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

Mechanism of the hydrodenitrogenation of neopentylamine and adamantylamine on sulfided NiMo/Al2O3

Neopentanethiol, 1-adamantanethiol, and 2-adamantanethiol were primary products and neopentane and adamantane were secondary products in the hydrodenitrogenation of neopentylamine, 1-adamantylamine, and 2-adamantylamine, respectively, over sulfided NiMo/Al2O3. Dialkylamines and dialkylimines were formed as primary products in the reactions of 2-adamantylamine and neopentylamine as well. None of the three amines can react by ammonia elimination and a classic SN2 substitution of the NH2 group by H2S is not possible for the adamantylamines either. The formation of di(2-adamantyl)imine and di(neopentyl)imine indicates that dehydrogenation and hydrogenation reactions occur and that imine or iminium-cation intermediates play an important role. NH2-SH substitution takes place by dehydrogenation of the amine to an imine or iminium cation, which adds H2S and eliminates NH3. The secondary character of adamantane and neopentane demonstrates that hydrogenolysis of the aliphatic C-N bond does not take place over sulfided NiMo/Al2O3 below 340°C. Even though 1-adamantylamine can neither react by classic SN2, E1, and E2 reactions, nor via an imine or iminium cation, it formed 1-adamanethiol at 300°C. This reaction might take place by an SN1 reaction or by adsorption of the amine at a surface vacancy, followed by a shift of the adamantyl group to a neighboring sulfur ato

Synthesis and structure characterization of two cadmium coordination polymers based on μ2-bridging bidentate hydrazine ligand

Synthesis, single crystal structures, spectral and thermal characteristics of two cadmium coordination polymers, viz., [Cd(NO3)2(N2H4)2] (1) [Cd(C3H2O4)(N2H4)] (where C3H2O4 is malonate) (2) are reported. The μ2-bridging bidentate binding mode of the crystallographically unique hydrazine ligands in (1) leads to a one-dimensional polymeric structure extending along c axis. The central Cd(II) in (2) exhibits hepta-coordination and is bonded to a unique malonate anion which exhibits a μ3-bridging pentadentate coordination, extending the structure along the a axis. The bridging bidentate binding of the crystallographically independent hydrazine ligand extends along b axis resulting in a 2-D structure

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

Children pillion rider safety awareness among motorcycle users in Malaysia

Motorcycle is one of the more popular modes of transport for Malaysian people due to its low price and easy usability. This paper reviews the current safety initiatives undertaken to address the need to enhance children safety whilst riding as pillion on motorcycles and suggest possible remedial action to counter the possible lack of awareness for child pillion riders. A search was undertaken of all the major database of articles. Articles related to children’s safety systems, children related injuries, children related accident data, available laws and legislation were reviewed. There is a greater need for the stricter enforcement of safety laws in Malaysia due to the fact that the accident statistics show a large percentage of motorcycle accidents involve pillion riding children. However, enforcement of laws in developing countries is not easy and one has to start at the root of the problem, i.e. the parents and adults who ride these children as pillion on motorcycles. This paper highlights the need for new safety initiatives and programmes to be undertaken by the government, law agencies and non-governmental organisations for parents and adults to understand the importance of their children safety while riding on motorcycles. Engineering countermeasures and intervention are needed to protect these vulnerable users. Besides the helmet, a device capable of providing some sort of protection to the child whilst riding pillion should be designed and developed

Cross-Sample Validation Provides Enhanced Proteome Coverage in Rat Vocal Fold Mucosa

The vocal fold mucosa is a biomechanically unique tissue comprised of a densely cellular epithelium, superficial to an extracellular matrix (ECM)-rich lamina propria. Such ECM-rich tissues are challenging to analyze using proteomic assays, primarily due to extensive crosslinking and glycosylation of the majority of high Mr ECM proteins. In this study, we implemented an LC-MS/MS-based strategy to characterize the rat vocal fold mucosa proteome. Our sample preparation protocol successfully solubilized both proteins and certain high Mr glycoconjugates and resulted in the identification of hundreds of mucosal proteins. A straightforward approach to the treatment of protein identifications attributed to single peptide hits allowed the retention of potentially important low abundance identifications (validated by a cross-sample match and de novo interpretation of relevant spectra) while still eliminating potentially spurious identifications (global single peptide hits with no cross-sample match). The resulting vocal fold mucosa proteome was characterized by a wide range of cellular and extracellular proteins spanning 12 functional categories

A potential new, stable state of the E-cadherin strand-swapped dimer in solution

E-cadherin is a transmembrane glycoprotein that facilitates inter-cellular adhesion in the epithelium. The ectodomain of the native structure is comprised of five repeated immunoglobulin-like domains. All E-cadherin crystal structures show the protein in one of three alternative conformations: a monomer, a strand-swapped trans homodimer and the so-called X-dimer, which is proposed to be a kinetic intermediate to forming the strand-swapped trans homodimer. However, previous studies have indicated that even once the trans strand-swapped dimer is formed, the complex is highly dynamic and the E-cadherin monomers may reorient relative to each other. Here, molecular dynamics simulations have been used to investigate the stability and conformational flexibility of the human E-cadherin trans strand-swapped dimer. In four independent, 100 ns simulations, the dimer moved away from the starting structure and converged to a previously unreported structure, which we call the Y-dimer. The Y-dimer was present for over 90% of the combined simulation time, suggesting that it represents a stable conformation of the E-cadherin dimer in solution. The Y-dimer conformation is stabilised by interactions present in both the trans strand-swapped dimer and X-dimer crystal structures, as well as additional interactions not found in any E-cadherin dimer crystal structures. The Y-dimer represents a previously unreported, stable conformation of the human E-cadherin trans strand-swapped dimer and suggests that the available crystal structures do not fully capture the conformations that the human E-cadherin trans homodimer adopts in solution

Prediction of risk and incidence of dry eye in critical patients

Objectives: to estimate the incidence of dry eye, to identify risk factors and to establish a risk prediction model for its development in adult patients admitted to the intensive care unit of a public hospital. Method: concurrent cohort, conducted between March and June, 2014, with 230 patients admitted to an intensive care unit. Data were analyzed by bivariate descriptive statistics, with multivariate survival analysis and Cox regression. Results: 53% out of 230 patients have developed dry eye, with onset mean time of 3.5 days. Independent variables that significantly and concurrently impacted the time for dry eye to occur were: O2 in room air, blinking more than five times per minute (lower risk factors) and presence of vascular disease (higher risk factor). Conclusion: dry eye is a common finding in patients admitted to adults intensive care units, and care for its prevention should be established

Internet of Things in Sustainable Energy Systems

Our planet has abundant renewable and conventional energy resources but technological capability and capacity gaps coupled with water-energy needs limit the benefits of these resources to citizens. Through IoT technology solutions and state-of-the-art IoT sensing and communications approaches, the sustainable energy-related research and innovation can bring a revolution in this area. Moreover, by the leveraging current infrastructure, including renewable energy technologies, microgrids, and power-to-gas (P2G) hydrogen systems, the Internet of Things in sustainable energy systems can address challenges in energy security to the community, with a minimal trade-off to environment and culture. In this chapter, the IoT in sustainable energy systems approaches, methodologies, scenarios, and tools is presented with a detailed discussion of different sensing and communications techniques. This IoT approach in energy systems is envisioned to enhance the bidirectional interchange of network services in grid by using Internet of Things in grid that will result in enhanced system resilience, reliable data flow, and connectivity optimization. Moreover, the sustainable energy IoT research challenges and innovation opportunities are also discussed to address the complex energy needs of our community and promote a strong energy sector economy