cssi/SciSciGPT-SciSciNet huggingface dataset:
Transfer of calcium through a stearic acid bilayer

Abstract Transfer of calcium through a stearic acid bilayer on glass was studied. It was found that calcium moves readily through the bilayer, but that ion movement is not related to exchange of the lipid molecules in one layer with those in another. Rather, a displacement mechanism appears to apply. On the other hand, calculations indicated that water patches or pores of significant capacity do not exist. Thus, in this model system calcium movement does not appear to occur either by a carrier mechanism or by movement through aqueous pores, but direct exchange of external calcium with bound calcium is facile.
Placement Services in Today's Economy

To fully understand placement issues at the University of MissouriColumbia (MU) one must realize that career services functions are decentralized. MU has eight individual career services offices that focus on issues related to careers, primarily for juniors and seniors. These career services are supported by the following schools: Business & Public Administration; Engineering; Education; Human and Environmental Sciences; Library Science; Agriculture, Food and Natural Resources; Law; and Journalism. This structure leaves Arts and Sciences students and freshmen and sophomore students, as well as deciding students to be served by the Career Center (CPPC). To develop and encourage open communication between the various career services offices at MU, a Placement Council has been established. The group meets once a semester to articulate changes and concerns in career services. Nationally, approximately 77% of MU's student body is still in the process of deciding a major (Rayman, 1993), therefore CPPC is more of a broad information center that is able to provide a variety of services, instead of a placement office serving only seniors. Therefore, the CPPC philosophy is to educate students about self exploration, possible majors and careers, job search strategies, networking, resume writing, interviewing, etc., so that he/she can conduct a job search independently. An important part of this education is the Job Development Program: cooperative education, internship, part-time
Not Without Hope: A Reformed Analysis of Sickness and Sin

A Reformed understanding of sickness requires that connections be drawn between the structural effects of sin and the ways that sickness is experienced in people's lives. Such an understanding can be an important resource for the bioethicist, both the bioethicist who speaks from the Reformed tradition and the bioethicist who speaks to patients and caregivers who may assume that sin and sickness are connected, but may understand that linkage in overly simplistic ways.
Writing in Cyberspaces

Advances in technology, such as the word-processor, have long supported the pedagogy of composition. However, in the Internet environment a variety of electronic tools and multimedia can further enhance best practices in teaching writing: the integration of reading and writing, recursive drafting, targeted grammar and vocabulary study, peer review, and publication.
Effects of prior aging at 288°C in argon environment on time‐dependent deformation behavior of a thermoset polymer at elevated temperature, part 1: Experiments

The inelastic deformation behavior of PMR-15 neat resin, a high-temperature thermoset polymer, aged at 288°C in argon environment for up to 2000 h was investigated. The experimental program was designed to explore the inﬂuence of prior isothermal aging on monotonic loading and unloading at various strain rates. In addition, the relaxation response and the creep behavior of specimens subjected to prior aging of various durations were evaluated. All tests were performed at 288°C. The time-dependent mechanical behavior of the PMR-15 polymer is strongly influenced by prior isothermal aging. The elastic modulus increased and the departure from quasi-linear behavior was delayed with prior aging time. Stress levels in the region of inelastic flow increased with prior aging time. Furthermore, prior aging significantly decreased the polymer's capacity for inelastic straining, including the material's capacity to accumulate creep strain. Conversely, the relaxation response was not affected by the prior aging. © 2009 Wiley Periodicals, Inc.† J Appl Polym Sci, 2009
The Meta-Green Fluorescent Protein Chromophore

m-Hydroxy isomer of the green fluorescent protein synthetic analogue (m-HBDI) was synthesized. By analogy to hydroxystilbenes, longer singlet lifetimes and lower isomerization quantum yields were observed for the meta versus para isomer of the chromophore
Impairment and deportment responses to different methylphenidate doses in children with ADHD: the MTA titration trial.

ABSTRACT Objective Results of the NIMH Collaborative Multisite Multimodal Treatment Study of Children With Attention-Deficit/Hyperactivity Disorder (MTA) were analyzed to determine whether a double-blind, placebo-controlled methylphenidate (MPH) titration trial identified the best MPH dose for each child with attention-deficit/hyperactivity disorder (ADHD). Method Children with ADHD assigned to MTA medication treatment groups ( n = 289) underwent a controlled 28-day titration protocol that administered different MPH doses (placebo, low, middle, and high) on successive days. Results A repeated-measures analysis of variance revealed main effects for MPH dose with greater effects on teacher ratings of impairment and deportment ( F 3 = 100.6, n = 223, p = .0001; effect sizes 0.8–1.3) than on parent ratings of similar endpoints ( F 3 = 55.61, n = 253, p = .00001; effect sizes 0.4–0.6). Dose did not interact with period, dose order, comorbid diagnosis, site, or treatment group. Conclusions The MTA titration protocol validated the efficacy of weekend MPH dosing and established a total daily dose limit of 35 mg of MPH for children weighing less than 25 kg. It replicated previously reported MPH response rates (77%), distribution of best doses (10–50 mg/day) across subjects, effect sizes on impairment and deportment, as well as dose-related adverse events.
Renegotiating expertise: an examination of PACS and the challenges to radiology using a medical anthropologic approach.

