cssi/SciSciGPT-SciSciNet huggingface dataset:
Near real-time vaccine safety surveillance with partially accrued data†

Purpose The Vaccine Safety Datalink (VSD) Project conducts near real-time vaccine safety surveillance using sequential analytic methods. Timely surveillance is critical in identifying potential safety problems and preventing additional exposure before most vaccines are administered. For vaccines that are administered during a short period, such as influenza vaccines, timeliness can be improved by undertaking analyses while risk windows following vaccination are ongoing and by accommodating predictable and unpredictable data accrual delays. We describe practical solutions to these challenges, which were adopted by the VSD Project during pandemic and seasonal influenza vaccine safety surveillance in 2009/2010. Methods Adjustments were made to two sequential analytic approaches. The Poisson-based approach compared the number of pre-defined adverse events observed following vaccination with the number expected using historical data. The expected number was adjusted for the proportion of the risk window elapsed and the proportion of inpatient data estimated to have accrued. The binomial-based approach used a self-controlled design, comparing the observed numbers of events in risk versus comparison windows. Events were included in analysis only if they occurred during a week that had already passed for both windows. Results Analyzing data before risk windows fully elapsed improved the timeliness of safety surveillance. Adjustments for data accrual lags were tailored to each data source and avoided biasing analyses away from detecting a potential safety problem, particularly early during surveillance. Conclusions The timeliness of vaccine and drug safety surveillance can be improved by properly accounting for partially elapsed windows and data accrual delays. Copyright © 2011 John Wiley & Sons, Ltd.
Events: a structuring mechanism for a real-time runtime system

Recent progress in the implementation of the ORE real-time programming language is reported. A summary of the important features of the language is included. Progress in designing a runtime system for the language is reported. The design issues are discussed. A model of ORE processes is described. The set of operations defined on events, strips, and processes is described. Examples of the implementation of specific ORE features using this mechanism are illustrated. >
Response by Carcelén-Estrada to “Betraying Empire: Translation and the Ideology of Conquest”

Vicente Rafael and I share a host of common interests regarding empire and translation: the use of translation as a colonial tool for the codification of postcolonial subjects within the grammar of...
DILITHIATION OF 1-BENZENESULFONYLINDOLES

Benzenesulfonylindole is converted to a dilithio derivative by 2.2 equivalents of lithiating reagent. The dilithio derivative gives rise to sultones on reaction with carbonyl compounds. This reaction proceeds by an intramolecular displacement of the indole group from the bis-adduct. Fair to poor yields of the 2-indolycarbinols can also be isolated. Benzoyl chloride forms a thiazine dioxide ring by addition at both the 2-indolyl and 2′-phenylsulfonyl positions. 3-Methyl-1-benzenesulfonylindole is also easily dilithiated.
Presenilin modulates Pen-2 levels posttranslationally by protecting it from proteasomal degradation.

The γ-secretase complex functions to cleave several type I transmembrane proteins within their transmembrane domains. These include the amyloid precursor protein, which is central to Alzheimer's disease pathogenesis, as well as N-cadherin and Notch, which regulate transcription. This complex is composed of four requisite integral membrane proteins: presenilin 1 (PS1) or presenilin 2 (PS2), nicastrin, Pen-2, and Aph-1. How these proteins coordinately regulate one another and assemble to form a functional complex is not well understood. In this report we demonstrate that PS1 selectively enhances the stability of Pen-2 protein but not that of nicastrin or Aph-1. In the absence of PS1, Pen-2 was rapidly degraded by the proteasome. As PS1 levels increased, so too did the half-life of Pen-2 and therefore its steady-state levels. In addition, Pen-2 protein levels correlated with PS1 levels not only in cell culture but in transgenic mouse models as well. The genetic absence of PS1 and PS2, and therefore of γ-sec...
Generalized order statistics, Bahadur representations, and sequential nonparametric fixed-width confidence intervals☆

Abstract Let X 1 ,…, X n be an i.i.d. sample from df F , let H F be the df of h ( X 1 ,…, X m ), based on a given ‘kernel’ h ( x 1 ,…, x m ), and consider confidence interval estimation of a parameter of the form H -1 F ( p ). This paper introduces confidence intervals formed by a pair of ‘generalized order statistics’, develops Bahadur-type representation theory for these order statistics, and constructs corresponding sequential fixed-width confidence interval procedures. Previous work of Bahadur (1966) and Geertsema (1970) is sharpened and extended.
The Strong Stability and Instability of a Fluid-Structure Semigroup

