A naïve Gaussian Bayes classifier for detection of mental activity in gait signature

A probabilistic modelling is presented to detect mental activity from gait signature recorded from healthy subjects. The proposed scheme is based on principal component analysis with reduced feature dimension followed by a naïve Gaussian Bayes classifier. The leave-one-out cross-validation shows the detection accuracy of 94% with specificity and sensitivity of 96% and 98.3%, respectively. The research has a potential application in the prevention of elderly risk falls, lie detection and rehabilitation among Parkinson's patients.     

Classification of complete blood count and haemoglobin typing data by a C4.5 decision tree,a naïve Bayes classifier and a multilayer perceptron for thalassaemia screening

This article presents the classification of blood characteristics by a C4.5 decision tree, a naïve Bayes classifier and a multilayer perceptron for thalassaemia screening. The aim is to classify eighteen classes of thalassaemia abnormality, which have a high prevalence in Thailand, and one control class by inspecting data characterised by a complete blood count (CBC) and haemoglobin typing. Two indices namely a haemoglobin concentration (HB) and a mean corpuscular volume (MCV) are the chosen CBC attributes. On the other hand, known types of haemoglobin from six ranges of retention time identified via high performance liquid chromatography (HPLC) are the chosen haemoglobin typing attributes. The stratified 10-fold cross-validation results indicate that the best classification performance with average accuracy of 93.23% (standard deviation = 1.67%) and 92.60% (standard deviation = 1.75%) is achieved when the naïve Bayes classifier and the multilayer perceptron are respectively applied to samples which have been pre-processed by attribute discretisation. The results also suggest that the HB attribute is redundant. Moreover, the achieved classification performance is significantly higher than that obtained using only haemoglobin typing attributes as classifier inputs. Subsequently, the naïve Bayes classifier and the multilayer perceptron are applied to an additional data set in a clinical trial which respectively results in accuracy of 99.39% and 99.71%. These results suggest that a combination of CBC and haemoglobin typing analysis with a naïve Bayes classifier or a multilayer perceptron is highly suitable for automatic thalassaemia screening.     

A naïve Gaussian Bayes classifier for detection of mental activity in gait signature

A probabilistic modelling is presented to detect mental activity from gait signature recorded from healthy subjects. The proposed scheme is based on principal component analysis with reduced feature dimension followed by a na?ve Gaussian Bayes classifier. The leave-one-out cross-validation shows the detection accuracy of 94% with specificity and sensitivity of 96% and 98.3%, respectively. The research has a potential application in the prevention of elderly risk falls, lie detection and rehabilitation among Parkinson's patients.     

Protein structure and fold prediction using Tree-Augmented naïve Bayesian classifier

Due to the large volume of protein sequence data, computational methods to determine the structure class and the fold class of a protein sequence have become essential. Several techniques based on sequence similarity, Neural Networks, Support Vector Machines (SVMs), etc. have been applied. Since most of these classifiers use binary classifiers for multi-classification, there may be (N) c2 classifiers required. This paper presents a framework using the Tree-Augmented Bayesian Networks (TAN) which performs multi-classification based on the theory of learning Bayesian Networks and using improved feature vector representation of (Ding et al., 2001). In order to enhance TAN's performance, pre-processing of data is done by feature discretization and post-processing is done by using Mean Probability Voting (MPV) scheme. The advantage of using Bayesian approach over other learning methods is that the network structure is intuitive. In addition, one can read off the TAN structure probabilities to determine the significance of each feature (say, hydrophobicity) for each class, which helps to further understand the complexity in protein structure. The experiments on the datasets used in three prominent recent works show that our approach is more accurate than other discriminative methods. The framework is implemented on the BAYESPROT web server and it is available at http://www-appn.comp.nus.edu.sg/~bioinfo/bayesprot/Default.htm. More detailed results are also available on the above website.     

