cssi/SciSciGPT-SciSciNet huggingface dataset:
New Obligate Methylotroph

A new and unique obligate methylotroph was isolated from enrichment cultures with methanol as the sole source of carbon and energy. The organism grows only on methanol and methylamine and not on methane. It does not have a complex intracellular membrane system. 14C-acetate was assimilated by growing cultures and cell suspensions but was incorporated into only a limited number of cell constituents. 14C-acetate incorporation was strictly dependent on the oxidation of methanol or methylamine as a source of energy. Extracts had relatively low levels of enzymes of the tricarboxylic acid cycle, and α-ketoglutarate dehydrogenase was not detected. Comparisons were made with a facultative methylotroph isolated from the same enrichment cultures. The new obligate methylotroph contained hexose phosphate synthetase, a key enzyme in the ribose phosphate cycle of methyl metabolism.
Merlin/NF2 regulates angiogenesis in schwannomas through a Rac1/semaphorin 3F-dependent mechanism.

Neurofibromatosis type 2 (NF2) is an autosomal-dominant multiple neoplasia syndrome that results from mutations in the NF2 tumor suppressor gene. Patients with NF2 develop hallmark schwannomas that require surgery or radiation, both of which have significant adverse effects. Recent studies have indicated that the tumor microenvironment—in particular, tumor blood vessels—of schwannomas may be an important therapeutic target. Furthermore, although much has been done to understand how merlin, the NF2 gene product, functions as a tumor suppressor gene in schwannoma cells, the functional role of merlin in the tumor microenvironment and the mechanism(s) by which merlin regulates angiogenesis to support schwannoma growth is largely unexplored. Here we report that the expression of semaphorin 3F (SEMA3F) was specifically downregulated in schwannoma cells lacking merlin/NF2. When we reintroduced SEMA3F in schwannoma cells, we observed normalized tumor blood vessels, reduced tumor burden, and extended survival in nude mice bearing merlin-deficient brain tumors. Next, using chemical inhibitors and gene knockdown with RNA interference, we found that merlin regulated expression of SEMA3F through Rho GTPase family member Rac1. This study shows that, in addition to the tumor-suppressing activity of merlin, it also functions to maintain physiological angiogenesis in the nervous system by regulating antiangiogenic factors such as SEMA3F. Restoring the relative balance of proangiogenic and antiangiogenic factors, such as increases in SEMA3F, in schwannoma microenvironment may represent a novel strategy to alleviate the clinical symptoms of NF2-related schwannomas.
A formal knowledge management ontology: Conduct, activities, resources, and influences: Research Articles

This article describes a collaboratively engineered general-purpose knowledge management (KM) ontology that can be used by practitioners, researchers, and educators. The ontology is formally characterized in terms of nearly one hundred definitions and axioms that evolved from a Delphi-like process involving a diverse panel of over 30 KM practitioners and researchers. The ontology identifies and relates knowledge manipulation activities that an entity (e.g., an organization) can perform to operate on knowledge resources. It introduces a taxonomy for these resources, which indicates classes of knowledge that may be stored, embedded, andsor represented in an entity. It recognizes factors that influence the conduct of KM both within and across KM episodes. The Delphi panelists judge the ontology favorably overall: its ability to unify KM concepts, its comprehensiveness, and utility. Moreover, various implications of the ontology for the KM field are examined as indicators of its utility for practitioners, educators, and researchers. © 2005 Wiley Periodicals, Inc.
Consistency of Maximum Likelihood and Pseudo-Likelihood Estimators for Gibbs Distributions

We prove that the Maximum Likelihood and Pseudo-likelihood estimators for the parameters of Gibbs distributions (equivalently Markov Random Fields) over ℤd, d≥l, are consistent even at points of “first” or “higher-order” phase transitions. The distributions are parametrized by points in a finite-dimensional Euclidean space ℝm, m≥l, and the single spin state space is either a finite set or a compact metric space. Also, the underlying interactions need not be of finite range.
An evolutionary approach for finding optimal automatic vehicle identification reader locations in transportation networks

A modified distance-based genetic algorithm is proposed to solve the multi-objective automatic vehicle identification (AVI) reader location problem studied in this paper. The objectives are: (1) minimizing the number of AVI readers, (2) maximizing the coverage of origin-destination (O-D) pairs, and (3) maximizing the number of AVI readings. These three objectives are strategically designed to catch the maximum number of trips covering the maximum number of AVI readers. In order to study the trade-off among the three objectives, non-dominated solutions are retained and analyzed. The results show that there is a trade-off between the quality (measured by objectives 2 and 3) and cost (measured by objective 1) of coverage.
Some Objects Are More Equal Than Others: Measuring and Predicting Importance

We observe that everyday images contain dozens of objects, and that humans, in describing these images, give different priority to these objects. We argue that a goal of visual recognition is, therefore, not only to detect and classify objects but also to associate with each a level of priority which we call `importance'. We propose a definition of importance and show how this may be estimated reliably from data harvested from human observers. We conclude by showing that a first-order estimate of importance may be computed from a number of simple image region measurements and does not require access to image meaning.
All-sputtered CdTe/CdS thin film solar cells with indium doped highly resistive absorber layer

