cssi/SciSciGPT-SciSciNet huggingface dataset:
Finding Repeated Elements

Two algorithms are presented for finding the values that occur more than $n \div k$ times in array b[O:n-1]. The second algorithm requires time $O(n \log(k))$ and extra space $O(k)$. We prove that $O(n \log(k))$ is a lower bound on the time required for any algorithm based on comparing array elements, so that the second algorithm is optimal. As special cases, determining whether a value occurs more than $n \div 2$ times requires linear time, but determining whether there are duplicates the case $k=n$ requires time $O(n \log(n))$. The algorithms may be interesting from a standpoint of programming methodology; each was developed as an extension of an algorithm for the simple case $k=2$.
The Vulgar Conception of Objects in "Of Skepticism with Regard to the Senses"

In this paper, we see that contrary to most readings of T 1.4.2 in the Treatise ("Of Skepticism with Regard to the Senses"), Hume does not think that objects are sense impressions. This means that Hume's position on objects (whatever that may be) is not to be conflated with the vulgar perspective. Moreover, the vulgar perspective undergoes a marked transition in T 1.4.2, evolving from what we may call vulgar perspective I into vulgar perspective II. This paper presents the first detailed analysis of this evolution, which includes an explanation of T 1.4.2's four-part system.
First catch urine sediment for Chlamydia trachomatis and Neisseria gonorrhoeae culture in adolescent males with pyuria

Traditionally, only symptomatic males or those with a history of exposure are tested for sexually transmitted diseases (STDs). Since urethral infections with Chlamydia trachomatis and Neisseria gonorrhoeae are frequently asymptomatic, a practical, sensitive, and acceptable screening method is desirable. Fifty sexually active males with pyuria (age 13 to 22 years old) diagnosed with 1+ or 2+ leukocyte esterase (LE) dipstick on first catch urine (FCU) were further evaluated by culture of urethral swabs and centrifuged FCU samples for N. gonorrhoeae and C. trachomatis. Eighty-six percent had one or more positive cultures: 17 (34%) N. gonorrhoeae, 18 (36%) C. trachomatis, and 8 (16%) both organisms. FCU culture for N. gonorrhoeae had a 100% sensitivity, specificity, and positive and negative predictive value when compared to urethral swab cultures. FCU culture for C. trachomatis had a 32% sensitivity, 95% specificity, 89% positive predictive value, and a 53% negative predictive value compared to urethral culture. On the basis of the results of this study, one urethral swab can be eliminated when evaluating male adolescents for urethritis by using spun FCU culture for N. gonorrhoeae. Continued efforts should be made to develop optimal tests to detect STDs which are reliable and encourage compliance in this high-risk group.
Factors predicting patterns of recurrence after resection of N1 non-small cell lung carcinoma

Abstract Background . Although irradiation and chemotherapy are unproved adjuvant treatments for completely resected N1 non–small cell lung carcinoma, previous studies may have been diluted by the inclusion of low-risk patients. Risk factors in this situation, however, are not yet well defined. Methods . One hundred seven consecutive patients with complete resection of N1 disease who received no other therapy were studied to identify factors independently predicting the risk of freedom from local recurrence (FFLR), freedom from distant metastasis (FFDM), and overall survival (OS). Results . Twelve factors were assessed for a potential prognostic relationship with FFLR, FFDM, and OS. Regression analyses revealed that the factors independently associated with an improved outcome were positive bronchoscopic findings (FFLR, p = 0.005), a greater number of dissected N1 nodes (FFDM, p = 0.02), and a lesser T stage (OS, p = 0.01). Classification and regression tree analyses were then used to separate the patients into risk groups. Conclusions . Although these results require corroboration in further studies, they may aid the design of trials examining therapies used to decrease rates of local recurrence or distant metastasis.
Retail Philanthropy: Firm Size, Industry, and Business Cycle

This article investigates the effects of firm size, profitability, industry affiliation, and the business cycle on retailer philanthropy. The importance of industry and firm effects on giving was analyzed with regression models using industry-fixed effects as well as firm strategy variables. The analysis included instrumental variables methodology to account for simultaneity in the charitable giving–profits relationship. Data were gathered from the IRS Corporate Statistics of Income Sourcebook, data that provide firm size class measures covering the entire firm size distribution ranging from small retailers up to large multi-national retail firms. Retailer philanthropy was measured as the ratio of charitable contributions to total receipts. Important findings include a cubic relationship between retailer philanthropy and firm size; industry effects stronger than those observed for retail profit; and the absence of business cycle effects. The empirical research relating retail charitable giving to firm attributes including firm size and advertising, industry and business cycle factors are unique in the business ethics literature. Prior studies regarding the importance of industry on charitable giving utilized data across broad sectors of the economy. Firms from different sectors could be expected to differ in philanthropic approach due to differences in public contact as well as differences in public relations exposure. The strong industry effects reported for this sample of exclusively retail firms, with similar public contact, provide strong evidence for the importance of industry in determining firms’ charitable strategies.
Differential responses to line orientation after training to a blank stimulus

