Reporting on methods of subgroup analysis in clinical trials: a survey of four scientific journals

Results of subgroup analysis (SA) reported in randomized clinical trials (RCT) cannot be adequately interpreted without information about the methods used in the study design and the data analysis. Our aim was to show how often inaccurate or incomplete reports occur. First, we selected eight methodological aspects of SA on the basis of their importance to a reader in determining the confidence that should be placed in the author's conclusions regarding such analysis. Then, we reviewed the current practice of reporting these methodological aspects of SA in clinical trials in four leading journals, i.e., the New England Journal of Medicine, the Journal of the American Medical Association, the Lancet, and the American Journal of Public Health. Eight consecutive reports from each journal published after July 1, 1998 were included. Of the 32 trials surveyed, 17 (53%) had at least one SA. Overall, the proportion of RCT reporting a particular methodological aspect ranged from 23 to 94%. Information on whether the SA preceded/followed the analysis was reported in only 7 (41%) of the studies. Of the total possible number of items to be reported, NEJM, JAMA, Lancet and AJPH clearly mentioned 59, 67, 58 and 72%, respectively. We conclude that current reporting of SA in RCT is incomplete and inaccurate. The results of such SA may have harmful effects on treatment recommendations if accepted without judicious scrutiny. We recommend that editors improve the reporting of SA in RCT by giving authors a list of the important items to be reported.

Comparison of the Polar S810i monitor and the ECG for the analysis of heart rate variability in the time and frequency domains

The aim of the present study was to compare heart rate variability (HRV) at rest and during exercise using a temporal series obtained with the Polar S810i monitor and a signal from a LYNX® signal conditioner (BIO EMG 1000 model) with a channel configured for the acquisition of ECG signals. Fifteen healthy subjects aged 20.9 ± 1.4 years were analyzed. The subjects remained at rest for 20 min and performed exercise for another 20 min with the workload selected to achieve 60% of submaximal heart rate. RR series were obtained for each individual with a Polar S810i instrument and with an ECG analyzed with a biological signal conditioner. The HRV indices (rMSSD, pNN50, LFnu, HFnu, and LF/HF) were calculated after signal processing and analysis. The unpaired Student t-test and intraclass correlation coefficient were used for data analysis. No statistically significant differences were observed when comparing the values analyzed by means of the two devices for HRV at rest and during exercise. The intraclass correlation coefficient demonstrated satisfactory correlation between the values obtained by the devices at rest (pNN50 = 0.994; rMSSD = 0.995; LFnu = 0.978; HFnu = 0.978; LF/HF = 0.982) and during exercise (pNN50 = 0.869; rMSSD = 0.929; LFnu = 0.973; HFnu = 0.973; LF/HF = 0.942). The calculation of HRV values by means of temporal series obtained from the Polar S810i instrument appears to be as reliable as those obtained by processing the ECG signal captured with a signal conditioner.

Analysis of testicular cell populations using flow cytometry

Studying testis is complex, because the tissue has a very heterogeneous cell composition and its structure changes dynamically during development. In reproductive field, the cell composition is traditionally studied by morphometric methods such as immunohistochemistry and immunofluorescence. These techniques provide accurate quantitative information about cell composition, cell-cell association and localization of the cells of interest. However, the sample preparation, processing, staining and data analysis are laborious and may take several working days. Flow cytometry protocols coupled with DNA stains have played an important role in providing quantitative information of testicular cells populations ex vivo and in vitro studies. Nevertheless, the addition of specific cells markers such as intracellular antibodies would allow the more specific identification of cells of crucial interest during spermatogenesis. For this study, adult rat Sprague-Dawley rats were used for optimization of the flow cytometry protocol. Specific steps within the protocol were optimized to obtain a singlecell suspension representative of the cell composition of the starting material. Fixation and permeabilization procedure were optimized to be compatible with DNA stains and fluorescent intracellular antibodies. Optimization was achieved by quantitative analysis of specific parameters such as recovery of meiotic cells, amount of debris and comparison of the proportions of the various cell populations with already published data. As a result, a new and fast flow cytometry method coupled with DNA stain and intracellular antigen detection was developed. This new technique is suitable for analysis of population behavior and specific cells during postnatal testis development and spermatogenesis in rodents. This rapid protocol recapitulated the known vimentin and γH2AX protein expression patterns during rodent testis ontogenesis. Moreover, the assay was applicable for phenotype characterization of SCRbKO and E2F1KO mouse models.

