Neural network assessment of herbal protection against chemotherapeutic-induced reproductive toxicity

The aim of this study is to assess the protective effects of Ginkgo biloba's (GB) extract against chemotherapeutic-induced reproductive toxicity using a data mining tool, namely Neural Network Clustering (NNC) on two types of data: biochemical & fertility indicators and Texture Analysis (TA) parameters. GB extract (1 g/kg/day) was given orally to male albino rats for 26 days. This period began 21 days before a single cisplatin (CIS) intraperitoneal injection (10 mg/kg body weight). GB given orally significantly restored reproductive function. Tested extract also notably reduced the CIS-induced reproductive toxicity, as evidenced by restoring normal morphology of testes. In GB, the attenuation of CIS-induced damage was associated with less apoptotic cell death both in the testicular tissue and in the sperms. CIS-induced alterations of testicular lipid peroxidation were markedly improved by the examined plant extract. NNC has been used for classifying animal groups based on the quantified biochemical & fertility indicators and microscopic image texture parameters extracted by TA. NNC showed the separation of two clusters and the distribution of groups among them in a way that signifies the dose-dependent protective effect of GB. The present study introduces the neural network as a powerful tool to assess both biochemical and histopathological data. We also show here that herbal protection against CIS-induced reproductive toxicity utilizing classic methodologies is validated using neural network analysis.     

The protection of mice against x-radiation using sodium succinate

Dynamics of mouse resistance to X-radiation was studied after single and double injection of sodium succinate in doses of 2.5 and 10 mmol/kg. The criteria by which the radioprotective effect of the agent was estimated were: survival rate, spleen mass, and DNA content in the bone marrow.     

Splice sites detection using chaos game representation and neural network

A novel method is proposed to detect the acceptor and donor splice sites using chaos game representation and artificial neural network. In order to achieve high accuracy, inputs to the neural network, or feature vector, shall reflect the true nature of the DNA segments. Therefore it is important to have one-to-one numerical representation, i.e. a feature vector should be able to represent the original data. Chaos game representation (CGR) is an iterative mapping technique that assigns each nucleotide in a DNA sequence to a respective position on the plane in a one-to-one manner. Using CGR, a DNA sequence can be mapped to a numerical sequence that reflects the true nature of the original sequence. In this research, we propose to use CGR as feature input to a neural network to detect splice sites on the NN269 dataset. Computational experiments indicate that this approach gives good accuracy while being simpler than other methods in the literature, with only one neural network component. The code and data for our method can be accessed from this link: https://github.com/thoang3/portfolio/tree/SpliceSites_ANN_CGR.     

The intrinsic chaperone network of Arabidopsis stem cells confers protection against proteotoxic stress

The biological purpose of plant stem cells is to maintain themselves while providing new pools of differentiated cells that form organs and rejuvenate or replace damaged tissues. Protein homeostasis or proteostasis is required for cell function and viability. However, the link between proteostasis and plant stem cell identity remains unknown. In contrast to their differentiated counterparts, we find that root stem cells can prevent the accumulation of aggregated proteins even under proteotoxic stress conditions such as heat stress or proteasome inhibition. Notably, root stem cells exhibit enhanced expression of distinct chaperones that maintain proteome integrity. Particularly, intrinsic high levels of the T‐complex protein‐1 ring complex/chaperonin containing TCP1 (TRiC/CCT) complex determine stem cell maintenance and their remarkable ability to suppress protein aggregation. Overexpression of CCT8, a key activator of TRiC/CCT assembly, is sufficient to ameliorate protein aggregation in differentiated cells and confer resistance to proteotoxic stress in plants. Taken together, our results indicate that enhanced proteostasis mechanisms in stem cells could be an important requirement for plants to persist under extreme environmental conditions and reach extreme long ages. Thus, proteostasis of stem cells can provide insights to design and breed plants tolerant to environmental challenges caused by the climate change.     

