Bacteria classification using Cyranose 320 electronic nose

Background An electronic nose (e-nose), the Cyrano Sciences' Cyranose 320, comprising an array of thirty-two polymer carbon black composite sensors has been used to identify six species of bacteria responsible for eye infections when present at a range of concentrations in saline solutions. Readings were taken from the headspace of the samples by manually introducing the portable e-nose system into a sterile glass containing a fixed volume of bacteria in suspension. Gathered data were a very complex mixture of different chemical compounds. Method Linear Principal Component Analysis (PCA) method was able to classify four classes of bacteria out of six classes though in reality other two classes were not better evident from PCA analysis and we got 74% classification accuracy from PCA. An innovative data clustering approach was investigated for these bacteria data by combining the 3-dimensional scatter plot, Fuzzy C Means (FCM) and Self Organizing Map (SOM) network. Using these three data clustering algorithms simultaneously better 'classification' of six eye bacteria classes were represented. Then three supervised classifiers, namely Multi Layer Perceptron (MLP), Probabilistic Neural network (PNN) and Radial basis function network (RBF), were used to classify the six bacteria classes. Results A [6 × 1] SOM network gave 96% accuracy for bacteria classification which was best accuracy. A comparative evaluation of the classifiers was conducted for this application. The best results suggest that we are able to predict six classes of bacteria with up to 98% accuracy with the application of the RBF network. Conclusion This type of bacteria data analysis and feature extraction is very difficult. But we can conclude that this combined use of three nonlinear methods can solve the feature extraction problem with very complex data and enhance the performance of Cyranose 320

Intelligent Bayes Classifier (IBC) for ENT infection classification in hospital environment

Electronic Nose based ENT bacteria identification in hospital environment is a classical and challenging problem of classification. In this paper an electronic nose (e-nose), comprising a hybrid array of 12 tin oxide sensors (SnO(2)) and 6 conducting polymer sensors has been used to identify three species of bacteria, Escherichia coli (E. coli), Staphylococcus aureus (S. aureus), and Pseudomonas aeruginosa (P. aeruginosa) responsible for ear nose and throat (ENT) infections when collected as swab sample from infected patients and kept in ISO agar solution in the hospital environment. In the next stage a sub-classification technique has been developed for the classification of two different species of S. aureus, namely Methicillin-Resistant S. aureus (MRSA) and Methicillin Susceptible S. aureus (MSSA). An innovative Intelligent Bayes Classifier (IBC) based on "Baye's theorem" and "maximum probability rule" was developed and investigated for these three main groups of ENT bacteria. Along with the IBC three other supervised classifiers (namely, Multilayer Perceptron (MLP), Probabilistic neural network (PNN), and Radial Basis Function Network (RBFN)) were used to classify the three main bacteria classes. A comparative evaluation of the classifiers was conducted for this application. IBC outperformed MLP, PNN and RBFN. The best results suggest that we are able to identify and classify three bacteria main classes with up to 100% accuracy rate using IBC. We have also achieved 100% classification accuracy for the classification of MRSA and MSSA samples with IBC. We can conclude that this study proves that IBC based e-nose can provide very strong and rapid solution for the identification of ENT infections in hospital environment

Inverse bifurcation analysis: application to simple gene systems

BACKGROUND: Bifurcation analysis has proven to be a powerful method for understanding the qualitative behavior of gene regulatory networks. In addition to the more traditional forward problem of determining the mapping from parameter space to the space of model behavior, the inverse problem of determining model parameters to result in certain desired properties of the bifurcation diagram provides an attractive methodology for addressing important biological problems. These include understanding how the robustness of qualitative behavior arises from system design as well as providing a way to engineer biological networks with qualitative properties. RESULTS: We demonstrate that certain inverse bifurcation problems of biological interest may be cast as optimization problems involving minimal distances of reference parameter sets to bifurcation manifolds. This formulation allows for an iterative solution procedure based on performing a sequence of eigen-system computations and one-parameter continuations of solutions, the latter being a standard capability in existing numerical bifurcation software. As applications of the proposed method, we show that the problem of maximizing regions of a given qualitative behavior as well as the reverse engineering of bistable gene switches can be modelled and efficiently solved