Purpose The aim of this study was to examine how the adoption of PACS has affected the professional relationships among radiologists and referring providers and to evaluate the effect of PACS on perceptions of radiologists' roles in patient care. Methods A medical anthropologic approach was used to assess the impact of PACS among radiologists and a community of clinical subspecialists at a large academic medical center (n = 40). Data collection techniques included 3 months of ethnographic participant observation during the routine medical practice of study participants as well as semistructured interviews and archival research. These data were then analyzed to identify behavioral and narrative patterns and themes among the study populations. Results The difficulty of establishing and maintaining relationships of trust between referring providers and radiologists due to the drop in post-PACS reading room visits emerged as a major source of concern for study participants. By interacting primarily over the phone or at weekly conferences, radiologists felt that they had fewer opportunities to build personal relationships with other clinicians. Meanwhile, the specialist referring providers stated they generally consulted only radiologists with whom they had established personal relationships and otherwise preferred to interpret their patients' images themselves. Conclusions Generating and sustaining relationships of trust and effective communication are vital for radiologists to communicate their expertise in medical imaging to referring providers. Because PACS have caused a reduction in referring provider visits to the reading room, radiologists must seek out new opportunities to form personal relationships with other physicians.
Field investigation of roadside vegetative and structural barrier impact on near-road ultrafine particle concentrations under a variety of wind conditions

Roadside barriers, such as tree stands or noise barriers, are prevalent in many populated areas and have been shown to affect the dispersion of traffic emissions. If roadside noise barriers or tree stands are found to consistently lower ground-level air pollution concentrations in the near-road environment, this may be a practical strategy for reducing exposures to air contaminants along populated traffic corridors. This study measured ultrafine particle (UFP) concentrations using an instrumented mobile measurement approach, collecting data on major roadways and in near-road locations for more than forty sampling sessions at three locations in central North Carolina, USA. Two of the sampling sites had relatively thin tree stands, one evergreen and one deciduous, along a portion of the roadway. The third sampling site had a brick noise wall along a portion of the road. At 10 m from the road, UFPs measured using a mobile sampling platform were lower by approximately 50% behind the brick noise wall relative to a nearby location without a barrier for multiple meteorological conditions. The UFP trends at the vegetative barrier sites were variable and the barrier effect is uncertain. In some cases, higher concentrations were observed behind the vegetative barrier, with respect to the clearing, which may be due to gaps in the thin tree stands allowing the transport of traffic-related air pollution to near-road areas behind the vegetation. On-road sampling revealed no consistent difference in UFP levels in on-road portions of the road with or without a roadside barrier present. These findings support the notion that solid roadside barriers may mitigate near-road impact. Given the co-benefits of vegetative barriers in the urban landscape, research regarding the mitigation potential of vegetative barriers of other configurations (e.g., greater density, wider buffer) is encouraged.
Narrating Suffering, Remembering Hope: Metz's Theology as Paradigm for Examining Mental Illness and Disability Theology

This article proposes to explore new ways of speaking about disability by drawing from the theology of Johann Baptist Metz. Specifically, it uses Metz's ideas of subjectivity, narrative, memory, and hope and applies them to mental illness, with the intent to enable theologians to respond to mental health issues in a more nuanced way and to encourage Christians to foster a deeper solidarity with those suffering from mental illness. The article then briefly considers how Metz's paradigm may be used to enhance our understanding of other categories of disability.
Growth, endocrinological and behavioral deficits after monosodium l-glutamate in the neonatal rat: possible involvement of arcuate dopamine neuron damage

Abstract (1) The syndrome induced by the systemic administration of monosodium l -glutamate (MSG) to neonatal rats was investigated. (2) Animals receiving five injections of 4 mg/g of MSG (MSG V) in the first 10 days of life showed, as adults, growth, endocrinological, and behavioral abnormalities, whereas those receiving one injection (MSG I) showed few of the characteristic symptoms associated with neonatal MSG treatment. (3) MSG V females were markedly hypoactive ten weeks after weaning as measured in circular photocell activity cages in the dark part of the rats' day-night cycle. (4) MSG V rats were extremely stunted and obese (as determined by the Lee index) but appeared normophagic. (5) A previously unreported aspect of MSG toxicity, tail automutilation, occurred in a large proportion of MSG I and MSG V animals, with the highest incidence in MSG V females. (6) MSG V animals were hypothyroid as measured by radioimmunological determinations of serum triiodothyronine (T3) and free thyroxine index (FTI). In addition, MSG V females had smaller ovaries, uteri, and pituitaries when compared with saline-treated controls. (7) Histochemical examination of the hypothalamic arcuate area revealed a marked loss of dopaminergic perikarya in MSG V, but not MSG I animals; other catecholamine systems appeared intact. This raises the possibility that damage to the tubero-infundibular dopamine system may contribute to endocrinological and other deficits observed after neonatal MSG treatment.
Studies of the c-Harvey-Ras gene in psychiatric disorders