Immunity and protection against Brucella abortus

Brucella abortus is an intracellular pathogen that causes disease in cattle and in humans. The response against B. abortus involves the whole gamut of the immune system, from innate to adaptive immunity resulting from stimulation of antigen-presenting cells, NK cells, CD4(+) and CD8(+) T cells, and B cells.     

Constructing software countermeasures against instruction manipulation attacks: an approach based on vulnerability evaluation using fault simulator

Cluster Computing - Fault injection attacks (FIA), which cause information leakage by injecting intentional faults into the data or operations of devices, are one of the most powerful methods...     

i‐Patch: Interprotein contact prediction using local network information

Biological processes are commonly controlled by precise protein‐protein interactions. These connections rely on specific amino acids at the binding interfaces. Here we predict the binding residues of such interprotein complexes. We have developed a suite of methods, i‐Patch, which predict the interprotein contact sites by considering the two proteins as a network, with residues as nodes and contacts as edges. i‐Patch starts with two proteins, A and B, which are assumed to interact, but for which the structure of the complex is not available. However, we assume that for each protein, we have a reference structure and a multiple sequence alignment of homologues. i‐Patch then uses the propensities of patches of residues to interact, to predict interprotein contact sites. i‐Patch outperforms several other tested algorithms for prediction of interprotein contact sites. It gives 59% precision with 20% recall on a blind test set of 31 protein pairs. Combining the i‐Patch scores with an existing correlated mutation algorithm, McBASC, using a logistic model gave little improvement. Results from a case study, on bacterial chemotaxis protein complexes, demonstrate that our predictions can identify contact residues, as well as suggesting unknown interfaces in multiprotein complexes. Proteins 2010. © 2010 Wiley‐Liss, Inc.     

On-line estimation of biomass concentration using a neural network and information about metabolic state

This paper deals with the design of a neural network-based biomass concentration estimation system. This system is enhanced by the incorporation of information about the actual metabolism of the microorganism cultivated, which is taken from an on-line knowledge-based system. Two different design approaches have been investigated using the fed-batch cultivation of bakers yeast as the model process. In the first, metabolic state (MS) data were passed as additional input to the neural network; in the second, these data were used to select a neural network suitable for the specific MS. Two neural network types—feed-forward (Levenberg-Marquardt) and cascade correlation—were applied to this system and tested, and the performances of these neural networks were compared.     

Distributed anomaly detection using concept drift detection based hybrid ensemble techniques in streamed network data

Cluster Computing - Ever since the internet became part of the everyday lives of humans providing network security has been considered of utmost importance. Over the years lot of time and energy...     

Origin of cells and network information

All cells are derived from one cell, and the origin of different cell types is a subject of curiosity. Cells construct life through appropriately timed networks at each stage of development. Communication among cells and intracellular signaling are essential for cell differentiation and for life processes. Cellular molecular networks establish cell diversity and life. The investigation of the regulation of each gene in the genome within the cellular network is therefore of interest. Stem cells produce various cells that are suitable for specific purposes. The dynamics of the information in the cellular network changes as the status of cells is altered. The components of each cell are subject to investigation.     

Kin-selection,reciprocal altruism,and information sharing among Maine lobstermen

In this paper, the sharing of information about the location of lobsters among lobstermen in two Maine harbors is described. First, why the sharing of such information is likely to entail an economic loss for the transmitters is explained. Then, the extent to which the principles of kin-selection and reciprocal altruism can account for the sharing of information is determined. Many cases of information sharing in one of the harbors do not appear to be the type of kin-directed or reciprocal acts expected to be produced by kin-selection or reciprocal altruism as they are usually conceived. The behavior of these lobstermen may be the result of the advantages of maintaining a complex web of social relationships among them. Failure to appreciate the complexity of such relationships in some fishing communities is suggested to be a major shortcoming in the economic models previously used to explain information management among commercial fishermen. I conclude that a more complex model of reciprocal altruism is needed to account for the information sharing among this group of Maine lobstermen, and perhaps many other human social groups.     

