Models and Estimation for Phylogenetic Trees

In this thesis, we consider Markov models for matched sequences. De¯ne fij(t) = P(X(t) = i; Y (t) = jjX(0) = Y (0)); where fij is the joint probability that, for a given site, the ¯rst and second sequences have the values i and j at a given site, given that they were the same at time 0. This can generalized to several sequences. The sequences (taxa) are then arranged in an evolutionary tree (phylogenetic tree) depicting how taxa diverge from their common ancestors. We develop tests and estimation methods for the parameters of di®erent models. Standard phylogenetic methods assume stationarity, homogeneity and reversibility for the Markov processes, and often impose further restrictions on the parameters. The parameters in these cases are estimated using many popular packages, including PHYLIP and PAUP*. We describe a new and more general method for calculating the joint probability distribution under stationary and homogeneous models for the more general models with some weakening of the stationarity and homogeneity assumptions. We describe the method for a two edged tree and then extend it to the case for a K tipped tree. We discuss the case of a ¯ve edged tree for a set of bacterial sequences for which stationarity and homogeneity are not present. This data set is very similar to that of Galtier and Gouy (1995), and the search for methods appropriate for its analysis has provided the raison d'etre for this work. The extension we propose is to allow non-stationarity, so that from the root of the tree we permit di®erent Markov processes to operate along different descendant lineages; furthermore, we permit non-homogeneous Markov processes to operate across the tree. We obtain methods tha

Quantification of benzene in groundwater sources and risk analysis in a popular South Indian Pilgrimage City – A GIS based approach

AbstractThe present research work quantified the concentration of benzene in a total of hundred groundwater samples at the proximity of petrol bunks and residential places in Madurai District. The average values recorded in Jan 2011, Feb 2011 and Mar 2011 were 0.100mgL−1 (10 times of PL), 0.138mgL−1 (14 times of PL) and 0.060mgL−1 (6 times of PL) respectively. A significant variation in the benzene level during February–March 2011 was validated through Student’s t-test analysis. Hierarchical cluster analysis using dendograms revealed the un-symmetric distribution of benzene during the study period. The cancer risk analysis at corporate locations among children was seven folds higher as compared to the risk of adults. The benzene concentration levels are interpreted using Arc Geographical Information System (Arc GIS) through thematic maps

A HIGH EFFICIENCY DC/DC CONVERTER WITH HYBRID-TYPE FULL-BRIDGE

This paper presents a hybrid-type full-bridge dc/dc converter with high efficiency. Using a hybrid control scheme with a simple circuit structure, the proposed dc/dc converter has a hybrid operation mode. Under a normal input range, the proposed converter operates as a phase-shift full-bridge series resonant converter that provides high efficiency by applying soft switching on all switches and rectifier diodes and reducing conduction losses. When the input is lower than the normal input range, the converter operates as an active-clamp step-up converter that enhances an operation range. Due to the hybrid operation, the proposed converter operates with larger phase shift value than the conventional converters under the normal input range. Thus, the proposed converter is capable of being designed to give high power conversion efficiency and its operation range is extended. A 1kW prototype is implemented to confirm the theoretical analysis and validity of the proposed converter

Electro-coagulation coupled Electro-floatation process: Feasible choice in Doxycycline removal from Pharmaceutical effluents

Article CC-BYInternational audienceElectrochemical treatment involving a coupled coagulation and floatation was performed in the removal of Doxycycline Hyclate (DCH) from aqueous solutions. All the experiments were carried out in an electrochemical reactor of 1.5 L which contained aluminium electrodes as cathode and anode. The removal of doxycycline hyclate (DCH) species by EC/EF was determined as a function of electrolysis time, pH, current intensity, flow rate and DCH concentration. From the observed results, it was corroborated that the DCH removal through the EC/EF process was excellent. The effective contribution from initial pH (7.03) and current intensity (5.39 mA cm-2) was very much remarkable and well apparent from flocs of good buoyancy. The removal of DCH was inversely proportional to spacing between electrodes (SBE) and circulating flow rate in the presence of the supporting NaCl electrolyte of 1 g L-1. It was also highly promoted by the addition of NaCl in comparison to NaNO3 and KCl to the electrolytic system. The compliance of four kinetic models was verified with DCH removal system. The free energy values from DKR model suggested the nature of bonding by chemical forces. Characterization by FTIR, SEM and XRD interpreted the assignments of various functional groups, surface morphology and crystalline incorporated amorphous nature, respectively of electro – generated flocs. The current efficiency and specific electrical energy consumption at optimized conditions of the EC/EF system were calculate

