A Multiplex Real-Time PCR with High Resolution Melting Analysis for the Characterization of Antimicrobial Resistance in Neisseria gonorrhoeae.

Resistance to antibiotics used against Neisseria gonorrhoeae infections is a major public health concern. Antimicrobial resistance (AMR) testing relies on time-consuming culture-based methods. Development of rapid molecular tests for detecting AMR determinants could provide valuable tools for surveillance, epidemiological studies and to inform individual case management. We developed a fast (<1.5 hrs) SYBR-green based real-time PCR method with high resolution melting (HRM) analysis. One triplex and three duplex reactions included two sequences for N. gonorrhoeae identification and seven determinants of resistance to extended-spectrum cephalosporins (ESCs), azithromycin, ciprofloxacin, and spectinomycin. The method was validated by testing 39 previously fully-characterized N. gonorrhoeae strains, 19 commensal Neisseria spp., and an additional panel of 193 gonococcal isolates. Results were compared with culture-based AMR determination. The assay correctly identified N. gonorrhoeae and the presence or absence of the seven AMR determinants. There was some cross-reactivity with non-gonococcal Neisseria species and the detection limit was 10(3)-10(4) gDNA copies/reaction. Overall, the platform accurately detected resistance to ciprofloxacin (sensitivity and specificity, 100%), ceftriaxone (sensitivity 100%, specificity 90%), cefixime (sensitivity 92%, specificity 94%), azithromycin and spectinomycin (both sensitivity and specificity, 100%). In conclusion, our methodology accurately detects mutations generating resistance to antibiotics used to treat gonorrhea. Low assay sensitivity prevents direct diagnostic testing of clinical specimens but this method can be used to screen collections of gonococcal isolates for AMR more quickly than with current culture-based AMR testing.

Approaches and Strategy for Cancer Research and Surveillance Data: Integration, Information Pipeline, Data Models, and Informatics Opportunities

Thesis (Ph.D.)--University of Washington, 2016-04

Relational incentive policies in cross-border interfirm relationships

How an exporter can effectively craft a distributor agreement that encourages its network of foreign distributors to respond in pro-relational ways? This is an important issue as previous research has shown that relationship quality was linked to export performance. However, research failed to propose managerial tools that allowed exporters to foster relational phenomena in cross-border relationships. In this study, we suggest that exporters can influence importers' attitudes and behaviors with relational incentives policies. We also show that the impact of these policies is impervious to the noise, i.e., psychic distance and information asymmetry, that characterizes international business relationships. Our hypotheses are tested via structural equations modeling with data from a sample of French exporters.

Selection of simulation tools for improving supply chain performance

Simulation is an effective method for improving supply chain performance. However, there is limited advice available to assist practitioners in selecting the most appropriate method for a given problem. Much of the advice that does exist relies on custom and practice rather than a rigorous conceptual or empirical analysis. An analysis of the different modelling techniques applied in the supply chain domain was conducted, and the three main approaches to simulation used were identified; these are System Dynamics (SD), Discrete Event Simulation (DES) and Agent Based Modelling (ABM). This research has examined these approaches in two stages. Firstly, a first principles analysis was carried out in order to challenge the received wisdom about their strengths and weaknesses and a series of propositions were developed from this initial analysis. The second stage was to use the case study approach to test these propositions and to provide further empirical evidence to support their comparison. The contributions of this research are both in terms of knowledge and practice. In terms of knowledge, this research is the first holistic cross paradigm comparison of the three main approaches in the supply chain domain. Case studies have involved building ‘back to back’ models of the same supply chain problem using SD and a discrete approach (either DES or ABM). This has led to contributions concerning the limitations of applying SD to operational problem types. SD has also been found to have risks when applied to strategic and policy problems. Discrete methods have been found to have potential for exploring strategic problem types. It has been found that discrete simulation methods can model material and information feedback successfully. Further insights have been gained into the relationship between modelling purpose and modelling approach. In terms of practice, the findings have been summarised in the form of a framework linking modelling purpose, problem characteristics and simulation approach.

