cssi/SciSciGPT-SciSciNet huggingface dataset:
Optical Methods for Measuring Single-Molecule Orientation and Position: Implications for Super-Resolution Microscopy

The quadrated pupil and double-helix PSF are modifications of epifluorescence microscopes that enable precise measurements of the single-molecule orientation. We explore how position estimation beyond the diffraction limit is affected by single-molecule orientation within cells.
Inhibition of CD1d1‐mediated antigen presentation by the vaccinia virus B1R and H5R molecules

Vaccinia virus (VV) has been most commonly used as the vaccine to protect individuals against the causative agent of smallpox (variola virus), but it also uses a number of strategies meant to evade or blunt the host's antiviral immune response. Natural killer T (NKT) cells are a subset of immunoregulatory CD1d-restricted T lymphocytes believed to bridge the innate and adaptive immune responses. It is shown here that the VV-encoded molecules, B1R and H5R, play a role in the ability of VV to inhibit CD1d-mediated antigen presentation to NKT cells. These are the first poxvirus-encoded molecules identified that can play such a role in the evasion of an important component of the innate immune response.
An observation of crack propagation in anti- plane shear

It is shown experimentally that in the absence of plasticity crack propagation in anti-plane shear occurs by the opening of semi-penny-shaped cracks which straddle the crack front at an angle of 45 degrees. It follows that if crack instability calculations are based on the assumption that a planar crack propagates in its own plane they are valid only if all shear stresses vanish along the crack periphery, i.e., if KIII is zero along that boundary.
Attribution of team members' responsibility: the effect of temporal pattern of performance

Two experiments were conducted to assess the effects of an individual's temporal pattern of success on attributions of responsibility for winning or losing a simulated free throw contest. In Experiment 1, subjects observed, via videotape, two teammates shooting free throws against an opposing team who had already completed their shots. The outcome (win or lose) of the contest was manipulated as well as the time at which one player made his shots (beginning or end of game). In Experiment 2, individual and team performance information was given to subjects without the videotape. In both experiments the player on a winning team who scored at the end was judged as more responsible for the outcome than when he succeeded at the beginning. When the team lost, however, succeeding at the beginning or end did not have an effect on responsibility attributions.
A comparison of general and explicit delay cues to reinforcement for tangible-maintained challenging behaviour

AbstractObjectives: This compares effects of explicit delay cue to reinforcement to general delay cue to reinforcement when attempting to decrease tangible-maintained challenging behaviours of children with autism spectrum disorder (ASD).Methods: Two school-age children with ASD participated in this study. In order to evaluate the effects of a general cue versus an explicit cue on the participants’ tangibly maintained challenging behaviours, a multiple baseline design across settings with an embedded alternating treatments design was used.Results: Results suggested that both types of delay cue to reinforcement demonstrated effectiveness on decreasing tangible-maintained behaviours of the participant. For both participants, an explicit delay cue demonstrated slightly better effects on the participants’ challenging behaviours then a general delay cue.Conclusions: This study adds an evidence to support that delayed reinforcement can be used as an effective strategy to reduce both escape and tangible-maintain...
AMNIOTIC FLUID INFECTIONS, A PROSPECTIVE STUDY

Fatal amniotic fluid infections were studied in a prospective analysis of 59,379 pregnancies. 31,494 well preserved placentas and approximately 60,000,000 pieces of medical, demographic, hereditary, social and postmortem data were analyzed using a log-linear model analysis of contingency tables to determine the significance of data. 386 cases were classified as amniotic fluid infections with intact membranes when acute chorioamnionitis, funisitis and inflammation of the chorionic plate were associated with acute congenital pneumonia. The fatal disorder had a frequency of 6.3/1000 live births making it the most common cause of perinatal death in the study. The disorder decreased after 27 wks gestation correlating with the appearance of antimicrobial activity in the amniotic fluid. It increased again after 37 wks when more bacteria gain access to the amniotic fluid. It was most common when gravida made few prenatal clinic visits. Many factors lost their association with the disorder when gravida made clinic visits, i.e. race, socioeconomic status, maternal age and numbers of prior pregnancies, abortions, fetal deaths and preterm deliveries. The disorder was strongly associated with gravida suboptimal weight gain suggesting that undernutrition may have a role in its genesis. The neonates had a pattern of growth retardation characteristic of undernutrition. Gravida who made few clinic visits had smaller weight gains than those who made more visits. Polyhydramnios was also correlated with the fatal disorder. (Supported by USPHS contract N01-NS-3-2311).
Assessment of Roles for Calreticulin in the Cross-Presentation of Soluble and Bead-Associated Antigens