The strong stability problem for a fluid-structure interactive partial differential equation (PDE) is considered. The PDE comprises a coupling of the linearized Stokes equations to the classical system of elasticity, with the coupling occurring on the boundary interface between the fluid and solid media. Because of the nature of the unbounded coupling between fluid and structure, the resolvent of the associated semigroup generator will not be a compact operator. In consequence, the classical solution to the stability problem, by means of the Nagy-Foias decomposition, will not avail here. Moreover, it is not practicable to write down explicitly the resolvent of the fluid-structure generator; this situation thus makes it problematic to use the well-known semigroup stability result of Arendt-Batty and Lyubich-Phong. When a locally supported boundary dissipative mechanism is in place, we derive here a result of strong decay for this fluid-structure PDE. In the absence of said dissipative mechanism, we show the lack of asymptotic decay for solutions corresponding to arbitary initial data of finite energy.
INTERNATIONAL DIFFERENCES IN CAPITAL RETURNS AND WAGE RATES

SUMMARY The disparities in international differences between wage rates and between the rates of return on capital cannot be fully explained by using the functional relationship between the wage/rental ratio and the capital/labor ratio. Nor can it be explained adequately by the differences in the degree of international mobility of the two factors. This paper presents an alternative explanation of the disparities. They are attributed to the fact that the output/labor ratios vary across countries much more widely than the output/capital ratios, which fact in turn may be explained by the typically greater degree of labor/capital substitutability toward the higher labor/capital end of the isoquants, and the international differences in the efficiency of production functions.
Regulation of mammalian mitochondrial translation by post-translational modifications.

Abstract Mitochondria are responsible for the production of over 90% of the energy in eukaryotes through oxidative phosphorylation performed by electron transfer and ATP synthase complexes. Mitochondrial translation machinery is responsible for the synthesis of 13 essential proteins of these complexes encoded by the mitochondrial genome. Emerging data suggest that acetyl-CoA, NAD + , and ATP are involved in regulation of this machinery through post-translational modifications of its protein components. Recent high-throughput proteomics analyses and mapping studies have provided further evidence for phosphorylation and acetylation of ribosomal proteins and translation factors. Here, we will review our current knowledge related to these modifications and their possible role(s) in the regulation of mitochondrial protein synthesis using the homology between mitochondrial and bacterial translation machineries. However, we have yet to determine the effects of phosphorylation and acetylation of translation components in mammalian mitochondrial biogenesis. This article is part of a Special Issue entitled: Mitochondrial Gene Expression.
A recent version of MELCOR for fusion safety applications

Abstract During the engineering design activity (EDA) of ITER, the MELCOR 1.8.2 code was selected as one of several codes to be used to perform ITER safety analyses. MELCOR was chosen because it has the capabilities of predicting thermal–hydraulic transients and self-consistently accounting for aerosol transport in nuclear facilities and reactor cooling systems. The Idaho National Laboratory (INL) Fusion Safety Program (FSP) organization made fusion specific modifications to the MELCOR 1.8.2 code that allows MELCOR to assess the thermal–hydraulic response of fusion reactor cooling systems and the transport of radionuclides as aerosols during accident conditions. The ITER International Organization (IO) used this version of MELCOR to perform accident analyses for ITER's “Rapport Preliminaire de Surete” (Report Preliminary on Safety – RPrS). Because MELCOR has undergone many improvements since version 1.8.2 was released, the INL FSP introduced these same fusion modifications into MELCOR 1.8.6, and thereby produced a version of MELCOR 1.8.6 with similar capabilities to the version of MELCOR used by the ITER IO for the ITER RPrS. We have applied this recent version of MELCOR to the analysis of a large in-vessel water leak event examined in the ITER Generic Site Safety Report (GSSR). This paper presents the results of this analysis and compares these results to those obtained from the MELCOR 1.8.2 code.
Role perceptions, satisfaction, and performance: moderating effects of self-esteem and organizational level.

Abstract The moderating effects of organizational level and self-esteem on the relationships between role perceptions (i.e., role ambiguity and role conflict) and employee satisfaction and performance were examined. Previous research suggested that self-esteem, as an indicator of perceived self-competence, should act as a buffering element contingent upon an individual's organizational level. To test this possibility, data were collected from a sample of 161 hospital professional and support personnel. It was hypothesized that the negative effects of role ambiguity and conflict on satisfaction and performance would be attenuated by high self-esteem at lower organizational levels. Two of the four predicted interactions (ambiguity—satisfaction and conflict—performance) were obtained. The importance of considering the combined effects of both situational and individual difference variables as potential buffers against aversive role perceptions was discussed.
Perspectives on psychogenic versus biogenic factors in pain

T he focus article has served well to point out the ambiguity and controversy of psychogenic pain. It is far too often that a diagnosis of “psychogenic pain” is made by exclusion rather than the appropriate inclusive criteria. Keeping this in mind, it is understandable that the author has focused on establishing what psychogenic pain refers to (i.e., what is the “concept” and its implications). I address the central positions taken in the focus article separately. Psychogenic pain is a theoretical possibility that can stimulate new ways of thinking about pain. Dworkin theorizes that if the psychological process allowed the body to yield pain that in turn motivated pain behavior, this would allow for research to define which brain process caused the reaction. Fordyce has pointed out that too often a patient’s pain experiences are labeled “psychogenic” when repeated failures using the biomedical model result in persistence of pain.* This and the broad exclusionary criteria often related to treatment failure or the inability to uncover an obvious cause described in the American Psychiatric Association’ and the International Association for the Study of Pain5 classification systems solidifies the conclusion that pain of unknown origin implies our need to reexamine our limited understanding of pain, rather than leaping to the conclusion that such pains must be psychogenic. Table 1 of the focus article further enhances the view that in orofacial pains where the pathophysiologic mechanism is unclear, the suspected psycho-
Constructing load-balanced virtual backbones in probabilistic wireless sensor networks via multi-objective genetic algorithm

