined by the colorings of its pattern and companion knots together with the winding number.
Euclid: An Open, Cross-Platform, Cloud Geometry Optimizer and Library

We present an open, cross-platform, cloud-scalable tool for architectural geometry optimization. Many existing tools for architectural geometry optimization are proprietary, implement slow algorithms such as genetic fitness, are limited to specific CAD software, or cannot take advantage of cloud computation. Here we present a new engine for architectural geometry optimization that provides solvers for problems such as integral curve generation, arrangement decomposition, surface fitting, and that is fast, multi-threadable, cloud scalable, and platform-independent. It will be freely distributed either as executables or as a standalone library that can be integrated into other applications. The tool is designed to allow real-time geometric analysis of complex architectural geomoetry problems on the cloud.
Structural Reforms in Latin America: What Has Been Reformed and How to Measure it (Updated Version)

This paper discusses the major changes that took place in the key areas of structural economic policy in Latin America between 1985 and 2009 and presents a set of indexes that attempt to measure how favorable trade, financial, tax, privatization and labor policies are for the free working of markets. On a scale from 0 to 1, the average index for all the countries and all the structural policy areas increased from 0. 39 in 1985 to 0. 6 at the end of the 1990s, and to 0. 65 at the end of the 2000s. The structural reforms have been far-reaching, especially in the trade and financial areas, and to a lesser extent in the areas of taxation and of infrastructure privatization. The indexes can be used to make comparisons over time between areas and between countries. However, they are not adequate for measuring structural policies in Argentina and Venezuela in the 2000s, since some of the heterodox policies that these countries have adopted are not covered by the indexes.
Emergency Department Tachypnea Predicts Transfer to a Higher Level of Care in the First 24 hours After ED Admission

Objectives: The authors hypothesized that vital sign abnormalities detected in the emergency department (ED) can be used to forecast clinical deterioration occurring within 24 hours of hospital admission. Methods: This was a retrospective case-control study performed after implementation of a hospitalwide rapid response team (RRT) system. Inclusion criteria for study patients consisted of age ‡ 18 years, admission to the general floor though the ED, and RRT activation and subsequent transfer to a higher level of care in the first 24 hours. Control patients were ‡18 years, were admitted to the floor though the ED, never required RRT or transfer to a higher level of care, and were matched to cases by risk of mortality. Multilevel logistic regression was used to model the odds of an adverse outcome as a function of race and sex, respiratory rate (RR), heart rate (HR), and systolic (sBP) and diastolic blood pressure (dBP) at time of transfer from the ED. Results: A total of 74 cases and 246 controls were used. RR (odds ratio [OR] = 2.79 per 10-point change, 95% confidence interval [CI] = 1.41 to 5.51) and to a lesser extent dBP (OR = 0.81, 95% CI = 0.67 to 0.97) contributed significantly to the odds of intensive care unit (ICU) or intermediate care transfer within 24 hours of admission; HR (OR = 1.15, 95% CI = 0.98 to 1.37) did not.
Life’s Duplicities: Sex, Death, and Valis

Is there a unifying principle in biology that can be deciphered from the structures of all the present day genomes? Can one hope to determine the general structure and organization of cellular information as well as elucidate the underlying evolutionary dynamics, by systematically exploring various statistical characteristics of the genomic and proteomic data at many levels? A large-scale software and hardware system, Valis, developed by NYU bioinformatics group, aims to do just that. We analyze word-frequency and domain family size distributions across various genomes, and the distribution of the potential “hot-spots” for segmental duplications in the human genome. We hypothesize and test, by computational analysis, that such a pattern is the result of a generic dominating evolution mechanism, ”evolution by duplication”, originally suggested by Susumu Ohno. We examine what implications these duplications may have in determining the translocations of male-biased genes from sex chromosomes, genome structure of sex chromosomes, copy-number fluctuations (amplifications of oncogenes and homozygous or homozygous deletions of tumor suppressor genes) in cancer genomes, etc. We examine, through our explorations with Valis, how important a role information technology is likely to play in elucidating biology at all levels.
How well do we understand quasi-elastic reactions at energies close to the barrier

In collisions between too heavy nuclei a wide spectrum of different reaction modes is observed covering the range from simple processes like elastic scattering to complicated multistep transfers and fusion. On the theoretical side heavy ion reactions are usually analyzed using models that were developed first for light ion induced reactions: the optical model for elastic scattering and the DWBA for more inelastic processes like transfer and inelastic scattering. Some of the assumptions going into these approximations, however, are not valid for heavy ion induced reactions. The region between fusion and quasi-elastic reactions is not well understood theoretically. This region is associated with deep inelastic collisions, which are complex multiparticle reactions involving transfer of several protons and neutrons. In this paper, the author discusses to what extent experiments in the field of quasi-elastic scattering are understood within the framework of various theoretical models and in what areas more work is needed.
Tight-binding based non-collinear spin model and magnetic correlations in iron

