cssi/SciSciGPT-SciSciNet huggingface dataset:
GTP-binding protein-independent potentiation by mastoparan of IL-1β-induced nitric oxide release from insulin-secreting HIT-T15 cells

Our recent data implicated small molecular weight G-proteins (e.g., H-Ras) in interleukin 1β (IL 1β)-induced metabolic dysfunction and apoptotic demise of the islet β cell (Tannous et al., Biochem Pharmacol 2001; 62:1459–1468, Kowluru and Morgan, Biochem Pharmacol, 2002; 63:1027–1035, Chen et al. Biochem Pharmacol, 2003; 66:1681–1694). Recently, we have shown that mastoparan, a tetradecapeptide from wasp venom, has been shown to directly activate islet endogenous G-proteins and regulate islet function (Amin et al., Endocrinology 2003; 144: 4508–4518). Herein, we investigated potential contributory roles, if any, of mastoparan (Mas)-sensitive G-proteins in IL-induced nitric oxide (NO) release from insulin-secreting HIT-T15 cells. While, ineffective by itself, Mas significantly potentiated IL-induced NO release from HIT-T15 cells. Interestingly, Mas-17, an inactive analog of Mas, also potentiated IL-induced NO release, suggesting that the potentiating effect of Mas may not involve activation of specific G-proteins. Such potentiating effects on IL-induced NO release were also demonstrable in the presence of another polycationic compound, melittin. Together, these findings suggest that Mas-induced potentiation of IL-induced NO release may in part be due to its amphiphilic and polycationic nature. These data also warrant caution in the use of Mas to study its regulation of cellular function without the use of an appropriate negative control, such as Mas-17.
Management of the diethylstilbestrol-exposed pregnant patient: A prospective study

Over a 5-year period we have managed 63 diethylstilbestrol-exposed pregnant patients with a standardized protocol requiring weekly cervical examination and decreased physical activity of the patient. Twenty-six patients (42%) underwent a prophylactic cerclage for a history of second-trimester loss or a hypoplastic cervix on initial clinical examination (group I). Thirty-six patients (58%) were followed expectantly (group II). Sixteen patients (44%) in group II demonstrated cervical change and required an emergency cerclage: Twenty-one patients were managed expectantly with no cerclage. The gestational age at delivery for group I was 37.7 ± 2.80 versus 34.5 ± 6.9 weeks for patients without a cerclage ( p = 0.04). There were no perinatal deaths if a cerclage was performed, whereas there were five deaths (24%) in the group without cerclage. The five deaths occurred at a mean gestational age of 24.40 ± 4.0 weeks and a mean birth weight of 614.00 ± 441.73 gm. Patients with a hypoplastic cervix or prior reproductive loss had a better outcome with early cerclage than patients with a normal cervix followed expectantly. We presently lack a reliable method to detect the diethylstilbestrol-exposed patient at greatest risk for perinatal loss. Based on our experience we believe that placement of a cerclage early in pregnancy should be a strong consideration.
Molecular dynamics simulations and functional characterization of the interactions of the PAR2 ectodomain with factor VIIa.

Signaling of the tissue factor-FVIIa complex regulates angiogenesis, tumor growth, and inflammation. TF-FVIIa triggers cell signaling events by cleavage of protease activated receptor (PAR2) at the Arg36-Ser37 scissile bond. The recognition of PAR2 by the FVIIa protease domain is poorly understood. We perform molecular modeling and dynamics simulations to derive the PAR2-FVIIa interactions. Docking of the PAR2 Arg36-Ser37 scissile bond to the S1 site and subsequent molecular dynamics leads to interactions of the PAR2 ectodomain with P and P′ sites of the FVIIa catalytic cleft as well as to electrostatic interactions between a stably folded region of PAR2 and a cluster of basic residues remote from the catalytic cleft of FVIIa. To address the functional significance of this interaction for PAR2 cleavage, we employed two antibodies with epitopes previously mapped to this cluster of basic residues. Although these antibodies do not block the catalytic cleft, both antibodies completely abrogated PAR2 activation by TF-FVIIa. Our simulations indicate a conformation of the PAR2 ectodomain that limits the cleavage site to no more than 33 A from its membrane proximal residue. Since the active site of FVIIa in the TF-FVIIa complex is ∼75 A above the membrane, cleavage of the folded conformation of PAR2 would require tilting of the TF-FVIIa complex toward the membrane, indicating that additional cellular factors may be required to properly align the scissile bond of PAR2 with TF-FVIIa. Proteins 2009. © 2009 Wiley-Liss, Inc.
Relationships between sulfate and nitrate ion concentrations and rainfall pH for use in modeling applications

Abstract Precipitation chemistry data for the north-east United States are analysed to test relationships between anthropogenic sulfate and nitrate ion contributions and rainfall pH. Results are presented and an application of a derived regression equation is made to estimate rainfall pH values from long-range transport model deposition predictions.
Techniques for visualizing 3-dimensional manifolds