Predicting antigenicity of proteins in a bacterial proteome; a protein microarray and naïve Bayes classification approach

Discovery of novel antigens associated with infectious diseases is fundamental to the development of serodiagnostic tests and protein subunit vaccines against existing and emerging pathogens. Efforts to predict antigenicity have relied on a few computational algorithms predicting signal peptide sequences (SignalP), transmembrane domains, or subcellular localization (pSort). An empirical protein microarray approach was developed to scan the entire proteome of any infectious microorganism and empirically determine immunoglobulin reactivity against all the antigens from a microorganism in infected individuals. The current database from this activity contains quantitative antibody reactivity data against 35,000 proteins derived from 25 infectious microorganisms and more than 30 million data points derived from 15,000 patient sera. Interrogation of these data sets has revealed ten proteomic features that are associated with antigenicity, allowing an in silico protein sequence and functional annotation based approach to triage the least likely antigenic proteins from those that are more likely to be antigenic. The first iteration of this approach applied to Brucella melitensis predicted 37% of the bacterial proteome containing 91% of the antigens empirically identified by probing proteome microarrays. In this study, we describe a na?ve Bayes classification approach that can be used to assign a relative score to the likelihood that an antigen will be immunoreactive and serodiagnostic in a bacterial proteome. This algorithm predicted 20% of the B. melitensis proteome including 91% of the serodiagnostic antigens, a nearly twofold improvement in specificity of the predictor. These results give us confidence that further development of this approach will lead to further improvements in the sensitivity and specificity of this in silico predictive algorithm.     

Susceptibility of a naïve population of house finches to Mycoplasma gallisepticum

Since 1994 an epidemic of mycoplasmal conjunctivitis has spread throughout the eastern house finch (Carpodacus mexicanus) population leading to a significant decline in this population. The infection has not yet been reported from house finch populations west of the Great Plains. We hypothesized that the western population, like the eastern population, is susceptible to infection, and we tested this hypothesis by experimentally infecting house finches from Missoula, Montana (USA) with the house finch strain of Mycoplasma gallisepticum (MG). We compared the response of finches from Montana infected with MG to that of finches from Auburn, Alabama (USA) (October 1999-February 2000). Fifteen house finches from Montana were shipped to Auburn and quarantined for 6 wk at the Auburn University aviary. All birds were negative for MG antibodies when tested by serum plate agglutination assay and MG could not be detected in any bird by polymerase chain reaction. We tested two methods of inoculation, ocular inoculation and contact exposure to an infected finch. Seven house finches from Montana and four house finches from Alabama were infected by bilateral ocular inoculation with 20 microliters of a culture containing 1 x 10(6) color changing units of the house finch strain of MG. The remaining eight house finches from Montana were co-housed with a house finch from Alabama exhibiting mycoplasmal conjunctivitis. After exposure to the pathogen, all house finches became infected, regardless of origin or method of exposure, and all developed conjunctivitis. All birds seroconverted, and evidence of infection could be detected in every bird at some point during the course of disease. Our results suggest that house finches from the western United States are highly susceptible to infection with the house finch strain of MG.     

Regulation of naïve and memory T-cell homeostasis

Recent work has confirmed the existence of homeostatic mechanisms that regulate the overall size and composition of the mature T-cell pool. Homeostatic mechanisms not only control total T-cell numbers but appear to act differently on na?ve vs. memory cells. The roles of self-MHC/peptide ligands and certain cytokines in T-cell homeostasis are discussed.     

