Transporter associated with antigen processing preselection of peptides binding to the MHC:a bioinformatic evaluation

TAP is responsible for the transit of peptides from the cytosol to the lumen of the endoplasmic reticulum. In an immunological context, this event is followed by the binding of peptides to MHC molecules before export to the cell surface and recognition by T cells. Because TAP transport precedes MHC binding, TAP preferences may make a significant contribution to epitope selection. To assess the impact of this preselection, we have developed a scoring function for TAP affinity prediction using the additive method, have used it to analyze and extend the TAP binding motif, and have evaluated how well this model acts as a preselection step in predicting MHC binding peptides. To distinguish between MHC alleles that are exclusively dependent on TAP and those exhibiting only a partial dependence on TAP, two sets of MHC binding peptides were examined: HLA-A*0201 was selected as a representative of partially TAP-dependent HLA alleles, and HLA-A*0301 represented fully TAP-dependent HLA alleles. TAP preselection has a greater impact on TAP-dependent alleles than on TAP-independent alleles. The reduction in the number of nonbinders varied from 10% (TAP-independent) to 33% (TAP-dependent), suggesting that TAP preselection is an important component in the successful in silico prediction of T cell epitopes.

Channel estimation and compensation in chromatic dispersion limited optical fast OFDM systems

We experimentally investigate the channel estimation and compensation in a chromatic dispersion (CD) limited 20Gbit/s optical fast orthogonal frequency division multiplexing (F-OFDM) system with up to 840km transmission. It is shown that symmetric extension based guard interval (GI) is required to enable CD compensation using one-tap equalizers. As few as one optical F-OFDM symbol with four and six pilot tones per symbol can achieve near-optimal channel estimation and compensation performance for 600km and 840km respectively.

JenPep : a novel computational information resource for immunobiology and vaccinology

JenPep is a relational database containing a compendium of thermodynamic binding data for the interaction of peptides with a range of important immunological molecules:  the major histocompatibility complex, TAP transporter, and T cell receptor. The database also includes annotated lists of B cell and T cell epitopes. Version 2.0 of the database is implemented in a bespoke postgreSQL database system and is fully searchable online via a perl/HTML interface (URL:  http://www.jenner.ac.uk/JenPep).

Genetic Algorithm Approach for Solving the Task Assignment Problem

This research was partially supported by the Serbian Ministry of Science and Ecology under project 144007. The authors are grateful to Ivana Ljubić for help in testing and to Vladimir Filipović for useful suggestions and comments.

Why do doctored images distort memory?

Doctored images can cause people to believe in and remember experiences that never occurred, yet the underlying mechanism(s) responsible are not well understood. How does compelling false evidence distort autobiographical memory? Subjects were filmed observing and copying a Research Assistant performing simple actions, then they returned 2 days later for a memory test. Before taking the test, subjects viewed video-clips of simple actions, including actions that they neither observed nor performed earlier. We varied the format of the video-clips between-subjects to tap into the source-monitoring mechanisms responsible for the 'doctored-evidence effect.' The distribution of belief and memory distortions across conditions suggests that at least two mechanisms are involved: doctored images create an illusion of familiarity, and also enhance the perceived credibility of false suggestions. These findings offer insight into how external evidence influences source-monitoring. © 2009 Elsevier Inc. All rights reserved.

