A two-stage SVM method to predict membrane protein types by incorporating amino acid classifications and physicochemical properties into a general form of Chou's PseAAC

Membrane proteins play important roles in many biochemical processes and are also attractive targets of drug discovery for various diseases. The elucidation of membrane protein types provides clues for understanding the structure and function of proteins. Recently we developed a novel system for predicting protein subnuclear localizations. In this paper, we propose a simplified version of our system for predicting membrane protein types directly from primary protein structures, which incorporates amino acid classifications and physicochemical properties into a general form of pseudo-amino acid composition. In this simplified system, we will design a two-stage multi-class support vector machine combined with a two-step optimal feature selection process, which proves very effective in our experiments. The performance of the present method is evaluated on two benchmark datasets consisting of five types of membrane proteins. The overall accuracies of prediction for five types are 93.25% and 96.61% via the jackknife test and independent dataset test, respectively. These results indicate that our method is effective and valuable for predicting membrane protein types. A web server for the proposed method is available at http://www.juemengt.com/jcc/memty_page.php

Spatiotemporal transmission dynamics of hemorrhagic fever with renal syndrome in China, 2005-2012

Background Hemorrhagic fever with renal syndrome (HFRS) is a rodent-borne disease caused by many serotypes of hantaviruses. In China, HFRS has been recognized as a severe public health problem with 90% of the total reported cases in the world. This study describes the spatiotemporal dynamics of HFRS cases in China and identifies the regions, time, and populations at highest risk, which could help the planning and implementation of key preventative measures. Methods Data on all reported HFRS cases at the county level from January 2005 to December 2012 were collected from Chinese Center for Disease Control and Prevention. Geographic Information System-based spatiotemporal analyses including Local Indicators of Spatial Association and Kulldorff's space-time scan statistic were performed to detect local high-risk space-time clusters of HFRS in China. In addition, cases from high-risk and low-risk counties were compared to identify significant demographic differences. Results A total of 100,868 cases were reported during 2005–2012 in mainland China. There were significant variations in the spatiotemporal dynamics of HFRS. HFRS cases occurred most frequently in June, November, and December. There was a significant positive spatial autocorrelation of HFRS incidence during the study periods, with Moran's I values ranging from 0.46 to 0.56 (P<0.05). Several distinct HFRS cluster areas were identified, mainly concentrated in northeastern, central, and eastern of China. Compared with cases from low-risk areas, a higher proportion of cases were younger, non-farmer, and floating residents in high-risk counties. Conclusions This study identified significant space-time clusters of HFRS in China during 2005–2012 indicating that preventative strategies for HFRS should be particularly focused on the northeastern, central, and eastern of China to achieve the most cost-effective outcomes.

The return to work experiences of middle-aged Australian workers diagnosed with colorectal cancer: a matched cohort study

Background Few studies have been undertaken to understand the employment impact in patients with colorectal cancer and none in middle-aged individuals with cancer. This study described transitions in, and key factors influencing, work participation during the 12 months following a diagnosis of colorectal cancer. Methods We enrolled 239 adults during 2010 and 2011who were employed at the time of their colorectal cancer diagnosis and were prospectively followed over 12 months. They were compared to an age- and gender-matched general population group of 717 adults from the Household, Income and Labour Dynamics in Australia (HILDA) Survey. Data were collected using telephone and postal surveys. Primary outcomes included work participation at 12 months, changes in hours worked and time to work re-entry. Multivariable logistic and Cox proportional hazards models were undertaken. Results A significantly higher proportion of participants with colorectal cancer (27%) had stopped working at 12 months than participants from the comparison group (8%) (p < 0.001). Participants with cancer who returned to work took a median of 91 days off work (25–75 percentiles: 14–183 days). For participants with cancer, predictors of not working at 12 months included: being older, lower BMI and lower physical well-being. Factors related to delayed work re-entry included not being university-educated, working for an employer with more than 20 employees in a non-professional or managerial role, longer hospital stay, poorer perceived financial status and having or had chemotherapy. Conclusions In middle-adulthood, those working and diagnosed with colorectal cancer can expect to take around three months off work. Individuals treated with chemotherapy, without a university degree and from large employers could be targeted for specific assistance for a more timely work entry.