Pigeons were trained to respond with variable-interval food reinforcement in the presence of a green key. During extinction, lines of different orientation were projected on the green field. Responding to these stimuli was differential but idiosyncratic. These findings may present methodological problems to Es using two dimensions to measure gradients of generalization of inhibition.
Advances in therapy for melanoma brain metastases

Melanoma cells frequently metastasize to the brain, and approximately 50% of patients with metastatic melanoma develop intracranial disease. Historically, central nervous system dissemination has portended a very poor prognosis. Recent advances in systemic therapies for melanoma, supported by improved local therapy control of brain lesions, have resulted in better median survival for these patients. We review current local and systemic approaches for patients with melanoma brain metastases.
Grain foods and health: a primer for clinicians

AbstractPreventing many chronic diseases in North America requires substantial changes in dietary habits. Achieving a better balance of grain-based foods through the inclusion of whole grains is one scientifically supported dietary recommendation. Epidemiological and other types of research continue to document health benefits for diverse populations who have adequate intakes of both folic acid-fortified grain foods and whole grains. Folic acid fortification of grains is associated with reduced incidence of neural tube and other birth defects and may be related to decreased risk of other chronic disease. Whole grain intake is associated with reduced risk of chronic disease. Specifically, there is a decreased risk of obesity, coronary heart disease, hypertension, stroke, metabolic syndrome, type 2 diabetes, and some cancers observed among the highest whole grain eaters compared with those eating little or no whole grains. Nationally promulgated dietary recommendations such as those in the US Dietary Guidel...
Method for recording and analyzing visual fixations in the unrestrained monkey.

Adaptation of the Mackworth wide-angle reflection eye camera for the collection and analysis of visual scanning behavior in the relatively unrestrained rhesus monkey is described. Crucial changes i...
Effect of prostaglandins E2 and F2α on umbilical blood flow and fetal hemodynamics

Abstract The hemodynamic effects of PGF2α, PGE2, and norepinephrine injected into the umbilical arterial circulation were compared in nine fetal lambs in utero . Umbilical blood flow was measured with radioactive microspheres and an electromagnetic flow transducer implanted on the distal aorta of the fetus after ligation of external iliac arteries and other accessible distal aortic branches. PGF2α and norepinephrine increased fetal arterial pressure and umbilical blood flow while umbilical vascular resistance increased slightly (PGF2α) or not at all (norepinephrine). PGE2 increased fetal arterial pressure, decreased umbilical blood flow, and exerted a profound active vasoconstrictor effect on the fetal placental bed. Our data taken together with the observations of others suggest that prostaglandins may play a role in the circulatory adaptations of the fetus at birth and that PGE2 in high concentrations is likely to have deleterious hemodynamic consequences in the fetus in utero .
Flow‐adaptive moderation of spurious ensemble correlations and its use in ensemble‐based data assimilation

Many ensemble Kalman filter (EnKF) data assimilation (DA) schemes reduce the effect of spurious ensemble correlations caused by small ensemble size by multiplying the correlations by moderation functions. Moderation functions envelop true error correlation functions. Ideal moderation functions would adapt to variations in the movement and width of true error correlation functions. Here, we describe a new method in which flow-dependent moderation functions are built from powers of smoothed ensemble correlations. The approach imparts to the moderation function movement and width information retained by the smoothed ensemble correlations. Spurious smoothed ensemble correlations are attenuated by raising them to a power. Simple systems were used to compare DA performance using such Smoothed ENsemble COrrelations Raised to a Power (SENCORP) moderation functions against DA performance using optimally tuned but non-adaptive moderation functions. The simple systems considered feature propagating error correlation functions and error correlation functions with variable width. It was found that when significant spatio-temporal variations in the true error correlation function are present, SENCORP moderation functions are superior to non-adaptive moderation functions. In the absence of spatio-temporal variations, the DA performance of SENCORP moderation functions was found to be statistically indistinguishable from the DA performance of non-adaptive moderation functions. An example using a primitive equation global model is given to illustrate how the method could be used to improve the performance of a local ensemble Kalman filter/smoother, particularly when larger observation volumes are used, to better account for error propagation and/or observations that represent vertically averaged variables. Published in 2007 by John Wiley & Sons, Ltd.
The triage efficacy of fine needle aspiration biopsy for follicular variant of papillary thyroid carcinoma using the Bethesda reporting guidelines.