Computer graphics has long been concerned with representing and displaying surfaces in 3-dimensional space R3. We address the questions of representation and display in a higher dimensional setting, specifically, that of 3-manifolds immersed in R4. We describe techniques for visualizing the cross-section surfaces of a 3-manifold formed by a cutting hyperplane. The manifold is first triangulated, so that the cross-section may be computed on a per tetrahedron basis. The triangulated manifold is stored in a data structure which efficiently supports calculation of curvature. We expect the techniques, which we have implemented on the Personal IRIS, will support a highly-interactive system when implemented on a fine-grain parallel computer such as the Connection Machine.
Ionic Conductances of the Surface and Transverse Tubular Membranes of Frog Sartorius Fibers

The resting ionic conductances of frog sartorius muscle fibers have been determined in a variety of conditions in order to measure the potassium conductance of the tubular and surface membranes ( g K t and g K s ) and the chloride conductance of the tubular and surface membranes ( g Cl t and g Cl s ). In both normal fibers and fibers without tubules, measurements of input resistance and diameter were made at normal pH and at low pH when the chloride conductance was very small. These measurements permitted the separation of the ionic conductances: g Cl s = 219 µmhos/cm2; g Cl t = 0 µmhos/cm2; g K s = 28 µmhos/cm2; g K t = 55 µmhos/cm2. Possible sources of systematic error are discussed and a statistical analysis of the effects of random error is presented. The implications of the nonuniformity of membrane properties are discussed along with possible anatomical explanations.
Natural abundance 15N NMR assignments delineate structural differences between intact and reactive-site hydrolyzed Cucurbita maxima trypsin inhibitor III.

15N NMR assignments were made to the backbone amide nitrogen atoms at natural isotopic abundance of intact and reactive-site (Arg5—Ile6) hydrolyzed Cucurbita maxima trypsin inhibitor III (CMTI-III and CMTI-III*, respectively) by means of 2D proton-detected heteronuclear single bond chemical shift correlation (HSBC) spectroscopy, utilizing the previously made sequence-specific 1H NMR assignments (Krishnamoorthi et al. (1992) Biochemistry 31. 898–904). Comparison of the 15N chemical shifts of the two forms of the inhibitor molecule revealed significant changes not only for residues located near the reactive-site region, but also for those distantly located. Residues Cys3, Arg5, Leu7, Met8, Cys10, Cys16, Glu19, His25, Tyr27, Cys28 and Gly28 showed significant chemical shift changes ranging from 0.3 to 6.1 ppm, thus indicating structural perturbations that were transmitted throughout the molecule. These findings confirm the earlier conclusions based on 1H NMR investigations.
Understanding the phase equilibrium and irradiation effects in Fe-Zr diffusion couples

Abstract We have studied the radiation effects in Fe–Zr diffusion couples, formed by thermal annealing of a mechanically bonded binary system at 850 °C for 15 days. After irradiation with 3.5 MeV Fe ions at 600 °C, a cross sectional specimen was prepared by using a focused-ion-beam-based lift out technique and was characterized using scanning/transmission electron microscopy, selected-area diffraction and X-ray energy dispersive spectroscopy analyses. Comparison studies were performed in localized regions within and beyond the ion projected range and the following observations were obtained: (1) the interaction layer consists of FeZr3, FeZr2, Fe2Zr, and Fe23Zr6; (2) large Fe23Zr6 particles with smaller core particles of Zr-rich Fe2Zr are found within the α-Fe matrix; (3) Zr diffusion is significantly enhanced in the ion bombarded region, leading to the formation of an Fe–Zr compound; (4) grains located within the interaction layer are much smaller in the ion bombarded region and are associated with new crystal growth and nanocrystal formation; and (5) large α-Fe particles form on the surface of the Fe side, but the particles are limited to the region close to the interaction layer. These studies reveal the complexity of the interaction phase formation in an Fe–Zr binary system and the accelerated microstructural changes under irradiation.
Atomic-layer by atomic-layer compositional depth profiling: Surface segregation and impurity cosegregation of Pt-Rh and Pt-Ru alloys.

Absolute composition depth profiles of true single-atomic-layer depth resolution have been obtained for the near surface layers of the (001) and (111) planes of Pt-Rh and Pt-Ru alloys in surface segregation and cosegregation with sulfur of these alloys. For both alloys, the segregation species is found to be Pt, and its concentration approaches the bulk value nonmonotonically; the composition of the second layer is reversed. We did not detect a significant dependence of surface segregation on crystal planes and also find the plane-edge effect to be very small for Pt-Rh alloy. Also no reversed segregation at the two dilute ends of the alloy composition of Pt-Rh is found. For Pt-Rh, if the sample contains a very small amount of sulfur, then sulfur and Rh cosegregate to the surface, with sulfur forming an adsorption overlayer. This reversal of segregation species by impurity sulfur is not observed for Pt-Ru alloys. We believe that atom-probe composition depth profiles can also be used as references for calibrating other surface analytical techniques.
Relaxant Effect of U0126 in Hemolysate-, Oxyhemoglobin-, and Bloody Cerebrospinal Fluid–Induced Contraction in Rabbit Basilar Artery

