A Phylogenetic Mixture Model for Detecting Pattern-Heterogeneity in Gene Sequence or Character-State Data

Mark Pagel, Andrew Meade (2004). A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data. Systematic Biology, 53(4), 571-581. RAE2008

Modeling the evolution of regulatory elements by simultaneous detection and alignment with phylogenetic pair HMMs.

The computational detection of regulatory elements in DNA is a difficult but important problem impacting our progress in understanding the complex nature of eukaryotic gene regulation. Attempts to utilize cross-species conservation for this task have been hampered both by evolutionary changes of functional sites and poor performance of general-purpose alignment programs when applied to non-coding sequence. We describe a new and flexible framework for modeling binding site evolution in multiple related genomes, based on phylogenetic pair hidden Markov models which explicitly model the gain and loss of binding sites along a phylogeny. We demonstrate the value of this framework for both the alignment of regulatory regions and the inference of precise binding-site locations within those regions. As the underlying formalism is a stochastic, generative model, it can also be used to simulate the evolution of regulatory elements. Our implementation is scalable in terms of numbers of species and sequence lengths and can produce alignments and binding-site predictions with accuracy rivaling or exceeding current systems that specialize in only alignment or only binding-site prediction. We demonstrate the validity and power of various model components on extensive simulations of realistic sequence data and apply a specific model to study Drosophila enhancers in as many as ten related genomes and in the presence of gain and loss of binding sites. Different models and modeling assumptions can be easily specified, thus providing an invaluable tool for the exploration of biological hypotheses that can drive improvements in our understanding of the mechanisms and evolution of gene regulation.

Performance and wear of coated carbide drill in machining of carbon fibre reinforced composite/titanium stack

In this research we investigate the performance of drilling process in carbon fibre reinforced composite (CFC) material, titanium alloy and the hybrid stack of these two materials, using coated carbide drill bit. We study the effect of the process parameters such as the feed rate and speed on the induced forces and torques, also on the wear of drill and surface roughness of the holes. In the composite material the percentage of surface damage in both drilling CFC on its own and drilling in stack form is estimated. Also, the effect of worn drill on the surface damage is identified. In the titanium, the burr formation in stack and non-stack form is investigated. The wear of the drill results in increased forces and torques required for drilling. This increases the surface delaminations substantially at the entrance in drilling of CFC. However, the surface roughness of the holes reduces with the wear of the drill in CFC drilling. Also, the surface delamination and surface roughness of the holes in the CFC whilst drilled in hybrid form reduces significantly. This is despite the increase of the forces and torques required in drilling CFC in stack form. Copyright © 2012 Inderscience Enterprises Ltd.

Role Ambiguity and Perceived Organizational Politics in Wolf Recovery: Washington State Wildlife Agency Personnel Perspectives

Thesis (Master's)--University of Washington, 2015-12

A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data

We describe a general likelihood-based 'mixture model' for inferring phylogenetic trees from gene-sequence or other character-state data. The model accommodates cases in which different sites in the alignment evolve in qualitatively distinct ways, but does not require prior knowledge of these patterns or partitioning of the data. We call this qualitative variability in the pattern of evolution across sites "pattern-heterogeneity" to distinguish it from both a homogenous process of evolution and from one characterized principally by differences in rates of evolution. We present studies to show that the model correctly retrieves the signals of pattern-heterogeneity from simulated gene-sequence data, and we apply the method to protein-coding genes and to a ribosomal 12S data set. The mixture model outperforms conventional partitioning in both these data sets. We implement the mixture model such that it can simultaneously detect rate- and pattern-heterogeneity. The model simplifies to a homogeneous model or a rate- variability model as special cases, and therefore always performs at least as well as these two approaches, and often considerably improves upon them. We make the model available within a Bayesian Markov-chain Monte Carlo framework for phylogenetic inference, as an easy-to-use computer program.

Polymorphism in [Co(SCN)(4)(ppz-H)(2)] (ppz, piperazine)

A one-pot reaction of [Co(NO3)(2)center dot 6H(2)O and piperazine] with NH4SCN/NaSCN in water-methanol (1:1) solvent leads to two polymorphs of [Co(SCN)(4)(ppz-H)(2)] (ppz, piperazine) (I and II). X-ray crystal structure reveals both have same space group but the differences in the alignment of pendant SCN- leads to two polymorphs. In I, trifurcated N-H...S hydrogen bonding plays a prominent role in crystal packing leading to S...S interactions between SCN fragments but in II, no such trifurcation arises and thereby the crystal packing occurs through hydrogen bonding interactions only leading to a distinctly different network topology. TG/DSC and FT-IR study reveal they are enantiotropically related. (c) 2007 Elsevier Ltd. All rights reserved.

