cssi/SciSciGPT-SciSciNet huggingface dataset:
A hybrid method for protein–protein interface prediction

The growing structural coverage of proteomes is making structural comparison a powerful tool for function annotation. Such template-based approaches are based on the observation that structural similarity is often sufficient to infer similar function. However, it seems clear that, in addition to structural similarity, the specific characteristics of a given protein should also be taken into account in predicting function. Here we describe PredUs 2.0, a method to predict regions on a protein surface likely to bind other proteins, that is, interfacial residues. PredUs 2.0 is based on the PredUs method that is entirely template-based and uses known binding sites in structurally similar proteins to predict interfacial residues. PredUs 2.0 uses a Bayesian approach to combine the template-based scoring of PredUs with a score that reflects the propensities of individual amino acids to be in interfaces. PredUs 2.0 includes a novel protein size dependent metric to determine the number of residues that should be reported as interfacial. PredUs 2.0 significantly outperforms PredUs as well as other published interface prediction methods.
Nucleic acid binding properties of Escherichia coli ribosomal protein S1. I. Structure and interactions of binding site I.

Abstract Escherichia coli ribosomal protein S1 plays a central role in initiation of protein synthesis, perhaps via participation in the binding of messenger RNA to the ribosome. S1 protein has two nucleic acid binding sites with very different properties: site I binds either single-stranded DNA or RNA, while site II binds single-stranded RNA only (Draper et al., 1977). The nucleic acid binding properties of these sites have been explored using the quenching of intrinsic protein fluorescence which results from binding of oligo- and polynucleotides, and are reported in this and the accompanying paper (Draper & von Hippel, 1978). Site I has been studied primarily using DNA oligomers and polymers, and has been found to have the following properties. (1) The intrinsic binding constant (K) of site I for poly(dA) and poly(dC) is ~3 × 106 m −1 at 0.12 m -Na+, and the site size (n, the number of nucleotide residues covered per S1 bound) is 5.1 ± 1.0 residues. (2) Binding of site I to polynucleotides is non-co-operative. (3) The K value for binding of S1 to single-stranded polynucleotides is ~103 larger than K for binding to double-stranded polynucleotides, meaning that S1 (via site I) is a potential “melting” or “double-helix destabilizing” protein. (4) The dependence of log K on log [Na+] is linear, and analysis of the data according to Record et al. (1976) shows that two basic residues in site I form charge-charge interactions with two DNA phosphates. In addition, a major part of the binding free energy of site I with the nucleic acid chain appears to involve non-electrostatic interactions. (5) Oligonucleotides bound in site II somewhat weaken the binding affinity of site I. (6) Binding affin is virtually independent of base and sugar composition of the nucleic acid ligand; in fact, the total absence of the base appears to have little effect on the binding, since the association constant for 2′-deoxyribose 5′-phosphate is approximately the same as that for dAMP or dCMP. (7) Two molecules of d(ApA) can bind to site I, suggesting the presence of two “subsites” within site I. (8) Iodide quenching experiments with S1-oligonucleotide complexes show differential exposure of tryptophans in and near the subsites of site I, depending upon whether neither, one, or both subsites are complexed with an oligonucleotide.
Cell Surface Components of Intestinal Epithelial Cells and their Relationship to Cellular Differentiation

The surfaces of the epithelial cells of the rat small intestine were studied by fluorescence microscopy using various fluorescein isothiocyanate-conjugated lectins. Throughout most of the adult intestine changes were detected in the luminal surfaces as the cells differentiate and move from the crypts to the villi. These changes in cell surface material depend upon the region of intestine in which the villi are located. By the end of the second week of postnatal development the cell surface components detected by the lectins used in this study have appeared at all levels of the small intestine. The maturational and regional differences begin to appear during the third week of postnatal development, and the adult pattern of distribution of surface components is established by 30 days after birth. By eight weeks after proximal jejunal-ileal resectioning or transposition of ileal segments to the jejunum, the epithelial cell surfaces of the relocated ileum had acquired the surface properties characteristic of the jejunal cells. However, jejunal segments transposed to the ileum maintained their original cell surface characteristics and influenced the properties of ileal cell surfaces distally adjacent to the transposed segment. The cell surface material detected by the Ricinus communis (RCAI) lectin was extracted from crypt cells of adult rat jejunum and isolated by affinity chromatography. The isolated material was found to contain at least two components, and its distribution in the jejunum was examined by fluorescence microscopy using antibodies prepared against the isolated material.
El Estado en América Latina

£En que medida es competente el Estado en America Latina? Este articulo analiza el sistema fiscal, Ia Administracion publica y datos electorales, asi como los indicadores de cambio en âmbitos como Ia seguridad publica, el derecho, Ias regulaciones economicas y los servidos sociales, a fin de poder comparar la region con otras partes del mundo y definir Ias disparidades intrarregionales. El Estado latinoamericano, en general, no es muy fuerte ni efectivo, pero los estados chileno y brasileno pueden ser el mejor ejemplo para la region.
Emission estimates of HCFCs and HFCs in California from the 2010 CalNex study