Epilepsy seizure detection using eigen-system spectral estimation and Multiple Layer Perceptron neural network

In this paper, a new approach based on eigen-systems pseudo-spectral estimation methods, namely Eigenvector (EV) and MUSIC, and Multiple Layer Perceptron (MLP) neural network is introduced. In this approach, the calculated EEG (electroencephalogram) spectrum is divided into smaller frequency sub-bands. Then, a set of features, {maximum, entropy, average, standard deviation, mobility}, are extracted from these sub-bands. Next, incorporating a set of the EEG time domain features {standard deviation, complexity measure} with the spectral feature set, a feature vector is formed. The feature vector is then fetched into a MLP neural network to classify the signal into the following three states: normal (healthy), epileptic patient signal in a seizure-free interval (inter-ictal), and epileptic patient signal in a full seizure interval (ictal). The experimental results show that the classification of the EEG signals maybe achieved with approximately 97.5% accuracy and the variance of 0.095% using an available public EEG signals database. The results are among the best reported methods for classifying the three states aforementioned. This is a high speed with high accuracy as well as low misclassifying rate method so it can make the practical and real-time detection of this chronic disease feasible.     

Vaccine protection against simian immunodeficiency virus in monkeys using recombinant gamma-2 herpesvirus

Recombinant strains of replication-competent rhesus monkey rhadinovirus (RRV) were constructed in which strong promoter/enhancer elements were used to drive expression of simian immunodeficiency virus (SIV) Env or Gag or a Rev-Tat-Nef fusion protein. Cultured rhesus monkey fibroblasts infected with each recombinant strain were shown to express the expected protein. Three RRV-negative and two RRV-positive rhesus monkeys were inoculated intravenously with a mixture of these three recombinant RRVs. Expression of SIV Gag was readily detected in lymph node biopsy specimens taken at 3 weeks postimmunization. Impressive anti-SIV cellular immune responses were elicited on the basis of major histocompatibility complex (MHC) tetramer staining and gamma interferon enzyme-linked immunospot (ELISPOT) assays. Responses were much greater in magnitude in the monkeys that were initially RRV negative but were still readily detected in the two monkeys that were naturally infected with RRV at the time of immunization. By 3 weeks postimmunization, responses measured by MHC tetramer staining in the two Mamu-A*01(+) RRV-negative monkeys reached 9.3% and 13.1% of all CD8(+) T cells in peripheral blood to the Gag CM9 epitope and 2.3% and 7.3% of all CD8(+) T cells in peripheral blood to the Tat SL8 epitope. Virus-specific CD8(+) T cell responses persisted at high levels up to the time of challenge at 18 weeks postimmunization, and responding cells maintained an effector memory phenotype. Despite the ability of the RRVenv recombinant to express high levels of Env in cultured cells, and despite the appearance of strong anti-RRV antibody responses in immunized monkeys, anti-Env antibody responses were below our ability to detect them. Immunized monkeys, together with three unimmunized controls, were challenged intravenously with 10 monkey infectious doses of SIVmac239. All five immunized monkeys and all three controls became infected with SIV, but peak viral loads were 1.2 to 3.0 log(10) units lower and chronic-phase viral loads were 1.0 to 3.0 log(10) units lower in immunized animals than the geometric mean of unimmunized controls. These differences were statistically significant. Anti-Env antibody responses following challenge indicated an anamnestic response in the vaccinated monkeys. These findings further demonstrate the potential of recombinant herpesviruses as preventive vaccines for AIDS. We hypothesize that this live, replication-competent, persistent herpesvirus vector could match, or come close to matching, live attenuated strains of SIV in the degree of protection if the difficulty with elicitation of anti-Env antibody responses can be overcome.     

