Explicit solution for vibrating bar with viscous boundaries and internal damper

We investigate longitudinal vibrations of a bar subjected to viscous boundary conditions at each end, and an internal damper at an arbitrary point along the bar's length. The system is described by four independent parameters and exhibits a variety of behaviors including rigid motion, super stability/instability and zero damping. The solution is obtained by applying the Laplace transform to the equation of motion and computing the Green's function of the transformed problem. This leads to an unconventional eigenvalue-like problem with the spectral variable in the boundary conditions. The eigenmodes of the problem are necessarily complex-valued and are not orthogonal in the usual inner product. Nonetheless, in generic cases we obtain an explicit eigenmode expansion for the response of the bar to initial conditions and external force. For some special values of parameters the system of eigenmodes may become incomplete, or no non-trivial eigenmodes may exist at all. We thoroughly analyze physical and mathematical reasons for this behavior and explicitly identify the corresponding parameter values. In particular, when no eigenmodes exist, we obtain closed form solutions. Theoretical analysis is complemented by numerical simulations, and analytic solutions are compared to computations using finite elements.Comment: 29 pages, 6 figure

Adaptive targeting in online advertisement: models based on relative influence of factors

We consider the problem of adaptive targeting for real-time bidding for internet advertisement. This problem involves making fast decisions on whether to show a given ad to a particular user. For demand partners, these decisions are based on information extracted from big data sets containing records of previous impressions, clicks and subsequent purchases. We discuss several criteria which allow us to assess the significance of different factors on probabilities of clicks and conversions. We then devise simple strategies that are based on the use of the most influential factors and compare their performance with strategies that are much more computationally demanding. To make the numerical comparison, we use real data collected by Crimtan in the process of running several recent ad campaigns

Demographic, risk behaviour and personal network variables associated with prevalent hepatitis C, hepatitis B, and HIV infection in injection drug users in Winnipeg, Canada

BACKGROUND: Previous studies have used social network variables to improve our understanding of HIV transmission. Similar analytic approaches have not been undertaken for hepatitis C (HCV) or B (HBV), nor used to conduct comparative studies on these pathogens within a single setting. METHODS: A cross-sectional survey consisting of a questionnaire and blood sample was conducted on injection drug users in Winnipeg between December 2003 and September 2004. Logistic regression analyses were used to correlate respondent and personal network data with HCV, HBV and HIV prevalence. RESULTS: At the multivariate level, pathogen prevalence was correlated with both respondent and IDU risk network variables. Pathogen transmission was associated with several distinct types of high-risk networks formed around specific venues (shooting galleries, hotels) or within users who are linked by their drug use preferences. Smaller, isolated pockets of IDUs also appear to exist within the larger population where behavioural patterns pose a lesser risk, unless or until, a given pathogen enters those networks. CONCLUSION: The findings suggest that consideration of both respondent and personal network variables can assist in understanding the transmission patterns of HCV, HBV, and HIV. It is important to assess these effects for multiple pathogens within one setting as the associations identified and the direction of those associations can differ between pathogens

Big-Data-Driven Materials Science and its FAIR Data Infrastructure

This chapter addresses the forth paradigm of materials research -- big-data driven materials science. Its concepts and state-of-the-art are described, and its challenges and chances are discussed. For furthering the field, Open Data and an all-embracing sharing, an efficient data infrastructure, and the rich ecosystem of computer codes used in the community are of critical importance. For shaping this forth paradigm and contributing to the development or discovery of improved and novel materials, data must be what is now called FAIR -- Findable, Accessible, Interoperable and Re-purposable/Re-usable. This sets the stage for advances of methods from artificial intelligence that operate on large data sets to find trends and patterns that cannot be obtained from individual calculations and not even directly from high-throughput studies. Recent progress is reviewed and demonstrated, and the chapter is concluded by a forward-looking perspective, addressing important not yet solved challenges.Comment: submitted to the Handbook of Materials Modeling (eds. S. Yip and W. Andreoni), Springer 2018/201