[1] The CalNex 2010 (California Research at the Nexus of Air Quality and Climate Change) study was designed to evaluate the chemical composition of air masses over key source regions in California. During May to June 2010, air samples were collected on board a National Oceanic and Atmospheric Administration (NOAA) WP-3D aircraft over the South Coast Air Basin of California (SoCAB) and the Central Valley (CV). This paper analyzes six effective greenhouse gases—chlorodifluoromethane (HCFC-22), 1,1-dichloro-1-fluoroethane (HCFC-141b), 1-chloro-1,1-difluoroethane (HCFC-142b), 2-chloro-1,1,1,2-tetrafluoroethane (HCFC-124), 1,1,1,2-tetrafluoroethane (HFC-134a), and 1,1-difluoroethane (HFC-152a)—providing the most comprehensive characterization of chlorofluorocarbon (CFC) replacement compound emissions in California. Concentrations of measured HCFCs and HFCs are enhanced greatly throughout the SoCAB and CV, with highest levels observed in the SoCAB: 310 ± 92 pptv for HCFC-22, 30.7 ± 18.6 pptv for HCFC-141b, 22.9 ± 2.0 pptv for HCFC-142b, 4.86 ± 2.56 pptv for HCFC-124, 109 ± 46.4 pptv for HFC-134a, and 91.2 ± 63.9 pptv for HFC-152a. Annual emission rates are estimated for all six compounds in the SoCAB using the measured halocarbon to carbon monoxide (CO) mixing ratios and CO emissions inventories. Emission rates of 3.05 ± 0.70 Gg for HCFC-22, 0.27 ± 0.07 Gg for HCFC-141b, 0.06 ± 0.01 Gg for HCFC-142b, 0.11 ± 0.03 Gg for HCFC-124, 1.89 ± 0.43 Gg for HFC-134a, and 1.94 ± 0.45 Gg for HFC-152b for the year 2010 are calculated for the SoCAB. These emissions are extrapolated from the SoCAB region to the state of California using population data. Results from this study provide a baseline emission rate that will help future studies determine if HCFC and HFC mitigation strategies are successful.
Cumulative Incidence Association Models for Bivariate Competing Risks Data

Association models, like frailty and copula models, are frequently used to analyze clustered survival data and evaluate within-cluster associations. The assumption of noninformative censoring is commonly applied to these models, though it may not be true in many situations. In this paper, we consider bivariate competing risk data and focus on association models specified for the bivariate cumulative incidence function (CIF), a nonparametrically identifiable quantity. Copula models are proposed which relate the bivariate CIF to its corresponding univariate CIFs, similarly to independently right censored data, and accommodate frailty models for the bivariate CIF. Two estimating equations are developed to estimate the association parameter, permitting the univariate CIFs to be estimated either parametrically or nonparametrically. Goodness-of-fit tests are presented for formally evaluating the parametric models. Both estimators perform well with moderate sample sizes in simulation studies. The practical use of the methodology is illustrated in an analysis of dementia associations.
Use of multiple markers for investigation of an epidemic of Shigella sonnei infections in Monroe County, New York.

Antibiotic susceptibility patterns, plasmid profiles, and endonuclease restriction analysis of plasmid DNA were used in the investigation of an epidemic of Shigella sonnei infections in Monroe County, New York, in 1988 and 1989. The epidemic peaked during the winter, included the simultaneous transmission of the disease from person to person and from common food sources, and especially affected inhabitants of the poor, inner-city neighborhoods, young children of both sexes, and women. Resistance to ampicillin, tetracycline, or trimethoprim-sulfamethoxazole, encoded in a 70-MDa plasmid, was found in most of the examined isolates. Unexpectedly, isolates from patients involved in a food-borne outbreak exhibited three different antibiotic susceptibility patterns, suggesting deletion of antibiotic resistance determinants in some strains. Antibiograms clearly separated food-borne outbreak-related and non-foodborne outbreak-related strains, distinguished more strains than did the plasmid profiles, and were useful in tracing the dissemination of individual isolates in the community. Restriction endonuclease analysis substantially increased the discriminatory value of plasmid profiles and validated the antibiogram results. The present study illustrates the complexity of epidemics of S. sonnei infections and shows the value of combining different biological markers in the investigation. Images
Soluble and insoluble nickel compounds induce DNA repair synthesis in cultured mammalian cells

Abstract The induction of DNA repair was investigated in cultured Syrian hamster embryo (SHE) cells and Chinese hamster ovary (CHO) cells by cesium chloride equilibrium gradient sedimentation techniques following exposure to NiCl 2 , amorphous NiS, crystalline NiS and crystalline Ni 3 S 2 . Significant repair was induced in CHO cells by 1 μg/ml of crystalline NiS following 24 h of treatment while 5 μg/ml caused more than twice the repair activity. In contrast amorphous NiS at 10 μg/ml for 24 h induced little repair in these cells. Similarly amorphous NiS did not induce repair at 5–10 μg/ml for 24 h in SHO cells while crystalline Ni 3 S 2 , and NiCl 2 caused substantial induction of DNA repair synthesis at 10 μg/ml or 100 μM, respectively. These results demonstrate that nickel compounds which are potent transforming agents and induce damage to DNA also result in the induction of DNA repair. Repair synthesis was detected at concentrations of metal compounds which result in no detectable damage to DNA.
Flavor Fade in Peanuts During Short-term Storage

