A comparison of four DNA extraction protocols for the analysis of urine from patients with visceral leishmaniasis

Introduction Polymerase chain reaction (PCR) may offer an alternative diagnostic option when clinical signs and symptoms suggest visceral leishmaniasis (VL) but microscopic scanning and serological tests provide negative results. PCR using urine is sensitive enough to diagnose human visceral leishmaniasis (VL). However, DNA quality is a crucial factor for successful amplification. Methods A comparative performance evaluation of DNA extraction methods from the urine of patients with VL using two commercially available extraction kits and two phenol-chloroform protocols was conducted to determine which method produces the highest quality DNA suitable for PCR amplification, as well as the most sensitive, fast and inexpensive method. All commercially available kits were able to shorten the duration of DNA extraction. Results With regard to detection limits, both phenol: chloroform extraction and the QIAamp DNA Mini Kit provided good results (0.1 pg of DNA) for the extraction of DNA from a parasite smaller than Leishmania (Leishmania) infantum (< 100fg of DNA). However, among 11 urine samples from subjects with VL, better performance was achieved with the phenol:chloroform method (8/11) relative to the QIAamp DNA Mini Kit (4/11), with a greater number of positive samples detected at a lower cost using PCR. Conclusion Our results demonstrate that phenol:chloroform with an ethanol precipitation prior to extraction is the most efficient method in terms of yield and cost, using urine as a non-invasive source of DNA and providing an alternative diagnostic method at a low cost.

Rely-guarantee protocols for safe interference over shared memory

Mutable state can be useful in certain algorithms, to structure programs, or for efficiency purposes. However, when shared mutable state is used in non-local or nonobvious ways, the interactions that can occur via aliases to that shared memory can be a source of program errors. Undisciplined uses of shared state may unsafely interfere with local reasoning as other aliases may interleave their changes to the shared state in unexpected ways. We propose a novel technique, rely-guarantee protocols, that structures the interactions between aliases and ensures that only safe interference is possible. We present a linear type system outfitted with our novel sharing mechanism that enables controlled interference over shared mutable resources. Each alias is assigned separate, local roles encoded in a protocol abstraction that constrains how an alias can legally use that shared state. By following the spirit of rely-guarantee reasoning, our rely-guarantee protocols ensure that only safe interference can occur but still allow many interesting uses of shared state, such as going beyond invariant and monotonic usages. This thesis describes the three core mechanisms that enable our type-based technique to work: 1) we show how a protocol models an alias’s perspective on how the shared state evolves and constrains that alias’s interactions with the shared state; 2) we show how protocols can be used while enforcing the agreed interference contract; and finally, 3) we show how to check that all local protocols to some shared state can be safely composed to ensure globally safe interference over that shared memory. The interference caused by shared state is rooted at how the uses of di↵erent aliases to that state may be interleaved (perhaps even in non-deterministic ways) at run-time. Therefore, our technique is mostly agnostic as to whether this interference was the result of alias interleaving caused by sequential or concurrent semantics. We show implementations of our technique in both settings, and highlight their di↵erences. Because sharing is “first-class” (and not tied to a module), we show a polymorphic procedure that enables abstract compositions of protocols. Thus, protocols can be specialized or extended without requiring specific knowledge of the interference produce by other protocols to that state. We show that protocol composition can ensure safety even when considering abstracted protocols. We show that this core composition mechanism is sound, decidable (without the need for manual intervention), and provide an algorithm implementation.

Secure multiParty computation protocols

Dissertação de Mestrado em Engenharia Informática

A hybrid MAC Scheme to improve the transmission performance in body sensor networks

Wireless body sensor networks (WBSNs) constitute a key technology for closing the loop between patients and healthcare providers, as WBSNs provide sensing ability, as well as mobility and portability, essential characteristics for wide acceptance of wireless healthcare technology. However, one important and difficult aspect of WBSNs is to provide data transmissions with quality of service, among other factors due to the antennas being small size and placed close to the body. Such transmissions cannot be fully provided without the assumption of a MAC protocol that solves the problems of the medium sharing. A vast number of MAC protocols conceived for wireless networks are based on random or scheduled schemes. This paper studies firstly the suitability of two MAC protocols, one using CSMA and the other TDMA, to transmit directly to the base station the signals collected continuously from multiple sensor nodes placed on the human body. Tests in a real scenario show that the beaconed TDMA MAC protocol presents an average packet loss ratio lower than CSMA. However, the average packet loss ratio is above 1.0 %. To improve this performance, which is of vital importance in areas such as e-health and ambient assisted living, a hybrid TDMA/CSMA scheme is proposed and tested in a real scenario with two WBSNs and four sensor nodes per WBSN. An average packet loss ratio lower than 0.2 % was obtained with the hybrid scheme. To achieve this significant improvement, the hybrid scheme uses a lightweight algorithm to control dynamically the start of the superframes. Scalability and traffic rate variation tests show that this strategy allows approximately ten WBSNs operating simultaneously without significant performance degradation.