A connected dominating set CDS is used as a virtual backbone VB for efficient routing and broadcasting in wireless sensor networks WSNs. Currently, almost all existing works focus on constructing minimum-sized CDS under the deterministic network model. However, because of the existence of many probabilistic lossy links in WSNs, it is more practical to obtain a VB under the realistic probabilistic network model PNM. Moreover, load-balance factor cannot be neglected when constructing a VB to prolong network lifetime. Hence, in this paper, we propose a multi-objective genetic algorithm to construct a load-balanced VB under PNM. Through simulations, we demonstrate that our proposed methods extend network lifetime by 69% on average compared with the existing state-of-the-art approaches. Copyright © 2014 John Wiley & Sons, Ltd.
Pregnancy Outcomes after Fallopian Tube Recanalization: Oil-based versus Water-soluble Contrast Agents

PURPOSE To determine the pregnancy outcomes in patients undergoing fallopian tube recanalization (FTR) with use of oil-based versus water-soluble contrast agents. MATERIALS AND METHODS Ninety-three patients with unilateral or bilateral proximal tubal occlusion confirmed by hysterosalpingography or laparoscopy underwent FTR with use of water-soluble contrast material alone ( n = 50) or also had an oil-based agent injected into each tube after recanalization ( n = 43). Pregnancy rates and outcomes of the two groups were studied retrospectively. RESULTS With respect to differences between groups, only the body mass index proved to be a significant predictor (oil, 28.4; water, 24.7; P =.008). Mean age, duration of infertility, type of infertility, and initial diagnosis were comparable. There was a weak trend toward a higher pregnancy rate in the oil-based contrast material group, but it was not significant ( P =.64). The average time to pregnancy was 4.4 months with use of oil-based contrast material, compared to 7.7 months with use of only water-soluble contrast material ( P =.03). CONCLUSION The use of an oil-based agent had little effect on the rate of conception, but time to conception was reduced by more than 3 months.
Numerical simulation of nucleation, solidification, and microstructure formation in thermal spraying

Abstract A splat formation model has been developed based on the classic nucleation theory accounting for heterogeneous nucleation kinetic and crystal growth to predict the nucleation temperature and grain size distribution. The predicted grain size distribution has been compared with experimental data for molybdenum (Mo) splats on different substrates. The influence of the substrate material, interfacial thermal contact resistance, and wettability on the nucleation, grain size distribution, and rapid solidification process has been investigated. Based on scaling analysis, the nucleation delay and solidification times have been derived and compared with simulation results.
Photobioelectronic studies with thylakoid membranes

The research described in this paper presents a method for chemically modifying the surface of plant photosynthetic membranes in such a way that electrical contact can be made. Colloidal platinum was prepared, precipitated directly onto thylakoid membranes from aqueous solution, and entrapped on fiberglass filter paper. This composition of matter was capable of sustained simultaneous photoevolution of hydrogen and oxygen when irradiated at any wavelength (400–700 nm) in the chlorophyll absorption spectrum. Experimental data support the interpretation that part of the platinum metal catalyst is precipitated adjacent to the photosystem-I reduction site of photosynthesis and that electron transfer occurs across the interface between photosystem I and the catalyst. When contacted with metal electrodes, the thylakoid-platinum combination was capable of generating a sustained flow of current through an external load resistor. Procedures for preparing this material and experimental data on its catalytic and electronic properties are presented. Also presented is an analysis of the flow of photocurrent in terms of the interfacial electron transfer reactions that occur at the interfaces of the components of the assembly.
p38 Pathway Kinases as Anti-inflammatory Drug Targets

Mitogen-activated protein kinases (MAPK) are intracellular signaling molecules involved in cytokine synthesis. Several classes of mammalian MAPK have been identified, including extracellular signal-regulated kinase, c-jun N-terminal kinase, and p38 MAP kinase. p38alpha is a key MAPK involved in tumor necrosis factor alpha and other cytokine production, as well as enzyme induction (cyclooxygenase-2, inducible nitric oxide synthase, and matrix metalloproteinases) and adhesion molecule expression. An understanding of the broad biologic and pathophysiological roles of p38 MAPK family members has grown significantly over the past decade, as has the complexity of the signaling network leading to their activation. Downstream substrates of MAPK include other kinases (e.g., mitogen-activated protein-kinase-activated protein kinase 2) and factors that regulate transcription, nuclear export, and mRNA stability and translation. The high-resolution crystal structure of p38alpha has led to the design of selective inhibitors that have good pharmacological activity. Despite the strong rationale for MAPK inhibitors in human disease, direct proof of concept in the clinic has yet to be demonstrated, with most compounds demonstrating dose-limiting adverse effects. The role of MAPK in inflammation makes them attractive targets for new therapies, and efforts are continuing to identify newer, more selective inhibitors for inflammatory diseases.
Continuous tubular polymerization reactors—I.A detailed model

