AceCloud: Molecular Dynamics Simulations in the Cloud.

We present AceCloud, an on-demand service for molecular dynamics simulations. AceCloud is designed to facilitate the secure execution of large ensembles of simulations on an external cloud computing service (currently Amazon Web Services). The AceCloud client, integrated into the ACEMD molecular dynamics package, provides an easy-to-use interface that abstracts all aspects of interaction with the cloud services. This gives the user the experience that all simulations are running on their local machine, minimizing the learning curve typically associated with the transition to using high performance computing services.

Kinetic characterization of fragment binding in AmpC ß-lactamase by high-throughput molecular simulations.

Small molecules used in fragment-based drug discovery form multiple, promiscuous binding complexes difficult to capture experimentally. Here, we identify such binding poses and their associated energetics and kinetics using molecular dynamics simulations on AmpC ß-lactamase. Only one of the crystallographic binding poses was found to be thermodynamically favorable; however, the ligand shows several binding poses within the pocket. This study demonstrates free-binding molecular simulations in the context of fragment-to-lead development and its potential application in drug design.

Reranking docking poses using molecular simulations and approximate free energy methods.

Fast and accurate identification of active compounds is essential for effective use of virtual screening workflows. Here, we have compared the ligand-ranking efficiency of the linear interaction energy (LIE) method against standard docking approaches. Using a trypsin set of 1549 compounds, we performed 12,250 molecular dynamics simulations. The LIE method proved effective but did not yield results significantly better than those obtained with docking codes. The entire database of simulations is released.

High-throughput all-atom molecular dynamics simulations using distributed computing.

Although molecular dynamics simulation methods are useful in the modeling of macromolecular systems, they remain computationally expensive, with production work requiring costly high-performance computing (HPC) resources. We review recent innovations in accelerating molecular dynamics on graphics processing units (GPUs), and we describe GPUGRID, a volunteer computing project that uses the GPU resources of nondedicated desktop and workstation computers. In particular, we demonstrate the capability of simulating thousands of all-atom molecular trajectories generated at an average of 20 ns/day each (for systems of approximately 30 000-80 000 atoms). In conjunction with a potential of mean force (PMF) protocol for computing binding free energies, we demonstrate the use of GPUGRID in the computation of accurate binding affinities of the Src SH2 domain/pYEEI ligand complex by reconstructing the PMF over 373 umbrella sampling windows of 55 ns each (20.5 mus of total data). We obtain a standard free energy of binding of -8.7 +/- 0.4 kcal/mol within 0.7 kcal/mol from experimental results. This infrastructure will provide the basis for a robust system for high-throughput accurate binding affinity prediction.

Global Research Alliance N2 O chamber methodology guidelines: Recommendations for air sample collection, storage, and analysis.

Certain aspects in the collection, handling, storage, and subsequent analysis of discrete air samples from non-steady-state flux chambers are critical to generating accurate and unbiased estimates of nitrous oxide (N2 O) fluxes. The focus of this paper is on air sample collection and storage in small vials (<12 ml) primarily for gas chromatography (GC) analysis. Sample integrity is assured through following simple procedures including storage under pressure and analysis within a few months of collection. Concurrent storage of standards in an identical manner to samples is recommended and allows the storage period to be reliably extended. In the laboratory, an autosampler is typically used in batch analysis of ∼200 sequentially analyzed samples by GC with an electron capture detector (ECD). Some comparisons are given between GC and alternatives including optical N2 O detectors that are increasingly being used for high-precision N2 O measurement. The importance of calibration and traceability of gas standards is discussed, where high-quality standards ensure the most accurate assessment of N2 O concentration and comparability between laboratories. The calibration allows a consistent and best estimate of flux to be derived.

The impact of accelerator processors for high-throughput molecular modeling and simulation.

The recent introduction of cost-effective accelerator processors (APs), such as the IBM Cell processor and Nvidia's graphics processing units (GPUs), represents an important technological innovation which promises to unleash the full potential of atomistic molecular modeling and simulation for the biotechnology industry. Present APs can deliver over an order of magnitude more floating-point operations per second (flops) than standard processors, broadly equivalent to a decade of Moore's law growth, and significantly reduce the cost of current atom-based molecular simulations. In conjunction with distributed and grid-computing solutions, accelerated molecular simulations may finally be used to extend current in silico protocols by the use of accurate thermodynamic calculations instead of approximate methods and simulate hundreds of protein-ligand complexes with full molecular specificity, a crucial requirement of in silico drug discovery workflows.