: Flavor characteristics of roasted peanuts over short-term storage were explored through sensory and chemical analyses. The volatiles from freshly roasted peanuts were evaluated over short-time (21 d) storage using gas chromatography, chemosensory techniques, and a sensory panel to quantify and identify pyrazines and hexanal over a 21-d storage period. A significant decrease (P 0.05) was noted in the 2-methylpyrazine and 2-ethylpyrazine concentrations. The hexanal concentration significantly increased (P < 0.05) over the 21-d period. The peroxide values and sensory analysis agreed with these results. A significant increase (P < 0.05) in peroxide value was seen at days 14 and 21, and a significant decrease (P < 0.05) in fresh roasted peanuty flavor from day 0 to 21 and significant increases (P < 0.05) in painty, cardboardy, and bitter flavors from day 7 to 21 with the sensory analysis. The electronic nose successfully separated day 0 and 21 samples from day 7 and 14 samples, which were also separated but with some overlap.
Role of tissue transglutaminase type 2 in calbindin-D28k interaction with ataxin-1.

Abstract Spinocerebellar ataxia-1 (SCA1) is caused by the expansion of a polyglutamine repeats within the disease protein, ataxin-1. The mutant ataxin-1 precipitates as large intranuclear aggregates in the affected neurons. These aggregates may protect neurons from mutant protein and/or trigger neuronal degeneration by encouraging recruitment of other essential proteins. Our previous studies have shown that calcium binding protein calbindin–D28k (CaB) associated with SCAl pathogenesis is recruited to ataxin-l aggregates in Purkinje cells of SCAl mice. Since our recent findings suggest that tissue transglutaminase 2 (TG2) may be involved in crosslinking and aggregation of ataxin-l, the present study was initiated to determine if TG2 has any role in CaB–ataxin-l interaction. The guinea pig TG2 covalently crosslinked purified rat brain CaB. Time dependent progressive increase in aggregation produced large multimers, which stayed on top of the gel. CaB interaction with ataxin-l was studied using HeLa cell lysates expressing GFP and GFP tagged ataxin-l with normal and expanded polyglutamine repeats (Q2, Q30 and Q82). The reaction products were analyzed by Western blots using anti-polyglutamine, CaB or GFP antibodies. CaB interacted with ataxin-1 independent of TG2 as the protein–protein crosslinker DSS stabilized CaB–ataxin-l complex. TG2 crosslinked CaB preferentially with Q82 ataxin-1. The crosslinking was inhibited with EGTA or TG2 inhibitor cystamine. The present data indicate that CaB may be a TG2 substrate. In addition, aggregates of mutant ataxin-l may recruit CaB via TG2 mediated covalent crosslinking, further supporting the argument that ataxin-l aggregates may be toxic to neurons.
Seismic Analysis of Structures with Viscoelastic Dampers

Viscoelastic dampers are being used in structures to mitigate dynamic effects. The models of varying complexities from simple maxwell element to differential models with fractional and complex order derivatives have been used to represent their frequency-dependent force deformation characteristics. More complex models are able to capture the frequency dependence of the material properties better, but are difficult to use in analyses. However, the classical models consisting of assemblies of Kelvin and/or Maxwell elements with an adequate number of parameters can be formed to capture the frequency dependence as accurately as the more sophisticated fractional derivative models can do. The main advantage in adopting these classical models is a simpler and smaller system of equations, which can be conveniently analyzed for nonlinear and linear systems. In this study, the two classical mechanical models consisting of Kelvin chains and Maxwell ladder are used. It is shown that these mechanical models are as effective as the fractional derivative model in capturing the effect of the frequency dependence of the material properties in response calculations and are more convenient to use in dynamic response analyses.
Maternal antimullerian hormone levels do not predict fetal aneuploidy

To determine if diminished ovarian reserve (measured by maternal antimullerian hormone (AMH) levels), is associated with fetal aneuploidy (determined by prenatal karyotype). This case-control study included 213 women with singleton pregnancies who underwent both serum aneuploidy screening and invasive prenatal diagnosis. 18 patients carrying an aneuploid fetus served as cases and the remaining 195 women with a euploid fetus were controls. Serum AMH was measured using two assays: AMHbc (Beckman-Coulter) and AMHdsl (Diagnostic Systems Laboratories). Karyotypes were determined by chorionic villus sampling or amniocentesis. AMHbc levels did not differ between women with an aneuploid fetus and women with a euploid fetus (p = 0.46) and did not predict aneuploidy (ROC Area = 0.57). Additionally, AMHbc values declined significantly with advancing gestational age. Maternal AMH does not appear to be a marker of fetal aneuploidy in ongoing pregnancies. Contrary to previous reports, we found a significant decline in maternal AMH levels with advancing gestational age.
Measurement of Fallout Cesium in the Pacific Ocean and in Terrestrial Effluents likely to alter Coastal Waters