Abstract The mass and energy balances describing free-radical solution polymerizations in a tubular reactor are numerically solved. The kinetic expressions developed are general and include the branching mechanisms of transfer to polymer and terminal-double-bond polymerizations. The attendant equations of motion are solved for both the axial and radial velocity profiles. This resulting simulator is used to show the effect of design parameters and operating conditions on the performance of the reactor in terms of the quality and quantity of polymer produced. The parametric sensitivity shown by tubular polymerization reactors makes a detailed simulator invaluable for their proper operation and optimization.
Merocyanine 540-sensitized photoinactivation of leukemia cells : effects of dose fractionation

The differential sensitivity to merocyanine 540 (MC540)-sensitized photoirradiation of leukemia cells, selected solid tumor cells, and normal pluripotent hematopoietic stem cells has been successfully exploited for the extracorporeal purging of simulated autologous remission bone marrow grafts. In this communication, we compare the effects of fractionated vs continuous irradiation upon the MC540-sensitized photoinactivation of L1210 and K562 leukemia cells. Exposure to MC540 (15 micrograms/mL) and fractionated doses of white light inactivated fewer in vitro clonogenic cells than exposure to an equivalent dose of continuous irradiation, provided the irradiation doses were small (8.1-16.2 kJ/m2) and spaced 1-2 h apart. The dye-sensitized photoinactivation of leukemia cells was enhanced when cells were stored at 4 degrees C instead of 37 degrees C between irradiation periods, most likely in part because the cells were unable to repair sublethal photodynamic damages at the lower temperature. These data suggest that cells can recover from sublethal damage inflicted by the plasma membrane-active photosensitizer, MC540.
Dewatering of coalbed methane wells with hydraulic gas pump

The coalbed methane industry has become an important source of natural gas production. Proper dewatering of coalbed methane (CBM) wells is the key to efficient gas production from these reservoirs. This paper presents the Hydraulic Gas Pump as a new alternative dewatering system for CBM wells. The Hydraulic Gas Pump (HGP) concept offers several operational advantages for CBM wells. Gas interference does not affect its operation. It resists solids damage by eliminating the lift mechanism and reducing the number of moving parts. The HGP has a flexible production rate and is suitable for all production phases of CBM wells. It can also be designed as a wireline retrievable system. We conclude that the Hydraulic Gas Pump is a suitable dewatering system for coalbed methane wells.
Preference for signaled vs unsignaled shock in pigeons with implanted electrodes

Treadle presses in two pigeons produced changeover from a program of unsignaled, unavoidable, and inescapable shock to a program in which such shock was preceded by a 5.0-sec visual and auditory preshock signal. Different houselight colors were correlated with the two programs. Both Ss, albeit marginal in one S, spent more session time in the signaled shock program when the above conditions prevailed than if (a) only the stimulus correlated with the signaled shock program but not the preshock signal occurred or (b) neither preshock signal nor correlated stimulus occurred.
Timing and intensity of exercise for glucose control. Reply to Chacko E. [letter].

Keywords Aerobicfitness .Exerciseprescription .Glycaemiccontrol .LeanbodymassTo the Editor:DrChacko[1] is to be congratulated for herconsideration of the timing and intensity of physical activityupon improvements in glycaemic control in type 2 diabeticpatients. She suggests that the best timing for moderate exer-cise to improve glycaemic control in patients with type 2diabetesisbetween the 30and 90min post-meal mark. Whileher and the field’s focus on improving glycaemia with exer-cise is a valuable starting place, this exercise prescription isunlikely to produce the optimal health benefits for longevitythat exercise can provide in this growing population. Tooptimally improve health, increasing and maintaining fitnessand lean body mass must be considered. As regards fitness, a60 min/day walking only prescription would not meet theweeklymetabolicequivalents(METS)thresholdthathasbeenshown to result in a 10 year reduction in coronary heartdisease risk in high-risk patients [2]. Furthermore, walkingexercise alone may not maximally increase, or maintain, car-diovascular fitness and lean muscle mass, the latter of whichmustbemaintainedinordertocontinue walkingand physicalactivity throughout the ageing process. Our point here issimple: although our first goal should be to increase physicalactivity,wemustalsoprovidetype2diabeticpatientswiththecrucial ammunition needed for battling further disease devel-opmentandlivingahealthy,longlife[3].Thus,usingexerciseto improve glycaemic control in addition to maintaining aer-obic fitness and leanbodymass (strength)should all bea partofthe ‘exerciseformula’ prescribedtopatientswith, or atriskof developing, type 2 diabetes.
Confidentiality-preserving and fault-tolerant in-network aggregation for Collaborative WSNs