Long-term self-renewal of naïve neural stem cells in a defined condition

During embryonic development, neural stem cells (NSCs) emerge as early as the neural plate stage and give rise to the nervous system. Early-stage NSCs express Sry-related-HMG box-1 (Sox1) and are biased towards neuronal differentiation. However, long-term maintenance of early-stage NSCs in vitro remains a challenge. Here, we report development of a defined culture condition for the long-term maintenance of Sox1-positive early-stage mouse NSCs. The proliferative ability of these Sox1-positive NSCs was confirmed by clonal propagation. Compared to the NSCs cultured using the traditional culture condition, the long-term self-renewing Sox1-positive NSCs efficiently differentiate into neurons and exhibit an identity representative of the anterior and midbrain regions. These early-stage Sox1-positive NSCs could also be switched to late-stage NSCs by being cultured with bFGF/EGF, which can then differentiate into astrocytes and oligodendrocytes. The long-term self-renewing Sox1-positive NSCs were defined as naïve NSCs, based on their high neuronal differentiation capacity and anterior regional identity. This culture condition provides a robust platform for further dissection of the NSC self-renewal mechanism and promotes potential applications of NSCs for cell-based therapy on nervous system disorders.     

Generation of a naïve/synthetic antibody specific to botulinum neurotoxin via motif-grafting

In this study, we describe a new approach to the production of naïve/synthetic human antibodies against the botulinum neurotoxin (BoNT). First, peptides that bind to BoNT serotype A (BoNT/A) were screened from a phage display of a combinatorial peptide library. One peptide, designated ANT 12-2 (TLPSPLALLTVH), was determined to interact with BoNT/A, as well as with other serotypes of BoNT. This peptide specifically reacted with the native form of BoNT/A, but not with its formalin-inactivated form. Next, a hybrid naïve/synthetic human Fab library was generated via the grafting of a peptide motif from ANT 12-2 into HCDR3 with randomized flanking residues. Through biopanning, the Fab clone, ANTHU-1, which harbors the HCDR3 sequence of VRIQRSPLALLSWGDV, was selected and confirmed in order to retain the same BoNT-binding characteristics as ANT 12-2.     

Study of naïve and memory cells in a cohort of Egyptian chronic granulomatous disease patients

Abstract

Context: Chronic granulomatous disease (CGD) is a primary immunodeficiency disorder caused by inherited defects in the NADPH oxidase complex which may be involved in important pathways that connect innate and adaptive immunity. Objectives: Characterize the naive and memory compartment of B and T lymphocytes in patients with CGD. Methods: Twenty CGD patients and twenty healthy controls matched for age and sex were enrolled in this study. Flow cytometric assessment of the naïve and memory compartments of peripheral blood lymphocytes was done using cell surface markers CD45RO, CD45RA, CD27, CD3 and CD19. Results: There were 15 (79%) autosomal recessive CGD patients (8 females (53%) and 7 males (47%), 100% positive parental consanguinity) and four (21%) X-linked CGD patients. On comparing the 3 groups; AR CGD, X-linked CGD and controls, there was a positive statistical significant difference for the percentage and absolute count of CD19?+?CD27+ memory B cell (p?=?0.028 and p?=?0.047 respectively), CD45RA cells (with p values of p?=?0.000 and 0.033, respectively), the naïve compartment CD3?+?CD45RA+ cells percentage and absolute counts (p?=?0.005, 0.01respectively), CD3?+?CD27?+?cells percentage and absolute counts (p?=?0.001, 0.012 respectively), CD3?+?CD45RA?+?CD27+ cells percentage and absolute counts (p?=?0.015, 0.005, respectively). The significance was mainly attributed to the decrease in the X-linked group than control group. Conclusion: There was an altered naïve and memory B profile in CGD patients, this may increase susceptibility of the patients to opportunistic infections and autoimmune disorders. T-cell alterations have to be interpreted cautiously especially in the presence of infections.     

