Optimization of protein crystallization:the OptiCryst project

Protein crystallization has gained a new strategic and commercial relevance in the postgenomic era due to its pivotal role in structural genomics. Producing high quality crystals has always been a bottleneck to efficient structure determination, and this problem is becoming increasingly acute. This is especially true for challenging, therapeutically important proteins that typically do not form suitable crystals. The OptiCryst consortium has focused on relieving this bottleneck by making a concerted effort to improve the crystallization techniques usually employed, designing new crystallization tools, and applying such developments to the optimization of target protein crystals. In particular, the focus has been on the novel application of dual polarization interferometry (DPI) to detect suitable nucleation; the application of in situ dynamic light scattering (DLS) to monitor and analyze the process of crystallization; the use of UV-fluorescence to differentiate protein crystals from salt; the design of novel nucleants and seeding technologies; and the development of kits for capillary counterdiffusion and crystal growth in gels. The consortium collectively handled 60 new target proteins that had not been crystallized previously. From these, we generated 39 crystals with improved diffraction properties. Fourteen of these 39 were only obtainable using OptiCryst methods. For the remaining 25, OptiCryst methods were used in combination with standard crystallization techniques. Eighteen structures have already been solved (30% success rate), with several more in the pipeline.

AstonCAT-plus:an efficient specialist for the TAC market design tournament

This paper describes the strategies used by AstonCAT-Plus, the post-tournament version of the specialist designed for the TAC Market Design Tournament 2010. It details how AstonCATPlus accepts shouts, clears market, sets transaction prices and charges fees. Through empirical evaluation, we show that AstonCAT-Plus not only outperforms AstonCAT (tournament version) significantly but also achieves the second best overall score against some top entrants of the competition. In particular, it achieves the highest allocative efficiency, transaction success rate and average trader profit among all the specialists in our controlled experiments.

Neuronal network dynamics during epileptogenesis in the medial temporal lobe

Epilepsy is one of the most common neurological disorders, a large fraction of which is resistant to pharmacotherapy. In this light, understanding the mechanisms of epilepsy and its intractable forms in particular could create new targets for pharmacotherapeutic intervention. The current project explores the dynamic changes in neuronal network function in the chronic temporal lobe epilepsy (TLE) in rat and human brain in vitro. I focused on the process of establishment of epilepsy (epileptogenesis) in the temporal lobe. Rhythmic behaviour of the hippocampal neuronal networks in healthy animals was explored using spontaneous oscillations in the gamma frequency band (SγO). The use of an improved brain slice preparation technique resulted in the natural occurence (in the absence of pharmacological stimulation) of rhythmic activity, which was then pharmacologically characterised and compared to other models of gamma oscillations (KA- and CCh-induced oscillations) using local field potential recording technique. The results showed that SγO differed from pharmacologically driven models, suggesting higher physiological relevance of SγO. Network activity was also explored in the medial entorhinal cortex (mEC), where spontaneous slow wave oscillations (SWO) were detected. To investigate the course of chronic TLE establishment, a refined Li-pilocarpine-based model of epilepsy (RISE) was developed. The model significantly reduced animal mortality and demonstrated reduced intensity, yet high morbidy with almost 70% mean success rate of developing spontaneous recurrent seizures. We used SγO to characterize changes in the hippocampal neuronal networks throughout the epileptogenesis. The results showed that the network remained largely intact, demonstrating the subtle nature of the RISE model. Despite this, a reduction in network activity was detected during the so-called latent (no seizure) period, which was hypothesized to occur due to network fragmentation and an abnormal function of kainate receptors (KAr). We therefore explored the function of KAr by challenging SγO with kainic acid (KA). The results demonstrated a remarkable decrease in KAr response during the latent period, suggesting KAr dysfunction or altered expression, which will be further investigated using a variety of electrophysiological and immunocytochemical methods. The entorhinal cortex, together with the hippocampus, is known to play an important role in the TLE. Considering this, we investigated neuronal network function of the mEC during epileptogenesis using SWO. The results demonstrated a striking difference in AMPAr function, with possible receptor upregulation or abnormal composition in the early development of epilepsy. Alterations in receptor function inevitably lead to changes in the network function, which may play an important role in the development of epilepsy. Preliminary investigations were made using slices of human brain tissue taken following surgery for intratctable epilepsy. Initial results showed that oscillogenesis could be induced in human brain slices and that such network activity was pharmacologically similar to that observed in rodent brain. Overall, our findings suggest that excitatory glutamatergic transmission is heavily involved in the process of epileptogenesis. Together with other types of receptors, KAr and AMPAr contribute to epilepsy establishment and may be the key to uncovering its mechanism.