The performance of CdTe-based thin film solar cells is dependent on intrinsic crystal properties such as carrier concentration, mobility, life time and resistivity. Improving crystal quality, in particular for photovoltaic energy conversion purposes, will lead to improvements in cell efficiency. Investigating the best initial CdTe material quality for conversion efficiency and cost efficiency is important to the scientific community as a whole. As a part of our systematic investigation, CdTe crystals doped with indium were grown using the vertical Bridgman method and a sputtering target of 3″ is prepared. The resistivity of the bulk crystal was measured at ∼109 Ω.cm. Thin film solar cells were fabricated using standard superstrate configuration using Pilkington TEC 10 soda lime glasses for substrate. The structure of the layers were glass/SnO2:F/CdS/CdTe/Cu/Au. The fabricated solar cells were found to have small shunt resistance and larger series resistance. The efficiencies varied from near zero percent to 5%.
Inherent oxidation protection of Fe-5Cr-15Ni-2Si-4.5Mo

The oxidation mechanism of Fe-5Cr-15Ni-2Si-4.5Mo alloy was investigated in order to determine the role of Si and Mo in providing oxidation resistance. It was determined that the oxidation protection in the temperature range 750–950°C resulted from formation of a continuous oxide sublayer of SiO 2 (or possibly Fe 2 SiO 4).Molybdenum formed an intermetallic Fe 2 Mo 1−x Si x that eventually diffused out into the grain boundaries and formed a protective barrier to the oxidation process. The mechanism behind the improved oxidation is the formation of a SiO 2 layer at the metal-oxide interface that retards the outward diffusion of Fe. It was also established that the oxidation mechanism was controlled by an activation energy equal to that of Fe 3+ ions diffusing through SiO 2.
High-pressure phase transitions in diamond and zinc-blende semiconductors

With the advent of accurate total-energy methods for solids, it has become feasible to determine the relative structural energies of simple solids as a function of pressure. We use such a method coupled with an empirical ionicity scale to predict phase transitions as a function of pressure for all diamond and zinc-blende semiconductors of the form ${A}^{N}$${B}^{8\mathrm{\ensuremath{-}}N}$ where A and B are simple metals or metalloids and N is the number of valence electrons for species A. We find satisfactory agreement between the predicted transition from zinc-blende structure to rocksalt or \ensuremath{\beta}-Sn structures and high-pressure experiments. In addition, we find that changes in ionicity to a large extent control whether the diamond or zinc-blende structure will transform preferentially to rocksalt or to \ensuremath{\beta}-Sn; whereas, for changes in the equilibrium crystal volume, we find the magnitude of the transition pressure changes, but not the structural preference.
Approximation Theorems on Some Classes of Automata

This paper considers a machine as a pair $(G,M)$, where G is a group or a semigroup and where M is a state-space. The first part of the paper considers the case where G is a locally compact group and M is any locally compact space. The essential requirement is that $(x,p) \to x(p)$ be continuous where $x \in G$, $p \in M$ and $x(p) \in M$: i.e., we require that the next state function be continuous. The notion of projective limit is discussed and a criterion is given as to when G is the projective limit of some of its quotient groups. Next an infinitesimal element is defined. An identification is then made near the respective identities of G and the set of infinitesimal operations.The second part of the paper treats the case when G is a so-called amenable semigroup, having a representation of bounded operators on a Hilbert space. In the case in which the representation is an isometry, weakly continuous, a decomposition theorem is given. On a particular subspace the representation turns out to be a direct ...
WinAgent: a system for creating and executing personal information assistants using a web browser

WinAgent is a software system for creating and executing Personal Information Assistants (PIAs). These are software robots that can locate and extract targeted data buried deep within a web site. They do so by automatically navigating to relevant sites, locating the correct Web pages (which can be either directly accessed by traversing appropriate links or by filling out HTML forms), and extracting, structuring, and organizing data of interest from these pages into XML. The primary thrust of WinAgent technology effort was to make these tools easy-to-use by users who are not necessarily trained in computing. In particular users create and execute PIAs through a Web Browser.
Two components of Ca-dependent potassium current in identified neurons of Aplysia californica.

Outward tail currents measured inAplysia neurones after termination of depolarizing voltage-clamp pulses consist of rapidly decaying voltage-dependent K currents and slow tail currents of much slower time course. The rapidly decaying voltage-dependent tail currents were blocked with aminopyridines, and measurements of the slow tail currents were made following decay of any residual rapid tail currents. The slow tail current exhibited two components of differing sensitivity to externally applied tetraethylammonium (TEA) ions. In some neurones of the abdominal ganglion (L-2, L-4), virtually all of the slow tail current was resistant to blockage by TEA, while in others (L-3, L-6) 80% or more of the slow tail current was blocked by low TEA concentrations (KD<1 mM), the remaining slow tail current being resistant to TEA. This TEA-resistant slow tail current was identified as a K current because it reversed near the K equilibrium potential (EK), the reversal potential was shifted by changes in the external K concentration, and it could be blocked by injection of Cs+. It was abolished by replacement of external Ca2+ by Co2+ or Ba2+, by addition of Cd2+, or by injection of EGTA, and thus determined to be a Ca-dependent current. Intracellular injection of TEA or external application of aminopyridine or apamine had little or no effect on the TEA-resistant slow tail current. Quinidine reduced the TEA-sensitive, but not the TEA-resistant current. Both the TEA-sensitive and the TEA-resistant components of the slow tail current exhibited similar time courses of decay. Thus, neurones ofAplysia appear to contain different proportions of two classes of Ca-dependent K channels that differ in their sensitivity to certain channel blocking agents.
Immunogenicity of the 23-valent pneumococcal polysaccharide vaccine in Alaska native chronic alcoholics compared with nonalcoholic native and non-native controls☆