Herault et al. (1993) previously reported a significant association between autism and the larger fragments of the c-Harvey-Ras (HRAS) Bam H1 polymorphism. We have sought to verify this finding and determine if there was any evidence for an association with other psychiatric disorders. Because of its greater sensitivity, we have examined the HRAS Msp 1 polymorphism. We found a just significant increase in the prevalence of the > 2.1 kb alleles in 48 subjects with autism versus 50 control subjects. There was no increase in the prevalence of the > 2.1 kb alleles in 164 probands with Tourette's syndrome. Examination of 16 preselected symptom clusters, however, showed a significant trend toward higher scores for obsessive-compulsive and phobic symptoms in > 2.1 kb homozygotes. While this locus requires further study, in conjunction with the results of Herault et al., the present findings suggest that genetic defects in HRAS, and possibly other components of the G protein secondary messenger system, may play a role in some psychiatric disorders.
Effects of forest-management activities on runoff components and ground-water recharge to Quabbin Reservoir, central Massachusetts

Abstract The effects of forest-management activities (timber cutting and herbicide application) on runoff components (total streamflow, direct runoff, and base flow) and on ground-water recharge per unit area were evaluated for two separate paired drainage basins of Quabbin Reservoir in central Massachusetts. The Cadwell Creek study area, studied from 1962–1973, included an experimental basin (Upper Cadwell Creek) and a control basin (Lower Cadwell Creek). In the experimental basin, herbicide was applied to mixed oaks, northern hardwoods, and understory vegetation in different riparian zones during the summers of 1967 and 1968, and some pine plantations were thinned or clear-cut during the winter of 1967–1968. These forest-management activities decreased the total basal area by about 34%. The decrease in total basal area resulted in an increase in total streamflow, direct runoff (total streamflow minus base flow), and ground-water recharge for six dormant seasons (October–April) and six growing seasons (May–September) during 1968–1973. Base flow increased for three dormant seasons and two growing seasons during 1968–1970 and the dormant seasons of 1971 and 1973. Base flow accounted for 34% and direct runoff accounted for 66% of the 94 mm (15%) increase in total streamflow during water years 1968–1973. Sixty-one percent of this increase in total streamflow occurred in the dormant seasons. The Dickey Brook study area, studied from 1985–1989, included an experimental basin (Dickey Brook) and a control basin (Dickey Brook Tributary). Some pine plantations were thinned or clear-cut in the headwaters of the experimental basin from October 1986 to March 1987 and October to December 1988. These forest-management activities decreased the total basal area by 24% during 1986–1987 and an additional 8% during 1988. The decrease in total basal area resulted in an increase in total streamflow, base flow, and ground-water recharge for only one dormant season and one growing season in 1987. Direct runoff only increased slightly during the 1987 dormant season. Base flow accounted for 91% and direct runoff accounted for 9% of the 92 mm (21%) increase in total streamflow during water year 1987. Seventy-seven percent of this increase in total streamflow occurred in the dormant season.
Probing planetary pollution from space

The data sets obtained from instruments that have measured carbon monoxide and tropospheric ozone from space are reviewed. These instruments include a gas cell correlation radiometer named MAPS (Measurement of Air Pollution from Satellites), the Total Ozone Mapping Spectrometer, and the Stratospheric Aerosol and Gas Experiment. Particular attention is given to differential absorption lidar technology which can determine the vertical distribution of aerosols and selected trace gases with considerably more resolution than passive remote sensing techniques. The current plans for monitoring pollution from spaceborne platforms are also discussed.
Evolving Systems: Adaptive Key Component Control and Inheritance of Passivity and Dissipativity

We propose a new framework called Evolving Systems to describe the self-assembly, or autonomous assembly, of actively controlled dynamical subsystems into an Evolved System with a higher purpose. Autonomous assembly of large, complex flexible structures in space is a target application for Evolving Systems. A critical requirement for autonomous assembling structures is that they remain stable during and after assembly. The fundamental topic of inheritance of stability, dissipativity, and passivity in Evolving Systems is the primary focus of this research. In this paper, we develop an adaptive key component controller to restore stability in Nonlinear Evolving Systems that would otherwise fail to inherit the stability traits of their components. We provide sufficient conditions for the use of this novel control method and demonstrate its use on an illustrative example.
Aminoguanidine-mediated inactivation and alteration of neuronal nitric-oxide synthase.

It is established that aminoguanidine (AG) is a metabolism-based inactivator of the three major isoforms of nitric-oxide synthase. AG is thought to be of potential use in diseases, such as diabetes, where pathological overproduction of NO is implicated. We show here that during the inactivation of neuronal nitric-oxide synthase (nNOS) by AG that the prosthetic heme is altered, in part, to dissociable and protein-bound adducts. The protein-bound heme adduct is the result of cross-linking of the heme to residues in the oxygenase domain of nNOS. The dissociable heme product is unstable and reverts back to heme upon isolation. The alteration of the heme is concomitant with the loss in the ability to form the ferrous-CO complex of nNOS and accounts for at least two-thirds of the activity loss. Studies with [14C]AG indicate that alteration of the protein, in part on the reductase domain of nNOS, also occurs but at low levels. Thus, heme alteration appears to be the major cause of nNOS inactivation. The elucidation of the mechanism of inactivation of nNOS will likely lead to a better understanding of the in vivo effects of NOS inhibitors such as AG.
Kinetics and specificities of two closely related β‐glucosidases secreted by Schizophyllum commune