On the occurrence of buckler crab Cryptopodia angulata in the coastal waters of India

464-467The trend of marine non-indigenous species in India has been increasing, with more than half of the species probably being introduced by shipping. A live specimen of buckler crab Cryptopodia angulata was found along the west coast of India at 40 m depth. The recent new records at different Indian coastal locations suggest that the crab is widening its distribution. Shipping is thought to be the possible introduction vector (via ballast) for the spread of C. angulata in the coastal waters of India. Further, the favorable environmental conditions prevalent in the Indian coastal waters may facilitate the establishment and subsequent spread of C. angulata. The invasion of this buckler crab may have negative impact on the native species. Although not present in detectable numbers, C. angulata may pose a major threat to the native species, if it establishes. Information on the establishment and distribution of C. angulata from other locations along the Indian coast would be essential to comprehensively and effectively address the threat

Risk factors of musculoskeletal disorders (MSD) among palm oil mill workers

The palm oil industry is the fourth largest contributor to the Malaysian Gross National Income (GNI) but the importance of this industry to the nation’s economy does not preclude them from the risk of being affected by the occurrence of musculoskeletal disorders (MSD) among the workers in palm oil mills. Previous studies carried out have not properly explained the exact reasons for the occurrence of musculoskeletal disorders (MSD) among the palm oil mill workers. Thus, this study aim to determine the association between risk factors and MSD among palm oil mill workers. A total of 120 male workers were consecutively enrolled in this crosssectional study. Information on sociodemographic, working, lifestyle, health and injury factors were collected via questionnaire and face-to-face interviews. A high lifetime prevalence of MSD (71.7 percent) among palm oil mill workers was found. However, the one-year prevalence of MSD among the same population was only 50.8 percent. Logistic regression analysis adjusted for age, Body Mass Index (BMI) and smoking revealed that the risk factors: history of previous injury [2.35, 95 percent CI 1.12-4.93], Osteoarthritis [3.9, 95 percent CI 1.568-9.708] and perception of exertion [8.09, 95 percent CI 1.358-48.170] was found to be significantly associated with MSD symptoms reported in the past 12 months. As a conclusion, exposure to the combination of these risk factors may lead to an increased risk of developing MSD among palm oil mill workers

Tight Junction-Related Barrier Contributes to the Electrophysiological Asymmetry across Vocal Fold Epithelium

Electrophysiological homeostasis is indispensable to vocal fold hydration. We investigate tight junction (TJ)-associated components, occludin and ZO-1, and permeability with or without the challenge of a permeability-augmenting agent, histamine. Freshly excised ovine larynges are obtained from a local abattoir. TJ markers are explored via reverse transcriptase polymerase chain reaction (RT-PCR). Paracellular permeabilities are measured in an Ussing system. The gene expression of both TJ markers is detected in native ovine vocal fold epithelium. Luminal histamine treatment significantly decreases transepithelial resistance (TER) (N = 72, p<0.01) and increases penetration of protein tracer (N = 35, p<0.001), respectively, in a time-, and dose-dependent fashion. The present study demonstrates that histamine compromises TJ-related paracellular barrier across vocal fold epithelium. The detection of TJ markers indicates the existence of typical TJ components in non-keratinized, stratified vocal fold epithelium. The responsiveness of paracellular permeabilities to histamine would highlight the functional significance of this TJ-equivalent system to the electrophysiological homeostasis, which, in turn, regulates the vocal fold superficial hydration

Complex regulation by Apetala2 domain-containing transcription factors revealed through analysis of the stress-responsive TdCor410b promoter from durum wheat