A biophysical model of cell adhesion mediated by immunoadhesin drugs and antibodies

A promising direction in drug development is to exploit the ability of natural killer cells to kill antibody-labeled target cells. Monoclonal antibodies and drugs designed to elicit this effect typically bind cell-surface epitopes that are overexpressed on target cells but also present on other cells. Thus it is important to understand adhesion of cells by antibodies and similar molecules. We present an equilibrium model of such adhesion, incorporating heterogeneity in target cell epitope density and epitope immobility. We compare with experiments on the adhesion of Jurkat T cells to bilayers containing the relevant natural killer cell receptor, with adhesion mediated by the drug alefacept. We show that a model in which all target cell epitopes are mobile and available is inconsistent with the data, suggesting that more complex mechanisms are at work. We hypothesize that the immobile epitope fraction may change with cell adhesion, and we find that such a model is more consistent with the data. We also quantitatively describe the parameter space in which binding occurs. Our results point toward mechanisms relating epitope immobility to cell adhesion and offer insight into the activity of an important class of drugs.Comment: 13 pages, 5 figure

Coevolved mutations reveal distinct architectures for two core proteins in the bacterial flagellar motor

Switching of bacterial flagellar rotation is caused by large domain movements of the FliG protein triggered by binding of the signal protein CheY to FliM. FliG and FliM form adjacent multi-subunit arrays within the basal body C-ring. The movements alter the interaction of the FliG C-terminal (FliGC) "torque" helix with the stator complexes. Atomic models based on the Salmonella entrovar C-ring electron microscopy reconstruction have implications for switching, but lack consensus on the relative locations of the FliG armadillo (ARM) domains (amino-terminal (FliGN), middle (FliGM) and FliGC) as well as changes during chemotaxis. The generality of the Salmonella model is challenged by the variation in motor morphology and response between species. We studied coevolved residue mutations to determine the unifying elements of switch architecture. Residue interactions, measured by their coevolution, were formalized as a network, guided by structural data. Our measurements reveal a common design with dedicated switch and motor modules. The FliM middle domain (FliMM) has extensive connectivity most simply explained by conserved intra and inter-subunit contacts. In contrast, FliG has patchy, complex architecture. Conserved structural motifs form interacting nodes in the coevolution network that wire FliMM to the FliGC C-terminal, four-helix motor module (C3-6). FliG C3-6 coevolution is organized around the torque helix, differently from other ARM domains. The nodes form separated, surface-proximal patches that are targeted by deleterious mutations as in other allosteric systems. The dominant node is formed by the EHPQ motif at the FliMMFliGM contact interface and adjacent helix residues at a central location within FliGM. The node interacts with nodes in the N-terminal FliGc α-helix triad (ARM-C) and FliGN. ARM-C, separated from C3-6 by the MFVF motif, has poor intra-network connectivity consistent with its variable orientation revealed by structural data. ARM-C could be the convertor element that provides mechanistic and species diversity.JK was supported by Medical Research Council grant U117581331. SK was supported by seed funds from Lahore University of Managment Sciences (LUMS) and the Molecular Biology Consortium

How are falls and fear of falling associated with objectively measured physical activity in a cohort of community-dwelling older men?