Transcranial direct current stimulation based metaplasticity protocols in working memory

It has been already shown that delivering tDCS that are spaced by an interval alters its impact on motor plasticity. These effects can be explained, based on metaplasticity in which a previous modification of activity in a neuronal network can change the effects of subsequent interventions in the same network. But to date there is limited data assessing metaplasticity effects in cognitive functioning.

Assessment of the DIXTAL DX-2710 Automated Oscillometric Device for Blood Pressure Measurement with the Validation Protocols of the British Hypertension Society (BHS) and the Association for the Advancement of Medical Instrumentation (AAMI)

OBJECTIVE: To assess the Dixtal DX2710 automated oscillometric device used for blood pressure measurement according to the protocols of the BHS and the AAMI. METHODS: Three blood pressure measurements were taken in 94 patients (53 females 15 to 80 years). The measurements were taken randomly by 2 observers trained to measure blood pressure with a mercury column device connected with an automated device. The device was classified according to the protocols of the BHS and AAMI. RESULT: The mean of blood pressure levels obtained by the observers was 148±38/93±25 mmHg and that obtained with the device was 148±37/89±26 mmHg. Considering the differences between the measurements obtained by the observer and those obtained with the automated device according to the criteria of the BHS, the following classification was adopted: "A" for systolic pressure (69% of the differences < 5; 90% < 10; and 97% < 15 mmHg); and "B" for diastolic pressure (63% of the differences < 5; 83% < 10; and 93% < 15 mmHg). The mean and standard deviation of the differences were 0±6.27 mmHg for systolic pressure and 3.82±6.21 mmHg for diastolic pressure. CONCLUSION: The Dixtal DX2710 device was approved according to the international recommendations.

Comparison of Contemporary Protocols for High-speed Data Transport via 10 Gbps WAN Connections

This work is dedicated to comparison of open source as well as proprietary transport protocols for highspeed data transmission via IP networks. The contemporary common TCP needs significant improvement since it was developed as general-purpose transport protocol and firstly introduced four decades ago. In nowadays networks, TCP fits not all communication needs that society has. Caused of it another transport protocols have been developed and successfully used for e.g. Big Data movement. In scope of this research the following protocols have been investigated for its efficiency on 10Gbps links: UDT, RBUDP, MTP and RWTP. The protocols were tested under different impairments such as Round Trip Time up to 400 ms and packet losses up to 2%. Investigated parameters are the data rate under different conditions of the network, the CPU load by sender andreceiver during the experiments, size of feedback data, CPU usage per Gbps and the amount of feedback data per GiByte of effectively transmitted data. The best performance and fair resources consumption was observed by RWTP. From the opensource projects, the best behavior is showed by RBUDP.

Instal·lació i disseny de protocols d'operació del subdetector SPD. de LHCb. Algorismes de trigger.

Estudi elaborat a partir d’una estada al Laboratori Europeu de Física de Partícules (CERN), Suissa, entre maig i setembre del 2006. L’estada al laboratori CERN ha tingut dues vessants complementàries, les dues relacionades amb la imminent posada en marxa de l'experiment LHCb a finals del 2007, quan l'accelerador LHC comenci a funcionar. D'una banda, s’ha treballat en la integració del subdetector SPD en LHCb, i de l'altra al desenvolupament dels algorismes de trigger de LHCb.

Subgroup analyses in randomised controlled trials: cohort study on trial protocols and journal publications

