Correlating liposomal adjuvant characteristics to in-vivo cell-mediated immunity using a novel Mycobacterium tuberculosis fusion protein:a multivariate analysis study

Objective In this study, we have used a chemometrics-based method to correlate key liposomal adjuvant attributes with in-vivo immune responses based on multivariate analysis. Methods The liposomal adjuvant composed of the cationic lipid dimethyldioctadecylammonium bromide (DDA) and trehalose 6,6-dibehenate (TDB) was modified with 1,2-distearoyl-sn-glycero-3-phosphocholine at a range of mol% ratios, and the main liposomal characteristics (liposome size and zeta potential) was measured along with their immunological performance as an adjuvant for the novel, postexposure fusion tuberculosis vaccine, Ag85B-ESAT-6-Rv2660c (H56 vaccine). Partial least square regression analysis was applied to correlate and cluster liposomal adjuvants particle characteristics with in-vivo derived immunological performances (IgG, IgG1, IgG2b, spleen proliferation, IL-2, IL-5, IL-6, IL-10, IFN-γ). Key findings While a range of factors varied in the formulations, decreasing the 1,2-distearoyl-sn-glycero-3-phosphocholine content (and subsequent zeta potential) together built the strongest variables in the model. Enhanced DDA and TDB content (and subsequent zeta potential) stimulated a response skewed towards a cell mediated immunity, with the model identifying correlations with IFN-γ, IL-2 and IL-6. Conclusion This study demonstrates the application of chemometrics-based correlations and clustering, which can inform liposomal adjuvant design.

Dynamical Systems in Description of Nonlinear Recursive Regression Transformers

The task of approximation-forecasting for a function, represented by empirical data was investigated. Certain class of the functions as forecasting tools: so called RFT-transformers, – was proposed. Least Square Method and superposition are the principal composing means for the function generating. Besides, the special classes of beam dynamics with delay were introduced and investigated to get classical results regarding gradients. These results were applied to optimize the RFT-transformers. The effectiveness of the forecast was demonstrated on the empirical data from the Forex market.

Comparing Several Methods of Discriminant Analysis on the Case of Wine Data

2000 Mathematics Subject Classification: 62H30, 62J20, 62P12, 68T99

PDNAsite:identification of DNA-binding site from protein sequence by incorporating spatial and sequence context

Protein-DNA interactions are involved in many fundamental biological processes essential for cellular function. Most of the existing computational approaches employed only the sequence context of the target residue for its prediction. In the present study, for each target residue, we applied both the spatial context and the sequence context to construct the feature space. Subsequently, Latent Semantic Analysis (LSA) was applied to remove the redundancies in the feature space. Finally, a predictor (PDNAsite) was developed through the integration of the support vector machines (SVM) classifier and ensemble learning. Results on the PDNA-62 and the PDNA-224 datasets demonstrate that features extracted from spatial context provide more information than those from sequence context and the combination of them gives more performance gain. An analysis of the number of binding sites in the spatial context of the target site indicates that the interactions between binding sites next to each other are important for protein-DNA recognition and their binding ability. The comparison between our proposed PDNAsite method and the existing methods indicate that PDNAsite outperforms most of the existing methods and is a useful tool for DNA-binding site identification. A web-server of our predictor (http://hlt.hitsz.edu.cn:8080/PDNAsite/) is made available for free public accessible to the biological research community.

Multidimensional classification and diagnosis of leukemia in flow cytometry

This research is to establish new optimization methods for pattern recognition and classification of different white blood cells in actual patient data to enhance the process of diagnosis. Beckman-Coulter Corporation supplied flow cytometry data of numerous patients that are used as training sets to exploit the different physiological characteristics of the different samples provided. The methods of Support Vector Machines (SVM) and Artificial Neural Networks (ANN) were used as promising pattern classification techniques to identify different white blood cell samples and provide information to medical doctors in the form of diagnostic references for the specific disease states, leukemia. The obtained results prove that when a neural network classifier is well configured and trained with cross-validation, it can perform better than support vector classifiers alone for this type of data. Furthermore, a new unsupervised learning algorithm---Density based Adaptive Window Clustering algorithm (DAWC) was designed to process large volumes of data for finding location of high data cluster in real-time. It reduces the computational load to ∼O(N) number of computations, and thus making the algorithm more attractive and faster than current hierarchical algorithms.

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).