Robust Detection of Hierarchical Communities from Escherichia coli Gene Expression Data

Determining the functional structure of biological networks is a central goal of systems biology. One approach is to analyze gene expression data to infer a network of gene interactions on the basis of their correlated responses to environmental and genetic perturbations. The inferred network can then be analyzed to identify functional communities. However, commonly used algorithms can yield unreliable results due to experimental noise, algorithmic stochasticity, and the influence of arbitrarily chosen parameter values. Furthermore, the results obtained typically provide only a simplistic view of the network partitioned into disjoint communities and provide no information of the relationship between communities. Here, we present methods to robustly detect coregulated and functionally enriched gene communities and demonstrate their application and validity for Escherichia coli gene expression data. Applying a recently developed community detection algorithm to the network of interactions identified with the context likelihood of relatedness (CLR) method, we show that a hierarchy of network communities can be identified. These communities significantly enrich for gene ontology (GO) terms, consistent with them representing biologically meaningful groups. Further, analysis of the most significantly enriched communities identified several candidate new regulatory interactions. The robustness of our methods is demonstrated by showing that a core set of functional communities is reliably found when artificial noise, modeling experimental noise, is added to the data. We find that noise mainly acts conservatively, increasing the relatedness required for a network link to be reliably assigned and decreasing the size of the core communities, rather than causing association of genes into new communities.Comment: Due to appear in PLoS Computational Biology. Supplementary Figure S1 was not uploaded but is available by contacting the author. 27 pages, 5 figures, 15 supplementary file

Mohs math – where the error hides

BACKGROUND: Mohs surgical technique allows a full view of surgical margins and has a reported cure rate approaching 100%. METHOD: A survey amongst Mohs surgeons was performed to assess operator technique. In addition, an animated clay model was constructed to identify and quantify tissue movement seen during the processing of Mohs surgical specimens. RESULTS: There is variability in technique used in Mohs surgery in regards to the thickness of layers, and the number of blocks layers are cut into. A mathematical model is described which assesses the clinical impact of this variability. CONCLUSION: Our mathematical model identifies key aspects of technique that may contribute to error. To keep the inherent error rate at a minimum, we advocate minimal division and minimal physical thickness of Mohs specimens

Mechanisms of CFTR Functional Variants That Impair Regulated Bicarbonate Permeation and Increase Risk for Pancreatitis but Not for Cystic Fibrosis

CFTR is a dynamically regulated anion channel. Intracellular WNK1-SPAK activation causes CFTR to change permeability and conductance characteristics from a chloride-preferring to bicarbonate-preferring channel through unknown mechanisms. Two severe CFTR mutations (CFTRsev) cause complete loss of CFTR function and result in cystic fibrosis (CF), a severe genetic disorder affecting sweat glands, nasal sinuses, lungs, pancreas, liver, intestines, and male reproductive system. We hypothesize that those CFTR mutations that disrupt the WNK1-SPAK activation mechanisms cause a selective, bicarbonate defect in channel function (CFTRBD) affecting organs that utilize CFTR for bicarbonate secretion (e.g. the pancreas, nasal sinus, vas deferens) but do not cause typical CF. To understand the structural and functional requirements of the CFTR bicarbonate-preferring channel, we (a) screened 984 well-phenotyped pancreatitis cases for candidate CFTRBD mutations from among 81 previously described CFTR variants; (b) conducted electrophysiology studies on clones of variants found in pancreatitis but not CF; (c) computationally constructed a new, complete structural model of CFTR for molecular dynamics simulation of wild-type and mutant variants; and (d) tested the newly defined CFTRBD variants for disease in non-pancreas organs utilizing CFTR for bicarbonate secretion. Nine variants (CFTR R74Q, R75Q, R117H, R170H, L967S, L997F, D1152H, S1235R, and D1270N) not associated with typical CF were associated with pancreatitis (OR 1.5, p = 0.002). Clones expressed in HEK 293T cells had normal chloride but not bicarbonate permeability and conductance with WNK1-SPAK activation. Molecular dynamics simulations suggest physical restriction of the CFTR channel and altered dynamic channel regulation. Comparing pancreatitis patients and controls, CFTRBD increased risk for rhinosinusitis (OR 2.3, p<0.005) and male infertility (OR 395, p≪0.0001). WNK1-SPAK pathway-activated increases in CFTR bicarbonate permeability are altered by CFTRBD variants through multiple mechanisms. CFTRBD variants are associated with clinically significant disorders of the pancreas, sinuses, and male reproductive system. © 2014 Whitcomb et al