EpiJen:a server for multistep T cell epitope prediction

Background - The main processing pathway for MHC class I ligands involves degradation of proteins by the proteasome, followed by transport of products by the transporter associated with antigen processing (TAP) to the endoplasmic reticulum (ER), where peptides are bound by MHC class I molecules, and then presented on the cell surface by MHCs. The whole process is modeled here using an integrated approach, which we call EpiJen. EpiJen is based on quantitative matrices, derived by the additive method, and applied successively to select epitopes. EpiJen is available free online. Results - To identify epitopes, a source protein is passed through four steps: proteasome cleavage, TAP transport, MHC binding and epitope selection. At each stage, different proportions of non-epitopes are eliminated. The final set of peptides represents no more than 5% of the whole protein sequence and will contain 85% of the true epitopes, as indicated by external validation. Compared to other integrated methods (NetCTL, WAPP and SMM), EpiJen performs best, predicting 61 of the 99 HIV epitopes used in this study. Conclusion - EpiJen is a reliable multi-step algorithm for T cell epitope prediction, which belongs to the next generation of in silico T cell epitope identification methods. These methods aim to reduce subsequent experimental work by improving the success rate of epitope prediction.

The influence of organizational and national culture on new product performance

The authors conduct a meta-analysis on the combined influence of organizational and national culture on new product performance. For this purpose, they refer to the effectiveness of value congruency and develop a conceptual model describing the fit between organizational culture types as suggested by the competing values framework and national culture, as described by Hofstede's cultural dimensions. The meta-analysis is based on 489 effect sizes taken from 123 manuscripts. The findings show that organizations with a market culture show the highest new product performance, while hierarchy-type organizations show the lowest performance. The influence of national culture variables supports the effect of value congruency, and shows that in individualistic cultures the impact of a clan culture decreases, the impact of an adhocracy culture type decreases with uncertainty avoidance, and the influence of a hierarchy culture type increases with power distance. The superior effect of a market culture type can be matched by other organizational orientations, but in particular national cultures only. The combined findings underline the importance for firms that seek to improve the success rate of new products on international markets to consider the fit of a national culture with a firm's organizational culture.

Use of Google as a tool to aid diagnosis by optometry students

Background: Previous work has shown that medical problems can be diagnosed by practitioners using Google. The aim of this study was to determine whether optometry students would benefit from using Google when diagnosing eye diseases. Methods: Participants were given symptoms and signs and instructed to list three key words and use them to search Aston University e-Library and Google UK. Results: Aston University e-Library only search resulted in correct diagnosis in 16 of 60 simulated cases. Aston e-Library plus Google search resulted in correct diagnosis in 31 of 60 simulated cases. Conclusion: Google is a useful aid to help optometry students improve their success rate when diagnosing eye conditions.

Self-adaptive probabilistic roadmap generation for intelligent virtual agents

Agents inhabiting large scale environments are faced with the problem of generating maps by which they can navigate. One solution to this problem is to use probabilistic roadmaps which rely on selecting and connecting a set of points that describe the interconnectivity of free space. However, the time required to generate these maps can be prohibitive, and agents do not typically know the environment in advance. In this paper we show that the optimal combination of different point selection methods used to create the map is dependent on the environment, no point selection method dominates. This motivates a novel self-adaptive approach for an agent to combine several point selection methods. The success rate of our approach is comparable to the state of the art and the generation cost is substantially reduced. Self-adaptation therefore enables a more efficient use of the agent's resources. Results are presented for both a set of archetypal scenarios and large scale virtual environments based in Second Life, representing real locations in London.