Quality of experience evaluation of voice communication: an affect-based approach

Voice communication systems such as Voice-over IP (VoIP), Public Switched Telephone Networks, and Mobile Telephone Networks, are an integral means of human tele-interaction. These systems pose distinctive challenges due to their unique characteristics such as low volume, burstiness and stringent delay/loss requirements across heterogeneous underlying network technologies. Effective quality evaluation methodologies are important for system development and refinement, particularly by adopting user feedback based measurement. Presently, most of the evaluation models are system-centric (Quality of Service or QoS-based), which questioned us to explore a user-centric (Quality of Experience or QoE-based) approach as a step towards the human-centric paradigm of system design. We research an affect-based QoE evaluation framework which attempts to capture users' perception while they are engaged in voice communication. Our modular approach consists of feature extraction from multiple information sources including various affective cues and different classification procedures such as Support Vector Machines (SVM) and k-Nearest Neighbor (kNN). The experimental study is illustrated in depth with detailed analysis of results. The evidences collected provide the potential feasibility of our approach for QoE evaluation and suggest the consideration of human affective attributes in modeling user experience.

Effect of Hydrologic Restoration on the Habitat of The Cape Sable Seaside Sparrow, Annual Report of 2004-2005

The major activities in Year 3 on ‘Effect of hydrologic restoration on the habitat of the Cape Sable seaside sparrow (CSSS)’ included presentations, field work, data analysis, and report preparation. During this period, we made 4 presentations, two at the CSSS – fire planning workshops at Everglades National Park (ENP), one at the Society of Wetland Scientists’ meeting in Charleston, SC, and a fourth at the Marl Prairie/CSSS performance measure workshop at ENP. We started field work in the third week of January and continued till June 3, 2005. Early in the field season, we completed vegetation surveys along two transects, B and C (~15.1 km). During April and May, vegetation sampling was completed at 199 census sites, bringing to 608 the total number of CSSS census sites with quantitative vegetation data. We updated data sets from all three years, 2003-05, and analyzed them using cluster analysis and ordination as in previous two years. However, instead of weighted averaging, we used weighted-averaging partial least square regression (WA-PLS) model, as this method is considered an improvement over WA for inferring values of environmental variables from biological species composition. We also validated the predictive power of the WA-PLS regression model by applying it to a sub-set of 100 census sites for which hydroperiods were “known” from two sources, i.e., from elevations calculated from concurrent water depth measurements onsite and at nearby water level recorders, and from USGS digital elevation data. Additionally, we collected biomass samples at 88 census sites, and determined live and dead aboveground plant biomass. Using vegetation structure and biomass data from those sites, we developed a regression model that we used to predict aboveground biomass at all transects and census sites. Finally, biomass data was analyzed in relation to hydroperiod and fire frequency.

Can minority language proficiency pay: a study on the return on English-Spanish fluent bilingualism in South Florida

This thesis studies the economic return for fluent-bilingualism in South Florida among native-born whites using IPUMS (Integrated Public Use Microdata Series) data for Miami-Dade County (1990). Previous mainstream-oriented theories focus on the benefit in English acquisition for immigrants and their descendants, either denying or ignoring the possible benefit of minority language retention in addition to English acquisition. An alternative literature, on the other hand, suggests that minority language retention can be beneficial in at least three areas: 1) enhancing cognitive ability; 2) accessing community-level social capital; and 3) serving as human capital. This study assesses economic returns in employment and earnings, using logistic and OLS (Ordinary Least Square) regression respectively. The results, countering the mainstream-oriented theories, suggest that fluent bilingualism does have economic consequences. Rather than fully supporting the positive effects thesis, the patterns shown are much more complicated, contingent on an individual's ethnic membership and educational level. Theoretical and substantive implications are discussed and suggestions for future research are made.

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).