Software for Transport Accessibility Analysis: The Case of Moscow

In this thesis the process of building a software for transport accessibility analysis is described. The goal was to create a software which is easy to distribute and simple to use for the user without particular background in the field of the geographical data analysis. It was shown that existing tools do not suit for this particular task due to complex interface or significant rendering time. The goal was accomplished by applying modern approaches in the process of building web applications such as maps based on vector tiles, FLUX architecture design pattern and module bundling. It was discovered that vector tiles have considerable advantages over image-based tiles such as faster rendering and real-time styling.

Controlling full penetration in MAG welding by the application of infrared thermography and neural network

In this study, an infrared thermography based sensor was studied with regard to usability and the accuracy of sensor data as a weld penetration signal in gas metal arc welding. The object of the study was to evaluate a specific sensor type which measures thermography from solidified weld surface. The purpose of the study was to provide expert data for developing a sensor system in adaptive metal active gas (MAG) welding. Welding experiments with considered process variables and recorded thermal profiles were saved to a database for further analysis. To perform the analysis within a reasonable amount of experiments, the process parameter variables were gradually altered by at least 10 %. Later, the effects of process variables on weld penetration and thermography itself were considered. SFS-EN ISO 5817 standard (2014) was applied for classifying the quality of the experiments. As a final step, a neural network was taught based on the experiments. The experiments show that the studied thermography sensor and the neural network can be used for controlling full penetration though they have minor limitations, which are presented in results and discussion. The results are consistent with previous studies and experiments found in the literature.

Effects of isometric elbow flexion on electromyographic spike analysis

The main objective of this research was to examine the relationship between surface electromyographic (SEMG) spike activity and force. The secondary objective was to determine to what extent subcutaneous tissue impacts the high frequency component of the signal, as well as, examining the relationship between measures of SEMG spike shape and their traditional time and frequency analogues. A total of96 participants (46 males and 50 females) ranging in age (18-35 years), generated three 5-second isometric step contractions at each force level of 40, 60, 80, and 100 percent of maximal voluntary contraction (MVC). The presentation of the contractions was balanced across subjects. The right arm of the subject was positioned in the sagittal plane, with the shoulder and elbow flexed to 90 degrees. The elbow rested on a support in a neutral position (mid pronation/mid supination) and placed within a wrist cuff, fastened below the styloid process. The wrist cuff was attached to a load cell (JR3 Inc., Woodland, CA) recording the force produced. Biceps brachii activity was monitored with a pair of Ag/AgCI recording electrodes (Grass F-E9, Astro-Med Inc., West Warwick, RI) placed in a bipolar configuration, with an interelectrode distance (lED) of 2cm distal to the motor point. Data analysis was performed on a I second window of data in the middle of the 5-second contraction. The results indicated that all spike shape measures exhibited significant (p < 0.01) differences as force increase~ from 40 to 100% MVC. The spike shape measures suggest that increased motor unit (MU) recruitment was responsible for increasing force up to 80% MVC. The results suggested that further increases in force relied on MU III synchronization. The results also revealed that the subcutaneous tissue (skin fold thickness) had no relationship (r = 0.02; P > 0.05) with the mean number of peaks per spike (MNPPS), which was the high frequency component of the signal. Mean spike amplitude (MSA) and mean spike frequency (MSF) were highly correlated with their traditional measures root mean square (RMS) and mean power frequency (MPF), respectively (r = 0.99; r = 0.97; P < 0.01).

A qualitative analysis of reflection in undergraduate and graduate programs

The purpose ofthis study was to explore various types ofreflection and to explore reflection on action, reflection as a practice, and reflection as a process. In doing this, the intent was to discover the perceived benefits of reflection in the classroom and to provide guidelines for future use at the undergraduate and graduate level. The qualitative components in this study included the data collection strategy of semistructured interviews with 2 undergraduate students, 2 graduate students, 1 undergraduate studies professor, and 1 graduate studies professor. The data analysis strategies included a within-case analysis and a cross-case analysis. Through the interviews participants discussed their experiences with the use ofreflection in the classroom. Through the completion ofthis analysis the researcher expected to discover the benefits ofreflection at this level of education, as well as provide suggestions for future use. Both undergraduate and graduate students and professors were found to benefit from the use of reflection in the classroom. The use ofreflection in the undergraduate and graduate classroom was found to improve student/teacher and student/peer relationships, foster critical thinking, allow for connections between learned theory and life experience, and improve students' writing abilities. Based on the results ofthe study the implications ofreflection for the undergraduate and graduate classroom and for further research are provided.