Abstract purpose: This study was designed to evaluate the immunogenicity of the 23-valent pneumococcal polysaccharide vaccine in Alaska Native chronic alcoholics and compare these responses with those in age- and sex-matched nonalcoholic, Native and non-Native control subjects. patients and methods: Native alcoholic patients were recruited from the inpatient medical service and outpatient clinics. Healthy age- and sex-matched Alaska Native and non-Native nonalcoholics were recruited from hospital employees. At the initial visit, a standardized questionnaire, the Alcohol Dependency Scale, was administered to all participants. Participants were examined for liver diseases; blood was drawn for liver function tests and prevaccination pneumococcal antibody levels. Charts of all Native participants were reviewed for alcohol-related diseases. Participants received one dose of the 23-valent pneumococcal vaccine at the time of the initial visit and returned 20 to 55 days after immunization for liver function tests and pneumococcal antibody level measurement. Serotype-specific pneumococcal antibody levels were measured by radioimmunoassay. Logistic regression analysis was used to examine the proportion of persons whose serotype-specific antibody level doubled following vaccination. A model including adjustments for age, sex, and initial antibody level was used to examine the effect of alcohol status and ethnicity on response to the vaccine. Eighty-five persons completed the study. Of these, 41 were chronic alcoholics and 44 were nonalcoholic. Of these, 21 were Alaska Natives and 23 were non-Natives. results: Before vaccination, the geometric mean titers (GMTs) were similar in all 3 groups but were slightly higher in Native alcoholic participants for 11 of 12 serotypes tested. For 11 or more serotypes tested, 46% of alcoholics and 27% of nonalcoholics had total antibody levels at or above 500 nanograms of antibody nitrogen per milliliter (p = 0.11). After vaccination, the GMTs were higher in nonalcoholic than in alcoholic participants for serotypes 3, 7F, and 19F (p conclusion: In this study of Alaska Natives with chronic alcoholism, Native and non-Native participants responded adequately to immunization with the 23-valent pneumococcal vaccine, although significant differences in some serotypes were evident.
Underwater acoustic network protocol stacks: Simulator-based vs. OS-based

As underwater acoustic network technologies become relatively mature, several protocol stack frameworks have been proposed and implemented. However, it is still an open problem to evaluate protocol stack frameworks. To evaluate their performance and help users to choose a proper solution, we propose several performance criteria, namely, timing accuracy, memory usage, power consumption, learning curve, and support of both simulation and emulation. As a case study, we evaluate and compare the performance of Sunset and Sealinx, which are Simulator-based and OS-based respectively. Through the tests, we find that Sealinx outperforms Sunset in terms of timing accuracy and memory usage efficiency. As for support of simulation, Sunset can run at simulation scale while Sealinx still runs in realtime. However, the results from Sunset's simulation mode and emulation mode could be inconsistent, due to the timing accuracy issue in its emulation mode.
Mixed finite element and atomistic formulation for complex crystals

A general formulation for the analysis of complex Bravais crystals using atomic energy functionals embedded within a finite element framework is presented. The method uses atomistic potentials to determine the constitutive response of the system. Unlike traditional finite element methods, the nonlinear elastic effects, the symmetries of the underlying crystal, and the possibility of uniform structural phase transformations are naturally included in this formulation. Explicit expressions for empirical energy functionals with separable two- and three-body potentials, and semiempirical tight-binding energy functionals with two-center integrals are presented. A simple application to silicon underscores the importance of including internal relaxation in a finite element treatment of a complex crystal. In a forthcoming companion paper, the method presented here is applied to the nanoindentation of silicon.
Factors that Influence PKR Dimerization and Activation

Protein kinase R (PKR) is a key component of the interferon-induced innate immunity pathway. It is expressed in a latent, inactive form and is activated upon binding dsRNA and subsequent autophosphorylation. PKR contains a C-terminal kinase domain and two tandem dsRNA binding motifs (dsRBMs) at the N-terminus. These regions are separated by a 90-residue, unstructured linker. Dimerization is believed to play a critical role in the mechanism of PKR activation by dsRNA. Activation requires dsRNAs long enough to accommodate two PKR monomers. However, there is no direct evidence for dimerization of PKR on dsRNA lattices. Under certain conditions, shorter RNAs bind multiple PKRs but fail to activate, suggesting that additional factors are involved. It is believed that binding of the second dsRBM is required for PKR activation. We have characterized the role of the second dsRBM by introducing mutations that block its interaction with dsRNA. The distance dependence of PKR dimerization and activation were probed using synthetic RNAs that function as molecular rulers. These molecules consist of two 15 bp duplex regions separated by variable length regions of 2′-O-methyl modified dsRNA that act as rigid and inert barriers. The effect of linker length was investigated using a PKR homolog containing a short, 25-residue linker. We developed a fluorescence assay to quantitatively probe PKR dimerization upon binding to RNA. The fluorescence anisotropy of a probe placed near the kinase dimer interface decreases upon PKR binding to an activating 40 bp dsRNA due to depolarization induced by homo-FRET. Thus, the kinase domains form a dimer when two PKR monomers bind to this dsRNA. Surprisingly, several non-activating dsRNAs also induce dimerization, suggesting that PKR dimerization is necessary but not sufficient for activation.
Demand evolution in stochastic inventory systems: Riskiness increase