Expression of the wheat dehydrin gene Cor410b is induced several fold above its non-stressed levels upon exposure to stresses such as cold, drought and wounding. Deletion analysis of the TdCor410b promoter revealed a single functional C-repeat (CRT) element. Seven transcription factors (TFs) were shown to bind to this CRT element using yeast one-hybrid screens of wheat and barley cDNA libraries, of which only one belonged to the DREB class of TFs. The remaining six encoded ethylene response factors (ERFs) belong to three separate subfamilies. Analysis of binding selectivity of these TFs indicated that all seven could bind to the CRT element (GCCGAC), and that three of the six ERFs could bind both to the CRT element and the ethylene-responsive GCC-box (GCCGCC). The TaERF4 subfamily members specifically bound the CRT element, and did not bind either the GCC-box or DRE element (ACCGAC). Molecular modeling and site-directed mutagenesis identified a single residue Pro42 in the Apetala2 (AP2) domain of TaERF4-like proteins that is conserved in monocotyledonous plants and is responsible for the recognition selectivity of this subfamily. We suggest that both DREB and ERF proteins regulate expression of the Cor410b gene through a single, critical CRT element. Members of the TaERF4 subfamily are specific, positive regulators of Cor410b gene expression.Omid Eini, Nannan Yang, Tatiana Pyvovarenko, Katherine Pillman, Natalia Bazanova, Natalia Tikhomirov, Serik Eliby, Neil Shirley, Shoba Sivasankar, Scott Tingey, Peter Langridge, Maria Hrmova, Sergiy Lopat

A Randomised Controlled Trial Comparing Ketamine versus Fentanyl for Procedural Sedation in the Emergency Department for Adults with Isolated Extremity Injury

Introduction: Alleviating pain and anxiety of patients during procedures is an essential skill for an Emergency Physician (EP). Several sedatives and dissociative agents are used for PSA (Procedural Sedation and Analgesia). In this study, we aimed to compare two drugs that is, ketamine and fentanyl for procedural sedation in adults with isolated limb injuries in the Emergency Department (ED). Materials and methods: In this prospective, randomised controlled interventional trial, patients aged between 18 to 65 years with isolated extremity injury requiring PSA in the ED were recruited. A total of 200 subjects were included in the study and randomly allocated to either the fentanyl (n=100) or the ketamine (n=100) group. Patients were blinded to the intervention and subsequently premedicated with Midazolam. Following this, they received either ketamine or fentanyl based on the group they were allocated to. Vital signs, including but not limited to the level of sedation, were measured at predetermined time intervals. A Modified Aldrete Score of >8 was used as a criterion for disposition from the ED. Data were collected in a pre-designed proforma. We aimed to compare the effectiveness as well as ascertain the safety profile of the two drugs for PSA in the ED. Results: There was no significant difference between the two groups when age, gender, mechanism of injury and comorbidities were compared. We found that there was no statistically significant difference between the two groups when blood pressure, respiratory rate and depth of sedation were compared. In both groups, there was a significant decrease in pain on the Numerical Rating Scale (NRS) following drug administration from 8 to 3 (p<0.001). Patients in the fentanyl group had an increased incidence of transient oxygen desaturation (p<0.001). Vomiting was more common in the ketamine group (p<0.001). Conclusion: PSA is a safe and efficacious procedure for patients undergoing painful procedures in ED. Patients in both the groups maintained hemodynamic stability throughout the procedure. From our study, we were able to conclude that both ketamine and fentanyl are similar in efficacy for PSA in the ED for adults with isolated limb injuries. In addition, no significant cardiovascular adverse events were noted in either group in our study

Reap the crop wild relatives for breeding future crops

Crop wild relatives (CWRs) have provided breeders with several 'game-changing' traits or genes that have boosted crop resilience and global agricultural production. Advances in breeding and genomics have accelerated the identification of valuable CWRs for use in crop improvement. The enhanced genetic diversity of breeding pools carrying optimum combinations of favorable alleles for targeted crop-growing regions is crucial to sustain genetic gain. In parallel, growing sequence information on wild genomes in combination with precise gene-editing tools provide a fast-track route to transform CWRs into ideal future crops. Data-informed germplasm collection and management strategies together with adequate policy support will be equally important to improve access to CWRs and their sustainable use to meet food and nutrition security targets