Background and Purpose —It has been suggested that mitogen-activated protein kinase (MAPK) is involved in cerebral vasospasm after subarachnoid hemorrhage. The present study was undertaken to explore the inhibitory effect of U0126, a novel MAPK inhibitor, in the contraction of the rabbit basilar artery by 3 spasmogens: hemolysate, oxyhemoglobin, and bloody cerebrospinal fluid (CSF) from patients with vasospasm. Methods —The contraction and relaxation of rabbit basilar arteries were measured by isometric tension. MAPK immunoprecipitation was assessed by Western blot analysis. Results —(1) Pretreatment of the rabbit basilar arteries with U0126 reduced contractions to hemolysate, oxyhemoglobin, or bloody CSF applied subsequently. (2) In the absence of endothelial cells, U0126 produced an inhibitory effect similar to the contractions induced by hemolysate, oxyhemoglobin, or bloody CSF. (3) U0126 relaxed the sustained contraction induced by hemolysate, oxyhemoglobin, or bloody CSF. (4) Hemolysate, oxyhemoglobin, and bloody CSF enhanced MAPK immunoprecipitation. (5) U0126 reduced MAPK immunoprecipitation induced by hemolysate, oxyhemoglobin, and bloody CSF. (6) Hemolysate, oxyhemoglobin, and bloody CSF significantly increased MAPK activity in the rabbit basilar artery. (7) U0126 abolished the effect of hemolysate, oxyhemoglobin, or bloody CSF on MAPK activation. Conclusions —This study demonstrated a role of MAPK in the contraction of rabbit basilar arteries by hemolysate, oxyhemoglobin, and bloody CSF. MAPK inhibitor U0126 may be useful in the treatment of cerebral vasospasm.
Older Adults' Use of Technology

In this article, we will discuss the “digital divide” as it relates to the use and acceptance of technology by older people, particularly in the realm of health care. We will review potential barri...
The PbSSi heterojunction III: Optical properties

Abstract The optical properties of the PbSSi heterojunctions were investigated at 300 and 77 K. A maximum D∗ value of 1010 cm Hz 1 2 W−1 was found at 3 μm near 200 K. The activation energy for recombination of the PbS film was determined. Finally, the IR imaging application of the heterojunction is briefly discussed.
CDC plenary: “Hybrid dynamical systems and robust feedback control”

A bouncing ball, a network of impulsive biological oscillators, a sampled-data and networked control system, and a supervisory-based feedback control loop are examples of hybrid dynamical systems. These systems contain variables that, in some regions of the state space, change continuously and, in other regions, change instantaneously. Hybrid systems have been studied extensively over the last two decades, with important contributions generated by computer scientists, mathematicians, and control engineers. Interest from the control community is due, primarily, to the recognition that advances in modeling and analysis of hybrid systems may spawn a variety of novel feedback control ideas. This lecture emphasizes a dynamical systems approach to hybrid systems. It describes a modeling framework and a set of structural properties under which the dynamic behavior of a hybrid system is robust. Robustness means that small perturbations to the system lead to correspondingly small changes in the qualitative behavior of the system. This feature is a requirement for feedback control systems of all types, including hybrid control systems. Moreover, the properties that yield robustness also confer to hybrid systems many classical stability analysis tools from continuous-time and discretetime nonlinear systems. These and other hybrid-specific tools serve as the genesis for several hybrid feedback control algorithms. A selection of analysis tools and control algorithms are presented to illustrate recent advances in the field of hybrid systems.
Pseudomodulation : a computer-based strategy for resolution enhancement

Abstract Pseudomodulation is defined as computer simulation of the effect on a magnetic resonance spectrum that would be obtained if a sinusoidal field modulation were applied followed by phase-sensitive detection at the fundamental frequency or at one of its harmonics. Since it is done by computer, it is not necessary that it actually be possible to modulate the field. The algorithm is developed here for EPR spectroscopy, but can be applied to any function or to any digitized signal, including an NMR signal, and there can be more than one independent parameter, as, for example, an MR image or a 2D NMR spectrum where there are two. Pseudomodulation transforms and filters a digitized spectrum. Subtraction or addition of various amounts of the even harmonics of the digitized spectral data from or to the original spectrum results in resolution enhancement. Other resolution-enhancement algorithms that use pseudomodulation are also presented. Resolution enhancement by pseudomodulation is tested on simulated spectra to which computer-generated noise has been added and is applied to the EPR S-band spectrum of the blue copper protein azurin.
Stainless steel capacitive pressure sensor for high pressure and corrosive media applications

This paper reports an assembly-type, stainless steel (SS) capacitive gage pressure sensor comprising three key elements: two SS dies and a commercial SS Swagelok fitting that also serves as the package. The sensor is realized by placing a patterned silicon dioxide film deposited on the thinner of the two SS dies (diaphragm die) against a silicon nitride film deposited on the other SS die (backing plate) and housing the combination in a Swagelok fitting. Pressure measurements up to 1500 psi have been demonstrated using corrosive and benign media. Tested media include 45% wt. potassium hydroxide (KOH), 25% wt. tetramethylammonium hydroxide (TMAH), deionized (DI) water, and nitrogen gas. Extended-duration tests with a sensor subjected to KOH solution for 30 days demonstrate excellent repeatability. Random pressure fluctuation tests over a 15-day period also demonstrate good repeatability.
The development of a Mentor Program to foster career management