Antigen cross-presentation involves the uptake and processing of exogenously derived antigens and their assembly with major histocompatibility complex (MHC) class I molecules. Antigen presenting cells (APC) load peptides derived from the exogenous antigens onto MHC class I molecules for presentation to CD8 T cells. Calreticulin has been suggested to mediate and enhance antigen cross-presentation of soluble and cell-derived antigens. In this study, we examined roles for calreticulin in cross-presentation of ovalbumin using a number of models. Our findings indicate that calreticulin does not enhance in vitro cross-presentation of an ovalbumin-derived peptide, or of fused or bead-associated ovalbumin. Additionally, in vivo, calreticulin fusion or co-conjugation does not enhance the efficiency of CD8 T cell activation by soluble or bead-associated ovalbumin either in wild type mice or in mice lacking Toll-like receptor 4 (TLR4). Furthermore, we detect no significant differences in cross-presentation efficiencies of glycosylated vs. non-glycosylated forms of ovalbumin. Together, these results point to the redundancies in pathways for uptake of soluble and bead-associated antigens.
Statistical methods for dependent competing risks

Many biological and medical studies have as a response of interest the time to occurrence of some event, X, such as the occurrence of cessation of smoking, conception, a particular symptom or disease, remission, relapse, death due to some specific disease, or simply death. Often it is impossible to measure X due to the occurrence of some other competing event, usually termed a competing risk. This competing event may be the withdrawal of the subject from the study (for whatever reason), death from some cause other than the one of interest, or any eventuality that precludes the main event of interest from occurring. Usually the assumption is made that all such censoring times and lifetimes are independent. In this case one uses either the Kaplan-Meier estimator or the Nelson-Aalen estimator to estimate the survival function. However, if the competing risk or censoring times are not independent of X, then there is no generally acceptable way to estimate the survival function. There has been considerable work devoted to this problem of dependent competing risks scattered throughout the statistical literature in the past several years and this paper presents a survey of such work.
A Semiparametric Factor Model of Interest Rates and Tests of the Affine Term Structure

Many continuous-time term structure of interest rate models assume a factor structure where the drift and volatility functions are affine functions of the state-variable process. These models involve very specific parametric choices of factors and functional specifications of the drift and volatility. Moreover, under the affine term structure restrictions not all factors necessarily affect interest rates at all maturities simultaneously. This class of so-called affine models covers a wide variety of existing empirical as well as theoretical models in the literature. In this paper we take a very agnostic approach to the specification of these diffusion functions and test implications of the affine term structure restrictions. We do not test a specific model among the class of affine models per se. Instead, the affine term structure restrictions we test are based on the derivatives of the responses of interest rates to the factors. We also test how many and which factors affect a particular rate. These test...
Laser traps for radioactive isotopes

The techniques of laser cooling and trapping now make it possible to observe large samples of stable atoms in a small volume at low temperature. This capability was recently extended to radioactive isotopes. This opens up new opportunities for the investigation of fundamental symmetries through measurements using radioactive atoms. In this paper we will discuss several fundamental measurements in atomic systems and how the ability to trap radioactive atoms will play an important role in improving the precision of such measurements. Measurements of the effects of the weak interaction are of particular note since they are becoming quite precise. In particular, we will describe in detail the system developed at Stony Brook to trap radioactive alkali atoms and measure weak interaction effects in francium isotopes.
Aspects of the water relations of the Formosan and eastern subterranean termites (Isoptera: rhinotermitidae)

Aspects of the water relations of worker and soldier Formosan subterranean, Coptotermes formosanus Shiraki, and eastern subterranean, Reticuliiermes flavipes (Kollar), termites were investigated. The percentage of total body water ranged from 55.68 ± 0.42% for C. formosanus female alates to 75.88 ± 0.36% for R. flavipes workers. Body water loss of both species increased linearly from 2 to 10 h at 30°C and 0–2% RH. Cuticular permeabilities ranged from 15.22 ± 0.93 μg cm−2 h−1 mmHg−1 for C. formosanus soldiers to 42.53 ± 0.21 μg cm−2 h−1 mmHg−1 for C. formosanus male alates. Cuticular permeability of C. formosanus soldiers was also significantly less than that of any stage of R. flavipes . Water loss at death ranged from 35.30 to 55.49% for C. formosanus soldiers and R. flavipes male alates, respectively. Water content of nest material ranged from 16.3 to 67.7% for both species.
SU-E-T-218: In Vivo 3D Dose Verification for IMRT Using Electronic Portal Imaging Device (EPID)

Purpose: To provide in vivo 3D dose verification for IMRT treatment sessions using an FFT‐based dose calculation method for heterogeneous media. Methods: Dosimetriccalibration of the EPID is performed using an ionization chamber with mini‐phantom. Optical scattering within the EPID is corrected to minimize systemic error. The dose‐response of EPID, i.e. EPID reading as a function of dose, is linear with dose. A fast ray‐tracing algorithm is developed to calculate the full 3D radiological length distribution within the heterogeneous phantom/patient and up to the EPID active imaging plane. Attenuation of the primary beam as a function of radiological length is approximated by a linear quadratic exponential function and its off‐axis variation is determined experimentally by transmittance measurements in order to account for the polyenergetic MV beams. An iterative algorithm is used to find a self‐consistent solution separating the total dose measured by the EPID into primary and scatter contributions through a phantom/patient. Calculation of the scatter contribution from phantom to EPID is achieved by first deconvolving the effect of EPID's internal lateral scattering, followed by the convolution of a 2D scatter kernel accounting for the patient scatter to EPID. Results: The dose‐response for the amorphous‐silicon (aSi) EPID has been obtained. The fast ray‐tracing algorithm has been developed and tested on both phantom and Rando phantom patient geometry. The linear quadratic parameters for our clinical 6MV beam have been estimated both on the central axis and off‐axis, and used for initial validation of this exit dose verification method. First result has shown that the estimated patient dose is within 5% of that calculated by the treatment planning system. Conclusions: With a fast kernel‐based 3D dose calculation algorithm, aSi EPID can potentially be used for dose verification as a routine patient QA procedure.
L-SELECTIN IS DOWN-REGULATED IN MURINE BLOOD AND BONE MARROW NEUTROPHILS FOLLOWING ENDOTOXIN STIMULATION. • 56