In Collaborative WSNs, sensing devices are owned and operated by different stakeholders with incentive to preserve the confidentiality of their individual sensors readings while contributing to statistics computed by the group. In such systems, in-network data processing presents high efficiency for energy and bandwidth, but unfortunately introduces several challenges related to data security and fault tolerance.
Bioethics and Deliberative Democracy: Five Warnings from Hobbes

Thomas Hobbes is one of the most ardent and thoroughgoing opponents of participatory democracy among Western political philosophers. Though Hobbes's alternative to participatory democracy-assent by subjects to rule by an absolute sovereign-no longer constitutes a viable political alternative for Westerners, his critique of participatory democracy is a potentially valuable source of insight about its liabilities. This essay elaborates five theses from Hobbes that stand as cogent warnings to those who embrace participatory democracy, especially those (such as most bioethicists) advocating for deliberative democracy based on a rational consensus model. In light of these warnings, the author suggests an alternative, modus vivendi approach to deliberative democracy that would radically alter the current practice of bioethics.
Structural integration, an alternative method of manual therapy and sensorimotor education.

Abstract Objectives: The objectives of this report are to review the clinical practice of Structural Integration (SI), an alternative method of soft-tissue manipulation and sensorimotor education, and to summarize the evidence to date for mechanism and clinical efficacy. Methods: The author's personal knowledge of SI literature, theory, and practice was supplemented by a database search, consultation with other senior SI practitioners, and examination of published bibliographies and websites that archive SI literature. Results: SI purports to improve biomechanical functioning as a whole by progressively approximating specific ideals of posture and movement, rather than to treat particular symptoms. Hypothesized mechanisms at the level of local tissue change include increases in soft-tissue pliability, release of adhesions between adjacent soft-tissue structures, and increased interstitial fluid flow with consequently improved clearance of nociceptive potentiators. Hypothesized mechanisms for more global c...
Abdominopelvic hemorrhage: correlation of CT positivity with the subsequent decision to perform blood transfusion.

The purpose of this study is to determine the role of computed tomography (CT) on the decision to administer blood transfusions in patients with abdominopelvic hemorrhage (trauma, surgery, invasive procedure, and spontaneous) and to determine the clinical parameters most likely to influence the decision to administer blood transfusions in patients with spontaneous abdominopelvic hemorrhage. In this IRB approved and HIPPA compliant study, retrospective analysis was performed on 298 patients undergoing abdominal and pelvic CT for suspected abdominopelvic hemorrhage and the CT reports and electronic medical records were reviewed. Odds ratios and 95% CI were calculated to compare the odds of abdominopelvic hemorrhage and transfusion for categorical and continuous predictors. The presence of abdominopelvic hemorrhage by CT was significantly associated with blood transfusions for trauma patients (p-value <0.0001) only. 106 patients with suspected spontaneous abdominopelvic hemorrhage had the lowest CT positivity rate (n = 23, 21.7%) but the highest blood transfusion rate (n = 62, 58.5%) compared to the patients with abdominopelvic hemorrhage from known preceding causes. In patients with spontaneous abdominopelvic hemorrhage, low hemoglobin and hematocrit levels immediately prior to obtaining the CT study were more predictive for receiving a blood transfusion (p-value <0.0001) than the presence of hemorrhage by CT. CT positivity is strongly correlated with the decision to administer blood transfusions for patients with abdominopelvic hemorrhage from trauma, indicating that CT studies play a significant role in determining the clinical management of trauma patients. For patients with spontaneous abdominopelvic hemorrhage, the decision to transfuse depends not on the CT study but on the patient’s hemoglobin and hematocrit levels. CT studies should therefore not be performed for the sole purpose of determining the need for blood transfusion in patients with spontaneous abdominopelvic hemorrhage.
A college course in cryptography and computer security

Back in 1978, when I was chairman of the Data Processing Department at SUNY/Farmingdale, which is located in the heart of the electronics and aerospace area on Long Island, I created a course in computer security. Since the intensive program's objective was programming efficiency [36 credits in computing and knowledge of at least two programming languages were required for a two-year degree], I decided to include several aspects of cryptography. Doing this helped to create student interest and also it provided an opportunity for mystudents to do some special programming.
Magnetic field gradient system for nuclear magnetic resonance microimaging

In this study we present an orthogonal magnetic field gradient system for nuclear magnetic resonance (NMR) microimaging applications. The construction details are given for a prototype assembly for proton microscopy inside a 50-mm vertical bore magnet, which is designed to fit into a commercial 300-MHz NMR probe. This system has been used to acquire images of the human spinal cord in vitro. Its performance has been evaluated and compared to that predicted by computer simulation.
Uncovering Nuclear Pore Complexity with Innovation