Accuracy of the lattice-Boltzmann method using the Cell processor.

Accelerator processors like the new Cell processor are extending the traditional platforms for scientific computation, allowing orders of magnitude more floating-point operations per second (flops) compared to standard central processing units. However, they currently lack double-precision support and support for some IEEE 754 capabilities. In this work, we develop a lattice-Boltzmann (LB) code to run on the Cell processor and test the accuracy of this lattice method on this platform. We run tests for different flow topologies, boundary conditions, and Reynolds numbers in the range Re=6-350 . In one case, simulation results show a reduced mass and momentum conservation compared to an equivalent double-precision LB implementation. All other cases demonstrate the utility of the Cell processor for fluid dynamics simulations. Benchmarks on two Cell-based platforms are performed, the Sony Playstation3 and the QS20/QS21 IBM blade, obtaining a speed-up factor of 7 and 21, respectively, compared to the original PC version of the code, and a conservative sustained performance of 28 gigaflops per single Cell processor. Our results suggest that choice of IEEE 754 rounding mode is possibly as important as double-precision support for this specific scientific application.

Determining the optimal strategy for the live-attenuated herpes zoster vaccine in adults.

The optimal strategy for the vaccinating against herpes zoster (HZ) vaccine remains unknown. Cost-effectiveness analyses provide insight to the most cost-effective age groups but results vary across studies. The optimal strategy is important given that vaccine efficacy and duration vary depending on vaccination age. Therefore, small changes from the optimal age can affect long-term outcomes and produce sub-optimal results. The objective of this research was to determine the optimal timing policy for HZ vaccination. We simulated cohorts of men and women and use stochastic dynamic programming to evaluate the decision to vaccinate or defer each year from age 50 to 100. If the decision was to defer, the cohort risked developing HZ. If HZ occurred, the cohort was subjected to cost and quality-adjusted life year (QALY) loss for a typical HZ infection (including complications) at that age. If HZ did not occur, the decision was evaluated at the next age. Then, we extend the model to consider the case in which a booster vaccine is available. A set of probabilistic sensitivity analyses were conducted to check model robustness. Results show the optimal policy for women is to vaccinate between ages 66 and 77, and for men between ages 66 and 74, assuming a willingness to pay (WTP) of $100,000 per QALY. It becomes optimal to vaccinate earlier if a booster vaccine is available, and women have a wider range of ages than men. This research is the first to examine exactly when the HZ vaccine should be administered. It is also the first study, to our knowledge, that used stochastic dynamic programming to examine the question of a second dose for any vaccine. This research provides the first simple policy on when to vaccinate and re-vaccinate against HZ.

Respiratory-syncytial-virus- and rhinovirus-related bronchiolitis in children aged <2 years in an English district general hospital.

BACKGROUND: Bronchiolitis is the most common reason for hospitalization in young children. In addition to respiratory syncytial virus (RSV), other viruses have been increasingly implicated. Guidance on testing has also changed. AIMS: To compare clinicopathological outcomes in young children admitted with bronchiolitis due to RSV in comparison with rhinovirus (RV), and identify associated risk/epidemiological factors. METHODS: Children aged less than two years admitted to hospital with a clinical diagnosis of bronchiolitis with positive results for either RSV or RV were included in this study. Polymerase-chain-reaction-negative cases using an extended respiratory virus panel served as a control group. Retrospective data were collected on sex, risk factors, respiratory support, intravenous fluids and antibiotics. Outcomes such as length of stay (LOS) and need for transfer to the high-dependency unit/paediatric intensive care unit were included. FINDINGS: Two hundred and twenty-seven out of 437 nasopharyngeal aspirate samples were positive for either RSV (N = 162) or RV (N = 65). The median age of cases was three months and 75% had at least one risk factor. Risk factors were higher in the RV group (P = 0.004). RV accounted for the majority of cases outside the RSV season (P < 0.01). RV-associated bronchiolitis had a longer LOS (more than seven days) (P < 0.05) and increased need for chest X-rays and/or antibiotics (P < 0.05). Use of intravenous fluids and respiratory support were higher in the RV group, but the difference was not significant. CONCLUSIONS: RV is the second most common pathogen associated with bronchiolitis and is isolated all year round. This may be important in those with risk factors resulting in prolonged LOS. Further research is necessary to establish the exact role of RV in this common condition, particularly outside the traditional RSV season.