L-selectin, a surface neutrophil (PMN) adhesion molecule important in inflammatory endothelial interactions, may mediate the maturity-directed egress of marrow PMNs into the circulation. Surface L-selectin levels, high on myeloid progenitors, are diminished during PMN maturation and again up-regulated on mature PMNs (Lund-Johansen, Tersappen). L-selectin appears to be involved in the egress of bone marrow PMNs following cardiopulmonary bypass(Van Eeden et al.), and in vivo studies have shown that inflammatory cytokines and lipopolysaccharide (LPS) induce PMN egress. To test the hypothesis that bacterial endotoxin may alter surface expression of L-selectin on blood and marrow PMNs in vivo, we compared surface L-selectin expression on marrow and blood PMNs from adult mice (129Sv) after LPS injection. Paired intracardiac blood and femoral marrow samples were collected from controls (n=5) or 4 hr after 50 ug intraperitoneal LPS (n=5). Samples were indirectly stained with anti-murine L-selectin (Mel-14) or isotype control IgG, and analyzed by flow cytometry. L-selectin levels are shown below as mean channel fluorescence values, X ± SEM:Table We conclude that endotoxin down-regulates surface L-selectin levels on both bone marrow and blood PMNs, and speculate that its diminished effect on marrow PMNs may reflect differences in their maturational stage.
Depth from physics: develpoment of a robust classifier for 2D image analysis

Blood vessels overlying one another at distinct depths (and hence appearing to intersect) in the sclera of the eye can be distinguished reliably from those that in fact do branch within the same depth, using only the information contained in a single photograph of the conjunctiva. That conclusion arises from extension of earlier work that qualitatively inferred relative depth of vessels. The current research was motivated by the need to quantify such inferences in terms of their sensitivities and robustness. A physics first principles model forms the basis for selection of features that capture blood vessel depth information. Features extracted from the image are shown to be useful in that effort; their utility is verified with phantoms that mimic the behavior of the conjunctiva and sclera. Because no special preparations are needed, the method works as well on archived images as on newly-acquired ones, and thus can be used in retrospective studies of images of the eye and other diffuse media.
Optimal stocking densities of walleye fingerlings in Minnesota lakes

Abstract A generalized additive model was developed that described the effects of fingerling stocking density on the abundance of walleyes Sander vitreus in 551 lakes in Minnesota. Walleye abundance was measured as a catch per effort (CPE) from 1,511 standard Minnesota Department of Natural Resources gill-net assessments conducted during 1986–2004. In addition to fingerling stocking, the effects of lake morphometry, productivity, and fish community variables on walleye CPE were also described using a generalized additive model. Lake morphometry variables had sharply nonlinear effects on walleye abundance. Walleye abundance declined in lakes with areas less than 1,000 acres and increased rapidly in lakes with depths of less than 30 ft. The lake productivity variable, total alkalinity, was positively related to walleye abundance. Abundance of northern pike Esox lucius had a negative effect and abundance of yellow perch Perca flavescens a positive effect on walleye abundance. The response of walleye abundanc...
Increasing seasonal upwelling in the subtropical South Atlantic over the past 700,000 yrs: Evidence from deep-living planktonic foraminifera

Abstract The distribution and character of deep-living planktonic foraminifera (such asGloborotalia truncatulinoides andG. hirsuta) are particularly sensitive to the structure of the upper ocean because of the wide range of water depths over which their life cycles extend. Like other planktonic foraminifera, the deep-living species begin growing in shallow surface waters, but unlike the other species they continue growing while sinking into much deeper water. Their reproduction is synchronized with the seasonal deep-mixing and upwelling of nutrient-rich waters that precedes spring bloom. Where deep-mixing is curtailed the abundances of the deeper-dwelling species (G. hirsuta), the deeper-dwelling varieties (e.g., left-coilingG. truncatulinoides), and the larger (presumably faster-sinking) shells are reduced (leading to an apparent acceleration in shell development). These changes are observed today in transects from the seasonally deep-mixed subtropical gyres to the seasonally-stable surface waters equatorward of the subtropical convergences. Past changes in the abundance and character of these deep-living planktonic foraminifera have been measured in a Late Pleistocene record from the subtropical western South Atlantic Ocean. Over the past 700 kyrs, abundances of these species have increased,G. truncatulinoides has changed from the predominantly shallower-dwelling right-coiling to the deeper-dwelling left-coiling variety, and the accelerated shell development characteristic of shallow mixing has shifted toward the rates normally associated with deep mixing. All this indicates that the structure of the upper ocean in the subtropical South Atlantic before 700 kyrs ago was more like that nearer the equator today where mixing is limited to the upper 100–200 m. Since that time the scale of mixing has gradually increased to more than 400 m. This implies a gradual increase through the Late Pleistocene in the seasonal upwelling of nutrients in the subtropical South Atlantic and, consequently, in the intensity of the seasonal maximum in organic productivity.
An extension of the cross-depolarization method: Subspectral editing in CP/MAS NMR