Advances in imaging and reductionist approaches have provided a high-resolution understanding of nuclear pore complex structure and transport, revealing unexpected mechanistic complexities based on nucleoporin functions and specialized import and export pathways.
Characterizing climate-change impacts on the 1.5-yr flood flow in selected basins across the United States: a probabilistic approach

AbstractThe U.S. Geological Survey Precipitation-Runoff Modeling System (PRMS) model was applied to basins in 14 different hydroclimatic regions to determine the sensitivity and variability of the freshwater resources of the United States in the face of current climate-change projections. Rather than attempting to choose a most likely scenario from the results of the Intergovernmental Panel on Climate Change, an ensemble of climate simulations from five models under three emissions scenarios each was used to drive the basin models.Climate-change scenarios were generated for PRMS by modifying historical precipitation and temperature inputs; mean monthly climate change was derived by calculating changes in mean climates from current to various future decades in the ensemble of climate projections. Empirical orthogonal functions (EOFs) were fitted to the PRMS model output driven by the ensemble of climate projections and provided a basis for randomly (but representatively) generating realizations of hydrolog...
Nucleotide usage, synonymous substitution pattern, and past recombination in genomes of Streptococcus pyogenes.

Abstract We examined (1) five variables summarizing nucleotide usage at synonymous sites; (2) pairwise patterns of nucleotide substitution among five genomes of Streptococcus pyogenes in order to examine the extent to which these variables are associated with past recombination events. Predicted prophage genes of MGAS10394 were characterized by an average pattern of nucleotide usage at synonymous sites that was distinct from that seen at most other genes. Ribosomal protein genes also showed a distinctive pattern, but one that differed from prophage genes in several key respects. The six most anomalous genes with respect to synonymous substitution in pairwise comparisons among the genomes included four prophage genes; these six genes were characterized by unusually high values of dS, suggesting that these genes had different evolutionary histories from those of the other shared genes in the genome. This hypothesis was supported by phylogenetic analyses, which revealed phylogenies inconsistent with that of the majority of genes. Eighty-nine genes outside prophage regions were found to resemble prophage genes with respect to nucleotide content and the pattern of synonymous substitution, suggesting that these genes may have been involved in horizontal gene transfers. Although prophage genes do show distinctive patterns of nucleotide composition, the results indicated that those patterns were not in themselves sufficient to distinguish all known prophage genes from other genes. On the other hand, nucleotide content, when suitably measured, can form one of a set of biological indicators that can be used to identify candidate genes for horizontal gene transfer.
A new method to address verification bias in studies of clinical screening tests: cervical cancer screening assays as an example.

Abstract Objectives Studies to evaluate clinical screening tests often face the problem that the “gold standard” diagnostic approach is costly and/or invasive. It is therefore common to verify only a subset of negative screening tests using the gold standard method. However, undersampling the screen negatives can lead to substantial overestimation of the sensitivity and underestimation of the specificity of the diagnostic test. Our objective was to develop a simple and accurate statistical method to address this “verification bias.” Study Design and Setting We developed a weighted generalized estimating equation approach to estimate, in a single model, the accuracy (eg, sensitivity/specificity) of multiple assays and simultaneously compare results between assays while addressing verification bias. This approach can be implemented using standard statistical software. Simulations were conducted to assess the proposed method. An example is provided using a cervical cancer screening trial that compared the accuracy of human papillomavirus and Pap tests, with histologic data as the gold standard. Results The proposed approach performed well in estimating and comparing the accuracy of multiple assays in the presence of verification bias. Conclusion The proposed approach is an easy to apply and accurate method for addressing verification bias in studies of multiple screening methods.
Parasitic Infections in Solid Organ Transplant Recipients

Parasitic diseases are rare infections after a solid organ transplant (SOT). Toxoplasmosis, Trypanosoma cruzi, and visceral leishmanias are the 3 main opportunistic protozoal infections that have the potential to be lethal if not diagnosed early and treated appropriately after SOT. Strongyloides stercoralis is the one helminthic disease that is life-threatening after transplant. This review addresses modes of transmission, methods of diagnosis, and treatment of the most serious parasitic infections in SOT. The role of targeted pretransplant screening of the donor and recipient for parasitic diseases is also discussed.
Source Apportionment of Fine (PM1.8) and Ultrafine (PM0.1) Airborne Particulate Matter during a Severe Winter Pollution Episode

Size-resolved samples of airborne particulate matter (PM) collected during a severe winter pollution episode at three sites in the San Joaquin Valley of California were extracted with organic solvents and analyzed for detailed organic compounds using GC-MS. Six particle size fractions were characterized with diameter (Dp) < 1.8 μm; the smallest size fraction was 0.056 < Dp < 0.1 μm which accounts for the majority of the mass in the ultrafine (PM0.1) size range. Source profiles for ultrafine particles developed during previous studies were applied to the measurements at each sampling site to calculate source contributions to organic carbon (OC) and elemental carbon (EC) concentrations. Ultrafine EC concentrations ranged from 0.03 μg m−3 during the daytime to 0.18 μg m−3 during the nighttime. Gasoline fuel, diesel fuel, and lubricating oil combustion products accounted for the majority of the ultrafine EC concentrations, with relatively minor contributions from biomass combustion and meat cooking. Ultrafine...
A TRAFFIC ASSIGNMENT PLANNING MODEL: THE LOAD-NODE CONCEPT