OBJECTIVE: To investigate the planning of subgroup analyses in protocols of randomised controlled trials and the agreement with corresponding full journal publications. DESIGN: Cohort of protocols of randomised controlled trial and subsequent full journal publications. SETTING: Six research ethics committees in Switzerland, Germany, and Canada. DATA SOURCES: 894 protocols of randomised controlled trial involving patients approved by participating research ethics committees between 2000 and 2003 and 515 subsequent full journal publications. RESULTS: Of 894 protocols of randomised controlled trials, 252 (28.2%) included one or more planned subgroup analyses. Of those, 17 (6.7%) provided a clear hypothesis for at least one subgroup analysis, 10 (4.0%) anticipated the direction of a subgroup effect, and 87 (34.5%) planned a statistical test for interaction. Industry sponsored trials more often planned subgroup analyses compared with investigator sponsored trials (195/551 (35.4%) v 57/343 (16.6%), P<0.001). Of 515 identified journal publications, 246 (47.8%) reported at least one subgroup analysis. In 81 (32.9%) of the 246 publications reporting subgroup analyses, authors stated that subgroup analyses were prespecified, but this was not supported by 28 (34.6%) corresponding protocols. In 86 publications, authors claimed a subgroup effect, but only 36 (41.9%) corresponding protocols reported a planned subgroup analysis. CONCLUSIONS: Subgroup analyses are insufficiently described in the protocols of randomised controlled trials submitted to research ethics committees, and investigators rarely specify the anticipated direction of subgroup effects. More than one third of statements in publications of randomised controlled trials about subgroup prespecification had no documentation in the corresponding protocols. Definitive judgments regarding credibility of claimed subgroup effects are not possible without access to protocols and analysis plans of randomised controlled trials.

Medium-term protocols for in vivo evaluation of chemical modifiers of carcinogenesis

Cancer development is a long-term multistep process which allows interventional measure before the clincial disease emerges. the detection of natural substances which can block the process of carcinogenesis is a important as the identification of anti-tumoral drugs since they might be used in chemoprevention of cancer in high-risk groups. In vivo rodent models of chemical caecinogenesis have been used to study plant-derived inhibitors of carcinofenesis such as indols, coumarins, isothiocyanates, flavones, phenols and allyl-sulfides. Since the standard in vivo rodent bioassay is prolonged and expensive, shorter reliable protocols are needed. Two in vivo medium-term protocols for evaluation of modifiers of carcinogenesis are presented, one related to liver and the other to bladder cancer. Both protocols use rats, last 8 and 36 weeks and are based on the two-step concept of carcinogenesis: initiation and promotion. The protocols use respectively the development of altered foci of hepatocytes expressing immunochistochemically the placental form of gluthation S-transferase and the appearence of pre-neoplastic urothelium and papillomas as the "end-points". the use of these protocols for detection of plantpderived inhibitors of carcinogenesis appear warranted.

Assessment of statistical iterative reconstructions to optimize CT examination protocols for children and young adults