Two β-glucosidases (I and II) were isolated from Schizophyllum commune, and their physical and chemical properties studied. The two enzymes have very similar sequences, as shown by HPLC analysis of tryptic digests and partial amino acid sequencing. As judged by their circular dichroism spectra, they have almost identical secondary structure. The estimates for α-helix, β-sheet, and other structures were 21%, 40% and 39%, respectively, for β-glucosidase I and 27%, 32% and 41% for β-glucosidase II. Their near-ultraviolet spectra were identical. β-Glucosidase I was more highly glycosylated than β-glucosidase II, having 2 mol N-acetylglucosamine/mol enzyme 36, mol mannose/mol enzyme and 1.2 mol glucose/mol enzyme vs 1.2, 17 and 3 mol/mol, respectively, in β-glucosidase II. The native glycosylated form of β-glucosidase I had a molecular mass of 102 kDa, and that of β-glucosidase II, 96 kDa. As estimated from sensitivity to N-glycanase, β-glucosidase II sugars were mainly asparagine linked, but much of the sugar in β-glucosidase I was not removed by this treatment and was apparently serine or threonine linked. Kinetic analysis showed that both forms had similar Km values (0.3–2.1 mM) for oligosaccharides of 2–6 residues, but the kcat values of β-glucosidase II were lower by 30–75% than those of β-glucosidase I. The substrate dependence of kcat/Km indicated that both enzymes had binding sites for three glucose residues. The pH optimum of β-glucosidase I was higher than that of β-glucosidase II (5.8 vs 5.1). Both had similar specificities for several (R)-β-D-glucosides tested. Both enzymes were competitively inhibited by their glucose product, but β-glucosidase II was consistently less inhibited than β-glucosidase I. Cellobiase activity was much more markedly inhibited than the activity with higher oligosaccharides, and the result of this, plus the lower hydrolytic rate with cellobiose, resulted in an accumulation of cellobiose as higher oligosaccharides were digested. Glucono-δ-lactone inhibited both enzymes and the hydrolysis of all oligosaccharide substrates similarly (Ki= 4 μM). We conclude that the catalytic site is identical in both enzymes, but subtle structural differences are reflected in a differential activity on the higher oligosaccharides and in the differential effects of the glucose product as an inhibitor. Furthermore, ethanol had a stimulatory effect on β-glucosidase I but inhibited β-glucosidase II, which presumably reflects differential effects of ethanol on the conformations of the two species.
Classification of premalignant pancreatic cancer mass-spectrometry data using decision tree ensembles

Pancreatic cancer is the fourth leading cause of cancer death in the United States. Consequently, identification of clinically relevant biomarkers for the early detection of this cancer type is urgently needed. In recent years, proteomics profiling techniques combined with various data analysis methods have been successfully used to gain critical insights into processes and mechanisms underlying pathologic conditions, particularly as they relate to cancer. However, the high dimensionality of proteomics data combined with their relatively small sample sizes poses a significant challenge to current data mining methodology where many of the standard methods cannot be applied directly. Here, we propose a novel methodological framework using machine learning method, in which decision tree based classifier ensembles coupled with feature selection methods, is applied to proteomics data generated from premalignant pancreatic cancer. This study explores the utility of three different feature selection schemas (Student t test, Wilcoxon rank sum test and genetic algorithm) to reduce the high dimensionality of a pancreatic cancer proteomic dataset. Using the top features selected from each method, we compared the prediction performances of a single decision tree algorithm C4.5 with six different decision-tree based classifier ensembles (Random forest, Stacked generalization, Bagging, Adaboost, Logitboost and Multiboost). We show that ensemble classifiers always outperform single decision tree classifier in having greater accuracies and smaller prediction errors when applied to a pancreatic cancer proteomics dataset. In our cross validation framework, classifier ensembles generally have better classification accuracies compared to that of a single decision tree when applied to a pancreatic cancer proteomic dataset, thus suggesting its utility in future proteomics data analysis. Additionally, the use of feature selection method allows us to select biomarkers with potentially important roles in cancer development, therefore highlighting the validity of this method.
Water Leaching of Chelated Pb Complexes from Post-Phytoremediation Biomass