An analysis of penalty kicks in elite football post 1997

The penalty kick in football is a seemingly simplistic play; however, it has increased in complexity since 1997 when the rules changed allowing goalkeepers to move laterally along their goal line before the ball was kicked. Prior to 1997 goalkeepers were required to remain still until the ball was struck. The objective of this study was to determine the importance of the penalty kick in the modern game of football. A retrospective study of the 2002, 2006 and 2010 World Cup and the 2000, 2004 and 2008 European Championship tournaments was carried out, assessing the importance of the penalty kick in match play and shootouts and the effect of the time of the game on the shooter's success rate. This study demonstrated the conversion rate of penalties was 73% in shootouts and 68% in match play. Significantly more penalties were awarded late in the game: twice as many penalties in the second half than the first and close to four times as many in the fourth quarter vs. the first. Teams awarded penalty kicks during match play won 52%, drew 30% and lost 18% of the time; chances of winning increased to 61% if the penalty was scored, but decreased to 29% if missed. Teams participating in either the World Cup or European Championship final match had roughly a 50% chance of being involved in a penalty shootout during the tournament. Penalty shots and their outcome significantly impact match results in post 1997 football.

The management of posterior vitreous detachment by an optometrist

Acute posterior vitreous detachment (PVD) is the most common cause of retinal detachment. The management of this condition can be variable and often undue reliance is placed upon associated signs and symptoms which can be a poor indicator of pathology. Optometrists undertake a number of extended roles, however involvement in vitreo-retinal sub-specialities appears to be limited. One objective was to directly compare an optometrist and ophthalmologist in the assessment of patients with PVD, for this a high level of agreement was found (95% sensitivity, 99% specificity, 0.94 kappa). A review of 1107 patients diagnosed with acute PVD that were re-evaluated in a PVD clinic a few weeks later was undertaken to determine whether such reviews are necessary. One-fifth of patients were found to have conditions undiagnosed at the initial assessment, overall 4% of patients had retinal breaks when examined in the PVD clinic and a total of 7% required further intervention. The sensitivity of fundus examination with +90D and 3-mirror lenses was 85-88% for detecting retinal breaks and 7-85% for pigment in the anterior vitreous for the presence of retinal breaks. Therefore patients with acute PVD should be examined by indirect ophthalmoscopy with indentation at the onset of PVD and 4-6 weeks later. The treatment of retinal breaks with laser retinopexy is performed by ophthalmologists with a primary success rate 54-85%. In a pioneering development, an optometrist undertaking this role achieved a comparable primary success rate (79%). Mid-vitreous opacities associated with PVD are described, and noted in 100% of eyes with PVD. The recognition of this sign is important in the diagnosis of PVD and retinal breaks. The importance of diagnostic imaging is also demonstrated, however the timing in relation to onset may be vital.

The impact of the Florida state -mandated Basic Skills Exit Tests at Miami -Dade Community College

The purpose of this study was to explore the impact of the Florida State-mandated Basic Skills Exit Tests (BSET) on the effectiveness of remedial instruction programs to adequately serve the academically underprepared student population. The primary research question concerned whether the introduction of the BSET has resulted in remedial completers who are better prepared for college-level coursework. ^ This study consisted of an ex post facto research design to examine the impact of the BSET on student readiness for subsequent college-level coursework at Miami-Dade Community College. Two way analysis of variance was used to compare the performance of remedial and college-ready students before and after the introduction of the BSET requirement. Chi-square analysis was used to explore changes in the proportion of students completing and passing remedial courses. Finally, correlation analysis was used to explore the utility of the BSET in predicting subsequent college-level course performance. Differences based on subject area and race/ethnicity were explored. ^ The introduction of the BSET did not improve the performance of remedial completers in subsequent college-level courses in any of the subject areas. The BSET did have a negative impact on the success rate of students in remedial reading and mathematics courses. There was a significant decrease in minority students' likelihood of passing remedial reading and mathematics courses after the BSET was introduced. The reliability of the BSET is unacceptably low for all subject areas, based on estimates derived from administrations at M-DCC. Nevertheless, there was a significant positive relationship between BSET score and grade point average in subsequent college-level courses. This relationship varied by subject area and ethnicity, with the BSET reading score having no relationship with subsequent course performance for Black non-Hispanic students. ^ The BSET had no discernable positive effect on remedial student performance in subsequent college-level courses. In other words, the BSET has not enhanced the effectiveness of the remedial programs to prepare students for later coursework at M-DCC. The BSET had a negative impact on the progress and success of students in remedial reading and mathematics. ^