Abstract A modification of the cross-depolarization method in CP/MAS NMR is described which allows simultaneous nulling of both methine and methylene carbon signals despite their different sensitivities to cross depolarization. Extension of the cross-depolarization time, partially inverting methine as well as methylene carbon signals, followed by a suitably chosen brief period of normal cross polarization (“cross repolarization”), nulls all signals arising from proton-bearing carbons in rigid-lattice environments. Since selective nulling of methylene or methine carbon signals is also possible by cross depolarization, spectral editing readily gives separate methine and methylene subspectra.
Toward Developing an Objective 4DVAR BDA Scheme for Hurricane Initialization Based on TPC Observed Parameters

Abstract This study aims to make the four-dimensional variational (4DVAR) bogus data assimilation (BDA) scheme for hurricane initialization first proposed by Zou and Xiao more objective. The BDA scheme consists of two steps: (i) specifying a bogus sea level pressure (SLP) field based on parameters observed by the Tropical Prediction Center (TPC) and (ii) assimilating the bogus SLP field under a forecast model constraint adjusting all model variables. In previous studies, specification of the bogus SLP was based on Fujita's formula, requiring the central SLP pressure (Pc), the radius of the outermost closed isobar (Rout), and the radius of the maximum SLP gradient (R0) as inputs. Although the parameters Pc and Rout are provided directly by the TPC, R0 is not. In this research, an empirical linear model designed to determine the value of R0 (the size of the bogus vortex) from the TPC observed radius of 34-kt wind (R34kt) is developed. Numerical experiments are carried out for the initialization and predicti...
E4DVar: Coupling an Ensemble Kalman Filter with Four-Dimensional Variational Data Assimilation in a Limited-Area Weather Prediction Model

AbstractA hybrid data assimilation approach that couples the ensemble Kalman filter (EnKF) and four-dimensional variational (4DVar) methods is implemented for the first time in a limited-area weather prediction model. In this coupled system, denoted E4DVar, the EnKF and 4DVar systems run in parallel while feeding into each other. The multivariate, flow-dependent background error covariance estimated from the EnKF ensemble is used in the 4DVar minimization and the ensemble mean in the EnKF analysis is replaced by the 4DVar analysis, while updating the analysis perturbations for the next cycle of ensemble forecasts with the EnKF. Therefore, the E4DVar can obtain flow-dependent information from both the explicit covariance matrix derived from ensemble forecasts, as well as implicitly from the 4DVar trajectory. The performance of an E4DVar system is compared with the uncoupled 4DVar and EnKF for a limited-area model by assimilating various conventional observations over the contiguous United States for June 2...
Bax does not have to adopt its final form to drive T cell death

The introduction of antigen into animals causes antigen-specific T cells to divide and then die. Activated T cell death requires either of the death effector molecules, Bak or Bax. When T cells die, Bak and Bax change their conformations, a phenomenon that is thought to be required for Bak or Bax to drive cell death. Here we show that Bak changes conformation before activated T cells die, as detected by an antibody specific for a peptide near the NH2 terminus of Bak, but Bax does not change its shape markedly until after the cells are dead, as detected by an antibody specific for a peptide near the NH2 terminus of Bax. This latter finding is also true in activated T cells that lack Bak and are therefore dependent on Bax to die. This result suggests that Bax does not have to adopt its final, completely unfolded form until after the cells are dead.
A Historical Overview of Health Disparities and the Potential of eHealth Solutions

Over the past decade, a rapidly expanding body of literature has demonstrated the existence of disparities in health and health care. While consensus has not emerged regarding the causes of disparities, they are generally thought to be related to sociocultural, behavioral, economic, environmental, biologic, or societal factors. To effectively address disparities, several authorities have suggested the need for greater information technology research and investments. eHealth researchers may be able to make significant contributions in this area through research and its applications. This paper begins with a historical overview of health disparities in the United States and Europe. It then discusses the role that the Internet, and access to the Internet, may play in the genesis of health disparities. Finally, this paper closes with a discussion of the potential benefits of eHealth applications and the possible contributions of the field to overcoming disparities in health and health care.
Developing a novel test to detect cancer genes from microarray data

