cssi/SciSciGPT-SciSciNet huggingface dataset:
The GREAT FIRE OF 1660 AND THE ISLAMIZATION OF CHRISTIAN AND JEWISH SPACE IN ISTANBUL

On 24 July 1660, a great conflagration broke out in Istanbul. An Ottoman writer conveys the horror of the event: “[t]housands of homes and households burned with fire. And in accordance with God's eternal will, God changed the distinguishing marks of night and day by making the very dark night luminous with flames bearing sparks, and darkening the light-filled day with black smoke and soot.” The fire began in a store that sold straw products outside the appropriately named Firewood Gate (Odun kapisi) west of Eminonu, and it devastated densely crowded neighborhoods consisting of wooden homes. The strong winds of Istanbul caused the fire to spread violently in all directions, despite the efforts of the deputy grand vizier (kaimmakam) and others who attempted the impossible task of holding it back with hooks, axes, and water carriers. Sultan Mehmed IV's boon companion and chronicler, Abdi Pasa, notes that the fire marched across the city like an invading army: the flames “split into divisions, and every single division, by the decree of God, spread to a different district.” The fire spread north, west, and to Unkapani. According to Mehmed Halife, in Suleymaniye the spires of the four minarets of the great mosque burned like candles. The blaze reached Bayezid and then moved south and west to Davud Pasa, Kumkapi, and even as far west as Samatya. The flames did not spare the Hippodrome (At Meydani) in the east or Mahmud Pasa and the markets at the center of the peninsula, either. Abdi Pasa estimated that the fire reduced 280,000 households to ashes as the city burned for exactly forty-nine hours. Two-thirds of Istanbul was destroyed in the conflagration, and as many as 40,000 people lost their lives. Although fire was a frequent occurrence in 17th-century Istanbul, this was the worst the city had ever experienced. Thousands died in the plague that followed the fire as rats feasted on unburied corpses and spread disease. Because three months prior to this fire a conflagration had broken out in the heart of the district of Galata, across the Golden Horn from Eminonu, much of the city lay in ruins in the summer of 1660.
Punitive legal approaches to the problem of prenatal drug exposure

Le corps legislatif et les tribunaux ont repondu prematurement aux problemes d'exposition prenatale a la drogue en donnant une variete de sanctions legales civiles et criminelles pour decourager l'utilisation de stupefiants et proteger la sante du fœtus. Une etude des cas juridiques demontre que d'importantes difficultes constitutionnelles et statutaires limitent l'efficacite de ces sanctions et en fin de compte empeche leur application. Ces contraintes exigent que toute intervention gouvernementale a travers les tribunaux soit basee sur des preuves judiciaires individuelles de dommage imminent a l'enfant et d'inaptitude maternelle durant les poursuites legales pour negligence
Vibrational energy redistribution in Cp*Ir(CO)2 (Cp*=η5-pentamethylcyclopentadienyl) studied by broadband transient infrared spectroscopy

Picosecond vibrational energy dynamics involving the symmetric (2020 cm−1 and asymmetric (1953 cm−1) CO-stretching modes of Cp*Ir(CO)2 in room temperature n-hexane is measured using mode specific infrared excitation followed by broadband infrared multichannel probing to generate a transient spectrum. The recovery of the transient bleaching and absorption bands, following 2020 or 1953 cm−1 excitation, yields a v=1 CO-stretching lifetime T1=28±7 (1σ) ps. The transitions from v=1 vibrational states give rise to new absorption features in the transient spectra at 2008, 1994, 1941 and 1930 cm−1. The time evolution of these absorptions monitors rapid energy redistribution and equilibration (<10 ps) between the symmetric and asymmetric CO-stretching modes prior to ground state recovery.
Accelerating High Performance Computing Applications: Using CPUs, GPUs, Hybrid CPU/GPU, and FPGAs

Most modern scientific research requires significant advanced modeling, simulation, and visualization. Due to the growing complexity of physical models, these research activities increasingly are requiring more and more High Performance Computing (HPC) resources and this trend is predicted to grow even stronger. Considering this growth in HPC applications, the traditional parallel computing model based solely on Central Processing Units (CPUs) is unable to meet the scientific needs of the researchers. HPC requirements are expected to reach exascale in this decade. There are several approaches to enhance and speed up HPC, some of the most promising involve hybrid solutions. In this paper, we describe existing state of hardware and accelerators for HPC. Such components include CPUs, Graphics Processing Units (GPU), and Field-Programmable Gate Arrays (FPGAs). Various hybrid implementations of these accelerators are presented and compared. Examples of the top supercomputers are included as well, together with their hardware configurations. Concluding this paper, we discuss our prediction of further HPC hardware trends in support of advanced modeling, simulation, and visualization.
Land use and economic change in the post-frontier upland Philippines