Abstract The use of the traffic assignment model in urban transportation planning is universal; however, traffic assignment in its present form is expensive, cumbersome, and has serious limitations. In this research the authors have developed and tested the load-node concept of traffic assignment which reduces many of these problems. In the load-node concept the corners of zone boundaries are used for points of trip origins and destinations. In this manner the zone centroids and associated connector linkages of the network are removed. This results in a substantial reduction in network coding. In this study the total number of nodes required to define the network decreased by almost 3000 to 995 and the number of links in the network decreased by two-thirds. The forecasted 1990 Phoenix metropolitan area was used to test this approach and the average link volumes of all-or-nothing capacity restraint assignments using both the load-node and zone centroid concepts formed the basis of the comparison. The analyses indicated the average link volumes of the two concepts are comparable. A probable reduction in computer time of 40 + per cent was obtained when the load-node concept was used. The authors suggest that this approach is primarily adaptable for planning purposes and not design. With respect to the design use of traffic assignment results, the travel between adjacent zones is seldom included in the major arterial street and freeway traffic volumes obtained from zone centroid assignment. This may result in a substantial underestimation of future traffic volume and turning movements particularly if stepped down 24-hr assignments are used for design purposes. The load-node approach does assign travel between adjacent zones.
Comparison of Thermal and Non-Thermal Ablation of Tumor Using Focused Short Pulse Laser Beam

For last few decades laser-induced tumor ablation has attracted significant attention of researchers. The accessibility of tumors located deep inside the body organ using fiber-optic probe without any major surgical resection has made this method an alternative for conventional surgical resection. Various minimally invasive techniques have been developed are used to ablate the tumor successfully with minimum collateral damages [1, 2]. All these techniques utilize the photo-thermal mechanism where conversion of laser energy (mainly from CW or long pulsed laser source) to heat energy leads to necrosis of the tissue through photocoagulation. Since, the necrosis of tumor is achieved by volumetric heating of the whole tumor there remains a significant chance of heat spreading out of the tumor volume damaging surrounding healthy tissue. Therefore, precise control of treatment parameters (laser pulse width, laser power, and irradiation time) is required to restrict the heat spread to the healthy tissue surrounding the tumor.Copyright © 2007 by ASME
The vasculopathy of autosomal dominant polycystic kidney disease: Insights from animal models

A 37-year-old white man with autosomal dominant polycystic kidney disease (ADPKD) was admitted to Boston's Beth Israel Hospital with sudden severe headache of two-hour duration. He was unconscious on admission. Emergency angiography revealed a ruptured 15 mm cerebral aneurysm. Emergency surgery to clip the aneurysm was unsuccessful, and the patient died 36 hours after admission. His serum creatinine was 3.2 mg/dL on admission; the rest of his laboratory values were within normal limits. A request for an autopsy was denied. At age 20, the patient and his then 15-year-old sister had abdominal ultrasound examinations that revealed bilateral renal cysts, consistent with the diagnosis of ADPKD. At age 32, the patient had a sudden, relatively severe, acute myocardial infarction (MI). Cardiac catheterization revealed three-vessel disease, and he subsequently underwent a triple coronary artery bypass operation. Throughout his medical course, the patient's blood pressure was in the 120/80 to 140/80 mm Hg range while he was taking lisinopril, 10 mg/day, which was started after his MI. The patient's mother has ADPKD and end-stage renal disease, and she is on hemodialysis. She recently underwent unsuccessful renal transplantation. There is no known family history of cerebral aneurysms. However, the mother had two cerebrovascular accidents and recovered from both. The patient's father had an MI at age 32, but he lived to age 64. A paternal uncle also died at an early age of an MI. The patient's younger sister was later screened for cerebral aneurysms and the test was negative. The patient's two young children have not been screened for ADPKD.
Lysophosphatidic acid promotes survival of androgen-insensitive prostate cancer PC3 cells via activation of NF-κB

