Expression of an anti-CD33 single-chain antibody by Pichia pastoris

CD33 is a cell surface glycoprotein expressed on cells of myelomonocytic lineage, leukaemic cells, but not haematopoietic stem cells. By virtue of its expression pattern, CD33 has become a popular target for new immunotherapeutic approaches to treat acute myeloid leukaemia. The methylotrophic yeast Pichia pastoris strain KM71H was used to produce an anti-CD33 single chain variable fragment (scFv), with the intention of conjugation to a radioisotope, for therapeutic use. To direct secreted expression of the anti-CD33-scFv the alpha-mating factor secretory signal sequence (alpha-MF) was used, with constructs containing a complete (CS) and incomplete (INCS) cleavage site to accommodate the potential outcomes of dibasic endopeptidase, Kex2, and dipeptidyl amino peptidase, Ste13, processing. The anti-CD33-scFv was expressed in BMMY cultures using both constructs, with a final yield of 48 mg/l (CS) and 11 mg/l (INCS). N-terminal sequencing showed that the CS-scFv had not been cleaved by Ste13, leaving amino acids EAEA at the N-terminus. The INCS-scFv construct produced a mixture of 50% authentic scFv and 50% with 11 amino acids from the alpha-MF remaining at the N-terminus. Despite the aberrations in alpha-MF processing, the anti-CD33-scFv's produced from both constructs were found to be functional. Flow cytometry and Biacore analysis demonstrated binding to target antigen CD33 on the surface of human leukaemic cell line HL-60, and to recombinant soluble CD33 respectively

Interpolation in waveform space: enhancing the accuracy of gravitational waveform families using numerical relativity

Matched-filtering for the identification of compact object mergers in gravitational-wave antenna data involves the comparison of the data stream to a bank of template gravitational waveforms. Typically the template bank is constructed from phenomenological waveform models since these can be evaluated for an arbitrary choice of physical parameters. Recently it has been proposed that singular value decomposition (SVD) can be used to reduce the number of templates required for detection. As we show here, another benefit of SVD is its removal of biases from the phenomenological templates along with a corresponding improvement in their ability to represent waveform signals obtained from numerical relativity (NR) simulations. Using these ideas, we present a method that calibrates a reduced SVD basis of phenomenological waveforms against NR waveforms in order to construct a new waveform approximant with improved accuracy and faithfulness compared to the original phenomenological model. The new waveform family is given numerically through the interpolation of the projection coefficients of NR waveforms expanded onto the reduced basis and provides a generalized scheme for enhancing phenomenological models.Comment: 10 pages, 7 figure

High Performance P3M N-body code: CUBEP3M

This paper presents CUBEP3M, a publicly-available high performance cosmological N-body code and describes many utilities and extensions that have been added to the standard package. These include a memory-light runtime SO halo finder, a non-Gaussian initial conditions generator, and a system of unique particle identification. CUBEP3M is fast, its accuracy is tuneable to optimize speed or memory, and has been run on more than 27,000 cores, achieving within a factor of two of ideal weak scaling even at this problem size. The code can be run in an extra-lean mode where the peak memory imprint for large runs is as low as 37 bytes per particles, which is almost two times leaner than other widely used N-body codes. However, load imbalances can increase this requirement by a factor of two, such that fast configurations with all the utilities enabled and load imbalances factored in require between 70 and 120 bytes per particles. CUBEP3M is well designed to study large scales cosmological systems, where imbalances are not too large and adaptive time-stepping not essential. It has already been used for a broad number of science applications that require either large samples of non-linear realizations or very large dark matter N-body simulations, including cosmological reionization, halo formation, baryonic acoustic oscillations, weak lensing or non-Gaussian statistics. We discuss the structure, the accuracy, known systematic effects and the scaling performance of the code and its utilities, when applicable.Comment: 20 pages, 17 figures, added halo profiles, updated to match MNRAS accepted versio

Lincoln University entomological expedition to Pitt Island

The expedition had two objectives: 1. To search for the Pitt Island longhorn beetle, Xylotoles costatus and determine its distribution, abundance and conservation status. 2. To undertake general entomological survey work, particularly in the orders Coleoptera, Diptera, Lepidoptera and Hymenoptera by using trapping methods not previously used on Pitt Island

Do selective cyclo-oxygenase-2 inhibitors and traditional non-steroidal anti-inflammatory drugs increase the risk of atherothrombosis? Meta-analysis of randomised trials