Changes in land use and in the nature of farm enterprises in the upland Philippines are examined through the lens of household economic strategies, using data obtained on Palawan Island and with particular attention to non-agricultural employment diversification. Short fallow intervals and small farm sizes are today common throughout upland Palawan. In addition, as upland farming has become more of an occupation of specific household members and less the way of life of entire households, many upland farms are specialized in particular crops. Such specializations, however, change over time as households undergo growth and domestic cycling and some members establish new income sources and residential bases in the lowlands. Meanwhile, restrictions on new forest clearance and other developments that make it difficult for upland households to secure an adequate living from farming alone have greatly increased collection pressures on non-timber forest products. These and other changes are reconfiguring the role of women in household economy and generating new axes of regional economic integration. Despite considerable land and other resource degradation in the uplands, some causes for optimism are found in the spontaneous adoption of agroforestry practices and in the emergence of new identities configured in part around notions of environmental well-being. Copyright © 2006 John Wiley & Sons, Ltd.
Evaluation of Minnesota and Illinois Hospital Respiratory Protection Programs and Health Care Worker Respirator Use

The objective of this study was to assess respiratory protection programs for aerosol-transmissible diseases in acute care hospitals for conformance with regulatory requirements and public health guidelines. Twenty-eight representative hospitals were selected by size, location, and ownership in Minnesota and Illinois. Interviews were conducted with 363 health care workers and 171 managers from high-risk departments. Written programs from each hospital were reviewed for required elements. Seventy-seven health care workers were observed donning and doffing a FFR. The most serious deficiency in many written programs was failure to identify a program administrator. Most written programs lacked adequate details about medical evaluation, fit-testing, and training and did not include a comprehensive risk assessment for aerosol transmissible diseases; tuberculosis was often the only pathogen addressed. Employees with the highest probability of tuberculosis exposure were most likely to pick a respirator for close ...
Frozen yogurt near deep-freeze

Abstract Certain nutritionists advocate yogurt as having significant benefit, citing it as an important reason for longevity in the Caucasus area of Russia. 1 The frozen version of yogurt was designed to capture some of the multimillion dollar ice dessert market while advertising significant benefits compared with ice cream. We report a near-death experience associated with frozen yogurt in order to put the advertised risk/benefit ratio in proper perspective.
Dijkgraaf-Vafa matrix models and integrable systems

We review the Dijkgraaf-Vafa correspondence and give some mathematical details of the associated matrix contour integrals, before discussing recent work relating supersymmetric vacua to integrable systems.
SOCIALSENSE: Graphical user interface design considerations for social network experiment software

Using networked computers in laboratory experiments to investigate group dynamics currently requires the creation of special program application software. Design considerations for a useable graphical user interface (GUI) in such software are discussed in this paper. We describe SOCIALSENSE communication software created to experimentally test the effect of different social network configurations, group membership, and group integration on patterns of rumor self-organization. The software connected 16 participants using several different network configurations via a web-accessible Java applet, tasked them with making sense of rumors presented to them, enabled ''neighbors'' to synchronously or asynchronously communicate, and recorded their selections and beliefs. Four principles of design were followed: employ reading gravity, minimize cognitive load, use pre-existing mental models, and select color to direct attention. A description of each principle is presented, how it was applied to the GUI, and how it could be applied to other social network experiment program interfaces.
Social comparison in virtual work environments: An examination of contemporary referent selection

The current trend with organizations is to streamline operations, cut cost, and operate with fewer employees (i.e., to do more with less). This trend has encouraged events such as downsizing and mergers as well as fostered the development of virtual work environments and new organizational forms like virtual organizations. Consequently, this change in organizational forms and the context of work has the potential to cause other associated consequences. One possible consequence is a change in the availability and type of referent others available. Likewise, a better understanding of worker referent choice remains a common issue of debate among researchers of comparison theories. This paper examines how referent selection relative to worker social comparison is (and will be) affected by the changing nature of organizations and the context of work.
Mechanism of Binding Site Conformational Switching in the CD44–Hyaluronan Protein–Carbohydrate Binding Interaction

Abstract The transmembrane protein CD44, which has been implicated in cancer biology and inflammation, mediates cell adhesion through multimeric interactions with the linear extracellular glycosaminoglycan hyaluronan (HA; in megadaltons). Affinity switching of CD44 from a low-affinity state to a high-affinity state is required for normal CD44 physiological function; crystal structures of the CD44 hyaluronan binding domain complexed with HA oligomers point to a conformational rearrangement at a binding site loop, leading to the formation of direct contact between the oligomer and an arginine side chain as a molecular basis for affinity switching. Here, all-atom explicit-solvent molecular dynamics simulations were used to characterize the dynamics and thermodynamics of oligomeric hyaluronan (oHA) and its two crystallographic complexes with the CD44 hyaluronan binding domain: the “A-form,” which lacks arginine–HA close contact, and the “B-form,” which has direct arginine side-chain–HA contact. From the simulations, the conformational properties of oHA are essentially unaltered in going from the unbound state to either the A-form or the B-form bound state, with the oligomer retaining its flexibility when bound and with only two of the eight monosaccharides in the oligomer maintaining uninterrupted contact with the protein. Biased simulations revealed that altering the backbone conformation of a tyrosine residue in the arginine loop can induce the A-form → B-form conformational transition and that a large free-energy barrier prevents ready interconversion between the two forms, thereby suggesting that the tyrosine backbone forms a molecular switch.
Fluorescence as a conformational probe of beef liver phenylalanine transfer RNA.