Abstract Because of dramatic changes in the employment environment and the increased frequency with which employees change jobs and careers, career management has become increasingly important. This article introduces and evaluates an academic Mentor Program that was developed in response to these changes. The Mentor Program provides students with many benefits including career counseling, practical work experience, employment opportunities, and networking.
New metaphors for understanding the new machines

Though frequently misunderstood and dismissed as irrelevant ornamentation, metaphors are useful tools for writers in the computer industry. Metaphors are especially useful for presenting information about new technologies because they help readers grasp whole concepts immediately and because they illuminate concepts that are difficult to communicate otherwise. It is important to distinguish this use of metaphors from their use in literature and advertisement.Participants in the workshop will follow procedures for investigating the suitability of several metaphors. They will analyze the power and appropriateness of metaphors currently used in the computer industry by applying seven criteria: Is the metaphor useful? understood? close? illuminating? acceptable? economical? memorable?
Predicting Attrition to Prevent Service Gaps in Serving Juvenile Offenders

Abstract Objective: The purpose of this study was to: (a) investigate differences in demographic variables, previous delinquent/criminal behavior variables, family system variables, juvenile court system variables, and subsequent delinquent behavior variables between youth who received services and those who did not among court-involved juvenile delinquent youth; and (b) create a predictive model that would correctly identify youth at the greatest risk of not receiving services. Method: The study employed an analysis of 244 youth, 182 (75%) service recipients and 62 (25%) non-recipients, randomly selected from a larger pool of 500 juvenile court-involved youth. Results: Analysis indicated that very few of the demographic variables, delinquent/criminal behavior variables, family system variables, and juvenile court system variables differentiated between service recipients and non-recipients. However, a logistic regression model was developed that correctly predicted service receipt for 78% of the sample, ...
Active proton transport stimulated by CO2/HCO3-, blocked by cyanide.

EXPOSURE of a cell to increased CO2 levels causes a drop in the intracellular pH (pHi) (ref. 1). The time development of this acidification has been monitored in snail giant neurones2 and squid giant axons3 by means of glass microelectrodes. It was found that pHi does not simply fall to a new steady value during CO2 exposure, but, given sufficient time, will slowly recover; and that, on return to a CO2-free solution, a higher pHi value (more alkaline) than the initial one is attained. The slow, secondary alkalinisation observed during exposure to CO2 cannot be accounted for by any passive mechanism, since the electrochemical gradients for H+, OH− and HCO3− all favour further acidification. For example, during the alkalinisation, the external pH (pHo) in squid axons is typically 7.7 and pHi 7.0; hence, the Nernst potentials for H+ (EH), OH−, and HCO3− are all ∼ −40 mV, compared with a membrane potential (Km) of −60 mV. Thus, a proton extruding pump, or its equivalent, must be postulated. We now report that the rate of alkalinisation is at least partially dependent on the CO2 and/or HCO3− content of the bathing medium, that it is reversibly blocked by metabolic inhibitors and that an extracellular acidification accompanies the intracellular alkalinisation.
Generating Kolmogorov phase screens for modeling optical turbulence

Accurate modeling of turbulence is required for investigating interactions between turbulence, blooming, and environmental and laser beam characteristics. A layered model propagates the optic field across each layer by Fresnel diffraction and a phase screen. Turbulence is modeled statistically with the Kolmogorov spectrum which goes to infinity as spatial frequency decreases. Below a cut-off frequency, the spectrum transitions to zero at a point corresponding to the largest eddies in the turbulence. Two different approaches for computing phase screens with this spectrum are considered. In the first approach, the phase screens are computed directly from the spectrum by inverse transformation. Gaussian random numbers are molded to the spectrum. A discrete 2D Fourier transform provides sample random phase screens. We show that the discrete Fourier transform cannot provide an accurate transform because of the character of the Kolmogorov spectrum. In the second approach, a covariance matrix is developed using structure functions. This avoids the need to compute a Fourier transform. The eigenvalues and eigenvectors are computed for the matrix. Eigenvalue weighted Gaussian random variables are premultiplied by the eigenvector array to generate phase screens. The advantages, disadvantages, and computational effort are discussed.
A typology of de-coupling strategies in mixed services

Abstract A typology of a class of service systems is proposed. The typology links strategic operational objectives to the decision to de-couple work between the front and back offices of a service system. Four specific ideal types of a strategy/de-coupling mix are described; each of which has distinct operational, marketing and human resource ramifications. A type that has had significant representation in traditional literature is the “Cost Leader” type, where back-office activities are de-coupled from the front office for the purpose of lowering costs. Another traditional type representative of the craftsman legacy is the “Personal Service” type, which retains back-office tasks in the front office to pursue non-cost-oriented strategic goals. Theoretical and empirical evidence is also given for two non-traditional types: the “Kiosk” type, where all tasks remain in the front office to achieve lower costs, and the “Focused Professional” type, which de-couples front- and back-office activities to enable front-office workers to provide higher service, rather than to reduce costs. Empirically, retail bank lending systems are analyzed to support the typology.
Parents, Friends, and Familial Sex Role Attitudes*

