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N-(4-chlorobenzyl)triflupromazinium chloride, a known antitubercular agent, has been found to also be active against HSV-1. A preliminary structure-activity relation has been explored to determine which groups are crucial to viral inhibition. Antiviral assessments such as GFP reduction, plaque reduction, treatment timing and wash-out studies have also been probed to determine a mode of action for QPD-1. Based on this preliminary data, it appears that QPD-1 is a reversible inhibitor, suspected to inhibit early stages of viral replication of HSV-1 at 50 μM, equipotent to acyclovir.

We thank the Scottish Universities Life Sciences Alliance (SULSA) and the Scottish Overseas Research Student Awards Scheme of the Scottish Funding Council (SFC) for financial support. Background: We investigate the relationships between the EC (Enzyme Commission) class, the associated chemical reaction, and the reaction mechanism by building predictive models using Support Vector Machine (SVM), Random Forest (RF) and k-Nearest Neighbours (kNN). We consider two ways of encoding the reaction mechanism in descriptors, and also three approaches that encode only the overall chemical reaction. Both cross-validation and also an external test set are used. Results: The three descriptor sets encoding overall chemical transformation perform better than the two descriptions of mechanism. SVM and RF models perform comparably well; kNN is less successful. Oxidoreductases and hydrolases are relatively well predicted by all types of descriptor; isomerases are well predicted by overall reaction descriptors but not by mechanistic ones. Conclusions: Our results suggest that pairs of similar enzyme reactions tend to proceed by different mechanisms. Oxidoreductases, hydrolases, and to some extent isomerases and ligases, have clear chemical signatures, making them easier to predict than transferases and lyases. We find evidence that isomerases as a class are notably mechanistically diverse and that their one shared property, of substrate and product being isomers, can arise in various unrelated ways. The performance of the different machine learning algorithms is in line with many cheminformatics applications, with SVM and RF being roughly equally effective. kNN is less successful, given the role that non-local information plays in successful classification. We note also that, despite a lack of clarity in the literature, EC number prediction is not a single problem; the challenge of predicting protein function from available sequence data is quite different from assigning an EC classification from a cheminformatics representation of a reaction. Publisher PDF

The mechanism of phospholipidosis is still not well understood. Numerous different mechanisms have been proposed, varying from direct inhibition of the breakdown of phospholipids to the binding of a drug compound to the phospholipid, preventing breakdown. We have used a probabilistic method, the Parzen-Rosenblatt Window approach, to build a model from the ChEMBL dataset which can predict from a compound's structure both its primary pharmaceutical target and other targets with which it forms off-target, usually weaker, interactions. Using a small dataset of 182 phospholipidosis-inducing and non-inducing compounds, we predict their off-target activity against targets which could relate to phospholipidosis as a side-effect of a drug. We link these targets to specific mechanisms of inducing this lysosomal build-up of phospholipids in cells. Thus, we show that the induction of phospholipidosis is likely to occur by separate mechanisms when triggered by different cationic amphiphilic drugs. We find that both inhibition of phospholipase activity and enhanced cholesterol biosynthesis are likely to be important mechanisms. Furthermore, we provide evidence suggesting four specific protein targets. Sphingomyelin phosphodiesterase, phospholipase A2 and lysosomal phospholipase A1 are shown to be likely targets for the induction of phospholipidosis by inhibition of phospholipase activity, while lanosterol synthase is predicted to be associated with phospholipidosis being induced by enhanced cholesterol biosynthesis. This analysis provides the impetus for further experimental tests of these hypotheses. Publisher PDF

Epitheliocystis, a disease characterised by cytoplasmic bacterial inclusions (cysts) in the gill and less commonly skin epithelial cells, has been reported in many marine and freshwater fish species and may be associated with mortality. Previously, molecular and ultrastructural analyses have exclusively associated members of the Chlamydiae with such inclusions. Here we investigated a population of farmed Atlantic salmon from the west coast of Norway displaying gill epitheliocystis. Although ‘Candidatus Piscichlamydia salmonis’, previously reported to be present in such cysts, was detected by PCR in most of the gill samples analysed, this bacterium was found to be a rare member of the gill microbiota, and not associated with the observed cysts as demonstrated by fluorescence in situ hybridization assays. The application of a broad range 16 S rRNA targeted PCR assay instead identified a novel betaproteobacterium as an abundant member of the gill microbiota. Fluorescence in situ hybridization demonstrated that this bacterium, tentatively classified as ‘Candidatus Branchiomonas cysticola’, was the cyst-forming agent in these samples. While histology and ultrastructure of ‘Ca. B. cysticola’ cysts revealed forms similar to the reticulate and intermediate bodies described in earlier reports from salmon in seawater, no elementary bodies typical of the chlamydial developmental cycle were observed. In conclusion, this study identified a novel agent of epitheliocystis in sea-farmed Atlantic salmon and demonstrated that these cysts can be caused by bacteria phylogenetically distinct from the Chlamydiae.

We investigate the suggestion that aromatic rings can act as hydrogen-bond acceptors in proteins, by an analysis of 55 non-homologous high-resolution protein chain structures. Approximately 10% of interactions between sp2 hybridized nitrogen atoms, from either side-chains or main-chains, and phenylalanine or tyrosine rings have the nitrogen atom positioned above the ring. In these instances, however, the sp2 nitrogen atoms tend to form stacked interactions with the aromatic rings, these geometries outnumbering amino/aromatic hydrogen bonds by around 2.5:1. The statistically expected distribution, in contrast, would have only a few stacked structures and many more with larger interplanar angles, corresponding to amino/aromatic hydrogen bonds. Thus, although we do find some of these unconventional hydrogen bonds, they are clearly disfavoured relative to stacked geometries. In stacked geometries, the nitrogen-bearing groups are observed to fulfil their hydrogen-bonding potential by forming conventional, energetically stronger, hydrogen bonds with other groups in protein or solvent. This may explain the favourability of stacking. Thus, although ab initio calculations of the gas phase interaction energies for three model systems generally favour the amino/aromatic hydrogen-bonded over the stacked geometries, the differences are small enough to be outweighed easily by the additional conventional hydrogen bonding in stacked structures.