Cognitive Behavior Therapy for Obsessive-Compulsive Behavior in Children with Autism Spectrum Disorder: A Comparison of Hierarchical Linear Modelling and Visual Analysis

Behavioral researchers commonly use single subject designs to evaluate the effects of a given treatment. Several different methods of data analysis are used, each with their own set of methodological strengths and limitations. Visual inspection is commonly used as a method of analyzing data which assesses the variability, level, and trend both within and between conditions (Cooper, Heron, & Heward, 2007). In an attempt to quantify treatment outcomes, researchers developed two methods for analysing data called Percentage of Non-overlapping Data Points (PND) and Percentage of Data Points Exceeding the Median (PEM). The purpose of the present study is to compare and contrast the use of Hierarchical Linear Modelling (HLM), PND and PEM in single subject research. The present study used 39 behaviours, across 17 participants to compare treatment outcomes of a group cognitive behavioural therapy program, using PND, PEM, and HLM on three response classes of Obsessive Compulsive Behaviour in children with Autism Spectrum Disorder. Findings suggest that PEM and HLM complement each other and both add invaluable information to the overall treatment results. Future research should consider using both PEM and HLM when analysing single subject designs, specifically grouped data with variability.

AnaBench: a Web/CORBA-based workbench for biomolecular sequence analysis

Affiliation: Département de biochimie, Faculté de médecine, Université de Montréal

Nouvelles limites sur la détection directe de la matière sombre avec l’expérience PICASSO

Les observations astronomiques et cosmologiques suggèrent fortement la présence d’une matière exotique, non-relativiste et non-baryonique qui représenterait 26% du contenu de masse-énergie de l’Univers actuel. Cette matière dite sombre et froide serait compo- sée de particules neutres, massives et interagissant faiblement avec la matière ordinaire (WIMP : Weakly Interactive Massive Particles). Le projet PICASSO (Projet d’Identification des CAndidats Supersymétriques de la matière SOmbre) est une des expériences installées dans le site souterrain de SNOLAB à Sudbury en Ontario, qui tente de détecter directement un des candidats de la matière sombre, proposé dans le cadre des extensions supersymétriques du modèle standard : le neutralino. Pour cela, PICASSO utilise des détecteurs à gouttelettes surchauffées de C4F10, basés sur le principe de la chambre à bulles. Les transitions de phase dans les liquides surchauffés peuvent être déclenchées par le recul du 19 F, causé par une collision élastique avec les neutralinos. La nucléation de la gouttelette génère une onde sonore enregistrée par des senseurs piézo-électriques. Cette thèse présentera les récents progrès de l’expérience PICASSO qui ont conduit à une augmentation substantielle de sa sensibilité dans la recherche du neutralino. En effet, de nouvelles procédures de fabrication et de purification ont permis de réduire à un facteur de 10, la contamination majeure des détecteurs, causée par les émetteurs alpha. L’étude de cette contamination dans les détecteurs a permis de localiser la source de ces émetteurs. Les efforts effectués dans le cadre de l’analyse des données, ont permis d’améliorer l’effet de discrimination entre des évènements engendrés par les particules alpha et par les reculs nucléaires. De nouveaux outils d’analyse ont également été implémentés dans le but de discriminer les évènements générés par des particules de ceux générés par des bruits de fond électroniques ou acoustiques. De plus, un mécanisme important de suppression de bruit de fond indésirable à haute température, a permis à l’expérience PICASSO d’être maintenant sensible aux WIMPs de faibles masses.

Détection et caractérisation de naines brunes et exoplanètes avec un filtre accordable pour applications dans l'espace