Abstract 1. 1. Purified beef liver phenylalanine tRNA (tRNA Phe ) exhibits a 4-fold increase in fluorescence intensity upon the addition of low concentrations (0.3–1.0 mM) of Mg 2+ . This enhancement of fluorescence by Mg 2+ is reversible and ribonuclease-sensitive. It occurs instantaneously and completely at both 1.4 and 27.0° and is accompanied by a 4% hypochromicity (260 nm) at the latter temperature. 2. 2. Simultaneous measurement of the optical rotatory dispersion (ORD) revealed that tRNA Phe exhibits a correspondingly sharp increase in optical rotation over the same concentration range of Mg 2+ . This transition was accompanied by a blue shift of the optical rotatory dispersion spectrum of approx. 3 nm. 3. 3. On the basis of the coincidence of these Mg 2+ -induced fluorescence and rotational changes, it is concluded that fluorescence spectroscopy is a valid and sensitive probe for the study of conformational changes in tRNA Phe . 4. 4. High concentrations (2.0 M) of NaCl mimic to a certain extent (61%) the effect of these lower concentrations of Mg 2+ on the fluorescence of tRNA Phe . NaCl competitively inhibited the enhancement of the fluorescence intensity of tRNA Phe by Mg 2+ . 5. 5. These results are discussed in relation to the effect of Mg 2+ and Na + on the biological activity of tRNA's in general.
The barriers to using urban infill development to achieve smart growth

Abstract The smart growth movement of the 1990s has seen many development and planning associations, state and local governments, and the Clinton administration encourage significant infill development to control sprawl and promote revitalization. Will the 123 million projected increase in population in the next 50 years be attracted to infill development or to outlying growth areas? A review of 22 major central cities shows that they captured only 5.2 percent of total new metropolitan housing permits over the decade: 2.2 percent of single‐family pemits and 14.9 percent of multifamily permits. This analysis identifies the practical barriers to urban infill development, including land assembly and infrastructure costs, unwillingness to condemn, municipal social goal and regulatory policies, difficulty of finding developers, complexities of public‐private partnerships, excessive risks, resistance from local residents, and stakeholder conflicts and political constraints. While supporting infill, smart growth...
Principles of uncertainty: what are they? Why do we need them?

Abstract The meaning and utility of three principles of uncertainty is discussed. These principles, which are referred to as a principle of minimum uncertainty, a principle of maximum uncertainty, and a principle of uncertainty invariance, depend on the theory in which uncertainty is conceptualized. Due to a connection between uncertainty and information, the principles may also be conceived as principles of information. To make the principles operational in a particular uncertainty theory, we need to measure the amount of relevant uncertainty (and associated information) in each problem situation describable within the theory. Well justified measures of uncertainty have thus far been established only in some uncertainty theories. These theories, their uncertainty measures, and the associated uncertainty principles are overviewed in the paper.
Approximate solutions for batch, packed tube and radial flow adsorbers—comparison with experiment

Abstract Taking the intraparticle concentration profile to be parabolic leads to important simplifications in the theory of chromatography. For systems whereby solid diffusion and film resistance are important, the parabolic model leads to simple, exact and well-known mathematical solutions which are widely tabulated. Analytical solutions for three types of configuration are presented: Batch, packed tube and radial-flow adsorbers. Experiments using bifunctional resin in saline solutions are used to test the theoretical predictions for batch and packed tube systems.
Treated municipal wastewater for citrus irrigation 1

Abstract Treated, reclaimed municipal wastewater was evaluated on citrus trees in central Florida for over six years. The effects of irrigation with reclaimed wastewater on soil water content, soil chemical analysis, leaf mineral status, and fruit quality were compared with those of irrigation with well water. Irrigation with reclaimed water increased mineral residues in the soil profile, altered leaf mineral concentration and fruit quality, and promoted better tree performance and more weed growth relative to irrigation with well water. Higher accumulation of nitrogen (N), potassium (K), calcium (Ca), and magnesium (Mg) in soils irrigated with reclaimed water were not significantly reflected in leaf mineral status. Although leaf sodium (Na), chloride (Cl), and boron (B) concentrations were noticeably higher in reclaimed water treatments than in those of well water, they are still far below the toxicity levels. This highly treated wastewater in central Florida has been found to be a very safe and good opt...
Spectra of fluctuations of velocity, kinetic energy, and the dissipation rate in strong turbulence.