Study Design. Prospective single-center case cohort study. Objective. Evaluation of clinical and radiographic outcomes of a consecutive 122-patient cohort with discogenic back pain, at 2 - to 10-year follow-up periods, treated by a single surgeon, with CHARITE® Artificial Disc (DePuy Spine, Raynham, MA, USA). Summary of Background Data. Minimum two-year clinical and radiographic Level 1 data for the first lumbar artificial disc, the CHARITE® Artificial Disc, has recently been published, demonstrating sustained clinical benefit of the device for the treatment of degenerative disc disease (DDD). Methods. Patients were assessed preoperatively using clinical outcome measures, including Visual Analogue Score (VAS) back and leg, Oswestry Disability Index (ODI), Short Form - 36 (SF-36), and Roland-Morris Questionnaires (RMDQ), and further assessed postoperatively, 3-months, 6-months, 12-months, and yearly thereafter. Results. Average follow-up was 44.9±23.3 months (n = 122). The median age at surgery was 43.0±9.0 years. Preoperative diagnosis included DDD in 118 (96.7%) and internal disc disruption (IDD) in 4 (3.3%). Surgery was performed at L5-S1 in 96 (77.9%) patients and at L4-5 in 27 (22.1%). Statistically significant clinical improvements from baseline were observed on VAS (back and leg), ODI, SF-36 PCS, SF-36 MCS, and RMDQ from 3 months onwards. Back VAS scores decreased from 78.2±21.3 preoperatively to 21.9±27.8 by final follow-up. ODI scores decreased from 51.1±17.3 to 16.2±17.9 at last follow-up. The RMDQ scores also decreased, from 16.7±4.7 to 4.2±5.8. SF-36 PCS and MCS increased from 25.7±11.0 to 46.4±10.3 for PCS and from 35.5±17.4 to 51.6±10.8 for MCS. Patient satisfaction surveys indicated that 90.56% patients rated their satisfaction with the surgery as “excellent” or “good” at 2 years. Range of motion averaged 8.6°±3.5° (median: 8.0°) at the last follow-up time point. Conclusions. Outcomes verify the clinical efficacy of total disc replacement (TDR) for treatment of discogenic back pain with or without radiculopathy. The outcomes instruments demonstrated statistically significant improvements from 3 months onwards.

A study of four marine salmon farms was undertaken in Ireland in 2008, with a focus on gill health and disease. All four farms suffered severe gill disease resulting in mortalities and, in some cases, failure to thrive. The aetiology of the gill pathologies in some cases was associated with small gelatinous zooplankton and bacteria, but also involved epitheliocystis and parasites such as marine costia (Ichthyobodo species) and amoebae (Neoparamoeba species). Treatments with oral broad-spectrum antibiotics and/or freshwater baths had equivocal benefits. There was a strong association of susceptibility to gill disease with one genetic strain of salmon.

This article reviews the use of informatics and computational chemistry methods in medicinal chemistry, with special consideration of how computational techniques can be adapted and extended to obtain more and higher-quality information. Special consideration is given to the computation of protein–ligand binding affinities, to the prediction of off-target bioactivities, bioactivity spectra and computational toxicology, and also to calculating absorption-, distribution-, metabolism- and excretion-relevant properties, such as solubility.

We present a Trusted Platform Module (TPM) application protocol that detects a certain man in the middle attack where an adversary captures and replaces a legitimate computing platform with an imposter that forwards platform authentication challenges to the captive over a high speed data link. This revised Cuckoo attack allows the imposter to satisfy a user's query of platform integrity, tricking the user into divulging sensitive information to the imposter. Our protocol uses an ordinary smart card to verify the platform boot integrity through TPM quote requests, and to verify TPM proximity by measuring TPM tickstamp times required to answer the quotes. Quotes not answered in an expected amount of time may indicate the presence of an imposter's data link, revealing the Cuckoo attack. We describe a timing model for the Cuckoo attack, and summarize experimental results that demonstrate the feasibility of using timing to detect the Cuckoo attack over practical levels of adversary link speeds.

The rapid increase in the number of high-quality protein structures provides an expanding knowledge resource about interactions involved in stabilizing protein three-dimensional structures and the complexes they form with other molecules. In this paper we first review the results of some recent analyses of protein structure, including restrictions on local conformation, and a study of the geometry of hydrogen bonds. Then we consider how such empirical data can be used as a test bed for energy calculations, by using the observed spatial distributions of side chain/atom interactions to assess three different methods for modelling atomic interactions in proteins. We have also derived a new empirical solvation potential which aims to reproduce the hydrophobic effect. To conclude we address the problem of molecular recognition and consider what we can deduce about the interactions involved in the binding of peptides to proteins.

Gastric fundoplication (GF) for gastroesophageal reflux disease (GERD) may protect against the progression of chronic rejection in lung transplant (LT) recipients. However, the association of GERD with acute rejection episodes (ARE) is uncertain. This study sought to identify if ARE were linked to GERD in LT patients.This single-center retrospective observational study, of patients transplanted from January 1, 2000, to January 31, 2009, correlated results of pH probe testing for GERD with ARE (≥International Society for Heart and Lung Transplantation A1 or B1). We compared the rates of ARE among patients with GERD (DeMeester Score14.7) versus without GERD as number of ARE per 1,000 patient-days after LT. Patients undergoing GF prior to LT were excluded.The analysis included 60 LT subjects and 9,249 patient-days: 33 with GERD versus 27 without GERD. We observed 51 ARE among 60 LT recipients. The rate of ARE was highest among patients with GERD: 8.49 versus 2.58, an incidence density ratio (IDR) of 3.29 (P = .00016). Upon multivariate negative binomial regression modeling, only GERD was associated with ARE (IDR 2.15; P = .009). Furthermore, GERD was associated with multiple ARE (36.4% vs 0%; P.0001) and earlier onset compared with patients without GERD: ARE proportion at 2 months was 0.55 versus 0.26 P = .004).In LT recipients, GERD was associated with a higher rate, multiple events, and earlier onset of ARE. The efficacy of GF to reduce ARE among patients with GERD needs further evaluation.

Thiomethylation of indole and haloindoles has been achieved via their zinc salts. This one-pot reaction uses methyl disulfide as electrophile. Isolation of thiomethylated indole products in moderate yields requires the addition of a thiol (e.g., cysteine hydrochloride) during aqueous workup, facilitating the displacement of the thiomethylated product from a water-insoluble zinc salt.