Flow evaluation and hemolysis analysis of BVAD centrifugal blood pump by computational fluids dynamics

Computational fluid dynamics (CFD) and particle image velocimetry (PIV) are commonly used techniques to evaluate the flow characteristics in the development stage of blood pumps. CFD technique allows rapid change to pump parameters to optimize the pump performance without having to construct a costly prototype model. These techniques are used in the construction of a bi-ventricular assist device (BVAD) which combines the functions of LVAD and RVAD in a compact unit. The BVAD construction consists of two separate chambers with similar impellers, volutes, inlet and output sections. To achieve the required flow characteristics of an average flow rate of 5 l/min and different pressure heads (left – 100mmHg and right – 20mmHg), the impellers were set at different rotating speeds. From the CFD results, a six-blade impeller design was adopted for the development of the BVAD. It was also observed that the fluid can flow smoothly through the pump with minimum shear stress and area of stagnation which are related to haemolysis and thrombosis. Based on the compatible Reynolds number the flow through the model was calculated for the left and the right pumps. As it was not possible to have both the left and right chambers in the experimental model, the left and right pumps were tested separately.

Stochastic dynamics of interacting haematopoietic stem cell niche lineages

Since we still know very little about stem cells in their natural environment, it is useful to explore their dynamics through modelling and simulation, as well as experimentally. Most models of stem cell systems are based on deterministic differential equations that ignore the natural heterogeneity of stem cell populations. This is not appropriate at the level of individual cells and niches, when randomness is more likely to affect dynamics. In this paper, we introduce a fast stochastic method for simulating a metapopulation of stem cell niche lineages, that is, many sub-populations that together form a heterogeneous metapopulation, over time. By selecting the common limiting timestep, our method ensures that the entire metapopulation is simulated synchronously. This is important, as it allows us to introduce interactions between separate niche lineages, which would otherwise be impossible. We expand our method to enable the coupling of many lineages into niche groups, where differentiated cells are pooled within each niche group. Using this method, we explore the dynamics of the haematopoietic system from a demand control system perspective. We find that coupling together niche lineages allows the organism to regulate blood cell numbers as closely as possible to the homeostatic optimum. Furthermore, coupled lineages respond better than uncoupled ones to random perturbations, here the loss of some myeloid cells. This could imply that it is advantageous for an organism to connect together its niche lineages into groups. Our results suggest that a potential fruitful empirical direction will be to understand how stem cell descendants communicate with the niche and how cancer may arise as a result of a failure of such communication.

Fractal and complex network analyses of protein molecular dynamics

Based on protein molecular dynamics, we investigate the fractal properties of energy, pressure and volume time series using the multifractal detrended fluctuation analysis (MF-DFA) and the topological and fractal properties of their converted horizontal visibility graphs (HVGs). The energy parameters of protein dynamics we considered are bonded potential, angle potential, dihedral potential, improper potential, kinetic energy, Van der Waals potential, electrostatic potential, total energy and potential energy. The shape of the h(q)h(q) curves from MF-DFA indicates that these time series are multifractal. The numerical values of the exponent h(2)h(2) of MF-DFA show that the series of total energy and potential energy are non-stationary and anti-persistent; the other time series are stationary and persistent apart from series of pressure (with H≈0.5H≈0.5 indicating the absence of long-range correlation). The degree distributions of their converted HVGs show that these networks are exponential. The results of fractal analysis show that fractality exists in these converted HVGs. For each energy, pressure or volume parameter, it is found that the values of h(2)h(2) of MF-DFA on the time series, exponent λλ of the exponential degree distribution and fractal dimension dBdB of their converted HVGs do not change much for different proteins (indicating some universality). We also found that after taking average over all proteins, there is a linear relationship between 〈h(2)〉〈h(2)〉 (from MF-DFA on time series) and 〈dB〉〈dB〉 of the converted HVGs for different energy, pressure and volume.