Objective: To assess the effects of selective cyclo-oxygenase-2 (COX 2) inhibitors and traditional non-steroidal anti-inflammatory drugs (NSAIDs) on the risk of vascular events. Design: Meta-analysis of published and unpublished tabular data from randomised trials, with indirect estimation of the effects of traditional NSAIDs. Data sources: Medline and Embase (January 1966 to April 2005); Food and Drug Administration records; and data on file from Novartis, Pfizer, and Merck. Review methods: Eligible studies were randomised trials that included a comparison of a selective COX 2 inhibitor versus placebo or a selective COX 2 inhibitor versus a traditional NSAID, of at least four weeks' duration, with information on serious vascular events (defined as myocardial infarction, stroke, or vascular death). Individual investigators and manufacturers provided information on the number of patients randomised, numbers of vascular events, and the person time of follow-up for each randomised group. Results: In placebo comparisons, allocation to a selective COX 2 inhibitor was associated with a 42% relative increase in the incidence of serious vascular events (1.2%/year v 0.9%/year; rate ratio 1.42, 95% confidence interval 1.13 to 1.78; P = 0.003), with no significant heterogeneity among the different selective COX 2 inhibitors. This was chiefly attributable to an increased risk of myocardial infarction (0.6%/year v 0.3%/year; 1.86, 1.33 to 2.59; P = 0.0003), with little apparent difference in other vascular outcomes. Among trials of at least one year's duration (mean 2.7 years), the rate ratio for vascular events was 1.45 (1.12 to 1.89; P = 0.005). Overall, the incidence of serious vascular events was similar between a selective COX 2 inhibitor and any traditional NSAID (1.0%/year v 0.9/%year; 1.16, 0.97 to 1.38; P = 0.1). However, statistical heterogeneity (P = 0.001) was found between trials of a selective COX 2 inhibitor versus naproxen (1.57, 1.21 to 2.03) and of a selective COX 2 inhibitor versus non-naproxen NSAIDs (0.88, 0.69 to 1.12). The summary rate ratio for vascular events, compared with placebo, was 0.92 (0.67 to 1.26) for naproxen, 1.51 (0.96 to 2.37) for ibuprofen, and 1.63 (1.12 to 2.37) for diclofenac. Conclusions: Selective COX 2 inhibitors are associated with a moderate increase in the risk of vascular events, as are high dose regimens of ibuprofen and diclofenac, but high dose naproxen is not associated with such an excess

Neural Signatures of Spatial Statistical Learning: Characterizing the Extraction of Structure from Complex Visual Scenes

Behavioral evidence has shown that humans automatically develop internal representations adapted to the temporal and spatial statistics of the environment. Building on prior fMRI studies that have focused on statistical learning of temporal sequences, we investigated the neural substrates and mechanisms underlying statistical learning from scenes with a structured spatial layout. Our goals were twofold: (1) to determine discrete brain regions in which degree of learning (i.e., behavioral performance) was a significant predictor of neural activity during acquisition of spatial regularities and (2) to examine how connectivity between this set of areas and the rest of the brain changed over the course of learning. Univariate activity analyses indicated a diffuse set of dorsal striatal and occipitoparietal activations correlated with individual differences in participants' ability to acquire the underlying spatial structure of the scenes. In addition, bilateral medial-temporal activation was linked to participants' behavioral performance, suggesting that spatial statistical learning recruits additional resources from the limbic system. Connectivity analyses examined, across the time course of learning, psychophysiological interactions with peak regions defined by the initial univariate analysis. Generally, we find that task-based connectivity with these regions was significantly greater in early relative to later periods of learning. Moreover, in certain cases, decreased task-based connectivity between time points was predicted by overall posttest performance. Results suggest a narrowing mechanism whereby the brain, confronted with a novel structured environment, initially boosts overall functional integration and then reduces interregional coupling over time

Randomized multicentre pilot study of sacubitril/valsartan versus irbesartan in patients with chronic kidney disease: United Kingdom Heart and Renal Protection (HARP)- III—rationale, trial design and baseline data

