Combining epidemiology and economics to assess control of a viral endemic animal disease: Porcine Reproductive and Respiratory Syndrome (PRRS).

Porcine reproductive and respiratory syndrome (PRRS) is an extremely contagious disease that causes great damage to the U.S. pork industry. PRRS is not subject to official control in the U.S., but most producers adopt control strategies, including vaccination. However, the PRRS virus mutates frequently, facilitating its ability to infect even vaccinated animals. In this paper we analyze how increased vaccination on sow farms reduces PRRS losses and when vaccination is profitable. We develop a SIR model to simulate the spread of an outbreak between and within swine farms located in a region of Minnesota. Then, we estimate economic losses due to PRRS and calculate the benefits of vaccination. We find that increased vaccination of sow farms increases the private profitability of vaccination, and also transmits positive externalities to farms that do not vaccinate. Although vaccination reduces industry losses, a low to moderate vaccine efficacy implies that large PRRS losses remain, even on vaccinated farms. Our approach provides useful insight into the dynamics of an endemic animal disease and the benefits of different vaccination regimens.

Serum-Stable and Selective Backbone-N-Methylated Cyclic Peptides That Inhibit Prokaryotic Glycolytic Mutases.

N-Methylated amino acids (N-MeAAs) are privileged residues of naturally occurring peptides critical to bioactivity. However, de novo discovery from ribosome display is limited by poor incorporation of N-methylated amino acids into the nascent peptide chain attributed to a poor EF-Tu affinity for the N-methyl-aminoacyl-tRNA. By reconfiguring the tRNA's T-stem region to compensate and tune the EF-Tu affinity, we conducted Random nonstandard Peptides Integrated Discovery (RaPID) display of a macrocyclic peptide (MCP) library containing six different N-MeAAs. We have here devised a "pool-and-split" enrichment strategy using the RaPID display and identified N-methylated MCPs against three species of prokaryotic metal-ion-dependent phosphoglycerate mutases. The enriched MCPs reached 57% N-methylation with up to three consecutively incorporated N-MeAAs, rivaling natural products. Potent nanomolar inhibitors ranging in ortholog selectivity, strongly mediated by N-methylation, were identified. Co-crystal structures reveal an architecturally related Ce-2 Ipglycermide active-site metal-ion-coordinating Cys lariat MCP, functionally dependent on two cis N-MeAAs with broadened iPGM species selectivity over the original nematode-selective MCPs. Furthermore, the isolation of a novel metal-ion-independent Staphylococcus aureus iPGM inhibitor utilizing a phosphoglycerate mimetic mechanism illustrates the diversity of possible chemotypes encoded by the N-MeAA MCP library.

Production Losses From an Endemic Animal Disease: Porcine Reproductive and Respiratory Syndrome (PRRS) in Selected Midwest US Sow Farms.

Porcine reproductive and respiratory syndrome (PRRS) is an endemic disease causing important economic losses to the US swine industry. The complex epidemiology of the disease, along with the diverse clinical outputs observed in different types of infected farms, have hampered efforts to quantify PRRS' impact on production over time. We measured the impact of PRRS on the production of weaned pigs using a log-linear fixed effects model to evaluate longitudinal data collected from 16 sow farms belonging to a specific firm. We measured seven additional indicators of farm performance to gain insight into disease dynamics. We used pre-outbreak longitudinal data to establish a baseline that was then used to estimate the decrease in production. A significant rise of abortions in the week before the outbreak was reported was the strongest signal of PRRSV activity. In addition, production declined slightly one week before the outbreak and then fell markedly until weeks 5 and 6 post-outbreak. Recovery was not monotonic, cycling gently around a rising trend. At the end of the study period (35 weeks post-outbreak), neither the production of weaned pigs nor any of the performance indicators had fully recovered to baseline levels. This result suggests PRSS outbreaks may last longer than has been found in most other studies. We assessed PRRS' effect on farm efficiency as measured by changes in sow production of weaned pigs per year. We translated production losses into revenue losses assuming an average market price of $45.2/weaned pig. We estimate that the average PRSS outbreak reduced production by approximately 7.4%, relative to annual output in the absence of an outbreak. PRRS reduced production by 1.92 weaned pigs per sow when adjusted to an annual basis. This decrease is substantially larger than the 1.44 decrease of weaned pigs per sow/year reported elsewhere.

