Predicting MoRFs in protein sequences using HMM profiles

Background: Intrinsically Disordered Proteins (IDPs) lack an ordered three-dimensional structure and are enriched in various biological processes. The Molecular Recognition Features (MoRFs) are functional regions within IDPs that undergo a disorder-to-order transition on binding to a partner protein. Identifying MoRFs in IDPs using computational methods is a challenging task. Methods: In this study, we introduce hidden Markov model (HMM) profiles to accurately identify the location of MoRFs in disordered protein sequences. Using windowing technique, HMM profiles are utilised to extract features from protein sequences and support vector machines (SVM) are used to calculate a propensity score for each residue. Two different SVM kernels with high noise tolerance are evaluated with a varying window size and the scores of the SVM models are combined to generate the final propensity score to predict MoRF residues. The SVM models are designed to extract maximal information between MoRF residues, its neighboring regions (Flanks) and the remainder of the sequence (Others). Results: To evaluate the proposed method, its performance was compared to that of other MoRF predictors; MoRFpred and ANCHOR. The results show that the proposed method outperforms these two predictors. Conclusions: Using HMM profile as a source of feature extraction, the proposed method indicates improvement in predicting MoRFs in disordered protein sequence

Interface induced perpendicular magnetic anisotropy in Co/CoO/Co thin film structure: An in-situ MOKE investigation

Co /CoO/Co polycrystalline film was grown on Si (001) substrate and magnetic properties have been investigated using in-situ magneto-optic Kerr effect during growth of the sample. Magnetic anisotropy with easy axis perpendicular to the film surface has been observed in top Co layer, whereas bottom layer was found to be soft with in-plane magnetization without any influence of top layer. Ex-situ in-plane and out-of-plane diffraction measurements revealed that the growth of Co on oxidized interface takes place with preferential orientation of c-axis perpendicular to the film plane, which results in the observed perpendicular magnetic anisotropy. Texturing of the c-axis is expected to be a result of minimization of the interface energy due to hybridization between Co and oxygen at the interface.Comment: 9 pages, 3 figures, under review in IOP journa

Application of cepstrum analysis and linear predictive coding for motor imaginary task classification

In this paper, classification of electroencephalography (EEG) signals of motor imaginary tasks is studied using cepstrum analysis and linear predictive coding (LPC). The Brain-Computer Interface (BCI) competition III dataset IVa containing motor imaginary tasks for right hand and foot of five subjects are used. The data was preprocessed by applying whitening and then filtering the signal followed by feature extraction. A random forest classifier is then trained using the cepstrum and LPC features to classify the motor imaginary tasks. The resulting classification accuracy is found to be over 90%. This research shows that concatenating appropriate different types of features such as cepstrum and LPC features hold some promise for the classification of motor imaginary tasks, which can be helpful in the BCI context

Ectoparasite of Rodents Collected from International Seaport, Gujarat (India) with Special Reference to Plague & Scrub Typhus

Background: Rodents are well established at port areas and their arthropod ectoparasite can be vectors of many diseases. Ships play an important role in spreading disease by transporting infected vectors.Objective: In view of the seriousness of the problem the present study was undertaken to assess the prevalence of rodent–ectoparasite association at KPT, Kandla (India).Results: Four species of rodents: Tatera indica (Hardwicke), Bandicota indica (Bechstein), Rattus norvegicus (Berkenhout), Rattus rattus (Linnaeus) were trapped from the port area. Rodent Infestation rate was 84.9 per cent. Lice (46.5%) were the predominant ectoparasites retrieved from the rodents followed by mites and fleas. The rodent ectoparasite index was 13.6 per rat. A total of 32 vector larval trombiculid chigger mite (Leptotrombidium deliense, Walch) were collected from various species of rats. Chigger infestation rate was found to be 8.0 per rat. A total of 96% chigger mites were retrieved from R. norvagicus trapped from canteen area. A total 234 fleas were retrieved giving an overall flea index of 2.5 per rat. The flea species collected from rodents were Xenopsylla cheopis (Rothschild) and X. astia (Rothschild). Serological & bacteriological examination of rodent samples showed no Orentia and plague bacilli activity.Conclusion: Result of the study suggests routine surveillance for rodent and their arthropods ectoparasite to apply appropriate control measure to prevent the spreading of rodent borne diseases