Governing the working population : knowledge, self and power in workplace health programs

This paper reports a case study of a workplace health programme in an international information technology company. Discourse analysis was used to identify how specific forms of knowledge create understandings of health and influence power relations between employee and organization. These forms of knowledge are shown to make employee health both visible and invisible in particular ways. Workplace health discourse encourages the employee to take responsibility for self-assessment and behaviour adjustment to become healthier employees. This is shown to be an ethical project which results in the alignment of personal and corporate goals.

Modelling the health impact of environmentally sustainable dietary scenarios in the UK

BACKGROUND/OBJECTIVES:


Food is responsible for around one-fifth of all greenhouse gas (GHG) emissions from products consumed in the UK, the largest contributor of which is meat and dairy. The Committee on Climate Change have modelled the impact on GHG emissions of three dietary scenarios for food consumption in the UK. This paper models the impact of the three scenarios on mortality from cardiovascular disease and cancer.
SUBJECTS/METHODS:


A previously published model (DIETRON) was used. The three scenarios were parameterised by fruit and vegetables, fibre, total fat, saturated fat, monounsaturated fatty acids, polyunsaturated fatty acids, cholesterol and salt using the 2008 Family Food Survey. A Monte Carlo simulation generated 95% credible intervals.
RESULTS:


Scenario 1 (50% reduction in meat and dairy replaced by fruit, vegetables and cereals: 19% reduction in GHG emissions) resulted in 36 910 (30 192 to 43 592) deaths delayed or averted per year. Scenario 2 (75% reduction in cow and sheep meat replaced by pigs and poultry: 9% reduction in GHG emissions) resulted in 1999 (1739 to 2389) deaths delayed or averted. Scenario 3 (50% reduction in pigs and poultry replaced with fruit, vegetables and cereals: 3% reduction in GHG emissions) resulted in 9297 (7288 to 11 301) deaths delayed or averted.
CONCLUSION:


Modelled results suggest that public health and climate change dietary goals are in broad alignment with the largest results in both domains occurring when consumption of all meat and dairy products are reduced. Further work in real-life settings is needed to confirm these results.

Anisotropic MRI contrast reveals enhanced ionic transport in plastic crystals

Organic ionic plastic crystals (OIPCs) are attractive as solid-state electrolytes for electrochemical devices such as lithium-ion batteries and solar and fuel cells. OIPCs offer high ionic conductivity, nonflammability, and versatility of molecular design. Nevertheless, intrinsic ion transport behavior of OIPCs is not fully understood, and their measured properties depend heavily on thermal history. Solid-state magnetic resonance imaging experiments reveal a striking image contrast anisotropy sensitive to the orientation of grain boundaries in polycrystalline OIPCs. Probing triethyl(methyl)phosphonium bis(fluorosulfonyl)imide (P1222FSI) samples with different thermal history demonstrates vast variations in microcrystallite alignment. Upon slow cooling from the melt, microcrystallites exhibit a preferred orientation throughout the entire sample, leading to an order of magnitude increase in conductivity as probed using impedance spectroscopy. This investigation describes both a new conceptual window and a new characterization method for understanding polycrystalline domain structure and transport in plastic crystals and other solid-state conductors.

Estudo do processo de combustão in-situ usando poços horizontais como produtores de óleo (Toe-to-Hell Air Injection)

The method "toe-to-heel air injection" (THAITM) is a process of enhanced oil recovery, which is the integration of in-situ combustion with technological advances in drilling horizontal wells. This method uses horizontal wells as producers of oil, keeping vertical injection wells to inject air. This process has not yet been applied in Brazil, making it necessary, evaluation of these new technologies applied to local realities, therefore, this study aimed to perform a parametric study of the combustion process with in-situ oil production in horizontal wells, using a semi synthetic reservoir, with characteristics of the Brazilian Northeast basin. The simulations were performed in a commercial software "STARS" (Steam, Thermal, and Advanced Processes Reservoir Simulator), from CMG (Computer Modelling Group). The following operating parameters were analyzed: air rate, configuration of producer wells and oxygen concentration. A sensitivity study on cumulative oil (Np) was performed with the technique of experimental design, with a mixed model of two and three levels (32x22), a total of 36 runs. Also, it was done a technical economic estimative for each model of fluid. The results showed that injection rate was the most influence parameter on oil recovery, for both studied models, well arrangement depends on fluid model, and oxygen concentration favors recovery oil. The process can be profitable depends on air rate

Boron transport in Eucalyptus. 2. Identification in silico of a putative boron transporter for xylem loading in eucalypt

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Iliac osteosynthesis with nylon clamp associated to polymethylmethacrylate bone cement - experimental study in dogs cadavers

