cssi/SciSciGPT-SciSciNet huggingface dataset:
Transforming Growth Factor-β1 Modifies Fibroblast Growth Factor-2 Production in Type II Cells

Transforming growth factor (TGF)-β 1 is an inflammatory cytokine that plays multiple roles in pulmonary fibrosis. In vascular epithelium, it has been shown to regulate production and activity of fibroblast growth factor (FGF)-2, a potent type II cell mitogen in the lung. Such a relationship could have important consequences in prefibrotic change in the lung alveolus, where reepithelialization of alveolar surfaces is crucial. The goal of this study was to determine if FGF-2 production by alveolar type II cells is modulated by TGF-β 1 or FGF-1, another type II cell mitogen. Isolated rat type II cells were exposed to 0 to 40 ng/mL of TGF-β 1 or 0 to 500 ng/mL of FGF-1 in serum-free medium for 1 to 3 days. Using a specific immunoassay, significant increases in FGF-2 protein in type II cell lysates were achieved after 1 day of exposure to 100 ng/mL of FGF-1 and after 3 days of treatment with 8 ng/mL of TGF-β 1 . Similarly, transcripts for FGF-2 were dramatically increased with TGF-β 1 or FGF-1, as were those for FGF receptor (FGFR)-1. These interactions were dramatically effected by the addition of heparin, a model sulfated extracellular matrix (ECM). Heparin as low as 0.01 mg/mL significantly downregulated expression of TGF-β 1 and FGF-1–stimulated FGF-2 and FGFR-1. These results demonstrate important regulatory links between FGF-2, sulfated ECMs, and both TGF-β 1 and FGF-1, which could contribute to the modulation of normal cell turnover, development, and repair processes attendant to fibrosis in the lung.
Tyrosine oxidation products: analysis and biological relevance

Dityrosine is found in several proteins as a product of UV irradiation, γ-irradiation, aging, exposure to oxygen free radicals, nitrogen dioxide, peroxynitrite, and lipid hydroperoxides. Interest of dityrosine in proteins is based on its potential as a specific marker for oxidatively damaged proteins and their selective proteolysis, hence it could be used as a marker for oxidative stress. Dityrosine is also the product of normal post-translational processes affecting specific structural proteins. Since post-translational modification of a given amino acid in a protein is equivalent to the substitution of that residue by an analogue, it has been proposed that the covalent modification of amino acids may serve as a “marking” step for protein degradation.
Finding a space for the public's health in bioterrorism funding: a commentary.

Thomas May (2005) provides a compelling case for a shift in funding priorities, but overstates the benefits of biosecurity as a means to improve the public's health. He assumes that the vast increa...
Victim Notification and Public Support for the Criminal Justice System

Dutch criminal justice policy assumes that people's faith in the criminal justice system depends largely on its ability to sanction offenders. In this article arguments are offered which question this assumption. Victimological research shows that the treatment of victims in the criminal justice process is important to victims and more important than the ability of police to catch the offender. The impact of treatment on victims' satisfaction and support for the police and sentencing practices is examined. By notifying victims of the developments in their case, police can improve victim satisfaction and support for them as well as increase support for sentencing practices. Failure to recognise the victim, regardless of the severity of the punishment imposed upon the offender, results in a significant decrease in victim satisfaction and support for the police. The paper closes with a discussion of the implications of the findings for criminal justice policy.
A Hybrid Trust Management System for automated fine-grained access control

An organization consists of many resources and entities who want to access those resources. Not all entities are granted full access rights to every resource, so there must be a Trust Management System (TMS) in place to enforce access rights. In this paper, we present a new Hybrid Trust Management System (HTMS) that combines Role Based Trust Management (RBTM) with Reputation Systems (RS). At any point in time, the privilege level of an entity is determined not only by its role in the system, but also by its reputation score, which in turn is based on its behavior. If a privileged node becomes compromised and conducts several malicious or risky transactions, its privilege level is quickly reduced to limit its access to resources and minimize the damage it can inflict further. The system uses a global, network-wide perspective in order to thwart global attacks. Such fine-grained variations of access control and dynamically assigning privilege levels would be very difficult to accomplish manually. We evaluated HTMS by comparing an implementation of it against an ideal response. We show that HTMS performs very close to the ideal if we can accurately estimate the proportion of malicious nodes in the network. We suggest using sampling to estimate this proportion. However, even if this estimate is not accurate, the results are still much better than using RBTM by itself.
Photochemical Inactivation of Deoxyribonucleic and Ribonucleic Acid Viruses by Chlorpromazine

Chlorpromazine, a widely used tranquilizing drug of the phenothiazine group, was found to be a very potent photochemical inactivator of both deoxyribonucleic acid and ribonucleic acid viruses in the presence of long-wave ultraviolet light (320 to 380 nm). Neither the light alone nor chlorpromazine alone caused any appreciable inactivation. The known chlorpromazine photoreactions with nucleic acids are somewhat similar to those of psoralen (furocoumarin) derivatives. As in the case of the psoralens, chlorpromazine is capable of photoinactivating viruses totally within a few minutes under near-physiological or other gentle conditions. The antiviral effects of the chlorpromazine photoreaction could make it valuable for the development of inactivated viral vaccines as well as for use in the photochemotherapy of viral dermatoses.
An unusual outbreak of rotavirus genotype G2P[6] during the 2005–2006 epidemic season in Philadelphia

