Miracle-dz/UniFAR-FTUs huggingface dataset:
Hybrid systems and biology: continuous and discrete modeling for systems biology

Hybrid Systems are dynamical systems presenting both discrete and continuous evolution. Hybrid Automata are a formal model for hybrid systems, originally proposed to study embedded systems, where a discrete control acts on a continuously changing environment. The presence of both discrete and continuous dynamics makes this formalism appealing also for modeling biological systems. However, the situation in this case is subtler, as there is no natural separation into discrete and continuous components. No surprise, then, that hybrid automata have been used in systems biology in rather different ways. Some approaches, like the description of biological switches, concentrate on the use of model-checking routines. Other applications, like the switching between continuous and discrete/stochastic simulation, focus on the exploitation of the interplay between discreteness and continuity in order to reduce the computational burden of numerical simulation, yet maintaining an acceptable precision. We will survey the use of hybrid automata in systems biology, through a series of cases studies that we deem interesting and paradigmatic.
2411: A pilot study: Using computational fluid dynamics to model physiologic airflow through an ovine tissue engineered tracheal graft

those patients with protective immunity to live vaccines prior to cancer therapy will lose it at the end of therapy. DISCUSSION/SIGNIFICANCE OF IMPACT: Loss of protective immunity to live vaccines has been reported in patients with hematologic malignancies after cancer therapy. This lack of protective immunity, which puts patients at higher risk of acquiring vaccine preventable diseases, has been limited studied in patients with solid tumors. The Center for Diseases Control has been established that it is safe to immunize cancer survivors with live vaccines 3 months post Tx. However, no clear guidelines for revaccination have been provided for this population. Understanding the protective immunity variation against live vaccines in children with solid tumors will allow us to identify the need for revaccination with live vaccines in this vulnerable population.
Clinical Consequences of Posttraumatic Bone Bruise in the Knee

Background Bone bruise is often seen in posttraumatic knees, but the clinical relevance is unclear. Hypothesis The presence of bone bruise is associated with increased pain severity in patients with sustained knee trauma. Study Design Cohort study; Level of evidence, 2. Methods We collected prospective data of 132 patients visiting their general practitioner after sustained knee trauma. Patients with bone bruise underwent a magnetic resonance imaging follow-up study that was discontinued when the bone bruise could no longer be discerned or after 1 year of follow-up. Bone bruise was assessed on magnetic resonance imaging, and pain severity was scored on a numeric rating scale (0-10) at baseline, and at 3, 6, and 12 months after trauma. The presence of bone bruise and pain severity (over time) were compared using linear regression analyses for repeated measurements. Adjustment was made for possible confounders: presence of meniscal tears, cruciate or collateral ligament ruptures, severe effusion, osteoarthritis, obesity, age, gender, work load, and sports load. Results At baseline as well as during follow-up, bone bruise was associated with a slightly higher pain score. The differences, however, were very small (adjusted difference in pain severity 0.34 or less) and not statistically significant nor clinically relevant. Conclusion There is no statistically significant relationship, nor a clinically relevant relationship, between the presence of bone bruise and pain severity in patients with sustained knee injury in general practice.
Widely Separated Frequencies in Coupled Oscillators with Energy-preserving Quadratic Nonlinearity

In this paper we present an analysis of a system of coupled-oscillators. We make two assumptions for our system. The first assumption is that the frequencies of the characteristic oscillations are widely separated, and the second is that the nonlinear part of the vector field preserves the distance to the origin. Using the first assumption, we prove that the reduced normal form of our system, exhibits an invariant manifold which, exists for all values of the parameters and cannot be perturbed away by including higher order terms in the normal form. Using the second assumption, we view the normal form as an energy-preserving three-dimensional system which is linearly perturbed. Restricting our selves to a small perturbation, the flow of the energy-preserving system is used to study the flow in general. We present a complete study of the flow of energy-preserving system and the bifurcations in it. Using these results, we provide the condition for having a Hopf bifurcation of one of the two equilibria. We also numerically follow the periodic solution created via the Hopf bifurcation and find a sequence of period-doubling and fold bifurcations, and also a torus (or Naimark-Sacker) bifurcation.
An Eyetracking Study on Online Hotel Decision Making: The Effects of Images and umber of Options