We have extended a first principles tight-binding total energy model to include magnetic correlations. We have tested the validity of the model against ab-initio calculations for bcc and fcc Fe. We find that our model can quantitatively describe the pressure dependence of magnetic moments and magnetization energy for bcc and fcc Fe. Moreover, in fcc Fe with increasing pressures it is able to capture the transitions from ferromagnetic to non-collinear spin to antiferromagnetic and finally to the non-magnetic state. PACS numbers: 71.55 Ak, 64.30 +t.
The Rising Rate of Rural Hospital Closures

Purpose Since 2010, the rate of rural hospital closures has increased significantly. This study is a preliminary look at recent closures and a formative step in research to understand the causes and the impact on rural communities. Methods The 2009 financial performance and market characteristics of rural hospitals that closed from 2010 through 2014 were compared to rural hospitals that remained open during the same period, stratified by critical access hospitals (CAHs) and other rural hospitals (ORHs). Differences were tested using Pearson's chi-square (categorical variables) and Wilcoxon rank test of medians. The relationships between negative operating margin and (1) market factors and (2) utilization/staffing factors were explored using logistic regression. Findings In 2009, CAHs that subsequently closed from 2010 through 2014 had, in general, lower levels of profitability, liquidity, equity, patient volume, and staffing. In addition, ORHs that closed had smaller market shares and operated in markets with smaller populations compared to ORHs that remained open. Odds of unprofitability were associated with both market and utilization factors. Although half of the closed hospitals ceased providing health services altogether, the remainder have since converted to an alternative health care delivery model. Conclusions Financial and market characteristics appear to be associated with closure of rural hospitals from 2010 through 2014, suggesting that it is possible to identify hospitals at risk of closure. As closure rates show no sign of abating, it is important to study the drivers of distress in rural hospitals, as well as the potential for alternative health care delivery models.
Preinstallation testing of TFTR long pulse ion sources correlated with reliability

The operational performance of the long-pulse ion sources (LPISs) installed and operated on the Tokamak Fusion Test Reactor (TFTR) neutral beam injection system has been compared with preinstallation test data. A direct correlation between unsatisfactory performance and/or failure and preinstallation test results can be made. Upon disassembly of the LPISs, causes for the failure were found. Improved cleaning processes and inspection procedures have been implemented. More stringent testing during the assembly phase and stricter acceptance criteria for preinstallation tests have helped avoid failures. The more stringent procedures are discussed, preinstallation test data is presented, and operational reliability is described. >
Applications of RNA minimum free energy computations

Several applications of RNA secondary structure energy minimization are surveyed, including a recent noncoding RNA gene finder. Keywords: RNA; energy minimization; applications; noncoding RNA gene finder
Abelian Chern-Simons theory with toral gauge group, modular tensor categories, and group categories

Classical and quantum Chern-Simons with gauge group $\text{U}(1)^N$ were classified by Belov and Moore in \cite{belov_moore}. They studied both ordinary topological quantum field theories as well as spin theories. On the other hand a correspondence is well known between ordinary $(2+1)$-dimensional TQFTs and modular tensor categories. We study group categories and extend them slightly to produce modular tensor categories that correspond to toral Chern-Simons. Group categories have been widely studied in other contexts in the literature \cite{frolich_kerler},\cite{quinn},\cite{joyal_street},\cite{eno},\cite{dgno}. The main result is a proof that the associated projective representation of the mapping class group is isomorphic to the one from toral Chern-Simons. We also remark on an algebraic theorem of Nikulin that is used in this paper.
Genomic signatures from DNA word graphs

Genomes have both deterministic and random aspects, with the underlying DNA sequences exhibiting features at numerous scales, from codons and cis-elements through genes and on to regions of conserved or divergent gene order. The DNA Words program aims to identify mathematical structures that characterize genomes at multiple scales. The focus of this work is the fine structure of genomic sequences, the manner in which short nucleotide sequences fit together to comprise the genome as an abstract sequence, within a graph-theoretic setting. A DNA word graph is a generalization of a de Bruijn graph that records the occurrence counts of node and edges in a genomic sequence. A DNA word graph can be derived from a genomic sequence generated by a finite Markov chain or a subsequence of a sequenced genome. Both theoretically and empirically, DNA word graphs give rise to genomic signatures. Several genomic signatures are derived from the structure of a DNA word graph, including an information-rich and visually appealing genomic bar code. Application of genomic signatures to several genomes demonstrate their practical value in identifying and distinguishing genomic sequences.
Phase I and pharmacokinetic study of etoposide phosphate by protracted venous infusion in patients with advanced cancer.