Using Machine Learning to Predict Swine Movements within a Regional Program to Improve Control of Infectious Diseases in the US.

Between-farm animal movement is one of the most important factors influencing the spread of infectious diseases in food animals, including in the US swine industry. Understanding the structural network of contacts in a food animal industry is prerequisite to planning for efficient production strategies and for effective disease control measures. Unfortunately, data regarding between-farm animal movements in the US are not systematically collected and thus, such information is often unavailable. In this paper, we develop a procedure to replicate the structure of a network, making use of partial data available, and subsequently use the model developed to predict animal movements among sites in 34 Minnesota counties. First, we summarized two networks of swine producing facilities in Minnesota, then we used a machine learning technique referred to as random forest, an ensemble of independent classification trees, to estimate the probability of pig movements between farms and/or markets sites located in two counties in Minnesota. The model was calibrated and tested by comparing predicted data and observed data in those two counties for which data were available. Finally, the model was used to predict animal movements in sites located across 34 Minnesota counties. Variables that were important in predicting pig movements included between-site distance, ownership, and production type of the sending and receiving farms and/or markets. Using a weighted-kernel approach to describe spatial variation in the centrality measures of the predicted network, we showed that the south-central region of the study area exhibited high aggregation of predicted pig movements. Our results show an overlap with the distribution of outbreaks of porcine reproductive and respiratory syndrome, which is believed to be transmitted, at least in part, though animal movements. While the correspondence of movements and disease is not a causal test, it suggests that the predicted network may approximate actual movements. Accordingly, the predictions provided here might help to design and implement control strategies in the region. Additionally, the methodology here may be used to estimate contact networks for other livestock systems when only incomplete information regarding animal movements is available.

Measuring Progress on the Control of Porcine Reproductive and Respiratory Syndrome (PRRS) at a Regional Level: The Minnesota N212 Regional Control Project (Rcp) as a Working Example.

Due to the highly transmissible nature of porcine reproductive and respiratory syndrome (PRRS), implementation of regional programs to control the disease may be critical. Because PRRS is not reported in the US, numerous voluntary regional control projects (RCPs) have been established. However, the effect of RCPs on PRRS control has not been assessed yet. This study aims to quantify the extent to which RCPs contribute to PRRS control by proposing a methodological framework to evaluate the progress of RCPs. Information collected between July 2012 and June 2015 from the Minnesota Voluntary Regional PRRS Elimination Project (RCP-N212) was used. Demography of premises (e.g. composition of farms with sows = SS and without sows = NSS) was assessed by a repeated analysis of variance. By using general linear mixed-effects models, active participation of farms enrolled in the RCP-N212, defined as the decision to share (or not to share) PRRS status, was evaluated and used as a predictor, along with other variables, to assess the PRRS trend over time. Additionally, spatial and temporal patterns of farmers' participation and the disease dynamics were investigated. The number of farms enrolled in RCP-N212 and its geographical coverage increased, but the proportion of SS and NSS did not vary significantly over time. A significant increasing (p<0.001) trend in farmers' decision to share PRRS status was observed, but with NSS producers less willing to report and a large variability between counties. The incidence of PRRS significantly (p<0.001) decreased, showing a negative correlation between degree of participation and occurrence of PRRS (p<0.001) and a positive correlation with farm density at the county level (p = 0.02). Despite a noted decrease in PRRS, significant spatio-temporal patterns of incidence of the disease over 3-weeks and 3-kms during the entire study period were identified. This study established a systematic approach to quantify the effect of RCPs on PRRS control. Despite an increase in number of farms enrolled in the RCP-N212, active participation is not ensured. By evaluating the effect of participation on the occurrence of PRRS, the value of sharing information among producers may be demonstrated, in turn justifying the existence of RCPs.