Following the ideas of operator product expansion, the velocity v, kinetic energy K=1/2${\mathit{v}}^{2}$, and dissipation rate \ensuremath{\epsilon}=${\ensuremath{\nu}}_{0}$(\ensuremath{\partial}${\mathit{v}}_{\mathit{i}}$/\ensuremath{\partial}${\mathit{x}}_{\mathit{j}}$${)}^{2}$ are treated as independent dynamical variables, each obeying its own equation of motion. The relations \ensuremath{\Delta}u(\ensuremath{\Delta}K${)}^{2}$ \ensuremath{\propto} r, \ensuremath{\Delta}u(\ensuremath{\Delta}\ensuremath{\epsilon}${)}^{2}$ \ensuremath{\propto} ${\mathit{r}}^{0}$, and (\ensuremath{\Delta}u${)}^{5}$\ensuremath{\approxeq}r\ensuremath{\Delta}\ensuremath{\epsilon}\ensuremath{\Delta}K are derived. If velocity scales as (\ensuremath{\Delta}v${)}_{\mathrm{rms}}$\ensuremath{\propto} ${\mathit{r}}^{(\ensuremath{\gamma}/3)\mathrm{\ensuremath{-}}1}$, then simple power counting gives (\ensuremath{\Delta}K${)}_{\mathrm{rms}}$ \ensuremath{\propto} ${\mathit{r}}^{1\mathrm{\ensuremath{-}}(\ensuremath{\gamma}/6)}$ and (\ensuremath{\Delta}\ensuremath{\epsilon}${)}_{\mathrm{rms}}$ \ensuremath{\propto} 1/\ensuremath{\surd}(\ensuremath{\Delta}v${)}_{\mathrm{rms}}$ \ensuremath{\propto} ${\mathit{r}}^{(1/2)\mathrm{\ensuremath{-}}(\ensuremath{\gamma}/6)}$. In the Kolmogorov turbulence (\ensuremath{\gamma}=4) the intermittency exponent \ensuremath{\mu}=(\ensuremath{\gamma}/3)-1=1/3 and (\ensuremath{\Delta}\ensuremath{\epsilon}${)}^{2}$=O(${\mathrm{Re}}^{1/4}$). The scaling relation for the \ensuremath{\epsilon} fluctuations is a consequence of cancellation of ultraviolet divergences in the equation of motion for the dissipation rate.
Rent seeking and economic liberalization: why are China and Vietnam different from Eastern Europe?

Why did a gradualist transition approach achieve different performances among socialist economies in the 1980s? Why did some socialist economies never try a gradualist approach to economic liberalization? This paper develops a model to show that the liberalization of a socialist economy has two opposite effects on the rent captured by government. The initial economic condition determines the relative strength of the two effects, and consequently the transition path and performance. In addition, a gradualist reform strategy adopted by a rent-seeking government cannot finish the transition toward a complete market economy. To achieve that goal, a new constitutional order and the rule of law are necessary.
Some properties of synthetic blocky and blurry artifacts

This work addresses the problem of studying and characterizing individual artifacts found in digital video applications (e.g., blockiness, blurriness). In particular, the goal of this paper was to examine the properties of synthetic blocky and blurry artifacts, designed to be relatively pure, and a combination of these two artifacts. We performed a psychophysical experiment in which human subjects were asked to detect these artifacts, identify their types, and rate their annoyance. In most cases, the blocky and blurry artifacts were identified as blocky and blurry, respectively. In combined blocky-blurry artifacts the salience of blockiness increased and blurriness decreased as artifact strength increased. The blocky artifacts produced higher annoyance values than the blurry ones when the total squared error was the same.
Sex differences in the effects of voluntary activity on sucrose-induced obesity

Sedentary, adult rats of both sexes fed Purina chow and a 32% sucrose solution overate, gained excess weight and had higher Lee Indexes of obesity than control animals fed only Purina chow. The magnitude of these effects was similar in the males and females. Animals of both sexes fed the sucrose diet showed a slower rate of weight loss during food deprivation than the chow controls. Access to an activity wheel led to a reduction in caloric intake and the elimination of obesity in male rats. In the chow fed male rats activity led to a smaller, transient suppression in caloric intake and a slightly lower level of body weight than the sedentary chow controls. Access to activity did not affect body weight in the female rats in either dietary condition. Rather, both active groups of female rats appeared to compensate for the energy cost of voluntary activity by a small increase in food consumption. Long-term exposure to activity was associated with more rapid weight loss during food deprivation in both males and females. These data reveal that high levels of activity and obesity can co-exist when normal female rats are fed a palatable diet but that activity eliminates this form of obesity in the male rat.
Nitrogen Contribution of Peanut Residue to Cotton in a Conservation Tillage System

Leguminous crops, particularly winter annuals, have been utilized in conservation systems to partially meet nitrogen (N) requirements of succeeding summer cash crops. Previous research also highlights the benefits of utilizing summer annual legumes in rotation with non-leguminous crops. This study assessed the N contribution of peanut (Arachis hypogaea L.) residues to a subsequent cotton (Gossypium hirsitum L.) crop in a conservation system on a Dothan sandy loam (fine-loamy, kaolinitic, thermic Plinthic Kandiudults) at Headland, AL during the 2003‐2005 growing seasons. Treatments were arranged in a split plot design, with main plots of peanut residue retained or removed from the soil surface, and subplots as N application rates (0, 34, 67, and 101 kg ha −1 ) applied in fall and spring. Peanut residue did not influence seed cotton yields, leaf N concentrations, or plant N uptake for either growth stage or year of the experiment. There was a trend for peanut residue to increase whole plant biomass measured at the first square in two of three years. Seed cotton yields and plant parameters measured at the first square and mid-bloom responded favorably to spring N applications, but the recommended 101 kg N ha −1 did not maximize yields. The results from this study indicate
Time-metric equivalence and dimension change under time reparameterizations