Degradação fotocatalítica oxidativa do fenol utilizando carvão obtido da pirólise de diferentes biomassas

The modern industrial progress has been contaminating water with phenolic compounds. These are toxic and carcinogenic substances and it is essential to reduce its concentration in water to a tolerable one, determined by CONAMA, in order to protect the living organisms. In this context, this work focuses on the treatment and characterization of catalysts derived from the bio-coal, by-product of biomass pyrolysis (avelós and wood dust) as well as its evaluation in the phenol photocatalytic degradation reaction. Assays were carried out in a slurry bed reactor, which enables instantaneous measurements of temperature, pH and dissolved oxygen. The experiments were performed in the following operating conditions: temperature of 50 °C, oxygen flow equals to 410 mL min-1 , volume of reagent solution equals to 3.2 L, 400 W UV lamp, at 1 atm pressure, with a 2 hours run. The parameters evaluated were the pH (3.0, 6.9 and 10.7), initial concentration of commercial phenol (250, 500 and 1000 ppm), catalyst concentration (0, 1, 2, and 3 g L-1 ), nature of the catalyst (activated avelós carbon washed with dichloromethane, CAADCM, and CMADCM, activated dust wood carbon washed with dichloromethane). The results of XRF, XRD and BET confirmed the presence of iron and potassium in satisfactory amounts to the CAADCM catalyst and on a reduced amount to CMADCM catalyst, and also the surface area increase of the materials after a chemical and physical activation. The phenol degradation curves indicate that pH has a significant effect on the phenol conversion, showing better results for lowers pH. The optimum concentration of catalyst is observed equals to 1 g L-1 , and the increase of the initial phenol concentration exerts a negative influence in the reaction execution. It was also observed positive effect of the presence of iron and potassium in the catalyst structure: betters conversions were observed for tests conducted with the catalyst CAADCM compared to CMADCM catalyst under the same conditions. The higher conversion was achieved for the test carried out at acid pH (3.0) with an initial concentration of phenol at 250 ppm catalyst in the presence of CAADCM at 1 g L-1 . The liquid samples taken every 15 minutes were analyzed by liquid chromatography identifying and quantifying hydroquinone, p-benzoquinone, catechol and maleic acid. Finally, a reaction mechanism is proposed, cogitating the phenol is transformed into the homogeneous phase and the others react on the catalyst surface. Applying the model of Langmuir-Hinshelwood along with a mass balance it was obtained a system of differential equations that were solved using the Runge-Kutta 4th order method associated with a optimization routine called SWARM (particle swarm) aiming to minimize the least square objective function for obtaining the kinetic and adsorption parameters. Related to the kinetic rate constant, it was obtained a magnitude of 10-3 for the phenol degradation, 10-4 to 10-2 for forming the acids, 10-6 to 10-9 for the mineralization of quinones (hydroquinone, p-benzoquinone and catechol), 10-3 to 10-2 for the mineralization of acids.

Radiotherapy Assessment Using Diffusion Weighted MRI

Purpose: There are two goals of this study. The first goal of this study is to investigate the feasibility of using classic textural feature extraction in radiotherapy response assessment among a unique cohort of early stage breast cancer patients who received the single-dose preoperative radiotherapy. The second goal of this study is to investigate the clinical feasibility of using classic texture features as potential biomarkers which are supplementary to regional apparent diffusion coefficient in gynecological cancer radiotherapy response assessment.

Methods and Materials: For the breast cancer study, 15 patients with early stage breast cancer were enrolled in this retrospective study. Each patient received a single-fraction radiation treatment, and DWI and DCE-MRI scans were conducted before and after the radiotherapy. DWI scans were acquired using a spin-echo EPI sequence with diffusion weighting factors of b = 0 and b = 500 mm2/s, and the apparent diffusion coefficient (ADC) maps were calculated. DCE-MRI scans were acquired using a T1-weighted 3D SPGR sequence with a temporal resolution of about 1 minute. The contrast agent (CA) was intravenously injected with a 0.1 mmol/kg bodyweight dose at 2 ml/s. Two parameters, volume transfer constant (Ktrans) and kep were analyzed using the two-compartment Tofts pharmacokinetic model. For pharmacokinetic parametric maps and ADC maps, 33 textural features were generated from the clinical target volume (CTV) in a 3D fashion using the classic gray level co-occurrence matrix (GLCOM) and gray level run length matrix (GLRLM). Wilcoxon signed-rank test was used to determine the significance of each texture feature’s change after the radiotherapy. The significance was set to 0.05 with Bonferroni correction.