A Phase I study of cyclin-dependent kinase inhibitor, AT7519, in patients with advanced cancer: NCIC Clinical Trials Group IND 177.

BACKGROUND: AT7519 is a small-molecular inhibitor of multiple cyclin-dependent kinases (CDKs). It shows encouraging anti-cancer activity against multiple cell lines and in tumour xenografts. This phase I study was conducted to evaluate the safety and tolerability of AT7519 given as 1-h intravenous infusion on days 1, 4, 8 and 11 every 3 weeks. METHODS: Patients with advanced refractory solid tumours or non-Hodgkin's lymphoma were enroled. Dose escalation occurred in a 3+3 manner based on toxicity assessment. Pharmacokinetic samples were collected after first AT7519 infusion, whereas pharmacodynamics (PD) samples were obtained in selected patients. RESULTS: Thirty-four patients were enroled, and 32 received study treatments over 4 dose levels. Dose-limiting toxicities included mucositis, febrile neutropenia, rash, fatigue and hypokalemia. The recommended phase II dose (RP2D) was 27.0 mg m(-2). Ten of 19 patients evaluable for efficacy had stable disease as the best response (median duration: 3.3 months; range: 2.5 to 11.1 months). There was no clinically significant QTc prolongation. There was an apparent dose proportional increase in AT7519 exposure. The PD studies showed reduction in markers of CDK activity in selected patients' skin biopsies post treatment. CONCLUSIONS: AT7519, when administered as an intravenous infusion on days 1, 4, 8 and 11, was well tolerated. The RP2D is 27.0 mg m(-2). At this dose level, plasma AT7519 concentrations were above the biologically active concentrations, and preliminary anti-cancer activity was observed in patients. This dosing schedule is being further evaluated in multiple phase II studies.

SU-E-T-125: High-Resolution Linear Diode Array for Use in Stereotactic Beam Commissioning.

PURPOSE: Task Group 106 discusses detector arrays and their usefulness in "soft-wedge" profile measurements. This study verifies an extension of their use; where a high-resolution linear diode array is used to measure profile scans for use in commissioning stereotactic beam. Small-field data is acquired with the LDA-99sc (IBA Dosimetry America, Memphis, TN), an array of 99 two-mm-diameter Hi-pSi diodes. These data are compared to data collected during serial scanning with an IBA SFD stereotactic diode. METHODS: Field measurements were taken at varying depths using an LDA-99sc in 1×1 cm2 , 2×2cm2 , and 3×3cm2 fields of a Trilogy accelerator (Varian Medical Systems, Palo Alto, CA). These scans were duplicated in resolution and sample rate with an SFD scanning diode. Both techniques acquired point data in 1.0mm increments. RESULTS: In identical conditions, the LDA-99sc provided readings with significantly less signal fluctuation than with traditional diode scanning; which is attributed to the reduction of water motion associated with detector travel during traditional scanning. This smoother data precluded the use of smoothing and filtration algorithms; allowing the beam to be modeled using raw data. The LDA-99sc measured an average penumbra of 0.1 mm wider than that which was measured with the diode. The LDA-99sc also measured an average field size of 0.3mm wider than that which was measured with the diode. With respect to time, a single profile scan (30cm-depth, 3×3cm2 field) using the LDA-99sc took 31 seconds, while a diode scan took 229 seconds. CONCLUSIONS: The LDA99 provided accurate commissioning-grade small-field beam profile data, as verified by comparison with diode scans, with a reduction of uncertainty in readings and a substantial reduction in time. Variation in penumbra and beam widths were deemed acceptable and can be attributed to the LDA-99sc data being raw, while the diode data was processed. Research supported in-part by IBA Dosimetry America.

The leucine-rich repeat structure.