Millions of travelers visit various online travel sites looking for inexpensive products and convenient and enjoyable shopping experience. Especially, online hotel booking contributes to a large proportion of hotel sales (Carroll and Siguaw 2003). However, proving a satisfactory online shopping experience within limited space on web pages demands a thorough understanding of travelers’ online decision making process in order for designers to customize and personalize websites (Argo, White, and Dahl 2006). Currently the most dominant travel websites (e.g. Expedia, Travelocity, Priceline, Orbitz, and Hotels.com) display a list of hotels sorted by recommendation, price, brand or location. Each hotel listing has one or more pictures, a brief introduction, hotel rates, and location information. How the consumers make decisions in this interactive and rich environment is largely unknown. In terms of the process of decision making, psychologists have proposed the additive utility model which asserts that the decision makers use utility function to evaluate different alternatives and pick an option (Tversky 1967). However, when facing many choices, decision makers tend to use frugal and convenient heuristics to save evaluation time and reduce cognitive load (.Gigerenzer and Todd 1999). For example, a study showed that decision makers followed a pairwise comparison when making purchases of automobiles (Russo and Rosen 1975). Using eye tracking methodology, Russo and Leclerc (1994) also demonstrated three stages of a nondurable purchase decision: orientation, evaluation, and verification. In tourism research area, research shows many attributes of a hotel influence travelers’ choices, including rate, service quality, location, and value (Wong and Chi-Yung 2002). Past studies have revealed that the gender of the subjects, the complexity of web pages, and the viewing sequence will determine the cognitive process on web pages (Pan et al. 2004). Furthermore, web site characteristics such as color and image may affect social presence perception or information recall (Cyr et al. 2009; Zhang et al. 2003). The purpose of this study is to use a mixed methodology (eyetracking, verbal protocol, and surveys) to examine the effects of images and the sizes of choice sets on the process of online hotel decision making.
MULTI-USER DETECTION IN DS-CDMA SYSTEMS USING A GENETIC ALGORITHM WITH REDUNDANCY SAVING STRATEGY

This study demonstrates that the configuration of a fixed generation number in the conventional genetic algorithm–based multi-user detector (GA-MUD) induces considerable redundant iterations and thus results in a computational inefficiency. To overcome this difficulty, this research suggests a redundancy saving strategy for the GAMUD (RSGA-MUD) based on the cost statistics of the GA solutions in a synchronous direct-sequence code division multiple access (DS-CDMA) system. Computer simulations for the synchronous DS-CDMA systems in perfect power control, near-far, and increased population scenarios are conducted to examine the performance of the proposed RSGA-MUD. Experimental results show that the RSGA-MUD can significantly reduce the computational burden of the conventional GA-MUD with only a slight performance degradation in perfect-power control and near-far scenarios. Furthermore, in the increased population scenario, the bit error rate (BER) performance is comparable to that of the optimum multi-user detector (OMD) with a computational complexity less than that of the conventional GA-MUD. Moreover, this study provides a novel mechanism that allows for a trade-off between computational reduction and acceptable degradation of GA-MUD performance by simply adjusting the cost threshold. Notably, the proposed redundancy saving strategy can be applied directly to various GA-based MUDs in order to increase their computational efficiency since it does not alter the essential structure of GA.
Voltage control solutions to face the CPL instability in MVDC shipboard power systems

Voltage control represents one of the main challenges in the development of Medium Voltage DC power systems on ships. The presence of non-linear loads (high-bandwidth controlled converters, CPLs) may cause dangerous voltage oscillations or even instability in presence of small or large disturbances (e.g. connection/disconnection of loads). To face this important issue, the voltage actuator approach appears as an effective solution by using DC/DC converters as sources of stabilizing power. Such controlling action is obtained by imposing control signals determined by different techniques. In this regard, the main goal of this paper is to analyze the action of three control techniques (State Feedback, Active Damping and Linearization via State Feedback) in order to suggest the implementation considering the system criticality (e.g. the CPL power or the filter damping factor). Numerical simulations are useful to compare the proposed methods by observing the control action in presence of growing disturbances.
Virus-induced immunosuppression: immune system-mediated destruction of virus-infected dendritic cells results in generalized immune suppression

Despite the clinical importance of virus-induced immunosuppression, how virus infection may lead to a generalized suppression of the host immune response is poorly understood. To elucidate the principles involved, we analyzed the mechanism by which a lymphocytic choriomeningitis virus (LCMV) variant produces a generalized immune suppression in its natural host, the mouse. Whereas adult mice inoculated intravenously with LCMV Armstrong rapidly clear the infection and remain immunocompetent, inoculation with the Armstrong-derived LCMV variant clone 13, which differs from its parent virus at only two amino acid positions, by contrast results in persistent infection and a generalized deficit in responsiveness to subsequent immune challenge. Here we show that the immune suppression induced by LCMV clone 13 is associated with a CD8-dependent loss of interdigitating dendritic cells from periarteriolar lymphoid sheaths in the spleen and, functionally, with a deficit in the ability of splenocytes from infected mice to stimulate the proliferation of naive T cells in a primary mixed lymphocyte reaction. Dendritic cells are not depleted in immunocompetent Armstrong-infected mice. LCMV Armstrong and clone 13 exhibit differences in their tropism within the spleen, with clone 13 causing a higher level of infection of antigen-presenting cells in the white pulp, including periarterial interdigitating dendritic cells, than Armstrong, thereby rendering these cells targets for destruction by the antiviral CD8+ cytotoxic T-lymphocyte response which is induced at early times following infection with either virus. Our findings illustrate the key role that virus tropism may play in determining pathogenicity and, further, document a mechanism for virus-induced immunosuppression which may contribute to the clinically important immune suppression associated with many virus infections, including human immunodeficiency virus type 1.
Explaining trends in Scottish coronary heart disease mortality between 2000 and 2010 using IMPACTSEC model: retrospective analysis using routine data

