Admissibility of a wide cluster solution in "anisotropic" higher-order traffic flow models

We analytically investigate a wide cluster solution and show that it is not admitted in some of the traffic flow models in the literature. For those traffic flow models that admit the wide cluster solution, the relationship between two important control parameters and the critical densities that divide an equilibrium solution into stable and unstable regions is thoroughly discussed in detail. We find that such wide clusters exist with a free traffic density in an unstable region, and with one or three critical densities. These results are different from the cases in the well-known higher-order traffic flow models of Payne and Whitham [H. J. Payne, "Models of freeway traffic and control," in Mathematical Models of Public Systems, A. G. Bekey, ed., Simulation Council Proc. Ser. 1, La Jolla, CA, 1971, pp. 51-61], [G. B. Whitham, Linear and Nonlinear Waves, John Wiley and Sons, New York, 1974], Kühne [R. D. Kühne, "Macroscopic freeway model for dense traffic-stop-start waves and incident detection," in Proceedings of the 9th International Symposium on Transportation and Traffic Theory, J. Volmuller and R. Hamerslag, eds., VNU Science Press, Utrecht, 1984, pp. 21-42], and Kerner and Konhäuser [B. S. Kerner and P. Konhäuser, Phys. Rev. E (3), 50 (1994), pp. 54-83]. © 2007 Society for Industrial and Applied Mathematics.published_or_final_versio

Solitary wave solution to Aw-Rascle viscous model of traffic flow

A traveling wave solution to the Aw-Rascle traffic flow model that includes the relaxation and diffusion terms is investigated. The model can be approximated by the well-known Kortweg-de Vries (KdV) equation. A numerical simulation is conducted by the first-order accurate Lax-Friedrichs scheme, which is known for its ability to capture the entropy solution to hyperbolic conservation laws. Periodic boundary conditions are applied to simulate a lengthy propagation, where the profile of the derived KdV solution is taken as the initial condition to observe the change of the profile. The simulation shows good agreement between the approximated KdV solution and the numerical solution.postprin

Short circuit current improvement in planar heterojunction organic solar cells by multijunction charge transfer

A multijunction structure was applied on an organic photovoltaic (OPV) device for broadening the absorption spectrum and enhancing the power conversion efficiency through charge transfer process. By inserting the tris[4-(2-thienyl)]amine (TTPA) into a boron subphthalocyanine chloride (SubPc)/C 60 OPV device, the short circuit current density (J sc) showed a 47.5% increases from 3.05 to 4.50 mA/cm 2 in the bilayer planar heterojunction device, while the open circuit voltage (V oc) remained constant. Based on the single junction (TTPA/SubPc) device and photoluminescence absorption results, we confirmed both TTPA/SubPc and SubPc/C 60 junctions are contributing to the exciton dissociation process hence the efficiency enhancement. © 2012 American Institute of Physics.published_or_final_versio

Secondhand smoke (SHS) exposures: Workplace exposures, related perceptions of SHS risk, and reactions to smoking in catering workers in smoking and nonsmoking premises

Introduction: Smoke-free workplace legislation often exempts certain venues. Do smoking (exempted) and nonsmoking (nonexempted) catering premises' workers in Hong Kong report different perceptions of risk from and reactions to nearby smoking as well as actual exposure to secondhand smoke (SHS)? Methods: In a cross-sectional survey of 204 nonsmoking catering workers, those from 67 premises where smoking is allowed were compared with workers from 36 nonsmoking premises in Hong Kong on measures of perceptions of risk and behavioral responses to self-reported SHS exposure, plus independent exposure assessment using urinary cotinine. Results: Self-reported workplace SHS exposure prevalence was 57% (95% CI = 49%-65%) in premises prohibiting and 100% (95% CI = 92%-100%) in premises permitting smoking (p < .001). Workers in smoking-permitted premises perceived workplace air quality as poorer (odds ratio [OR] = 9.3, 95% CI = 4.2-20.9) with higher associated risks (OR = 3.7, 95% CI = 1.6-8.6) than workers in smoking-prohibited premises. Workers in smoking-prohibited premises were more bothered by (OR = 0.2, 95% CI = 0.1-0.5) and took more protective action to avoid SHS (OR = 0.2, 95% CI = 0.1-0.4) than workers in smoking-permitted premises. Nonwork exposure was negatively associated with being always bothered by nearby smoking (OR = 0.3, 95% CI = 0.1-0.9), discouraging nearby smoking (OR = 0.5, 95% CI = 0.2-1.1), and discouraging home smoking (OR = 0.4, 95% CI = 0.2-0.9). Urinary cotinine levels were inversely related to workers' avoidance behavior but positively related to their perceived exposure-related risks. Conclusions: Different workplace smoking restrictions predicted actual SHS exposure, exposure-related risk perception, and protective behaviors. Workers from smoking-permitted premises perceived greater SHS exposure-related risks but were more tolerant of these than workers in smoking-prohibited premises. This tolerance might indirectly increase both work and nonwork exposures. © The Author 2011. Published by Oxford University Press on behalf of the Society for Research on Nicotine and Tobacco. All rights reserved.postprin