Deoxypseudophrynaminol, 1 , is a potent antibacterial agent that inhibits the in vitro growth of vancomycin-resistant Enterococci and methicillin-resistant Staphylococcus aureus with MIC values ⩽40 μg/mL.

Intracellular inclusions containing chlamydia-like organisms are frequently observed in the gill epithelial cells of Atlantic salmon, Salmo salar L., cultured in fresh water in Ireland. In this study, the causative agent was identified in four separate freshwater sites, using 16s rRNA sequencing, as 'Candidatus Clavochlamydia salmonicola'. Histopathology and real-time (RT) PCR were used to further assess infections. The prevalence of infection ranged from 75-100% between sites and infection intensity was highly variable. No significant lesions were associated with these infections. As a diagnostic tool, RT-PCR proved marginally more sensitive than histopathology. The fate of 'Candidatus Clavochlamydia salmonicola' in Atlantic salmon post-seawater transfer was investigated in a 12-week marine longitudinal study. Both RT-PCR and histopathological examination indicate that the organism disappears from the gills 4-6 weeks post-transfer.

Selective human butyrylcholinesterase (BChE) inhibitors such as cymserine have shown considerable promise for restoring cognition in Alzheimer's disease. Recently, (-)-debromoflustramine B, 1, a hexahydropyrrolo-[2,3-b]indole natural product isolated from the marine bryozoan Flustra foliacea, has demonstrated micromolar potency as a selective BChE inhibitor. Since (±)-demethyldebromoflustramine B, (±)-2, has an even lower IC(50), and the active enantiomer is (-)-2, derivatives of (-)-2 were constructed in silico and docked into the active site of BChE. Several compounds exhibited improved inhibitor potency and could be candidates for future synthesis and in vitro enzyme inhibition study.

Dietary fluid and sodium intake may influence the risk for vasoocclusive events in persons with sickle cell anemia (SCA). The objective of this study was to examine the dietary intake of water and sodium in children and adolescents with SCA and identify possible factors influencing intake. We compared water (mL) and sodium (mg) intake in 21 patients with SCA, aged 5 to 18 years, to reported adequate intake for water, daily fluid requirement, upper limit for sodium, and National Health and Nutrition Examination Survey 2005 to 2006 data for sodium, and sociodemographic factors. Dietary intake from 3-day food records was evaluated retrospectively. Median water intake was significantly lower than adequate intake, and median sodium intake was significantly higher than sodium upper limit. Sociodemographic factors were not associated with dietary water or sodium intake. Our results suggest that children and adolescents with SCA would benefit from education regarding increasing fluid intake and limiting high sodium foods.

Functionally analogous enzymes are those that catalyze similar reactions on similar substrates but do not share common ancestry, providing a window on the different structural strategies nature has used to evolve required catalysts. Identification and use of this information to improve reaction classification and computational annotation of enzymes newly discovered in the genome projects would benefit from systematic determination of reaction similarities. Here, we quantified similarity in bond changes for overall reactions and catalytic mechanisms for 95 pairs of functionally analogous enzymes (non-homologous enzymes with identical first three numbers of their EC codes) from the MACiE database. Similarity of overall reactions was computed by comparing the sets of bond changes in the transformations from substrates to products. For similarity of mechanisms, sets of bond changes occurring in each mechanistic step were compared; these similarities were then used to guide global and local alignments of mechanistic steps. Using this metric, only 44% of pairs of functionally analogous enzymes in the dataset had significantly similar overall reactions. For these enzymes, convergence to the same mechanism occurred in 33% of cases, with most pairs having at least one identical mechanistic step. Using our metric, overall reaction similarity serves as an upper bound for mechanistic similarity in functional analogs. For example, the four carbon-oxygen lyases acting on phosphates (EC 4.2.3) show neither significant overall reaction similarity nor significant mechanistic similarity. By contrast, the three carboxylic-ester hydrolases (EC 3.1.1) catalyze overall reactions with identical bond changes and have converged to almost identical mechanisms. The large proportion of enzyme pairs that do not show significant overall reaction similarity (56%) suggests that at least for the functionally analogous enzymes studied here, more stringent criteria could be used to refine definitions of EC sub-subclasses for improved discrimination in their classification of enzyme reactions. The results also indicate that mechanistic convergence of reaction steps is widespread, suggesting that quantitative measurement of mechanistic similarity can inform approaches for functional annotation., Author Summary When species evolve, their genes duplicate and diverge to allow for adaptation of their functional repertoires to the changing environment. In this scenario, unrelated genes can convergently evolve to produce proteins with the same molecular function, termed “functionally analogous.” A quantitative determination of the reaction similarities among functionally analogous enzymes could provide insight about the different structural solutions nature has used to evolve similar catalysts. Bond changes between substrates and products, and between successive reaction intermediates, were used to compare the reactions catalyzed and the mechanisms of catalysis for 95 pairs of functionally analogous enzymes. Less than half of the reactions catalyzed by unrelated enzymes, but defined as similar by the Enzyme Commission (EC) classification, are similar in terms of bond changes, suggesting that this classification often fails to capture quantitative differences between many enzyme reactions. Furthermore, we addressed for the first time whether the chemical mechanisms by which similar overall reactions are achieved in functional analogs are also similar. We conclude that convergence of reaction is often accompanied by convergence of chemical mechanism. These results will be useful for classifying enzymes, guiding functional annotation of newly determined enzyme sequences and structures and for informing the engineering of enzymes with new functions.

Development of primary graft dysfunction (PGD) is associated with poor outcomes after transplantation. We hypothesized that Receptor for Advanced Glycation End-products (RAGE) levels in donor lungs is associated with the development of PGD. Furthermore, we hypothesized that RAGE levels would be increased with PGD in recipients after transplantation. We measured RAGE in bronchoalveolar lavage fluid (BALf) from 25 donors and 34 recipients. RAGE was also detected in biopsies (transbronchial biopsy) from recipients with and without PGD. RAGE levels were significantly higher in donor lungs that subsequently developed sustained PGD versus transplanted lungs that did not display PGD. Donor RAGE level was a predictor of recipient PGD (odds ratio = 1.768 per 0.25 ng/mL increase in donor RAGE level). In addition, RAGE levels remained high for 14 days in those recipients that developed severe graft dysfunction. Recipients may be at higher risk for developing PGD if they receive transplanted organs that have higher levels of soluble RAGE prior to explantation. Moreover, the clinical and pathologic abnormalities associated with PGD posttransplantation are associated with increased RAGE expression. These findings also raise the possibility that targeting the RAGE signaling pathway could be a novel strategy for treatment and/or prevention of PGD.