BACKGROUND: Falls affect approximately one third of community-dwelling older adults each year and have serious health and social consequences. Fear of falling (FOF) (lack of confidence in maintaining balance during normal activities) affects many older adults, irrespective of whether they have actually experienced falls. Both falls and fear of falls may result in restrictions of physical activity, which in turn have health consequences. To date the relation between (i) falls and (ii) fear of falling with physical activity have not been investigated using objectively measured activity data which permits examination of different intensities of activity and sedentary behaviour. METHODS: Cross-sectional study of 1680 men aged 71-92 years recruited from primary care practices who were part of an on-going population-based cohort. Men reported falls history in previous 12 months, FOF, health status and demographic characteristics. Men wore a GT3x accelerometer over the hip for 7 days. RESULTS: Among the 12% of men who had recurrent falls, daily activity levels were lower than among non-fallers; 942 (95% CI 503, 1381) fewer steps/day, 12(95% CI 2, 22) minutes less in light activity, 10(95% CI 5, 15) minutes less in moderate to vigorous PA [MVPA] and 22(95% CI 9, 35) minutes more in sedentary behaviour. 16% (n = 254) of men reported FOF, of whom 52% (n = 133) had fallen in the past year. Physical activity deficits were even greater in the men who reported that they were fearful of falling than in men who had fallen. Men who were fearful of falling took 1766(95% CI 1391, 2142) fewer steps/day than men who were not fearful, and spent 27(95% CI 18, 36) minutes less in light PA, 18(95% CI 13, 22) minutes less in MVPA, and 45(95% CI 34, 56) minutes more in sedentary behaviour. The significant differences in activity levels between (i) fallers and non-fallers and (ii) men who were fearful of falling or not fearful, were mediated by similar variables; lower exercise self-efficacy, fewer excursions from home and more mobility difficulties. CONCLUSIONS: Falls and in particular fear of falling are important barriers to older people gaining health benefits of walking and MVPA. Future studies should assess the longitudinal associations between falls and physical activity

PPLook: an automated data mining tool for protein-protein interaction

<p>Abstract</p> <p>Background</p> <p>Extracting and visualizing of protein-protein interaction (PPI) from text literatures are a meaningful topic in protein science. It assists the identification of interactions among proteins. There is a lack of tools to extract PPI, visualize and classify the results.</p> <p>Results</p> <p>We developed a PPI search system, termed PPLook, which automatically extracts and visualizes protein-protein interaction (PPI) from text. Given a query protein name, PPLook can search a dataset for other proteins interacting with it by using a keywords dictionary pattern-matching algorithm, and display the topological parameters, such as the number of nodes, edges, and connected components. The visualization component of PPLook enables us to view the interaction relationship among the proteins in a three-dimensional space based on the OpenGL graphics interface technology. PPLook can also provide the functions of selecting protein semantic class, counting the number of semantic class proteins which interact with query protein, counting the literature number of articles appearing the interaction relationship about the query protein. Moreover, PPLook provides heterogeneous search and a user-friendly graphical interface.</p> <p>Conclusions</p> <p>PPLook is an effective tool for biologists and biosystem developers who need to access PPI information from the literature. PPLook is freely available for non-commercial users at <url>http://meta.usc.edu/softs/PPLook</url>.</p

Gravitational waves from single neutron stars: an advanced detector era survey

With the doors beginning to swing open on the new gravitational wave astronomy, this review provides an up-to-date survey of the most important physical mechanisms that could lead to emission of potentially detectable gravitational radiation from isolated and accreting neutron stars. In particular we discuss the gravitational wave-driven instability and asteroseismology formalism of the f- and r-modes, the different ways that a neutron star could form and sustain a non-axisymmetric quadrupolar "mountain" deformation, the excitation of oscillations during magnetar flares and the possible gravitational wave signature of pulsar glitches. We focus on progress made in the recent years in each topic, make a fresh assessment of the gravitational wave detectability of each mechanism and, finally, highlight key problems and desiderata for future work.Comment: 39 pages, 12 figures, 2 tables. Chapter of the book "Physics and Astrophysics of Neutron Stars", NewCompStar COST Action 1304. Minor corrections to match published versio

Thoracic empyema with scarlatiniform rash and acral desquamation: a case report

A 5 year old girl with thoracic empyema developed a scarlatiniform rash and acral desquamation. Cultures from blood, throat, and pleural fluid all grew Streptococcus pyogenes, a common etiologic agent of pediatric thoracic empyema. The presence of a scarlatiniform rash and acral desquamation in children with a thoracic empyema may help identify the causative organism