The leucine-rich repeat is a widespread structural motif of 20-30 amino acids with a characteristic repetitive sequence pattern rich in leucines. Leucine-rich repeat domains are built from tandems of two or more repeats and form curved solenoid structures that are particularly suitable for protein-protein interactions. Thousands of protein sequences containing leucine-rich repeats have been identified by automatic annotation methods. Three-dimensional structures of leucine-rich repeat domains determined to date reveal a degree of structural variability that translates into the considerable functional versatility of this protein superfamily. As the essential structural principles become well established, the leucine-rich repeat architecture is emerging as an attractive framework for structural prediction and protein engineering. This review presents an update of the current understanding of leucine-rich repeat structure at the primary, secondary, tertiary and quaternary levels and discusses specific examples from recently determined three-dimensional structures.

Underestimation of severity of previous whiplash injuries.

INTRODUCTION: We noted a report that more significant symptoms may be expressed after second whiplash injuries by a suggested cumulative effect, including degeneration. We wondered if patients were underestimating the severity of their earlier injury. PATIENTS AND METHODS: We studied recent medicolegal reports, to assess subjects with a second whiplash injury. They had been asked whether their earlier injury was worse, the same or lesser in severity. RESULTS: From the study cohort, 101 patients (87%) felt that they had fully recovered from their first injury and 15 (13%) had not. Seventy-six subjects considered their first injury of lesser severity, 24 worse and 16 the same. Of the 24 that felt the violence of their first accident was worse, only 8 had worse symptoms, and 16 felt their symptoms were mainly the same or less than their symptoms from their second injury. Statistical analysis of the data revealed that the proportion of those claiming a difference who said the previous injury was lesser was 76% (95% CI 66-84%). The observed proportion with a lesser injury was considerably higher than the 50% anticipated. CONCLUSIONS: We feel that subjects may underestimate the severity of an earlier injury and associated symptoms. Reasons for this may include secondary gain rather than any proposed cumulative effect.

Manipulating enteric methane emissions and animal performance of late-lactation dairy cows through concentrate supplementation at pasture.

The objective of this study was to determine the potential of increased fiber-based concentrates to reduce methane (CH(4)) production in relation to milk yield from late-lactation dairy cows. The effect of 2 levels of concentrate supplementation (0.87 vs. 5.24 kg on a dry matter basis) on herbage voluntary intake, total dry matter intake, milk yield, milk composition, and CH(4) production were determined by way of a randomized block designed grazing trial using lactating Holstein-Friesian cows (231 +/- 44 d in milk) grazing a mixed-grass sward with a regrowth aged 36 d. Increased concentrate supplementation resulted in a significant increase in total dry matter intake, milk yield, fat-corrected milk (FCM) yield, and daily CH(4) production. However, herbage intake and milk composition were unaffected. Although daily CH(4) production increased with fibrous concentrate use the increase was not as great as that observed for milk yield. The decline in CH(4) production per kilogram of milk was nonsignificant; however, when relating CH(4) production to FCM(FCM at 35 g of fat/kg of milk), a declining trend was identified within increasing concentrate supplementation (19.26 and 16.02 g of CH(4)/kg of FCM). These results suggest that increased fibrous concentrate use at pasture, even at modest levels, could reduce enteric CH(4) production per kilogram of animal product. However, the effectiveness of such a strategy is dependent on the maintenance of production quotas and a subsequent decline in the number of livestock needed to fulfill the specified production level.

Properties of polyproline II, a secondary structure element implicated in protein-protein interactions.

The polyproline II (PPII) conformation of protein backbone is an important secondary structure type. It is unusual in that, due to steric constraints, its main-chain hydrogen-bond donors and acceptors cannot easily be satisfied. It is unable to make local hydrogen bonds, in a manner similar to that of alpha-helices, and it cannot easily satisfy the hydrogen-bonding potential of neighboring residues in polyproline conformation in a manner analogous to beta-strands. Here we describe an analysis of polyproline conformations using the HOMSTRAD database of structurally aligned proteins. This allows us not only to determine amino acid propensities from a much larger database than previously but also to investigate conservation of amino acids in polyproline conformations, and the conservation of the conformation itself. Although proline is common in polyproline helices, helices without proline represent 46% of the total. No other amino acid appears to be greatly preferred; glycine and aromatic amino acids have low propensities for PPII. Accordingly, the hydrogen-bonding potential of PPII main-chain is mainly satisfied by water molecules and by other parts of the main-chain. Side-chain to main-chain interactions are mostly nonlocal. Interestingly, the increased number of nonsatisfied H-bond donors and acceptors (as compared with alpha-helices and beta-strands) makes PPII conformers well suited to take part in protein-protein interactions.