Objective To quantify the contributions of prevention and treatment to the trends in mortality due to coronary heart disease in Scotland. Design Retrospective analysis using IMPACTSEC, a previously validated policy model, to apportion the recent decline in coronary heart disease mortality to changes in major cardiovascular risk factors and to increases in more than 40 treatments in nine non-overlapping groups of patients. Setting Scotland. Participants All adults aged 25 years or over, stratified by sex, age group, and fifths of Scottish Index of Multiple Deprivation. Main outcome measure Deaths prevented or postponed. Results 5770 fewer deaths from coronary heart disease occurred in 2010 than would be expected if the 2000 mortality rates had persisted (8042 rather than 13 813). This reflected a 43% fall in coronary heart disease mortality rates (from 262 to 148 deaths per 100 000). Improved treatments accounted for approximately 43% (95% confidence interval 33% to 61%) of the fall in mortality, and this benefit was evenly distributed across deprivation fifths. Notable treatment contributions came from primary prevention for hypercholesterolaemia (13%), secondary prevention drugs (11%), and chronic angina treatments (7%). Risk factor improvements accounted for approximately 39% (28% to 49%) of the fall in mortality (44% in the most deprived fifth compared with only 36% in the most affluent fifth). Reductions in systolic blood pressure contributed more than one third (37%) of the decline in mortality, with no socioeconomic patterning. Smaller contributions came from falls in total cholesterol (9%), smoking (4%), and inactivity (2%). However, increases in obesity and diabetes offset some of these benefits, potentially increasing mortality by 4% and 8% respectively. Diabetes showed strong socioeconomic patterning (12% increase in the most deprived fifth compared with 5% for the most affluent fifth). Conclusions Increases in medical treatments accounted for almost half of the large recent decline in mortality due to coronary heart disease in Scotland. Furthermore, the Scottish National Health Service seems to have delivered these benefits equitably. However, the substantial contributions from population falls in blood pressure and other risk factors were diminished by adverse trends in obesity and diabetes. Additional population-wide interventions are urgently needed to reduce coronary heart disease mortality and inequalities in future decades.
Participative decision-making and job satisfaction for teachers in the UAE

Purpose – Knowledge of teachers’ participative decision making (PDM) and job satisfaction (JS) is important, as teachers comprise most of a school’s staff. The purpose of this paper is to examine the effect of teacher gender, nationality and school type on teachers’ PDM and JS in Abu Dhabi’s schools and to determine whether there any significant differences in PDM and teachers’ JS among teachers of different genders, school types and nationalities. Design/methodology/approach – A questionnaire was used to collect data for the study by measuring each responding teacher’s involvement in making school decisions in both the instructional and managerial domains and JS. The questionnaire was distributed among teachers in 28 different schools around the Emirate of Abu Dhabi. Findings – The primary results demonstrated that teachers’ PDM differs by teacher gender, nationality and school type, whereas teacher’s JS differs by teacher gender and nationality, with school type having in general no significant effect o.
SDN Based Control Plane Extensions for Mobility Management Improvement in Next Generation ETArch Networks

Mobility support is a requirement in next generation networks. The entity Title Architecture (ETArch) is a clean-slate network architecture that uses a naming and addressing scheme based on the Title and has a natural match with Software Defined Networking (SDN) paradigm. ETArch aims at satisfying applications requirements such as mobility. On a previous work, we demonstrated the use of ETArch in order to keep ongoing sessions during handover with no packet loss. The initial approach however, performed the handover without taking into account QoS guarantees during the selection of new Point of Attachments (PoAs). This work proposes an extension to the legacy ETArch Mobility Manager, called Quality-oriented Mobility Management Approach (QoMMA), to support a quality-oriented handover management. This extension enables a network-initiated mobility control that improves resources allocation and execute a quality-oriented access point selection. The QoMMA also performs a mobility load balancing in order to maximize admissions of mobile sessions in conditions of congestion. The evaluations were carried out on a testbed that considered real events, and provided evidence that the proposal outperforms legacy ETArch mobility control functionalities.
Identification Robust Predictive Ability Testing Most recent version : here