PURPOSEEtoposide has schedule-dependent cytotoxic activity, and clinical resistance may be overcome with prolonged low-dose therapy. Oral bioavailability is variable, and protracted intravenous administration is limited by water insolubility, which requires large infusion volumes. Etoposide phosphate (EP) is a water-soluble prodrug that is rapidly converted in vivo to etoposide, and may be administered in concentrated solution. A phase I study was conducted to determine the toxicity, pharmacokinetics, and pharmacodynamics of EP administered as a protracted venous infusion in the ambulatory setting.METHODSTwenty-three patients with advanced cancer were treated with a continuous infusion of EP using ambulatory pumps for 6 weeks followed by a 2-week rest. Cohorts were treated with EP at 10, 20, 25, and 30 mg/m2/d. Steady-state plasma etoposide levels (Css) and stability of EP in infusion pumps were measured using high performance liquid chromatography (HPLC).RESULTSMyelosuppression, mucositis, and fatigue we...
Self-Monitoring, Trust, and Commitment in Romantic Relationships

Abstract This study examined the relationship between self-monitoring and trust with a focus on commitment among college students in the United States. Both partners in 38 heterosexual dating couples filled out questionnaires that included the Self-Monitoring Scale (M. Snyder, 1974) and the Trust Scale (J. K. Remple, J. G. Holmes, M. P. Zanna, 1985). Findings indicated that there was a significant positive correlation between the self-monitoring scores of the dating partners. Those couples consisting of 2 high self-monitors were significantly less likely to believe that they would marry their current partners than couples that included at least 1 low self-monitor, and they scored significantly lower on the subscale of the Trust Scale that assessed continuing commitment to the relationship.
The inhibition of Listeria monocytogenes in milk by pediococci

Abstract Each of five strains of pediococci was tested in milk for its ability to control each one of four strains of Listeria monocytogenes. Four out of the five strains of pediococci were either bacteriostatic or bactericidal toward the pathogen. One of the strains of the pediococci did not control the growth of L. monocytogenes in milk. Pure cultures of the strains of L. monocytogenes in milk at 4·5 and 32°C attained populations of about log 10 9·0 cfu ml -1 after 6 and 4 days, respectively. Some of the pediococci not only prevented L. monocytogenes strains from attaining populations it would have in pure culture (P 4·0 log 10 cfu ml -1 . The Pediococcus strain PAC was the least antagonistic toward the strains of Listeria; while L. monocytogenes strain SA was the most resistant to the pediococcal action. The pH of the milk never dropped below 5·3, an indication that acid may have played a role in concert with other factors in the observed inhibition of Listeria.
Cytolytic activity of Ia-restricted T cell clones and hybridomas: Evidence for a cytolytic mechanism independent of interferon-γ, lymphotoxin, and tumor necrosis factor-α

Abstract Ten different helper T cell (Th) hybridomas that are specific to Ia or antigen plus Ia were found to express nonspecific cytolytic activity toward the cytotoxin (CT)-resistant P815 cells upon activation with either Con A or a monoclonal anti-T3 antibody (T3-mAb). In contrast to cytolytic Th1 clones which secrete high levels of interferon-γ (IFN-γ) and cytotoxin (CT) (lymphotoxin (LT, also known as TNF-β) or tumor necrosis factor-α (TNF-α)), these Th hybridomas produce low or undetectable levels of IFN-γ and CT. No inhibitory activity of IFN-γ and CT was observed in culture supernatants of activated Th hybridomas. Double-chamber experiments demonstrated that CT-sensitive L929 cells when physically separated from activated Th1 clones were killed by membrane-permeable CT. Under identical experimental conditions, lysis of P815 cells did not occur. Moreover, activation of Th hybridomas directly in wells containing the CT-sensitive L929 cells failed to induce target cell lysis. This confirms that these Th hybridomas produce little CT and argues against high local concentrations of CT being responsible for Th hybridoma-mediated killing of P815 cells. Finally, a polyclonal rabbit antiserum to rTNF-α, which strongly and specifically inhibited CT-mediated and Th1 clone-mediated killing of L929 cells, failed to inhibit P815 lysis by activated Th1 clones and Th hybridomas. These observations establish that a cytolytic mechanism independent of IFN-γ, LT, and TNF-α is responsible for lysis of CT-resistant target cells.
Combined Thrombolytic and Platelet Glycoprotein IIb/IIIa Inhibitor Therapy for Acute Myocardial Infarction: Will Pharmacological Therapy Ever Equal Primary Angioplasty?

The management of acute myocardial infarction (AMI) was altered dramatically with the introduction of intracoronary thrombolytic therapy in the late l970s by Rentrop and others.1 The visualization of coronary artery occlusion by angiography performed during the first few hours of AMI and the removal of some of these thrombi at the time of emergent coronary artery bypass surgery convinced the medical community that AMI was, as was thought years earlier, due to “coronary thrombosis.” After the publication of a number of randomized clinical trials (RCTs) of intracoronary and intravenous lytic therapy, reperfusion of acutely occluded coronary artery beds with thrombolytic therapy became a standard treatment of AMI by the mid-1980s.2 While thrombolytic therapy was gaining early acceptance as a means to achieve reperfusion, a parallel pathway for achieving reperfusion was developing with catheter-based techniques. Reports of PTCA for the management of AMI appeared in 1983.3 Soon a vigorous competition developed between pharmacological and mechanical methods of reperfusion. Important differences between these 2 competing approaches were apparent. Thrombolytic therapy could be initiated rapidly once the diagnosis was made, with treatment instituted in the emergency department or even before hospitalization,4 and it did not require the technical skills of a proceduralist for its implementation. However, because reperfusion did not occur until 60 to 90 minutes after the onset of treatment, the occurrence of successful reperfusion (or its failure) could not be ascertained with certainty by use of clinical markers, and there was an obligatory risk of intracranial hemorrhage (ICH) of 0.5% to 1.0%, with higher rates experienced in elderly patients.5 With PTCA, on the other hand, there was an obligatory delay between diagnosis and initiation of the procedure, and highly skilled procedural cardiologists and technical staff were required to be available 24 hours a day. Because a …
The ataxia telangiectasia group D associated gene confers a cellular survival advantage in pancreatic adenocarcinoma