Hot spot detection and spatio-temporal dynamics of dengue in Queensland, Australia

Dengue has been a major public health concern in Australia since it re-emerged in Queensland in 1992-1993. This study explored spatio-temporal distribution and clustering of locally-acquired dengue cases in Queensland State, Australia and identified target areas for effective interventions. A computerised locally-acquired dengue case dataset was collected from Queensland Health for Queensland from 1993 to 2012. Descriptive spatial and temporal analyses were conducted using geographic information system tools and geostatistical techniques. Dengue hot spots were detected using SatScan method. Descriptive spatial analysis showed that a total of 2,398 locally-acquired dengue cases were recorded in central and northern regions of tropical Queensland. A seasonal pattern was observed with most of the cases occurring in autumn. Spatial and temporal variation of dengue cases was observed in the geographic areas affected by dengue over time. Tropical areas are potential high-risk areas for mosquito-borne diseases such as dengue. This study demonstrated that the locally-acquired dengue cases have exhibited a spatial and temporal variation over the past twenty years in tropical Queensland, Australia. There is a clear evidence for the existence of statistically significant clusters of dengue and these clusters varied over time. These findings enabled us to detect and target dengue clusters suggesting that the use of geospatial information can assist the health authority in planning dengue control activities and it would allow for better design and implementation of dengue management programs.

Linear and weakly nonlinear stability analyses of cooperative car-following models

Stability analyses have been widely used to better understand the mechanism of traffic jam formation. In this paper, we consider the impact of cooperative systems (a.k.a. connected vehicles) on traffic dynamics and, more precisely, on flow stability. Cooperative systems are emerging technologies enabling communication between vehicles and/or with the infrastructure. In a distributed communication framework, equipped vehicles are able to send and receive information to/from other equipped vehicles. Here, the effects of cooperative traffic are modeled through a general bilateral multianticipative car-following law that improves cooperative drivers' perception of their surrounding traffic conditions within a given communication range. Linear stability analyses are performed for a broad class of car-following models. They point out different stability conditions in both multianticipative and nonmultianticipative situations. To better understand what happens in unstable conditions, information on the shock wave structure is studied in the weakly nonlinear regime by the mean of the reductive perturbation method. The shock wave equation is obtained for generic car-following models by deriving the Korteweg de Vries equations. We then derive traffic-state-dependent conditions for the sign of the solitary wave (soliton) amplitude. This analytical result is verified through simulations. Simulation results confirm the validity of the speed estimate. The variation of the soliton amplitude as a function of the communication range is provided. The performed linear and weakly nonlinear analyses help justify the potential benefits of vehicle-integrated communication systems and provide new insights supporting the future implementation of cooperative systems.

General practitioners learning qualitative research: A case study of postgraduate education

Background Qualitative research is increasingly being recognised as a vital aspect of primary healthcare research. Teaching and learning how to conduct qualitative research is especially important for general practitioners and other clinicians in the professional educational setting. This article examines a case study of postgraduate professional education in qualitative research for clinicians, for the purpose of enabling a robust discussion around teaching and learning in medicine and the health sciences. Method A series of three workshops was delivered for primary healthcare academics. The workshops were evaluated using a quantitative survey and qualitative free-text responses to enable descriptive analyses. Results Participants found qualitative philosophy and theory the most difficult areas to engage with, and learning qualitative coding and analysis was considered the easiest to learn. Discussion Key elements for successful teaching were identified, including the use of adult learning principles, the value of an experienced facilitator and an awareness of the impact of clinical subcultures on learning.

Voice, deliberation, resistance and persuasion through networked journalism

The pervasive use of the World Wide Web by the general population has created a cultural shift in “our living world”. It has enabled more people to share more information about more events and issues in the world than was possible before its general use. As a consequence, it has transformed traditional news media’s approach to almost every aspect of journalism, with many organisations restructuring their philosophy and practice to include a variety of participatory spaces/forums where people are free to engage in deliberative dialogue about matters of public importance. Moreover, while news media were the traditional gatekeepers of information, today many organisations allow, to different degrees, the general public and other independent journalism entities to participate in the news production process, which may include agenda setting and content production. This paper draws from an international collective case study that showcases various approaches to networked online news journalism. It examines the ways in which different traditional news media models use digital tools and technologies for participatory communication of information about matters of public interest. The research finds differences between the ways in which public service, commercial and independent news media give voice to the public and ultimately their approach to journalism’s role as the Fourth Estate––one of the key institutions of democracy. The work is framed by the notion that journalism in democratic societies has a key role in ensuring citizens are informed and engaged with public affairs. An examination of four media models, the British Broadcasting Corporation (BBC), the Guardian, News Limited and OhmyNews, showcases the various approaches to networked online news journalism and how each provides different avenues for citizen empowerment. The cases are described and analysed in the context of their own social, political and economic setting. Semi-structured in-depth interviews with key senior journalists and editors provide specific information on comparisons between the distinctive practices of their own organisation. In particular these show how the ideal of democracy can be used as a tool of persuasion as much as a method of deliberation.

