Mean CD4 cell count changes in patients failing a first-line antiretroviral therapy in resource-limited settings

Background Changes in CD4 cell counts are poorly documented in individuals with low or moderate-level viremia while on antiretroviral treatment (ART) in resource-limited settings. We assessed the impact of on-going HIV-RNA replication on CD4 cell count slopes in patients treated with a first-line combination ART. Method Naïve patients on a first-line ART regimen with at least two measures of HIV-RNA available after ART initiation were included in the study. The relationships between mean CD4 cell count change and HIV-RNA at 6 and 12 months after ART initiation (M6 and M12) were assessed by linear mixed models adjusted for gender, age, clinical stage and year of starting ART. Results 3,338 patients were included (14 cohorts, 64% female) and the group had the following characteristics: a median follow-up time of 1.6 years, a median age of 34 years, and a median CD4 cell count at ART initiation of 107 cells/μL. All patients with suppressed HIV-RNA at M12 had a continuous increase in CD4 cell count up to 18 months after treatment initiation. By contrast, any degree of HIV-RNA replication both at M6 and M12 was associated with a flat or a decreasing CD4 cell count slope. Multivariable analysis using HIV-RNA thresholds of 10,000 and 5,000 copies confirmed the significant effect of HIV-RNA on CD4 cell counts both at M6 and M12. Conclusion In routinely monitored patients on an NNRTI-based first-line ART, on-going low-level HIV-RNA replication was associated with a poor immune outcome in patients who had detectable levels of the virus after one year of ART.

PyGirl Generating Whole-System VMs from high-level models using PyPy

Virtual machines emulating hardware devices are generally implemented in low-level languages and using a low-level style for performance reasons. This trend results in largely difficult to understand, difficult to extend and unmaintainable systems. As new general techniques for virtual machines arise, it gets harder to incorporate or test these techniques because of early design and optimization decisions. In this paper we show how such decisions can be postponed to later phases by separating virtual machine implementation issues from the high-level machine-specific model. We construct compact models of whole-system VMs in a high-level language, which exclude all low-level implementation details. We use the pluggable translation toolchain PyPy to translate those models to executables. During the translation process, the toolchain reintroduces the VM implementation and optimization details for specific target platforms. As a case study we implement an executable model of a hardware gaming device. We show that our approach to VM building increases understandability, maintainability and extendability while preserving performance.

PyGirl: Generating Whole-System VMs from High-Level Prototypes Using PyPy

Virtual machines (VMs) emulating hardware devices are generally implemented in low-level languages for performance reasons. This results in unmaintainable systems that are difficult to understand. In this paper we report on our experience using the PyPy toolchain to improve the portability and reduce the complexity of whole-system VM implementations. As a case study we implement a VM prototype for a Nintendo Game Boy, called PyGirl, in which the high-level model is separated from low-level VM implementation issues. We shed light on the process of refactoring from a low-level VM implementation in Java to a high-level model in RPython. We show that our whole-system VM written with PyPy is significantly less complex than standard implementations, without substantial loss in performance.

Analysis of ⁸⁵Kr: a comparison at the 10-14 level using micro-liter samples

The isotopic abundance of 85Kr in the atmosphere, currently at the level of 10−11, has increased by orders of magnitude since the dawn of nuclear age. With a half-life of 10.76 years, 85Kr is of great interest as tracers for environmental samples such as air, groundwater and ice. Atom Trap Trace Analysis (ATTA) is an emerging method for the analysis of rare krypton isotopes at isotopic abundance levels as low as 10−14 using krypton gas samples of a few micro-liters. Both the reliability and reproducibility of the method are examined in the present study by an inter-comparison among different instruments. The 85Kr/Kr ratios of 12 samples, in the range of 10−13 to 10−10, are measured independently in three laboratories: a low-level counting laboratory in Bern, Switzerland, and two ATTA laboratories, one in Hefei, China, and another in Argonne, USA. The results are in agreement at the precision level of 5%.