Responses of naïve and experienced European rabbits to predator odour

The response of prey species to predator scent has been investigated in many mammalian species; however, there is little information about the responses of European wild rabbits at the population level. Therefore, we conducted a simple experiment to investigate the behavioural response of a rabbit population to native predator cues in the wild. We compared the response to the scent of a predator (red fox) in a wild rabbit population bred in semi-natural conditions and naïve to terrestrial predators with the response of a population in a similar environment where terrestrial predators were present. The response to predators was based on rabbit abundance, inferred from pellet counts and measured by the defecation rate per day (DRD). Our results indicate that rabbits responded to the odour of fox faeces in the treatment warrens, resulting in a lower DRD. The main anti-predator behaviour observed was spatial avoidance (warren abandonment), which seemed to be more accentuated for rabbits who had not previously had contact with foxes in the plot where terrestrial predators were excluded. In both the fenced and the unfenced plot, the differences in the effect of the predator odour between the control and treatment warrens disappeared after cessation of treatment, suggesting a flexible and adaptive behaviour of rabbits to predator cues.

     

The testosterone binding mechanism of an antibody derived from a naïve human scFv library

A testosterone binding scFv antibody was isolated from a naïve human library with a modest size of 10⁸ clones. The crystal structure of the Fab fragment form of the 5F2 antibody clone complexed with testosterone determined at 1.5 Å resolution shows that the hapten is bound deeply in the antibody binding pocket. In addition to the interactions with framework residues only CDR‐L3 and CDR‐H3 loops interact with testosterone and the heavy chain forms the majority of the contacts with the hapten. The testosterone binding site of the 5F2 antibody with a high abundance of aromatic amino acid residues shows similarity with an in vitro affinity matured antibody having around 300 times higher affinity. The moderate affinity of the 5F2 antibody originates from the different orientation of the hapten and few light chain contacts. This is the first three‐dimensional structure of a human steroid hormone binding antibody that has been isolated from a naïve human repertoire. Copyright © 2010 John Wiley & Sons, Ltd.     

MHC-dependent survival of naïve T cells? A complicated answer to a simple question

The differentiation and survival of developing alpha beta thymocytes depends on effective T-cell receptor (TCR) signaling upon recognition of self peptide/major histocompatibility complex (MHC) molecule ligands. Although this concept is uniformly accepted with regard to immature thymocytes, there are conflicting reports as to whether or not MHC recognition is required for survival of mature peripheral na?ve T cells. In this review, we assess these reports critically and conclude that in many cases, the differences observed in CD4(+) T-cell recovery between MHC-expressing and MHC-deficient animals can be attributed to proliferation occurring only in the MHC-expressing lymphopenic animals studied in these models systems, rather than to effects of MHC recognition on cell viability per se. Still other reports involve experimental manipulations that may have affected the intrathymic development of the T cells such that they receive a "poor" selecting signal, fail to fully mature, and thus behave more like thymocytes in their survival characteristics (i.e., show MHC dependence). With respect to CD8(+) T cells, we discuss data suggesting that some clones are more dependent upon the presence of MHC class I for survival than others. We propose that some CD8(+) T cells even in a wild-type host may behave like the manipulated CD4(+) T cells just described, and fail to mature completely with respect to their survival requirements. Although the proportion of CD8(+) cells in this MHC-dependent state is not known, the corresponding fraction among CD4(+) T cells seems to be rather small. Overall, our analysis of the available data suggests that most or all mature CD4(+) (and perhaps also many CD8(+)) T lymphocytes do not depend on self-recognition for their viability in the periphery.     

Glycans define the stemness of naïve and primed pluripotent stem cells

Cell surface glycans are tissue-specific and developmentally regulated. They function as essential modulators in cell-cell interactions, cell-extracellular matrix interactions, and ligand-receptor interactions, binding to various ligands, including Wnt, fibroblast growth factors, and bone morphogenetic proteins. Embryonic stem (ES) cells, originally derived from the inner cell mass of blastocysts, have the essential characteristics of pluripotency and self-renewal. Recently, it has been proposed that mouse and human conventional ES cells are present in different developmental stages, namely pre-implantation blastocyst and post-implantation blastocyst stages, also called the naïve state and the primed state, respectively. They therefore require different extrinsic signals for the maintenance of self-renewal and pluripotency, and also appear to require different surface glycans. Understanding of molecular mechanisms involving glycans in self-renewal and pluripotency of ES cells is increasingly important for potential clinical applications, as well as for basic research. This review focuses on the roles of glycans in the two different states of pluripotent stem cells, namely the naïve state and the primed state, and the transition between these two states.     