Abstract This paper characterizes demand evolution in the steady state under common inventory policies in a single-location stochastic inventory system. Our results show that downstream demand nonstrictly second-degree stochastically dominates upstream orders and the bullwhip effect occurs. We provide the link between demand evolution and utility theory for stochastic inventory systems. Our model is general in that ultimate customer demand follows an arbitrary stationary distribution and the facility may arbitrarily select policy parameters.
Computational Study of Proton Binding at the Rutile/Electrolyte Solution Interface

Quantum chemistry methods are used to study the properties (charges, proton affinity constants) of isolated surface sites originating from (100), (110), and (001) rutile surfaces. Energetic profiles of water adsorption on rutile suggest that the dissociative adsorption is energetically favorable, so surface hydrolysis is a probable mechanism of rutile surface charging. Moreover, on the basis of energetic profiles of proton binding we conclude that this process is exothermic with the highest heat effect at (110) surface. The ab initio results are compared with the multisite complexation model predictions, and next they are used as input data for the grand canonical Monte Carlo simulations of proton binding, which are carried out to predict the adsorption isotherms for isolated unreconstructed and reconstructed surfaces. The solvent effects are modeled using the conductor-like screening model for real solvents model in the ab initio calculations and the Borkovec potential in the Monte Carlo simulations.
Hybrid partial evaluation

Hybrid partial evaluation (HPE) is a pragmatic approach to partial evaluation that borrows ideas from both online and offline partial evaluation. HPE performs offline-style specialization using an online approach without static binding time analysis. The goal of HPE is to provide a practical and predictable level of optimization for programmers, with an implementation strategy that fits well within existing compilers or interpreters. HPE requires the programmer to specify where partial evaluation should be applied. It provides no termination guarantee and reports errors in situations that violate simple binding time rules, or have incorrect use of side effects in compile-time code. We formalize HPE for a small imperative object-oriented language and describe Civet, a straightforward implementation of HPE as a relatively simple extension of a Java compiler. Code optimized by Civet performs as well as the output of a state-of-the-art offline partial evaluator.
Captopril reduces the proteinuric effect of human growth hormone in adriamycin nephrosis.

Developing male Sprague-Dawley rats (125 g) with adriamycin (doxorubicin hydrochloride) nephrosis (AN) were treated with growth hormone (GH) which may induce hyperfiltration potentiating glomerulosclerosis. Since captopril (CAP) reduces hyperfiltration, we studied its effects in GH-treated rats with AN. After 41, 76, and 90 days of therapy, urine protein excretion was significantly (P<0.05) reduced in GH-treated AN plus CAP compared with AN rats receiving GH alone. After 90 days, urine protein, creatinine ratio was significantly (P<0.05) increased in GH-treated AN (95.2±13.9) compared with untreated AN (64.8±7.8) and GH-treated AN rats plus CAP (41.8±8.8). The mean serum cholesterol level was significantly (P<0.05) reduced in GH-treated AN rats receiving CAP compared with AN rats receiving GH alone and untreated AN controls. Histologically tubular dilation was significantly (P<0.05) reduced in GH-treated AN rats plus CAP compared with AN rats receiving GH alone. Tubular atrophy and scarring were significantly (P<0.05) increased in AN rats treated with GH compared with untreated AN rats, and normalized in GH-treated AN rats plus CAP. We conclude that CAP reduces the proteinuric response of GH in rats with AN and ameliorates tubular injury.
Recall of sex-role appropriate and inappropriate models in children's songs

The function of sex of model and sex-role appropriateness of models' behavior in facilitating children's recall of song characters and content was explored. Fifty-eight boys and girls, aged 6 1/2, listened to two songs in one of three treatment conditions. The songs had male-dominant/female-subordinant, female-dominant/male-subordinant, or neutral-dominant/neutral-subordinant lyrics. As expected, children attended selectively to same-sex characters, recalling more when the same-sex character was dominant. Boys reported liking males more than females, while girls had no sexual preference. Surprisingly, both boys and girls more frequently reported that they wanted to be like the subordinant characters than like the dominant characters.
Quasi-superconformal algebras in two dimensions and hamiltonian reduction