A chemical technique was developed for concentrating traces of Cs/sup 137/ fallout in sea water (and in sewage), so that assay can be made rapidly with a gamma spectrometer. Measurements were made of Cs/sup 137/ in surface waters of the eastern Pacific, especially near the shore, and data are compared with fallout contamination reported elsewhere. Also, a contemporary vertical profile of Cs/sup 137/ activity in the Pacific is given. The behavior of fallout activity in a large modern sewage treatment plant and in its oceanic outfall is discussed, and estimates are made of the probable effects in coastal areas. (Abstr. Japan Med., 2: No. 12, Dec. 1962)
Motor Vehicle Theft at the Shopping Centre: An Application of the Routine Activities Approach

Using a national survey of self-reported shopping centre crime, this study examines how one of the most commonly reported shopping centre offences, namely, motor vehicle theft, is associated with the three critical elements of the ‘routine activities’ approach to crime distribution. As expected, the presence of motivated offenders and the absence of capable guardians both have a significant effect on the rates of auto theft occurring at 265 major US shopping centres and malls. However, contrary to the model, the availability of suitable targets does not predict auto theft in the regression equation. Theoretical discussion considers several possible explanations for this partial support for the routine activities model.
Changes in extracellular pH are neither required nor sufficient for activation of mitogen-activated protein kinases (MAPKs) in response to systemin and fusicoccin in tomato

Leaf wounding and the wound signaling peptide systemin induce expression of wound response genes while the fungal toxin fusicoccin (FC) induces expression of pathogenesis-related genes. Consistent with their functional differences, FC and systemin regulate the extracellular pH in opposite ways, with systemin inducing an alkalinization and FC an acidification response. Here we show that systemin, wounding and FC activate the same mitogen-activated protein kinases (MAPKs; MPKs) MPK1 and 2 in tomato (Lycopersicon esculentum) leaves and L. peruvianum suspension-cultured cells. Wounding and FC activated an additional MAPK, MPK3. Pronounced differences were observed with regard to MAPK activation kinetics. FC induced prolonged, and systemin transient activity of the MAPKs. This shows that functionally different elicitors engage the same signaling components, yet induce signal-specific activation dynamics. A comparative analysis of pH effects and MAPK activity in response to specific treatments revealed that the kinetics of pH changes and MAPK activation did not correlate. Simultaneous application of FC and systemin did not lead to immediate pH changes but resulted in rapid increases in MAPK activity. Furthermore, changes in extracellular pH could be induced without concomitant MAPK activation by exchanging conditioned medium with fresh medium. This shows that changes in the extracellular pH are neither required nor sufficient for MAPK activation, suggesting that signaling pathways involving MAPKs and extracellular pH changes operate in parallel and are not part of the same linear pathway.
Magnetic Exchange-Coupling in CoPt/Co Bilayer thin Films

Thin film CoPt/Co bilayers have been prepared as a model system to investigate the relationship between microstructure and exchange coupling in two-phase hard/soft composite magnets. CoPt films, with a thickness of 25 nm, were sputter-deposited from a nearly equiatomic alloy target onto oxidized Si wafers. The films were subsequently annealed at 700 C and fully transformed from the FCC phase to the magnetically hard, ordered L1{sub 0} phase. The coercivity of the films increased rapidly with annealing time until it reached a plateau at approximately 9.5 kOe. Fully-ordered CoPt films were then used as substrates for deposition of Co layers, with thicknesses in the range of 2.8--225 nm, in order to produce the hard/soft composite bilayers. As predicted by theory, the magnetic coherency between the soft Co phase and the hard, ordered CoPt phase decreased as the thickness of the soft phase increased. This decrease in coupling was clearly seen in the magnetic hysteresis loops of the bilayers. At small thicknesses of Co (a few nanometers), the shape of the loop was one of a uniform material showing no indication of the presence of two phases with extremely different coercivities. At larger Co thicknesses, constricted loops, i.e., ones showing the presence of a mixture of two ferromagnetic phases of different hardnesses, were obtained. The magnetic exchange present in the bilayer samples was qualitatively analyzed using magnetic recoil curves and the dependence of exchange coupling on the soft phase dimension in the bilayer hard/soft composite magnet films is discussed.
David Byar as a teacher

For me and for everyone at this workshop, this is a bittersweet occasion. Bitter because of the loss of a colleague, friend, and teacher, but sweet because we have the opportunity to come together and continue to learn from, and honor, a truly remarkable person. I was originally asked to speak about "Dave Byar as a Supervisor," but I've changed it to "David Byar as a Teacher" because it's more in keeping with his intentions and style of what we might otherwise call supervision. I'm very grateful for the opportunity to speak well of Dave Byar as a teacher. I was a medical staff fellow and senior staff fellow in the Biometry Branch at the National Cancer Institute (NCI) from 1982 to 1988, a relatively short exposure compared with some of the participants and attendees at this workshop. I've tried to extract some of the principles that I perceived and that Dave openly advocated in his supervisory style, using his own as well as other people's words. There is observer bias here because ray personality, needs, and aspirations, combined with the chance events that rule all of ot,.r lives, have caused me to remember and emphasize things that others would not, and perhaps even to neglect some things that others would hold dear. So I have no special insight hereI have only this opportunity. To me, this quote is pure David Byar:
Datagram authentication in internet gateways: implications of fragmentation and dynamic routing