Cette thèse porte sur la capacité à détecter des compagnons de faible intensité en présence de bruit de tavelures dans le contexte de l’imagerie à haute gamme dynamique pour l’astronomie spatiale. On s’intéressera plus particulièrement à l’imagerie spectrale différentielle (ISD) obtenue en utilisant un étalon Fabry-Pérot comme filtre accordable. Les performances d’un tel filtre accordable sont présentées dans le cadre du Tunable Filter Imager (TFI), instrument conçu pour le télescope spatial James Webb (JWST). La capacité de l’étalon à supprimer les tavelures avec ISD est démontrée expérimentalement grâce à un prototype de l’étalon installé sur un banc de laboratoire. Les améliorations de contraste varient en fonction de la séparation, s’étendant d’un facteur 10 pour les séparations supérieures à 11 lambda/D jusqu’à un facteur 60 à 5 lambda/D. Ces résultats sont cohérents avec une étude théorique qui utilise un modèle basé sur la propagation de Fresnel pour montrer que les performances de suppression de tavelures sont limitées par le banc optique et non pas par l’étalon. De plus, il est démontré qu’un filtre accordable est une option séduisante pour l’imagerie à haute gamme dynamique combinée à la technique ISD. Une seconde étude basée sur la propagation de Fresnel de l’instrument TFI et du télescope, a permis de définir les performances de la technique ISD combinée avec un étalon pour l’astronomie spatiale. Les résultats prévoient une amélioration de contraste de l’ordre de 7 jusqu’à 100, selon la configuration de l’instrument. Une comparaison entre ISD et la soustraction par rotation a également été simulée. Enfin, la dernière partie de ce chapitre porte sur les performances de la technique ISD dans le cadre de l’instrument Near-Infrared Imager and Slitless Spectrograph (NIRISS), conçu pour remplacer TFI comme module scientifique à bord du Fine Guidance Sensor du JWST. Cent quatre objets localisés vers la région centrale de la nébuleuse d’Orion ont été caractérisés grâce à un spectrographe multi-objet, de basse résolution et multi-bande (0.85-2.4 um). Cette étude a relevé 7 nouvelles naines brunes et 4 nouveaux candidats de masse planétaire. Ces objets sont utiles pour déterminer la fonction de masse initiale sous-stellaire et pour évaluer les modèles atmosphériques et évolutifs futurs des jeunes objets stellaires et sous-stellaires. Combinant les magnitudes en bande H mesurées et les valeurs d’extinction, les objets classifiés sont utilisés pour créer un diagramme de Hertzsprung-Russell de cet amas stellaire. En accord avec des études antérieures, nos résultats montrent qu’il existe une seule époque de formation d’étoiles qui a débuté il y a environ 1 million d’années. La fonction de masse initiale qui en dérive est en accord avec des études antérieures portant sur d’autres amas jeunes et sur le disque galactique.

Analyse et modélisation de la réponse des détecteurs du projet PICASSO pour la recherche de la matière sombre

Les mesures cosmologiques les plus récentes ont montré la présence d’un type de matière exotique constituant 85% de la masse de l’univers. Ce type de matière non baryonique serait formé de particules neutres, non relativistes, massives et interagissant faiblement avec la matière baryonique. L’ensemble des candidats est regroupé sous le nom générique WIMP (Weakly Interactive Massive Particles). L’expérience PICASSO (Projet d’Identification des CAndidats Supersymétriques de la matière SOmbre) est une expérience utilisant des détecteurs à seuil d’énergie contenant des gouttelettes surchauffées constituées de C4F10. Cette technique de détection est basée sur le principe de la chambre à bulles. Le projet PICASSO a pour but de détecter directement une particule de matière sombre. Le principe de détection est qu’une particule de matière sombre interagissant avec le liquide actif engendre un recul nucléaire du 19F. L’énergie de recul serait suffisante pour engendrer une transition de phase accompagnée d’un signal acoustique enregistrée par des senseurs piézoélectriques. Dans le cadre de ce mémoire, une simulation du taux de comptage de l’étalonnage des détecteurs PICASSO soumis à des neutrons monoénergétiques a été effectuée en utilisant la théorie de Seitz qui décrit les critères pour qu’une transition de phase ait lieu pour un liquide en état de surchauffe. De plus, un modèle calculant le signal acoustique émis lors d’une transition de phase engendré par différents types de radiations a été créé permettant de caractériser la discrimination entre différents bruits de fond en fonction de l’énergie de seuil. Finalement, un outil d’analyse, la localisation des évènements, a été utilisé pour appliquer des coupures sur le volume dans le but d’améliorer la discrimination alpha-neutron.

Assessment of Tandem Mass Spectrometry and High Resolution Mass Spectrometry for the Analysis of Bupivacaine in Plasma