Short circuit current improvement in planar heterojunction organic solar cells by multijunction charge transfer

Author name used in this publication: S. Q. ShiAuthor name used in this publication: P. K. L. Chan2011-2012 > Academic research: refereed > Publication in refereed journalVersion of RecordPublishe

Identification of single nucleotide variants using position-specific error estimation in deep sequencing data

BACKGROUND: Targeted deep sequencing is a highly effective technology to identify known and novel single nucleotide variants (SNVs) with many applications in translational medicine, disease monitoring and cancer profiling. However, identification of SNVs using deep sequencing data is a challenging computational problem as different sequencing artifacts limit the analytical sensitivity of SNV detection, especially at low variant allele frequencies (VAFs). METHODS: To address the problem of relatively high noise levels in amplicon-based deep sequencing data (e.g. with the Ion AmpliSeq technology) in the context of SNV calling, we have developed a new bioinformatics tool called AmpliSolve. AmpliSolve uses a set of normal samples to model position-specific, strand-specific and nucleotide-specific background artifacts (noise), and deploys a Poisson model-based statistical framework for SNV detection. RESULTS: Our tests on both synthetic and real data indicate that AmpliSolve achieves a good trade-off between precision and sensitivity, even at VAF below 5% and as low as 1%. We further validate AmpliSolve by applying it to the detection of SNVs in 96 circulating tumor DNA samples at three clinically relevant genomic positions and compare the results to digital droplet PCR experiments. CONCLUSIONS: AmpliSolve is a new tool for in-silico estimation of background noise and for detection of low frequency SNVs in targeted deep sequencing data. Although AmpliSolve has been specifically designed for and tested on amplicon-based libraries sequenced with the Ion Torrent platform it can, in principle, be applied to other sequencing platforms as well. AmpliSolve is freely available at https://github.com/dkleftogi/AmpliSolve

Identification of single nucleotide variants using position-specific error estimation in deep sequencing data.

Background Targeted deep sequencing is a highly effective technology to identify known and novel single nucleotide variants (SNVs) with many applications in translational medicine, disease monitoring and cancer profiling. However, identification of SNVs using deep sequencing data is a challenging computational problem as different sequencing artifacts limit the analytical sensitivity of SNV detection, especially at low variant allele frequencies (VAFs).Methods To address the problem of relatively high noise levels in amplicon-based deep sequencing data (e.g. with the Ion AmpliSeq technology) in the context of SNV calling, we have developed a new bioinformatics tool called AmpliSolve. AmpliSolve uses a set of normal samples to model position-specific, strand-specific and nucleotide-specific background artifacts (noise), and deploys a Poisson model-based statistical framework for SNV detection.Results Our tests on both synthetic and real data indicate that AmpliSolve achieves a good trade-off between precision and sensitivity, even at VAF below 5% and as low as 1%. We further validate AmpliSolve by applying it to the detection of SNVs in 96 circulating tumor DNA samples at three clinically relevant genomic positions and compare the results to digital droplet PCR experiments.Conclusions AmpliSolve is a new tool for in-silico estimation of background noise and for detection of low frequency SNVs in targeted deep sequencing data. Although AmpliSolve has been specifically designed for and tested on amplicon-based libraries sequenced with the Ion Torrent platform it can, in principle, be applied to other sequencing platforms as well. AmpliSolve is freely available at https://github.com/dkleftogi/AmpliSolve

Acquisition of pneumococci specific effector and regulatory Cd4+ T cells localising within human upper respiratory-tract mucosal lymphoid tissue