The implications of fragmentation and dynamic routing for datagram authentication at the gateway level are discussed. Two protocols are presented that permit varying degrees of fragmentation and dynamic routing, while allowing the gateways to authenticate successive packets belonging to authorized connections. The first adapts to changing paths and fragmentation by keeping state information on a per-packet basis, while the second restricts fragmentation but incurs little state overhead. The two methods vary in implementation complexity, overhead, number of extra packets sent, and host modification requirements. They were designed with different network characteristics in mind, and, since they are not mutually exclusive, both can be incorporated and used depending on the nature of communication. >
Suppressor cells of mitogen-induced lymphocyte proliferation in the peripheral blood of patients with common variable hypogammaglobulinemia.

Abstract Diminished lymphocyte proliferative responses to several mitogens have been demonstrated in peripheral blood lymphocytes (PBL) from patients with common variable hypogammaglobulinemia. The mechanism is obscure, although intrinsic cellular defects have been suggested in both T and B cells. We studied PBL from three patients with this disease, who showed diminished lymphocyte proliferative responses to pokeweed mitogen and/or concanavalin A. Decreased OKT4-reactive helper T-cell subsets as well as increased OKT8-reactive suppressor T-cell subsets, as defined by recently developed monoclonal antibodies, were identified in PBL from these patients. In addition, activated suppressor T-cell function modulating the proliferative responses of autologous and/or allogeneic lymphocytes was demonstrated in these patients by coculture of the patients' PBL with allogeneic PBL and by elimination of T-cell subsets from the patients' PBL.
Improvement of etching selectivity for 32-nm node mask making

As the geometry of semiconductor devices continue to scale down, high-NA imaging will be used to enhance the resolution. Sub-resolution assistant features are used to gain depth of focus at the wafer. One of the challenges in patterning small assistant features during mask fabricating is resist collapse. Reducing resist thickness is one of the solutions. This necessitates an increase in the selectivity of chromium (Cr) to photo-resist (PR). The selectivity determines the PR remaining on the mask after Cr etching. Insufficient remaining PR will induce pinhole-type clear defect and poor line edge roughness (LER). In this paper, the Cr-to-PR selectivity was studied under induced couple plasma (ICP) and quasi-remote plasma environment. PR remaining, etching bias, and critical dimension uniformity (CDU) are the main subjects for evaluation. To understand the etching behavior for higher selectivity, design of experiment (DOE) L4 by Taguchi method is used to find the dominating factors. By adopting the optimized etching recipe, the resist can be thinned down to effectively improve its collapse margin, especially for smaller assistant features. The results show that 72-nm assistant features on mask can be patterned for early 32-nm node development. This paper also suggests several approaches that can be used to reduce the required resist thickness, such as hard-mask, film thickness reduction, and etcher hardware modification.
Purification of S-acyl fatty acid synthase thioester hydrolase by affinity chromatography with fatty acid synthase attached to Sepharose.

S-Acyl fatty acid synthase thioester hydrolase, the enzyme responsible for release of short-chain fatty acids from fatty acid synthase, was purified to homogeniety in 50–60% yield by a procedure involving affinity chromatography with fatty acid synthase as the affinity ligand attached to Sepharose. This procedure gave a 10- to 12-fold increase in yield over the previously available method.
Reexamination of the arguments of Einstein, Podolsky, and Rosen

Verifiable physical theories can deal only with reproducible phenomena. To the extent that some objectively real aspects of quantum phenomena are inherently not reproducible, to that extent quantum theory cannot be expected to provide a complete description of reality. Einstein, Podolsky, and Rosen argued, however, that quantum mechanics does not even provide a complete description of reproducible reality. But their reasoning fails to distinguish between the “predictability” and the “predictedness” of a physical quantity. It is shown that in quantum mechanics, as in classical mechanics, predictability is not affected by a nondisturbing measurement, only predictedness is affected. Since Einstein, Podolsky, and Rosen define the (reproducible) reality of a quantity on the basis of its predictability, we find that the quantum mechanical description of this reproducible reality is unaffected by nondisturbing measurements and does not need to be considered incomplete.
Cardiac rehabilitation today: programs, their effects and practical guidelines

Cardiac rehabilitation programs started to develop in the early 1970s. At that time the emphasis was on physical training. The goal was early return to work and lowering of mortality. Today, cardiac rehabilitation also includes risk factor modification and stress management. From 1972 to 1986, 22 randomized, controlled trials were performed to evaluate whether cardiac rehabilitation would be able to decrease mortality and improve people's ability to return to work. Although all of them reported an increase in physical working capacity, only one reported a decrease in mortality. However, a meta-analysis of the 22 trials was reported in 1989. The study found a 20% decrease in total mortality and a 22% decrease in cardiovascular mortality, both significant. This article describes the principles of cardiac rehabilitation and different types of program models with a detailed description of 3 different programs. It also reviews the effect of cardiac rehabilitation on mortality and its use in primary prevention.
Emerging macrolide resistance in Mycoplasma pneumoniae in children: detection and characterization of resistant isolates.