The present study treats parental and friendship interaction as predictors of familial sex role attitudes for each sex, taking into account mother's socioeconomic status and work experience. The data are based on a random sample of college students. The findings show that parental interaction is more important than peer associations in influencing familial sex role attitudes, particularly among men. Mother's socioeconomic status and work experience condition the effects of reference group interaction on a daughter's and son's familial sex role attitudes differently and contrary to expectations. The findings are discussed in the context of reference group theory and attitude formation with a focus on the mother as a role model.
Self-assembly of hydrogen-bonded two-dimensional quasicrystals

Scanning tunnelling microscopy reveals that molecules of ferrocenecarboxylic acid can self-assemble into quasicrystal monolayers containing highly unusual cyclic hydrogen-bonded pentamers; this molecular framework could form the basis of a large range of supramolecular assemblies. The range of systems in which non-periodic quasicrystalline ordering has been observed continues to increase, with small-molecule self-assembled monolayers now entering the arena. Specifically, Natalie Wasio and colleagues find that the hydrogen-bonding patterns of ferrocenecarboxylic acid drive the assembly of these molecules into unusual cyclic pentamers, whose five-fold symmetry facilitates a two-dimensional quasicrystalline arrangement. The authors anticipate that a large range of novel quasicrystalline supramolecular assemblies could be formed based on this molecular framework. The process of molecular self-assembly on solid surfaces is essentially one of crystallization in two dimensions, and the structures that result depend on the interplay between intermolecular forces and the interaction between adsorbates and the underlying substrate1. Because a single hydrogen bond typically has an energy between 15 and 35 kilojoules per mole, hydrogen bonding can be a strong driver of molecular assembly; this is apparent from the dominant role of hydrogen bonding in nucleic-acid base pairing, as well as in the secondary structure of proteins. Carboxylic acid functional groups, which provide two hydrogen bonds, are particularly promising and reliable in creating and maintaining surface order, and self-assembled monolayers of benzoic acids produce structure that depends on the number and relative placement of carboxylic acid groups2,3,4,5,6. Here we use scanning tunnelling microscopy to study self-assembled monolayers of ferrocenecarboxylic acid (FcCOOH), and find that, rather than producing dimeric or linear structures typical of carboxylic acids, FcCOOH forms highly unusual cyclic hydrogen-bonded pentamers, which combine with simultaneously formed FcCOOH dimers to form two-dimensional quasicrystallites that exhibit local five-fold symmetry and maintain translational and rotational order (without periodicity) for distances of more than 400 angstroms.
Soft plaque detected on intravascular ultrasound is the strongest predictor of in-stent restenosis: an intravascular ultrasound study.

Aims Although various predictors of in-stent restenosis (ISR) have been reported, the subject of parameters relating to ISR on intravascular ultrasound (IVUS) still leaves room for discussion. The aim of this study was to clarify the strongest predictors of ISR using IVUS. Methods and results Ninety-two native coronary lesions undergoing single bare-metallic stent implantation were investigated retrospectively. We classified them into the ISR (n = 46) and non-ISR (n = 46) groups using quantitative coronary angiography. On serial IVUS studies, plaque morphology, and areas and volumes of each component in vessel were evaluated. Among all parameters, diabetes mellitus and soft plaque appearing hypoechoic on IVUS were associated with ISR. By multivariate analysis, soft plaque was the only independent predictor of ISR (p = 0.0057). Compared with non-soft plaque, soft plaque had a larger plaque reduction rate (-7.1% vs. -1.6%, p=0.0613) and smaller percent plaque volume (53.0% vs. 55.5%, p=0.0273) after stenting. Conversely, soft plaque had a larger neointimal area (4.39 vs. 3.33 mm 2 , p = 0.0437) and percent plaque area (80.5% vs. 75.1%, p = 0.0503) at follow-up. Conclusion Soft plaque detected on IVUS was the strongest predictor of ISR. Soft plaque was compressed more easily by stenting, however, causing more proliferation of neointima subsequently and resulted in a worse prognosis.
How well is enzyme function conserved as a function of pairwise sequence identity

Enzyme function conservation has been used to derive the threshold of sequence identity necessary to transfer function from a protein of known function to an unknown protein. Using pairwise sequence comparison, several studies suggested that when the sequence identity is above 40%, enzyme function is well conserved. In contrast, Rost argued that because of database bias, the results from such simple pairwise comparisons might be misleading. Thus, by grouping enzyme sequences into families based on sequence similarity and selecting representative sequences for comparison, he showed that enzyme function starts to diverge quickly when the sequence identity is below 70%. Here, we employ a strategy similar to Rost's to reduce the database bias; however, we classify enzyme families based not only on sequence similarity, but also on functional similarity, i.e. sequences in each family must have the same four digits or the same first three digits of the enzyme commission (EC) number. Furthermore, instead of selecting representative sequences for comparison, we calculate the function conservation of each enzyme family and then average the degree of enzyme function conservation across all enzyme families. Our analysis suggests that for functional transferability, 40% sequence identity can still be used as a confident threshold to transfer the first three digits of an EC number; however, to transfer all four digits of an EC number, above 60% sequence identity is needed to have at least 90% accuracy. Moreover, when PSI-BLAST is used, the magnitude of the E-value is found to be weakly correlated with the extent of enzyme function conservation in the third iteration of PSI-BLAST. As a result, functional annotation based on the E-values from PSI-BLAST should be used with caution. We also show that by employing an enzyme family-specific sequence identity threshold above which 100% functional conservation is required, functional inference of unknown sequences can be accurately accomplished. However, this comes at a cost: those true positive sequences below this threshold cannot be uniquely identified.
In the Wake of Terrorist Attack, Hatred May Mask Fear