DNA microarray technology can simultaneously screen thousands of gene expression profiles, transforming how genetics is applied in medicine. However, the lack of normality in microarray data renders common statistical methods ineffective. We propose a novel statistical method which does not require stringent assumptions but is still more powerful than some of its competitors. Using both simulation studies and clinical data, we show that our novel method outperforms previous methods. The limiting distribution for the proposed test is obtained for under null and alternative hypotheses. The proposed test will help make cancer treatment and gene therapy more successful, and it may facilitate research regarding cancer vaccinations. The proposed test may also help in the development of a prediction model in genetic profiling studies built on a subset of differentially expressed genes and the clinical data to assess the accuracy of the clinical prediction.
Multifunctional Unmanned Aerial Vehicle Wing Spar for Low-Power Generation and Storage

DOI: 10.2514/1.C031542 This paper presents the investigation of a multifunctional energy harvesting and energy-storage wing spar for unmanned aerial vehicles. Multifunctional material systems combine several functionalities into a single device in order to increase performance while limiting mass and volume. Multifunctional energy harvesting can be used to provide power to remote low-power sensors on unmanned aerial vehicles, where the added weight or volume of conventional harvesting designs can hinder flight performance. In this paper, a prototype self-charging wing spar containing embedded piezoelectric and battery elements is modeled, fabricated, and tested to evaluate its energy harvesting and storage performance. A coupled electromechanical model based on the assumed modes method is developedtopredictthevibrationresponseandvoltageresponseofacantileveredwingsparexcitedunderharmonic base excitation. Experiments are performed on a representative self-charging wing spar, and the results are used to verify the electromechanical model. The power-generation performance of the self-charging wing spar is investigatedindetailforharmonicexcitationinclamped–freeboundaryconditions.Experimentsarealsoconducted to demonstrate the ability of the wing spar to simultaneously harvest and store electrical energy in a multifunctional manner.Itisshownthat,foraninputbaseaccelerationlevelof0:25 gat28.4Hzatthebaseofthestructure,1.5mW of regulated dc power isdelivered from the piezoelectric layers to the thin-film battery, resulting in a stored capacity of 0.362 mAh in 1 h.
Adaptive arrays&#8212;An introduction

Adaptive array antenna systems are currently the subject of intense interest and investigation/development for radar and communications applications. The principal reason for the interest is their ability to automatically steer nulls onto undesired sources of interference, thereby reducing output noise and enhancing the detection of desired signals. These systems usually consist of an array of antenna elements and a real-time adaptive receiver-processor which has feedback control over the element weights. This paper provides a tutorial introduction to adaptive arrays from the viewpoint of antenna beam-forming and null steering. The particular vehicle chosen for discussion is the Howells-Applebaum analog servo-control-loop processor. This processor derives feedback control error signals from the correlations between element signals, i.e., on the basis of the covariance matrix of the set of system inputs. A simple two-element array with a single adaptive control loop is addressed first, in order to set the stage for analysis of a basic K-element linear array with K adaptive control loops. The set of linear differential equations associated with the controlloop network can be solved by a Q-matrix transformation into orthonormal eigenvector space. The purely mathematical Q-matrix is interpreted in terms of orthogonal beam-forming networks, similar in principle to a Butler matrix beam-forming network. The Q-matrix network produces a set of K orthogonal normalized eigenvector beams whose output powers are proportional to the eigenvalues of the covariance matrix. These beams are utilized in a convenient expression for calculating the time-dependent output pattern function for the array. Performance characteristics have been calculated for different distributions of interference sources to demonstrate the effects of power level, source location with respect to the quiescent beam pattern, source spacing in terms of array resolution, source bandwidth, continuous source distributions, and the array "degrees of freedom" captured. Two modifications of the basic system are also included: the addition of a hard-limiter in the control loops, and a change in the antenna aperture element arrangement to a circular array with an omni "mainbeam."
Effects of meal size, meal type, and body temperature on the specific dynamic action of anurans

Specific dynamic action (SDA), the increase in metabolism stemming from meal digestion and assimilation, varies as a function of meal size, meal type, and body temperature. To test predictions of these three determinants of SDA, we quantified and compared the SDA responses of nine species of anurans, Bombina orientalis, Bufo cognatus, Ceratophrys ornata, Dyscophus antongilli, Hyla cinerea, Kassina maculata, Kassina senegalensis, Pyxicephalus adspersus, and Rana catesbeiana subjected to meal size, meal type, and body temperature treatments. Over a three to seven-fold increase in meal size, anurans experienced predicted increases in postprandial rates of oxygen consumption \((\dot{\text{V}}\hbox{O}_{2}),\) the duration of elevated \(\dot{\text{V}}\hbox{O}_{2},\) and SDA. Meal type had a significant influence on the SDA response, as the digestion and assimilation of hard-bodied, chitinous crickets, mealworms, and superworms required 76% more energy than the digestion and assimilation of soft-bodied earthworms, waxworms, and neonate rodents. Body temperature largely effected the shape of the postprandial metabolic profile; peak \(\dot{\text{V}}\hbox{O}_{2}\) increased and the duration of the response decreased with an increase in body temperature. Variation in body temperature did not significantly alter SDA for four species, whereas both H. cinerea and R. catesbeiana experienced significant increases in SDA with body temperature. For 13 or 15 species of anurans ranging in mass from 2.4 to 270 g, SMR, postprandial peak \(\dot{\text{V}}\hbox{O}_{2},\) and SDA scaled with body mass (log–log) with mass exponents of 0.79, 0.93, and 1.05, respectively.
Evolving hard problems: Generating human genetics datasets with a complex etiology.