Most rotavirus gastroenteritis is caused by G1P[8] strains. When G2 infections are encountered, the P type has most often been reported to be P[4]. The purpose of our study was to describe an unusual outbreak of G2P[6] cases. Children presenting to The Children's Hospital of Philadelphia with acute gastroenteritis have been monitored for rotavirus antigen in stool by ELISA (with G-typing if ELISA positive) since 1994-1995. Compared to the last 12 rotavirus seasons before the 2006 introduction of a new rotavirus vaccine, the 2005-2006 season had by far the highest number of evaluable rotavirus infections [n = 275 from September 2005 through June 2006, of which 261 (95%) were G typed] and the greatest number of G2 cases (n = 101, 39% of typed strains). Only 16% of G2 strains were associated with P[4], whereas genotype G2P[6] was responsible for 83% of the G2 infections. Eighty-eight percent of the 84 G2P[6] cases occurred in the 60% of patients who were African-Americans, most of whom were urban residents. Among 157 African-American patients, G2 cases (n = 80; 52%) predominated, including 74 due to G2P[6]. Children <6 months old accounted for 27% of cases overall, but 36% of the G2P[6] cases. G2 rotaviruses caused over a third of the community-acquired rotavirus cases in children presenting to CHOP in 2005-2006, attesting to the potential impact of G2 strains during some epidemics. The large majority of G2 strains had the rare P[6] genotype. Urban African-American children under 6 months of age were disproportionately affected.
Analytical results for mixed action SU(2) lattice gauge theory

Abstract Strong and weak coupling expansions for the SU(2), mixed action lattice gauge theories are given. Nonperturbative configurations are identified and their contribution is also estimated. A comparison with Monte Carlo data is presented.
Trends in pharmacotherapy in patients referred to a bipolar specialty clinic, 2000-2011

Abstract Objective To assess mood stabilizer (MS) and second-generation antipsychotic (SGA) prescribing trends in bipolar disorder (BD) outpatients referred to a bipolar disorder specialty clinic over the past 12 years. Method BD outpatients referred to the Stanford University Bipolar Disorder Clinic during 2000–2011 were assessed with the Systematic Treatment Enhancement Program for BD (STEP-BD) Affective Disorders Evaluation. Prescription rates for MSs and SGAs were compared during the first (2000–2005) and second (2006–2011) six years. Results Among 597 BD patients (mean±SD age 35.4±8.6 years; 58.1% female; 40.7% Type I, 43.6% Type II, and 15.7% Type Not Otherwise Specified; taking 2.6±1.7 prescription psychotropic medications), lamotrigine, quetiapine, and aripiprazole usage more than doubled, from 14.7% to 37.2% (p Conclusions Over 12 years, in patients referred to a BD specialty clinic, lamotrigine, quetiapine, and aripiprazole use more than doubled, and olanzapine and risperidone use decreased by more than half. Tolerability (for lamotrigine, aripiprazole, olanzapine, and risperidone) more than efficacy (for quetiapine) differences may have driven these findings. Additional studies are needed to explore the relative influences of enhanced tolerability versus efficacy upon prescribing practices in BD patients.
Negative Interpretation Bias in Individuals with Depressive Symptoms

Negative interpretations are a central component of cognitive models of depression. Previous research on interpretation biases in depression has relied on self-report measures. Self-report measures have limited validity because they may measure a response bias rather than a cognitive bias. To overcome this limitation, recent investigations have used response latencies as a measure of interpretation bias with mixed results. We examined interpretation bias using a modified word sentence association paradigm (Beard and Amir in Cogn Therapy Res 33:406–415, 2009). In comparison with individuals without dysphoria, dysphoric individuals were significantly faster to endorse the association between negative words and ambiguous sentences. These results suggest that negative interpretations are primed in depression, suggesting that training towards benign interpretations may have therapeutic value.
Issues in the assessment of personality disorder and substance abuse using the millon clinical multiaxial inventory (MCMI-II)

Substance abuse treatment clients often present other severe mental health problems that affect treatment outcomes. Hence, screening and assessment for psychological distress and personality disorder are an important part of effective treatment, discharge, and aftercare planning. The Millon Clinical Multiaxial Inventory-II (MCMI-II) frequently is used for this purpose. In this paper, several issues of concern to MCMI-II users are addressed. These include the extent to which MCMI-II scales correspond to DSM-III-R disorders; overdiagnosis of disorders using the MCMI-II; accuracy of MCMI-II diagnostic cut-off scores; and the clinical utility of MCMI-II diagnostic algorithms. Approaches to addressing these issues are offered.
Does detritus quality predict the effect of native and non-native plants on the performance of larval amphibians?