International session at the BCLA conference

Full text: It seems a long time ago now since we were at the BCLA conference. The excellent FIFA World Cup in Brazil kept us occupied over the summer as well as Formula 1, Wimbledon, Tour de France, Commonwealth Games and of course exam paper marking! The BCLA conference this year was held in Birmingham at the International Convention Centre which again proved to be a great venue. The number of attendees overall was up on previous years, and at a record high of 1500 people. Amongst the highlights at this year's annual conference was the live surgery link where Professor Sunil Shah demonstrated the differences in technique between traditional phacoemulsification cataract surgery and femtosecond assisted phacoemulsification cataract surgery. Dr. Raquel Gil Cazorla, a research optometrist at Aston University, assisted in the procedure including calibrating the femtosecond laser. Another highlight for me was the session that I chaired, which was the international session organised by IACLE (International Association of CL Educators). There was a talk by Mirjam van Tilborg about dry eye prevalence in the Netherlands and how it was managed by medical general practitioners (GPs) or optometrists. It was interesting to know that there are only 2 schools of optometry there and currently under 1000 registered optometrists there. It also seems that GPs were more likely to blame CL as the cause for dry eye whereas optometrists who had a fuller range of tests were better at solving the issue. The next part of the session included the presentation of 5 selected posters from around the world. The posters were also displayed in the main poster area but were selected to be presented here as they had international relevance. The posters were: 1. Motivators and Barriers for Contact Lens Recommendation and Wear by Nilesh Thite (India) 2. Contact lens hygiene among Saudi wearers by Dr. Ali Masmaly (Saudi) 3. Trends of contact lens prescribing and patterns of contact lens practice in Jordan by Dr. Mera Haddad (Jordan) 4. Contact Lens Behaviour in Greece by Dr. Dimitra Makrynioti (Greece) 5. How practitioners inform ametropes about the benefits of contact lenses and overcome the potential barriers: an Italian survey, by Dr. Fabrizio Zeri (Italy) It was interesting to learn about CL practice in different parts, for example the CL wearing population ration in Saudi Arabia is around 1:2 Male:Female (similar to other parts of the world) and although the sale of CL is restricted to registered practitioners there are many unregistered outlets, like clothing stores, that flout the rules. In Jordan some older practitioners will still advise patients to use tap water or even saliva! But thankfully the newer generation of practitioners have been educated not to advise this. In Greece one of the concerns was that some practitioners may advise patients to use disposable lenses for longer than they should and again it seems to be the practitioners with inadequate education that would do this. In India it was found that cost was one barrier to using contact lenses but also some practitioners felt that they shouldn’t offer CLs due to cost too. In Italy sensitive eyes and CL care and maintenance were the barriers to CL wear but the motivators were vision and comfort and aesthetics. Finally the international session ended with the IACLE travel award and educator awards presented by IACLE president Shehzad Naroo and BCLA President Andrew Yorke. The travel award went to Wang Ling, Jinling Institute of Technology, Nanjing, China. There were 3 regional Contact Lens Educator of the Year Awards sponsored by Coopervision and presented by Dr. J.C. Aragorn of Coopervision. 1. Asia Pacific Region – Dr. Rajeswari Mahadevan of Sankara Nethralaya Medical Research Foundation, Chennai, India 2. Americas Region – Dr. Sergio Garcia of University of La Salle, Bogotá and the University Santo Tomás, Bucaramanga, Colombia 3. Europe/Africa – Middle East Region: Dr. Eef van der Worp, affiliated with the University of Maastricht, the Netherlands The posters above were just a small selection of those displayed at this year's BCLA conference. If you missed the BCLA conference then you can see the abstracts for all posters and talks in a virtual issue of CLAE very soon. The poster competition was kindly sponsored by Elsevier. The poster winner this year was: Joan Gispets – Corneal and Anterior Chamber Parameters in Keratoconus The 3 runners up were: Debby Yeung – Scleral Lens Central Corneal Clearance Assessment with Biomicroscopy Sarah L. Smith – Subjective Grading of Lid Margin Staining Heiko Pult – Impact of Soft Contact Lenses on Lid Parallel Conjunctival Folds My final two highlights are a little more personal. Firstly, I was awarded Honorary Life Fellowship of the BCLA for my work with the Journal, and I would like to thank the BCLA, Elsevier, the editorial board of CLAE, the reviewers and the authors for their support of my role. My final highlight from the BCLA conference this year was the final presentation of the conference – the BCLA Gold Medal award. The recipient this year was Professor Philip Morgan with his talk ‘Changing the world with contact lenses’. Phil was the person who advised me to go to my first BCLA conference in 1994 (funnily he didn’t attend himself as he was busy getting married!) and now 20 years later he was being honoured with the accolade of being the BCLA Gold Medallist. The date of his BCLA medal addressed was shared with his father's birthday so a double celebration for Phil. Well done to outgoing BCLA President Andy Yorke and his team at the BCLA (including Nick Rumney, Cheryl Donnelly, Sarah Greenwood and Amir Khan) on an excellent conference. And finally welcome to new President Susan Bowers. Copyright © 2014 British Contact Lens Association. Published by Elsevier Ltd. All rights reserved.