Horizontal transmissible protection against myxomatosis and rabbit hemorrhagic disease by using a recombinant myxoma virus

We have developed a new strategy for immunization of wild rabbit populations against myxomatosis and rabbit hemorrhagic disease (RHD) that uses recombinant viruses based on a naturally attenuated field strain of myxoma virus (MV). The recombinant viruses expressed the RHDV major capsid protein (VP60) including a linear epitope tag from the transmissible gastroenteritis virus (TGEV) nucleoprotein. Following inoculation, the recombinant viruses induced specific antibody responses against MV, RHDV, and the TGEV tag. Immunization of wild rabbits by the subcutaneous and oral routes conferred protection against virulent RHDV and MV challenges. The recombinant viruses showed a limited horizontal transmission capacity, either by direct contact or in a flea-mediated process, promoting immunization of contact uninoculated animals.     

Temperature-dependent protection against Ichthyophthirius multifiliis following immunisation of rainbow trout using live theronts

Rainbow trout Oncorhynchus mykiss Walbaum, 1792 fingerlings were vaccinated by intraperitoneal (i.p.) injection using live theronts of the skin parasitic ciliate Ichthyophthirius multifiliis Fouquet, 1876 at 2 temperatures (12 and 20 degrees C), and protection against challenge infections was subsequently evaluated by bath exposure to live theronts. Vaccination conferred a relative protection (evaluated as the decrease in the number of established theronts) at 12 degrees C and almost complete immunity at 20 degrees C. Significantly increased immobilisation titers (using plasma immobilisation of live theronts) were found in immunised fish at Week 2 and 4 post-vaccination. Lysozyme activity of plasma from vaccinated fish increased from Week 1 to 4. Both immobilisation titers and lysozyme activity were significantly higher at 20 degrees C. This study demonstrated that live theronts are good candidates for an antigen source for development of effective vaccines against white spot disease in this fish host, and further indicated that the protection of rainbow trout against I. multifiliis infection is highly temperature dependent and may be associated with both adaptive and innate response mechanisms.     

Personal protection against biting insects and ticks

Recent events with the first cases of local transmission of chikungunya and dengue fever virus in southern France by Aedes albopictus, adding to the nuisance and potential vectors that can be encountered when traveling in tropical or sub-tropical countries, has shown the value of a reflection on the Personal protection against vectors (PPAV). It is seen during an outbreak of vector-borne disease, or simply because of nuisance arthropods, that our fellow citizens try to protect themselves individually by using an arsenal of resources available on the market. Yet most of these means have been neither checked for effectiveness or safety tests, however, essential. Travellers, staff on mission or assignment, are looking for specific information on how to protect themselves or their families. Health workers had at their disposal so far indications that vary widely from one source to another. Therefore it seemed important to the Society of Travel Medicine (SMV) and the French Society of Parasitology (SFP) to initiate a reflection on this theme. This reflection took the form of recommendations for good practice, following the outline established by the French High Health Authority (HAS). The aim was to gather all relevant information, verified and validated and the format to be used not only by health personnel (doctors, pharmacists, nurses), but also by travel agents and individuals. This document highlights the need to take into account the risk of vector-borne diseases, some deadly, and the benefit of various methods of personal protection. The choice of methods is clearly oriented towards those whose effectiveness has been proven and potential risks assessed. The paper finally proposes two decision trees based on the transmission type (day or night) and kind of stay (short or roaming, long and steady). It concerns travellers, but also expatriates, residents and nomads.     

More robust detection of motifs in coexpressed genes by using phylogenetic information

Background  

Several motif detection algorithms have been developed to discover overrepresented motifs in sets of coexpressed genes. However, in a noisy gene list, the number of genes containing the motif versus the number lacking the motif might not be sufficiently high to allow detection by classical motif detection tools. To still recover motifs which are not significantly enriched but still present, we developed a procedure in which we use phylogenetic footprinting to first delineate all potential motifs in each gene. Then we mutually compare all detected motifs and identify the ones that are shared by at least a few genes in the data set as potential candidates.