Reactions of anger, rage, and hatred in the wake of September 11 terrorist attack are considered in light of the psychology of emotion and stress. Acknowledging underlying grief and fear through self-reflection, writing, and social communication is likely to reduce unchecked anger, rage, and hatred. Hate crimes may also have some psychological bases in responses to stress called “flight-or-fight.” When flight is not an option, identifying and hating an enemy may have had evolutionary value for survival. This response creates harm in the current situation. An alternative cooperative response to stress, called “tend-and-befriend” by researchers, will be more helpful. In Wyoming an angry group of shoppers chased a woman and her children from a Wal-Mart, apparently because the woman and children were Muslim. In New York a young Manhattan couple yelled insults at a Lebanese American who was searching for survivors from the arts center he had run at the World Trade Center. A mosque in Denton, Texas, was fire-bombed. Why have these and other similar expressions of hostility toward people of Middle Eastern heritage already occurred across the United States following the September 11 terrorist attack (cnn.com, 2001; Thomson, 2001)? Surely we know that all Arabs or all Muslims are no more responsible for the horrific tragedy than are all Irish or all Christians responsible for terrorism in northern Ireland. Surely we do not want to repeat acts reminiscent of our own history of severely mistreating innocent Japanese Americans during World War II. Surely we don’t want to engage in the same sort of racism and hatred of innocent people that we find so Analyses of Social Issues and Public Policy, 2002, pp. 5–8
Phenotype of chromosome 14–linked familial Alzheimer's disease in a large kindred

We report the clinical and neuropathological features of chromosome 14–linked familial Alzheimer's disease (14qF AD) in affected members of the L family. Some clinical information on all 16 known affected individuals and detailed neuropathological findings in 6 family members were available for review. Common features of the phenotype of 14qFAD in the L family included onset of dementia before the age of 50, early progressive aphasia, early-appearing myoclonus and generalized seizures, paratonia, cortical atrophy, numerous and extensive senile plaques and neurofibrillary tangles, and prominent amyloid angiopathy. Descriptions of phenotypic features were available for six additional recently defined 14q-linked FAD kindreds: the findings in four of them (FAD4, FAD2, A, B) indicated a relatively consistently shared 14qFAD phenotype, conforming closely with the specific clinical and neuropathological characteristics noted in the L family. Comparisons also suggested several ostensible phenotypic variants in 14qFAD: (1) In two 14q-linked kindreds (SNW/FAD3, FAD1), affected individuals in some instances were noted to survive to age 70 or beyond and the mean age at onset (> 49 years) in these two kindreds was somewhat higher than in their five 14qFAD counterparts (< 48 years in each) (2) in the SNW/FAD3 kindred, seizures and myoclonus were absent in all 10 subjects examined; and (3) cerebellar amyloid plaques were variably present within and among several 14qFAD kindreds. Comparisons with phenotypic features recently detailed in three kindreds (TOR3, F19, ROM) with codon 717 amyloid precursor protein gene mutations (i.e., APP717 FAD) suggested several distinctions: Prominent progressive aphasia, myoclonus, seizures, and paratonia were all apparently less prevalent in APP717 FAD, with language function predominantly spared over the initial disease course. The extent of homogeneity and heterogeneity in the clinical and neuropathological phenotype of 14q-linked FAD and its possible meaningful distinctions from the phenotypes of APP717 FAD await further determination.
Cluster-Based Back-Pressure Routing Algorithm

We study scalable, distributed, and adaptive routing algorithms for communication networks. The back-pressure algorithm introduced in [21] is a well-known distributed and adaptive routing/scheduling algorithm where nodes only need the queue length information of neighboring nodes to make routing decisions, and packets are adaptively routed in the network according to congestion information, which makes the algorithm resilient to traffic and topology changes. However, the back-pressure algorithm requires routers to maintain a separate queue for each destination, which prevents its implementation in large-scale networks like the Internet. In this paper, we propose a cluster-based back-pressure routing algorithm, which retains the distributability and adaptability of back-pressure routing, while significantly reducing the number of queues that have to be maintained at each node. Since the cluster-based algorithm performs adaptive load-balancing in the network, it has the potential to eliminate the need for off-line traffic engineering in the Internet.
De⁄Re-Centring Work and Class?: A Review and Critique of Labour Geography