Introduction: Recently we have determined that the gene Ataxia-Telangiectasia Group D Associated (ATDC) is significantly over- expressed in >90% of human pancreatic adenocarcinomas. The role of ATDC in tumorigenesis is unknown. We hypothesize that ATDC promotes growth and confers survival advantage after radiation exposure in pancreatic cancer. Methods: To examine the role of ATDC in pancreatic cancer, we designed an anti-ATDC small inhibitory RNA (siRNA) as well as a mutated anti-ATDC siRNA (msiRNA) to serve as a control. Stable expression of both the anti-ATDC siRNA and the msiRNA was established in BxPC-3 cells, a pancreatic cancer cell line with high endogenous ATDC expression. ATDC expression was assessed by Western blotting. Cell growth was calculated by counting cell number. Following exposure to ionizing radiation (0–10 gy), the surviving fraction of cells after 2 weeks was analyzed by clonigenic assay. The effect of radiation exposure (5 gy) on cell cycle distribution was assessed by FACS analysis of propidium iodide stained cells. Results: Silencing of ATDC was confirmed by Western blotting in BxPC-3 cells expressing anti-ATDC siRNA, while the control msiRNA had little effect. Cellular proliferation in ATDC silenced cells was significantly inhibited compared to msiRNA and WT cells (fold change compared to time 0: siRNA = 0.97 ± 0.29∗, msiRNA = 2.92 ± 0.43, WT = 4.19 ± 0.79, ∗p < 0.05 vs. WT and msiRNA at 96 hours). Clonigenic assays revealed that following exposure to ionizing radiation, BxPC-3 cells with silenced ATDC were more sensitive to the effects of ionizing radiation than control cells (radiation dose for 1% survival: WT = 11.60 ± 0.06 gy; siRNA = 10.16 ± 0.70 gy). Preliminary analysis of cell cycle distribution 12 hours after exposure to 5 gy ionizing radiation showed an increased S phase fraction in ATDC silenced cells compared to msiRNA and WT (siRNA = 37.2%, msiRNA = 3.2%, WT = 3.5%), suggesting a role for ATDC in repair of DNA damage. Conclusion: Silencing of ATDC expression in BxPC-3 cells leads to decreased growth rate and increased sensitivity to ionizing radiation. Our data indicate that ATDC may be a therapeutic target in pancreatic cancer by inhibiting tumor growth and increasing sensitivity to radiation therapy.
Relative growth rates and the grazing optimization hypothesis.

A mathematical analysis of the changes in plant relative growth rates necessary to increase aboveground production following grazing was conducted. The equation derived gives an isoline where production of a grazed and ungrazed plant will be the same. The equation has four variables (mean shoot relative growth rate, change in relative growth rate after grazing, grazing intensity, and recovery time) and may be analyzed graphically in a number of ways.
A new formulation for developing CVBEM approximation functions

The complex variable boundary element method, or CVBEM, is a numerical technique that exactly solves the Laplace or many forms of the Poisson equation, over a two-dimensional domain. A considerable effort is expended, however, in developing formulations involving higher order trial function CVBEM approximations. In this work, a new expansion of the CVBEM is developed that significantly mitigates the complexity involved in preparing such higher order trial function approximations.
Some Issues in Noncommutative Solitons as D-branes

We investigate and interpret a large class of soliton solutions found in noncommutative tachyon condensation. These constructions make extensive use of the idea that Dp-branes may be built out of lower dimensional branes. Finally we comment on a recently proposed solution generating technique.
School Mental Health's Response to Terrorism and Disaster.

The events of September 11, 2001, have underscored the mental health needs of youth and families, and amplified the advantages of proactively bringing a range of mental health services to them, where they are, in natural settings such as schools. Further, there is increasing momentum for the enhancement of coordinated and comprehensive school-based approaches that seek to effectively respond to significant crises such as terrorist attacks and disaster. This article explores key themes related to school mental health's response to terrorism and disaster. Following review of background literature on child and adult reactions to trauma, we discuss the development of crisis response teams, and present a range of strategies for schools to respond to crises and disaster. The experiences of one elementary school in responding to the events of September 11 are presented, followed by review of critical challenges facing schools and school mental health programs in improving their ability to respond to significant crises.
A comparison of the attraction of nymphs and adults of the ticksAmblyomma hebraeum andA. variegatum to carbon dioxide and the male-produced aggregation-attachment pheromone