BACKGROUND Dysregulated cell survival contributes to the poor efficacy of many chemotherapeutic regimens for patients with advanced prostate cancer. In this study we examined ability of the lipid growth factor lysophosphatidic acid (LPA), a G protein-coupled receptor (GPCR) ligand, to promote prostate cell survival. METHODS PC3 cells were used as a model to study mechanisms involved in survival of androgen-insensitive prostate cancer cells. Cell survival was measured by FACS analysis of cell cycle parameters after propidium iodide or annexin V and 7-AAD immunostaining. Activation state of nuclear facor-κB (NF-κB) was determined biochemically by nuclear translocation and transcriptional activation. Human tissue was analyzed for nuclear expression of NF-κB by immunohistochemistry. RESULTS Molecular dissection of the LPA-regulated PC3 cell survival revealed the sequential phosphorylation of Akt, IκB, and transcriptional activation of NF-κB. Both Akt and NF-κB were required to escape serum deprivation-induced cell death since their inhibition abrogated the LPA-mediated PC3 cell survival. Data from archival human tissue show that NF-κB is constitutively activated in prostate cancers, but not in benign prostate tissues. CONCLUSIONS Targeted disruption of the LPA receptor-Akt–NF-κB signaling axis may be effective for the treatment of androgen-insensitive prostate cancer. © 2004 Wiley-Liss, Inc.
Experimental examination of the “energy upconversion” theory for green plant photosynthesis

Abstract Spinach chloroplasts, dark adapted for periods of three days to three months, yield P700+ formation (electron spin resonance signal 1) on the first as well as the following flashes in an actinic series of xenon light flashes of 10 μs duration. These data are in contradiction with the prediction of the “energy upconversion” theory [F. K. Fong (1975) Appl. Phys. 6, 151-156] that only the second flash would be effective.
A modified position sensitive proportional counter with improved particle identification capability

Abstract A position sensitive proportional counter with a d E d x region has been modified to contain a section of plastic scintillator which is used to produce a signal proportional to particle energy. When used with the modified broad range magnetic spectrograph, excellent particle identification capability has been achieved. The design and performance of this detector are discussed.
A scanning electron microscopic study of arterial endothelial repair under turbulent flow conditions.

In order to study the role of hemodynamic factors on the healing and native morphology of endothelium in vivo, turbulent arterial flow was created using a loop bypass model, with and without occlusion in the recipient vessel. In this model, several different patterns of turbulent arterial blood flow resulted. The scanning electron microscope (SEM) was used to evaluate endothelial morphology in the area of the anastomoses at 3 and 14 days post-operatively. Morphological changes in the native endothelium along the recipient vessel correlated well with the direction of blood flow and predicted patterns of turbulence. The morphology of the native endothelium was altered to reflect the direction and pattern (laminar versus turbulent) of blood flow by 3 days post-operatively. Based on endothelial morphology, very narrow zones of separation could be demonstrated between areas of laminar and turbulent blood flow. The degree of reendothelialization across the suture itself was greatly variable at 3 days and there seemed to be no relationship to the location of turbulent flow.
Chronic inflammation and cancer: potential role of Bcl-2 gene family members as regulators of cellular antioxidant status

The incidence of cancer is increased in all gastrointestinal (GI) tissues as a result of chronic inflammation. These cancers may develop in cells that are selected for resistance to inflammatory products by virtue of overexpressing the antioxidant protein Bcl-2 or other Bcl-2 gene family members that have antioxidant activity. Unfortunately, Bcl-2 also functions as an anti-apoptotic. Bcl-2 overexpression can increase cellular lifetime and increase the likelihood that other cancer-related mutations will accumulate in individual cells. Thus, Bcl-2 expression is cytoprotective, but its expression also increases the risk of cancer incidence. This is perhaps more evident in the GI tract, which is exposed to more potential mutagens relative to other tissues.
Elastases and Elastin Degradation

The metabolic turnover of mature elastin fibers in adult animals is relatively slow. Although only small amounts of elastin are degraded normally, increased degradation and fragmentation of elastic fibers may play a significant role in disease processes. Elastinolytic enzymes are found in microorganisms, snake venoms, and in a number of mammalian cells and tissues, including pancreas, polymorphonuclear leukocytes, and macrophages. Elastinolytic enzymes fall into all 4 classes of proteinases (aspartic, cysteine, serine, and metallo) and show a spectrum of different specificities. All elastases studied to date have catalytic activity against protein and peptide substrates other than elastin. The presence of elastase activity is a virulence factor associated with the pathogenicity of Pseudomonas and other bacteria, dermatophytic fungi, and necrosis by rattlesnake venoms. Only elastinolytic enzymes are capable of inducing experimental pulmonary emphysema. Elastin degradation mediated by living macrophages and trophoblasts is confined to the immediate pericellular environment. Destruction of mature elastin by other mammalian elastases is probably the result of an imbalance in the normal inhibitor-proteinase ratio. The major plasma inhibitors contributing to the regulatory balance are α1-proteinase inhibitor and α2-macroglobulin.
Spirituality and Cognition: Does Spirituality Influence What We Attend to and Remember?

This study investigated how spirituality as a positive life theme might be related to one’s unique style of cognitive processing. Study participants included 80 individuals; 40 older adults and 40 younger adults. Word recall and recognition tasks assessed memory for positive, negative, neutral, and religious words. Results indicated that spirituality does not appear to be related to cognitive bias, but that words with either positive, negative, neutral, or religious connotations are recalled and recognized at different rates.