Diagnosis of follicular variant of papillary thyroid carcinoma (FVPTC) by ultrasound-guided fine-needle aspiration (FNA) is challenging. In this retrospective review, we evaluated triage efficacy (i.e., potential for triggering surgical intervention) in 44 archived FNA biopsies of surgically confirmed FVPTC obtained between December 2006 and December 2008. We compared the original FNA diagnoses with reclassified diagnoses based on 2007 National Cancer Institute (NCI)/Bethesda recommendations, and reviewed FNA cytologic features. Original FNA diagnoses included colloid nodule (7%, 3/44), atypical follicular cells (5%, 2/44), follicular lesion (11%, 5/44), follicular neoplasm (16%, 7/44), suspicious for malignancy/PTC (27%, 12/44), and papillary thyroid carcinoma (34%, 15/44). Reclassified diagnoses included indeterminate (5%, 2/44), colloid nodule (7%, 3/44), atypical cells of undetermined significance [ACUS] (7%, 3/44), Hurthle cell neoplasm (2%, 1/44), follicular neoplasm (7%, 3/44), suspicious for malignancy/PTC (25%, 11/44), and PTC (48%, 21/44). Triage efficacy was 77% (34/44) for original diagnoses versus 82% (36/44) for reclassified FNA diagnoses. We frequently observed cytologic features of PTC, such as nuclear grooves and fine chromatin; conversely, intranuclear inclusions, though present in 77% cases, were scant. Our review findings suggest that lack of characteristic cytologic features of PTC,coexistence with other thyroid lesions, and small tumor size arethe major obstacles to FNA diagnosis of FVPTC. Reclassification of thyroid FNA diagnoses does not significantly improve triage efficacy. Furthermore, FNA diagnoses of follicular neoplasm and suspicious for malignancy are valuable in patients with FVPTC because they trigger triage toward surgical intervention. Diagn. Cytopathol. 2012;40:E69–E73. © 2011 Wiley Periodicals, Inc.
Autism Spectrum in the College Classroom: Strategies for Instructors

Autism spectrum disorder (ASD) refers to several conditions that share the feature of persistent social impairment. The rate of ASD diagnosis has climbed to one in 88 (CDC, 2012), and increasing numbers of individuals with ASD attend college. College students with ASD may share academic challenges related to critical thinking, executive functioning, and classroom anxiety. These challenges can manifest in the classroom, and there are a number of simple strategies for instructors that directly address characteristics of ASD. These strategies are not just good for students on the spectrum, but they can benefit other learners as well.
Prediction of bone mineral density and content from measures of physical activity and sedentary behavior in younger and older females

Abstract Background Little is known regarding the extent to which physical activity (PA) and sedentary behavior (SB) influence bone mineral content (BMC) and bone mineral density (BMD) in females across the lifespan. Methods Data from 2232 females aged 12 years and older collected as part of the 2007–2008 National Health and Nutrition Examination Survey were analyzed. Categories of PA and SB were used to predict femoral and spinal BMD and BMC in four age groups (G1: 12–17; G2: 18–39; G3: 40–64; G4: ≥ 65 years). Self-reported PA categories included sufficient moderate-to-vigorous recreational PA (S-MVRPA) and insufficient MVRPA (I-MVRPA). Results G1 females who accumulated S-MVRPA displayed greater femoral and spinal BMC and BMD compared to G1 females who displayed I-MVRPA. For G4 females, higher levels of SB were associated with lower femoral BMC and BMD. Conclusions These findings highlight the importance of engaging in sufficient moderate-to-vigorous physical activity during adolescence and reducing sedentary behavior in older adults to improve bone health in females.
Responses of ventromedial hypothalamic neurons in vitro to norepinephrine: dependence on dose and receptor type

Application of norepinephrine (NE) at 12.5 microM in the bath surrounding hypothalamic slices from ovariectomized rats could evoke excitation, inhibition, or biphasic inhibition-excitation from single neurons in the ventromedial nucleus. Whether the rats were treated with estrogen or not did not alter the distribution of the type of neuronal responses to NE in vitro. Altering the composition of the bathing solution to achieve synaptic blockade did not abolish or alter the type of responses, indicating that all these types of NE responses, including both phases of the biphasic response, were mediated by postsynaptic receptors. Experiments with varying doses of NE showed that the inhibitory response could be evoked at doses lower than those required to evoke the excitatory response. The effective dose for 50% of the responsive neurons (ED50) was lower than 1.25 microM for inhibitions and higher than 5 microM for excitations. Using specific adrenergic receptor agonists and antagonists, it was found that the excitation and the inhibition were mediated, primarily, by alpha 1- and alpha 2-receptors, respectively. beta-Receptors played only a minor role, but might be related to both excitation and inhibition. Study with adrenergic agents further revealed that different types of adrenergic receptors co-localized not only in neurons showing the biphasic response, but also in a major portion of neurons showing monophasic excitation or inhibition. Because of the co-localization and the differential sensitivities to NE, alteration of the dose of NE or the ratio of excitatory/inhibitor receptors co-localized on a neuron should be able to reverse the type of a neuronal response to NE.
Guided-wave methods for optical configurations

Guided-wave methods used in the past to treat electromagnetic problems and applications in the microwave area have recently been extended to cover work in fiber and integrated optics. The basic principles of these methods are reviewed briefly and, in particular, the “open” properties of optical configurations are contrasted to the “closed” characteristics that describe most microwave applications. These aspects are illustrated in the context of beam couplers of uniform and periodic varieties, which are shown to lend themselves to rigorous treatment by microwave guided-wave methods that include both theoretical and experimental facets.
‘Let's Talk about the Books’: The Complexity of Book Discussions in a Multilingual Preschool Classroom