The attraction of nymphs of the ticksAmblyomma hebraeum andA. variegatum to CO2 alone and CO2 together with the male-produced aggregation-attachment pheromone (AAP) was investigated. Matching experiments on the attraction of the adults of the two species were run for comparison. Nymphs ofA. hebraeum were strongly attracted to sources of CO2 and CO2/AAP at distances of 10 and 15 m. At distances of 20 and 25 m significantly more nymphs were attracted to CO2/AAP than to CO2 alone. Adults ofA. hebraeum were not attracted to CO2 alone at any distance; these ticks were attracted to CO2 and AAP together for distances of up to 25 m. The patterns of attraction of nymphs and adults ofA. variegatum at 10 m were similar to those recorded inA. hebraeum.
Effect of pavement roughness on user costs

After the construction of a pavement system, deterioration occurs because of traffic loading and weathering action and results in the formation of various types of distresses and an increase in pavement roughness. "Roughness" can be defined as irregularities of pavement surface that affect driver safety and increase user costs, including fuel consumption, repair and maintenance, depreciation, and tire costs. In this study, pavement roughness was predicted with the use of the newly released Mechanistic-Empirical Pavement Design Guide for levels of initial roughness condition. Four alternative maintenance and rehabilitation (M&R) strategies were used to estimate the life-cycle cost of pavement over a 35-year analysis period. Various categories of user costs were calculated on the basis of different cost models and from data reported in the literature. From this analysis, pavement roughness was found to affect user costs dramatically. A comparison was made between agency investment and user costs related to ...
Energy status in anoxic rat hepatocytes: Effects of isoflurane, solution composition, and hypothermia

Both cold and warm ischemia occur during liver transplantation. Hypothermia and Wisconsin solution preserve adenine nucleotide energy status, which is crucial to hepatic function and viability. The volatile anesthetic isoflurane has been shown to preserve energy status in anoxic isolated hepatocytes in warm Krebs solution. The present study examined isoflurane effects on energy status during incubation also in Wisconsin or Krebs-plus-adenosine solution at 37 degrees or 4 degrees. Hepatocytes were isolated from rat liver after perfusion with Krebs + collagenase. In 25-mL flasks, 12.5 million cells in 2.5 mL of Krebs, Krebs plus 5 mmol/L adenosine, or Wisconsin solution were incubated under an atmosphere of O2/CO2 or N2/CO2 (19:1) +/- isoflurane (3 volumes% = 2ED50), for 30 minutes at 37 degrees C or 4 degrees C. Adenine nucleotides were measured by high-performance liquid chromatography (HPLC), lactate enzymatically. During warm (37 degrees) anoxia, Wisconsin solution preserved energy status; Krebs plus adenosine did not. Isoflurane further protected energy status in all three solutions. Hypothermia (4 degrees) alone greatly decreased anoxic loss of energy status in all solutions. In Wisconsin solution only, energy status tended to be higher in anoxic than in oxygenated cells and was further enhanced by isoflurane, with corresponding increases in lactate. During 30 minutes of either warm or cold anoxia, isoflurane and Wisconsin solution each helped preserve adenine nucleotide energy status in isolated hepatocytes, at least in part through enhanced glycolysis.
Spacecraft expected-cost analysis with k-out-of-n:G subsystems

In designing a subsystem for a spacecraft, the design engineer is often faced with a number of options ranging from planning an inexpensive subsystem with low reliability to selecting a highly reliable system that would cost much more. We minimize the total of the cost of the subsytem and the costs that would occur if the subsystem fails. We choose the subsystem with the lowest total. A k-out-of-n:G subsystem has n modules, of which k are required to be good for the subsystem to be good. We examine two models to illustrate the principles of the k-out-of-n:G subsystem designs. For the first model, the following assumptions are necessary: the probability of failure of any module in the system is not affected by the failure of any other module; and each of the modules has the same probabillity of success. For the second model we are also free to choose k in our subsystem.
Liquid Phase Sintering in the Glass-Cordierite System - Effect of Melt Infiltration Distance

Effect of glass infiltration distance, controlled by particle sizes of glass and ceramic filler, and green density, on densification kinetics of glass-filled ceramics has been studied using borosilicate glass-cordierite as the model system. Within the particle size range investigated, the densification is found to be significantly enhanced by increasing cordierite size, reducing glass size and increasing green density. The above results are attributed to both increased driving force of densification by reducing glass particle size, and decreased glass redistribution distance by either increasing green density of compacts or increasing the particle size ratio between cordierite and glass powders.
A Novel Multiscale Model of Cell Adhesion and Migration on Defined Extracellular Matrices

While many of the molecules and signaling pathways that govern biophysical interactions between cells and the extracellular matrix (ECM) have been identified, the mechanisms through which these components cooperate to control whole-cell shape, adhesion, and motility remain incompletely understood. This is due in part to the absence of multiscale models that integrate local activation of biochemical signals with adhesion and force generation. In this study, we present a novel computational model of cell migration on ECMs of defined biophysical properties that incorporates adhesion growth & rupture dynamics, stress fiber contractility, and a protrusive machinery. Critically, our model makes use of a reduced one-dimensional geometry, which enables us to systematically probe multiple intracellular and extracellular parameters in a computationally tractable framework. Using this model, we examine effects of substrate stiffness, ligand density, and Rho family GTPase activation on cellular adhesion, contractility, and migration speed and dynamics. Our simulations yield results that are in qualitative agreement with previously observed experimental observations, including a biphasic relationship between migration speed and ligand density, enhanced cell adhesion and faster random migration on stiffer ECMs, and recently-reported transitions from filopodial to “stick-slip” to gliding motility on ECMs of increasing stiffness (Ulrich et al., Cancer Research 2009). Our model enables us to investigate experimentally-inaccessible microscale relationships between mechanotransductive signaling, adhesion, and motility and offers novel insight into how these factors interact with one another to produce complex migration patterns across a variety of cell types and ECM conditions.
Effects of aging on event-related brain potentials (ERPs) in a visual detection task.