BACKGROUND: Epidemiologic data from Asia have documented the rapid and extensive emergence of macrolide resistance in Mycoplasma pneumoniae. This drug resistance has also been documented in Europe and recently in the United States, but there is very little information currently available on its prevalence. A rapid technique to identify macrolide-resistant M. pneumoniae is needed to guide management of patients with community-acquired respiratory infections. METHODS: Culture and Minimum Inhibitory Concentration testing identified macrolide-resistant M. pneumoniae infection in 2 seriously ill hospitalized children with community-acquired pneumonia. A portion of the 23S ribosomal RNA gene from 2 macrolide-resistant M. pneumoniae isolates from these children as well as 4 laboratoryinduced macrolide-resistant strains was amplified by PCR, and the PCR products were sequenced to identify mutations associated with macrolide resistance. A real-time PCR assay was designed to identify 3 known mutations in the 23S rRNA gene associated with macrolide resistance and applied to the clinical specimens from which these isolates were obtained and to the bacterial isolates. RESULTS:: Macrolideresistant M. pneumoniae from both children were found to carry an A2063G transition in the 23S rRNA gene previously identified in resistant isolates from China, Japan, France, and recently in an encephalitis outbreak in Rhode Island. Three laboratory-induced mutant strains had an A2064G mutation whereas the other one had an A2063G mutation. A real-time PCR assay successfully detected the macrolide-resistant M. pneumoniae directly in clinical specimens and discriminated them from wild-type isolates. CONCLUSIONS: Macrolide-resistant M. pneumoniae can be associated with prolonged severe respiratory infection in children. Real-time PCR offers a rapid method of diagnosing macrolide resistance in community-acquired respiratory infections due to M. pneumoniae.
On theory and modelling

Parisi, D., & Plunkett, K. (1996). Rethinking innateness: A connectionist perspective on development. Cambridge, Mass.: MIT Press. Goldman-Rakic, P. S. (1988). Topography of cognition: Parallel distributed networks in primate association cortex. Annual Review of Neuroscience, 11, 137–156. Kojima, S., & and, G.-R. P. S. (1982). Delay-related activity of prefrontal neurons in rhesus monkeys performing delayed response. Brain Research, 248, 43–49. Montague, P. R., Dayan, P., & Sejnowski, T. J. (1996). A framework for mesencephalic dopamine systems based on predictive Hebbian learning. Journal of Neuroscience, 16, 1936–1947. Munakata. (1997). Infant perseveration and implications for object permanence theories: A PDP model of the A-not-B task. Developmental Science, this issue. Niki, H., & Watanabe, M. (1976). Prefrontal unit activity and delayed response: relation to cue location versus direction of response. Brain Research, 105, 79–88. Quartz, S. R., & Sejnowski, T. J. (in press). The neural basis of cognitive development: A constructivist manifesto. Behavioral and Brain Sciences. 196Commentaries
Nature of deformation of sandy bed forms

[1] We explore a stochastic component of topographic evolution of sandy river beds and its relationship to bed material flux. The behavior of trains of mobile bed forms can be decomposed into two independent constituents, translation and deformation. Translation is the mean downstream migration of the bed at velocity that defines the Lagrangian reference frame of the bed. Deformation is the sum of all changes to the bed's topographic profile measured from within the bed's moving reference frame. The occurrence of deformation leads to exponential decorrelation of bed topography that is in dynamic equilibrium with flow conditions. For the field and laboratory data sets used, correlation decays to 0.5 by the time the bed translates 40% and 360% of the mean bed form length, respectively. Proportions of bed material flux responsible for translation and deformation can be straightforwardly calculated. Translation flux is measured using the traditional bed form-bed load equation. Deformation flux is determined by excess topographic change scaled by the ratio of horizontal sediment velocity to fall velocity. Deformation represents the sediment exchanged between bed load and suspended load. Because deformation is a stochastic process with zero mean, the apparent rate of deformation decreases as a function of time interval between bed surveys. For the field case, deformation accounts for 40% of bed material flux while it is only 1% of the flux in the laboratory.
Estimating the Consumptive Use Costs of Shale Natural Gas Extraction on Pennsylvania Roadways