Towards high-level execution primitives for and-parallelism: preliminary results

Most implementations of parallel logic programming rely on complex low-level machinery which is arguably difflcult to implement and modify. We explore an alternative approach aimed at taming that complexity by raising core parts of the implementation to the source language level for the particular case of and-parallelism. Therefore, we handle a signiflcant portion of the parallel implementation mechanism at the Prolog level with the help of a comparatively small number of concurrency-related primitives which take care of lower-level tasks such as locking, thread management, stack set management, etc. The approach does not eliminate altogether modiflcations to the abstract machine, but it does greatly simplify them and it also facilitates experimenting with different alternatives. We show how this approach allows implementing both restricted and unrestricted (i.e., non fork-join) parallelism. Preliminary experiments show that the amount of performance sacriflced is reasonable, although granularity control is required in some cases. Also, we observe that the availability of unrestricted parallelism contributes to better observed speedups.

The assessment of the level of knowledge about dietary fibre among the portuguese population

The aim of this work was to assess the degree of knowledge about dietary fibre (DF), as influenced by factors such as age, gender, level of education and living environment. For this, a descriptive cross- sectional study was undertaken by means of a questionnaire and the total number of respondents was 382. The results revealed that the participants had a not satisfying global level of knowledge (3.59 ± 0.64, on a scale from 1 to 5). The overall knowledge was found lower for young adults aged 19 to 30 years, when compared to adults aged over 31 and up to 65 years, being this difference statistically significant (p=0.030). However, no statistical significant differences were found between genders, levels of education or living environments. The low level of knowledge demonstrated by the enquired alerts for the need to plan some additional actions to further inform the Portuguese population about dietary fibre.

Why is Coccidoxenoides perminutus, a mealybug parasitoid, ineffective as a biocontrol agent - Inaccurate measures of parasitism or low adult survival?

Coccidoxenoides perminutus achieves only low levels of parasitism of its host Planococcus citri in southeast Queensland citrus. Two possible causes were investigated. Adult survival under natural conditions was assessed to determine whether providing adult food sources could enhance survival. Behavioural changes of hosts, induced by C perminutus parasitism, was also investigated to establish if parasitised P. citri move from their feeding site to seek protected shelters some distance away and are thus not accounted for in field assessments of parasitism rates. Unparasitised mealybugs placed in the field for two periods were retrieved before the effects of parasitism were manifested and parasitism rates were still low (0.3% at 5 days and 1.2% at 10 days). Levels of locomotion of P. citri exposed to C perminutus were compared with those of unexposed ones. Parasitised mealybugs, regardless of instar, undergo behavioural changes. In comparison to unparasitised controls, the mealybugs become highly active 7-14 days after exposure to wasps. All parasitised mealybugs undergo physical changes, their body becomes cylindrical, their legs go so rigid that the mealybugs become immobile, and this signifies the typical mummy appearance. All mealybugs that became mummies eventually fell from the host lemon fruit because of impaired locomotion and were caught on sticky traps that had been placed beneath the lemons. Consequently, their final site of mummification was not established. C perminutus adults provided with nectar or honey survived longer (about 5 days) in the field than those without food (about a day). Nectar from two plant species, Alpinia zerumbet and Datura candida, proved to be good sources of food for the adult wasps, and were comparable in quality to honey. The low level of parasitism achieved by C perminutus in southeast Queensland citrus thus appears to be a consequence of the short adult life and the negative effects of a harsh environment. Provision of a suitable food source (e.g., nectar) may well enhance levels of parasitism in the field. (c) 2005 Elsevier Inc. All rights reserved.

A DHA14 drug efflux gene from Xanthomonas albilineans confers high-level albicidin antibiotic resistance in Escherichia coli