Summary 1. The lack of consistent differences between the traits of native and non-native plant species makes it difficult to make general predictions about the ecological impact of invasive plants; however, the increasing number of non-native plants in many habitats makes the assessment of the impact of each individual species impracticable. General knowledge about how specific plant traits are linked to their effects on communities or ecosystems may be more useful for predicting the effect of plant invasions. Specifically, we hypothesised that higher carbon-to-nitrogen ratio (C:N) and percent lignin in plant detritus would reduce the rate of development and total mass at metamorphosis of tadpoles, resulting in lower metamorph production (total fresh biomass) and amphibian species richness. 2. To test these hypotheses, we raised five species of tadpoles in mesocosms containing senescent leaves of three common native and three common non-native wetland plants that varied in C:N ratio and % lignin. 3. Leaf mass loss, total metamorph production and the number of species that metamorphosed declined as a function of increasing C:N ratio of plant leaves. Plant lignin content was not related to the production of metamorphs or the number of species that metamorphosed. The percentage of wood frog (Lithobates sylvaticus) and American toad (Anaxyrus americanus) tadpoles reaching metamorphosis declined as a function of increasing plant C:N ratio. Mean time to metamorphosis increased and mean mass at metamorphosis declined as a function of increasing plant C:N ratio. Tadpole performance and metamorph diversity and production (biomass) were similar between native and non-native plant species with similar C:N ratio in leaves. Percent lignin was not a significant predictor of tadpole performance. 4. Our results show that the impact of a plant invasion on tadpole performance could depend on differences between the quality of the detritus produced by the invading species and that of the native species it replaces. We suggest that plant community changes that lead to dominance by more recalcitrant plant species (those with higher leaf C:N ratio) may negatively affect amphibian populations.
The demography of deinstitutionalization

Once defined as long-term residents of psychiatric hospitals, the chronically mentally ill today are a heterogeneous population living in a variety of institutional and community settings.
On the optimality of disk allocation for Cartesian product files (extended abstract)

In this paper we present a coding-theoretic analysis of the disk allocation problem. We provide both necessary and sufficient conditions for the existence of strictly optimal allocation methods. Based on a class of optimal codes, known as maximum distance separable codes, strictly optimal allocation methods are constructed. Using the necessary conditions proved, we argue that the standard definition of strict optimality is too strong, and cannot be attained in general. A new criterion for optimality is therefore defined whose objective is to design allocation methods that yield a response time of one for all queries with a minimum number of specified attributes. Using coding theory, we determined this minimum number for binary files, assuming that the number of disks is a power of two. In general, our approach provides better allocation methods than previous techniques.
Interest-rate volatility and volatility transmission in nine Latin American countries

With US monetary policy and financial markets exerting a strong influence on the region’s exchange rates, exports and investor confidence, Latin America is particularly vulnerable to international macroeconomic ‘contagion.’ Of the limited studies on the region, however, most attention has been drawn to the largest economies. This study models monthly short-term nominal interest-rate volatility for nine Latin American countries and the US, examining whether this volatility spills over within the region. GARCH and exponential GARCH methods provide univariate analyses, and multivariate GARCH techniques test for contagion. Relatively few instances of contagion are uncovered, with Argentina and Chile the most affected by external events. Paraguay and Uruguay (as well as Brazil) are more immune, most likely due to capital controls. An expanded model that includes exchange-rate volatility suggests that direct interest-rate linkages are rare, and that spillovers are primarily transmitted through currency markets.
Radioactive assay of folic acid polyglutamate conjugase(s).

Abstract In summary we report the development of a new nonmicrobiological assay for conjugases (pteroyglutamyl-γ-glutamyl peptidases). This method is comparable in sensitivity to the microbiological procedures, and may be modified to exceed that sensitivity. With the judicious use of selectively positioned glutamic acid-C 14 residues in the substrates, the procedure described allows the determination of preferred substrates and end products.
Specific and Nonspecific Membrane-binding Determinants Cooperate in Targeting Phosphatidylinositol Transfer Protein β-Isoform to the Mammalian Trans-Golgi Network

Phosphatidylinositol transfer proteins (PITPs) regulate the interface between lipid metabolism and specific steps in membrane trafficking through the secretory pathway in eukaryotes. Herein, we describe the cis-acting information that controls PITPbeta localization in mammalian cells. We demonstrate PITPbeta localizes predominantly to the trans-Golgi network (TGN) and that this localization is independent of the phospholipid-bound state of PITPbeta. Domain mapping analyses show the targeting information within PITPbeta consists of three short C-terminal specificity elements and a nonspecific membrane-binding element defined by a small motif consisting of adjacent tryptophan residues (the W(202)W(203) motif). Combination of the specificity elements with the W(202)W(203) motif is necessary and sufficient to generate an efficient TGN-targeting module. Finally, we demonstrate that PITPbeta association with the TGN is tolerant to a range of missense mutations at residue serine 262, we describe the TGN localization of a novel PITPbeta isoform with a naturally occurring S262Q polymorphism, and we find no other genetic or pharmacological evidence to support the concept that PITPbeta localization to the TGN is obligately regulated by conventional protein kinase C (PKC) or the Golgi-localized PKC isoforms delta or epsilon. These latter findings are at odds with a previous report that conventional PKC-mediated phosphorylation of residue Ser262 is required for PITPbeta targeting to Golgi membranes.
Micro-scale components from high-strength nanostructured alloys