This sociolinguistic study explores complexities of supporting preschool emergent bilinguals' communicative competence in multilingual classrooms. These complexities were highlighted in the author'...
Lack of dispersion cancellation with classical phase-sensitive light

Shapiro recently argued that nonlocal dispersion cancellation using entangled pairs of photons is essentially classical in nature, based on a comparison with a classical model in which two stationary, chaotic beams of light have phases and frequencies that are anticorrelated, which he refers to as 'phase-sensitive' light [J. H. Shapiro, Phys. Rev. A 81, 023824 (2010)]. It is shown here that there is no physical cancellation of dispersion for classical light of that kind and Shapiro's results merely reflect the fact that identical dispersion occurs in both beams. The origin of the cross correlations between the intensities of the two beams is shown to be completely different in the classical and quantum mechanical cases.
Efficient Identification of Phosphorylation by Mass Spectrometric Phosphopeptide Fingerprinting

We describe a rapid and efficient method for the identification of phosphopeptides, which we term mass spectrometric (MS) phosphopeptide fingerprinting. The method involves quantitative comparison of proteolytic peptides from native versus completely dephosphorylated proteins. Dephosphorylation of serine, threonine, and tyrosine residues is achieved by in-gel treatment of the separated proteins with hydrogen fluoride (HF). This chemical dephosphorylation results in enrichment of those unmodified peptides that correspond to previously phosphorylated peptides. Quantitative comparison of the signal-to-noise ratios of peaks in the treated versus untreated samples are used to identify phosphopeptides, which can be confirmed and further studied by tandem mass spectrometry (MS/MS). We have applied this method to identify eight known phosphorylation sites of Xenopus Aurora A kinase, as well as several novel sites in the Xenopus chromosome passenger complex (CPC).
pH dependence of stability of staphylococcal nuclease: evidence of substantial electrostatic interactions in the denatured state.

The pH dependence of stability of staphylococcal nuclease was studied with two independent equilibrium thermodynamic approaches. First, by measurement of stability in the pH range 9 to 3.5 by fluorescence-monitored denaturation with urea (Δ ), GdnHCl (Δ ), and heat (Δ ). Second, by numerical integration of H+ titration curves (Δ ) measured potentiometrically under native (100 mM KCl) and unfolding (6.0 M GdnHCl) conditions. The pH dependence of stability described by Δ , Δ , and Δ was comparable but significantly different from the one described by Δ . The decrease in Δ between pH 9 and pH 4 was 4 kcal/mol greater than the decrease in Δ , Δ , and Δ in the same pH range. In 6 M GdnHCl, all the ionizable groups titrated with the pKa values of model compounds. Therefore, Δ represents the free energy difference between the native state (N) and an ensemble of unstructured, or expanded, and highly screened conformations. In contrast, the shallower pH dependence of stability described by Δ and by Δ between pH 9 ...
Basal and exercise-induced regulation of skeletal muscle capillarization

Regulation of skeletal muscle capillarization involves distinct signaling pathways and growth factors including nitric oxide and vascular endothelial growth factor. Our understanding of this complex regulation continues to expand with the identification of new angiogenic growth factors. Future work needs to increase the use of advanced molecular techniques to expand our knowledge of the regulation of basal and exercise-induced capillarization.
Real-time simulation of dust behavior generated by a fast traveling vehicle

Simulation of physically realistic complex dust behavior is very useful in training, education, art, advertising, and entertainment. There are no published models for real-time simulation of dust behavior generated by a traveling vehicle. In this paper, we use particle systems, computational fluid dynamics, and behavioral simulation techniques to simulate dust behavior in real time. First, we analyze the forces and factors that affect dust generation and the behavior after dust particles are generated. Then, we construct physically-based empirical models to generate dust particles and control the behavior accordingly. We further simplify the numerical calculations by dividing dust behavior into three stages, and establishing simplified particle system models for each stage. We employ motion blur, particle blending texture mapping, and other computer graphics techniques to achieve the final results. Our contributions include constructing physically-based empirical models to generate dust behavior and achieving simulation of the behavior in real time.
RHESSI Microflare Statistics. I. Flare-Finding and Frequency Distributions

We present the first in-depth statistical survey of all X-ray microflares observed by RHESSI between 2002 March and 2007 March, a total of 25,705 events, an order of magnitude larger then previous studies. These microflares were found using a new flare-finding algorithm designed to search the 6-12 keV count rate when RHESSI's full sensitivity was available in order to find the smallest events. The peak and total count rate are automatically obtained along with count spectra at the peak and the microflare centroid position. Our microflare magnitudes are below GOES C class, on average GOES A class (background subtracted). They are found to occur only in active regions, not in the quiet Sun, and are similar to large flares. The monthly average microflaring rate is found to vary with the solar cycle and ranges from 90 to 5 flares a day during active and quiet times, respectively. Most flares are found to be impulsive (74%), with rise times shorter than decay times. The mean flare duration is ~6 minutes with a 1 minute minimum set by the flare-finding algorithm. The frequency distributions of the peak count rate in the energy bands, 3-6, 6-12, and 12-25 keV, can be represented by power-law distributions with a negative power-law index of -->1.50 ± 0.03, -->1.51 ± 0.03, and -->1.58 ± 0.02, respectively. We find that these power-law indices are constant as a function of time. The X-ray photon spectra for individual events can be approximated with a power-law spectrum [ -->dJ/d(hν) ~ (hν)−γ]. Using the ratio of photon fluxes between 10-15 and 15-20 keV, we find -->4 -1.7 ± 0.1. We estimate the total energy flux deposited in active regions by microflare-associated accelerated electrons (>10 keV) over the five years of observations to be, on average, below 1026 erg s−1.
Fine-grained object recognition with Gnostic Fields