Background: A goal of human genetics is to discover genetic factors that influence individuals’ susceptibility to common diseases. Most common diseases are thought to result from the joint failure of two or more interacting components instead of single component failures. This greatly complicates both the task of selecting informative genetic variants and the task of modeling interactions between them. We and others have previously developed algorithms to detect and model the relationships between these genetic factors and disease. Previously these methods have been evaluated with datasets simulated according to pre-defined genetic models. Results: Here we develop and evaluate a model free evolution strategy to generate datasets which display a complex relationship between individual genotype and disease susceptibility. We show that this model free approach is capable of generating a diverse array of datasets with distinct gene-disease relationships for an arbitrary interaction order and sample size. We specifically generate eight-hundred Pareto fronts; one for each independent run of our algorithm. In each run the predictiveness of single genetic variation and pairs of genetic variants have been minimized, while the predictiveness of third, fourth, or fifth-order combinations is maximized. Two hundred runs of the algorithm are further dedicated to creating datasets with predictive four or five order interactions and minimized lower-level effects. Conclusions: This method and the resulting datasets will allow the capabilities of novel methods to be tested without pre-specified genetic models. This allows researchers to evaluate which methods will succeed on human genetics problems where the model is not known in advance. We further make freely available to the community the entire Pareto-optimal front of datasets from each run so that novel methods may be rigorously evaluated. These 76,600 datasets are available from http://discovery.dartmouth.edu/model_free_data/.
Digital Frequency-Lock Generator

A digital frequency-lock generator has been developed which produces an output pulse train automatically locked to the pulse repetition rate, or frequency, of an input pulse train. This device, which exhibits a wide capture range and has no static output frequency drift, offers several advantages over a phase-lock loop in frequency-locking applications.
An educational approach to voluntary improvement of dental radiological practices

Seventy-two private practices in middle Tennessee were surveyed for types and speeds of radiographic film used, work loads, equipment operators, intraoral radiographic technique, and darkroom procedures, among other items. A year after the survey, the offices were again visited, to determine the extent of improvement it deficiencies had been found. An educational approach to improvement of radiographic practices has been tested in 72 randomly selected private dental offices. Results confirmed the effectiveness of the approach in achieving reductions in patient exposure to levels approaching the practical minimum for routine clinical use, while maintaining or improving film diagnostic quality.
Special Boundary Integral Equations for Approximate Solution of Potential Problems in Three-dimensional Regions with Slender Cavities of Circular Cross-section

Dans les processus de formage qui necessite un echange de chaleur entre un dispositif de fixation permanent et le materiau etant soumis au formage, le moule ou matrice doit normalement etre chauffe ou refroidi par des ouvertures circulaires internes. Pour concevoir la localisation de ces ouvertures, il faut pouvoir calculer les temperatures dans le moule ou la matrice, et il faut calculer le potentiel electrique entourant une configuration tridimensionnelle des conducteurs elances. Presentation d'une methode de calcul dans ce but
The Dynamics and Mechanics of Endothelial Cell Spreading

Cell adhesion to extracellular matrix is mediated by receptor-ligand interactions. When a cell first contacts a surface, it spreads, exerting traction forces against the surface and forming new bonds as its contact area expands. Here, we examined the changes in shape, actin polymerization, focal adhesion formation, and traction stress generation that accompany spreading of endothelial cells over a period of several hours. Bovine aortic endothelial cells were plated on polyacrylamide gels derivatized with a peptide containing the integrin binding sequence RGD, and changes in shape and traction force generation were measured. Notably, both the rate and extent of spreading increase with the density of substrate ligand. There are two prominent modes of spreading: at higher surface ligand densities cells tend to spread isotropically, whereas at lower densities of ligand the cells tend to spread anisotropically, by extending pseudopodia randomly distributed along the cell membrane. The extension of pseudopodia is followed by periods of growth in the cell body to interconnect these extensions. These cycles occur at very regular intervals and, furthermore, the extent of pseudopodial extension can be diminished by increasing the ligand density. Measurement of the traction forces exerted by the cell reveals that a cell is capable of exerting significant forces before either notable focal adhesion or stress fiber formation. Moreover, the total magnitude of force exerted by the cell is linearly related to the area of the cell during spreading. This study is the first to monitor the dynamic changes in the cell shape, spreading rate, and forces exerted during the early stages (first several hours) of endothelial cell adhesion.
Significance of flat epithelial atypia on mammotome core needle biopsy: should it be excised?