The use of ICT by logistics service providers and implications for training needs:a cross-country perspective

Changes in the international economic scenario in recent years have made it necessary for both industrial and service firms to reformulate their strategies, with a strong focus on the resources required for successful implementation. In this scenario, information and communication technologies (ICT) has a potentially vital role to play both as a key resource for re-engineering business processes within a framework of direct connection between suppliers and customers, and as a source of cost optimisation. There have also been innovations in the logistics and freight transport industry in relation to ICT diffusion. The implementation of such systems by third party logistics providers (3PL) allows the real-time exchange of information between supply chain partners, thereby improving planning capability and customer service. Unlike other industries, the logistics and freight transport industry is lagging somewhat behind other sectors in ICT diffusion. This situation is to be attributed to a series of both industry-specific and other factors, such as: (a) traditional resistance to change on the part of transport and logistics service providers; (b) the small size of firms that places considerable constraints upon investment in ICT; (c) the relative shortage of user-friendly applications; (d) the diffusion of internal standards on the part of the main providers in the industry whose aim is to protect company information, preventing its dissemination among customers and suppliers; (e) the insufficient degree of professional skills for using such technologies on the part of staff in such firms. The latter point is of critical importance insofar as the adoption of ICT is making it increasingly necessary both to develop new technical skills to use different hardware and new software tools, and to be able to plan processes of communication so as to allow the optimal use of ICT. The aim of this paper is to assess the impact of ICT on transport and logistics industry and to highlight how the use of such new technologies is affecting providers' training needs. The first part will provide a conceptual framework of the impact of ICT on the transport and logistics industry. In the second part the state of ICT dissemination in the Italian and Irish third party logistics industry will be outlined. In the third part, the impact of ICT on the training needs of transport and logistics service providers - based on case studies in both countries - are discussed. The implications of the foregoing for the development of appropriate training policies are considered. For the covering abstract see ITRD E126595.

A "Cross-technology" Software Development Approach

Contemporary web-based software solutions are usually composed of many interoperating applications. Classical approach is the different applications of the solution to be created inside one technology/platform, e.g. Java-technology, .NET-technology, etc. Wide spread technologies/platforms practically discourage (and sometime consciously make impossible) the cooperation with elements of the concurrent technologies/platforms. To make possible the usage of attractive features of one technology/platform in another technology/platform some “cross-technology” approach is necessary. In the paper is discussed the possibility to combine two existing instruments – interoperability protocols and “lifting” of procedures – in order to obtain such cross-technology approach.

How to Elaborate a Demonstrator in Inspiring Science Education Platform

Report published in the Proceedings of the National Conference on "Education and Research in the Information Society", Plovdiv, May, 2016

A research platform for artificial neural networks with applications in pediatric epilepsy

This dissertation established a state-of-the-art programming tool for designing and training artificial neural networks (ANNs) and showed its applicability to brain research. The developed tool, called NeuralStudio, allows users without programming skills to conduct studies based on ANNs in a powerful and very user friendly interface. A series of unique features has been implemented in NeuralStudio, such as ROC analysis, cross-validation, network averaging, topology optimization, and optimization of the activation function’s slopes. It also included a Support Vector Machines module for comparison purposes. Once the tool was fully developed, it was applied to two studies in brain research. In the first study, the goal was to create and train an ANN to detect epileptic seizures from subdural EEG. This analysis involved extracting features from the spectral power in the gamma frequencies. In the second application, a unique method was devised to link EEG recordings to epileptic and nonepileptic subjects. The contribution of this method consisted of developing a descriptor matrix that can be used to represent any EEG file regarding its duration and the number of electrodes. The first study showed that the inter-electrode mean of the spectral power in the gamma frequencies and its duration above a specific threshold performs better than the other frequencies in seizure detection, exhibiting an accuracy of 95.90%, a sensitivity of 92.59%, and a specificity of 96.84%. The second study yielded that Hjorth’s parameter activity is sufficient to accurately relate EEG to epileptic and non-epileptic subjects. After testing, accuracy, sensitivity and specificity of the classifier were all above 0.9667. Statistical tests measured the superiority of activity at over 99.99 % certainty. It was demonstrated that (1) the spectral power in the gamma frequencies is highly effective in locating seizures from EEG and (2) activity can be used to link EEG recordings to epileptic and non-epileptic subjects. These two studies required high computational load and could be addressed thanks to NeuralStudio. From a medical perspective, both methods proved the merits of NeuralStudio in brain research applications. For its outstanding features, NeuralStudio has been recently awarded a patent (US patent No. 7502763).

A Research Platform for Artificial Neural Networks with Applications in Pediatric Epilepsy