Seawater carbonate chemistry and sea urchin Paracentrotus lividus biological processes during experiments, 2011

Ocean acidification is predicted to have significant effects on benthic calcifying invertebrates, in particular on their early developmental stages. Echinoderm larvae could be particularly vulnerable to decreased pH, with major consequences for adult populations. The objective of this study was to understand how ocean acidification would affect the initial life stages of the sea urchin Paracentrotus lividus, a common species that is widely distributed in the Mediterranean Sea and the NE Atlantic. The effects of decreased pH (elevated PCO2) were investigated through physiological and molecular analyses on both embryonic and larval stages. Eggs and larvae were reared in Mediterranean seawater at six pH levels, i.e. pHT 8.1, 7.9, 7.7, 7.5, 7.25 and 7.0. Fertilization success, survival, growth and calcification rates were monitored over a 3 day period. The expression of genes coding for key proteins involved in development and biomineralization was also monitored. Paracentrotus lividus appears to be extremely resistant to low pH, with no effect on fertilization success or larval survival. Larval growth was slowed when exposed to low pH but with no direct impact on relative larval morphology or calcification down to pHT 7.25. Consequently, at a given time, larvae exposed to low pH were present at a normal but delayed larval stage. More surprisingly, candidate genes involved in development and biomineralization were upregulated by factors of up to 26 at low pH. Our results revealed plasticity at the gene expression level that allows a normal, but delayed, development under low pH conditions.

Search for associations containing young stars (SACY). VII. New stellar and substellar candidate members in the young associations

Context. The young associations offer us one of the best opportunities to study the properties of young stellar and substellar objects and to directly image planets thanks to their proximity (<200 pc) and age (≈5−150 Myr). However, many previous works have been limited to identifying the brighter, more active members (≈1 M_⊙) owing to photometric survey sensitivities limiting the detections of lower mass objects. Aims. We search the field of view of 542 previously identified members of the young associations to identify wide or extremely wide (1000−100 000 au in physical separation) companions. Methods. We combined 2MASS near-infrared photometry (J, H, K) with proper motion values (from UCAC4, PPMXL, NOMAD) to identify companions in the field of view of known members. We collated further photometry and spectroscopy from the literature and conducted our own high-resolution spectroscopic observations for a subsample of candidate members. This complementary information allowed us to assess the efficiency of our method. Results. We identified 84 targets (45: 0.2−1.3 M_⊙, 17: 0.08−0.2 M_⊙, 22: <0.08 M_⊙) in our analysis, ten of which have been identified from spectroscopic analysis in previous young association works. For 33 of these 84, we were able to further assess their membership using a variety of properties (X-ray emission, UV excess, Hα, lithium and K I equivalent widths, radial velocities, and CaH indices). We derive a success rate of 76–88% for this technique based on the consistency of these properties. Conclusions. Once confirmed, the targets identified in this work would significantly improve our knowledge of the lower mass end of the young associations. Additionally, these targets would make an ideal new sample for the identification and study of planets around nearby young stars. Given the predicted substellar mass of the majority of these new candidate members and their proximity, high-contrast imaging techniques would facilitate the search for new low-mass planets.

Ocean acidification and its potential effects on the early life-history of non-calcifying and calcifying echinoderm (Odontaster validus, Patiriella regularis and Arachnoides placenta) larvae, 2011