Triple quadrupole mass spectrometers coupled with high performance liquid chromatography are workhorses in quantitative bioanalyses. It provides substantial benefits including reproducibility, sensitivity and selectivity for trace analysis. Selected Reaction Monitoring allows targeted assay development but data sets generated contain very limited information. Data mining and analysis of non-targeted high-resolution mass spectrometry profiles of biological samples offer the opportunity to perform more exhaustive assessments, including quantitative and qualitative analysis. The objectives of this study was to test method precision and accuracy, statistically compare bupivacaine drug concentration in real study samples and verify if high resolution and accurate mass data collected in scan mode can actually permit retrospective data analysis, more specifically, extract metabolite related information. The precision and accuracy data presented using both instruments provided equivalent results. Overall, the accuracy was ranging from 106.2 to 113.2% and the precision observed was from 1.0 to 3.7%. Statistical comparisons using a linear regression between both methods reveal a coefficient of determination (R2) of 0.9996 and a slope of 1.02 demonstrating a very strong correlation between both methods. Individual sample comparison showed differences from -4.5% to 1.6% well within the accepted analytical error. Moreover, post acquisition extracted ion chromatograms at m/z 233.1648 ± 5 ppm (M-56) and m/z 305.2224 ± 5 ppm (M+16) revealed the presence of desbutyl-bupivacaine and three distinct hydroxylated bupivacaine metabolites. Post acquisition analysis allowed us to produce semiquantitative evaluations of the concentration-time profiles for bupicavaine metabolites.

Energy-Efficient Cluster based Routing Schemes for Static and Mobile Sensor Networks

The theme of the thesis is centred around one important aspect of wireless sensor networks; the energy-efficiency.The limited energy source of the sensor nodes calls for design of energy-efficient routing protocols. The schemes for protocol design should try to minimize the number of communications among the nodes to save energy. Cluster based techniques were found energy-efficient. In this method clusters are formed and data from different nodes are collected under a cluster head belonging to each clusters and then forwarded it to the base station.Appropriate cluster head selection process and generation of desirable distribution of the clusters can reduce energy consumption of the network and prolong the network lifetime. In this work two such schemes were developed for static wireless sensor networks.In the first scheme, the energy wastage due to cluster rebuilding incorporating all the nodes were addressed. A tree based scheme is presented to alleviate this problem by rebuilding only sub clusters of the network. An analytical model of energy consumption of proposed scheme is developed and the scheme is compared with existing cluster based scheme. The simulation study proved the energy savings observed.The second scheme concentrated to build load-balanced energy efficient clusters to prolong the lifetime of the network. A voting based approach to utilise the neighbor node information in the cluster head selection process is proposed. The number of nodes joining a cluster is restricted to have equal sized optimum clusters. Multi-hop communication among the cluster heads is also introduced to reduce the energy consumption. The simulation study has shown that the scheme results in balanced clusters and the network achieves reduction in energy consumption.The main conclusion from the study was the routing scheme should pay attention on successful data delivery from node to base station in addition to the energy-efficiency. The cluster based protocols are extended from static scenario to mobile scenario by various authors. None of the proposals addresses cluster head election appropriately in view of mobility. An elegant scheme for electing cluster heads is presented to meet the challenge of handling cluster durability when all the nodes in the network are moving. The scheme has been simulated and compared with a similar approach.The proliferation of sensor networks enables users with large set of sensor information to utilise them in various applications. The sensor network programming is inherently difficult due to various reasons. There must be an elegant way to collect the data gathered by sensor networks with out worrying about the underlying structure of the network. The final work presented addresses a way to collect data from a sensor network and present it to the users in a flexible way.A service oriented architecture based application is built and data collection task is presented as a web service. This will enable composition of sensor data from different sensor networks to build interesting applications. The main objective of the thesis was to design energy-efficient routing schemes for both static as well as mobile sensor networks. A progressive approach was followed to achieve this goal.

“Reconstruction of Gene Regulatory Network from Expression Profile of Plasma RNA Data of Colorectal Cancer Patients using Soft Computing Techniques”

Microarray data analysis is one of data mining tool which is used to extract meaningful information hidden in biological data. One of the major focuses on microarray data analysis is the reconstruction of gene regulatory network that may be used to provide a broader understanding on the functioning of complex cellular systems. Since cancer is a genetic disease arising from the abnormal gene function, the identification of cancerous genes and the regulatory pathways they control will provide a better platform for understanding the tumor formation and development. The major focus of this thesis is to understand the regulation of genes responsible for the development of cancer, particularly colorectal cancer by analyzing the microarray expression data. In this thesis, four computational algorithms namely fuzzy logic algorithm, modified genetic algorithm, dynamic neural fuzzy network and Takagi Sugeno Kang-type recurrent neural fuzzy network are used to extract cancer specific gene regulatory network from plasma RNA dataset of colorectal cancer patients. Plasma RNA is highly attractive for cancer analysis since it requires a collection of small amount of blood and it can be obtained at any time in repetitive fashion allowing the analysis of disease progression and treatment response.