Solving the Task Assignment Problem with a Variable Neighborhood Search

In this paper a variable neighborhood search (VNS) approach for the task assignment problem (TAP) is considered. An appropriate neighborhood scheme along with a shaking operator and local search procedure are constructed specifically for this problem. The computational results are presented for the instances from the literature, and compared to optimal solutions obtained by the CPLEX solver and heuristic solutions generated by the genetic algorithm. It can be seen that the proposed VNS approach reaches all optimal solutions in a quite short amount of computational time.

Analysis of carrier phase extraction methods in 112-Gbit/s NRZ-PDM-QPSK coherent transmission system

We present a comparative analysis on three carrier phase extraction approaches, including a one-tap normalized least mean square method, a block-average method, and a Viterbi-Viterbi method, in coherent transmission system considering equalization enhanced phase noise. © OSA 2012.

Environmental lead contamination in Miami inner-city area

The purpose of the study was to evaluate the magnitude of environmental lead contamination in the downtown area of Miami. Lead inspections took place at 121 homes in Little Haiti and Liberty City and involved the collection ofrepresentative samples from floors, window wells, tap water, soil and air. Community health workers (CHWs) trained in interview and safety techniques went from door to door to enlist participation. On-site investigations were tailored to areas most utilized by children underthe age of6 years. The presence of lead-containing paint was also investigated in situ via X-ray fluorescence (XRF) analysis. Results: Of the sampling areas, the window wells area had the most abundant occurrence of lead. On analysis, 24% of sites returned window well samples with lead levels above Department of Housing and Urban Development (HUD) guidelines. Of the soil samples, the playgrounds around the house had the highest concentration of lead. Soil sampling demonstrated that 27.5% of sites returned samples with lead levels (400 to 1600 ppm) inexcess of HUD/Environmental Protection Agency (EPA) standards. Positive XRF readings in one or more components were returned by 18% of sites. Conclusions: More than half of the houses in these two neighborhoods exhibited unacceptably high levels of lead dust and soil in areas where children live and play. Limitations of this study did not allow the assessment of how many children in this area are affected. A more comprehensive study including other areas of Miami-Dade County with older housing stock is recommended.

Assessing the construct validity of a measure of learning agility

This study examined the construct validity of the Choices questionnaire that purported to support the theory of Learning Agility. Specifically, Learning Agility attempts to predict an individual's potential performance in new tasks. The construct validity will be measured by examining the convergent/discriminant validity of the Choices Questionnaire against a cognitive ability measure and two personality measures. The Choices Questionnaire did tap a construct that is unique to the cognitive ability and the personality measures, thus suggesting that this measure may have considerable value in personnel selection. This study also examined the relationship of this pew measure to job performance and job promotability. Results of this study found that the Choices Questionnaire predicted job performance and job promotability above and beyond cognitive ability and personality. Data from 107 law enforcement officers, along with two of their co-workers and a supervisor resulted in a correlation of .08 between Learning Agility and cognitive ability. Learning Agility correlated .07 with Learning Goal Orientation and. 17 with Performance Goal Orientation. Correlations with the Big Five Personality factors ranged from −.06 to. 13 with Conscientiousness and Openness to Experience, respectively. Learning Agility correlated .40 with supervisory ratings of job promotability and correlated .3 7 with supervisory ratings of overall job performance. Hierarchical regression analysis found incremental validity for Learning Agility over cognitive ability and the Big Five factors of personality for supervisory ratings of both promotability and overall job performance. A literature review was completed to integrate the Learning Agility construct into a nomological net of personnel selection research. Additionally, practical applications and future research directions are discussed. ^