Much object recognition research is concerned with basic-level classification, in which objects differ greatly in visual shape and appearance, e.g., desk vs duck. In contrast, fine-grained classification involves recognizing objects at a subordinate level, e.g., Wood duck vs Mallard duck. At the basic-level objects tend to differ greatly in shape and appearance, but these differences are usually much more subtle at the subordinate level, making fine-grained classification especially challenging. In this work, we show that Gnostic Fields, a brain-inspired model of object categorization, excel at fine-grained recognition. Gnostic Fields exceeded state-of-the-art methods on benchmark bird classification and dog breed recognition datasets, achieving a relative improvement on the Caltech-UCSD Bird-200 (CUB-200) dataset of 30.5% over the state-of-the-art and a 25.5% relative improvement on the Stanford Dogs dataset. We also demonstrate that Gnostic Fields can be sped up, enabling real-time classification in less than 70 ms per image.
Instruction of Research-Based Comprehension Strategies in Basal Reading Programs

Research supports using research-based comprehension strategies; however, comprehension strategy instruction is not highly visible in basal reading programs or classroom instruction, resulting in many students who struggle with comprehension. A content analysis examined which research-based comprehension strategies were presented in five elementary school basal readers and how the basals suggest that the strategies be taught. The analysis found that two thirds of instructional recommendations were research-based strategies; several strategies did not appear in basals, and others received minimal attention. Findings suggest that though the state of comprehension instruction in basals is not as dire as previous research suggests, improvements can be made.
192 DECREASED SURVIVAL AND ALTERED MEMBRANE PROPERTIES OF RED BLOOD CELLS (RBC) IN THE NEWBORN RAT

Decreased survival has been noted for RBC of newborn man and rat(Ped.Res.11:1155,1977).The present studies investigate the possibility that decreased survival is due to an altered RBC membrane. Osmotic fragility of newborn(NB) rat RBC was increased (29% lysis in 0.5% NaCl;adult RBC:6%),increasing to 92% following 1 hr incubation at 20° in pH 9.2 borate buffer (adult RBC: no change). Filtration half-time of RBC suspensions was prolonged (NB:40 min; adult:2-3 min)and returned to normal with advancing age(16 min at 6 days,5 min at 12 days,3 min at 26 days). Splenic uptake at 24 hr was increased 15-fold & hepatic uptake increased 3-fold for 51Cr-labeled NB RBC as compared to adult RBC. Following treatment with the cross-linking agent dimethyladipimidate (DMA,2-5mM,pH 9.2),survival of 51Cr-labeled adult RBC was slightly reduced from 100&92% at 1&24 hr to 94&76%. DMA(2-5mM) caused marked further reduction in survival of NB RBC from 64&16% at 1&24 hr to 10&3%. Following incubation of intact RBC with glucose, electrophoresis of RBC membrane proteins yielded a pattern of high molecular weight complexes(HMWC) for NB,but not for adult, RBC. These results suggest an unstable RBC membrane in the newborn rat,leading to altered osmotic fragility,reduced deformability, splenic trapping, and reduced survival. Preferential hemolysis of DMA-treated NB rat RBC and HMWC formation suggest that an altered state of aggregation of membrane proteins may underlie these abnormalities.
The kinetics of growth of an aerosol in a flow reactor. I. Experimental

Abstract A novel and inexpensive design for an aerosol generator is described. The apparatus reliably and reproducibly generates nearly monodisperse aerosols in a size range convient for study by light scattering. With its use, we have examined the rate of growth of dibutyl phthalate aerosol droplets nucleated by sodium chloride particles in a supersaturated jet.
Drying kinetics of calcium caseinate.

Drying is a major component of the cost of making caseinate-based films. We determined the drying curves for making calcium caseinate/glycerol films at low and high relative humidity at 21−34 °C. The drying curves exhibited a very long constant rate period followed by a single falling rate period. Much of the drying was in the constant rate period and preceded the actual film formation. Normally, calcium caseinate solutions are dried from about 5% solids, but it was possible to start with a more concentrated solution, 10% solids, to avoid much of the constant rate period. The resulting films were equal to those prepared starting at high initial moisture. An estimate of the drying costs indicated it is much cheaper to start with the more concentrated solutions. Keywords: Casein; film; coating; drying curve
Modified replica exchange simulation methods for local structure refinement.