Aims: Identification of a gene for self-protection from the antibiotic-producing plant pathogen Xanthomonas albilineans, and functional testing by heterologous expression. Methods and Results: Albicidin antibiotics and phytotoxins are potent inhibitors of prokaryote DNA replication. A resistance gene (albF) isolated by shotgun cloning from the X. albilineans albicidin-biosynthesis region encodes a protein with typical features of DHA14 drug efflux pumps. Low-level expression of albF in Escherichia coli increased the MIC of albicidin 3000-fold, without affecting tsx-mediated albicidin uptake into the periplasm or resistance to other tested antibiotics. Bioinformatic analysis indicates more similarity to proteins involved in self-protection in polyketide-antibiotic-producing actinomycetes than to multi-drug resistance pumps in other Gram-negative bacteria. A complex promoter region may co-regulate albF with genes for hydrolases likely to be involved in albicidin activation or self-protection. Conclusions: AlbF is the first apparent single-component antibiotic-specific efflux pump from a Gram-negative antibiotic producer. It shows extraordinary efficiency as measured by resistance level conferred upon heterologous expression. Significance and Impact of the Study: Development of the clinical potential of albicidins as potent bactericidial antibiotics against diverse bacteria has been limited because of low yields in culture. Expression of albF with recently described albicidin-biosynthesis genes may enable large-scale production. Because albicidins are X. albilineans pathogenicity factors, interference with AlbF function is also an opportunity for control of the associated plant disease.

Low back pain patients demonstrate increased hip extensor muscle activity during standardized submaximal rotation efforts

Study Design. A comparative study of trunk and hip extensor muscle recruitment patterns in 2 subject groups. Objective. To examine for changes in recruitment of the hip and back extensor muscles during low level isometric trunk rotation efforts in chronic low back pain (CLBP) subjects by comparison with matched asymptomatic control subjects. Summary of Background Data. Anatomic and biomechanical models have provided evidence that muscles attaching to the thoracolumbar fascia (TLF) are important for providing stabilization to the lumbopelvic region during trunk rotation. This has guided rehabilitation programs. The muscles that link diagonally to the posterior layer of the TLF have not previously been examined individually and compared during low-level trunk rotation efforts in CLBP patients and matched controls. Methods. Thirty CLBP patients and 30 matched controls were assessed using surface electromyography (EMG) as they performed low-level isometric rotation efforts while standing upright. Muscles studied included latissimus dorsi, erector spinae, upper and lower gluteus maximus, and biceps femoris. Subjects performed the rotation exertion with various levels of external trunk support, related to different functional tasks. Results. EMG results demonstrated that subjects with CLBP had significantly higher levels of recruitment for the lower and upper gluteus maximus (P < 0.05), hamstrings (P < 0.05), and erector spinae muscles (P < 0.05) during rotation to the left compared with the control subjects. Conclusion. This study provided evidence of increased muscle recruitment in CLBP patients when performing a standardized trunk rotation task. These results may have implications for the design of therapeutic exercise programs for CLBP patients.

A co-ordinated business object approach for supporting tactical level management decisions

The proliferation of data throughout the strategic, tactical and operational areas within many organisations, has provided a need for the decision maker to be presented with structured information that is appropriate for achieving allocated tasks. However, despite this abundance of data, managers at all levels in the organisation commonly encounter a condition of ‘information overload’, that results in a paucity of the correct information. Specifically, this thesis will focus upon the tactical domain within the organisation and the information needs of management who reside at this level. In doing so, it will argue that the link between decision making at the tactical level in the organisation, and low-level transaction processing data, should be through a common object model that used a framework based upon knowledge leveraged from co-ordination theory. In order to achieve this, the Co-ordinated Business Object Model (CBOM) was created. Detailing a two-tier framework, the first tier models data based upon four interactive object models, namely, processes, activities, resources and actors. The second tier analyses the data captured by the four object models, and returns information that can be used to support tactical decision making. In addition, the Co-ordinated Business Object Support System (CBOSS), is a prototype tool that has been developed in order to both support the CBOM implementation, and to also demonstrate the functionality of the CBOM as a modelling approach for supporting tactical management decision making. Containing a graphical user interface, the system’s functionality allows the user to create and explore alternative implementations of an identified tactical level process. In order to validate the CBOM, three verification tests have been completed. The results provide evidence that the CBOM framework helps bridge the gap between low level transaction data, and the information that is used to support tactical level decision making.