Abstract Event-related brain potentials (ERPs) were recorded from 74 subjects (45 men) between 18 and 82 years of age in a simple visual detection task. On each trial the subject reported the location of a triangular flash of light presented briefly 20° laterally to the left or right visual field or to both fields simultaneously. ERPs to targets exhibited a similar morphology including P1, N1, P2, N2, and P3 components across all age groups. The principal effects of advancing age were (1) a marked reduction in amplitude of the posterior P1 component (75–150 latency) together with an amplitude increase of an anterior positivity at the same latency; (2) an increase in amplitude of the P3 component that was most prominent over frontal scalp areas; and (3) a linear increase in P3 peak latency. These results extend the findings of age-related changes in P3 peak latency and distribution to a non-oddball task in the visual modality and raise the possibility that short-latency ERPs may index changes in visual attention in the elderly.
Signaling cascades modulate the speed of signal propagation through space

Background Cells are not mixed bags of signaling molecules. As a consequence, signals must travel from their origin to distal locations. Much is understood about the purely diffusive propagation of signals through space. Many signals, however, propagate via signaling cascades. Here, we show that, depending on their kinetics, cascades speed up or slow down the propagation of signals through space, relative to pure diffusion. Methodology/Principal Findings We modeled simple cascades operating under different limits of Michaelis-Menten kinetics using deterministic reaction-diffusion equations. Cascades operating far from enzyme saturation speed up signal propagation; the second mobile species moves more quickly than the first through space, on average. The enhanced speed is due to more efficient serial activation of a downstream signaling module (by the signaling molecule immediately upstream in the cascade) at points distal from the signaling origin, compared to locations closer to the source. Conversely, cascades operating under saturated kinetics, which exhibit zero-order ultrasensitivity, can slow down signals, ultimately localizing them to regions around the origin. Conclusions/Significance Signal speed modulation may be a fundamental function of cascades, affecting the ability of signals to penetrate within a cell, to cross-react with other signals, and to activate distant targets. In particular, enhanced speeds provide a way to increase signal penetration into a cell without needing to flood the cell with large numbers of active signaling molecules; conversely, diminished speeds in zero-order ultrasensitive cascades facilitate strong, but localized, signaling.
Characterization of association microstructures in hydrometallurgical nickel extraction by di(2-ethylhexyl)phosphoric acid

Abstract The association microstructures which form in the hydrometallurgical extraction of nickel from nitrate media of ionic strength 0.25 M by di(2-ethylhexyl)phosphoric acid (HDEHP) in n -heptane were characterized under constant high loading conditions. Photon correlation spectroscopy, fluorescence polarization, small-angle neutron scattering. FT-IR spectroscopy, and various analytical techniques were employed to investigate the physicochemical nature of the molecular aggregates in the nonpolar organic phase. This study shows that the metal—extractant aggregates are cylindrical reversed micelles which contain between five and six water molecules per HDEHP monomer. Furthermore, it appears that the metal—extractant aggregates are mixed reversed micelles consisting of predominately nickel—HDEHP and to a lesser extent NaDEHP. The water in the metal—extractant reversed micelles exists mainly in three different states, namely, free water and bound water in the aqueous core of the aggregates, and trapped water in the interfacial layer among the hydrocarbon chains of the extractant molecules near the micellar core. The important role of reversed micelles in the liquid/liquid extraction of metal ions by acidic organophosphorus extractants is also briefly discussed.
Thermodynamics of Protein Hydration Computed by Molecular Dynamics and Normal Modes

Thermodynamic properties of bovine pancreatic trypsin inhibitor (BPTI) hydrated by up to 1600 water molecules, i.e., a ratio of the weight of water to that of protein, h, from 0 to ∼4.5, are studied by molecular dynamics (MD) simulation and normal-mode analysis (NMA). Temperatures range from 100 to 300 K to include the hydrated protein glass transition, Tg ≈ 200 K. The partial specific heat of BPTI computed by MD reaches fully hydrated values around h ≈ 0.7 below and above Tg. For smaller h, distinctly different variations in the apparent specific heat of BPTI with h below and above Tg are found and related to the respective decrease and increase in protein flexibility with h. Changes upon varying h in the energy landscape of hydrated BPTI near its native configuration are examined. The partial entropy of BPTI is computed with NMA up to Tg. Above 200 K, an increase in the partial entropy of BPTI is computed with specific heats of hydrated BPTI obtained by MD. The difference between the partial entropy of ...
s- AND p-WAVE NEUTRON SPECTROSCOPY. PART II. EVEN-EVEN NUCLEI