A general approach for manufacturing of micro-scale components from high-strength, nanostructured materials is presented. The approach utilizes severe plastic deformation by large-strain extrusion machining to create the nanostructured material in a high-strength alloy system, and conventional micro-machining to produce the components. Manufacture of small-scale gears from nickel-based superalloy Inconel 718 is illustrated.
The structure of adsorbed bromide concurrent with the underpotential deposition (UPD) of Cu on Pt(111)

Abstract The adsorption of bromide anions concurrent with the underpotential deposition (UPD) of Cu on Pt(111) was examined utilizing ex-situ LEED and in-situ surface X-ray scattering for structure determination, in combination with coverage determination by rotating ring disk flux measurements with the Pt(111) single crystal as the disk electrode. The results show definitively that Cu UPD on Pt(111) in the presence of bromide is a two-step process, with the total amount of Cu deposited at underpotentials ∼0.95 ± 5% ML (1 ML = 1 adatom per Pt atom). The results also indicate that the surface coverage by adsorbed bromide undergoes only a small (
Clot lifespan model analysis of the effects of warfarin on thrombus growth and fibrinolysis: Role of contact protein and tissue factor initiation

Warfarin therapy has served as the backbone of chronic anticoagulation therapy for decades to prevent thrombotic morbidity secondary to blood-biomaterial interfaces. Unfortunately, thrombotic and bleeding complications are observed despite maintenance of therapeutic international normalized ratio (INR) values. We proposed to define the effects of warfarin therapy on thrombus growth and disintegration following contact pathway protein or tissue factor (TF) initiation. Normal subject or patient plasma with INR values between 1.8 and 9.6 were exposed to TF or celite and tissue-type plasminogen activator (tPA). Thrombus growth/disintegration kinetics were determined by changes in resistance over time with the clot lifespan model (CSLM), a thrombelastographic-based methodology. Data were collected until clot lysis time was observed. Linear relationships of the difference between the CLSM parameter values obtained from paired celite and TF-activated samples and corresponding INR value were determined and reported as r2. The time to clot initiation was progressively prolonged with increasing INR values in all samples, and speed of clot formation, clot strength, and time to onset of fibrinolysis decreased as INR increased. Throughout the range of INR values tested, contact activation resulted in faster growing, stronger, and longer lived thrombi when compared with matched TF-activated plasma samples. Only the time to maximum rate of lysis was correlated with INR (r2 = 0.36, p = 0.005). INR values have little correlation with the difference between contact protein and TF-activated coagulation/fibrinolysis.
Red cell phosphoglycerate mutase and bisphosphoglycerate synthase: controlled modifications in coulombic properties in vitro.

Under controlled conditions, both phosphoglycerate mutase and bisphosphoglycerate synthase from outdated human erythrocytes can be made to manifest changes in coulombic properties as indicated by isoelectric focusing. This finding provides corroborative evidence for the hypothesis that each of the above enzymes arises from its own unique gene locus and is subsequently modified through post-translational events which give rise to other isomeric forms. In the presence of intracellular concentrations of glycerate-2,3-P2, phosphoglycerate mutase is fully phosphorylated, suggesting a scheme, other than that proposed earlier [Hass, L. F. and Miller, K. B. (1978) J. Biol. Chem. 253, 3798–3803], to account for all of the mutase isomers found in whole cells. Dephosphorylation of the various mutase species present in circulating cells is accelerated by glycolate-2-P, but not by the normal acceptor, glycerate-3-P, indicating that the enzyme in vivo may be phosphorylated at a site other than the mutase site.
Genetic moderators of naltrexone's effects on alcohol cue reactivity.

Background: Naltrexone (NTX) reduces drinking and craving in alcoholic individuals in treatment and also in heavy drinkers. Polymorphisms in the D4 dopamine receptor (DRD4) gene and μ-opiate receptor gene (OPRM1) may moderate NTX's effects on craving. This study examined these candidate genes as moderators of the effects of NTX on cue-elicited urge to drink in non–treatment-seeking heavy drinkers. Method: Data from the subset of 93 participants who consented for genetic testing in a larger study of medication effects were used to examine pharmacogenetic hypotheses. The non–treatment-seeking male and female heavy drinkers (62% alcohol dependent) were genotyped for the variable number of tandem repeats polymorphism in the DRD4 gene [L=7 or more (n=34), S=less than 7 (n=56)] and Asn40Asp single-nucleotide polymorphism in the OPRM1 gene [29 aspartate (Asp) carriers and 59 asparagine (Asn) homozygotes]. Ten days after randomization to NTX (50 mg) or placebo, participants completed an alcohol cue reactivity assessment. Results: Any medication effects were all accounted for by interaction with genotype. Naltrexone increased urge for alcohol in Asp carriers across alcohol and neutral beverage cue trials and had no effect on homozygous Asn carriers. Asp40 carriers on either medication had greater decreases (from resting baseline) in mean arterial blood pressure across all beverage cue trials compared with Asn carriers. For DRD4, no differential medication effects by DRD4 polymorphism were found. Alcohol dependence diagnosis did not moderate the effects of gene and medication on cue-elicited measures. Discussion: The differential responses to NTX due to variation in the OPRM1 gene may help explain conflicting results in clinical trials and suggest directions for patient-treatment matching.
SHORT‐TERM AND LONG‐TERM EFFECTS OF TEMPERATURE ON PHOTOSYNTHESIS IN THE DIATOM THALASSIOSIRA PSEUDONANA UNDER UVR EXPOSURES1