Absolute absorption cross sections of nitrogen dioxide were measured with a resolution of 0.008 nm in 470–490, 520–534, 588–601, and 603–616 nm spectral regions at temperatures of 295, 573, and 673 K. An absolute error of ±10% is due principally to uncertainty in the NO2 concentration. Absorption cross sections were also measured at these temperatures in the 450–650 nm spectral region with a resolution of 0.075 nm with an error of ±10%. All data were corrected for thermal decomposition of NO2 at the elevated temperatures. The spectral features show broadening at elevated temperatures consistent with the breakdown of ΔK selection rules for higher rotational levels.

Thoracic aortic aneurysms (TAA) have remained a formidable operative challenge. Open surgical techniques have been associated with high rates of morbidity and mortality. Thoracic endovascular aneurysm repair (TEVAR) has produced results equal to or better than the traditional open surgical approach. This report presents a patient with a complex thoracic aortic aneurysm involving the ascending, transverse, and proximal descending thoracic aorta. This patient was successfully managed by the creation of Landing Zone-Zero, arch vessel debranching, and endografting the entire aortic arch without the need for hypothermic circulatory arrest or cerebral perfusion strategies. Computer tomographic images demonstrate the repair to be durable at 18 months.

Type B aortic dissections have remained a difficult management problem. Open surgical techniques have had a very high perioperative mortality, and medical management has not produced satisfactory long-term results. Endovascular grafting techniques may provide a favorable alternative therapy. However, there are currently no endovascular stents approved by the United States Food and Drug Administration for treating Type B aortic dissections. Also, there is very little data from United States centers on the long-term efficacy of endovascular stents used "off-label" to treat aortic dissections. This report discusses the care of a patient with a Type B aortic dissection successfully treated by an endograft in a community hospital. In addition, serial follow-up computerized tomography demonstrates the durability of this repair at three years.

Chronic hypoxia contributes to pulmonary hypertension through complex mechanisms that include enhanced NADPH oxidase expression and reactive oxygen species (ROS) generation in the lung. Stimulation of peroxisome proliferator-activated receptor gamma (PPARgamma) reduces the expression and activity of NADPH oxidase. Therefore, we hypothesized that activating PPARgamma with rosiglitazone would attenuate chronic hypoxia-induced pulmonary hypertension, in part, through suppressing NADPH oxidase-derived ROS that stimulate proliferative signaling pathways. Male C57Bl/6 mice were exposed to chronic hypoxia (CH, Fi(O2) 10%) or room air for 3 or 5 weeks. During the last 10 days of exposure, each animal was treated daily by gavage with either the PPARgamma ligand, rosiglitazone (10 mg/kg/d) or with an equal volume of vehicle. CH increased: (1) right ventricular systolic pressure (RVSP), (2) right ventricle weight, (3) thickness of the walls of small pulmonary vessels, (4) superoxide production and Nox4 expression in the lung, and (5) platelet-derived growth factor receptor beta (PDGFRbeta) expression and activity and reduced phosphatase and tensin homolog deleted on chromosome 10 (PTEN) expression. Treatment with rosiglitazone prevented the development of pulmonary hypertension at 3 weeks; reversed established pulmonary hypertension at 5 weeks; and attenuated CH-stimulated Nox4 expression and superoxide production, PDGFRbeta activation, and reductions in PTEN expression. Rosiglitazone also attenuated hypoxia-induced increases in Nox4 expression in pulmonary endothelial cells in vitro despite hypoxia-induced reductions in PPARgamma expression. Collectively, these findings indicate that PPARgamma ligands attenuated hypoxia-induced pulmonary vascular remodeling and hypertension by suppressing oxidative and proliferative signals providing novel insights for mechanisms underlying therapeutic effects of PPARgamma activation in pulmonary hypertension.

The MACiE database contains 223 distinct step-wise enzyme reaction mechanisms and holds representatives from each EC sub-subclass where there is a crystal structure and sufficient evidence in the literature to support a mechanism. Each catalytic step of every reaction sequence in MACiE is fully annotated so that it includes the function of the catalytic residues involved in the reaction and the mechanism by which substrates are transformed into products. Using MACiE as a knowledge base, we have seen that the top 10 most catalytic residues are histidine, aspartate, glutamate, lysine, cysteine, arginine, serine, threonine, tyrosine and tryptophan. Of these only seven (cysteine, histidine, aspartate, lysine, serine, threonine and tyrosine) dominate catalysis and provide essentially five functional roles that are essential. Stabilisation is the most common and essential role for all classes of enzyme, followed by general acid/base (proton acceptor and proton donor) functionality, with nucleophilic addition following closely behind (nucleophile and nucleofuge). We investigated the occurrence of these residues in MACiE and the Catalytic Site Atlas and found that, as expected, certain residue types are associated with each functional role, with some residue types able to perform diverse roles. In addition, it was seen that different EC classes of enzyme have a tendency to employ different residues for catalysis. Further, we show that whilst the differences between EC classes in catalytic residue composition are not immediately obvious from the general classes of Ingold mechanisms, there is some weak correlation between the mechanisms involved in a given EC class and the functions that the catalytic amino acid residues are performing. The analysis presented here provides a valuable insight into the functional roles of catalytic amino acid residues, which may have applications in many aspects of enzymology, from the design of novel enzymes to the prediction and validation of enzyme reaction mechanisms.