We study the behavior of dynamical systems under time reparameterizations, which is important not only to characterize chaos in relativistic systems but also to probe the invariance of dynamical quantities. We first show that time transformations are locally equivalent to metric transformations, a result that leads to a transformation rule for all Lyapunov exponents on arbitrary Riemannian phase spaces. We then show that time transformations preserve the spectrum of generalized dimensions D_{q} except for the information dimension D1 , which, interestingly, transforms in a nontrivial way despite previous assertions of invariance. The discontinuous behavior at q=1 can be used to constrain and extend the formulation of the Kaplan-Yorke conjecture.
On Optimum and Nearly Optimum Data Quantization for Signal Detection

The application of companding approximation theory to the quantization of data for detection of coherent signals in a noisy environment is considered. This application is twofold, allowing for greater simplicity in both analysis and design of quantizers for detection systems. Most computational methods for designing optimum (most efficient) quantizers for signal detection systems are iterative and are extremely sensitive to initial conditions. Companding approximation theory is used here to obtain suitable initial conditions for this problem. Furthermore, the companding approximation idea is applied to design suboptimum quantizers which are nearly as efficient as optimum quantizers when the number of levels is large. In this design, iteration is not needed to derive the parameters of the quantizer, and the design procedure is very simple. In this paper, we explore this approach numerically and demonstrate its effectiveness for designing and analyzing quantizers in detection systems.
Periodontal disease, Porphyromonas gingivalis, and rheumatoid arthritis: what triggers autoimmunity and clinical disease?

Rheumatoid arthritis, currently regarded as a complex multifactorial disease, was initially characterized as such at the turn of the 19th century. Ever since, multiple lines of investigation have attempted to elucidate the etiological factor(s) involved in disease incidence. Genes – including those risk alleles within HLA-DR4 – have been implicated but are insufficient to explain the vast majority of cases. Several environmental factors, therefore, are being studied. Among them, the role of periodontal disease and Porphyromonas gingivalis in the pathogenesis of rheumatoid arthritis has attracted both clinical and bench interest given supportive epidemiologic and mechanistic data.
Serum proteomics reveals systemic dysregulation of innate immunity in type 1 diabetes

Using global liquid chromatography-mass spectrometry (LC-MS)–based proteomics analyses, we identified 24 serum proteins that were significantly variant between those with type 1 diabetes (T1D) and healthy controls. Functionally, these proteins represent innate immune responses, the activation cascade of complement, inflammatory responses, and blood coagulation. Targeted verification analyses were performed on 52 surrogate peptides representing these proteins, with serum samples from an antibody standardization program cohort of 100 healthy control and 50 type 1 diabetic subjects. 16 peptides were verified as having very good discriminating power, with areas under the receiver operating characteristic curve ≥0.8. Further validation with blinded serum samples from an independent cohort (10 healthy control and 10 type 1 diabetics) demonstrated that peptides from platelet basic protein and C1 inhibitor achieved both 100% sensitivity and 100% specificity for classification of samples. The disease specificity of these proteins was assessed using sera from 50 age-matched type 2 diabetic individuals, and a subset of proteins, C1 inhibitor in particular, were exceptionally good discriminators between these two forms of diabetes. The panel of biomarkers distinguishing those with T1D from healthy controls and those with type 2 diabetes suggests that dysregulated innate immune responses may be associated with the development of this disorder.
Protein Kinase C Is Involved in the Early Signals of Interferon-α But Not of Interferon-γ in U937 Cells

Increasing interest is being focused on the role of protein kinase C (PKC) in the mode of action of interferons (IFNs). Here we report that IFN-a induced a transient translocation of PKC from the cytosol to the particulate fraction of U937 cells. In contrast, after IFN-7 treatment, no significant change in PKC activity could be observed. IFN-induced changes in membrane potential were also examined by means of a potential sensitive oxonol dye and flow cytometry. Hyperpolarization was induced by both IFN-a and IFN-7. The protein kinase inhibitor H-7 blocked the hyperpolarization induced by IFN-a but not by IFN-7. These concordant results suggest that PKC is involved in the early signals of IFN-a but not of IFN-7 in U937 cells.
Volume doubling measurement of spherical and ellipsoidal tumors

Volume doubling rulers are described for rapid estimation of tumor volume using projection areas of single-plane images such as chest radiographs. The potential utility of the rulers derives in part from the convenient relationships that exist for the interconversion of volume, volume doubling number, and decimal log growth or cell kill. The traditional approach to tumor volume doubling time determination, originated by Collins [1] uses the average diameter of approximately spherical tumors; analysis of the geometry of volume doubling shows this method to be nearly as accurate as methods that assume elliptical eccentricity, but only up to a tumor image length/width ratio of 1.5. For ratios greater than 1.5, it is shown that the clinical practice of taking perpendicular diameters is inherently more accurate. Where two perpendicular radiographic views of a tumor ellipsoid are available, it is shown that calculation of volume using the longest projection radius should result in less than one single volume doubling underestimate due to out-of-plane orientation of the long axis of the tumor. These methods should find greatest utility in measurement of multiple metachronous tumors that are well-circumscribed, convex in perimeter, and have low length/width ratios.
Are the Inotropic and Antiarrhythmic Effects of Bradykinin Due to Increases in Coronary Flow