AbstractThe development of natural gas resources in the Marcellus Shale formation has progressed rapidly in the last several years, particularly in the Commonwealth of Pennsylvania. These activities require many heavy truck trips for equipment and materials, which can damage state and local roads that were not designed for high volumes of heavy truck traffic. For state transportation agencies, one measure of costs of shale gas development is the potential degradation of roadways resulting from shale gas development. This technical note, provides a first-order an estimate of roadway consumptive use costs of additional heavy truck traffic on Pennsylvania state-maintained roadways from Marcellus Shale natural gas development in 201, estimated at 1 about $13,000–$23,000 per well for all state roadway types, or $5,000–$10,000 per well if state roads with the lowest traffic volumes are excluded. This initial estimate of costs, is based on data on the distribution of well activity and roadway type in Pennsylvani...
Characterization of the Azoarcus ribozyme: tight binding to guanosine and substrate by an unusually small group I ribozyme

We report novel chemical properties of the ribozyme derived from the smallest group I intron (subgroup IC3) that comes from the pre-tRNA(Ile) of the bacterium Azoarcus sp. BH72. Despite the small size of the Azoarcus ribozyme (195 nucleotides (nt)), it binds tightly to the guanosine nucleophile (Kd = 15 +/- 3 microM) and exhibits activity at high temperatures (approximately 60-70 degrees C). These features may be due to the two GA3 tetraloop interactions postulated in the intron and the high GC content of the secondary structure. The second order rate constant for the Azoarcus ribozyme, ((k(cat)/Km)S = 8.4 +/- 2.1 x 10(-5) M(-1) min(-1)) is close to that found for the related ribozyme derived from the pre-tRNA(Ile) of the cyanobacterium Anabaena PCC7120. pH dependence studies and kinetic analyses of deoxy-substituted substrates suggest that the chemical cleavage step is the rate-determining process in the Azoarcus ribozyme. This may be due to the short 3-nt guide sequence-substrate pairing present in the Azoarcus ribozyme. Finally, the Azoarcus ribozyme shares features conserved in other group I ribozymes including the pH profile, the stereospecificity for the Rp-phosphorothioate at the cleavage site and the 1000-fold decrease in cleavage rate with a deoxyribonucleoside leaving group.
Rare-earth fatty liver.

THE biological behaviour of the rare earths has recently become a question of increasing importance1. Early recognition of the prominent occurrence of several of these elements in fission products2 stimulated a wide scope of distribution studies in animals and, to a limited extent, in man. Yet, we could find among these studies no mention of a specific biochemical or histological effect except for a brief communication from this laboratory on fatty liver degeneration3 and some earlier reports on rare earths as anticoagulants4.
The Effect of Transforming Growth Factor-β on Follicle-Stimulating Hormone-Induced Differentiation of Cultured Rat Granulosa Cells*

Growth factors have been shown to modulate differentiation of cultured ovarian granulosa cells. Transforming growth factors (TGFs) constitute a family of polypeptide growth factors capable of reversibly inducing anchorage-independent growth in normal cells. Epidermal growth factor (EGF), which has significant structural homology with TGF α, has been shown to modulate differentiation of granulosa cells in vitro. Similarly, TGFβ (TGFB) has been found to have significant structural homology with ovarian follicular fluid inhibin. To examine whether TGFB might affect granulosa cell growth or differentiation, rat granulosa cells were cultured in serumfree medium containing insulin for up to 3 days with varying concentrations of TGFB in the presence or absence of FSH. TGFB caused a dose-dependent increase in FSH-stimulated LH/hCG receptor binding, but had no effect on binding in the absence of FSH; TGFB (10.0 ng/ml) further increased FSHstimulated LH/hCG receptor binding by 48 ± 8% (P < 0.02). Similarly, FSH-sti...
A PROCESS MANAGEMENT MODEL OF CORPORATE SOCIAL RESPONSIBILITY

Review of Literature Social responsibility is a fairly old concept which took on new life in the 1960s. Corporate critics who questioned corporate performance, and even the legitimacy of corporate business, called for and got increased government control of business. Social responsibility became the “self‐control” alternative as criticism of business continued to grow. In general, social responsibility means that a private corporation has responsibilities to society that go beyond the production of goods and services at a profit (Davis, 1960; Starling, 1984). Many definitions go beyond this one and require more specific activities from corporations. Acceptance of social responsibility as an appropriate description of the business‐society relationship implies that the corporation's broader constituency includes not only stockholders but also other societal groups such as customers, employees, suppliers, and neighbouring communities.
Model studies on the effect of the intracardiac blood on the electrocardiogram.

Abstract Perfused dog bladders to simulate the intracardiac blood mass were placed in an electrolytic tank in the shape of an elliptical cylinder. An artificial dipole was placed adjacent to the preparation, and wall and limb potentials were measured. Measurements were made with the dipole axis tangential, radial, or at intermediate angles to the bladder wall. In one group of experiments the leads were measured for ratios of bladder fluid to tank fluid of from about 0.14 to 1.20. In the second series of experiments the ratio was kept constant at 0.15, and field potentials were measured as a function of the distance between the dipole and the bladder. The results show that the contribution of a dipole component to the potential at a given electrode depends on the ratio of the resistivity of the blood to the resistivity of myocardial and thorax tissue, the distance of the dipole from the cavity, its direction relative to the cavity wall, as well as on the orientation of the dipole with respect to the electrode.
The hydrolytic scavenging of metal ions by marine particulate matter