High Level Color Similarity Retrieval

In this paper a new method for image retrieval using high level color semantic features is proposed. It is based on extraction of low level color characteristics and their conversion into high level semantic features using Johannes Itten theory of color, Dempster-Shafer theory of evidence and fuzzy production rules.

Formal modeling and analysis techniques for high level Petri nets

Petri Nets are a formal, graphical and executable modeling technique for the specification and analysis of concurrent and distributed systems and have been widely applied in computer science and many other engineering disciplines. Low level Petri nets are simple and useful for modeling control flows but not powerful enough to define data and system functionality. High level Petri nets (HLPNs) have been developed to support data and functionality definitions, such as using complex structured data as tokens and algebraic expressions as transition formulas. Compared to low level Petri nets, HLPNs result in compact system models that are easier to be understood. Therefore, HLPNs are more useful in modeling complex systems. ^ There are two issues in using HLPNs—modeling and analysis. Modeling concerns the abstracting and representing the systems under consideration using HLPNs, and analysis deals with effective ways study the behaviors and properties of the resulting HLPN models. In this dissertation, several modeling and analysis techniques for HLPNs are studied, which are integrated into a framework that is supported by a tool. ^ For modeling, this framework integrates two formal languages: a type of HLPNs called Predicate Transition Net (PrT Net) is used to model a system's behavior and a first-order linear time temporal logic (FOLTL) to specify the system's properties. The main contribution of this dissertation with regard to modeling is to develop a software tool to support the formal modeling capabilities in this framework. ^ For analysis, this framework combines three complementary techniques, simulation, explicit state model checking and bounded model checking (BMC). Simulation is a straightforward and speedy method, but only covers some execution paths in a HLPN model. Explicit state model checking covers all the execution paths but suffers from the state explosion problem. BMC is a tradeoff as it provides a certain level of coverage while more efficient than explicit state model checking. The main contribution of this dissertation with regard to analysis is adapting BMC to analyze HLPN models and integrating the three complementary analysis techniques in a software tool to support the formal analysis capabilities in this framework. ^ The SAMTools developed for this framework in this dissertation integrates three tools: PIPE+ for HLPNs behavioral modeling and simulation, SAMAT for hierarchical structural modeling and property specification, and PIPE+Verifier for behavioral verification.^

Formal Modeling and Analysis Techniques for High Level Petri Nets

Petri Nets are a formal, graphical and executable modeling technique for the specification and analysis of concurrent and distributed systems and have been widely applied in computer science and many other engineering disciplines. Low level Petri nets are simple and useful for modeling control flows but not powerful enough to define data and system functionality. High level Petri nets (HLPNs) have been developed to support data and functionality definitions, such as using complex structured data as tokens and algebraic expressions as transition formulas. Compared to low level Petri nets, HLPNs result in compact system models that are easier to be understood. Therefore, HLPNs are more useful in modeling complex systems. There are two issues in using HLPNs - modeling and analysis. Modeling concerns the abstracting and representing the systems under consideration using HLPNs, and analysis deals with effective ways study the behaviors and properties of the resulting HLPN models. In this dissertation, several modeling and analysis techniques for HLPNs are studied, which are integrated into a framework that is supported by a tool. For modeling, this framework integrates two formal languages: a type of HLPNs called Predicate Transition Net (PrT Net) is used to model a system's behavior and a first-order linear time temporal logic (FOLTL) to specify the system's properties. The main contribution of this dissertation with regard to modeling is to develop a software tool to support the formal modeling capabilities in this framework. For analysis, this framework combines three complementary techniques, simulation, explicit state model checking and bounded model checking (BMC). Simulation is a straightforward and speedy method, but only covers some execution paths in a HLPN model. Explicit state model checking covers all the execution paths but suffers from the state explosion problem. BMC is a tradeoff as it provides a certain level of coverage while more efficient than explicit state model checking. The main contribution of this dissertation with regard to analysis is adapting BMC to analyze HLPN models and integrating the three complementary analysis techniques in a software tool to support the formal analysis capabilities in this framework. The SAMTools developed for this framework in this dissertation integrates three tools: PIPE+ for HLPNs behavioral modeling and simulation, SAMAT for hierarchical structural modeling and property specification, and PIPE+Verifier for behavioral verification.