Abstract In the standard quantum hamiltonian reduction, constraining the SL(3.ℝ) WZNW model leads to a model of Zamolodchikov's W 3 -symmetry. In recent work, Polyakov and Bershadsky have considered an alternative reduction which leads to a new algebra. W 3− 2 a nonlinear extension of the Virasoro algebra by a spin-1 current and two bosonic spin-2/3 currents. Motivated by this result, we display two new infinite series of nonlinear extended conformal algebras, containing 2 N bosonic spin-3/2 and spin-1 Kac-Moody currents for either U( N )or Sp(2 N ); the W 3 2 algebra appears as the N = 1 member of the U( N ) series. We discuss the relationship between these algebras and the Knizhnik-Bershadsky superconformal algebras, and provide realisations in terms of free fields coupled to Kac-Moody currents. We propose a specific procedure for obtaining the algebras for general N through hamiltonian reduction.
The backflow cell model of isothermal first order flow reactors with axial dispersion

Equations which predict the course of the reversible first order reaction A ⇄ R in backflow cell models of isothermal flow reactors are developed and compared to those of the continuous dispersion model. The conditions of convergence of the concentration A profile of the backflow cell model to that of the continuous dispersion model were investigated for isothermal first order irreversible (A ⇄ R) reactors of finite size. For this case figures are displayed which allow the models to be compared and the effects of axial mixing to be included in reactor design. The effect of backmixing upon the optimum temperature and maximum product yields of R is considered for the reversible reaction in the finite reactor.
Binding of myosin subfragment-1 to F-actin.

Abstract During a part of the hydrolytic cycle, myosin head (S1) carries no nucleotide and binds strongly to an actin filament forming a rigor bond. At saturating concentration of S1 in rigor, S1 is well known to form 1:1 complex with actin. However, we have provided evidence that under certain conditions S1 could also form a complex with 2 actin monomers in a filament (Andreev, O.A. & Borejdo, J. (1991) Biochem. Biophys. Res. Comm. 177 , 350–356). This view was recently challenged by Carlier & Didry (Carlier, M-F. & Didry, D. (1992) Biochem. Biophys. Res. Comm. 183 , 970–974) who interpreted our data by suggesting that F-actin underwent a simple depolymerization and implied that, when only actin in the F-form was scored, the real stoichiometry in our experiments was 1:1. We show here that under conditions of our experiments less than 8% of actin was depolymerized. Moreover, we have repeated the experiments in the presence of phalloidin and show that under these conditions too, when S1 was added slowly to a fixed concentration of F-actin, it formed a different complex with F-actin than when it was added quickly. This confirms our original conclusion that S1 can bind actin in two different ways and shows that depolymerization of F-actin is not responsible for this finding.
Antibodies in the breakdown lane.

An engineered IgG induces degradation of endogenous IgG, providing a potential therapeutic approach to autoimmune disease.
Deblurring images blurred by the discrete Gaussian

Abstract Gaussian blur is frequently used to model the degradation of images or signals. We will show how to clean the blurred image. We shall obtain exact formulas. To achieve this goal, we will make use of some formulas from the theory of basic hypergeometric series. We will also show how to deblur images blurred by a modified Gaussian blur.
Glial contribution to seizure: K+ activation of (Na+, K+)-ATPase in bulk isolated glial cells and synaptosomes of epileptogenic cortex

Abstract Glial and neuronal (Na+, K+)-ATPase have dissimilar apparent affinities for K+ ions. Glial (Na+, K+)-ATPase is maximally activated by 20 mM K+ while neuronal (Na+, K+)-ATPase is maximally stimulated by 3–5 mM K+. Because this glial property may play an important role in the clearance of [K+]0 during seizures, we investigated the K+ activation of (Na+, K+)-ATPase within bulk isolated glial cells and synaptosomes isolated from epileptogenic brains. The primary focus (F), the homolateral brain area around the focus (PF) and the mirror (M) or secondary focus induced by freezing lesions were studied. Results show that both glial and synaptosomal enzyme activities in the epileptogenic state change in comparison with controls, i.e. sham-operated cats. In F and M., glial enzyme decreased reaction velocities between 3 and 18 mM K+. In PF, maximum velocities increased in glial (Na+, K+)-ATPase. These results indicate that in actively firing epileptogenic tissue (F, M), glial (Na+, K+)-ATPase decreased rate reactions while the catalytic activity was increased in cortical tissues surrounding the focus. These phenomena appeared early, i.e. 1–3 days after production of the freezing lesion, and was associated with a sharp decrease in absolute levels of enzyme activity. Synaptosomal (Na+, K+)-ATPase from controls always exhibited a saturation curve at 3–6 mM K+. Synaptosomal enzyme activities in the primary (F) lesion increased slightly 24 h after lesion production, then progressively decreased 3 days after lesion production. No significant changes were seen in M and PF.
Exercise-Induced Asthma:

Exercise-induced asthma is a common complex pulmonary disorder associated with a diagnosis of chronic asthma including cough, dyspnea, wheezing, and chest tightness that affects millions of patients worldwide. Exercise-induced asthma patients are frequently inhibited from participating in physical activities because of the degree of pulmonary dysfunction. Pharmacological agents, the cornerstone of treatment for exercise-induced asthma, improve pulmonary function and quality of life. Short-term and long-term adrenergic β2sympathomimetics, mast cell stabilizers, leukotriene receptor antagonists, 5-lipoxygenase inhibitors, and corticosteroids are commonly used. β2sympathomimetics are the most potent bronchodilators and are considered the first drug of choice. Inhaled corticosteroids and mast cell stabilizers assist with the reduction of airway inflammation and response to exercise and are generally added in combination with β2sympathomimetics for maximum efficacy. Leukotriene receptor antagonists and inhibit...
Semen pH in patients with normal versus abnormal sperm characteristics.

