Pattern matching and pattern discovery algorithms for protein topologies

We describe algorithms for pattern matching and pattern learning in TOPS diagrams (formal descriptions of protein topologies). These problems can be reduced to checking for subgraph isomorphism and finding maximal common subgraphs in a restricted class of ordered graphs. We have developed a subgraph isomorphism algorithm for ordered graphs, which performs well on the given set of data. The maximal common subgraph problem then is solved by repeated subgraph extension and checking for isomorphisms. Despite the apparent inefficiency such approach gives an algorithm with time complexity proportional to the number of graphs in the input set and is still practical on the given set of data. As a result we obtain fast methods which can be used for building a database of protein topological motifs, and for the comparison of a given protein of known secondary structure against a motif database

Exact Path-Integral Representations for the TT-Matrix in Nonrelativistic Potential Scattering

Several path integral representations for the $T$-matrix in nonrelativistic potential scattering are given which produce the complete Born series when expanded to all orders and the eikonal approximation if the quantum fluctuations are suppressed. They are obtained with the help of "phantom" degrees of freedom which take away explicit phases that diverge for asymptotic times. Energy conservation is enforced by imposing a Faddeev-Popov-like constraint in the velocity path integral. An attempt is made to evaluate stochastically the real-time path integral for potential scattering and generalizations to relativistic scattering are discussed.Comment: 6 pages, 2 figures. Contribution to the workshop "Relativistic Description of Two- and Three-Body Systems in Nuclear Physics", ETC*, October 19-23, 2009. v2: typo corrected, matches published version + additional reference

Immunosuppressive/anti-inflammatory cytokines directly and indirectly inhibit endothelial dysfunction- a novel mechanism for maintaining vascular function

This study aims to elucidate in greater detail the dermal uptake of nicotine from air or from nicotine-exposed clothes, which was demonstrated recently in a preliminary study. Six non-smoking participants were exposed to gaseous nicotine (between 236 and 304 μg/m³) over 5 hours while breathing clean air through a hood. Four of the participants wore only shorts and 2 wore a set of clean clothes. One week later, 2 of the bare-skinned participants were again exposed in the chamber, but they showered immediately after exposure instead of the following morning. The 2 participants who wore clean clothes on week 1 were now exposed wearing a set of clothes that had been exposed to nicotine. All urine was collected for 84 hours after exposure and analyzed for nicotine and its metabolites, cotinine and 3OH-cotinine. All participants except those wearing fresh clothes excreted substantial amounts of biomarkers, comparable to levels expected from inhalation intake. Uptake for 1 participant wearing exposed clothes exceeded estimated intake via inhalation by >50%. Biomarker excretion continued during the entire urine collection period, indicating that nicotine accumulates in the skin and is released over several days. Absorbed nicotine was significantly lower after showering in 1 subject but not the other. Differences in the normalized uptakes and in the excretion patterns were observed among the participants. The observed cotinine half-lives suggest that non-smokers exposed to airborne nicotine may receive a substantial fraction through the dermal pathway. Washing skin and clothes exposed to nicotine may meaningfully decrease exposure

Understanding the association between sleep, shift work and COVID-19 vaccine immune response efficacy: protocol of the S-CORE study

This protocol describes an innovative study to investigate the relationship between sleep, shift work and the immune response to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2; coronavirus disease 2019 [COVID-19]) vaccination. As the COVID-19 pandemic is a global crisis with devastating health, social and economic impacts, there is a pressing need for effective vaccination programmes. Previous influenza and hepatitis vaccination studies suggest that lack of sleep can negatively alter immune responsiveness, while circadian misalignment most likely may also play an important role in the immune response to vaccination. Our present study will be the first to address this question in actual shift workers and in relation to COVID-19 vaccination. We hypothesise that the occurrence of recent night shifts and diminished sleep will negatively alter the immune response to vaccination in shift workers compared to dayworkers. We aim to recruit 50 shift workers and 50 dayworkers. Participants will receive an mRNA-based vaccination, through the Dutch vaccination programme. To assess immune responsiveness, blood will be drawn at baseline (before first vaccination), 10 days after first vaccination, the day prior to the second vaccination; and 28 days, 6 and 12 months after the second vaccination. Actigraphy and daily sleep e-diaries will be implemented for 7 days around each vaccination to assess sleep. The Pittsburgh Sleep Quality Index will be used to monitor sleep in the long term. Optimising the efficacy of the COVID-19 vaccines is of outmost importance and results of this study could provide insights to develop sleep and circadian-based interventions to enhance vaccination immunity, and thereby improve global health.Paroxysmal Cerebral Disorder

Semiclassical Trace Formulas for Noninteracting Identical Particles

We extend the Gutzwiller trace formula to systems of noninteracting identical particles. The standard relation for isolated orbits does not apply since the energy of each particle is separately conserved causing the periodic orbits to occur in continuous families. The identical nature of the particles also introduces discrete permutational symmetries. We exploit the formalism of Creagh and Littlejohn [Phys. Rev. A 44, 836 (1991)], who have studied semiclassical dynamics in the presence of continuous symmetries, to derive many-body trace formulas for the full and symmetry-reduced densities of states. Numerical studies of the three-particle cardioid billiard are used to explicitly illustrate and test the results of the theory.Comment: 29 pages, 11 figures, submitted to PR

Side branch healing patterns of the Tryton dedicated bifurcation stent: a 1-year optical coherence tomography follow-up study

The bare-metal Tryton Side Branch (SB) Stent™ (Tryton Medical, Durham, NC, USA) is used with a drug-eluting stent (DES) in the main branch (MB) to treat bifurcation lesions. It is argued that a drug-eluting Tryton-version is needed to improve clinical outcomes, although previous registries have shown good clinical results. More insights in neo-intimal hyperplasia (NIH) growth patterns of the Tryton treatment strategy are needed to decide if and where to drug-coat the stent. Ten patients returned for follow-up angiography (mean follow-up time 393 ± 103 days) and optical coherence tomography (OCT) pullbacks from the MB were obtained in all patients and from the SB in six patients. A per-strut analysis showed an uncovered strut rate of 0.7 % and an incompletely-apposed strut rate of 0.8 %. Most incompletely-apposed struts were found at the bifurcation region, in the luminal half facing towards the SB. Mean NIH thickness in the proximal MB, distal MB and SB were 0.14 ± 0.11, 0.19 ± 0.11, and 0.34 ± 0.19 mm, respectively, with a variety of growth patterns observed in the SB. We found good vascular healing of the DES in the MB, while healing was less favourably in the SB part. Furthermore, we observed a variety of NIH growth patterns in this SB part and more studies are needed to investigate the relation between growth patterns and clinical outcomes

Interstitials, Vacancies and Dislocations in Flux-Line Lattices: A Theory of Vortex Crystals, Supersolids and Liquids

We study a three dimensional Abrikosov vortex lattice in the presence of an equilibrium concentration of vacancy, interstitial and dislocation loops. Vacancies and interstitials renormalize the long-wavelength bulk and tilt elastic moduli. Dislocation loops lead to the vanishing of the long-wavelength shear modulus. The coupling to vacancies and interstitials - which are always present in the liquid state - allows dislocations to relax stresses by climbing out of their glide plane. Surprisingly, this mechanism does not yield any further independent renormalization of the tilt and compressional moduli at long wavelengths. The long wavelength properties of the resulting state are formally identical to that of the ``flux-line hexatic'' that is a candidate ``normal'' hexatically ordered vortex liquid state.Comment: 21 RevTeX pgs, 7 eps figures uuencoded; corrected typos, published versio