Non-random tissue distribution of human naïve umbilical cord matrix stem cells

AIM: To determine the tissue and temporal distribution of human umbilical cord matrix stem (hUCMS) cells in severe combined immunodeficiency (SCID) mice. METHODS: For studying the localization of hUCMS cells, tritiated thymidine-labeled hUCMS cells were injected in SCID mice and tissue distribution was quantitatively determined using a liquid scintillation counter at days 1, 3, 7 and 14. Furthermore, an immunofluorescence detection technique was employed in which anti-human mitochondrial antibody was used to identify hUCMS cells in mouse tissues. In order to visualize the distribution of transplanted hUCMS cells in H&E stained tissue sections, India Black ink 4415 was used to label the hUCMS cells. RESULTS: When tritiated thymidine-labeled hUCMS cells were injected systemically (iv) in female SCID mice, the lung was the major site of accumulation at 24 h after transplantation. With time, the cells migrated to other tissues, and on day three, the spleen, stomach, and small and large intestines were the major accumulation sites. On day seven, a relatively large amount of radioactivity was detected in the adrenal gland, uterus, spleen, lung, and digestive tract. In addition, labeled cells had crossed the blood brain barrier by day 1. CONCLUSION: These results indicate that peripherally injected hUCMS cells distribute quantitatively in a tissue-specific manner throughout the body.     

Differential expression of FCRLA in naïve and activated mouse B cells

FCRLA is an intracellular B cell protein that belongs to the FcR-like family. Using newly generated FCRLA-specific antibodies, we studied the constitutive expression pattern of mouse FCRLA and monitored changes during an immune response and following in vitro B cell activation. All B cell subpopulations examined expressed FCRLA. However, the level of FCRLA expression is determined by the stage of B cell differentiation. Low expression of FCRLA is characteristic of naïve follicular and marginal zone B cells. High expression was detected in a small fraction of activated B cells scattered along migratory pathways in the lymphoid tissues. FCRLA-bright cells could be subdivided into two subpopulations, with high and low/undetectable level of intracellular immunoglobulins, which phenotypically resemble either plasma or memory B cells. High expression of FCRLA in subset(s) of terminally differentiated B-cells suggests that, being an ER protein, FCRLA may participate in the regulation of immunoglobulin assembly and secretion.     

Screening for dihydrofolate reductase inhibitors using MOLPRINT 2D, a fast fragment-based method employing the naïve Bayesian classifier: limitations of the descriptor and the importance of balanced chemistry in training and test sets

A fragment-based similarity searching method, MOLPRINT 2D, was employed for virtual screening of Escherichia coli dihydrofolate reductase inhibitors. Using the original training set of 50,000 compounds, only marginal enrichment factors (between 1 and 3) could be achieved on the test library. The active structures contained in the training and test libraries represented different types of "chemistry", that is, different substructural features associated with activity. Training and test sets were pooled in a 2nd step and randomly split into training and test of equal size, with the objective of smoothing out the different chemical characteristics of both libraries. In a 10-fold cross-validation study on the new training and test sets, typically 10-fold enrichment could be found in the first 96 positions, 4-fold enrichment in the first 384 positions, and 3-fold enrichment in the first 1536 positions, corresponding to 6, 10, and 28 hits, respectively (out of a total of 307; activity defined as average residual activity of less than 80%). The conclusions are 2-fold. On one hand, the exact fragment-matching similarity searching method employed here is not capable of finding completely novel hit structures. On the other hand, this study emphasizes the requirement for a comparable distribution of chemical features of the training and test sets. MOLPRINT 2D is freely downloadable from http://www.cheminformatics.org.