Abstract Objective: The World Health Organization laboratory manual, last revised in 1992, states that the normal pH of semen ranges from 7.2 to 8.0. Our experience has been that values in our patient population are consistently higher than this range. To confirm this we reviewed >1100 semen records. Study Design: All patient records from January 1994 to December 1998 that had semen pH measurements and sperm concentration and motility measurements recorded were included in this study. We also determined the semen pH in a subgroup of patients who underwent sperm preparations for intrauterine inseminations that resulted in documented pregnancies. Histograms were used to describe the populations and the Mann-Whitney test was used for group comparisons. Results: For all patients (N = 1199) mean (±SD) semen pH was 8.2 ± 0.3. The range was 7.3 to 9.5, with pH
The potential in a cylindrical electrode partially submerged in a perfectly conducting medium

Abstract A method, well suited for use with digital computers, is given for determining the potential in a cylindrical electrode partially submerged in a conducting medium. Numerical illustrations and a brief proof of the convergence of the approximants are provided.
Diffusion of small solutes in cartilage as measured by nuclear magnetic resonance (NMR) spectroscopy and imaging

The ability of water and solutes to move through the cartilage matrix is important to the normal function of cartilage and is presumed to be altered in degenerative diseases of cartilage such as osteoarthritis and rheumatoid arthritis. Nuclear magnetic resonance (NMR) spectroscopy and magnetic resonance imaging (MRI) techniques were used to measure a self diffusion coefficient (D) for small solutes in samples of explanted cartilage for diffusion times ranging from 13 ms to 2s. With a diffusion time of 13 ms, the intratissue diffusivity of several small solutes (water, Na+, Li+, and CF3CO2−) was found consistently to be about 60% of the diffusivity of the same species in free solution. Equilibration of the samples at low pH (which titrates the charge groups so that the net matrix charge of −300 mM at pH 8 becomes approximately −50 mM at pH 2) did not affect the diffusivity of water or Na+. These data, and the similarity between the D in cartilage relative to free solution for water, anions, and cations, are consistent with the view that charge is not an important determinant of the intratissue diffusivity of small solutes in cartilage. With 35% compression, the diffusivity of water and Li+ dropped by 19 and 39%, respectively. In contrast, the diffusivity of water increased by 20% after treatment with trypsin (to remove the proteoglycans and noncollagenous proteins). These data and the lack of an effect of charge on diffusivity are consistent with D being dependent on the composition and density of the solid tissue matrix. A series of diffusion-weighted proton images demonstrated that D could be measured on a localized basis and that changes in D associated with an enzymatically depleted matrix could be clearly observed. Finally, evidence of restriction to diffusion within the tissue was found with studies in which D was measured as a function of diffusion time. The measured D for water in cartilage decreased with diffusion times ranging from 25 ms to 2 s, at which point the measured D was roughly 40% of the diffusivity in free solution. Although changes in matrix density by compression or digestion with trypsin led to a decrease or increase, respectively, in the measured D, the functional change in measured diffusivity with diffusion time remained essentially unchanged. In a different type of study, in which bulk transport could be observed over long periods of time, cartilage was submerged in 99% D2O and MRI studies were performed to demonstrate the bulk movement of water out of the cartilage matrix. These studies yielded a diffusivity estimated to be approximately 40% of the diffusivity of water in solution, which is in agreement with the value obtained for the diffusivity at a diffusion time of 2 s. These NMR measurements of diffusion can be totally noninvasive; thus, the results reported here can be extended to in vivo situations.
Mass Spectrometrically Detected Statistical Aspects of Ligand Populations in Mixed Monolayer Au25L18 Nanoparticles

Ligand exchange reactions of Au25(SCH2CH2Ph)18 with hexanethiol (HSC6) and thiophenol (HSPh) as incoming ligands, and Brust reaction nanoparticle syntheses using mixtures of thiols (HSCH2CH2Ph and HSC6), produce nanoparticles having different, ideally statistically determined, relative populations of the two thiolate ligands (X and Y), i.e., Au25(X)m(Y)m′, where m and m′ vary but always sum to 18. By choice of reactant concentrations, the exchange reaction can reach an equilibrium state or a near-complete exchange of ligands or be at a kinetically determined (nonequilibrium) mixed population, at the time of reaction quenching and subsequent matrix-assisted laser desorption ionization−time-of-flight (MALDI-TOF) mass spectrometric examination. With the assumption that the reactivities of the 18 ligand sites are identical and independent, the equilibrium distributions of ligand populations of the mixed monolayer exchange products should adhere to a binominal distribution. A simulated kinetic model for ligand...
The Mechanism by which DNA Adenine Methylase and PapI Activate the Pap Epigenetic Switch