The evolution of the urinary bladder as a storage organ: scent trails and selective pressure of the first land animals in a computational simulation

The function of waste control in all living organisms is one of the vital importance. Almost universally, terrestrial tetrapods have a urinary bladder with a storage function. It is well documented that many marine and aerial species do not have an organ of such a function, or have one with very depressed storage functionality. Bladder morphology indicates it has evolved from a thin-walled structure used for osmoregulatory purposes, as it is currently used in many marine animals. It is hypothesised that the storage function of the urinary bladder allows for an evolutionary selective advantage in reducing the likelihood of successful predation. Random walks simulating predator and prey movements with simplified scent trails were utilised to represent various stages of the hunt: Detection and pursuit. A final evolutionary model is proposed in order to display the advantages over inter-generational time scales and illustrates how a bladder may evolve from an osmoregulatory organ to one of the storage. Data sets were generated for each case and analysed indicating the viability of such advantages. From the highly consistent results, three distinct characteristics of having a storage function in the urinary bladder are suggested: reduced scent trail detection rate; increased prey–predator separation (upon scent trail detection); and a reduced probability of successful capture upon scent detection by the predator. Furthered by the evolutionary model indicating such characteristics are conserved and augmented over many generations, it is concluded that prey–predator interactions provide a large selective pressure in the evolution of the urinary bladder and its storage function

The malaria candidate vaccine liver stage antigen-3 is highly conserved in Plasmodium falciparum isolates from diverse geographical areas

<p>Abstract</p> <p>Background</p> <p>A high level of genetic stability has been formerly identified in segments of the gene coding for the liver stage antigen-3 (LSA-3), a subunit vaccine candidate against <it>Plasmodium falciparum</it>. The exploration of <it>lsa-3 </it>polymorphisms was extended to the whole sequence of this large antigen in 20 clinical isolates from four geographical areas; Senegal, Comoro islands, Brazil and Thailand.</p> <p>Methods</p> <p>The whole 4680 bp genomic sequence of <it>lsa-3 </it>was amplified by polymerase chain reaction and sequenced. The clinical isolate sequences were aligned on the sequence of the laboratory reference <it>P. falciparum </it>strain 3D7.</p> <p>Results</p> <p>The non-repeated sequence of <it>lsa-3 </it>was very well conserved with only a few allelic variations scattered along the sequence. Interestingly, a formerly identified immunodominant region, employed for the majority of pre-clinical vaccine development, was totally conserved at the genetic level. The most significant variations observed were in the number and organization of tetrapeptide repeated units, but not in their composition, resulting in different lengths of these repeated regions. The shorter repeated regions were from Brazilian origin. A correlation between the geographical distribution of the parasites with single nucleotide polymorphisms was not detected.</p> <p>Conclusion</p> <p>The lack of correlation between allelic polymorphisms with a specific transmission pressure suggests that LSA-3 is a structurally constrained molecule. The unusual characteristics of the <it>lsa-3 </it>gene make the molecule an interesting candidate for a subunit vaccine against malaria.</p

Circumstellar disks and planets. Science cases for next-generation optical/infrared long-baseline interferometers

We present a review of the interplay between the evolution of circumstellar disks and the formation of planets, both from the perspective of theoretical models and dedicated observations. Based on this, we identify and discuss fundamental questions concerning the formation and evolution of circumstellar disks and planets which can be addressed in the near future with optical and infrared long-baseline interferometers. Furthermore, the importance of complementary observations with long-baseline (sub)millimeter interferometers and high-sensitivity infrared observatories is outlined.Comment: 83 pages; Accepted for publication in "Astronomy and Astrophysics Review"; The final publication is available at http://www.springerlink.co