There is a pollution risk when disposing of post-remediation biomass from chelate-assisted metal phytoremediation. To assess this risk, we measured water extractable lead (Pb) in Brassica rapa tissues with ICP-MS, determined if chelated Pb was present with HPLC-MS, and identified Pb storage locations using electron microscopy with x-ray microanalysis. Ethylenediaminetetraacetic acid (EDTA) and ethylenediaminedisuccinic acid (EDDS) were used to enhance Pb movement from contaminated soil to above ground B. rapa tissues. With Pb-EDTA, 92 % (+/−5) of Pb was water extractable from dried tissues and complexed as Pb-EDTA. Electron microscopy and x-ray microanalysis showed Pb stored in xylem vessels. After composting of plant tissues, 79 % (+/−2) of Pb was water extractable and complexed as Pb-EDTA. Total plant Pb accumulation was lower from soils amended with EDDS, but only 6.7 % (+/−0.3) of Pb was water extractable from dried tissues and 55 % (+/−25) from wet tissues of plants grown in EDDS-amended soils. Pb-EDDS was detected in tissues but not at quantifiable levels. This work emphasizes the need for proper treatment and disposal of contaminated post-remediation plant tissues, especially when using EDTA. Composting of plant tissues containing Pb-EDTA was shown to significantly reduce waste material volume and slightly reduce the water extractable fraction, but further immobilization of Pb would be necessary to minimize transport risk. Amending Pb-contaminated soils with EDDS can result in plant biomass with a lower potential to leach Pb into groundwater, but the lower Pb accumulation with EDDS would require longer phytoremediation time compared with EDTA.
Effect of binary diffusion and chemical kinetic parameter uncertainties in simulations of premixed and non-premixed laminar hydrogen flames

Abstract Using a two-step approach, which includes a screening method (based on Morris Method) followed by global sensitivity analysis (based on High-Dimensional Model Representation), the uncertainty-based sensitivity of binary diffusion coefficients and chemical kinetic parameters over the full uncertainty range are presented for both simulations of premixed and non-premixed hydrogen-oxidizer-diluent mixtures. By implementing realistic uncertainty factors for binary diffusion coefficients and chemical kinetic parameters, the measured experimental uncertainty of laminar flame propagation velocity S L 0 is shown to be greater than the uncertainty on predicted S L 0 propagated from the binary diffusion coefficient parametric space. For 1 and 15 atm laminar flame speed simulations, the propagated uncertainties (ϵ) due to separate perturbation of the diffusion coefficients and chemical parameters are 3–5% and 12–41% respectively. The values of ϵ for the extinction strain rate at 1 atm are 6–8% and 19–28%. In premixed flames, the propagated uncertainty of chemical parameters increases with pressure, whereas the propagated uncertainty of binary diffusion coefficients is not affected. Based on current flame property measurements (about 5–10%), these results indicate that the fundamental flame properties clearly offer the possibility of reducing the chemical kinetic parameter uncertainties but marginal or no possibility of reducing the diffusion coefficient uncertainties.
The effects of health information technology on the costs and quality of medical care

Information technology has been linked to productivity growth in a wide variety of sectors, and health information technology (HIT) is a leading example of an innovation with the potential to transform industry-wide productivity. This paper analyzes the impact of health information technology (HIT) on the quality and intensity of medical care. Using Medicare claims data from 1998 to 2005, I estimate the effects of early investment in HIT by exploiting variation in hospitals' adoption statuses over time, analyzing 2.5 million inpatient admissions across 3900 hospitals. HIT is associated with a 1.3% increase in billed charges (p-value: 5.6%), and there is no evidence of cost savings even five years after adoption. Additionally, HIT adoption appears to have little impact on the quality of care, measured by patient mortality, adverse drug events, and readmission rates.
Growth structure of chemisorbed oxygen on GaAs(110) and InP(110) surfaces.

A study of oxygen chemisorption on GaAs(110) surfaces with both high-resolution synchrotron-photoemission spectroscopy and x-ray-photoemission spectroscopy of the oxygen 1s core level is presented in light of what can be learned about the atomic-scale structure during the growth of the first layers of oxide. Additional results for oxygen chemisorption on InP(110) are included for comparison with GaAs(110). Curve fitting of the synchrotron-photoemission data indicates that the spectra contain peaks due to direct oxygen bonding to semiconductor atoms, inducing large binding-energy shifts, as well as peaks arising from second-order charge transfer and structural relaxation, with smaller binding-energy shifts. These peak identifications are supported by the correlation between semiconductor and oxygen core-level intensities, the behavior of peak areas as a function of oxygen exposure, and the peak binding-energy spacings. The changes in intensity of the oxide peaks show that both Ga and As atoms are involved to an equal extent in the bonding with oxygen at coverages from 0.1 monolayers (ML) to at least 1.5 ML. Comparisons of the oxide peak areas for spectra taken with different surface sensitivity also demonstrate that oxygen chemisorption for InP and GaAs proceeds layer by layer, with large kinetic barriers to oxidation beyond the first two monolayers. The dominance of surface oxidation is confirmed by oxygen core-level spectroscopy and by calibration of the experimental surface sensitivity with surface-shifted peaks on the clean surface.
Modeling and simulation in engineering

This review article will explore the innovative and popular theme of engineering modeling and simulation, predominantly in the manufacturing industry and cybersecurity world, citing severe challenges, advantages and time- and budget saving solutions and its future. The power of simulation is not an exaggeration but an understatement. The favorable outcomes since the advent of digital computers and software revolution could not have been achieved, especially without the multiple benefits of statistical simulation, which underlies the widespread use of modeling and simulation in engineering and sciences, stretching from A (Astronomy) to Z (Zoology). This refers not only to research findings in verifying a certain piece of theory, such as that of the recently discovered Higgs Boson, but in testing new products to innovate new discoveries so as to make our universe a more peaceful place by modeling and simulating the future projects and taking precautions before disasters occur. The review explores a cross section of engineering modeling and simulation practices illustrating a window of numerical examples. WIREs Comput Stat 2013, 5:239–266. doi: 10.1002/wics.1254 Conflict of interest: The author has declared no conflicts of interest for this article. For further resources related to this article, please visit the WIREs website
Friendship as method

