Statistical Models of Reconstructed Phase Spaces for Signal Classification

This paper introduces a novel approach to the analysis and classification of time series signals using statistical models of reconstructed phase spaces. With sufficient dimension, such reconstructed phase spaces are, with probability one, guaranteed to be topologically equivalent to the state dynamics of the generating system, and, therefore, may contain information that is absent in analysis and classification methods rooted in linear assumptions. Parametric and nonparametric distributions are introduced as statistical representations over the multidimensional reconstructed phase space, with classification accomplished through methods such as Bayes maximum likelihood and artificial neural networks (ANNs). The technique is demonstrated on heart arrhythmia classification and speech recognition. This new approach is shown to be a viable and effective alternative to traditional signal classification approaches, particularly for signals with strong nonlinear characteristics

Time-Domain Isolated Phoneme Classification Using Reconstructed Phase Spaces

This paper introduces a novel time-domain approach to modeling and classifying speech phoneme waveforms. The approach is based on statistical models of reconstructed phase spaces, which offer significant theoretical benefits as representations that are known to be topologically equivalent to the state dynamics of the underlying production system. The lag and dimension parameters of the reconstruction process for speech are examined in detail, comparing common estimation heuristics for these parameters with corresponding maximum likelihood recognition accuracy over the TIMIT data set. Overall accuracies are compared with a Mel-frequency cepstral baseline system across five different phonetic classes within TIMIT, and a composite classifier using both cepstral and phase space features is developed. Results indicate that although the accuracy of the phase space approach by itself is still currently below that of baseline cepstral methods, a combined approach is capable of increasing speaker independent phoneme accuracy

Ameliorative Effect and Underlying Mechanisms of Total Triterpenoids from Psidium guajava Linn (Myrtaceae) Leaf on High-Fat Streptozotocin-induced Diabetic Peripheral Neuropathy in Rats

Purpose: To investigate whether the total triterpenoids extracted from Psidium Guajava leaves (TTPGL) attenuate the development of diabetic peripheral neuropathy in rats by regulating the NF-κB pathway of the inflammatory process and its signaling mediators.Methods: All the Sprague Dawley rats used were maintained in a clean environment on a 12 h light/12h dark cycle. High-fat feeding and intraperitoneal injection of 40 mg/kg streptozotocin (STZ) were used to induce diabetes in the rats. The rats were randomly divided into 5 groups: diabetic mellitus (DM) group; TTPGL - 30 group, TTPGL - 60 group and TTPGL - 120 group treated by intragastric administration (i.g) with 30, 100 and 120 mg/kg/day TTPGL, respectively. The well-established drug, rosiglitazone (RSG, 3 mg/k/d, i.g.), was used as positive control. Normal rats served as control group. Nerve conduction velocity and sensitive tests were measured on weeks 1, 4 and 8. After 8 weeks administration, expression of pro-inflammatory molecules (TNF - α, IL - 6 and iNOS) and tissue proteins (Akt, IKKα, and NF – κB - p65) were evaluated to assess biochemical changes.Results: Compared to DM group, TTPGL (especially 120 mg / kg dose) treatment improved (p < 0.05) physical functions and provided neuronal protection in high - fat/streptozotocin - induced peripheral neuropathy rats. We found that the expressions of several pro - inflammatory factors such as tumor necrosis factor - α (TNF - α), IL - 6 and inducible nitric oxide synthase (iNOS) were highly suppressed (p < 0.05 or p < 0.01) by TTPGL in sciatic nerve. Mechanism analysis indicated that the ameliorative effect of TTPGL, in part, is through suppression of the expression of pro - inflammatory cytokines by NF - κB pathway mediation.Conclusion: TTPGL offers a potential therapeutic approach for the treatment of diabetic peripheral neuropathy.Keywords: Triterpenoids, Psidium Guajava, Diabetic peripheral neuropathy, Pro inflammatory cytokines, NF-κB pathwa

Biochemical Characterization and Phylogenetic Analysis of the Virulence Factor Lysine Decarboxylase From Vibrio vulnificus

Cadaverine is produced in organisms from the amino acid lysine in a decarboxylation reaction catalyzed by lysine decarboxylase (EC 4.1.1.18). The inducible lysine decarboxylase CadA plays a vital role in acid stress response for enteric bacteria. Vibrio vulnificus is an extremely virulent human pathogen causing gastroenteritis when the acid conditions that prevent survival of V. vulnificus in the stomach or small intestine are overcome. A gene encoding CadA was identified from V. vulnificus. Subsequent analyses showed that CadA from V. vulnificus (VvCadA) is a decamer with a 82-kDa subunit. Homogenous VvCadA was purified from Escherichia coli and used for lysine decarboxylation with an optimal pH of 6.0 and optimal temperature of 37°C. The apparent Vmax and Km for lysine were 9.45 ± 0.24 μM/min and 0.45 ± 0.05 mM, respectively. Mutation analysis suggested that the amino-acid-binding pyridoxal phosphate, the cofactor of the enzyme, plays a vital role in the reaction. Mutation of the negatively charged residues interacting with lysine also affected the activity of the enzyme to some extent. Quantitative RT-PCR showed that expression of VvcadA was up-regulated under low pH, low salinity, and oxidative stresses. Furthermore, the concentration of cadaverine released to the cell exterior also increased under these stresses. Protein sequence similarity network (SSN) analysis indicated that lysine decarboxylases with ornithine decarboxylases and arginine decarboxylases shared a common ancestor, and that lysine decarboxylases are more conserved during evolution. Our data provide evidence for the biochemical characteristics and important roles of VvCadA under stress conditions