Fractures of iliac body are generally consequences of traumas of great impact. These fractures lead to a lack of locomotor response and in specific cases, surgery is needed. Among the possible therapeutic lines, implants become a good option. In this paper, the authors used dog corpses to develop a surgery technique of iliac osteosynthesis, employing nylon clamps and bone cement of polymethylmethacrylate (PMMA). Sixteen hemi pelvises of eight dog corpses, which had its iliac bodies totally fractured previously, were utilized. The osteosynthesis was reached through the implantation of six nylon clamps, distributed equally between the bone fragments. With the use of the nylon clamps there were bone realignment and a contact surface to fixation of the biomaterial. The technique developed in corpses was easily executed, effective in reduction, alignment and stabilization of the fracture. The authors suggest more studies in vitro to evaluate immobilization resistance and functionality in dogs with this condition.

Political Depolarization in German Public Opinion, 1980–2010

Little is known about political polarization in German public opinion. This article offers an issue-based perspective and explores trends of opinion polarization in Germany. Public opinion polarization is conceptualized and measured as alignment of attitudes. Data from the German General Social Survey (1980 to 2010) comprise attitudes towards manifold issues, which are classified into several dimensions. This study estimates multilevel models that reveal general and issue- as well as dimension-specific levels and trends in attitude alignment for both the whole German population and sub-groups. It finds that public opinion polarization has decreased over the last three decades in Germany. In particular, highly educated and more politically interested people have become less polarized over time. However, polarization seems to have increased in attitudes regarding gender issues. These findings provide interesting contrasts to existing research on the American public.

ParAlign: a parallel sequence alignment algorithm for rapid and sensitive database searches

There is a need for faster and more sensitive algorithms for sequence similarity searching in view of the rapidly increasing amounts of genomic sequence data available. Parallel processing capabilities in the form of the single instruction, multiple data (SIMD) technology are now available in common microprocessors and enable a single microprocessor to perform many operations in parallel. The ParAlign algorithm has been specifically designed to take advantage of this technology. The new algorithm initially exploits parallelism to perform a very rapid computation of the exact optimal ungapped alignment score for all diagonals in the alignment matrix. Then, a novel heuristic is employed to compute an approximate score of a gapped alignment by combining the scores of several diagonals. This approximate score is used to select the most interesting database sequences for a subsequent Smith–Waterman alignment, which is also parallelised. The resulting method represents a substantial improvement compared to existing heuristics. The sensitivity and specificity of ParAlign was found to be as good as Smith–Waterman implementations when the same method for computing the statistical significance of the matches was used. In terms of speed, only the significantly less sensitive NCBI BLAST 2 program was found to outperform the new approach. Online searches are available at http://dna.uio.no/search/

Investigating the Role of cAMP-Signaling in the Regulation of Vascular Endothelial Cell Adaptive Responses to Fluid Shear Stress

The circulating blood exerts a force on the vascular endothelium, termed fluid shear stress (FSS), which directly impacts numerous vascular endothelial cell (VEC) functions. For example, high rates of linear and undisturbed (i.e. laminar) blood flow maintains a protective and quiescent VEC phenotype. Meanwhile, deviations in blood flow, which can occur at vascular branchpoints and large curvatures, create areas of low, and/or oscillatory FSS, and promote a pro-inflammatory, pro-thrombotic and hyperpermeable phenotype. Indeed, it is known that these areas are prone to the development of atherosclerotic lesions. Herein, we show that cyclic nucleotide phosphodiesterase (PDE) 4D (PDE4D) activity is increased by FSS in human arterial endothelial cells (HAECs) and that this activation regulates the activity of cAMP-effector protein, Exchange Protein-activated by cAMP-1 (EPAC1), in these cells. Importantly, we also show that these events directly and critically impact HAEC responses to FSS, especially when FSS levels are low. Both morphological events induced by FSS, as measured by changes in cell alignment and elongation in the direction of FSS, and the expression of critical FSS-regulated genes, including Krüppel-like factor 2 (KLF2), endothelial nitric oxide synthase (eNOS) and thrombomodlin (TM), are mediated by EPAC1/PDE4D signaling. At a mechanistic level, we show that EPAC1/PDE4D acts through the vascular endothelial-cadherin (VECAD)/ platelet-cell adhesion molecule-1 (PECAM1)/vascular endothelial growth factor receptor 2 (VEGFR2) mechanosensor to activate downstream signaling though Akt. Given the critical role of PDE4D in mediating these effects, we also investigated the impact of various patterns of FSS on the expression of individual PDE genes in HAECs. Notably, PDE2A was significantly upregulated in response to high, laminar FSS, while PDE3A was upregulated under low, oscillatory FSS conditions only. These data may provide novel therapeutic targets to limit FSS-dependent endothelial cell dysfunction (ECD) and atherosclerotic development.