Abstract Total cross sections have been measured for Ni58, Ni60, Ce140, Ce142, Mg24, Mg25, Mg26, Si28, Zr90, Zr92, and Zr94 from 3 to 300 kev. Of the eight well separated levels found in Ni58, six are matched by levels in Ni60 at very nearly the same energies. This effect is very difficult to understand on the basis of conventional nuclear models. Strength functions ( Γ n 0 D ) of 3.4 × 10−4, 2.3 × 10−4, 1.0 × 10−4, and 1.2 × 10−4 and average level spacings of 23 kev, 21 kev, 3 kev, and 1 kev have been estimated for Ni58, Ni60, Ce140, and Ce142, respectively. The strength functions and level spacings of the Zr isotopes are difficult to interpret because of the importance of both s- and p-wave resonances; however, a preliminary average cross-section analysis of Zr and neighboring nuclei shows a very definite peak in the p-wave strength function at atomic weight 92. Resonance parameters have been obtained for resonances observed in the magnesium isotopes.
Vertical Distribution of PH3 in Saturn from Observations of Its 1-0 and 3-2 Rotational Lines

Far-infrared Fourier-transform spectrometer measurements of the 1-0 and 3-2 PH3 transitions in Saturn's disk near 267 and 800 GHz (8.9 and 26.7/cm), respectively, were analyzed simultaneously to derive a global mean profile for the PH3 vertical mixing ratio between 100 and 600 mbar total pressure. The far-infrared spectrum is relatively free from spectral interlopers, suffers minimal absorption or scattering by atmospheric particulates, and contains intrinsically weak PH3 lines that are sensitive to a range of atmospheric depths. The combined spectra are inconsistent with a uniform tropospheric mixing ratio, even with a stratospheric cut-off. They are consistent with a volume mixing ratio of PH3 that drops from 1.2 x 10(exp -5) at 645 mbar pressure to a value of 4.1 x 10(exp -7) at 150 mbar pressure, a decrease that is linear is log abundance vs log pressure. The mixing ratio could drop even more quickly at atmospheric pressures below 150 mbar and still be consistent with the data. The mixing ratio may well remain constant with depth for pressures above 630 mbar. The maximum PH3 mixing ratio in this model is consistent with a [P]/[H] ratio in the deep atmosphere that is about a factor of 10 higher than solar composition. Such a model is consistent with rapid mixing up to the radiative-convective boundary and transport by, for example, vertical waves just above this boundary. In the best fitting model, the eddy diffusion coefficient is approximately 10(exp 4) sq cm near 630 mbar, and it must increase with altitude. The predominant PH3 loss mechanisms are direct photolysis by UV radiation and scavenging by H atoms produced by the photolysis.
Systematic optimization of exterior measurement locations for the determination of interior magnetic field vector components in inaccessible regions

An experiment may face the challenge of real-time determination of the magnetic field vector components present within some interior region of the experimental apparatus over which it is impossible to directly measure the field components during the operation of the experiment. As a solution to this problem, we propose a general concept which provides for a unique determination of the field components within such an interior region solely from exterior measurements at fixed discrete locations. The method is general and does not require the field to possess any type of symmetry. We describe our systematic approach for optimizing the locations of these exterior measurements which maximizes their sensitivity to successive terms in a multipole expansion of the field.
Semantic based image retrieval: a probabilistic approach

This paper describes an approach to image retrieval based on the underlying semantics of images. To extract these semantics a hierarchical, probabilistic approach is proposed. The labels that are extracted in this case are man-made, natural, inside and outside. The hierarchical framework combines class likelihood probability estimates across a number of levels to form a posterior estimate of the probability of class membership. Unlike previous work in this field, the proposed algorithm can determine probabilities at any point in the scene and only a small number of images are required to train the system. To illustrate the potential of such an approach a prototype image retrieval system has been developed, initial results from this system are given in this paper.
Conserved amino acid markers from past influenza pandemic strains

Finding the amino acid mutations that affect the severity of influenza infections remains an open and challenging problem. Of special interest is better understanding how current circulating influenza strains could evolve into a new pandemic strain. Influenza proteomes from distinct viral phenotype classes were searched for class specific amino acid mutations conserved in past pandemics, using reverse engineered linear classifiers. Thirty-four amino acid markers associated with host specificity and high mortality rate were found. Some markers had little impact on distinguishing the functional classes by themselves, however in combination with other mutations they improved class prediction. Pairwise combinations of influenza genomes were checked for reassortment and mutation events needed to acquire the pandemic conserved markers. Evolutionary pathways involving H1N1 human and swine strains mixed with avian strains show the potential to acquire the pandemic markers with a double reassortment and one or two amino acid mutations. The small mutation combinations found at multiple protein positions associated with viral phenotype indicate that surveillance tools could monitor genetic variation beyond single point mutations to track influenza strains. Finding that certain strain combinations have the potential to acquire pandemic conserved markers through a limited number of reassortment and mutation events illustrates the potential for reassortment and mutation events to lead to new circulating influenza strains.
Meta-analysis of association of rare mutations and common sequence variants in the MSR1 gene and prostate cancer risk.