Parallel tempering, also known as replica exchange molecular dynamics (REMD), has recently been successfully used to study the structure and thermodynamic properties of biomolecules such as peptides and small proteins. For large systems, however, applying REMD can be costly since the number of replicas needed increases as the square root of the number of degrees of freedom in the system. Often, enhanced sampling is only needed for a subset of atoms, such as a loop region of a large protein or a small ligand binding to a receptor. In such applications, it is often reasonable to assume a weak dependence of the structure of the larger region on the instantaneous conformation of the smaller region of interest. For these cases, we derived two variant replica exchange methods, partial replica exchange molecular dynamics (PREMD) and local replica exchange molecular dynamics (LREMD). The Hamiltonian for the system is separated, with replica exchange carried out only for terms involving the subsystem of interest w...
Toward an effective automated tracing process

The research on automated tracing has noticeably advanced in the past few years. Various methodologies and tools have been proposed in the literature to provide automatic support for establishing and maintaining traceability information in software systems. This movement is motivated by the increasing attention traceability has been receiving as a de jure standard in software quality assurance. Following that effort, in this research proposal we describe several research directions related to enhancing the effectiveness of automated tracing tools and techniques. Our main research objective is to advance the state of the art in this filed. We present our suggested contributions through a set of incremental enhancements over the conventional automated tracing process, and briefly describe a set of strategies for assessing these contributions impact on the process.
Expression and localization of the prion protein PrPC in the olfactory system of the mouse

The normal physiological function of the prion protein PrPC remains elusive despite its widespread expression, particularly throughout the nervous system. A critical step toward identifying its function is to precisely localize its pattern of expression. Historically, the immunolocalization of PrPC has proved to be notoriously difficult and nonconsensual. We have thus undertaken a detailed expression analysis by means of a combination of in situ hybridization, knockout mice, and immunohistochemistry, using recently generated highly specific antibodies. We have attempted to accurately localize PrPC expression in a tissue that is highly structured and of crucial behavioral importance to mice, the olfactory system. We found that PrPC was expressed in both peripheral and central neurons of the olfactory system and that its distribution was axonal-specific in both olfactory sensory neurons of the olfactory epithelium and mitral cells of the olfactory bulb. Our detailed expression analysis and the axonal localization we observed may provide important hints toward potential functions of PrPC. J. Comp. Neurol. 508:487–499, 2008. © 2008 Wiley-Liss, Inc.
Cardiac dysfunction in aging conscious rats: altered cardiac cytoskeletal proteins as a potential mechanism

The objective of this study was to test the hypothesis that the mechanism mediating left ventricular (LV) dysfunction in the aging rat heart involves, in part, changes in cardiac cytoskeletal compo...
Doubling IT Innovation Spending: Laying the Foundation for IT-Enabled Business Process, Supply Chain, and Service Innovation in the Pharmaceutical Industry

This paper discusses the development and application of the methodology, which was part of a multi-year effort that I led on the part of Pfizer’s Global Business Technology organization. The effort resulted in a 30% reduction in IT support and maintenance expenses, a 75% reduction in service providers, a 50% reduction in the cost of global operations support, and a 50% reduction in the worldwide portfolio of applications and databases. The associated savings allowed Pfizer to double its level of investment in IT-enabled business innovation throughout its Worldwide Drug Development organization. For Pfizer, the methodology served as a catalyst for IT organizations to increase their efficiency and become more effective at leveraging information, improving business processes, and seeding IT-enabled business innovation. For the Industry, this work can serve as a roadmap for improving the efficiency of IT organizations and using that efficiency to drive IT-enabled business innovation across the enterprise.
Productivity of New England hemlock/hardwood stands as affected by species composition and canopy structure

Kelty, M.J., 1989. Productivity of New England hemlock/hardwood stands as affected by species composition and canopy structure. For. Ecol. Manage., 28:237-257 Canopy structure, yield, and current productivity of two even-aged stands (of ages 44 and 87 years) composed of hemlock (Tsuga canadensis (L.) Carr.) and hardwoods (primarily Quercus rubra L. and Acer rubrum L. ) were compared with that of adjacent hardwood stands of the same age, site conditions, and hardwood species composition, but which lacked hemlock. In the hemlock/hardwood mixtures, hemlock formed a dense understory beneath the hardwood overstory, while hardwood stands lacked comparably dense understories of any species. The mixed stands were found to have significantly greater yields and current production rates in total stand basal area than adjacent hardwood stands. Basal area yield and production of the hardwood component of the mixed stands were not significantly different from that of the adjacent hardwood stands, indicating that the hemlock growth was largely additive to that of the hardwood overstory. Similar patterns were observed when data were converted to stemwood volume or above-ground biomass measures, although not all differences were statistically significant. Published yield tables for hemlock indicate that basal area and biomass yield of pure hemlock stands of similar age and site conditions was also exceeded by that of the hemlock/hardwood mixtures in the present study. A review of plantation studies comparing mixed stands with adjacent pure stands of the component species indicates consistency with the results of the present study in the pattern of mixed stands with stratified canopies having greater yield than pure stands of the overstory species. There is some evidence to indicate that mixtures have greater yields than pure stands of the understory component as well, although fewer data exist for this comparison.
The Internal Enforcement of Norms