A Canonical Correlation Analysis of AIDS Restriction Genes and Metabolic Pathways Identifies Purine Metabolism as a Key Cooperator

Human immunodeficiency virus causes a severe disease in humans, referred to as immune deficiency syndrome. Studies on the interaction between host genetic factors and the virus have revealed dozens of genes that impact diverse processes in the AIDS disease. To resolve more genetic factors related to AIDS, a canonical correlation analysis was used to determine the correlation between AIDS restriction and metabolic pathway gene expression. The results show that HIV-1 postentry cellular viral cofactors from AIDS restriction genes are coexpressed in human transcriptome microarray datasets. Further, the purine metabolism pathway comprises novel host factors that are coexpressed with AIDS restriction genes. Using a canonical correlation analysis for expression is a reliable approach to exploring the mechanism underlying AIDS

Association of Lean Body Mass Index and Peritoneal Protein Clearance in Peritoneal Dialysis Patients

Background/Aims: The relationship between peritoneal protein clearance (PPCl) and nutritional status in peritoneal dialysis (PD) population have not been clarified. This study aims to investigate the relationship between PPCl and nutritional status in PD population. Methods: Prevalent PD patients were enrolled in the cross-sectional survey in a single center from April to November 2013. The total amount of protein loss in the dialysate was calculated. PPCl reflects the individual differences of peritoneal protein loss, and is calculated by the formula, that PPCl (ml/day)=24-h dialysate protein loss / (albumin/0.4783). Nutritional status measured by lean body mass index (LBMI) was assessed by multi-frequency bioelectrical impedance analysis (BIA). Results: Totally 351 PD patients (55% male, 17.1% with diabetes, mean age 47.7±14.3 years) were included. The median PPC l was 58 ml/day. Patients were divided into four groups for comparison according to the PPC quartiles. Compared with lower PPCl quartiles, patients with higher PPCl had higher body mass index (BMI) (P< 0.001), body surface area (BSA) (P < 0 .001), LBMI (P<0.001), 4-hour D/P creatinine ratio (P< 0.001), and lower residual renal CCl (P<0.001). Compared with conventional body index (BMI and BSA) in ROC analysis, LBMI (area under curve: 0.71, 95% confidence interval [CI]: 0.66-0.77) had better performance in predicting higher PPCl. After adjustment in logistic regression models, each 1 kg/m2 increase of LBMI (odd ratio[OR] =1.37; 95% CI: 1.17-1.60), each 0.1 increase of 4-hour D/P creatinine ratio (OR =1.47; 95% CI: 1.11-1.93), and every 1 L/week/1.73m2 decrease of residual renal CCl (OR =0.98; 95% CI: 0.96-0.99) were independently associated with higher PPCl (> 58 ml/day). Conclusion: Higher LBMI was independently associated with higher , indicating that better nutritional status dominates peritoneal protein metabolism in PD patients

Nearly a decade-long repeatable seasonal diversity patterns of bacterioplankton communities in the eutrophic Lake Donghu (Wuhan, China).

Uncovering which environmental factors govern community diversity patterns and how ecological processes drive community turnover are key questions related to understand the community assembly. However, the ecological mechanisms regulating long-term variations of bacterioplankton communities in lake ecosystems remain poorly understood. Here we present nearly a decade-long study of bacterioplankton communities from the eutrophic Lake Donghu (Wuhan, China) using 16S rRNA gene amplicon sequencing with MiSeq platform. We found strong repeatable seasonal diversity patterns in terms of both common (detected in more than 50% samples) and dominant (relative abundance >1%) bacterial taxa turnover. Moreover, community composition tracked the seasonal temperature gradient, indicating that temperature is a key environmental factor controlling observed diversity patterns. Total phosphorus also contributed significantly to the seasonal shifts in bacterioplankton composition. However, any spatial pattern of bacterioplankton communities across the main lake areas within season was overwhelmed by their temporal variabilities. Phylogenetic analysis further indicated that 75%-82% of community turnover was governed by homogeneous selection due to consistent environmental conditions within seasons, suggesting that the microbial communities in Lake Donghu are mainly controlled by niche-based processes. Therefore, dominant niches available within seasons might be occupied by similar combinations of bacterial taxa with modest dispersal rates throughout different lake areas