Egg-laying rhythm in Drosophila melanogaster

Extensive research has been carried out to understand how circadian clocks regulate various physiological processes in organisms. The discovery of clock genes and the molecular clockwork has helped researchers to understand the possible role of these genes in regulating various metabolic processes. In Drosophila melanogaster, many studies have shown that the basic architecture of circadian clocks is multi-oscillatory. In nature, different neuronal subgroups in the brain of D. melanogaster have been demonstrated to control different circadian behavioural rhythms or different aspects of the same circadian rhythm. Among the circadian phenomena that have been studied so far in Drosophila, the egg-laying rhythm is unique, and relatively less explored. Unlike most other circadian rhythms, the egg-laying rhythm is rhythmic under constant light conditions, and the endogenous or free-running period of the rhythm is greater than those of most other rhythms. Although the clock genes and neurons required for the persistence of adult emergence and activity/rest rhythms have been studied extensively, those underlying the circadian egg-laying rhythm still remain largely unknown. In this review, we discuss our current understanding of the circadian egg-laying rhythm in D. melanogaster, and the possible molecular and physiological mechanisms that control the rhythmic output of the egg-laying process

A simulation study of pearlite-to-austenite transformation kinetics in rapidly heated hot-rolled low carbon steel

The main aim of the present research was to obtain an optimized microstructure with adequate mechanical properties in a low carbon steel. The effect of microstructure on kinetics of austenite transformation was simulated. A 3.2 mm hot rolled steel was subjected to continuous annealing to obtain properties of Dual Phase 590 grade. Kinetics of austenite transformation was studied with respect to the condition of just pearlite dissolution to form austenite under rapid heating. Annealing parameters were based on process conditions of dual phase steel production in a continuous annealing line. DICTRA was used to simulate heating rates of the order 10–500 °C/s with peak temperatures in the range 750–850 °C to predict isothermal annealing time required for complete dissolution of pearlite into austenite under different temperature-heating rate conditions. Simulation results showed dependency of temperature and heating rate on austenite transformation time. Interestingly, no significant effect of heating rate on complete pearlite dissolution into austenite was evident. Results were validated with limited experimentation on Gleeble. Microstructure analysis validated the simulation results to be accurate. The observations have pertinent inputs while designing industrial continuous annealing line parameters where rapid heating rates are generally encountered (10–20 °C/s).A simulation study of pearlite-to-austenite transformation kinetics in rapidly heated hot-rolled low carbon steel (PDF Download Available). Availablefrom:https://www.researchgate.net/publication/303915593_A_simulation_study_of_pearlite-to austenite_transformation_kinetics_in_rapidly_heated_hot-rolled_low_carbon_steel [accessed Aug 14, 2017]

Combining ability and heterosis analysis for fibre yield and quality parameters in roselle (Hibiscus sabdariffa L.)

Roselle (Hibiscus sabdariffa L.) is second important bast fibre crop after jute in India. With an aim to ex-ploit non-additive genetic variance present experiment was designed to identify good general combining parents and specific cross combination for fibre yield and fibre quality parameters (fibre fineness, fibre tenacity) in roselle. A total of 11 parents were crossed in complete diallel fashion which resulted 55 F1, 55 RF1 (reciprocal F1). Parents, F1s and RF1s were grown in randomized block design. Analysis of variance revealed significant differences (P< 0.01, P<0.05) among the parents and their hybrids. The parents AMV 1, AMV 5, GR 27 and AHS 160 were identified as good combiners since they recorded significant general combining ability (GCA) effects for fibre yield and quality parameters. Further, For fibre yield only three crosses (AMV 1 × AMV 4, AMV 1 × GR 27, HS 4288 × JRR 07) showed significant specific combining ability (SCA) effects from them hybrid AMV 1 × GR 27 (fibre yield=27.37g/ plant) exhibited positively significant best parent (Non bris 4, Mean fibre yield=21.16g/plant) heterosis (29.35%). Similarly, for fibre tenacity, hybrid GR 27 × JRR 07 (fibre tenacity=23.47g/tex) exhibited positively significant best parent (HS 4288; fibre tenacity=20.35g/tex) heterosis (15.30%)