The expression of pyelonephritis-associated pili (Pap) in uropathogenic Escherichia coli is epigenetically controlled by a reversible OFF to ON switch. In phase OFF cells, the global regulator Lrp is bound to pap sites proximal to the pilin promoter, whereas in phase ON cells, Lrp is bound to promoter distal sites. We have found that the local regulator PapI increases the affinity of Lrp for the sequence "ACGATC," which contains the target "GATC" site for DNA adenine methylase (Dam) and is present in both promoter proximal and distal sites. Mutational analyses show that methylation of the promoter proximal GATC(prox) site by Dam is required for transition to the phase ON state by specifically blocking PapI-dependent binding of Lrp to promoter proximal sites. Furthermore, our data support the hypothesis that PapI-dependent binding of Lrp to a hemimethylated GATC(dist) site generated by DNA replication is a critical component of the switch mechanism.
Microscale Plasma-Initiated Patterning (μPIP)

A novel technique to create biomolecular micropatterns of varying complexity on several types of polymer substrates is presented. This method uses a patterned PDMS stamp to preferentially expose or protect areas of an underlying polymer substrate from oxygen plasma. Following plasma treatment, the substrate is immersed in a biomolecular ink, whereby molecules preferentially adsorb to either the plasma-exposed or plasma-protected substrate regions, depending on the particular substrate/ink combination. Using this method, polyethylene (PE), polystyrene (PS), poly(methyl methacrylate) (PMMA), poly(dimethylsiloxane) (PDMS), and poly(hydroxybutyrate/hydroxyvalerate) (PHBV) were micropatterned with different aqueous-based biomolecular inks (i.e., goat anti-rabbit immunoglobulin G, poly-l-lysine, and bovine serum albumin (BSA)). Water contact angle measurements performed on substrates after oxygen plasma exposure showed that the hydrophilicity of substrate areas exposed to plasma was significantly greater than t...
Two Classes of Calmodulin Binding to IQ Motifs of Voltage-Gated Sodium Channels

Voltage-dependent sodium channels (VDSCs) control the rising phase of action potentials in excitable cells. Channelopathies associated with these transmembrane proteins include Dravet syndrome, epilepsy, Long QT syndrome type 3, ventricular fibrillation, autism, and pain insensitivity. This family of ion channels is regulated by calmodulin (CaM), a small essential eukaryotic calcium sensor that contains two domains (N and C) with different affinity for calcium. CaM recognizes at least two regions of the Nav channels: the inactivation gate between transmembrane domains III and IV, and an IQ motif located in the intracellular C-terminal tail of the alpha subunit of Nav. In a genetic screen of Paramecium, the Kung laboratory discovered the first biological role for differences in the N and C domains of CaM. They identified N-domain mutations that specifically altered calcium-dependent regulation of sodium channels. However, the molecular mechanism is not understood. Our laboratory has quantitatively characterized the interactions of both domains of mammalian and Paramecium CaM with the IQ motif of NaV1.2. Under apo conditions, both mCaM and PCaM bind to the IQ motif of NaV1.2 exclusively via the CaM C-domain; Ca2+ binding to CaM lowers its affinity for the IQ motif. To understand calcium–mediated feedback control, we conducted thermodynamic analyses of CaM binding to IQ motif sequences from 9 members of the human Nav family. CaM association was detected as fractional disruption of FRET in a biosensor containing the NaV IQ motif sandwiched between YFP and CFP. We see two classes of IQ motifs in human sodium channels that differ in their relative binding affinity for apo and calcium-saturated CaM, and the roles of the two CaM domains. Support: NIH R01 GM57001 & Carver Charitable Trust Grant 01-224
Vertebrate Development: Taming the Nodal Waves

Recent results have provided evidence that regulatory loops operating in vertebrate embryos between the developmental signalling factors Nodal and Lefty may provide a real example of the kind of reaction-diffusion process long predicted to be a mechanism of pattern formation.
Dynamic mechanical analysis of the effect of water on glass bead-epoxy composites

Dynamic mechanical analysis (DMA) has been used to investigate the effect of water and glass bead surface treatment on the properties of glass bead–epoxy composites. By treating or not treating the glass beads with a silane coupling agent, we fabricated composites with ostensibly good or poor interfacial adhesion. SEM images of fracture surfaces and water uptake data confirmed this picture. We used dynamic mechanical tests to measure the material properties of dry and wet specimens. Temperature sweep tests of atmosphere-conditioned specimens indicated that the value of the loss tangent at the temperature of the α-α-relaxation peak was most sensitive to interfacial adhesion. For wet specimens, the magnitude of an additional relaxation process, denoted as the ω-relaxation, correlated strongly with water uptake and, indirectly, interfacial adhesion. Master curves constructed from frequency sweep tests also manifested differences among dry and wet specimens, but shift factor data suggested that these tests were more prone to complications due to water loss. Apparent activation energies of α- and β-relaxation processes were statistically significant indicators of interfacial adhesion in dry and wet composites, respectively. © 1996 John Wiley & Sons, Inc.
High-Speed Nonlinear Harmonic Generation Holographic Microscopy

We present three-dimensional images of biological samples using nonlinear optical, holographic microscopy. The oscillator operates at a wavelength with low scattering in the sample and its low average power prevents damage to the samples.
Regulation of potassium (K) handling in the renal collecting duct