Toxicology has the goal of ensuring the safety of humans, animals and the environment. Computational toxicology is an area of active development and great potential. There are tangible reasons for the emerging interest in this discipline from academia, industry, regulatory bodies and governments.Pharmaceuticals, personal health care products, nutritional ingredients and products of the chemical industries are all potential hazards and need to be assessed. Toxicological tests for these products are costly, frequently use laboratory animals and are time-consuming. This delays end-user access to improved products or, conversely, the timely withdrawal of dangerous substances from the market. The aim of computational toxicology is to accelerate the assessment of potentially dangerous substances through in silico models.In this review, we provide an overview of the development of models for computational toxicology. Addressing the significant divide between the experimental and computational worlds-believed to be a prime hindrance to computational toxicology-we briefly consider the fundamental issue of toxicological data and the assays they stem from. Different kinds of models that can be built using such data are presented: computational filters, models for specific toxicological endpoints and tools for the generation of testable hypotheses.

BACKGROUND Using an experimental model of airway fibrosis following lung transplantation, we recently showed that chronic alcohol ingestion by donor rats amplifies airway fibrosis in the recipient. Associated with alcohol-mediated amplification of airway fibrosis is increased transforming growth factor beta-1(TGFbeta(1)) and alpha-smooth muscle actin expression. Other studies have shown that interleukin-13 (IL-13) modulates TGFbeta(1) signaling during experimentally-induced airway fibrosis. Therefore, we hypothesized that IL-13 is a component of alcohol-mediated amplification of pro-fibrotic mediators in the alcoholic lung. METHODS To test this hypothesis, we analyzed tracheal epithelial cells and type II alveolar cells from control- or alcohol-fed rats, alcohol-treated mouse lung fibroblasts, and human bronchial epithelial cells in vitro for expression of various components of the IL-13 signaling pathway. Signaling via the IL-13 pathway was assessed by measuring levels of phosphorylated signal transducers and activators of transcription-6 (STAT6). In addition, we performed heterotopic tracheal transplantation using control-fed and alcohol-fed donor rats and analyzed tracheal allografts for expression of components of the IL-13 signaling pathway by RT-PCR and immunocytochemical analyses. RESULTS Interleukin-13 expression was detected in type II alveolar epithelial cells and human bronchial epithelial cells, but not in lung fibroblasts. IL-13 expression was decreased in whole lung and type II cells in response to alcohol exposure. In all cell types analyzed, expression of IL-13 signaling receptor (IL-13R alpha(1)) mRNA was markedly increased. In contrast, mRNA and protein expression of the IL-13 decoy receptor (IL-13R alpha(2)) were decreased in all cells analyzed. Exposure to alcohol also increased STAT6 phosphorylation in response to IL-13 and lipopolysaccharide. CONCLUSIONS Data from multiple cell types in the pulmonary system suggest that IL-13 and its receptors play a role in alcohol-mediated activation of pro-fibrotic pathways. Taken together, these data suggest that alcohol primes the airway for increased IL-13 signaling and subsequent tissue remodeling upon injury such as transplantation.

Background Respiratory syncytial virus (RSV) can cause severe lower respiratory tract infection (LRI) and is a risk factor for the development of bronchiolitis obliterans syndrome (BOS) after lung transplantation (LTx). Currently, the most widely used therapy for RSV is inhaled ribavirin. However, this therapy is costly and cumbersome. We investigated the utility of using oral ribavirin for the treatment of RSV infection after LTx. Methods RSV was identified in nasopharyngeal swabs (NPS) or bronchoalveolar lavage (BAL) using direct fluorescent antibody (DFA) in 5 symptomatic LTx patients diagnosed with LRI. Data were collected from December 2005 and August 2007 and included: age; gender; type of LTx; underlying disease; date of RSV; pulmonary function prior to, during and up to 565 days post-RSV infection; need for mechanical ventilation; concurrent infections; and radiographic features. Patients received oral ribavirin for 10 days with solumedrol (10 to 15 mg/kg/day intravenously) for 3 days, until repeat NPS were negative. Results Five patients had their RSV–LRI diagnosis made at a median of 300 days post-LTx. Mean forced expiratory volume in 1 second (FEV 1 ) fell 21% ( p 1 returned to baseline and was maintained at follow-up of 565 days. There were no complications and no deaths with oral therapy. A 10-day course of oral ribavirin cost $700 compared with $14,000 for nebulized ribavirin at 6 g/day. Conclusions Treatment of RSV after LTx with oral ribavirin and corticosteroids is well tolerated, effective and less costly than inhaled ribavirin. Further studies are needed to directly compare the long-term efficacy of oral vs nebulized therapy for RSV.

We have performed Hayes—Stone intermolecular perturbation theory (IMPT) calculations on amide…water and amide…amide complexes in order to estimate the change ΔW in intermolecular interaction energy associated with the hydrogen bond exchange process amide(NH)…water+water…(OC)amide⇔amide(NH)…(OC)amide+water…water. ΔW is found to be small and varies by almost 5 kJ/mol and in sign for the amides formamide, acetamide, N-methyl formamide and N-methyl acetamide. The main variations in the amide hydrogen bond energies occur in the electrostatic and exchange-repulsion contributions. This reflects the variation in the charge distributions of the hydrogen bonding groups between the different amides. Thus, we cannot quantify an isolated hydrogen bond strength with any great accuracy, and care must be used in extrapolating model potentials based on small model systems to peptides and proteins.

Vibration perception threshold (VPT) is increasingly used as a measure of large nerve fibre function in studies of patients with diabetes and in other disorders. In order to establish the influence of age, height, sex, and smoking on VPT values in the normal population and to allow the calculation of accurate age-related percentile charts, 1365 healthy volunteers were studied using a biothesiometer. Measurements were made bilaterally on thumbs, great toes, and over medial malleoli. Multivariate regression analysis confirmed age to be the major determinant of VPT levels at all sites (p less than 0.001). Height was a significant factor for toes and ankles (p less than 0.001) but not thumbs. Sex had no overall effect at toe or thumb but there were differences regarding ankle VPT (p less than 0.01). Log transformation of VPT data produced a linear relationship with age at all sites except at the thumbs in elderly females where there was significant deviation from this model (p less than 0.001) and inverse square root transformation was more appropriate. Smoking had no effect on VPT levels. Age-related centile charts were produced for each site and an easy-to-use computer program was developed to calculate centile values based on raw VPT data, age, height, and sex.