The order selection and lot sizing problem in the make-to-order environment

This research is motivated by the need for considering lot sizing while accepting customer orders in a make-to-order (MTO) environment, in which each customer order must be delivered by its due date. Job shop is the typical operation model used in an MTO operation, where the production planner must make three concurrent decisions; they are order selection, lot size, and job schedule. These decisions are usually treated separately in the literature and are mostly led to heuristic solutions. The first phase of the study is focused on a formal definition of the problem. Mathematical programming techniques are applied to modeling this problem in terms of its objective, decision variables, and constraints. A commercial solver, CPLEX is applied to solve the resulting mixed-integer linear programming model with small instances to validate the mathematical formulation. The computational result shows it is not practical for solving problems of industrial size, using a commercial solver. The second phase of this study is focused on development of an effective solution approach to this problem of large scale. The proposed solution approach is an iterative process involving three sequential decision steps of order selection, lot sizing, and lot scheduling. A range of simple sequencing rules are identified for each of the three subproblems. Using computer simulation as the tool, an experiment is designed to evaluate their performance against a set of system parameters. For order selection, the proposed weighted most profit rule performs the best. The shifting bottleneck and the earliest operation finish time both are the best scheduling rules. For lot sizing, the proposed minimum cost increase heuristic, based on the Dixon-Silver method performs the best, when the demand-to-capacity ratio at the bottleneck machine is high. The proposed minimum cost heuristic, based on the Wagner-Whitin algorithm is the best lot-sizing heuristic for shops of a low demand-to-capacity ratio. The proposed heuristic is applied to an industrial case to further evaluate its performance. The result shows it can improve an average of total profit by 16.62%. This research contributes to the production planning research community with a complete mathematical definition of the problem and an effective solution approach to solving the problem of industry scale.

Assessment of the occurrence and potential effects of pharmaceuticals and personal care products in South Florida waters and sediments

A LLE-GC-MS method was developed to detect PPCPs in surface water samples from Big Cypress National Park, Everglades National Park and Biscayne National Park in South Florida. The most frequently found PPCPs were caffeine, DEET and triclosan with detected maximum concentration of 169 ng/L, 27.9 ng/L and 10.9 ng/L, respectively. The detection frequencies of hormones were less than PPCPs. Detected maximal concentrations of estrone, 17β-estradiol, coprostan-3-ol, coprostane and coprostan-3-one were 5.98 ng/L, 3.34 ng/L, 16.5 ng/L, 13.5 ng/L and 6.79 ng/L, respectively. An ASE-SPE-GC-MS method was developed and applied to the analysis of the sediment and soil area where reclaimed water was used for irrigation. Most analytes were below detection limits, even though some of analytes were detected in the reclaimed water at relatively high concentrations corroborating the fact that PPCPs do not significantly partition to mineral phases. An online SPE-HPLC-APPI-MS/MS method and an online SPE-HPLC-HESI-MS/MS method were developed to analyze reclaimed water and drinking water samples. In the reclaimed water study, reclaimed water samples were collected from the sprinkler for a year-long period at Florida International University Biscayne Bay Campus, where reclaimed water was reused for irrigation. Analysis results showed that several analytes were continuously detected in all reclaimed water samples. Coprostanol, bisphenol A and DEET's maximum concentration exceeded 10 μg/L (ppb). The four most frequently detected compounds were diphenhydramine (100%), DEET (98%), atenolol (98%) and carbamazepine (96%). In the study of drinking water, 54 tap water samples were collected from the Miami-Dade area. The maximum concentrations of salicylic acid, ibuprofen and DEET were 521 ng/L, 301 ng/L and 290 ng/L, respectively. The three most frequently detected compounds were DEET (93%), carbamazepine (43%) and salicylic acid (37%), respectively. Because the source of drinking water in Miami-Dade County is the relatively pristine Biscayne aquifer, these findings suggest the presence of wastewater intrusions into the delivery system or the onset of direct influence of surface waters into the shallow aquifer.