La tomodensitométrie (CT) est une technique d'imagerie dont l'intérêt n'a cessé de croître depuis son apparition dans le début des années 70. Dans le domaine médical, son utilisation est incontournable à tel point que ce système d'imagerie pourrait être amené à devenir victime de son succès si son impact au niveau de l'exposition de la population ne fait pas l'objet d'une attention particulière. Bien évidemment, l'augmentation du nombre d'examens CT a permis d'améliorer la prise en charge des patients ou a rendu certaines procédures moins invasives. Toutefois, pour assurer que le compromis risque - bénéfice soit toujours en faveur du patient, il est nécessaire d'éviter de délivrer des doses non utiles au diagnostic.¦Si cette action est importante chez l'adulte elle doit être une priorité lorsque les examens se font chez l'enfant, en particulier lorsque l'on suit des pathologies qui nécessitent plusieurs examens CT au cours de la vie du patient. En effet, les enfants et jeunes adultes sont plus radiosensibles. De plus, leur espérance de vie étant supérieure à celle de l'adulte, ils présentent un risque accru de développer un cancer radio-induit dont la phase de latence peut être supérieure à vingt ans. Partant du principe que chaque examen radiologique est justifié, il devient dès lors nécessaire d'optimiser les protocoles d'acquisitions pour s'assurer que le patient ne soit pas irradié inutilement. L'avancée technologique au niveau du CT est très rapide et depuis 2009, de nouvelles techniques de reconstructions d'images, dites itératives, ont été introduites afin de réduire la dose et améliorer la qualité d'image.¦Le présent travail a pour objectif de déterminer le potentiel des reconstructions itératives statistiques pour réduire au minimum les doses délivrées lors d'examens CT chez l'enfant et le jeune adulte tout en conservant une qualité d'image permettant le diagnostic, ceci afin de proposer des protocoles optimisés.¦L'optimisation d'un protocole d'examen CT nécessite de pouvoir évaluer la dose délivrée et la qualité d'image utile au diagnostic. Alors que la dose est estimée au moyen d'indices CT (CTDIV0| et DLP), ce travail a la particularité d'utiliser deux approches radicalement différentes pour évaluer la qualité d'image. La première approche dite « physique », se base sur le calcul de métriques physiques (SD, MTF, NPS, etc.) mesurées dans des conditions bien définies, le plus souvent sur fantômes. Bien que cette démarche soit limitée car elle n'intègre pas la perception des radiologues, elle permet de caractériser de manière rapide et simple certaines propriétés d'une image. La seconde approche, dite « clinique », est basée sur l'évaluation de structures anatomiques (critères diagnostiques) présentes sur les images de patients. Des radiologues, impliqués dans l'étape d'évaluation, doivent qualifier la qualité des structures d'un point de vue diagnostique en utilisant une échelle de notation simple. Cette approche, lourde à mettre en place, a l'avantage d'être proche du travail du radiologue et peut être considérée comme méthode de référence.¦Parmi les principaux résultats de ce travail, il a été montré que les algorithmes itératifs statistiques étudiés en clinique (ASIR?, VEO?) ont un important potentiel pour réduire la dose au CT (jusqu'à-90%). Cependant, par leur fonctionnement, ils modifient l'apparence de l'image en entraînant un changement de texture qui pourrait affecter la qualité du diagnostic. En comparant les résultats fournis par les approches « clinique » et « physique », il a été montré que ce changement de texture se traduit par une modification du spectre fréquentiel du bruit dont l'analyse permet d'anticiper ou d'éviter une perte diagnostique. Ce travail montre également que l'intégration de ces nouvelles techniques de reconstruction en clinique ne peut se faire de manière simple sur la base de protocoles utilisant des reconstructions classiques. Les conclusions de ce travail ainsi que les outils développés pourront également guider de futures études dans le domaine de la qualité d'image, comme par exemple, l'analyse de textures ou la modélisation d'observateurs pour le CT.¦-¦Computed tomography (CT) is an imaging technique in which interest has been growing since it first began to be used in the early 1970s. In the clinical environment, this imaging system has emerged as the gold standard modality because of its high sensitivity in producing accurate diagnostic images. However, even if a direct benefit to patient healthcare is attributed to CT, the dramatic increase of the number of CT examinations performed has raised concerns about the potential negative effects of ionizing radiation on the population. To insure a benefit - risk that works in favor of a patient, it is important to balance image quality and dose in order to avoid unnecessary patient exposure.¦If this balance is important for adults, it should be an absolute priority for children undergoing CT examinations, especially for patients suffering from diseases requiring several follow-up examinations over the patient's lifetime. Indeed, children and young adults are more sensitive to ionizing radiation and have an extended life span in comparison to adults. For this population, the risk of developing cancer, whose latency period exceeds 20 years, is significantly higher than for adults. Assuming that each patient examination is justified, it then becomes a priority to optimize CT acquisition protocols in order to minimize the delivered dose to the patient. Over the past few years, CT advances have been developing at a rapid pace. Since 2009, new iterative image reconstruction techniques, called statistical iterative reconstructions, have been introduced in order to decrease patient exposure and improve image quality.¦The goal of the present work was to determine the potential of statistical iterative reconstructions to reduce dose as much as possible without compromising image quality and maintain diagnosis of children and young adult examinations.¦The optimization step requires the evaluation of the delivered dose and image quality useful to perform diagnosis. While the dose is estimated using CT indices (CTDIV0| and DLP), the particularity of this research was to use two radically different approaches to evaluate image quality. The first approach, called the "physical approach", computed physical metrics (SD, MTF, NPS, etc.) measured on phantoms in well-known conditions. Although this technique has some limitations because it does not take radiologist perspective into account, it enables the physical characterization of image properties in a simple and timely way. The second approach, called the "clinical approach", was based on the evaluation of anatomical structures (diagnostic criteria) present on patient images. Radiologists, involved in the assessment step, were asked to score image quality of structures for diagnostic purposes using a simple rating scale. This approach is relatively complicated to implement and also time-consuming. Nevertheless, it has the advantage of being very close to the practice of radiologists and is considered as a reference method.¦Primarily, this work revealed that the statistical iterative reconstructions studied in clinic (ASIR? and VECO have a strong potential to reduce CT dose (up to -90%). However, by their mechanisms, they lead to a modification of the image appearance with a change in image texture which may then effect the quality of the diagnosis. By comparing the results of the "clinical" and "physical" approach, it was showed that a change in texture is related to a modification of the noise spectrum bandwidth. The NPS analysis makes possible to anticipate or avoid a decrease in image quality. This project demonstrated that integrating these new statistical iterative reconstruction techniques can be complex and cannot be made on the basis of protocols using conventional reconstructions. The conclusions of this work and the image quality tools developed will be able to guide future studies in the field of image quality as texture analysis or model observers dedicated to CT.