HTMD: High-Throughput Molecular Dynamics for Molecular Discovery.

Recent advances in molecular simulations have allowed scientists to investigate slower biological processes than ever before. Together with these advances came an explosion of data that has transformed a traditionally computing-bound into a data-bound problem. Here, we present HTMD, a programmable, extensible platform written in Python that aims to solve the data generation and analysis problem as well as increase reproducibility by providing a complete workspace for simulation-based discovery. So far, HTMD includes system building for CHARMM and AMBER force fields, projection methods, clustering, molecular simulation production, adaptive sampling, an Amazon cloud interface, Markov state models, and visualization. As a result, a single, short HTMD script can lead from a PDB structure to useful quantities such as relaxation time scales, equilibrium populations, metastable conformations, and kinetic rates. In this paper, we focus on the adaptive sampling and Markov state modeling features.

On the disulfiram-like activity of moxalactam.

A three-way crossover study was undertaken in 10 healthy subjects to characterize the reported disulfiram-like activity of moxalactam and to assess its influence on ethanol and acetaldehyde metabolism. On different occasions separated by at least 2 wk subjects were given in random order: 0.5 gm/kg ethanol orally, 0.5 gm/kg ethanol followed in 1 hr by 1.0 gm IV moxalactam, and 1.0 gm IV moxalactam every 8 hr for four doses followed by 0.5 gm/kg ethanol. Mean ethanol elimination rates of 13.1 +/- 0.76, 10.1 +/- 1.11, and 10.9 +/- 1.06 mg/dl/hr (mean +/- SEM) were observed in the three protocols, respectively. Corresponding mean estimated acetaldehyde clearance rates were 103.7 +/- 15.55, 92.8 +/- 13.79, and 97.3 +/- 10.41 l/min (mean +/- SEM). While no consistent moxalactam effect on ethanol or acetaldehyde elimination was observed, two subjects experienced mild disulfiram-like reactions to ethanol after moxalactam pretreatment. In one subject this reaction was associated with markedly elevated blood acetaldehyde concentrations. We conclude that moxalactam pretreatment may induce a disulfiram-like reaction after ethanol ingestion in some, probably due to inhibition of aldehyde dehydrogenase, and that alcoholic beverages are contraindicated in patients receiving moxalactam. We suggest, however, that such reactions will not occur when moxalactam is given after ethanol ingestion.

Rapid isolation of human CD34 hematopoietic stem cells--purging of human tumor cells.

Human CD34+ hematopoietic stem cells were purified using a new technology in which monoclonal antibodies are covalently immobilized on polystyrene surfaces. The CD34+ cell isolation scheme involved three sequential processes: (1) purification of bone marrow mononuclear cells; (2) enrichment of CD34+ cells using covalently immobilized soybean agglutinin; and (3) positive selection of CD34+ cells using polystyrene surfaces coated with the anti-CD34 monoclonal antibody ICH3. CD34+ cells purified by this process have both low-to-medium forward light scatter and low 90 degrees light-scatter properties. Moreover, the purified CD34+ cells are greater than 85% viable, express appropriate characteristic surface antigens, and are 10-50-fold enriched in short- and long-term hematopoietic activity. CD34+ cells collected in this manner from bone marrow samples contaminated with radiolabeled breast carcinoma, neuroblastoma, acute myelogenous leukemia, or small cell lung carcinoma cells were 99.9% depleted of the tumor cells. The CD34+ cell selection devices are sterile and are easily scaled-up to process clinical scale bone marrow samples.

Effects of castration on luteinizing hormone secretion and response to gonadotrophin-releasing hormone in sheep infected with Trypanosoma congolense.