The study provides data regarding the effect of internalized norms on behaviour. I use the factorial vignette survey method to measure internalized giving norms and then conduct an experiment to test whether these norms predict participants'actual donations. The results are consistent with arguments that norms are at least partially internally enforced. They also point to the importance of context in predicting the effect of norms on behaviour
'Rough Consensus and Running Code' and the Internet-OSI Standards War

Internet historians recognize the technical achievements but often overlook the bureaucratic innovations of Internet pioneers. The phrase, "We reject: kings, presidents, and voting. We believe in: rough consensus and running code," was coined by David Clark in 1992. This article explains how the phrase captured the technical and political values of Internet engineers during a crucial phase in the Internet's growth
Structure of G Protein–Coupled Receptors and G Proteins

This Teaching Resource provides lecture notes and slides for a class covering the structure and function of G protein–coupled receptors and is part of the course "Cell Signaling Systems: A Course for Graduate Students." The lecture begins with a discussion of the crystal structure of rhodopsin and G protein subunits and then proceeds to describe the molecular mechanisms of receptor activation and the subsequent release of G proteins.
Examining the central and peripheral processes of written word production through meta-analysis.

Producing written words requires “central” cognitive processes (such as orthographic long-term and working memory) as well as more peripheral processes responsible for generating the motor actions needed for producing written words in a variety of formats (handwriting, typing, etc.). In recent years, various functional neuroimaging studies have examined the neural substrates underlying the central and peripheral processes of written word production. This study provides the first quantitative meta-analysis of these studies by applying Activation Likelihood Estimation methods (Turkeltaub et al., 2002). For alphabet languages, we identified 11 studies (with a total of 17 experimental contrasts) that had been designed to isolate central and/or peripheral processes of word spelling (total number of participants = 146). Three ALE meta-analyses were carried out. One involved the complete set of 17 contrasts; two others were applied to subsets of contrasts to distinguish the neural substrates of central from peripheral processes. These analyses identified a network of brain regions reliably associated with the central and peripheral processes of word spelling. Among the many significant results, is the finding that the regions with the greatest correspondence across studies were in the left inferior temporal/fusiform gyri and left inferior frontal gyrus. Furthermore, although the angular gyrus has traditionally been identified as a key site within the written word production network, none of the meta-analyses found it to be a consistent site of activation, identifying instead a region just superior/medial to the left angular gyrus in the left posterior intraparietal sulcus. In general these meta-analyses and the discussion of results provide a valuable foundation upon which future studies that examine the neural basis of written word production can build.
Modulators of Cytoskeletal Reorganization in CA1 Hippocampal Neurons Show Increased Expression in Patients at Mid-Stage Alzheimer's Disease

During the progression of Alzheimer's disease (AD), hippocampal neurons undergo cytoskeletal reorganization, resulting in degenerative as well as regenerative changes. As neurofibrillary tangles form and dystrophic neurites appear, sprouting neuronal processes with growth cones emerge. Actin and tubulin are indispensable for normal neurite development and regenerative responses to injury and neurodegenerative stimuli. We have previously shown that actin capping protein beta2 subunit, Capzb2, binds tubulin and, in the presence of tau, affects microtubule polymerization necessary for neurite outgrowth and normal growth cone morphology. Accordingly, Capzb2 silencing in hippocampal neurons resulted in short, dystrophic neurites, seen in neurodegenerative diseases including AD. Here we demonstrate the statistically significant increase in the Capzb2 expression in the postmortem hippocampi in persons at mid-stage, Braak and Braak stage (BB) III-IV, non-familial AD in comparison to controls. The dynamics of Capzb2 expression in progressive AD stages cannot be attributed to reactive astrocytosis. Moreover, the increased expression of Capzb2 mRNA in CA1 pyramidal neurons in AD BB III-IV is accompanied by an increased mRNA expression of brain derived neurotrophic factor (BDNF) receptor tyrosine kinase B (TrkB), mediator of synaptic plasticity in hippocampal neurons. Thus, the up-regulation of Capzb2 and TrkB may reflect cytoskeletal reorganization and/or regenerative response occurring in hippocampal CA1 neurons at a specific stage of AD progression.
Cost-effective use of echocardiography in children with Kawasaki disease.