We compared two algorithms for ligand-target prediction, namely, the Laplacian-modified Bayesian classifier and the Winnow algorithm. A dataset derived from the WOMBAT database, spanning 20 pharmaceutically relevant activity classes with 13 000 compounds, was used for performance assessment in 24 different experiments, each of which was assessed using a 15-fold Monte Carlo cross-validation. Compounds were described by different circular fingerprints, ECFP_4 and MOLPRINT 2D. A detailed analysis of the resulting approximately 2.4 million predictions led to very similar measures for overall accuracy for both classifiers, whereas we observed significant differences for individual activity classes. Moreover, we analyzed our data with respect to the numbers of compounds which are exclusively retrieved by either of the algorithmsbut never by the otheror by neither of them. This provided detailed information that can never be obtained by considering the overall performance statistics alone.

Obstructive sleep apnea, characterized by intermittent periods of hypoxemia, is an independent risk factor for the development of pulmonary hypertension. However, the exact mechanisms of this disorder remain to be defined. Enhanced NADPH oxidase expression and superoxide (O2(-).) generation in the pulmonary vasculature play a critical role in hypoxia-induced pulmonary hypertension. Therefore, the current study explores the hypothesis that chronic intermittent hypoxia (CIH) causes pulmonary hypertension, in part, by increasing NADPH oxidase-derived reactive oxygen species (ROS) that contribute to pulmonary vascular remodeling and hypertension. To test this hypothesis, male C57Bl/6 mice and gp91phox knockout mice were exposed to CIH for 8 hours per day, 5 days per week for 8 weeks. CIH mice were placed in a chamber where the oxygen concentration was cycled between 21% and 10% O2 45 times per hour. Exposure to CIH for 8 weeks increased right ventricular systolic pressure (RVSP), right ventricle (RV):left ventricle (LV) + septum (S) weight ratio, an index of RV hypertrophy, and thickness of the right ventricular anterior wall as measured by echocardiography. CIH exposure also caused pulmonary vascular remodeling as demonstrated by increased muscularization of the distal pulmonary vasculature. CIH-induced pulmonary hypertension was associated with increased lung levels of the NADPH oxidase subunits, Nox4 and p22phox, as well as increased activity of platelet-derived growth factor receptor beta and its associated downstream effector, Akt kinase. These CIH-induced derangements were attenuated in similarly treated gp91phox knockout mice. These findings demonstrate that NADPH oxidase-derived ROS contribute to the development of pulmonary vascular remodeling and hypertension caused by CIH.

The authors thank the BBSRC (NMOB and JBOM – grant BB/C51320X/1), Pfizer (DSP and JBOM – through the Pfizer Institute for Pharmaceutical Materials Science), and Unilever for funding FN and JBOM and for supporting the Centre for Molecular Science Informatics. Background We present a novel feature selection algorithm, Winnowing Artificial Ant Colony (WAAC), that performs simultaneous feature selection and model parameter optimisation for the development of predictive quantitative structure-property relationship (QSPR) models. The WAAC algorithm is an extension of the modified ant colony algorithm of Shen et al. (J Chem Inf Model 2005, 45: 1024–1029). We test the ability of the algorithm to develop a predictive partial least squares model for the Karthikeyan dataset (J Chem Inf Model 2005, 45: 581–590) of melting point values. We also test its ability to perform feature selection on a support vector machine model for the same dataset. Results Starting from an initial set of 203 descriptors, the WAAC algorithm selected a PLS model with 68 descriptors which has an RMSE on an external test set of 46.6°C and R2 of 0.51. The number of components chosen for the model was 49, which was close to optimal for this feature selection. The selected SVM model has 28 descriptors (cost of 5, ε of 0.21) and an RMSE of 45.1°C and R2 of 0.54. This model outperforms a kNN model (RMSE of 48.3°C, R2 of 0.47) for the same data and has similar performance to a Random Forest model (RMSE of 44.5°C, R2 of 0.55). However it is much less prone to bias at the extremes of the range of melting points as shown by the slope of the line through the residuals: -0.43 for WAAC/SVM, -0.53 for Random Forest. Conclusion With a careful choice of objective function, the WAAC algorithm can be used to optimise machine learning and regression models that suffer from overfitting. Where model parameters also need to be tuned, as is the case with support vector machine and partial least squares models, it can optimise these simultaneously. The moving probabilities used by the algorithm are easily interpreted in terms of the best and current models of the ants, and the winnowing procedure promotes the removal of irrelevant descriptors. Publisher PDF

A tripartate prodrug of S-trityl-L-cysteine was synthesized and investigated for antiprostatic potency versus the free anticancer agent (S-trityl-L-cysteine) in PSA-secreting cells (LNCap) and non-PSA-secreting cells (PC3). The prodrug did not inhibit cell growth as much as S-trityl-L-cysteine itself, was not selective for PSA-secreting cells, and did not release S-trityl-L-cysteine when treated with cell-free PSA. Interestingly, S-trityl-L-cysteine itself selectively inhibited the growth of LNCap versus PC3 cells.

Problem1. To determine if GM-CSF (granulocyte macrophage-colony stimulating factor) protects against fibrosis using an experimental animal model of tracheal injury. 2. To determine if GM-CSF prevents cytokine-induced expression of fibrotic markers in human bronchial epithelial cells in vitro.MethodsTracheae from GM-CSF (20ng) or vehicle (PBS) treated Sprague-Dawley donor rats were heterotopically transplanted into Fischer 344 recipients. Recipients were treated daily with either GM-CSF or vehicle for seven days. Allografts were harvested on days 14 or 21 post-transplantation and analyzed for luminal collagen deposition and the presence of intact epithelium. In parallel, human bronchial epithelial cells (Beas2B) were treated with pro-fibrotic cytokines (TGFbeta1, IL-13) with or without GM-CSF. Treated cells were harvested and processed for RT-PCR or immunocytochemical analyses for expression of fibrotic markers (alpha smooth muscle actin, fibroblast-specific protein 1).ResultsTracheal allografts treated wi...