The aim of this study was to determine the morphologic types, associations, and significance of flat epithelial atypia (FEA) with or without atypical ductal hyperplasia (ADH) in mammotome core needle biopsies. We evaluated the correlation of FEA in core biopsies with follow-up excision biopsies to predict the likelihood of upgrade to carcinoma. We also investigated the utility of Ki-67 in predicting which lesions were associated with carcinoma in the excisional biopsies. Core biopsies with a diagnosis of atypia were categorized as pure FEA, pure ADH, or both. The following parameters were recorded: indication for core biopsies, presence of microcalcifications, inflammation, and stromal changes. A total of 60 core biopsies from 56 patients were studied. Pure ADH, pure FEA, and concomitant FEA and ADH were seen in 13%, 23%, and 64% of core biopsies, respectively. The most common architectural pattern of FEA resembled blunt duct adenosis (52%), followed by cystically dilated ducts with secretions (38%) and apocrine features (10%). Chronic inflammation and stromal changes were noted in 29% and 36% of FEA, respectively. Excisional biopsies in 48 of 56 patients demonstrated ductal carcinoma in situ and/or invasive carcinoma in 10 patients (21%), lobular carcinoma in situ or atypical lobular hyperplasia in 5 (11%), residual ADH in 11 (23%), and no atypia in 24 patients (50%). Three (21%) of 14 pure FEA upgraded to ductal carcinoma in situ and/or invasive carcinoma on excisional biopsy. The staining for Ki-67 in FEA/ADH was similar regardless of whether they were upgraded to carcinoma or not. In summary, we found a strong association between FEA and ADH, which may reflect a biologic progression. Most FEAs have a low-power appearance of a well-circumscribed group of ducts. Chronic inflammation and stromal changes are present in a subset of cases. Flat epithelial atypia shows a risk of upgrade to carcinoma similar to that of ADH and, hence, should be recognized and warrants a follow-up excision.
Retinoic acid and dexamethasone affect RAR-β and surfactant protein C mRNA in the MLE lung cell line

Lung development and surfactant biosynthesis are affected by retinoic acid (RA) and dexamethasone (Dex). Using a mouse lung epithelial cell line, we are exploring RA-Dex interactions through the st...
Numerical and Experimental Study on Dynamic Behaviour of Concrete Sleeper Track Caused by Wheel Flat

ABSTRACTImpact loads caused by flat spots on railcar wheels impose a major maintenance burden on railroads and can cause severe damage to both railcar and track components. This paper discusses the dynamic behaviour of the railroad track system under impact loads. A finite element (FE) model with multiple crossties and their accompanying fastening systems is developed and validated using field data. The results of the parametric study indicate that impact loading consists of direct wheel impact loads and track system vibration–induced impact loads. Both of these impact mechanisms are sensitive to the stiffness of rail pad. It is observed that rail pad with a moderate stiffness provides the most effective impact attenuation.
Probing the Chemistry of Alumina Atomic Layer Deposition Using Operando Surface-Enhanced Raman Spectroscopy

This work demonstrates for the first time the capability of measuring surface vibrational spectra for adsorbates during atomic layer deposition (ALD) reactions using operando surface-enhanced Raman spectroscopy (SERS). We use SERS to study alumina ALD growth at 55 °C on bare silver film-over nanosphere (AgFON) substrates as well as AgFONs functionalized with thiol self-assembled monolayers (SAMs). On bare AgFONs, we observe the growth of Al–C stretches, symmetric C–H and asymmetric C–H stretches during the trimethylaluminum (TMA) dose half-cycle, and their subsequent decay after dosing with H2O. Al–C and C–H vibrational modes decay in intensity with time even without H2O exposure providing evidence that residual H2O in the ALD chamber reacts with −CH3 groups on AgFONs. The observed Al–C stretches are attributed to TMA dimeric species on the AgFON surface in agreement with density functional theory (DFT) studies. We observe Al–C stretches and no thiol vibrational frequency shifts after dosing TMA on AgFONs...
Bidirectional regulation of lysosomal enzyme secretion and phagocytosis in human neutrophils by guanosine 3',5'-monophosphate and adenosine 3',5'-monophosphate.

SummaryThe biologic roles of guanosine 3′,5′-monophosphate (cyclic GMP) and adenosine 3′,5′-monophosphate (cyclic AMP) in the secretion of lysosomal enzymes from, and in phagocytosis by, human neu-trophils were studied. Contact between neutrophils and particulate immunologic reactants results in both phagocytosis of the particles and secretion of lysosomal enzymes. These cellular events are accompanied by the accumulation of cyclic GMP and require the presence of extracellular calcium. Acetylcholine, pilocarpine, and cyclic GMP enhance, whereas epinephrine, cyclic AMP, and/or dibutyryl cyclic AMP inhibit, both phagocytosis and lysosomal enzyme secretion. The stimulatory action of cholinergic agents and the inhibitory action of epinephrine are accompanied by the accumulation of cyclic GMP and cyclic AMP, respectively, in human neutrophils. The data suggest that cyclic GMP mediates whereas cyclic AMP inhibits the major functions of human neutrophils. Moreover, by virtue of their effects on cyclic nucleotide...
A geographical and multi-criteria vulnerability assessment of transportation networks against extreme earthquakes