The relationship between early and intermediate level spatial vision during typical development and in autism spectrum disorder

Certaines recherches ont investigué le traitement visuel de bas et de plus hauts niveaux chez des personnes neurotypiques et chez des personnes ayant un trouble du spectre de l’autisme (TSA). Cependant, l’interaction développementale entre chacun de ces niveaux du traitement visuel n’est toujours pas bien comprise. La présente thèse a donc deux objectifs principaux. Le premier objectif (Étude 1) est d’évaluer l’interaction développementale entre l’analyse visuelle de bas niveaux et de niveaux intermédiaires à travers différentes périodes développementales (âge scolaire, adolescence et âge adulte). Le second objectif (Étude 2) est d’évaluer la relation fonctionnelle entre le traitement visuel de bas niveaux et de niveaux intermédiaires chez des adolescents et des adultes ayant un TSA. Ces deux objectifs ont été évalué en utilisant les mêmes stimuli et procédures. Plus précisément, la sensibilité de formes circulaires complexes (Formes de Fréquences Radiales ou FFR), définies par de la luminance ou par de la texture, a été mesurée avec une procédure à choix forcés à deux alternatives. Les résultats de la première étude ont illustré que l’information locale des FFR sous-jacents aux processus visuels de niveaux intermédiaires, affecte différemment la sensibilité à travers des périodes développementales distinctes. Plus précisément, lorsque le contour est défini par de la luminance, la performance des enfants est plus faible comparativement à celle des adolescents et des adultes pour les FFR sollicitant la perception globale. Lorsque les FFR sont définies par la texture, la sensibilité des enfants est plus faible comparativement à celle des adolescents et des adultes pour les conditions locales et globales. Par conséquent, le type d’information locale, qui définit les éléments locaux de la forme globale, influence la période à laquelle la sensibilité visuelle atteint un niveau développemental similaire à celle identifiée chez les adultes. Il est possible qu’une faible intégration visuelle entre les mécanismes de bas et de niveaux intermédiaires explique la sensibilité réduite des FFR chez les enfants. Ceci peut être attribué à des connexions descendantes et horizontales immatures ainsi qu’au sous-développement de certaines aires cérébrales du système visuel. Les résultats de la deuxième étude ont démontré que la sensibilité visuelle en autisme est influencée par la manipulation de l’information locale. Plus précisément, en présence de luminance, la sensibilité est seulement affectée pour les conditions sollicitant un traitement local chez les personnes avec un TSA. Cependant, en présence de texture, la sensibilité est réduite pour le traitement visuel global et local. Ces résultats suggèrent que la perception de formes en autisme est reliée à l’efficacité à laquelle les éléments locaux (luminance versus texture) sont traités. Les connexions latérales et ascendantes / descendantes des aires visuelles primaires sont possiblement tributaires d’un déséquilibre entre les signaux excitateurs et inhibiteurs, influençant ainsi l’efficacité à laquelle l’information visuelle de luminance et de texture est traitée en autisme. Ces résultats supportent l’hypothèse selon laquelle les altérations de la perception visuelle de bas niveaux (local) sont à l’origine des atypies de plus hauts niveaux chez les personnes avec un TSA.

Multi-purpose adaptable business tier components based on Call Level Interfaces

Call Level Interfaces (CLI) play a key role in business tiers of relational and on some NoSQL database applications whenever a fine tune control between application tiers and the host databases is a key requirement. Unfortunately, in spite of this significant advantage, CLI are low level API, this way not addressing high level architectural requirements. Among the examples we emphasize two situations: a) the need to decouple or not to decouple the development process of business tiers from the development process of application tiers and b) the need to automatically adapt business tiers to new business and/or security needs at runtime. To tackle these CLI drawbacks, and simultaneously keep their advantages, this paper proposes an architecture relying on CLI from which multi-purpose business tiers components are built, herein referred to as Adaptable Business Tier Components (ABTC). Beyond the reference architecture, this paper presents a proof of concept based on Java and Java Database Connectivity (an example of CLI).