Temperature is expected to modify the effects of ultraviolet radiation (UVR) on photosynthesis by affecting the rate of repair. We studied the effect of short-term (1 h) and long-term (days) acclimation to temperature on UVR photoinhibition in the diatom Thalassiosira pseudonana Hasle et Heimdal. Photosynthesis was measured during 1 h exposures to varying irradiances of PAR and UVR + PAR at 15, 20, and 25� C, the latter corresponding to the upper temperature limit for optimal growth in T. pseudonana. The exposures allowed the estimation of photosynthesis–irradiance (P–E) curves and biological weighting functions (BWFs) for photoinhibition. For the growth conditions used, temperature did not affect photosynthesis under PAR. However, photoinhibition by UVR was highly affected by temperature. For cultures preacclimated to 20� C, the extent of UVR photoinhibition increased with decreasing temperature, from 63% inhibition of PAR-only photosynthesis at 25� C to 71% at 20� C and 85% at 15� C. These effects were slightly modified after several days of acclimation: UVR photoinhibition increased from 63% to 75% at 25� C and decreased from 85% to 80% at 15� C. Time courses of photochemical efficiency (UPSII) under UVR + PAR were also fitted to a model of UVR photoinhibition, allowing the estimation of the rates of damage (k) and repair (r). The r ⁄k values obtained for each temperature treatment verified the responses observed with the BWF (R 2 = 0.94). The results demonstrated the relevance of temperature in determining primary productivity under UVR exposures. However, the results suggested that temperature and UVR interact mainly over short (hours) rather than long (days) timescales.
Experimental Studies of Phonon Dispersion and C-Axis Structure in Graphite Intercalation Compounds

In this paper we present new results, obtained from a variety of experiments, which probe the structure and lattice dynamics of donor- and acceptor-type graphite intercalation compounds (GIC’s). Specifically, we wish to discuss conclusions deduced from x-ray diffraction, Mossbauer, inelastic neutron scattering and Raman scattering investigations of well-staged GIC’s. The paper is organized as follows: in section II we discuss the experimental details, in section III we collect results pertaining to the chemistry, layer structure and c-axis dispersion of low-frequency phonon branches in SbCl5:graphite; in section IV and V we present the results of Raman scattering studies; section IV — the stage-dependence of two-phonon scattering from high-frequency graphitic modes in SbCl5:graphite (acceptor system) and Rb:graphite (donor system); section V- the observation and study of the temperature dependence of low frequency shear modes (ω ≃ 15, 20 cm-1) in stage 2 Rb:graphite.
Zhang Shiying and Chinese Appreciation of Hegelian Philosophy

This essay discusses Zhang Shiying (张世英), Professor of Philosophy in Peking University, China, a well-known contemporary Chinese scholar's study of Hegelian philosophy.
Novel, Highly Specific N-Demethylases Enable Bacteria To Live on Caffeine and Related Purine Alkaloids

The molecular basis for the ability of bacteria to live on caffeine as a sole carbon and nitrogen source is unknown. Pseudomonas putida CBB5, which grows on several purine alkaloids, metabolizes caffeine and related methylxanthines via sequential N-demethylation to xanthine. Metabolism of caffeine by CBB5 was previously attributed to one broad-specificity methylxanthine N-demethylase composed of two subunits, NdmA and NdmB. Here, we report that NdmA and NdmB are actually two independent Rieske nonheme iron monooxygenases with N(1)- and N(3)-specific N-demethylation activity, respectively. Activity for both enzymes is dependent on electron transfer from NADH via a redox-center-dense Rieske reductase, NdmD. NdmD itself is a novel protein with one Rieske [2Fe-2S] cluster, one plant-type [2Fe-2S] cluster, and one flavin mononucleotide (FMN) per enzyme. All ndm genes are located in a 13.2-kb genomic DNA fragment which also contained a formaldehyde dehydrogenase. ndmA, ndmB, and ndmD were cloned as His(6) fusion genes, expressed in Escherichia coli, and purified using a Ni-NTA column. NdmA-His(6) plus His(6)-NdmD catalyzed N(1)-demethylation of caffeine, theophylline, paraxanthine, and 1-methylxanthine to theobromine, 3-methylxanthine, 7-methylxanthine, and xanthine, respectively. NdmB-His(6) plus His(6)-NdmD catalyzed N(3)-demethylation of theobromine, 3-methylxanthine, caffeine, and theophylline to 7-methylxanthine, xanthine, paraxanthine, and 1-methylxanthine, respectively. One formaldehyde was produced from each methyl group removed. Activity of an N(7)-specific N-demethylase, NdmC, has been confirmed biochemically. This is the first report of bacterial N-demethylase genes that enable bacteria to live on caffeine. These genes represent a new class of Rieske oxygenases and have the potential to produce biofuels, animal feed, and pharmaceuticals from coffee and tea waste.
Characterization of Dissimilatory Fe(III) versus NO3− Reduction in the Hyperthermophilic Archaeon Pyrobaculum aerophilum