Abstract The purpose of this research was to test whether the positive inotropic and antiarrhythmic effects of bradykinin are due solely to increases in coronary flow. Rat hearts were perfused at constant pressure (75 cm H 2 O) and temperature (37°C). Coronary flow was measured using an electronic drop counter. Contractile force was assessed using a left ventricular balloon catheter. Bradykinin (10 nmol/L) significantly increased coronary flow by 55 ± 8% above the control level of 4.8 ± 0.5 mL/min (n = 20), while force was increased by 23.1 ± 3% (n = 20). Ramiprilat (10 nmol/L) potentiated the vasodilatory and inotropic responses to 10 nmol/L bradykinin by 58 ± 8% (n = 5). When hearts were perfused at constant flow, bradykinin no longer produced a positive inotropic effect. Bradykinin, 10 or 100 nmol/L, under these conditions actually caused a negative inotropic effect of −24.8 ± 5% (n = 8) and −35 ± 11% (n = 3), respectively. In another 2 groups of hearts, also perfused at constant pressure, reperfusion arrhythmias were elicited after a 20-min period of complete global ischemia. In control hearts, the mean period of fibrillation was 7.3 ± 1.8 min (n = 10). This period was significantly reduced to 2.7 ± 0.7 min (n = 10) in hearts receiving 10 nmol/L bradykinin. In untreated hearts, the coronary flow during the reperfusion period increased over the baseline flow by a factor of 1.8 ± 0.2, and this factor was not significantly effected by bradykinin. These results suggest that only the positive inotropic, but not the antiarrhythmic, action of bradykinin is due to coronary vasodilation.
Discovery of Novel DNA Gyrase Inhibitors by High-Throughput Virtual Screening

The bacterial type II topoisomerases DNA gyrase and topoisomerase IV are validated targets for clinically useful quinolone antimicrobial drugs. A significant limitation to widely utilized quinolone inhibitors is the emergence of drug-resistant bacteria due to an altered DNA gyrase. To address this problem, we have used structure-based molecular docking to identify novel drug-like small molecules that target sites distinct from those targeted by quinolone inhibitors. A chemical ligand database containing approximately 140,000 small molecules (molecular weight, <500) was molecularly docked onto two sites of Escherichia coli DNA gyrase targeting (i) a previously unexplored structural pocket formed at the dimer interface of subunit A and (ii) a small region of the ATP binding pocket on subunit B overlapping the site targeted by coumarin and cyclothialidine drugs. This approach identified several small-molecule compounds that inhibited the DNA supercoiling activity of purified E. coli DNA gyrase. These compounds are structurally unrelated to previously identified gyrase inhibitors and represent potential scaffolds for the optimization of novel antibacterial agents that act on fluoroquinolone-resistant strains.
Current distribution of a VLF electric dipole antenna in the plasmasphere

[1] In a recent paper (Inan et al., 2003) a method of remediating enhanced energetic electron fluxes in the radiation belt was proposed in which injection of VLF whistler mode waves from spacecraft within the radiation belts would dramatically increase the pitch angle scattering of the relativistic electrons and cause these particles to be rapidly lost from the belts, thereby mitigating the flux enhancement. The VLF wave transmitting system discussed by Inan et al. (2003) involves electric dipole antennas. One of the most important characteristics of such an antenna is the current distribution along the length of the dipole, since it is this current which ultimately determines the amount of VLF power which can be radiated from the antenna into the plasma. In past work it has been assumed without proof that the dipole current has a triangular distribution. In the present work we determine the dipole antenna current distribution from first principles, constructing an integral equation of the Hallen type relating the current distribution to the wave vector potential. In this development it is assumed that the length of the thin cylindrical dipole antenna is small compared to the wavelength of whistler mode waves which propagate parallel to the Earth's magnetic field Bo. In the case of the dipole antenna oriented parallel to Bo, it is found that the assumption of a triangular current distribution is reasonable for antenna lengths up to hundreds of meters. For the case of the antenna perpendicular to Bo, it is found that the current decays exponentially along the antenna from the feed points to the antenna ends. In this case we find the conditions under which a triangular current distribution is still a reasonable approximation. We also give the conditions under which the quasi-static model of Balmain (1964) reasonably describes the electric fields associated with the dipole antenna.
PVAAS: identify variants associated with aberrant splicing from RNA-seq