Branch and price solution approach for order acceptance and capacity planning in make -to -order operations

The increasing emphasis on mass customization, shortened product lifecycles, synchronized supply chains, when coupled with advances in information system, is driving most firms towards make-to-order (MTO) operations. Increasing global competition, lower profit margins, and higher customer expectations force the MTO firms to plan its capacity by managing the effective demand. The goal of this research was to maximize the operational profits of a make-to-order operation by selectively accepting incoming customer orders and simultaneously allocating capacity for them at the sales stage. ^ For integrating the two decisions, a Mixed-Integer Linear Program (MILP) was formulated which can aid an operations manager in an MTO environment to select a set of potential customer orders such that all the selected orders are fulfilled by their deadline. The proposed model combines order acceptance/rejection decision with detailed scheduling. Experiments with the formulation indicate that for larger problem sizes, the computational time required to determine an optimal solution is prohibitive. This formulation inherits a block diagonal structure, and can be decomposed into one or more sub-problems (i.e. one sub-problem for each customer order) and a master problem by applying Dantzig-Wolfe’s decomposition principles. To efficiently solve the original MILP, an exact Branch-and-Price algorithm was successfully developed. Various approximation algorithms were developed to further improve the runtime. Experiments conducted unequivocally show the efficiency of these algorithms compared to a commercial optimization solver.^ The existing literature addresses the static order acceptance problem for a single machine environment having regular capacity with an objective to maximize profits and a penalty for tardiness. This dissertation has solved the order acceptance and capacity planning problem for a job shop environment with multiple resources. Both regular and overtime resources is considered. ^ The Branch-and-Price algorithms developed in this dissertation are faster and can be incorporated in a decision support system which can be used on a daily basis to help make intelligent decisions in a MTO operation.^

Branch and Price Solution Approach for Order Acceptance and Capacity Planning in Make-to-Order Operations

The increasing emphasis on mass customization, shortened product lifecycles, synchronized supply chains, when coupled with advances in information system, is driving most firms towards make-to-order (MTO) operations. Increasing global competition, lower profit margins, and higher customer expectations force the MTO firms to plan its capacity by managing the effective demand. The goal of this research was to maximize the operational profits of a make-to-order operation by selectively accepting incoming customer orders and simultaneously allocating capacity for them at the sales stage. For integrating the two decisions, a Mixed-Integer Linear Program (MILP) was formulated which can aid an operations manager in an MTO environment to select a set of potential customer orders such that all the selected orders are fulfilled by their deadline. The proposed model combines order acceptance/rejection decision with detailed scheduling. Experiments with the formulation indicate that for larger problem sizes, the computational time required to determine an optimal solution is prohibitive. This formulation inherits a block diagonal structure, and can be decomposed into one or more sub-problems (i.e. one sub-problem for each customer order) and a master problem by applying Dantzig-Wolfe’s decomposition principles. To efficiently solve the original MILP, an exact Branch-and-Price algorithm was successfully developed. Various approximation algorithms were developed to further improve the runtime. Experiments conducted unequivocally show the efficiency of these algorithms compared to a commercial optimization solver. The existing literature addresses the static order acceptance problem for a single machine environment having regular capacity with an objective to maximize profits and a penalty for tardiness. This dissertation has solved the order acceptance and capacity planning problem for a job shop environment with multiple resources. Both regular and overtime resources is considered. The Branch-and-Price algorithms developed in this dissertation are faster and can be incorporated in a decision support system which can be used on a daily basis to help make intelligent decisions in a MTO operation.

Multi-media filtration for removal of petroleum contamination

A pilot scale multi-media filtration system was used to evaluate the effectiveness of filtration in removing petroleum hydrocarbons from a source water contaminated with diesel fuel. Source water was artificially prepared by mixing bentonite clay and tap water to produce a turbidity range of 10-15 NTU. Diesel fuel concentrations of 150 ppm or 750 ppm were used to contaminate the source water. The coagulants used included Cat Floc K-10 and Cat Floc T-2. The experimental phase was conducted under direct filtration conditions at constant head and constant rate filtration at 8.0 gpm. Filtration experiments were run until the filter reached its clogging point as noted by a measured peak pressure loss of 10 psi. The experimental variables include type of coagulant, oil concentration and source water. Filtration results were evaluated based on turbidity removal and petroleum hydrocarbon (PHC) removal efficiency as measured by gas chromatography. Experiments indicated that clogging was controlled by the clay loading on the filter and that inadequate destabilization of the contaminated water by the coagulant limited the PHC removal. ^