BACKGROUND MSR1 has been reported to be associated with increased risk of prostate cancer (PCa). METHODS We performed a meta-analysis of all eight published studies to evaluate the pooled effect of three rare mutations (R293X, S41T, and D174Y) and five common sequence variants (PRO3, INDEL1, IVS5-59, P275A, and INDEL7), stratified by race and sporadic/hereditary cancer. RESULTS Several variants were significantly or marginally significantly associated with sporadic, not hereditary PCa risk, including R293X in white men (random effect OR = 1.34, P = 0.09) and D174Y in black men (random effect OR = 2.41, P = 0.04). The associations were not significant when the initial study was excluded. However, the frequency of the D174Y mutation was consistently higher among cases in all three studies that examined black men. CONCLUSIONS Overall, this meta-analysis suggests the MSR1 gene does not independently confer a major risk to PCa but may confer a moderate risk to PCa, especially in black men. Prostate © 2006 Wiley-Liss, Inc.
Kainic acid-mediated upregulation of matrix metalloproteinase-9 promotes retinal degeneration.

PURPOSE. Excitotoxicity has been proposed to play a pivotal role in retinal damage, but the mechanisms that underlie retinal damage are not clearly understood. In this study, the role of matrix metalloproteinases in excitotoxin-mediated retinal damage was investigated. METHODS. KA, CNQX (6-cyano-7-nitroquinoxaline-2,3,-dione), NBQX (2,3-dihydroxy-6-nitro-7-sulfamoyl-benzo(F)quinoxaline), MK801, or PBS was injected into the vitreous of CD-1 mice. MMP expression in the retina was analyzed by zymography, Western blot, and immunohistochemistry. Retinal ganglion cells (RGCs) were retrogradely labeled with aminostilbamidine methanesulfonate (Molecular Probes, Eugene, OR), and loss of fluorescently labeled RGCs in retinal flatmounts was quantified. Apoptotic cell death was assessed by TUNEL staining. Astrocyte activation was determined by immunohistochemistry, and laminin decrease was determined by immunohistochemistry and Western blot analysis. RESULTS. Intravitreal injection of KA caused time- and dose-related MMP-9 upregulation in the retina. Increased MMP-9 activity and protein levels were associated with activation of astrocytes. Astrocyte-associated MMP-9 correlated with a decrease in laminin immunoreactivity in the ganglion cell layer and significant loss of retinal ganglion cells. KA-mediated upregulation of MMP-9 activity was associated with apoptosis of cells in the ganglion cell layer as early as 6 hours after injection, followed by apoptosis in cells in the inner nuclear layer by day 1. Intravitreal injection of the non-NMDA receptor antagonists, CNQX and NBQX decreased KA-induced MMP-9 activity and protein levels in the retina and attenuated retinal degeneration, whereas the NMDA receptor antagonist MK801 failed to offer protection. Further, a synthetic MMP inhibitor GM6001 decreased KA-mediated MMP-9 activity and offered significant protection against ganglion cell loss in the retina. CONCLUSIONS. These results indicate that KA-mediated upregulation of MMP-9 activity promotes retinal degeneration and suggest that inhibition of KA-mediated MMP activity may offer protection against excitotoxin-induced retinal damage.
Copulation in the lycosid spider Schizocosa saltatrix (Hentz): An analysis of palpal insertion patterns

Abstract Copulation in this wolf spider species was characterized by a pattern which involved successive isertions of one palp before a shift was made to the opposite palp. The observed pattern is probably characteristic for the genus. The duration of mating and number of insertions were relatively great in comparison with other lycosids. In all cases, insertion duration was positively linearly correlated with the numerical sequence of insertion. Fatigue was hypothesized to be the underlying factor which produced the incremental change in insertion duration. Partial or complete independence of the control mechanism of each palp was suggested by the differences in certain aspects of insertion between the right and left palps in some of the males.
Community Development Block Grant Spending Revisited: Patterns of Benefit and Program Institutionalization

This article analyzes Community Development Block Grant (CDBG) spending by local governments between 1988-1992. We address four issues examining actual expenditure patterns in a small central city and five satellite cities in Michigan: changes in CDBG expenditure patterns; levels of social targeting; the extent of institutionalization of expenditure patterns; and the level of privatization of CDBG spending. We conclude that while spending for housing and public works is related to the fiscal health of cities, expenditures for economic development and social services are related to political characteristics. Further, local governments exceed federal social targeting guidelines. Finally, while there is little privatization, the communities studied evidence modest levels of program innovation in the later years of the CDBG program.
Right thoracic ectopic kidney in a child with breathing difficulties—Sonographic diagnosis

Congenital intrathoracic ectopic kidney is a rare congenital abnormality that is usually found as an incidental lesion on chest radiographs. We report the case of a 6-month-old male with a 1-day history of breathing difficulties whose chest radiograph revealed a soft tissue right basilar mass. Further investigation utilizing ultrasound revealed a thoracic kidney. This case demonstrates the importance of sonography as a diagnostic tool in identifying thoracic kidneys in the pediatric age group.