The upper respiratory tract mucosa is the location for commensal Streptococcus (S.) pneumoniae colonization and therefore represents a major site of contact between host and bacteria. The CD4(+) T cell response to pneumococcus is increasingly recognised as an important mediator of immunity that protects against invasive disease, with data suggesting a critical role for Th17 cells in mucosal clearance. By assessing CD4 T cell proliferative responses we demonstrate age-related sequestration of Th1 and Th17 CD4(+) T cells reactive to pneumococcal protein antigens within mucosal lymphoid tissue. CD25(hi) T cell depletion and utilisation of pneumococcal specific MHCII tetramers revealed the presence of antigen specific Tregs that utilised CTLA-4 and PDL-1 surface molecules to suppress these responses. The balance between mucosal effector and regulatory CD4(+) T cell immunity is likely to be critical to pneumococcal commensalism and the prevention of unwanted pathology associated with carriage. However, if dysregulated, such responses may render the host more susceptible to invasive pneumococcal infection and adversely affect the successful implementation of both polysaccharide-conjugate and novel protein-based pneumococcal vaccines

Copy number architectures define treatment-mediated selection of lethal prostate cancer clones

Despite initial responses to hormone treatment, metastatic prostate cancer invariably evolves to a lethal state. To characterize the intra-patient evolutionary relationships of metastases that evade treatment, we perform genome-wide copy number profiling and bespoke approaches targeting the androgen receptor (AR) on 167 metastatic regions from 11 organs harvested post-mortem from 10 men who died from prostate cancer. We identify diverse and patient-unique alterations clustering around the AR in metastases from every patient with evidence of independent acquisition of related genomic changes within an individual and, in some patients, the co-existence of AR-neutral clones. Using the genomic boundaries of pan-autosome copy number changes, we confirm a common clone of origin across metastases and diagnostic biopsies, and identified in individual patients, clusters of metastases occupied by dominant clones with diverged autosomal copy number alterations. These autosome-defined clusters are characterized by cluster-specific AR gene architectures, and in two index cases are topologically more congruent than by chance (p-values 3.07 × 10-8 and 6.4 × 10-4). Integration with anatomical sites suggests patterns of spread and points of genomic divergence. Here, we show that copy number boundaries identify treatment-selected clones with putatively distinct lethal trajectories

A five-year retrospective study of the epidemiological characteristics and visual outcomes of patients hospitalized for ocular trauma in a Mediterranean area

<p>Abstract</p> <p>Background</p> <p>To determine the epidemiological characteristics and visual outcome of ocular trauma in southern Italy.</p> <p>Methods</p> <p>All cases of ocular trauma admitted to Department of Ophthalmology of Palermo University, Italy, from January 2001–December 2005 were retrospectively reviewed for open- or closed-globe injury (OGI or CGI). Data extracted included age, sex, residence, initial and final visual acuity (VA), cause and treatment of injury, hospitalization. The injuries were classified by Ocular Trauma Classification System (OTCS) and Birmingham Eye Trauma Terminology (BETT). We also referred to the Ocular Trauma Score (OTS) in evaluating the final visual outcome.</p> <p>Results</p> <p>Of the 298 eyes, there were 146 OGI and 152 CGI. Fifty eyes (16.8%) had an intraocular foreign body (IOFB). The annual incidence of eye injuries was 4.9 per 100,000. Most injuries occurred in men (84.6%, p < 0.0005), with an average age of 33.0 vs. 49.9 for women (p = 0.005). Cause of injury differed significantly by gender (p = 0.001) and urban vs. rural location (p = 0.009). The most frequent causes in men were outdoor activities related injuries (30.9%), work-related (25.4%), and sport-related (17.5%), and in women were home-related (52.2%) and outdoor activities related injuries (30.4%). In urban areas, road accidents were more frequent; in rural areas, work-related injuries were more frequent with a greater rate of IOFBs than in urban areas (p = 0.002).</p> <p>The incidence of OGI and CGI differed in work-related injuries (p < 0.0005), sport-related injuries (p < 0.0005), and assaults (p = 0.033). The final visual acuity was 20/40 (6/12) or better in 144 eyes (48.3%), 20/40–20/200 (6/12–6/60) in 90 eyes (30.2%), and <20/200 (6/60) or less in 46 eyes (15.5%). Eighteen eyes (6%) had a final acuity of no light perception. Of those eyes that presented with hand motion vision or better, 220 (86.6%) had a final vision of better than 20/200 (6/60). Initial visual acuity was found to be correlated with final visual acuity (Spearman's correlation coefficient = 0.658; p < 0.001). The likelihood of the final visual acuities in the OTS categories was correlated to that of the OTS study group in 12 of 14 cases (85.7%).</p> <p>Conclusion</p> <p>This analysis provides insight into the epidemiology of patients hospitalized for ocular trauma. The findings indicate that ocular trauma is a significant cause of visual loss in this population.</p