In this paper I examine how labour geographer’s research on the work-place, the wage relation and class have evolved and assess their implications for the sub-discipline. Since the early 1990s post-structural and post-structurally informed Marxist approaches have both challenged classical Marxism and added new insights. In particular, the former have de-centred the formal work-place as a site of value production, exploitation and class and emphasized the critical role of intersectionality of class with other identities such as gender and race. Paralleling and informing this shift has been a significant restructuring of capitalism as formerly stable employment is disrupted via (often global) outsourcing, downsizing and the blurring of enterprises and organizations. Thus post-structural perspectives have developed important insights into the active agency and the differentiated nature of labour, the work-place and class. Yet despite some congruence between post-structural and Marxist approaches I argue that there remain important empirical and theoretical concerning the work-place, the wage- relation and class. I conclude that while post-structural approaches are correct in arguing that the formal work-place and wage relation are not the exclusive sites of work, surplus production or class identity, over-emphasize the decline of the formal work-place and the wage relation’s role in collectivity and class identity more traditional Marxian concerning this relationship remain powerfully relevant to both labour geography and progressive politics.
Ziv–Zakai Time-Delay Estimation Bounds for Frequency-Hopping Waveforms Under Frequency-Selective Fading

Ziv-Zakai Bayesian lower bounds on time-delay estimation (TDE) are developed for frequency hopping waveforms. These wideband waveforms are readily employed for both communications and TDE. We consider random frequency-selective fading channels, described by a Gaussian tapped delay line model with inter-hop correlation. The receiver does not know the channel realization to assist in estimating the time delay but does know the channel statistics. The development incorporates a random uniform prior on the delay. The bounds provide tight mean-square error prediction for the maximum a posteriori (MAP) estimator performance over a large range of signal-to-noise ratios (SNRs). They also accurately predict the TDE frequency diversity gain from multi-frequency transmission in fading channels. The special case of independent fading is discussed, including both flat Rician and Rayleigh fading, and closed-form expressions enable easy study of the effects of SNR, frequency diversity, and channel statistics on TDE.
Molecular ordering in monolayers of an alkyl-substituted perylene-bisimide dye by attenuated total reflectance ultraviolet-visible spectroscopy.

Surface-relative orientational parameters were determined for monolayer films of N, N′-ditridecylperylenetetracarboxylic dianhydridediimide (C13-PTCDI) in terms of the relative electronic transition dipole strengths, providing a three-dimensional view of the absorption dipole distribution. In order to obtain a macroscopically ordered film, C13-PTCDI was deposited by (1) horizontal Lang-muir–Blodgett (LB) transfer onto methyl- and phenyl-silanized glass, and (2) vapor deposition onto oriented films of poly(tetrafluoroethylene) (PTFE) on glass. Films of LB-deposited C13-PTCDI were found to be completely isotropic prior to annealing. After annealing, these films remained isotropic in the plane of the substrate while the out-of-plane anisotropy was significantly enhanced. In contrast, films of C13-PTCDI vapor deposited onto oriented poly(tetrafluoroethylene) (PTFE)-modified substrates yielded films with a high degree of both in- and out-of-plane anisotropy. Atomic force microscopy (AFM) images of both the LB- and vapor-deposited films show substantial differences in film morphology and long-range order. These results demonstrate that molecular orientation in C13-PTCDI films can be controlled by varying substrate surface chemistry and post-deposition processing.
An extended finite element framework for slow-rate frictional faulting with bulk plasticity and variable friction

SUMMARY We present an extended finite element (FE) approach for the simulation of slow-rate frictional faulting in geologic media incorporating bulk plasticity and variable friction. The method allows the fault to pass through the interior of FEs without remeshing. The extended FE algorithm for frictional faulting, advocated in two recent articles, emanates from a variational equation formulated in terms of the relative displacement on the fault. In the present paper we consider the combined effects of bulk plasticity and variable friction in a two-dimensional plane strain setting. Bulk plasticity is localized to the fault tip and could potentially be used as a predictor for the initiation and propagation of new faults. We utilize a variable velocity- and state-dependent friction, known as the Dieterich–Ruina or ‘slowness’ law, formulated in a slip-weakening format. The slip-weakening/variable friction model is then time-integrated according to the generalized trapezoidal rule. We present numerical examples demonstrating the convergence properties of a global Newton-based iterative scheme, as well as illustrate some interesting properties of the variable friction model. Copyright q 2009 John Wiley & Sons, Ltd. Received 16 August 2008; Accepted 17 December 2008
Determination of rubidium in human erythrocytes, plasma, and urine by atomic absorption spectrophotometry.

Abstract A method for quantitation of stable Rb in human erythrocytes, plasma, and urine is described which is accurate, simple, and free from interference by other sample constituents. This method gives a percentual concentration limit (PCL) for Rb of 0.02 μg/ml.
Coupled m-component fields with cubic anisotropy

Abstract The critical behavior at phase transitions of two coupled, m -component systems with cubic anisotropy is studied by a simplified model in which the fluctuations are partially considered. The phase transition could be a new fluctuation-induced first order transition into the anisotropic phase, or a new second order phase transition. Unlike in uncoupled systems, the second order phase transition could be into either the anisotropic or isotropic phase. As expected, upon suppression of fluctuations, all results reduce to those of mean field theory.
Architecting millisecond test solutions for wireless phone RIFIC's

Today's low cost wireless phones have driven a need to be able to economically test high volumes of complex RF ICs at a fraction of the cost of the IC. In June of 2001 the IBM test development group developed a strategy and design to test complex wireless phone front end components for a fraction of the cost of using traditional ATE or rack and stack test solutions. In this paper, the architecture of the system is described as well as some of the design, maintenance and implementation considerations. The system is designed to bring the cost of complex manufacturing test of RF ICs equivalent to that of testing discrete components such as resistors or capacitors. Given the drastic reduction of test cost and the relative ease of implementation of this solution, this architecture sets the bar for future RF test solutions. To the best of our knowledge, this architecture has resulted in the fastest RF tester in the world.
Memories from My Gainesville Days as a Student of R.E. Kalman [Historical Perspectives]