The hyperthermophilic archaeon Pyrobaculum aerophilum used 20 mM Fe(III) citrate, 100 mM poorly crystalline Fe(III) oxide, and 10 mM KNO3 as terminal electron acceptors. The two forms of iron were reduced at different rates but with equal growth yields. The insoluble iron was reduced when segregated spatially by dialysis tubing, indicating that direct contact with the iron was not necessary for growth. When partitioned, there was no detectable Fe(III) or Fe(II) outside of the tubing after growth, suggesting that an electron shuttle, not a chelator, may be used as an extracellular mediator of iron reduction. The addition of 25 and 50% (vol vol(-1)) cell-free spent insoluble iron media to fresh media led to growth without a lag phase. Liquid chromatography analysis of spent media showed that cultures grown in iron, especially insoluble iron, produced soluble extracellular compounds that were absent or less abundant in spent nitrate medium. NADH-dependent ferric reductase activity increased approximately 100-fold, while nitrate reductase activity decreased 10-fold in whole-cell extracts from iron-grown cells relative to those from nitrate-grown cells, suggesting that dissimilatory iron reduction was regulated. A novel 2,6-anthrahydroquinone disulfonate oxidase activity was more than 580-fold higher in iron-grown cells than in nitrate-grown cells. The activity was primarily (>95%) associated with the membrane cellular fraction, but its physiological function is unknown. Nitrate-grown cultures produced two membrane-bound, c-type cytochromes that are predicted to be monoheme and part of nitrite reductase and a bc1 complex using genome analyses. Only one cytochrome was present in cells grown on Fe(III) citrate whose relative abundance was unchanged.
L 1 adaptive controller for a class of systems with unknown nonlinearities: Part I

This paper presents an extension of the L 1 adaptive controller to a class of general nonlinear uncertain systems, nonaffine in control. The control signal interacts with system states and time-varying uncertainties in an unknown nonlinear way. The adaptive controller ensures uniformly bounded transient for system's both input and output signals simultaneously. The performance bounds can be systematically improved by increasing the adaptation rate. Simulation results verify the theoretical findings.
An architecture study of infrastructure-based vehicular networks

There are various ways to organize and connect in-vehicle computing systems by exploiting existing wireless technologies. It is desired to provide a wireless infrastructure for vehicles (e.g., offering reliable broadband channels, transportation related services and Internet access). In this paper we identify several design options for infrastructure-based vehicular networks and evaluate these designs in a realistic vehicular environment.
Overweight children in Beirut: prevalence estimates and characteristics.

Objective To estimate, for the first time, overweight prevalence and associated characteristics in a representative sample of prepubertal children in Beirut, Lebanon's capital. Design A cross-sectional study with a home interview including measurements of weight and height and a structured questionnaire. Subjects A total of 234 children aged 6–8 years in Beirut: 131 boys, 103 girls. Methods Prevalence of overweight and obesity was based on the international cut-off points for body mass index (BMI) by age and gender proposed by the International Obesity Task Force. The characteristics of overweight examined were: age, gender, household and family size, single- vs. two-parent family, parents’ level of education and profession, physical activity and dietary intake of children. Results Prevalence of overweight and obesity was 26% and 7% respectively in boys, 25% and 6% in girls. Overweight was significantly associated with low physical activity (P < 0.05) and mother's BMI (P < 0.05). Conclusions This study identified a high proportion of overweight in 6- to 8-year-old children in Beirut. Reduced physical activity was the most significant factor associated with childhood overweight. Further studies in different regions in Lebanon are necessary to identify national characteristics; prevention efforts will be designed accordingly.
American College of Gastroenterology guideline on the management of Helicobacter pylori infection.

Helicobacter pylori (H. pylori) remains a prevalent, worldwide, chronic infection. Though the prevalence of this infection appears to be decreasing in many parts of the world, H. pylori remains an important factor linked to the development of peptic ulcer disease, gastric malignanc and dyspeptic symptoms. Whether to test for H. pylori in patients with functional dyspepsia, gastroesophageal reflux disease (GERD), patients taking nonsteroidal antiinflammatory drugs, with iron deficiency anemia, or who are at greater risk of developing gastric cancer remains controversial. H. pylori can be diagnosed by endoscopic or nonendoscopic methods. A variety of factors including the need for endoscopy, pretest probability of infection, local availability, and an understanding of the performance characteristics and cost of the individual tests influences choice of evaluation in a given patient. Testing to prove eradication should be performed in patients who receive treatment of H. pylori for peptic ulcer disease, individuals with persistent dyspeptic symptoms despite the test-and-treat strategy, those with H. pylori-associated MALT lymphoma, and individuals who have undergone resection of early gastric cancer. Recent studies suggest that eradication rates achieved by first-line treatment with a proton pump inhibitor (PPI), clarithromycin, and amoxicillin have decreased to 70‐85%, in part due to increasing clarithromycin resistance. Eradication rates may also be lower with 7 versus 14-day regimens. Bismuth-containing quadruple regimens for 7‐14 days are another first-line treatment option. Sequential therapy for 10 days has shown promise in Europe but requires validation in North America. The most commonly used salvage regimen in patients with persistent H. pylori is bismuth quadruple therapy. Recent data suggest that a PPI, levofloxacin, and amoxicillin for 10 days is more effective and better tolerated than bismuth quadruple therapy for persistent H. pylori infection, though this needs to be validated in the United States. (Am J Gastroenterol 2007;102:1808‐1825)
A Highly Compatible Architecture Design for Optimum FPGA to Structured-ASIC Migration