For the gynecological cancer study, 12 female patients with gynecologic cancer treated with fractionated external beam radiotherapy (EBRT) combined with high dose rate (HDR) intracavitary brachytherapy were studied. Each patient first received EBRT treatment followed by five fractions of HDR treatment. Before EBRT and before each fraction of brachytherapy, Diffusion Weighted MRI (DWI-MRI) and CT scans were acquired. DWI scans were acquired in sagittal plane utilizing a spin-echo echo-planar imaging sequence with weighting factors of b = 500 s/mm2 and b = 1000 s/mm2, one set of images of b = 0 s/mm2 were also acquired. ADC maps were calculated using linear least-square fitting method. Distributed diffusion coefficient (DDC) maps and stretching parameter α were calculated. For ADC and DDC maps, 33 classic texture features were generated utilizing the classic gray level run length matrix (GLRLM) and gray level co-occurrence matrix (GLCOM) from high-risk clinical target volume (HR-CTV). Wilcoxon signed-rank statistics test was applied to determine the significance of each feature’s numerical value change after radiotherapy. Significance level was set to 0.05 with multi-comparison correction if applicable.

Results: For the breast cancer study, regarding ADC maps calculated from DWI-MRI, 24 out of 33 CTV features changed significantly after the radiotherapy. For DCE-MRI pharmacokinetic parameters, all 33 CTV features of Ktrans and 33 features of kep changed significantly.

For the gynecological cancer study, regarding ADC maps, 28 out of 33 HR-CTV texture features showed significant changes after the EBRT treatment. 28 out of 33 HR-CTV texture features indicated significant changes after HDR treatments. The texture features that indicated significant changes after HDR treatments are the same as those after EBRT treatment. 28 out of 33 HR-CTV texture features showed significant changes after whole radiotherapy treatment process. The texture features that indicated significant changes for the whole treatment process are the same as those after HDR treatments.

Conclusion: Initial results indicate that certain classic texture features are sensitive to radiation-induced changes. Classic texture features with significant numerical changes can be used in monitoring radiotherapy effect. This might suggest that certain texture features might be used as biomarkers which are supplementary to ADC and DDC for assessment of radiotherapy response in breast cancer and gynecological cancer.

Near real time surface ocean velocity, Tyrrhenian Sea and Ligurian Sea in September 2016

The data set consists of maps of total velocity of the surface current in the North-Western Tyrrhenian Sea and Ligurian Sea averaged over a time interval of 1 hour around the cardinal hour. Surface ocean velocities estimated by HF Radar are representative of the upper 0.3-2.5 meters of the ocean. Total velocities are derived using least square fit that maps radial velocities measured from individual sites onto a cartesian grid. The final product is a map of the horizontal components of the ocean currents on a regular grid in the area of overlap of two or more radar stations.

Seawater carbonate chemistry and biological processes of Amphisorus hemprichii, Amphisorus kudakajimensis and Calcarina gaudichaudii during experiments, 2011

Ocean acidification, which like global warming is an outcome of anthropogenic CO2emissions, severely impacts marine calcifying organisms, especially those living in coral reef ecosystems. However, knowledge about the responses of reef calcifiers to ocean acidification is quite limited, although coral responses are known to be generally negative. In a culture experiment with two algal symbiont-bearing, reef-dwelling foraminifers, Amphisorus kudakajimensis and Calcarina gaudichaudii, in seawater under five different pCO2 conditions, 245, 375, 588, 763 and 907 µatm, maintained with a precise pCO2-controlling technique, net calcification of A. kudakajimensis was reduced under higher pCO2, whereas calcification of C. gaudichaudii generally increased with increased pCO2. In another culture experiment conducted in seawater in which bicarbonate ion concentrations were varied under a constant carbonate ion concentration, calcification was not significantly different between treatments in Amphisorus hemprichii, a species closely related to A. kudakajimensis, or in C. gaudichaudii. From these results, we concluded that carbonate ion and CO2 were the carbonate species that most affected growth ofAmphisorus and Calcarina, respectively. The opposite responses of these two foraminifer genera probably reflect different sensitivities to these carbonate species, which may be due to their different symbiotic algae.

Near real time surface ocean velocity in the Bay of Biscay - Basque Country from Mai to September 2016

The data set consists of maps of total velocity of the surface current in the Southeastern Bay of Biscay averaged over a time interval of 1 hour around the cardinal hour. Surface ocean velocities estimated by this HF Radar(4.65 MHz) are representative of the upper 2-3 meters of the ocean. The main objective of near real time processing is to produce the best product from available data at the time of processing. Total velocities are derived using least square fit that maps radial velocities measured from individual sites onto a cartesian grid. The final product is a map of the horizontal components of the ocean currents on a regular grid in the area of overlap of two or more radar stations.