Abstract The purpose of this study is to provide a geographical and multi-criteria vulnerability assessment method to quantify the impacts of extreme earthquakes on road networks. The method is applied to two US cities, Los Angeles and San Francisco, both of which are susceptible to severe seismic activities. Aided by the recent proliferation of data and the wide adoption of Geography Information Systems (GIS), we use a data-driven approach using USGS ShakeMaps to determine vulnerable locations in road networks. To simulate the extreme earthquake, we remove road sections within “very strong” intensities provided by USGS. Subsequently, we measure vulnerability as a percentage drop in four families of metrics: overall properties (length of remaining system); topological indicators (betweenness centrality); accessibility; and travel demand using Longitudinal Employment Household Dynamics (LEHD) data. The various metrics are then plotted on a Vulnerability Surface (VS), from which the area can be assimilated to an overall vulnerability indicator. This VS approach offers a simple and pertinent method to capture the impacts of extreme earthquake. It can also be useful to planners to assess the robustness of various alternative scenarios in their plans to ensure that cities located in seismic areas are better prepared to face severe earthquakes.
Study on the erosion mechanism of copper-infiltrated graphite throat insert

The erosion mechanism of the copper-infiltrated graphite throat insert (CIGTI) is obtained by means of studying the microcopic structure and the thermoconductivity of the copper-infiltrated graphite materials, analyzing the chemical reaction between the copper-infiltrated graphite and high-temperature gas. Some phenomena have been found, such as phase transformation of the copper, loss of the melting-copper on the insert surface, thermochemical ablation and mechanical exfoliation of the graphite matrix; but the self-transpiration of the copper hasn' t observed. It is also shown that the copper couldn' t react with combustion gas during ablating of the copper-infiltrnated graphite. The formula for the evaluation of steady erosion rate of CIGTI is obtained.
Utility of Pediatric Nerve Biopsy in Tertiary Care Referral

Investigators from Mayo Clinic in Rochester, MN, report the utility of nerve biopsy as a diagnostic tool in their institution.
Bayesian analysis of time-interval data for environmental radiation monitoring

Time-interval (time difference between two consecutive pulses) analysis based on the principles of Bayesian inference was compared with frequentist methods to determine the method with the highest detection probability and the shortest average run length. Using experimental and simulated data, Bayesian analysis of time-intervals (Bayesian (ti)) was compared with Bayesian and frequentist analyses of counts in a fixed count time (Bayesian (cnt) and 1.65σ, respectively). Experimental data were acquired with DGF-4C (XIA, Inc) system in list mode. Simulated data were obtained using Monte Carlo techniques to obtain a random sampling of the Poisson distribution. All statistical algorithms were developed using R (R Core Development Team, 2010). Detection probabilities and average run lengths for the three methods were compared. Bayesian analysis of time-interval information provided a similar detection probability as Bayesian analysis of count information, but was able to make a quicker decision with fewer pulses at relatively higher radiation levels. The relationships of the source time, change points and modifications to the Bayesian approach for increasing detection probability are presented.
Measuring AIDS Activism

Typically, emerging movements grow out of and remain dependent upon established institutions and organizations. Movements as diverse as a Texas antipornography effort, the Populist poarty, the Berkeley free speech movement, and the American civil rights movement of the 1950s and 1960s found their impetus in existing organizations. (McAdam, 1982: 162)
Dropout in clinical trials of pharmacological treatment for methamphetamine dependence: the role of initial abstinence.

Background and Aims High rates of loss to follow-up represent a significant challenge to clinical trials of pharmacological treatments for methamphetamine (MA) use disorder. We aimed to estimate and test the relationship between achieving and maintaining abstinence in the initial weeks of study participation and subsequent retention in such trials, hypothesizing that participants able to achieve early abstinence would be less likely to drop out. Design Data from four randomized controlled trials (RCTs) of pharmacological treatments for MA use disorder were pooled and analyzed using a random-effects approach. Setting All trials were conducted in the greater Los Angeles, CA, USA area. Participants A total of 440 participants were included; trials were conducted between 2004 and 2014. Measurements Participants’ ability to achieve a brief period of initial abstinence was measured as the number of MA-negative urine screens completed in the first 2 weeks of the trials. Outcomes were the likelihood of dropout, i.e. missing two consecutive weeks of scheduled urine drug screens, and the number of days participants were retained in the trials. Findings Study participants achieved an average of three (of six possible) negative urine screens during the first 2 weeks of the trials, 51% dropped out and the average number of days retained was 60 (of 90 maximum). Each additional negative urine screen achieved during the first 2 weeks of the study reduced multiplicatively the odds of dropout by 41% [odds ratio (OR) = 0.59, 95% confidence interval (CI) = 0.53, 0.66]. Abstinence was also a significant predictor of retention time; the hazard ratio for non-completion was 0.75 per additional negative urine screen (95% CI = 0.71, 0.80). Conclusions Participants in randomized controlled trials of pharmacological treatments for methamphetamine use disorder who are able to achieve a brief period of early abstinence are retained longer in the trials and are less likely to drop out overall.