BACKGROUND: Patients with chronic kidney disease (CKD) are at risk of progression to end-stage renal disease and cardiovascular disease. Data from other populations and animal experiments suggest that neprilysin inhibition (which augments the natriuretic peptide system) may reduce these risks, but clinical trials among patients with CKD are required to test this hypothesis. METHODS: UK Heart and Renal Protection III (HARP-III) is a multicentre, double-blind, randomized controlled trial comparing sacubitril/valsartan 97/103 mg two times daily (an angiotensin receptor-neprilysin inhibitor) with irbesartan 300 mg one time daily among 414 patients with CKD. Patients ≥18 years of age with an estimated glomerular filtration rate (eGFR) of ≥45 but <60 mL/min/1.73 m2 and urine albumin:creatinine ratio (uACR) >20 mg/mmol or eGFR ≥20 but <45 mL/min/1.73 m2 (regardless of uACR) were invited to be screened. Following a 4- to 7-week pre-randomization single-blind placebo run-in phase (during which any current renin-angiotensin system inhibitors were stopped), willing and eligible participants were randomly assigned either sacubitril/valsartan or irbesartan and followed-up for 12 months. The primary aim was to compare the effects of sacubitril/valsartan and irbesartan on measured GFR after 12 months of therapy. Important secondary outcomes include effects on albuminuria, change in eGFR over time and the safety and tolerability of sacubitril/valsartan in CKD. RESULTS: Between November 2014 and January 2016, 620 patients attended a screening visit and 566 (91%) entered the pre-randomization run-in phase. Of these, 414 (73%) participants were randomized (mean age 63 years; 72% male). The mean eGFR was 34.0 mL/min/1.73 m2 and the median uACR was 58.5 mg/mmol. CONCLUSIONS: UK HARP-III will provide important information on the short-term effects of sacubitril/valsartan on renal function, tolerability and safety among patients with CKD

Effectiveness and reach of a directed-population approach to improving dental health and reducing inequalities: a cross sectional study

Background Childsmile School adopts a directed-population approach to target fluoride varnish applications to 20% of the primary one (P1) population in priority schools selected on the basis of the proportion of enrolled children considered to be at increased-risk of developing dental caries. The study sought to compare the effectiveness of four different methods for identifying individuals most in need when a directed-population approach is taken. <p></p> Methods The 2008 Basic National Dental Inspection Programme (BNDIP) cross-sectional P1 Scottish epidemiological survey dataset was used to model four methods and test three definitions of increased-risk. Effectiveness was determined by the positive predictive value (PPV) and explored in relation to 1-sensitivity and 1-specificity. <p></p> Results Complete data was available on 43470 children (87% of the survey). At the Scotland level, at least half (50%) of the children targeted were at increased-risk irrespective of the method used to target or the definition of increased-risk. There was no one method across all definitions of <i>increased-risk</i> that maximised PPV. Instead, PPV was highest when the targeting method complimented the definition of <i>increased-risk</i>. There was a higher percentage of children at <i>increased-risk</i> who were not targeted (1-sensitivity) when caries experience (rather than deprivation) was used to define <i>increased-risk</i>, irrespective of the method used for targeting. Over all three definitions of <i>increased-risk</i>, there was no one method that minimised (1-sensitivity) although this was lowest when the method and definition of <i>increased-risk</i> were complimentary. The false positive rate (1-specificity) for all methods and all definitions of <i>increased-risk</i> was consistently low (<20%), again being lowest when the method and definition of <i>increased-risk</i> were complimentary. <p></p> Conclusion Developing a method to reach all (or even the vast majority) of individuals at <i>increased-risk</i> defined by either caries experience or deprivation is difficult using a directed-population approach at a group level. There is a need for a wider debate between politicians and public health experts to decide how best to reach those most at need of intervention to improve health and reduce inequalities. <p></p&gt

Comparison of different stomatal conductance algorithms for ozone flux modelling

A multiplicative and a semi-mechanistic, BWB-type [Ball, J.T., Woodrow, I.E., Berry, J.A., 1987. A model predicting stomatalconductance and its contribution to the control of photosynthesis under different environmental conditions. In: Biggens, J. (Ed.), Progress in Photosynthesis Research, vol. IV. Martinus Nijhoff, Dordrecht, pp. 221–224.] algorithm for calculating stomatalconductance (gs) at the leaf level have been parameterised for two crop and two tree species to test their use in regional scale ozone deposition modelling. The algorithms were tested against measured, site-specific data for durum wheat, grapevine, beech and birch of different European provenances. A direct comparison of both algorithms showed a similar performance in predicting hourly means and daily time-courses of gs, whereas the multiplicative algorithm outperformed the BWB-type algorithm in modelling seasonal time-courses due to the inclusion of a phenology function. The re-parameterisation of the algorithms for local conditions in order to validate ozone deposition modelling on a European scale reveals the higher input requirements of the BWB-type algorithm as compared to the multiplicative algorithm because of the need of the former to model net photosynthesis (An