69 research outputs found
An open problem in complex analytic geometry arising in harmonic analysis
In this paper, an open problem in the multidimensional complex analysis is
pesented that arises in the investigation of the regularity properties of
Fourier integral operators and in the regularity theory for hyperbolic partial
differential equations. The problem is discussed in a self-contained elementary
way and some results towards its resolution are presented. A conjecture
concerning the structure of appearing affine fibrations is formulated.Comment: 8 page
Reduced dimensionality spin-orbit dynamics of CH3 + HCl reversible arrow CH4 Cl on ab initio surfaces
A reduced dimensionality quantum scattering method is extended to the study of spin-orbit nonadiabatic transitions in the CH3 + HCl reversible arrow CH4 + Cl(P-2(J)) reaction. Three two-dimensional potential energy surfaces are developed by fitting a 29 parameter double-Morse function to CCSD(T)/IB//MP2/cc-pV(T+d)Z-dk ab initio data; interaction between surfaces is described by geometry-dependent spin-orbit coupling functions fit to MCSCF/cc-pV(T+d)Z-dk ab initio data. Spectator modes are treated adiabatically via inclusion of curvilinear projected frequencies. The total scattering wave function is expanded in a vibronic basis set and close-coupled equations are solved via R-matrix propagation. Ground state thermal rate constants for forward and reverse reactions agree well with experiment. Multi-surface reaction probabilities, integral cross sections, and initial-state selected branching ratios all highlight the importance of vibrational energy in mediating nonadiabatic transition. Electronically excited state dynamics are seen to play a small but significant role as consistent with experimental conclusions. (C) 2011 American Institute of Physics. [doi:10.1063/1.3592732
Public Health Governance and Population Health Outcomes
Research reviews have identified a gap in understanding the diversity of health department governance structures and in understanding how the variations in governing relates to health outcomes. This report details the categorization of local public health governance and reveals that certain governance types may be better suited to achieve better population health outcomes. State systems achieve the poorest health outcomes, but the best health outcomes are achieved when the political branches have a key role in local public health governance. Public health systems should consider greater local control and involvement in governance; but local governance should include the political branches -- and even the state -- to achieve more positive health outcomes
The effect of oxygenate fuels on PN emissions from a highly boosted GDI engine
Gasoline Direct Injection (GDI) engines are increasingly available in the market. Such engines are known to emit more Particulate Matter (PM) than their port-fuel injected predecessors. There is also a widespread use of oxygenate fuels in the market, up to blends of E85, and their impact on PN emissions is widely studied. However the impact of oxygenate fuels on PN emissions from downsized, and hence highly-boosted engines is not known. In this work, PN emissions from a highly boosted engine capable of running at up to 35 bar Brake Mean Effective Pressure (BMEP) have been measured from a baseline gasoline and three different oxygenate fuels (E20, E85, and GEM – a blend of gasoline, ethanol, and methanol) using a DMS500. The engine has been run at four different operating points, and a number of engine parameters relevant to highly-boosted engines (such as EGR, exhaust back pressure, and lambda) have been tested – the PN emissions and size distributions have been measured from all of these. The results show that the oxygenate content of the fuel has a very large impact on its PN emissions, with E85 giving low levels of PN emissions across the operating range, and GEM giving very low and extremely high levels of PN emissions depending on operating point. These results have been analysed and related back to key fuel properties
VarMod: modelling the functional effects of non-synonymous variants.
Unravelling the genotype–phenotype relationship in humans remains a challenging task in genomics studies. Recent advances in sequencing technologies mean there are now thousands of sequenced human genomes, revealing millions of single nucleotide variants (SNVs). For non-synonymous SNVs present in proteins the difficulties of the problem lie in first identifying those nsSNVs that result in a functional change in the protein among the many non-functional variants and in turn linking this functional change to phenotype. Here we present VarMod (Variant Modeller) a method that utilises both protein sequence and structural features to predict nsSNVs that alter protein function. VarMod develops recent observations that functional nsSNVs are enriched at protein–protein interfaces and protein–ligand binding sites and uses these characteristics to make predictions. In benchmarking on a set of nearly 3000 nsSNVs VarMod performance is comparable to an existing state of the art method. The VarMod web server provides extensive resources to investigate the sequence and structural features associated with the predictions including visualisation of protein models and complexes via an interactive JSmol molecular viewer.