Structured-ASIC design provides a mid-way point between FPGA and cell-based ASIC design for performance, area and power, but suffers from the same increasing verification burden associated with cell-based design. In this paper we address a structured ASIC architecture fabric directly tie to FPGA prototype and functional in-system verification with a clean migration path to structured ASIC. Our goal is to leverage the power/delay/area benefits of structured ASIC technology vs. FPGA with a simple flow which maintains the benefits of FPGAs for ease of test, prototyping, characterization and pre-verification. We will go over the introduction of FPGA to structured-ASIC migration, the architecture of the logic fabric follow by the Lcell to Hcell mapping methodology which can eliminate the need of complicated verification effort and overview of the CAD flow.
STUDIES ON BACTERIEMIA : III. THE BLOOD STREAM CLEARANCE OF ESCHERICHIA COLI IN RABBITS

Large numbers of E. coli were rapidly removed from the blood stream of rabbits at rates which initially paralleled the removal of similar numbers of staphylococci. Splanchnic tissues removed approximately two-thirds of the circulating bacilli in transit through the liver and spleen. In contrast to the cessation of splanchnic trapping noted 20 to 40 minutes following the injection of staphylococci, splanchnic trapping of E. coli continued unchanged for 3 to 5 hours unless the splanchnic tissues were dearly reseeding the blood stream. This resulted in the continued disappearance of E. coli over a 60 to 90 minute period, and differed from the constant bacteriemia maintained beyond 20 minutes after the injection of staphylococci. Some of the differences in the initial clearance of these two microorganisms appeared to relate to differences in host leukocyte-bacterium relationships. In vitro studies indicated that E. coli were rapidly killed following ingestion by rabbit polymorphonuclear leukocytes. Staphylococci survive such ingestion. The injection of E. coli was followed by a prolonged granulocytopenia with evidence of sequestration of granulocytes within the pulmonary vascular bed. The injection of staphylococci was followed by a transient leukopenia, with rapid return of granulocytes to the circulation (15). It appears probable that E. coli ingested by sequestered leukocytes are destroyed within the cell, and that leukocytes do not reenter the circulation containing living E. coli. Such intraleukocytic residence in the blood stream has been shown to be of possible importance in the maintenance of staphylococcal bacteriemia (14). An increasing E. coli bacteriemia occurred rapidly after the initial clearance period, indicating that many sequestered bacilli remained viable. Increasing bacteriemia also occurs 3 to 5 hours after the injection of staphylococci. The bacterial or host cell mechanisms which allow this secondary resurgence of bacterial populations are currently under investigation.
Infant Colic Syndrome—Maternal Fantasies of Aggression and Infanticide

This study examined the impact of infant colic on the emotional state of the mother. Subjects were 23 pairs of mothers and their colicky infants. Structured interviews were conducted with mothers to elicit details around the colic episode and included (1) the emotional state experienced by the mother, (2) the quality and content of the mother's fantasies in response to her infant, and (3) the emotional impact on the parents. Explicit aggressive thoughts and fantasies were revealed by 16 (70%) of the mothers while six (26%) admitted thoughts of infanticide during their infant's colic episodes, a finding notable because previously this has not been documented in medical literature. All mothers experienced physical and psychological symptoms in response to their infant's colic. More than 90% of the mothers with a colicky infant experienced significant marital tension and disruption in their social contacts. The findings suggest that physician receptivity and skill in uncovering the physical and psychological impact of colic on parents is essential for the physical and emotional well-being of the family. Active support and counseling by physicians is critical to diminish any potential for abuse and infanticide in these infants.
Photosynthetic Efficiency of CAM Plants in Relation to C3 and C4 Plants

An investigation of CAM with the use of the gas transfer equations, \({\rm{T = D\Delta /}}{{\rm{R}}_{\rm{a}}}{\rm{ + }}{{\rm{R}}_{\rm{s}}}\) and \({\rm{P = D'\Delta '/}}{{\rm{R}}_{\rm{a}}}{\rm{ + }}{{\rm{R}}_{\rm{s}}}{\rm{ + }}{{\rm{R}}_{\rm{m}}}\) suggests that CAM is adaptive to xeric conditions and similar to the C4 pathway. Transpiration ratios (TR) are low and on the order of 150 whereas for C4-piants and C3-plants they average 300 and 600 respectively. Carbon assimilation efficiency (CAE) estimates, the ratio of P to Pmax where Pmax = \( D'\Delta \sim '({{R}_{a}} + {{R}_{s}}) \) or the estimated CO2 assimilation rate at Rm = O, in the dark are about 0.7–0.9 similarly to C4 plants but unlike C3 estimates of 0.2 to 0.3. We have concluded that the CAM pathway for plants in an arid, desert environment has a two-fold interpretation: primarily, immediately after periods of rainfall and consequent high plant water potentials, nocturnal acidification rates are highest. Minimum TR of 25–70 and maximum CAE values of 0.75–0.82 occur. The level of acid metabolism decreases with decreasing water potential. Secondly, during periods of drought and water potentials of −15 to −20 bars a reduced, but steady level of acidification occurs by the reassimilation of endogenous CO2. Perhaps, further, these plants can shift from the CAM option to the C3 option under extended, favorable conditions.
SPIRIT: a runtime system for distributed irregular tree applications