This dissertation established a state-of-the-art programming tool for designing and training artificial neural networks (ANNs) and showed its applicability to brain research. The developed tool, called NeuralStudio, allows users without programming skills to conduct studies based on ANNs in a powerful and very user friendly interface. A series of unique features has been implemented in NeuralStudio, such as ROC analysis, cross-validation, network averaging, topology optimization, and optimization of the activation function’s slopes. It also included a Support Vector Machines module for comparison purposes. Once the tool was fully developed, it was applied to two studies in brain research. In the first study, the goal was to create and train an ANN to detect epileptic seizures from subdural EEG. This analysis involved extracting features from the spectral power in the gamma frequencies. In the second application, a unique method was devised to link EEG recordings to epileptic and non-epileptic subjects. The contribution of this method consisted of developing a descriptor matrix that can be used to represent any EEG file regarding its duration and the number of electrodes. The first study showed that the inter-electrode mean of the spectral power in the gamma frequencies and its duration above a specific threshold performs better than the other frequencies in seizure detection, exhibiting an accuracy of 95.90%, a sensitivity of 92.59%, and a specificity of 96.84%. The second study yielded that Hjorth’s parameter activity is sufficient to accurately relate EEG to epileptic and non-epileptic subjects. After testing, accuracy, sensitivity and specificity of the classifier were all above 0.9667. Statistical tests measured the superiority of activity at over 99.99 % certainty. It was demonstrated that 1) the spectral power in the gamma frequencies is highly effective in locating seizures from EEG and 2) activity can be used to link EEG recordings to epileptic and non-epileptic subjects. These two studies required high computational load and could be addressed thanks to NeuralStudio. From a medical perspective, both methods proved the merits of NeuralStudio in brain research applications. For its outstanding features, NeuralStudio has been recently awarded a patent (US patent No. 7502763).

Westminster Serious Games Platform (wmin-SGP) a tool for real-time authoring of roleplay simulations for learning

The use of serious games in education and their pedagogical benefit is being widely recognized. However, effective integration of serious games in education depends on addressing two big challenges: the successful incorporation of motivation and engagement that can lead to learning; and the highly specialised skills associated with customised development to meet the required pedagogical objectives. This paper presents the Westminster Serious Games Platform (wmin-SGP) an authoring tool that allows educators/domain experts without games design and development technical skills to create bespoke roleplay simulations in three dimensional scenes featuring fully embodied virtual humans capable of verbal and non-verbal interaction with users fit for specific educational objectives. The paper presents the wmin-SGP system architecture and it evaluates its effectiveness in fulfilling its purpose via the implementation of two roleplay simulations, one for Politics and one for Law. In addition, it presents the results of two types of evaluation that address how successfully the wmin-SGP combines usability principles and game core drives based on the Octalysis gamification framework that lead to motivating games experiences. The evaluation results shows that the wmin-SGP: provides an intuitive environment and tools that support users without advanced technical skills to create in real-time bespoke roleplay simulations in advanced graphical interfaces; satisfies most of the usability principles; and provides balanced simulations based on the Octalysis framework core drives. The paper concludes with a discussion of future extension of this real time authoring tool and directions for further development of the Octalysis framework to address learning.

The design and Evaluation of 'CAP Tools' - A computer aided parallelisation tool-kit

Abstract not available

Software tools for automating the parallelisation of FORTRAN computational mechanics codes

It is now clear that the concept of a HPC compiler which automatically produces highly efficient parallel implementations is a pipe-dream. Another route is to recognise from the outset that user information is required and to develop tools that embed user interaction in the transformation of code from scalar to parallel form, and then use conventional compilers with a set of communication calls. This represents the key idea underlying the development of the CAPTools software environment. The initial version of CAPTools is focused upon single block structured mesh computational mechanics codes. The capability for unstructured mesh codes is under test now and block structured meshes will be included next. The parallelisation process can be completed rapidly for modest codes and the parallel performance approaches that which is delivered by hand parallelisations.

New tools for cognitive and motor rehabilitation: development and clinical validation

Nervous system disorders are associated with cognitive and motor deficits, and are responsible for the highest disability rates and global burden of disease. Their recovery paths are vulnerable and dependent on the effective combination of plastic brain tissue properties, with complex, lengthy and expensive neurorehabilitation programs. This work explores two lines of research, envisioning sustainable solutions to improve treatment of cognitive and motor deficits. Both projects were developed in parallel and shared a new sensible approach, where low-cost technologies were integrated with common clinical operative procedures. The aim was to achieve more intensive treatments under specialized monitoring, improve clinical decision-making and increase access to healthcare. The first project (articles I – III) concerned the development and evaluation of a web-based cognitive training platform (COGWEB), suitable for intensive use, either at home or at institutions, and across a wide spectrum of ages and diseases that impair cognitive functioning. It was tested for usability in a memory clinic setting and implemented in a collaborative network, comprising 41 centers and 60 professionals. An adherence and intensity study revealed a compliance of 82.8% at six months and an average of six hours/week of continued online cognitive training activities. The second project (articles IV – VI) was designed to create and validate an intelligent rehabilitation device to administer proprioceptive stimuli on the hemiparetic side of stroke patients while performing ambulatory movement characterization (SWORD). Targeted vibratory stimulation was found to be well tolerated and an automatic motor characterization system retrieved results comparable to the first items of the Wolf Motor Function Test. The global system was tested in a randomized placebo controlled trial to assess its impact on a common motor rehabilitation task in a relevant clinical environment (early post-stroke). The number of correct movements on a hand-to-mouth task was increased by an average of 7.2/minute while the probability to perform an error decreased from 1:3 to 1:9. Neurorehabilitation and neuroplasticity are shifting to more neuroscience driven approaches. Simultaneously, their final utility for patients and society is largely dependent on the development of more effective technologies that facilitate the dissemination of knowledge produced during the process. The results attained through this work represent a step forward in that direction. Their impact on the quality of rehabilitation services and public health is discussed according to clinical, technological and organizational perspectives. Such a process of thinking and oriented speculation has led to the debate of subsequent hypotheses, already being explored in novel research paths.