Repositioning the innovation rationale for public service media

The values that gave rise to the ethos of public service broadcasting (PSB) almost a century ago, and which have provided the rationale for PSBs around the world across that time, are under question. This article argues that the process of reinvention of PSBs is enhanced through repositioning the innovation rationale for public service media (PSM). It is organized around a differentiation which is part of the standard repertoire of innovation studies – that between product, process and organizational innovation – as they are being practised by the two Australian PSBs, the Australian Broadcasting Corporation (ABC) and the Special Broadcasting Service (SBS). The article then considers the general problematics of innovation for PSBs through an analysis of the operations of the public value test in the context of European PSM, and its, to this stage, non-application in Australia. The innovation rationale is argued to be a distinctive via media between complementary and comprehensive roles for PSM, which in turn suggests an international, policy-relevant research agenda focusing on international circumstances in which the public broadcaster is not market dominant.

Self-organized criticality in dynamics without branching

We demonstrate the phenomenon of self-organized criticality (SOC) in a simple random walk model described by a random walk of a myopic ant, i.e., a walker who can see only nearest neighbors. The ant acts on the underlying lattice aiming at uniform digging, i.e., reduction of the height profile of the surface but is unaffected by the underlying lattice. In one, two, and three dimensions we have explored this model and have obtained power laws in the time intervals between consecutive events of "digging." Being a simple random walk, the power laws in space translate to power laws in time. We also study the finite size scaling of asymptotic scale invariant process as well as dynamic scaling in this system. This model differs qualitatively from the cascade models of SOC.

Shock propagation in gas dynamics: explicit form of higher order compatibility conditions

With the use of tensor analysis and the method of singular surfaces, an infinite system of equations can be derived to study the propagation of curved shocks of arbitrary strength in gas dynamics. The first three of these have been explicitly given here. This system is further reduced to one involving scalars only. The choice of dependent variables in the infinite system is quite important, it leads to coefficients free from singularities for all values of the shock strength.

Experiments on a plume with off-source heating: Implications for cloud fluid dynamics

We report here on a series of laboratory experiments on plumes, undertaken with the object of simulating the effect of the heat release that occurs in clouds on condensation of water vapor. The experimental technique used for this purpose relies on ohmic heating generated in an electrically conducting plume fluid subjected to a suitable alternating voltage across specified axial stations in the plume flow [Bhat et al., 1989]. The present series of experiments achieves a value of the Richardson number that is toward the lower end of the range that characteristics cumulus clouds. It is found that the buoyancy enhancement due to heating disrupts the eddy structures in the flow and reduces the dilution owing to entrainment of ambient fluid that would otherwise have occurred in the central region of the plume. Heating also reduces the spread rate of the plume, but as it accelerates the flow as well, the overall specific mass flux in the plume does not show a very significant change at the heat input employed in the experiment. However, there is some indication that the entrainment rate (proportional to the streamwise derivative of the mass flux) is slightly higher immediately after heat injection and slightly lower farther downstream. The measurements support a previous proposal for a cloud scenario [Bhat and Narasimha, 1996] and demonstrate how fresh insights into certain aspects of the fluid dynamics of clouds may be derived from the experimental techniques employed here.

Cell Dynamics of Model Proteins

We design rapidly folding sequences by assigning the strongest couplings to the contacts present in a target native state in a two dimensional model of heteropolymers. The pathways to folding and their dependence on the temperature are illustrated via a mapping of the dynamics into motion within the space of the maximally compact cells.