I graduated from the National Technical University of Athens in June of 1979. In the spring of 1979, shortly after I had expressed interest in joining Prof. Kalman's group at Gainesville, I met and was vetted by his former student Thanos Antoulas during one of Thanos' visits to Athens. I still have notes from that meeting, where I came to realize the beauty and breadth of the research program that I was soon going to be part of. I went to Gainesville in the fall of 1979 and was welcomed by fellow students Pramod Khargonekar, Bulent Ozguler, Jaime Ribera, and Erol Emre, who was R.E. Kalman's postdoc at the time. I met Prof. Kalman a month later when he returned to Gainesville from a trip. I distinctly recall that first meeting. After inquiring briefly about my own (limited at the time) research experience, he went on to discuss the importance of mathematics in engineering and science. He touched on modeling and how to discover structure from data as well as the fundamental role of minimality, both in the complexity of models as well as in our assumptions in developing them. Yet, with that in the background, he suggested that I take advanced algebra courses first, the importance of which became clear to me much later. From that point on, and for about a year, my interaction with Prof. Kalman was minimal. Apparently, he allowed time for osmosis to take place.
Self-organizing skill synthesis

Endowing robots with the ability of self-organizing learned skills enables them to learn a new skill from learned skills. This paper proposes a skill-synthesis framework to enable robots to self-organize learned skills for facilitating learning a new skill for accomplishing a new task. The proposed skill-synthesis framework differs from previous work in its capability of self-organizing learned skills into stimulus-response units (SRU), from which new skills can be quickly learned and synthesized. The proposed skill-synthesis framework can be realized by stages, which establish common SRUs between two similar skills and self-organize a new skill from these common SRUs and additional new SRUs with reinforcement learning. Computer simulations and experiments with a Pioneer 3-DX mobile robot were conducted to validate the self-organizing capability of the proposed skill-synthesis framework in identifying common SRUs between similar skills and learning new skills from learned skills.
Results of Elective Stenting of Branch-Ostial Lesions

Coronary stenting using both Palmaz-Schatz and Gianturco-Roubin stents for branch ostial lesions was performed in 48 patients with high success and low complication rates. The 6-month event-free survival rates were high in these patients.
Proteorhodopsin genes in giant viruses

Viruses with large genomes encode numerous proteins that do not directly participate in virus biogenesis but rather modify key functional systems of infected cells. We report that a distinct group of giant viruses infecting unicellular eukaryotes that includes Organic Lake Phycodnaviruses and Phaeocystis globosa virus encode predicted proteorhodopsins that have not been previously detected in viruses. Search of metagenomic sequence data shows that putative viral proteorhodopsins are extremely abundant in marine environments. Phylogenetic analysis suggests that giant viruses acquired proteorhodopsins via horizontal gene transfer from proteorhodopsin-encoding protists although the actual donor(s) could not be presently identified. The pattern of conservation of the predicted functionally important amino acid residues suggests that viral proteorhodopsin homologs function as sensory rhodopsins. We hypothesize that viral rhodopsins modulate light-dependent signaling, in particular phototaxis, in infected protists.
Structural Re-Alignment in an Immunogenic Surface Region of Ricin A Chain

We compared structure alignments generated by several protein structure comparison programs to determine whether existing methods would satisfactorily align residues at a highly conserved position within an immunogenic loop in ribosome inactivating proteins (RIPs). Using default settings, structure alignments generated by several programs (CE, DaliLite, FATCAT, LGA, MAMMOTH, MATRAS, SHEBA, SSM) failed to align the respective conserved residues, although LGA reported correct residue-residue (R-R) correspondences when the beta-carbon (Cb) position was used as the point of reference in the alignment calculations. Further tests using variable points of reference indicated that points distal from the beta carbon along a vector connecting the alpha and beta carbons yielded rigid structural alignments in which residues known to be highly conserved in RIPs were reported as corresponding residues in structural comparisons between ricin A chain, abrin-A, and other RIPs. Results suggest that approaches to structure alignment employing alternate point representations corresponding to side chain position may yield structure alignments that are more consistent with observed conservation of functional surface residues than do standard alignment programs, which apply uniform criteria for alignment (i.e. alpha carbon (Ca) as point of reference) along the entirety of the peptide chain. We present the results of tests that suggest the utility of allowing user-specified points of reference in generating alternate structural alignments, and we present a web server for automatically generating such alignments: http://as2ts.llnl.gov/AS2TS/LGA/lga_pdblist_plots.html.
Ranking Fuzzy Numbers by Using Dominance Based Approach

The most commonly used approach for ranking fuzzy numbers is ranking indices based on the centroids of fuzzy numbers. In this paper, we introduced a new ranking method which is based on multi-index such as relative dominance, priority weight and decision-maker s preference. In addition to this we determined the feasibility and validity of this method by providing nume rical examples.