The paper analyzes the predictive accuracy evaluation of models that are strongly identified in some part of the parameter space but non-identified or weakly identified in another part of the parameter space. We show that when comparing the predictive ability of models that might be affected by identification deficiencies, when the parameter estimation error is negligible, the null distribution of out-of-sample predictive ability tests is not well approximated by the standard normal distribution. As a result, employing a standard (strong) identification critical value can lead to misleading inference. We propose methods to make the out-of-sample predictive ability tests robust to identification loss. These methods use a different critical value than the standard one and include: a least-favorable critical value and a data dependent critical value. In settings where the parameter error is non-negligible, the paper shows that the asymptotic distribution of the predictive ability test in West(1996) is standard, even when one allows for the model(s) to be only semi-strongly identified. ∗Department of Economics, University of Warwick, email: a.a. naghi@warwick.ac. uk. I would like to thank Valentina Corradi for her guidance, helpful comments and advice. I also benefited from insightful discussions with Ana Galvao and Jeremy Smith. Feedback and helpful suggestions from Clement De Chaisemartin, Bo Honore, Arthur Lewbel and Giovanni Ricco helped improve the paper. Financial support from the ESRC and RES is gratefully acknowledged.
Effects of tracking technology, latency, and spatial jitter on object movement

We investigate the effects of input device latency and spatial jitter on 2D pointing tasks and 3D object movement tasks. First, we characterize jitter and latency in a 3D tracking device and an optical mouse used as a baseline comparison. We then present an experiment based on ISO 9241-9, which measures performance characteristics of pointing devices. We artificially introduce latency and jitter to the mouse and compared the results to the 3D tracker. Results indicate that latency has a much stronger effect on human performance than low amounts of spatial jitter. In a second study, we use a subset of conditions from the first to test latency and jitter on 3D object movement. The results indicate that large, uncharacterized jitter “spikes” significantly impact 3D performance.
An overlaid Hybrid-Duplex OFDMA system with partial frequency reuse

For the overlaid HDD cellular system, where TDD and FDD coexist in the inner region [1], we suggest a new frame structure adopting partial frequency reuse (PFR). We found that the overlaid HDD system with PFR outperforms other conventional systems by the optimal downlink power allocation. We also found that cooperative transmission with network coding improves the capacity of the cell border in the overlaid HDD. The simulation results are promising in that the performance gain in the overlaid HDD, mostly comes from multi-hop transmission in the uplink direction and from network-coded cooperative communication in the downlink.
Electrophysiological study of Drosophila rhodopsin mutants

Electrophysiological investigations were carried out on several independently isolated mutants of the ninaE gene, which encodes opsin in R1-6 photoreceptors, and a mutant of the ninaD gene, which is probably important in the formation of the rhodopsin chromophore. In these mutants, the rhodopsin content in R1-6 photoreceptors is reduced by 10(2)-10(6)-fold. Light-induced bumps recorded from even the most severely affected mutants are physiologically normal. Moreover, a detailed noise analysis shows that photoreceptor responses of both a ninaE mutant and a ninaD mutant follow the adapting bump model. Since any extensive rhodopsin-rhodopsin interactions are not likely in these mutants, the above results suggest that such interactions are not needed for the generation and adaptation of light-induced bumps. Mutant bumps are strikingly larger in amplitude than wild-type bumps. This difference is observed both in ninaD and ninaE mutants, which suggests that it is due to severe depletion of rhodopsin content, rather than to any specific alterations in the opsin protein. Lowering or buffering the intracellular calcium concentration by EGTA injection mimics the effects of the mutations on the bump amplitude, but, unlike the mutations, it also affects the latency and kinetics of light responses.
An Intrusive Analyzer for Hadoop Systems Based on Wireless Sensor Networks

Owing to the acceleration of IoT- (Internet of Things-) based wireless sensor networks, cloud-computing services using Big Data are rapidly growing. In order to manage and analyze Big Data efficiently, Hadoop frameworks have been used in a variety of fields. Hadoop processes Big Data as record values by using MapReduce programming in a distributed environment. Through MapReduce, data are stored in a Hadoop file system, and that form is not structured but unstructured. For this, it is not easy to grasp the cause, although inaccurate and unreliable data occur in the process of Hadoop-based MapReduce. As a result, Big Data may lead to a fatal flaw in the system, possibly paralyzing services. There are existing tools that monitor Hadoop systems' status. However, the status information is not related to inner structure of Hadoop system so it is not easy to analyze Hadoop systems. In this paper, we propose an intrusive analyzer that detects interesting events to occur in distributed processing systems with Hadoop in wireless sensor networks. This tool guarantees a transparent monitor as using the JDI (Java debug interface).