This review provides an overview of the molecular mechanisms of K transport in the mammalian connecting tubule (CNT) and cortical collecting duct (CCD), both nephron segments responsible for the regulation of renal K secretion. Aldosterone and dietary K intake are two of the most important factors regulating K secretion in the CNT and CCD. Recently, angiotensin II (AngII) has also been shown to play a role in the regulation of K secretion. In addition, genetic and molecular biological approaches have further identified new mechanisms by which aldosterone and dietary K intake regulate K transport. Thus, the interaction between serum-glucocorticoid-induced kinase 1 (SGK1) and with-no-lysine kinase 4 (WNK4) plays a significant role in mediating the effect of aldosterone on ROMK (Kir1.1), an important apical K channel modulating K secretion. Recent evidence suggests that WNK1, mitogen-activated protein kinases such as P38, ERK, and Src family protein tyrosine kinase are involved in mediating the effect of low K intake on apical K secretory channels.
Sensitivity of cycling measures derived from ecological flow analysis

Abstract Ecologists have developed and applied flow analyses to examine indirect interactions in ecosystem models. These methods generate measures of indirect influence such as recycling efficiencies, cycled throughflows, and cycling indices. Results of such analyses provide insight into the nature of interactions in ecosystems. This paper describes a sensitivity technique for examining flow structures of ecosystem models. The sensitivity technique relies on a method for determining the ‘condition’ of inverted matrices. Resulting sensitivity values describe effects of perturbations and errors on indirect flows, recycling efficiencies, cycling indices, cycled throughflows and other flow measures. I have applied the methods to three models of Ca flow for the Hubbard Brook forest.
Indexing and mining streams

How can we find patterns in a sequence of sensor measurements (eg., a sequence of temperatures, or water-pollutant measurements)? How can we compress it? What are the major tools for forecasting and outlier detection? The objective of this tutorial is to provide a concise and intuitive overview of the most important tools, that can help us find patterns in sensor sequences. Sensor data analysis becomes of increasingly high importance, thanks to the decreasing cost of hardware and the increasing on-sensor processing abilities. We review the state of the art in three related fields: (a) fast similarity search for time sequences, (b) linear forecasting with the traditional AR (autoregressive) and ARIMA methodologies and (c) non-linear forecasting, for chaotic/self-similar time sequences, using lag-plots and fractals. The emphasis of the tutorial is to give the intuition behind these powerful tools, which is usually lost in the technical literature, as well as to give case studies that illustrate their practical use.
Alcohol-nutrient interactions in cancer etiology

The cancers for which there is the most compelling epidemiologic evidence of associations with both diet and alcohol are oral, pharyngeal, laryngeal, esophageal, and liver cancer. For lung, breast, stomach, and colorectal cancer, there is reasonably strong epidemiologic evidence of associations with diet, but only moderate or equivocal evidence of associations with alcohol. For pancreatic cancer there is suggestive evidence of associations with both exposures. It is probable that the quantitative relationship and the underlying biological mechanisms of the diet-alcohol interaction will not be the same for all cancers. Heavy alcohol consumption and generally poor nutrition, possibly a deficiency of several micronutrients and food groups, were the major risk factors for esophageal cancer in a case-control study of the unusually high rates for this cancer among Washington, DC black men. It is proposed that alcohol might increase risk of esophageal cancer, in part, by reducing nutrient intake. Two descriptive studies are presented that suggest that as the percent of caloric intake from alcohol increases, the daily consumption of protein, carbohydrate, fiber, and many micronutrients steadily and significantly decreases. Alcohol consumption and low fruit and vegetable intake, as well as snuff dipping and cigarette smoking, were shown to be risk factors for oral-pharyngeal cancer in a case-control study of the high rates of these cancers among North Carolina women. Since these women were not heavy drinkers, it is not likely that alcohol functioned by altering nutritional status. A number of mechanisms for the action of alcohol in cancer etiology are presented.
Ethics of treating postoperative pain

You received a call advising that Mr S. H. Irk was in the emergency room having considerable wound pain following an above-knee amputation you performed 6 months ago. You discharged him from your clinic 6 weeks postoperatively to his primary care physician, still complaining of more pain than usual. Your examination, clinical lab tests, and X-rays do not reveal any serious problems, but he is writhing in pain and begging for relief. Mr Irk has been to a number of different physicians in the interlude including a chiropractor, a pain specialist, several primary care physicians, and a psychiatrist without relief. He has braced up with increasing amounts of analgesics, the latest of which was oral Dilaudid. His last source of pain meds on the street has dried up. You admit him with orders for analgesics. What should your treatment plan be?
Econometrics: Retrospect and prospect

I find the set of introductory essays remarkable insofar as, taken together, they illustrate beautifully what I consider to be three central themes in econometrics, perhaps the central themes, as we move into the new millennium. The first is the sweeping effect of improvements in information technology, broadly defined to include not only processing speed, but also data collection and storage capability, on both econometric theory and practice. The second is the distinct recognition that empirical finance and time-series econometrics are natural partners, and that the benefits from cross-fertilization are immense, resulting in a booming new area, financial econometrics. (As I write, the Journal of Financial Econometrics is being launched.) The third is the continued importance and rapid development of ideas and methods related to forecasting, whether in macroeconometrics, microeconometrics, or financial econometrics.