Oxygen consumption is increased relative to work rate in patients with McArdle's disease.

BACKGROUND: Patients with McArdle's disease suffer exercise incapacity as a result of myophosphorylase deficiency, and for a given work rate have excessive circulatory and ventilatory responses. We hypothesized that the rate of increase of oxygen consumption with work rate (DeltaVO2-DeltaWR slope) would also be elevated in such patients as a result of these excessive responses. PATIENTS AND METHODS: Five patients with McArdle's disease and five matched controls carried out a maximal incremental cardiopulmonary exercise test. Controls then carried out a second test matched to the maximal test of a paired patient. Venous blood was sampled at rest, peak exercise and recovery. RESULTS: During the matched test, the DeltaVO2-DeltaWR slope was higher in the patients than in the controls [19.9 (15.0-24.6) vs. 11.7 (9.2-13.5) mL min(-1) W(-1); mean (range); P = 0.022], and the peak-achieved VO2 was also greater in the patient group [1201 (890-1575) vs. 918 (599-1248) mL min(-1); P = 0.003]. A similar pattern was observed for heart rate [173 (165-182) vs. 108 (105-134) b.p.m.; P = 0.001] and plasma norepinephrine levels [12.6 (9.2-19.9) vs. 2.9 (2.2-4.9) nmol l(-1); P = 0.003]. CONCLUSION: There is an increased rate of rise in VO2 relative to work rate during exercise in patients with McArdle's disease. There is also a greater rise in catecholamines, which may be the result of a physiological response to substrate starvation, and is likely to contribute to the increase in VO2.

Why is there an "inert" metal center in the active site of nitrile hydratase? Reactivity and ligand dissociation from a five-coordinate Co(III) nitrile hydratase model.

To determine how a substitutionally inert metal can play a catalytic role in the metalloenzyme nitrile hydratase (NHase), a reactive five-coordinate Co(III) thiolate complex ([Co(III)(S(2)(Me2)N(3)(Pr,Pr))](PF(6)) (1)) that resembles the active site of cobalt containing nitrile hydratase (Co NHase) was prepared. This was screened for reactivity, by using low-temperature electronic absorption spectroscopy, toward a number of biologically relevant "substrates". It was determined 1 will react with azide, thiocyanate, and ammonia, but is unreactive toward nitriles, NO, and butyrate. Substrate-bound 1 has similar spectroscopic and structural properties as [Co(III)(ADIT(2))](PF(6)) (2). Complex 2 is a six-coordinate Co(III) complex containing cis-thiolates and imine nitrogens, and has properties similar to the cobalt center of Co NHase. Substrate binding to 1 is reversible and temperature-dependent, allowing for the determination of the thermodynamic parameters of azide and thiocyanate binding and the rates of ligand dissociation. Azide and thiocyanate bind trans to a thiolate, and with similar entropies and enthalpies (thiocyanate: DeltaH = -7.5 +/- 1.1 kcal/mol, DeltaS = -17.2 +/- 3.2 eu; azide: DeltaH = -6.5 +/- 1.0 kcal/mol, DeltaS = -12.6 +/- 2.4 eu). The rates of azide and thiocyanate displacement from the metal center are also comparable to one another (k(d) = (7.22 +/- 0.04) x 10(-)(1) s(-)(1) for thiocyanate and k(d) = (2.14 +/- 0.50) x 10(-)(2) s(-)(1) for azide), and are considerably faster than one would expect for a low-spin d(6) six-coordinate Co(III) complex. These rates are comparable to those of an analogous Fe(III) complex, demonstrating that Co(III) and Fe(III) react at comparable rates when in this ligand environment. This study therefore indicates that ligand displacement from a low-spin Co(III) center in a ligand environment that resembles NHase is not prohibitively slow so as to disallow catalytic action in nonredox active cobalt metalloenzymes.