Ocean acidification, as a result of increased atmospheric CO2, has the potential to adversely affect the larval stages of many marine organisms and hence have profound effects on marine ecosystems. This is the first study of its kind to investigate the effects of ocean acidification on the early life-history stages of three echinoderms species, two asteroids and one irregular echinoid. Potential latitudinal variations on the effects of ocean acidification were also investigated by selecting a polar species (Odontaster validus), a temperate species (Patiriella regularis), and a tropical species (Arachnoides placenta). The effects of reduced seawater pH levels on the fertilization of gametes, larval survival and morphometrics on the aforementioned species were evaluated under experimental conditions. The pH levels considered for this research include ambient seawater (pH 8.1 or pH 8.2), levels predicted for 2100 (pH 7.7 and pH 7.6) and the extreme pH of 7.0, adjusted by bubbling CO2 gas into filtered seawater. Fertilization for Odontaster validus and Patiriella regularis for the predicted scenarios for 2100 was robust, whereas fertilization was significantly reduced in Arachnoides placenta. Larval survival was robust for the three species at pH 7.8, but numbers declined when pH dropped below 7.6. Normal A. placenta larvae developed in pH 7.8, whereas smaller larvae were observed for O. validus and P. regularis under the same pH treatment. Seawater pH levels below 7.6 resulted in smaller and underdeveloped larvae for all three species. The greatest effects were expected for the Antarctic asteroid O. validus but overall the tropical sand dollar A. placenta was the most affected by the reduction in seawater pH. The effects of ocean acidification on the asteroids O. validus and P. regulars, and the sand dollar A. placenta are species-specific. Several parameters, such as taxonomic differences, physiology, genetic makeup and the population's evolutionary history may have contributed to this variability. This study highlights the vulnerability of the early developmental stages and the complexity of ocean acidification. However, future research is needed to understand the effects at individual, community and ecosystem levels.

Seawater carbonate chemistry and biological processes during experiments with oyster Crassostrea gigas, 2009

An increasing number of studies are now reporting the effects of ocean acidification on a broad range of marine species, processes and systems. Many of these are investigating the sensitive early life-history stages that several major reviews have highlighted as being potentially most susceptible to ocean acidification. Nonetheless there remain few investigations of the effects of ocean acidification on the very earliest, and critical, process of fertilization, and still fewer that have investigated levels of ocean acidification relevant for the coming century. Here we report the effects of near-future levels of ocean acidification (?0.35 pH unit change) on sperm swimming speed, sperm motility, and fertilization kinetics in a population of the Pacific oyster Crassostrea gigas from western Sweden. We found no significant effect of ocean acidification - a result that was well-supported by power analysis. Similar findings from Japan suggest that this may be a globally robust result, and we emphasise the need for experiments on multiple populations from throughout a species' range. We also discuss the importance of sound experimental design and power analysis in meaningful interpretation of non-significant results.

Feasibility of MR-Based Body Composition Analysis in Large Scale Population Studies

Introduction Quantitative and accurate measurements of fat and muscle in the body are important for prevention and diagnosis of diseases related to obesity and muscle degeneration. Manually segmenting muscle and fat compartments in MR body-images is laborious and time-consuming, hindering implementation in large cohorts. In the present study, the feasibility and success-rate of a Dixon-based MR scan followed by an intensity-normalised, non-rigid, multi-atlas based segmentation was investigated in a cohort of 3,000 subjects. Materials and Methods 3,000 participants in the in-depth phenotyping arm of the UK Biobank imaging study underwent a comprehensive MR examination. All subjects were scanned using a 1.5 T MR-scanner with the dual-echo Dixon Vibe protocol, covering neck to knees. Subjects were scanned with six slabs in supine position, without localizer. Automated body composition analysis was performed using the AMRA Profiler™ system, to segment and quantify visceral adipose tissue (VAT), abdominal subcutaneous adipose tissue (ASAT) and thigh muscles. Technical quality assurance was performed and a standard set of acceptance/rejection criteria was established. Descriptive statistics were calculated for all volume measurements and quality assurance metrics. Results Of the 3,000 subjects, 2,995 (99.83%) were analysable for body fat, 2,828 (94.27%) were analysable when body fat and one thigh was included, and 2,775 (92.50%) were fully analysable for body fat and both thigh muscles. Reasons for not being able to analyse datasets were mainly due to missing slabs in the acquisition, or patient positioned so that large parts of the volume was outside of the field-of-view. Discussion and Conclusions In conclusion, this study showed that the rapid UK Biobank MR-protocol was well tolerated by most subjects and sufficiently robust to achieve very high success-rate for body composition analysis. This research has been conducted using the UK Biobank Resource.