Objective. To determine whether a third echocardiogram, performed 6 months to 1 year after the onset of Kawasaki disease (KD), as recommended by current American Heart Association guidelines, identified any case of coronary artery abnormalities when previous echocardiograms were normal. Methods. Children diagnosed with KD were identified by searching our institution9s database. Cases were included in the study if diagnosed between June 1988 and December 1996 and if at least two echocardiograms were documented, including at least one study between 2 weeks and 2 months from the onset of KD and another in follow-up. The patients9 charts were reviewed and videotapes of the echocardiograms were reviewed if reports were unclear or contradictory. McNemar9s test for discordant pairs was used for statistical analysis. Additionally, a complete review was performed in all other cases of KD in the database in which a coronary artery abnormality had been identified. Results. There were 203 patients diagnosed during the study period who had 2 or more echocardiograms performed, and 67 had the requisite studies in the subacute period and later follow-up. The median age at onset of KD was 3.0 years (range: 0.2–16), the median duration of follow-up was 12.5 months (range: 1.7–100), and the median number of echocardiograms performed was 3 (range: 2–8). Intravenous immunoglobulin was given in 62 cases, and high-dose aspirin was given in 63. There were 35 children with no echocardiographic abnormalities at any point, and 15 other children had early abnormalities (including coronary ectasia, perivascular brightness, pericardial effusion, and ventricular dysfunction) but had a normal echocardiogram between 2 weeks and 2 months. Of these 50 children, none were noted to have abnormalities on later studies. Three children had effusion and/or perivascular brightness after 2 weeks; follow-up studies were normal in each. Six children had coronary ectasia after 2 weeks; it persisted on follow-up in 1 child and had resolved in 5 children. Eight children had coronary aneurysms on studies after 2 weeks; in 3 children, the aneurysm resolved on later follow-up. No coronary abnormalities were demonstrated on a late follow-up echocardiogram in any child with normal coronaries between 2 weeks and 2 months. Conclusions. All children with KD should have an echocardiogram at the time of diagnosis with a follow-up study 4 to 6 weeks after the onset of fever. In the current environment of cost-containment, additional echocardiographic studies are justified only if abnormalities are present at 4 to 6 weeks. Kawasaki disease, coronary artery aneurysm, echocardiography, coronary ectasia.
Plant Canopy Specular Reflectance Model

A model is derived for the amount of light specularly reflected and polarized by a plant canopy. The model is based on the morphological and phenological characteristics of the canopy and upon the Fresnel equations of optics. The theory demonstrates that the specular reflectance of the plant canopy is a function of the angle of incidence and potentially contains information to help discriminate between species. The theory relates the specular reflectance to botanical condition of the canopy-to factors such as development stage, plant vigor, and leaf area index (LAI).
Measuring Public Service Motivation: An Assessment of Construct Reliability and Validity

The public administration literature makes many assertions that the motivations of individuals who pursue public service careers differ in important ways from other members of American society. This research advances the study of these assertions by creating a scale to measure public service motivation. Public service motivation (PSM) represents an individual's predisposition to respond to motives grounded primarily or uniquely in public institutions. The construct is associated conceptually with six dimensions: attraction to public policy making, commitment to the public interest, civic duty, social justice, self-sacriflce, and compassion. Likert-type items are developed for each dimension to create the PSM scale. The measurement theory for the scale is tested using confirnatory factor analysis (CFA). The present study reports initial reliability and validity results.
Anti‐Gna a New Antibody Reacting with a High‐incidence Erythrocytic Antigen

An antibody found in the serum of a blood donor agglutinated all cells tested except those of the donor and of three relatives. This antibody was named anti-Gna and identified the previously unrecognized antigen, Gna, possessed by all persons thus far tested. The antibody is presumed to have developed in the course of pregnancy although there is no history of clinical erythroblastosis fetalis. Antibody reactions are demonstrated by means of the antiglobulin technic. No persons lacking the Gna antigen have been found in a study of 2,600 unselected group A and O Rh-negative donors and patients. Compatible relatives are most likely homozygous for rare alleles, gn. The Gna gene is not sex linked nor is it closely linked to the loci responsible for ABO, MNSs, P, Kell, Duffy, Kidd, Lewis, and Xg blood-group systems. Parents and grandparents of the compatible relatives were all born within an extremely small geographic area in Poland. Studies of this family for the possibility of consanguinity and for the distribution of the Gna antigen in Poland have been initiated.
Susceptibility of mosquito and lepidopteran cell lines to the mosquito iridescent virus (IIV-3) from Aedes taeniorhynchus

Mosquito iridescent viruses (MIV) are members of the genus Chloriridovirus that currently contains only the type IIV-3 from Aedestaeniorhynchus. The complete genome of invertebrate iridescent virus -3 (IIV-3) has been sequenced and the availability of a tissue culture system would facilitate functional genomic studies. This investigation, using quantitative PCR and electron microscopy, has determined that the mosquito cell lines Aedes aegypti (Aag2), Aedes albopictus (C6/36) and Anopheles gambiae (4a3A) as well as the lepidopteran cell line from Spodoptera frugiperda (SF9) are permissive to IIV-3 infection. However, IIV-3 infection remained longer in Aag2 and C6/36 cells. Virus produced in C6/36 cell line was infectious to larvae of A. taeniorhynchus by injection and per os. Ultrastructural examination of 4a3A and SF9 cells infected with IIV-3 revealed an unusual feature, where virions were localized to mitochondria. It is speculated that containment with mitochondria may play a role in the lack of persistence in these cell lines.