VarMod is available for use at http://www.wasslab.org/varmod
Psychosocial Predictors of Non-Adherence and Treatment Failure in a Large Scale Multi-National Trial of Antiretroviral Therapy for HIV: Data from the ACTG A5175/PEARLS Trial
Background: PEARLS, a large scale trial of antiretroviral therapy (ART) for HIV (n = 1,571, 9 countries, 4 continents), found that a once-daily protease inhibitor (PI) based regimen (ATV+DDI+FTC), but not a once-daily non-nucleoside reverse transcriptase inhibitor/nucleoside reverse transcriptase inhibitor (NNRTI/NRTI) regimen (EFV+FTC/TDF), had inferior efficacy compared to a standard of care twice-daily NNRTI/NRTI regimen (EFV+3TC/ZDV). The present study examined non-adherence in PEARLS. Methods: Outcomes: non-adherence assessed by pill count and by self-report, and time to treatment failure. Longitudinal predictors: regimen, quality of life (general health perceptions = QOL-health, mental health = QOL-mental health), social support, substance use, binge drinking, and sexual behaviors. “Life-Steps” adherence counseling was provided. Results: In both pill-count and self-report multivariable models, both once-a-day regimens had lower levels of non-adherence than the twice-a-day standard of care regimen; although these associations attenuated with time in the self-report model. In both multivariable models, hard-drug use was associated with non-adherence, living in Africa and better QOL-health were associated with less non-adherence. According to pill-count, unprotected sex was associated with non-adherence. According to self-report, soft-drug use was associated with non-adherence and living in Asia was associated with less non-adherence. Both pill-count (HR = 1.55, 95% CI: 1.15, 2.09, p<.01) and self-report (HR = 1.13, 95% CI: 1.08, 1.13, p<.01) non-adherence were significant predictors of treatment failure over 72 weeks. In multivariable models (including pill-count or self-report nonadherence), worse QOL-health, age group (younger), and region were also significant predictors of treatment failure. Conclusion: In the context of a large, multi-national, multi-continent, clinical trial there were variations in adherence over time, with more simplified regimens generally being associated with better adherence. Additionally, variables such as QOL-health, regimen, drug-use, and region play a role. Self-report and pill-count adherence, as well as additional psychosocial variables, such QOL-health, age, and region, were, in turn, associated with treatment failure
Integrative Genetic Manipulation of Plasmodium cynomolgi Reveals Multidrug Resistance-1 Y976F Associated With Increased In Vitro Susceptibility to Mefloquine
The lack of a long-term in vitro culture method has severely restricted the study of Plasmodium vivax, in part because it limits genetic manipulation and reverse genetics. We used the recently optimized Plasmodium cynomolgi Berok in vitro culture model to investigate the putative P. vivax drug resistance marker MDR1 Y976F. Introduction of this mutation using clustered regularly interspaced short palindromic repeats-CRISPR-associated protein 9 (CRISPR-Cas9) increased sensitivity to mefloquine, but had no significant effect on sensitivity to chloroquine, amodiaquine, piperaquine, and artesunate. To our knowledge, this is the first reported use of CRISPR-Cas9 in P. cynomolgi, and the first reported integrative genetic manipulation of this species
Structure of a Burkholderia pseudomallei Trimeric Autotransporter Adhesin Head
Pathogenic bacteria adhere to the host cell surface using a family of outer membrane proteins called Trimeric Autotransporter Adhesins (TAAs). Although TAAs are highly divergent in sequence and domain structure, they are all conceptually comprised of a C-terminal membrane anchoring domain and an N-terminal passenger domain. Passenger domains consist of a secretion sequence, a head region that facilitates binding to the host cell surface, and a stalk region.Pathogenic species of Burkholderia contain an overabundance of TAAs, some of which have been shown to elicit an immune response in the host. To understand the structural basis for host cell adhesion, we solved a 1.35 A resolution crystal structure of a BpaA TAA head domain from Burkholderia pseudomallei, the pathogen that causes melioidosis. The structure reveals a novel fold of an intricately intertwined trimer. The BpaA head is composed of structural elements that have been observed in other TAA head structures as well as several elements of previously unknown structure predicted from low sequence homology between TAAs. These elements are typically up to 40 amino acids long and are not domains, but rather modular structural elements that may be duplicated or omitted through evolution, creating molecular diversity among TAAs.The modular nature of BpaA, as demonstrated by its head domain crystal structure, and of TAAs in general provides insights into evolution of pathogen-host adhesion and may provide an avenue for diagnostics
Structure and non-structure of centrosomal proteins
Here we perform a large-scale study of the structural properties and the expression of proteins that constitute the human Centrosome. Centrosomal proteins tend to be larger than generic human proteins (control set), since their genes contain in average more exons (20.3 versus 14.6). They are rich in predicted disordered regions, which cover 57% of their length, compared to 39% in the general human proteome. They also contain several regions that are dually predicted to be disordered and coiled-coil at the same time: 55 proteins (15%) contain disordered and coiled-coil fragments that cover more than 20% of their length. Helices prevail over strands in regions homologous to known structures (47% predicted helical residues against 17% predicted as strands), and even more in the whole centrosomal proteome (52% against 7%), while for control human proteins 34.5% of the residues are predicted as helical and 12.8% are predicted as strands. This difference is mainly due to residues predicted as disordered and helical (30% in centrosomal and 9.4% in control proteins), which may correspond to alpha-helix forming molecular recognition features (α-MoRFs). We performed expression assays for 120 full-length centrosomal proteins and 72 domain constructs that we have predicted to be globular. These full-length proteins are often insoluble: Only 39 out of 120 expressed proteins (32%) and 19 out of 72 domains (26%) were soluble. We built or retrieved structural models for 277 out of 361 human proteins whose centrosomal localization has been experimentally verified. We could not find any suitable structural template with more than 20% sequence identity for 84 centrosomal proteins (23%), for which around 74% of the residues are predicted to be disordered or coiled-coils. The three-dimensional models that we built are available at http://ub.cbm.uam.es/centrosome/models/index.php
<i>De novo</i> design of a four-fold symmetric TIM-barrel protein with atomic-level accuracy
Despite efforts for over 25 years, de novo protein design has not succeeded in achieving the TIM-barrel fold. Here we describe the computational design of 4-fold symmetrical (β/α)(8)-barrels guided by geometrical and chemical principles. Experimental characterization of 33 designs revealed the importance of sidechain-backbone hydrogen bonding for defining the strand register between repeat units. The X-ray crystal structure of a designed thermostable 184-residue protein is nearly identical with the designed TIM-barrel model. PSI-BLAST searches do not identify sequence similarities to known TIM-barrel proteins, and sensitive profile-profile searches indicate that the design sequence is distant from other naturally occurring TIM-barrel superfamilies, suggesting that Nature has only sampled a subset of the sequence space available to the TIM-barrel fold. The ability to de novo design TIM-barrels opens new possibilities for custom-made enzymes
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