The effects of trypanosomiasis on the endocrine function of the hypothalamo-pituitary-gonadal axis were investigated before and after castration of Scottish Blackface rams infected with Trypanosoma congolense and uninfected controls. Blood samples were collected at 15-min intervals for 6 h before and at 10, 20, 40, 60, 80, 100 and 120 min after injection of synthetic gonadotrophin-releasing hormone (GnRH, 20 micrograms iv) 2 days before infection and 26 and 54 days after infection, with castration being performed 28 days after infection. Mean luteinizing hormone (LH) pulse amplitude was higher (3.3 +/- 0.2 vs 2.6 +/- 0.3 ng/ml) and mean plasma testosterone concentration was lower (4.1 +/- 0.6 vs 7.6 +/- 1.2 nmol/l) in infected vs control rams 26 days after infection (p < 0.05). Mean plasma LH concentration and pulse amplitude increased in both groups after castration but both were significantly lower in infected compared to control rams (6.6 +/- 1.5 and 13.0 +/- 2.2 ng/ml, p < 0.01; 7.7 +/- 0.9 and 11.6 +/- 0.9 ng/ml, p < 0.001), respectively. However, LH responses to exogenous GnRH were similar in infected and control rams at each stage of the experiment, suggesting that the smaller increase in plasma LH after castration in infected rams was not caused by reduced responsiveness of the pituitary to GnRH but by alterations in GnRH secretion by the hypothalamus or its transport to the adenohypophysis. These results also demonstrate that impairment of testosterone secretion within 4 weeks of T. congolense infection in sheep may be due to testicular rather than pituitary effects.

Monomeric uni-ligated aluminates.

The tetradentate ligand, common name Salban(But)H4 (N,N'-bis(2-hydroxy-3,5-di-tert-butylbenzyl)-1,4-diaminobutane) combines with appropriate amounts of LiAlH4 to produce the unique monomeric, uni-ligated aluminate [Salban(But)Al]Li(thf)2 (1) and the bimetallic derivative Salban(But)(AlH2Li(thf)2)2 (2).

Shaking pups: a disorder of central myelination in the Spaniel dog. Part 1. Clinical, genetic and light-microscopical observations.

A new disorder of central myelination has been recognised in male Springer Spaniel pups which is probably inherited in a sex-linked recessive mode. The affected animals were much reduced in weight an size and showed gross generalised tremor, particularly when aroused, at about 10-12 days of age. Affected pups were studied between 1 and 3 months of age. There was severe hypomyelination throughout the CNS which was more marked in the cerebrum and optic nerves than in the spinal cord. The amount of myelin at each location increased with age. Axonal calibre also increased and there was no difference between the axonal diameters of affected and age-matched normal pups. Axons were either naked or surrounded by a disproportionately thin layer of myelin. Myelinated internodes tended to be short and heminodes were frequent. Vacuoles were present adjacent to axons or within glia but there was no evidence of demyelination. Total glial numbers were not reduced and numerous oligodendroglial and astrocytic nuclei identified. Peripheral, cranial and autonomic nerves were myelinated normally. It is suggested that there is an abnormality of oligodendroglial metabolism such that they cannot form and maintain normal myelin. Consequently the radial and longitudinal extensions of their plasma membranes are reduced. The vacuoles may represent a breakdown of defective myelin lipids as suggested in certain murine mutants. This defect of myelination provides a further model in which normal and disordered myelinogenesis can be studied.

Relative in vitro affinity of hepatic metallothionein for metals.

The ability of selected metals (Ag, Al, As, Ca, Cd, Co, Cr, Cu, Fe, Hg, Mg, Mn, Mo, Ni, Pb, Tl and V) to displace Zn from Zn-metallothionein (Zn-MT) was quantitated. Of the metals tested Cd had the highest affinity for MT, with 1.33 microM displacing 50% of the 65Zn bound to MT (EC50), followed by Pb (1.46 microM), Cu (1.93 microM), Hg (3.93 microM), Zn (8.06 microM), Ag (10.4 microM), Ni (474 microM) and Co (880 microM). As, Ca and Mo had a limited ability to displace Zn from MT while Al, Cr, Fe, Mg, Mn, Tl and V had no effect on Zn binding even at 1.0 mM.