Repeated, depth-first traversal of trees is a common algorithmic pattern in an important set of applications from diverse domains such as cosmological simulations, data mining, and computer graphics. As these applications operate over massive data sets, it is often necessary to distribute the trees to process all of the data.In this work, we introduce SPIRIT, a runtime system to ease the writing of distributed tree applications. SPIRIT automates the challenging tasks of tree distribution, optimizing communication and parallelizing independent computations. The common algorithmic pattern in tree traversals is exploited to effectively schedule parallel computations and improve locality. As a result, pipeline parallelism in distributed traversals is identified, which is complemented by load-balancing, and locality-enhancing, message aggregation optimizations. Evaluation of SPIRIT on tree traversal in Point Correlation (PC) shows a scalable system, achieving speedups upto 38x on a 16-node, 64 process system compared to a 1-node, baseline configuration. We also find that SPIRIT results in substantially less communication and achieves significant performance improvements over implementations in other distributed graph systems.
Thermodynamics of Phase Coexistence and Metal–Nonmetal Transition in Mercury: Assessment of Effective Potentials via Expanded Wang–Landau Simulations

We present molecular simulation results on the thermodynamics of phase transitions (specifically, the vapor-liquid and metal-nonmetal transitions) in mercury, as predicted by effective potential models. We use a recently developed method, known as Expanded Wang-Landau simulations, to determine the grand-canonical partition function of systems of mercury atoms. Using the statistical mechanics formalism, we are then able to determine all thermodynamic properties of the system, including the Gibbs free energy and entropy. Prior experimental and theoretical work has emphasized the strong interplay between the vapor-liquid coexistence and the metal-nonmetal transition. We therefore start by assessing the accuracy of the effective potentials considered in this work through a comparison to the available experimental data. We then analyze the thermodynamics of the nonmetal liquid-metal liquid transition, characterized by sharp variations in the rate of change of Gibbs free energy and enthalpy as a function of density. We also identify a crossover density (10.5 g/cm(3)) consistent with the results of recent ab initio calculations and with the experiment.
Ross Versus Non-Ross Aortic Valve Replacement in Children: A 22-Year Single Institution Comparison of Outcomes.

Background The Ross aortic valve replacement (AVR) has been the AVR of choice for children at our center since 1993. Absence or inadequate quality of the pulmonary valve or, less commonly, family or surgeon preference caused us to select an alternative AVR prosthesis for some children. This review compares the outcomes of 42 children who received a non-Ross AVR with 115 children undergoing Ross root replacement at our institution during the most recent 22 years. Methods A retrospective chart review of the 42 pediatric non-Ross AVRs was compared with 115 Ross AVRs. The mean age at AVR was 11.0 ± 6.5 years (range, 1 month to 18 years) for the non-Ross and 11.4 ± 5.5 years (range, 6 weeks to 18 years) for the Ross groups. Follow-up was 7.8 ± 6.2 years for the Ross group and 8.7 ± 6.5 years for the non-Ross group. The Ross AVR technique was modified in 2000; these modifications were applied to 72 patients (63%) of the total Ross AVR group. Results All-cause early and late mortality of the non-Ross AVR group was 17% compared with 4% for the Ross cohort ( p = 0.017). The actuarial survival rate at 20 years for the non-Ross AVR group was 81% compared with 94% for the Ross group ( p = 0.018). Reintervention rate was 29% (12/38) in the non-Ross group and 28% (32/115) in the entire Ross group (60% [26/43] before 2000, and 8% [6/72] after 2000). Thromboemboli, bleeding, and endocarditis occurred in 2.4%, 1.4%, and 10% in the non-Ross group compared with 0.9%, 2.6%, and 1.7% in the Ross AVR group ( p = 0.46, 0.01, and 0.02), respectively. Patients in the non-Ross group had a significantly higher recurrent or persistent aortic valve gradient (>20 mm Hg) than did patients in the Ross group at most recent follow-up ( p Conclusions Lower mortality, valve-related complications, and better hemodynamics were seen after the Ross AVR than with other types of AVR prostheses. The Ross AVR remains the treatment of choice for children who have an adequate pulmonary valve. Reoperation for Ross root dilatation, regurgitation, or both (only 6% since our modifications in 2000) has markedly reduced the main drawbacks of this AVR technique. The Ross AVR affords the growing child the advantages of a growing, autologous, viable valve substitute and eliminates the lifelong disadvantages of mechanical and xenograft valves.