Motivation: RNA-seq has been widely used to study the transcriptome. Comparing to microarray, sequencing-based RNA-seq is able to identify splicing variants and single nucleotide variants in one experiment simultaneously. This provides unique opportunity to detect variants that associated with aberrant splicing. Despite the popularity of RNA-seq, no bioinformatics tool has been developed to leverage this advantage to identify variants associated with aberrant splicing. Results: We have developed PVAAS, a tool to identify single nucleotide variants that associated with aberrant alternative splicing from RNA-seq data. PVAAS works in three steps: (i) identify aberrant splicings; (ii) use user-provided variants or perform variant calling; (iii) assess the significance of association between variants and aberrant splicing events. Availability and implementation: PVAAS is written in Python and C. Source code and a comprehensive user’s manual are freely available at: http://pvaas.sourceforge.net/.
Possible role of Toxoplasma gondii in brain cancer through modulation of host microRNAs

Background: The obligate intracellular protozoan parasite Toxoplasma gondii infects humans and other warm-blooded animals and establishes a chronic infection in the central nervous system after invasion. Studies showing a positive correlation between anti-Toxoplasma antibodies and incidences of brain cancer have led to the notion that Toxoplasma infections increase the risk of brain cancer. However, molecular events involved in Toxoplasma induced brain cancers are not well understood. Presentation of the hypothesis: Toxoplasma gains control of host cell functions including proliferation and apoptosis by channelizing parasite proteins into the cell cytoplasm and some of the proteins are targeted to the host nucleus. Recent studies have shown that Toxoplasma is capable of manipulating host micro RNAs (miRNAs), which play a central role in post-transcriptional regulation of gene expression. Therefore, we hypothesize that Toxoplasma promotes brain carcinogenesis by altering the host miRNAome using parasitic proteins and/or miRNAs. Testing the hypothesis: The miRNA expression profiles of brain cancer specimens obtained from patients infected with Toxoplasma could be analyzed and compared with that of normal tissues as well as brain cancer tissues from Toxoplasma uninfected individuals to identify dysregulated miRNAs in Toxoplasma-driven brain cancer cells. Identified miRNAs will be further confirmed by studying cancer related miRNA profiles of the different types of brain cells before and after Toxoplasma infection using cell lines and experimental animals. Expected outcome: The miRNAs specifically associated with brain cancers that are caused by Toxoplasma infection will be identified. Implications of the hypothesis: Toxoplasma infection may promote initiation and progression of cancer by modifying the miRNAome in brain cells. If this hypothesis is true, the outcome of this research would lead to the development of novel biomarkers and therapeutic tools against Toxoplasma driven brain cancers.
Tweezer Dexterity Aptitude of Dental Students

The rationale for using the Perceptual Ability Test (PAT) as a component in admissions decisions for dental schools is that candidates vary in an underlying aptitude that is predictive of degree of success in technique course performance and perhaps in clinical performance. There have been periodic attempts to identify tests that more directly measure manual dexterity aptitude that would supplement the predictive power of admissions decisions. Previous research has demonstrated that a commercially available "speeded" tweezer dexterity test (Johnson O'Connor Test #32022) is not associated with performance in dental school or dental practice. Our research investigated both Test #32022 and Test #18 that measure both speed and accuracy as potential predictors of dental school performance in technical and clinical courses. This article reports the results of a longitudinal, comparative study of tweezer dexterity scores for students at the University of the Pacific School of Dentistry during their first and last quarters in school. The goals of the study were to 1) evaluate the correlation between beginning students' scores on two different types of tweezer dexterity tests; 2) compare dental students' scores to normative data for the general population; 3) determine the effect of a dental curriculum on students' performance on Test #18; and 4) evaluate the two tests as potential dental school admission screening instruments in comparison to the PAT. Fifty first-quarter students were tested from a class of 134. Forty-nine of these students were retested on Test #18 during their final quarter. The predictor value of the initial scores for the two dexterity tests was assessed for seven outcome measures reflecting student technique performance. Analysis showed a significant correlation (r=0.318, p 0.05). The correlation between the first and final quarter administrations for Test #18 was r=0.517 (p<0.01). The predictive power of these tests for the seven educational outcomes measures was weak. Results suggest that dental student tweezer dexterity is no different from that of the general population and is not changed by completing a dental school curriculum. The ability for an applicant to perform successfully in dental school will not be reliably predicted by tweezer dexterity score.
Lessons learned in modeling schizophrenic and depressed responsive virtual humans for training

This paper describes lessons learned in developing the linguistic, cognitive, emotional, and gestural models underlying virtual human behavior in a training application designed to train civilian police officers how to recognize gestures and verbal cues indicating different forms of mental illness and how to verbally interact with the mentally ill. Schizophrenia, paranoia, and depression were all modeled for the application. For linguistics, the application has quite complex language grammars that captured a range of syntactic structures and semantic categories. For cognition, there is a great deal of augmentation to a plan-based transition network needed to model the virtual humans knowledge. For emotions and gestures, virtual human behavior is based on expert-validated mapping tables specific to each mental illness. The paper presents five areas demanding continued research to improve virtual human behavior for use in training applications
Coherence masking protection for speech in children and adults