In this article, the author discusses friendship as a method of qualitative inquiry. After defining friendship and positing it as a kind of fieldwork, the methodological foundations of friendship as method are established. Next, it is proposed that friendship as method involves researching with the practices, at the pace, in the natural contexts, and with an ethic of friendship. Finally, the author describes this method's strengths and considerations for both researcher and participants.
Multilayer Optics for an Extreme Ultraviolet Lithography Tool with 70 nm Resolution

One of the most critical tasks in the development of extreme ultraviolet lithography (EUVL) is the accurate deposition of reflective multilayer coatings for the mirrors comprising the EUVL tool. The second set (Set 2) of four imaging optics for an alpha-class EUVL system has been coated successfully. All four mirrors (M1, M2, M3, M4) were Mo/Si- coated during a single-deposition run with a production- scale DC-magnetron sputtering system. Ideally, the multilayer coatings should not degrade the residual wavefront error of the imaging system design. For the present EUVL camera, this requirement is equivalent to depositing multilayer coatings that would add a figure error of less than 0.11 nm rms. In addition, all mirrors should be matched in centroid wavelength, in order to insure maximum throughput of the EUVL tool. In order to meet these constraints, the multilayer deposition process needs to be controlled to atomic precision. EUV measurements of the coated mirrors determined that the added figure errors due to the multilayer coatings are 0.032 nm rms (M1), 0.037 nm rms (M2), 0.040 nm rms (M3) and 0.015 nm rms (M4), well within the aforementioned requirement of 0.11 nm rms. The average wavelength among the four projection mirrors is 13.352 nm, with an optic-to-optic matching of 1(sigma) =0.010 nm. This outstanding level of wavelength matching produces 99.3% of the throughput of an ideally matched four-mirror system. Peak reflectances are 63.8% (M1), 65.2% (M2), 63.8% (M3) and 66.7% (M4). The variation in reflectance values between the four optics is consistent with their high frequency substrate roughness. It is predicted that the multilayer coatings will not introduce any aberrations in the lithographic system performance, for both static and scanned images of 70 nm - dense features.
Rewiring cellular morphology pathways with synthetic guanine nucleotide exchange factors

Eukaryotic cells mobilize the actin cytoskeleton to generate a remarkable diversity of morphological behaviours, including motility, phagocytosis and cytokinesis. Much of this diversity is mediated by guanine nucleotide exchange factors (GEFs) that activate Rho family GTPases-the master regulators of the actin cytoskeleton. There are over 80 Rho GEFs in the human genome (compared to only 22 genes for the Rho GTPases themselves), and the evolution of new and diverse GEFs is thought to provide a mechanism for linking the core cytoskeletal machinery to a wide range of new control inputs. Here we test this hypothesis and ask if we can systematically reprogramme cellular morphology by engineering synthetic GEF proteins. We focused on Dbl family Rho GEFs, which have a highly modular structure common to many signalling proteins: they contain a catalytic Dbl homology (DH) domain linked to diverse regulatory domains, many of which autoinhibit GEF activity. Here we show that by recombining catalytic GEF domains with new regulatory modules, we can generate synthetic GEFs that are activated by non-native inputs. We have used these synthetic GEFs to reprogramme cellular behaviour in diverse ways. The GEFs can be used to link specific cytoskeletal responses to normally unrelated upstream signalling pathways. In addition, multiple synthetic GEFs can be linked as components in series to form an artificial cascade with improved signal processing behaviour. These results show the high degree of evolutionary plasticity of this important family of modular signalling proteins, and indicate that it may be possible to use synthetic biology approaches to manipulate the complex spatio-temporal control of cell morphology.
Polyclonals to β-amyloid(1-42) identify most plaque and vascular deposits in Alzheimer cortex, but not striatum

Alzheimer's beta-peptides (A beta) aggregation rates depend on A beta length. We made synthetic peptide antisera to A beta 34-40 and 37-42. Purified anti-34-40 preferentially recognizes beta 1-40, vascular amyloid and a subset of plaques while purified anti-37-42 recognizes A beta 1-42 and not A beta 1-40 in dot and Western blots and immunoprecipitates; 37-42 precipitates a small percentage of fibroblast secreted A beta and strongly stains all deposits identified by monoclonals to A beta on adjacent sections from frontal cortex, but not in dorsal striatum.
An Ion Channel Platform for Detection of Small Molecule Analytes

The development of detection assays for small molecule analytes based on ion channel proteins makes it possible to exploit the amplification properties of membrane pores in response to specific external stimuli. Here, we used C-terminal derivatives of an ion channel-forming peptide, gramicidin A (gA), to explore an ion channel-based method for monitoring environmental contamination such as toxins or lethal microorganisms. Our initial results suggest that the modified ion channel-forming peptides can respond to a range of tailored, external, small molecule stimuli to produce detectable changes in electrophysiological properties.
Carotid artery reconstruction combined with myocutaneous flap coverage: A complex and durable rescue operation