The rapid rise in food prices has been a burden on the poor in developing countries, who spend roughly half of their household incomes on food. This paper examines the factors behind the rapid increase in internationally traded food prices since 2002 and estimates the contribution of various factors such as the increased production of biofuels from food grains and oilseeds, the weak dollar, and the increase in food production costs due to higher energy prices. It concludes that the most important factor was the large increase in biofuels production in the U.S. and the EU. Without these increases, global wheat and maize stocks would not have declined appreciably, oilseed prices would not have tripled, and price increases due to other factors, such as droughts, would have been more moderate. Recent export bans and speculative activities would probably not have occurred because they were largely responses to rising prices. While it is difficult to compare the results of this study with those of other studies due to differences in methodologies, time periods and prices considered, many other studies have also recognized biofuels production as a major driver of food prices. The contribution of biofuels to the rise in food prices raises an important policy issue, since much of the increase was due to EU and U.S. government policies that provided incentives to biofuels production, and biofuels policies which subsidize production need to be reconsidered in light of their impact on food prices.

The authors thank the EPSRC and Unilever plc for funding. Background We have introduced a new Hybrid descriptor composed of the MACCS key descriptor encoding topological information and Ballester and Richards' Ultrafast Shape Recognition (USR) descriptor. The latter one is calculated from the moments of the distribution of the interatomic distances, and in this work we also included higher moments than in the original implementation. Results The performance of this Hybrid descriptor is assessed using Random Forest and a dataset of 116,476 molecules. Our dataset includes 5,245 molecules in ten classes from the 2005 World Anti-Doping Agency (WADA) dataset and 111,231 molecules from the National Cancer Institute (NCI) database. In a 10-fold Monte Carlo cross-validation this dataset was partitioned into three distinct parts for training, optimisation of an internal threshold that we introduced, and validation of the resulting model. The standard errors obtained were used to assess statistical significance of observed improvements in performance of our new descriptor. Conclusion The Hybrid descriptor was compared to the MACCS key descriptor, USR with the first three (USR), four (UF4) and five (UF5) moments, and a combination of MACCS with USR (three moments). The MACCS key descriptor was not combined with UF5, due to similar performance of UF5 and UF4. Superior performance in terms of all figures of merit was found for the MACCS/UF4 Hybrid descriptor with respect to all other descriptors examined. These figures of merit include recall in the top 1% and top 5% of the ranked validation sets, precision, F-measure, area under the Receiver Operating Characteristic curve and Matthews Correlation Coefficient. Publisher PDF

In the present paper we combine the Winnow algorithm and an advanced scheme for feature generation into a tool for multiclass classification. The Winnow algorithm, specifically designed in the late 1980s to work well with high-dimensional data, by design ignores most of the irrelevant features for the scoring of each single training/test case. To augment the pool of available molecular features we use the Winnow algorithm in conjunction with a process that creates additional features from a set of given ones. We adapt a technique formerly employed in text classification termed "orthogonal sparse bigrams" and extend the use of that method to the domain of cheminformatics. Using circular molecular fingerprints as initial features, we create "molecular orthogonal sparse bigrams" (MOSBs) and report their successful application to the task of classification of bioactive molecules. Additionally, we introduce a memory-efficient way of bagging individual classifiers, avoiding the need to hold the complete training data set in memory. To compare the performance of our method with published results, we use the Hert data set of 8293 active molecules in 11 classes. We compare our method to Random Forest and find that our method not only is comparable or better in classification accuracy (up to 50% higher in MCC [Matthews correlation coefficient], 98% higher in fraction of correct predictions) but also is quicker to train (by a factor between 2 and 18, depending on the feature generation), more memory efficient, and able to cope more easily with large data sets when we seeded the actives into a pool of 94290 inactive molecules. It is shown that this method can be used with different fingerprints.

We have used Hayes-Stone Intermolecular Perturbation Theory (IMPT) to study the variation with distance and orientation of the various components of the interaction energy of the N H…O = C hydrogen bonded trans- formamide/formaldehyde complex, a model system for hydrogen bonding in proteins. The directionality of the total interaction energy is similar to that of the electrostatic component alone. We have analysed our data in terms of two model atom-atom intermolecular potentials, using an isotropic functional form and an anisotropic one. The anisotropic form gives an excellent representation of the IMPT potential energy surface, considerably better than the isotropic model, and is comprised entirely of theoretically justified, physically meaningful terms.

The first synthesis of (+) pseudophrynaminol, a unique pyrrolo [2,3b] indole recently isolated from the Australian frog Pseudophryne coriacea, is described.

Obliterative bronchiolitis (OB) after lung transplantation is triggered by alloimmunity, but is ultimately mediated by transforming growth factor (TGF)-beta(1)-dependent airway fibrosis.Chronic alcohol use increases TGF-beta(1) expression and renders the lung susceptible to injury. Therefore, we hypothesized that donor alcohol abuse could prime the lung allograft for OB, as many organ donors have a history of alcohol abuse.Tracheas from control and alcohol-fed rats (8 wk) were heterotopically transplanted into recipients with varying degrees of alloimmune mismatch and analyzed for obliterative airway disease severity on Postoperative Day 21.Although donor alcohol ingestion did not increase the number of antigen-presenting cells or infiltrating lymphocytes, it nevertheless increased allograft lumenal collagen content fourfold compared with allografts from control donors. In parallel, alcohol increased TGF-beta(1) and alpha-smooth muscle actin expression in allografts. Alcohol amplified airway disease even in isografts with minor alloimmune mismatches. In contrast, it did not cause any airway disease in isografts in a pure isogenic background, suggesting that a minimal alloimmune response is necessary to trigger alcohol-induced airway fibrosis.Although alloimmune inflammation is required to initiate airway disease, alcohol primes the allograft for greater TGF-beta(1) expression, myofibroblast transdifferentiation, and fibrosis than by alloimmune inflammation alone. This has serious clinical implications, as many lung donors have underlying alcohol abuse that may prime the allograft recipient for subsequent OB.

Airport security and efficiency are both compromised by the process of requiring passengers to remove their shoe. A novel shoe scanner developed at the GE Security San Diego Center of Excellence uses both Quadrupole Resonance (QR) and configuration-sensitive metal detection to identify threats hidden in shoes. The shoe scanner was developed with an open-access chassis and scanning chamber that allows passengers to stand in the system in a natural position during the scanning process. More traditional magnetic resonance systems are closed or partially closed and cannot be used for screening personnel because the scanning chambers confine the object in question. The shoe scanner's novelty lies in a particular chassis geometry that allows both QR and metal screening. The resulting scanning system achieves the same level of performance as a more confining system. The shoe scanner is small enough to allow integration with other sensors such as the GE Itemizer FXTM trace detection system. In fact, the first application of the novel shoe scanner is expected to be as a component in a multi-sensor verification and security system known as the Secure Registered Traveler (SRT) Kiosk. The SRT kiosk is designed to be used as part of the TSA's Registered Traveler Program.