Abstract A simple chemical model of hydrolytic scavenging by marine particulate matter is developed, incorporating adsorption of free metal ions and hydrolysis complexes and taking into account competitive complexation by major seawater anions. The model is applied to laboratory adsorption data and successfully predicts the trend in adsorption for a range of metals on different natural particles, but fails where adsorptive behaviour is dominated by oxide or mineral phases. Experimentally determined distribution coefficients and adsorption rate constants for strongly adsorbed metals such as Th, Pu and Sn appear to be consistent with those derived for Th from ocean data, at the same suspended particle concentration. Using Th as a model, the hydrolytic scavenging behaviour of metals (except oxyanions) in the ocean can be estimated from thermodynamic data for hydrolysis and complex formation with the major anions of seawater. An index of scavenging for over fifty metals is presented.
The impact of interprocedural analysis and optimization on the design of a software development environment

One of the primary goals of the IRn programming environment project is to mount a concerted attack on the problems of performing interprocedural analysis and optimization in a compiler. Few commercial optimizing compilers employ interprocedural techniques because the cost of gathering the requisite information in a traditional compiler is too great. Computing the side effects of a procedure call requires detailed knowledge of the internals of both the called procedure and any procedures invoked either directly or indirectly from it. Thus, the compiler potentially needs information about the internals of every procedure to determine the side effects of procedure calls, even separately compiled procedures. Gathering this information would require examining the source of every procedure in the program - an expensive process, particularly unfortunate since the primary goal of separate compilation is to reduce the amount of recompilation required in response to changes in an individual procedure.The existence of a software development environment like the IRn programming environment [HoKe 84] changes the compilation process enough to make computing such information palatable. Since all modules are developed and all programs are defined using tools of the environment, these tools can cooperate to record the information necessary to do a good job of interprocedural analysis and optimization. Whenever the compiler needs information about possible side effects of a particular procedure, it can simply extract this information from the environment's central database. Because the only mechanism for changing modules or programs is through the tools provided by the environment, the compiler is assured that it will be notified of any changes. Thus, it can use information derived from previous analysis with certain knowledge that the information reflects the current state of the program and its procedures.
Classification of blueberry fruit and leaves based on spectral signatures

Blueberry spectral analysis can provide necessary wavelengths, for use in multispectral imaging that could be applied in blueberry yield estimation system. Samples of fruit and leaves were obtained from a commercial blueberry field in Waldo, Florida and an experimental field in Citra, Florida, USA in 2011. Samples were also collected in 2010 in Waldo. Seven representative southern highbush varieties were chosen for the experiment. Spectral reflectance was measured in the 200–2500 nm with an increment of 1 nm. Samples were divided into leaf, mature fruit, near-mature fruit, near-young fruit and young fruit. Normalised indices were used as the candidate variables for classification. Each index was composed of the two wavelengths that had the greatest difference in reflectance between two classes. Classification tree, principal component analysis (PCA) and multinomial logistic regression (MNR) were conducted to develop classification models. An MNR model with six wavelengths (233, 551, 554, 691, 699 and 1373 nm) performed the best for the 2011 dataset, with a prediction accuracy of 100% for leaf and mature fruit, 97.8% for young fruit, 97.9% for near-young fruit and 94.6% for near-mature fruit. Four wavelengths (553, 688, 698 and 1373 nm) were used in the classification models of two years' data with four classes (mature fruit, intermediate fruit, young fruit and leaf), and accuracies of 100%, 100%, 99%, and 98.5% were obtained for the classification of leaf, mature fruit, intermediate fruit and young fruit, respectively. An easy-to-use and low cost blueberry fruit detector could thus be developed using multispectral imaging.
Application of a deflagration plasma gun as a space propulsion thruster

The application of the magnetized plasma deflagration process to space propulsion is introduced. The deflagration process has the unique capability of efficiently converting input energy into kinetic energy in the accelerating direction. Examples of the differences between deflagration and detonation are given, such as their current densities, their temperature, and their particle velocities. Magnetic field profiles of the two modes of discharges are measured. Preliminary temperature measuring technique is introduced. Specific impulses measured by piezoelectric probe and pendulum methods are presented. The influence of the transmission line in the discharge circuits on that of plasma velocity is measured by means of microwave time-of-flight method. The results for the deflagration gun are compared with other space thrust ers.
Macrophage Arginine Metabolism to Ornithine/Urea or Nitric Oxide/Citrulline: A Life or Death Issue

Macrophages can metabolize arginine to nitric oxide in quantities that inhibit pathogens or nearby host cells. They can instead metabolize arginine to ornithine (a precursor of polyamines and collagen) in quantities that stimulate pathogens or nearby host cells. Macrophages are essentially the only circulating cells that can make these life or death decisions with arginine. Macrophages expressing these destructive or constructive phenotypes have been termed M-1 or M-2 because they also stimulate TH1 or TH2 responses, respectively. Factors that influence whether a macrophage expresses the M-1 or M-2 phenotype and the real or potential impact on immune responses and other host processes are discussed.