In three experiments, we tested the hypothesis that children are more obliged than adults to fuse components of speech signals and asked whether the principle of harmonicity could explain the effect or whether it is, instead, due to children’s implementing speech-based mechanisms. Coherence masking protection (CMP) was used, which involves labeling a phonetically relevant formant (the target) presented in noise, either alone or in combination with a stable spectral band (the cosignal) that provides no additional information about phonetic identity and is well outside the critical band of the target. Adults and children (8 and 5 years old) heard stimuli that were either synthetic speech or hybrids consisting of sine wave targets and synthetic cosignals. The target and cosignal either shared a common harmonic structure or did not. An adaptive procedure located listeners’ thresholds for accurate labeling. Lower thresholds when the cosignal is present indicate CMP. Younger children demonstrated CMP effects that were both larger in magnitude and less susceptible to disruptions in harmonicity than those observed for adults. The conclusion was that children are obliged to integrate spectral components of speech signals, a perceptual strategy based on their recognition of when all components come from the same generator.
A clear test of rational voting

Two recent articles in Public Choice have provided empirical support for the rational hypothesis stating that differential voting turnout results from varying expected utility differences. (See Barzel and Silberburg, 1973.) Brody and Page used survey data to show that the likelihood of individual voting was increased by larger perceived differences between the candidates. Barzel and Silberberg found turnout to be positively related to the margin of victory. More essential to the issue of rationality is the extent to which voters make decisions coincident with their own self-interests. The inherent complexity of most electoral issues, with widely varying interpersonal costs and benefits, does not allow for a clear statement of the rational individual choice. rn this paper a unique electoral situation in Oregon will be explored to shed light on the ability of voters to make choices consistent with their own self-interests.
Response to Letter to the Editor: a counterweight is not necessary to implement simple, natural and comfortable single-leg cycle training

Dr. Dolmage and colleagues commented on a recent publication titled, "Cardiovascular responses to counterweighted single-leg cycling: implications for rehabilitation." They assert that a counterweight is not required to facilitate natural single-leg cycling, rather a fixed gear ergometer can also accomplish the same goal. We agree with Dolmage and colleagues that a fixed gear ergometer can facilitate natural single-leg cycling with minimal deviation in the angular velocity of the crank if the kinetic energy of the flywheel is large. We also present some simple comparisons between the two modalities.
Bilateral vs Single Internal Thoracic Artery Grafting for Left Main Coronary Artery Occlusion

This study was conducted to compare the coronary flow distributed by single and bilateral internal thoracic artery (ITA) grafts in the setting of the left main coronary occlusion. Ten dogs underwent coronary artery bypass grafting through a left thoracotomy, off pump, using a brief local occlusion to perform the anastomosis. Dogs were randomly assigned to receive either a single left ITA (LITA) graft to the circumflex coronary artery (CFX), or bilateral ITA grafts, with additional placement of the right ITA (RITA) to the left anterior descending artery (LAD). After the grafts were placed, the left main coronary artery was ligated. Electromagnetic flows were obtained in the LAD and the CFX proximally and distally to ITA grafts in both groups before grafting and after grafting. ITA flow in situ was also measured before rotation from the chest wall. Total left ventricular flow requirements were satisfied equally well by either a single LITA graft (116.7±11.6 mL/min) or bilateral ITA grafts (total, 116.8±9.6 mL/min divided as LITA, 55.9±7.4 mL/min; RITA, 60.9±12.0 mL/min). When two grafts were replaced, competitive flow in the proximal regions of both native vessels was noted, although basal flow requirements were maintained. When an individual graft was occluded in the bilaterally grafted system, the remaining graft immediately recruited the additional flow, demonstrating that either right or left ITA can support flow demands five to six times higher than in situ chest wall flow (RITA, 21.9±3.1 mL/min; LITA, 22.3±4.9 mL/min). These data suggest that in this canine model, a single ITA graft can support the entire flow requirements of the left ventricle. Assuming no intervening stenosis is present in native coronary systems, bilateral ITA grafting may provide a margin of safety, but under resting conditions, provides no perfusion advantages over a single ITA graft.
Computational Materials Data: An Update

The June 2011 announcement of the Materials Genome Initiative (MGI) by the National Science and Technology Council of the Executive Office of the President [1] spurred a significant amount of activity in the materials science and engineering world on issues related to materials data and data-driven approaches for developing new materials and processing methods. MGI, in many ways, builds on previous U.S. and international efforts to promote the development and use of integrated computational materials engineering (ICME) as a way to accelerate advanced materials discovery and deployment. In April 2012, one of the authors published a guest editorial in this journal [2] describing efforts being undertaken by ASM International to support the goals of the MGI. At that time, ASM had recently announced the launch of a national Center for Computational Materials Science and Engineering Data (CCMSED); the name was changed later that year to the current Computational Materials Data (CMD) Network. Then as now, the objective of the CMD Network is to collect, refine, and disseminate information and resources to assist the MGI/ ICME community with its materials data challenges and needs. Since its launch, the CMD Network has had an active role in a number of collaborative projects, providing materials data management guidance and support. The experience and insights gained in the course of this work, as noted in Table 1, are made available to all on the CMD Network web site [3]. Structural Materials Data Demonstration Project