C--N bond formation on addition of aryl carbanions to the electrophilic nitrido ligand in TpOs(N)Cl(2).

The osmium(VI) nitrido complex TpOs(N)Cl(2) (1) has been prepared from K[Os(N)O(3)] and KTp in aqueous ethanolic HCl. It reacts rapidly with PhMgCl and related reagents with transfer of a phenyl group to the nitrido ligand. This forms Os(IV) metalla-analido complexes, which are readily protonated to give the analido complex TpOs(NHPh)Cl(2) (4). The nitrido-phenyl derivatives TpOs(N)PhCl and TpOs(N)Ph(2) react more slowly with PhMgCl and are not competent intermediates for the reaction of 1 with PhMgCl. Reactions of 1 with alkyl- and arylboranes similarly result in transfer of one organic group to nitrogen, leading to isolable borylamido complexes such as TpOs[N(Ph)(BPh(2))]Cl(2) (11). This is an unprecedented insertion of a nitrido ligand into a boron--carbon bond. Hydrolysis of 11 gives 4. Mechanistic studies suggest that both the Grignard and borane reactions proceed by initial weak coordination of Mg or B to the nitrido ligand, followed by migration of the carbanion to nitrogen. The hydrocarbyl group does not go to osmium and then move to nitrogen--there is no change in the atoms bound to the osmium during the reactions. It is suggested that there may be a general preference for nucleophiles to add directly to the metal--ligand multiple bond rather than binding to the metal first and migrating. Ab initio calculations show that the unusual reactivity of 1 results from its accessible LUMO and LUMO + 1, which are the Os = N pi* orbitals. The bonding in 1 and its reactivity with organoboranes are reminiscent of CO.

Protonation and deprotonation of TpOs(NHPh)Cl(2): an unusually inert amido ligand.

Protonation of the Os(IV) amido complex TpOs(NHPh)Cl(2) (1) to give the aniline complex [TpOs(NH(2)Ph)Cl(2)]OTf (2) requires excess triflic acid (HOTf). Complex 1 is unreactive with HCl and other moderately strong acids. Consistent with the low basicity of 1, the aniline complex 2 is extremely acidic and is deprotonated by stoichiometric addition of weak bases such as Cl(-) or H(2)O. No reaction is observed between 1 and methyl triflate (CH(3)OTf) at ambient temperatures. Upon heating, CH(3)OTf removes the chloride ligands from 1 to give CH(3)Cl and the amidobis(triflate) complex TpOs(NHPh)(OTf)(2) (3). Attack at the amido nitrogen is not observed. Complex 1 is thus very inert to protonation and electrophilic attack at nitrogen. A deprotonated form of 1, TpOs[NPh(MgBr)]Cl(2) (4), is generated on reaction of PhMgBr with TpOs(N)Cl(2). Complex 4 is extremely basic and will protonate to 1 with weak acids such as CH(3)CN, DMSO, and acetic anhydride. Thus, 1 has a low acidity as well as a low basicity; it is both less acidic and less basic than aniline. The inertness of 1 is ascribed to partial Os-N pi bonding and to the oxidizing nature of the Os(IV) center.

Probing the influence of local coordination environment on the properties of Fe-type nitrile hydratase model complexes.