Efficacy of an anti-fertility vaccine based on mammalian gonadotrophin releasing hormone (GnRH-I)--a histological comparison in male animals.

A N-terminal modified gonadotrophin releasing hormone (GnRH-I, tetanus toxoid-CHWSYGLRPG-NH2) conjugate was evaluated histologically in a number of male animal species (mice, dogs and sheep). The immunogen has previously been shown to be highly effective in rats, by suppressing both steroidogenesis and spermatogenesis. However, cross-species efficacy of peptide vaccines is known to be highly variable. Therefore, a comparative evaluation of reproductive tissues from animals immunized against this immunogen adsorbed onto an alum-based adjuvant was made. The sheep and dogs were chosen, as use of anti-fertility vaccines in these species is important in farming and veterinary practice. Changes in testicular size were measured during the immunization period and the greatest alteration (attributed to gonadal atrophy) was observed in the rat. Following euthanasia, the testicular tissue was evaluated for spermatogenesis. The most susceptible species to GnRH-I ablation was the rat, which showed significant (P < 0.0001) arrest in spermatogenesis compared with untreated controls. Testicular sections taken from treated animals were completely devoid of spermatozoa or spermatids, in comparison with 94% of the untreated controls showing evidence of spermatogenesis. The immunized mice and rams also showed significant arrest (P < 0.0001). There was a 30-45% decrease in spermatogenesis and total azoospermia was not apparent. However, the least responsive were the dogs, which showed little significant variation compared to untreated animals and only a 5% decrease in activity. A comparison of the specific IgG response to GnRH-I indicated that in sheep and dogs the response was not maintained, unlike in rodents, suggesting that suppression of fertility may be due to differences in immune responses in different animal species.

A 14/20 Robertsonian translocation in Swiss Simmental cattle.

A chromosomal abnormality identified as a 14/20 Robertsonian translocation by measurement and banding studies has been found randomly in several Swiss Simmental cattle. These cases have all been traced back to one ancestral bull. The testicular function of three unselected male offspring, two heterozygotes and one normal was studied. All possessed apparently normal spermatogenesis. In a meiotic study no alteration of overall chiasma counts were found at diakinesis in the heterozygous bulls compared with the normal, while the presence of a trivalent confirmed the diagnosis of a Robertsonian translocation. Also in the heterozygotes a small number of secondary spermatocytes were identified but they were too few to draw any firm conclusions regarding alterations in non disjunction rate.

Comparison of endocrine changes and ultrasound as means of identifying ovulation in the bitch.

Twenty bitches were monitored through pro-oestrus and oestrus using both circulating plasma hormone levels and ultrasonic examination of the ovaries. Using luteinising hormone (LH) as being the generally accepted optimum indicator of the day of ovulation, comparisons were made of the accuracy of progesterone and ultrasound to identify ovulation. Progesterone agreed with LH in 12 of 20 bitches and was within one day in seven of the other eight. Ultrasound was less accurate in that only four of the 16 estimates agreed, with a further six being within one day. However, if only the bitches which were examined by ultrasound with the latest equipment were included, while only three of 11 coincided, six of the remaining eight were within one day of the LH estimated ovulation. It is concluded that, at present, of the rapid assessments, the measurement of plasma progesterone is a better estimator of ovulation than ultrasound.

The use of a bovine plasma progesterone ELISA kit to measure progesterone in equine, ovine and canine plasmas.

A commerical kit designed to measure the concentration of progesterone in bovine plasma using an enzyme-linked immunosorbent assay (ELISA) has been assessed for measuring progesterone in the plasma of horses, sheep and dogs. Without validation, an immunoassay developed for progesterone in one species should not be used to measure progesterone in the plasma of other species. The kit was assessed by using the criteria of parallelism to a standard curve, the recovery of added progesterone, the correlation with an established radioimmunoassay and the detection of physiological change for each of the species tested. The ELISA kit proved to be acceptable for the analysis of progesterone in the plasma of each species, and in particular for the detection of the low concentrations found during the follicular phase and of the subsequent rise during the luteal phase of the oestrous cycle.