New Library-curated Faculty Profile Platform Launches Through bepress

As faculty needs evolve and become increasingly digital, libraries are feeling the pressure to provide relevant new services. At the same time, faculty members are struggling to create and maintain their professional reputations online. We at bepress are happy to announce the new SelectedWorks, the fully hosted, library-curated faculty profile platform that positions the library to better support faculty as well as the institution at large. Beverly Lysobey, Digital Commons and Resource Management Librarian, at Sacred Heart University, says: “Both faculty and administration have been impressed with the services we provide through SelectedWorks; we’re able to show how much our faculty really publishes, and it’s great for professors to get that recognition. We’ve had several faculty members approach us for help making sure their record was complete when they were up for tenure, and we’ve even found articles that authors themselves no longer had access to.” With consistent, organized, institution-branded profiles, SelectedWorks increases campus-wide exposure and supports the research mission of the university. As the only profile platform integrated with the fully hosted Digital Commons suite of publishing and repository services, it also ensures that the institution retains management of its content. Powerful integration with the Digital Commons platform lets the home institution more fully capture the range of scholarship produced on campus, and hosted services facilitate resource consolidation and reduces strain on IT. The new SelectedWorks features a modern, streamlined design that provides compelling display options for the full range of faculty work. It beautifully showcases streaming media, images, data, teaching materials, books – any type of content that researchers now produce as part of their scholarship. Detailed analytics tools let authors and librarians measure global readership and track impact for a variety of campus stakeholders: authors can see the universities, agencies, and businesses that are reading their work, and can easily export reports to use in tenure and promotion dossiers. Janelle Wertzbeger, Assistant Dean and Director of Scholarly Communications at Gettysburg College’s Musselman Library, says, “The new author dashboard maps and enhanced readership are SO GOOD. Every professor up for promotion & tenure should use them!” And of course, SelectedWorks is fully backed by the continual efforts of the bepress development team to provide maximum discoverability to search engines, increasing impact for faculty and institutions alike: Reverend Edward R. Udovic, Vice President for Teaching and Learning Resources at DePaul University, says, “In the last several months downloads of my scholarship from my [SelectedWorks] site have far surpassed the total distribution of all my work in the previous twenty five years.”

How Psychiatry Journals Support the Unbiased Translation of Clinical Research. A Cross-Sectional Study of Editorial Policies

Introduction: Reporting guidelines (e. g. CONSORT) have been developed as tools to improve quality and reduce bias in reporting research findings. Trial registration has been recommended for countering selective publication. The International Committee of Medical Journal Editors (ICMJE) encourages the implementation of reporting guidelines and trial registration as uniform requirements (URM). For the last two decades, however, biased reporting and insufficient registration of clinical trials has been identified in several literature reviews and other investigations. No study has so far investigated the extent to which author instructions in psychiatry journals encourage following reporting guidelines and trial registration. Method: Psychiatry Journals were identified from the 2011 Journal Citation Report. Information given in the author instructions and during the submission procedure of all journals was assessed on whether major reporting guidelines, trial registration and the ICMJE's URM in general were mentioned and adherence recommended. Results: We included 123 psychiatry journals (English and German language) in our analysis. A minority recommend or require 1) following the URM (21%), 2) adherence to reporting guidelines such as CONSORT, PRISMA, STROBE (23%, 7%, 4%), or 3) registration of clinical trials (34%). The subsample of the top-10 psychiatry journals (ranked by impact factor) provided much better but still improvable rates. For example, 70% of the top-10 psychiatry journals do not ask for the specific trial registration number. Discussion: Under the assumption that better reported and better registered clinical research that does not lack substantial information will improve the understanding, credibility, and unbiased translation of clinical research findings, several stakeholders including readers (physicians, patients), authors, reviewers, and editors might benefit from improved author instructions in psychiatry journals. A first step of improvement would consist in requiring adherence to the broadly accepted reporting guidelines and to trial registration.