A series of four structurally related cis-dithiolate-ligated Fe(III) complexes, [Fe(III)(DITpy)2]Cl (1), [Fe(III)(DITIm)2]Cl (2), [Fe(III)(ADIT)2]Cl (3), and [Fe(III)(AMIT)2]Cl (4), are described. The structural characterization of 3 as well as the spectroscopic properties of 3 and 4 has been previously reported. Crystal data for 1, 2, and 4 are as follows: 1.3H2O crystallizes in the orthorhombic space group Pca2(1) with a = 19.800(4) A, b = 18.450(4) A, c = 14.800(3) A, and Z = 8. 2.(1/2)EtOH.1/2H2O crystallizes in the monoclinic space group Cc with a = 24.792(4) A, b = 14.364(3) A, c = 17.527(3) A, beta = 124.91(2) degrees, and Z = 8. 4 crystallizes in the triclinic space group P1 with a = 8.0152(6) A, b = 10.0221(8) A, c = 11.8384(10) A, alpha = 73.460(3) degrees, beta = 71.451(5) degrees, gamma = 72.856(4) degrees, and Z = 2. Complexes 1-4 share a common S2N4 coordination environment that consists of two cis-thiolates, two trans-imines, and two cis-terminal nitrogen donors: Nterm = pyridine (1), imidazole (2), and primary amine (3 and 4). The crystallographically determined mean Fe-S bond distances in 1-4 range from 2.196 to 2.232 A and are characteristic of low-spin Fe(III)-thiolate complexes. The low-spin S = 1/2 ground state was confirmed by both EPR and magnetic susceptibility measurements. The electronic spectra of these complexes are characterized by broad absorption bands centered near approximately 700 nm that are consistent with ligand-to-metal charge-transfer (CT) bands. The complexes were further characterized by cyclic voltammetry measurements, and all possess highly negative Fe(III)/Fe(II) redox couples ( approximately -1 V vs SCE, saturated calomel electrode) indicating that alkyl thiolate donors are effective at stabilizing Fe(III) centers. Both the redox couple and the 700 nm band in the visible spectra show solvent-dependent shifts that are dependent upon the H-bonding ability of the solvent. The implications of these results with respect to the active site of the iron-containing nitrile hydratases are also discussed.

Sequence-structure homology recognition by iterative alignment refinement and comparative modeling.

Our approach to fold recognition for the fourth critical assessment of techniques for protein structure prediction (CASP4) experiment involved the use of the FUGUE sequence-structure homology recognition program (http://www-cryst.bioc.cam.ac.uk/fugue), followed by model building. We treat models as hypotheses and examine these to determine whether they explain the available data. Our method depends heavily on environment-specific substitution tables derived from our database of structural alignments of homologous proteins (HOMSTRAD, http://www-cryst.bioc.cam.ac.uk/homstrad/). FUGUE uses these tables to incorporate structural information into profiles created from HOMSTRAD alignments that are matched against a profile created for the target from multiple sequence alignment. In addition, environment-specific substitution tables are used throughout the modeling procedure and as part of the model evaluation. Annotation of sequence alignments with JOY, to reflect local structural features, proved valuable, both for modifying hypotheses, and for rejecting predictions when the expected pattern of conservation is not observed. Our stringency in rejecting incorrect predictions led us to submit a relatively small number of models, including only a low number of false positives, resulting in a high average score.

Pharmacy-based needle exchange (PBNX) schemes in south east England: a survey of service providers.

AIMS: To describe the activities of service providers with regard to (i) the business operation and policies defining pharmacy-based needle exchange (PBNX) in South East England; (ii) the day-to-day work of PBNX outlets from the provider perspective; and (iii) problems encountered by PBNX providers. DESIGN: (i) Postal self-completion questionnaire to all participating PBNX community pharmacies in South East England; and (ii) postal self-completion questionnaire to needle exchange coordinators. SETTING: Community pharmacy needle exchanges. PARTICIPANTS: Pharmacists in charge of needle exchange; and needle exchange coordinators. FINDINGS: Data were collected (i) from 381/440 (86.7%) participating community pharmacists, and (ii) 32/36 (88.9%) of coordinators. The study found that PBNX was reaching injecting drug users (many of whom used PBNX regularly), and providing a wide range of injecting equipment. Although pharmacists reported that problems such as shoplifting occurred relatively frequently, more serious problems such as violence were relatively rare. However, PBNX pharmacists reported needing further training for themselves and their staff. Suggested improvements included better advertising of services and improving returns rates for used injecting equipment. CONCLUSION: Needle exchange can reasonably be provided by non-specialist health care professionals such as community pharmacists. However, attention should to be paid to the educational needs of service providers who also require adequate support.