Carotid reconstruction combined with myocutaneous flap coverage is a rare and challenging operation. We reviewed our experience to define the indications and outcome of this complex procedure. Clinical data and neurologic, wound, and vascular complications of all patients who underwent carotid artery reconstruction combined with myocutaneous flap coverage over a 17-year period were retrospectively reviewed. Results from this procedure indicate that pectoralis major myocutaneous flap is a safe and durable option for wound coverage in patients who undergo carotid endarterectomy, resection, and/or reconstruction for neck malignancy, previous irradiation or graft infection. Late outcome is favorable with low neurologic, vascular, and wound complication rates.
Plasmonic Microarrays for Biology

We will present a large-area and label-free plasmonic microarray with over one million sensor elements. Our system by enabling quantitative, real-time and high-throughput detection could become a powerful tool for biomedical sciences and pharmacology.
Inhibition of Tumor Necrosis Factor-α-Induced SHP-2 Phosphatase Activity by Shear Stress. A Mechanism to Reduce Endothelial Inflammation

Objectives— Atherosclerosis preferentially occurs in areas of turbulent flow, whereas laminar flow is atheroprotective. Inflammatory cytokines have been shown to stimulate adhesion molecule expression in endothelial cells that may promote atherosclerosis, in part, by stimulating c-Jun N -terminal kinase (JNK) and nuclear factor (NF)-κB transcriptional activity. Methods and Results— Because Src kinase family and Src homology region 2-domain phosphatase-2 (SHP-2) may regulate JNK activation, we studied the effect of shear stress on endothelial inflammation and JNK. Human umbilical vein endothelial cells preexposed to flow showed decreased tumor necrosis factor (TNF)-α–induced c-Jun and NF-κB transcriptional activation. TNF-α–mediated JNK, c-Jun, and NF-κB activation required Src and SHP-2 activity. Shear stress significantly inhibited SHP-2 phosphatase activity without affecting TNF-α–induced Src family kinase activation. Because MEKK3 and Gab1 are critical for TNF-α–induced c-Jun and NF-κB activation, we determined the role of SHP-2 phosphatase activity in MEKK3 signaling. A catalytically inactive form of SHP-2 increased MEKK3/Gab1 interaction and inhibited MEKK3 (but not MEKK1)-mediated c-Jun and NF-κB activation. Conclusions— These results suggest that SHP-2 is a key mediator for the inhibitory effects of shear stress on TNF-α signaling in part via regulating MEKK3/Gab1 interaction, MEKK3 signaling, and subsequent adhesion molecule expression.
The isolation and characterization of cDNA encoding human and rat brain inositol polyphosphate 4-phosphatase.

Inositol polyphosphate 4-phosphatase, an enzyme of the inositol phosphate signaling pathway, catalyzes the hydrolysis of the 4-position phosphate of inositol 3,4-bisphosphate, inositol 1,3,4-trisphosphate, and phosphatidylinositol 3,4-bisphosphate. The amino acid sequences of tryptic and CNBr peptides of the enzyme isolated from rat brain were determined. Degenerate oligonucleotide primers based on this sequence were used to amplify a 74-base pair polymerase chain reaction product. This product was used to isolate a 5607-base pair composite cDNA, which had an open reading frame encoding a protein with 939 amino acids with a predicted molecular mass of 105,588 Da. The rat brain polymerase chain reaction product was used as a probe to isolate a human brain cDNA that predicts a protein with 938 amino acids and a molecular mass of 105,710 Da. Remarkably, the human and rat proteins were 97% identical. Recombinant rat protein expressed in Escherichia coli catalyzed the hydrolysis of all three substrates of the 4-phosphatase. Northern blot hybridization indicates that the 4-phosphatase is widely expressed in rat tissues with the highest levels of expression occurring in brain, heart, and skeletal muscle. Polyclonal antiserum directed against the carboxyl terminus of the 4-phosphatase immunoprecipitated >95% of the 4-phosphatase activity in crude homogenates of rat brain, heart, skeletal muscle, and spleen, suggesting that this enzyme accounts for the 4-phosphate activ-ity present in rat tissues. This antiserum also immunoprecipitated the 4-phosphatase from human platelet sonicates.
Catastrophic overturn of the Earth's mantle driven by multiple phase changes and internal heat generation

The effects of phase changes and strong internal heat generation may combine to bring about brief, but extremely intense episodes of rapid thermal convection in the Earth's mantle. Numerical calculations using realistic thermodynamic properties for the exothermic Olivine → Spinel and endothermic Spinel → Perovskite + Magnesiowustite phase transitions suggest the transition region of the Earth's mantle may act as a capacitor for subducting slabs. Slab material accumulates in the transition region until a threshold level of thermal buoyancy is reached, and is then rapidly discharged into the lower mantle. In my calculations, this occurs as a catastrophic burst of convection lasting ∼10 Myr, with elevated heat transfer rates lasting ∼100 Myr. Such episodes may be analogs to superplume activity which has been hypothesized to give rise to an intense episode of intra-plate volcanism and stabilize the geodynamo against reversals. The topography on the two phase change boundaries is found to be negatively correlated, with the correlation becoming more negative during periods of rapid convection. Furthermore, the results of this study suggest the transition region of the Earth's mantle could be ∼250 K cooler on average, and consequently more viscous, than the surrounding mantle.
Differential Requirement for CD70 and CD80/CD86 in Dendritic Cell-Mediated Activation of Tumor-Tolerized CD8 T Cells