Epidemiological investigations into the pancreas disease (PD) of farmed salmon were conducted on populations of Atlantic salmon reared in Ireland during 2003 and 2004. The investigations surveyed all marine salmon farms operating in Ireland through a detailed questionnaire with follow-up farm visits. Information was gathered on 21 populations of fish in 2003 and 14 populations in 2004. Thirteen of the 21 populations suffered PD in 2003 and 12 of the 14 in 2004. The mean mortality due to PD on affected farms was 18.8% in 2003 and 14.8% in 2004 and the loss of growth due to PD was estimated at 11.4% over the 2-year period. The highest risk periods for outbreaks of PD were early summer and early autumn and the farms most seriously affected by PD mortality were in the western counties of Ireland. Factors which showed an indication of association with a PD outbreak or high mortality during a PD outbreak were: livestock movement to another sea site, high feeding rate prior to any PD outbreak, the presence of another PD positive farm in the same water body, greater than 250 000 fish on a site, a previous history of PD on a site, a high sea lice burden, and sites located in the western regions of Ireland which reared a specific strain of salmon.

The concept of reaction similarity has been well studied in terms of the overall transformation associated with a reaction, but not in terms of mechanism. We present the first method to give a quantitative measure of the similarity of reactions based upon their explicit mechanisms. Two approaches are presented to measure the similarity between individual steps of mechanisms: a fingerprint-based approach that incorporates relevant information on each mechanistic step; and an approach based only on bond formation, cleavage and changes in order. The overall similarity for two reaction mechanisms is then calculated using the Needleman-Wunsch alignment algorithm. An analysis of MACiE, a database of enzyme mechanisms, using our measure of similarity identifies some examples of convergent evolution of chemical mechanisms. In many cases, mechanism similarity is not reflected by similarity according to the EC system of enzyme classification. In particular, little mechanistic information is conveyed by the class level of the EC system.

Representative molecules from 10 classes of prohibited substances were taken from the World Anti-Doping Agency (WADA) list, augmented by molecules from corresponding activity classes found in the MDDR database. Together with some explicitly allowed compounds, these formed a set of 5245 molecules. Five types of fingerprints were calculated for these substances. The random forest classification method was used to predict membership of each prohibited class on the basis of each type of fingerprint, using 5-fold cross-validation. We also used a k-nearest neighbors (kNN) approach, which worked well for the smallest values of k. The most successful classifiers are based on Unity 2D fingerprints and give very similar Matthews correlation coefficients of 0.836 (kNN) and 0.829 (random forest). The kNN classifiers tend to give a higher recall of positives at the expense of lower precision. A naïve Bayesian classifier, however, lies much further toward the extreme of high recall and low precision. Our results suggest that it will be possible to produce a reliable and quantitative assignment of membership or otherwise of each class of prohibited substances. This should aid the fight against the use of bioactive novel compounds as doping agents, while also protecting athletes against unjust disqualification.

The process of deducing the catalytic mechanism of an enzyme from its structure is highly complex and requires extensive experimental work to validate a proposed mechanism. As one step towards improving the reliability of this process, we have gathered statistics describing the typical geometry of catalytic residues with regard to the substrate and one another. In order to analyse residue-substrate interactions, we have assembled a dataset of structures of enzymes of known mechanism bound to substrate, product, or a substrate analogue. Despite the challenges presented in obtaining such experimental data, we were able to include 42 enzyme structures. We have also assembled a separate dataset of catalytic residues which act upon other catalytic residues, using a set of 60 enzyme structures. For both datasets, we have extracted the distances between residues with a given catalytic function and their target moieties. The geometry of residues whose function involves the transfer or sharing of hydrogens (either with substrate or another residue) was analysed more closely. The results showed that the geometry for such productive interactions (prior to the transition state) closely resembles that seen in non-catalytic hydrogen bonds, with distances and angles in the normal expected range. Such statistics provide limits on "expected geometries" for catalytic residues, which will help to identify these residues and elucidate enzyme mechanisms.

Metal–oxide–semiconductor (MOS) capacitors were fabricated on in situ doped n- and p-type Si1−yCy/Si heterostructures grown on Si substrates by chemical vapor deposition. Strained Si1−yCy epitaxial layers with substitutional carbon contents up to 1.6% were studied. High frequency and quasistatic capacitance–voltage (C–V) measurements exhibit well-behaved MOS characteristics, indicating high electronic material quality. Band alignments were extracted from MOS C–V measurements and one-dimensional device simulations performed over a range of temperatures. The conduction band energy of strained Si1−yCy is lower than that of Si by approximately 65 meV for 1 at. % carbon, while the valence band shows negligible offset to Si valence band.

We investigate the classification performance of circular fingerprints in combination with the Naive Bayes Classifier (MP2D), Inductive Logic Programming (ILP) and Support Vector Inductive Logic Programming (SVILP) on a standard molecular benchmark dataset comprising 11 activity classes and about 102,000 structures. The Naive Bayes Classifier treats features independently while ILP combines structural fragments, and then creates new features with higher predictive power. SVILP is a very recently presented method which adds a support vector machine after common ILP procedures. The performance of the methods is evaluated via a number of statistical measures, namely recall, specificity, precision, F-measure, Matthews Correlation Coefficient, area under the Receiver Operating Characteristic (ROC) curve and enrichment factor (EF). According to the F-measure, which takes both recall and precision into account, SVILP is for seven out of the 11 classes the superior method. The results show that the Bayes Classifier gives the best recall performance for eight of the 11 targets, but has a much lower precision, specificity and F-measure. The SVILP model on the other hand has the highest recall for only three of the 11 classes, but generally far superior specificity and precision. To evaluate the statistical significance of the SVILP superiority, we employ McNemar’s test which shows that SVILP performs significantly (p < 5%) better than both other methods for six out of 11 activity classes, while being superior with less significance for three of the remaining classes. While previously the Bayes Classifier was shown to perform very well in molecular classification studies, these results suggest that SVILP is able to extract additional knowledge from the data, thus improving classification results further.