A major obstacle to efficacious T cell-based cancer immunotherapy is the tolerizing-tumor microenvironment that rapidly inactivates tumor-infiltrating lymphocytes. In an autochthonous model of prostate cancer, we have previously shown that intratumoral injection of Ag-loaded dendritic cells (DCs) delays T cell tolerance induction as well as refunctionalizes already tolerized T cells in the tumor tissue. In this study, we have defined molecular interactions that mediate the effects of DCs. We show that pretreating Ag-loaded DCs with anti-CD70 Ab abolishes the ability of DCs to delay tumor-mediated T cell tolerance induction, whereas interfering with 4-1BBL, CD80, CD86, or both CD80 and CD86 had no significant effect. In contrast, CD80(-/-) or CD80(-/-)CD86(-/-) DCs failed to reactivate already tolerized T cells in the tumor tissue, whereas interfering with CD70 and 4-1BBL had no effect. Furthermore, despite a high level of programmed death 1 expression by tumor-infiltrating T cells and programmed death ligand 1 expression in the prostate, disrupting programmed death 1/programmed death ligand 1 interaction did not enhance T cell function in this model. These findings reveal dynamic requirements for costimulatory signals to overcome tumor-induced tolerance and have significant implications for developing more effective cancer immunotherapies.
Comparison of thresholding techniques on nanoparticle images

Thresholding is an image processing procedure used to convert an image consisting of gray level pixels into a black and white binary image. One application of thresholding is particle analysis. Once foreground objects are separated from the background, a quantitative analysis that characterizes the number, size and shape of particles is obtained which can then be used to evaluate a series of nanoparticle samples. Numerous thresholding techniques exist differing primarily in how they deal with variations in noise, illumination and contrast. In this paper, several popular thresholding algorithms are qualitatively and quantitatively evaluated on transmission electron microscopy (TEM) and atomic force microscopy (AFM) images. Initially, six thresholding algorithms were investigated: Otsu, Riddler-Calvard, Kittler, Entropy, Tsai and Maximum Likelihood. The Riddler-Calvard algorithm was not included in the quantitative analysis because it did not produce acceptable qualitative results for the images in the series. Two quantitative measures were used to evaluate these algorithms. One is based on comparing object area the other on diameter before and after thresholding. For AFM images the Kittler algorithm yielded the best results followed by the Entropy and Maximum Likelihood techniques. The Tsai algorithm yielded the top results for TEM images followed by the Entropy and Kittler methods.
Influence of Test Conditions on Antifungal Time-Kill Curve Results: Proposal for Standardized Methods

This study was designed to examine the effects of antifungal carryover, agitation, and starting inoculum on the results of time-kill tests conducted with various Candida species. Two isolates each of Candida albicans, Candida tropicalis, and Candida glabrata were utilized. Test antifungal agents included fluconazole, amphotericin B, and LY303366. Time-kill tests were conducted in RPMI 1640 medium buffered with morpholinepropanesulfonic acid (MOPS) to a pH of 7.0 and incubated at 35 degrees C. Prior to testing, the existence of antifungal carryover was evaluated at antifungal concentrations ranging from 1x to 16x MIC by four plating methods: direct plating of 10, 30, and 100 microl of test suspension and filtration of 30 microl of test suspension through a 0.45-microm-pore-size filter. Time-kill curves were performed with each isolate at drug concentrations equal to 2 x MIC, using a starting inoculum of approximately 10(5) CFU/ml, and incubated with or without agitation. Last, inoculum experiments were conducted over three ranges of starting inocula: 5 x 10(2) to 1 x 10(4), >1 x 10(4) to 1 x 10(6), and >1 x 10(6) to 1 x 10(8) CFU/ml. Significant antifungal carryover (>25% reduction in CFU/milliliter from the control value) was observed with amphotericin B and fluconazole; however, carryover was eliminated with filtration. Agitation did not appreciably affect results. The starting inoculum did not significantly affect the activity of fluconazole or amphotericin B; however, the activity of LY303366 may be influenced by the starting inoculum. Before antifungal time-kill curve methods are routinely employed by investigators, methodology should be scrutinized and standardized procedures should be developed.
Preparation and magnetic properties of cobalt disulfide

Abstract A sample of CoS 1.97 was prepared by reacting CoS and S in an evacuated silica tube. Single crystals were grown by chemical transport using iodine as the transport agent. The ferro- magnetic transition temperature was found to be 122°K and from the saturation magnetization value of 38 e.m.u./g a magnetic moment of 0.84 μ B /molecule at 0°K was obtained.