Miracle-dz/UniFAR-FTUs huggingface dataset:
Phylodynamic Analysis of the Emergence and Epidemiological Impact of Transmissible Defective Dengue Viruses

Intra-host sequence data from RNA viruses have revealed the ubiquity of defective viruses in natural viral populations, sometimes at surprisingly high frequency. Although defective viruses have long been known to laboratory virologists, their relevance in clinical and epidemiological settings has not been established. The discovery of long-term transmission of a defective lineage of dengue virus type 1 (DENV-1) in Myanmar, first seen in 2001, raised important questions about the emergence of transmissible defective viruses and their role in viral epidemiology. By combining phylogenetic analyses and dynamical modeling, we investigate how evolutionary and ecological processes at the intra-host and inter-host scales shaped the emergence and spread of the defective DENV-1 lineage. We show that this lineage of defective viruses emerged between June 1998 and February 2001, and that the defective virus was transmitted primarily through co-transmission with the functional virus to uninfected individuals. We provide evidence that, surprisingly, this co-transmission route has a higher transmission potential than transmission of functional dengue viruses alone. Consequently, we predict that the defective lineage should increase overall incidence of dengue infection, which could account for the historically high dengue incidence reported in Myanmar in 2001–2002. Our results show the unappreciated potential for defective viruses to impact the epidemiology of human pathogens, possibly by modifying the virulence-transmissibility trade-off, or to emerge as circulating infections in their own right. They also demonstrate that interactions between viral variants, such as complementation, can open new pathways to viral emergence.
Fast Robust Non-Negative Matrix Factorization for Large-Scale Human Action Data Clustering

Human action recognition is important in improving human life in various aspects. However, the outliers and noise in data often bother the clustering tasks. Therefore, there is a great need for the robust data clustering techniques. Nonnegative matrix factorization (NMF) and Nonnegative Matrix Tri-Factorization (NMTF) methods have been widely researched these years and applied to many data clustering applications. With the presence of outliers, most previous NMF/NMTF models fail to achieve the optimal clustering performance. To address this challenge, in this paper, we propose three new NMF and NMTF models which are robust to outliers. Efficient algorithms are derived, which converge much faster than previous NMF methods and as fast as K-means algorithm, and scalable to large-scale data sets. Experimental results on both synthetic and real world data sets show that our methods outperform other NMF and NMTF methods in most cases, and in the meanwhile, take much less computational time.
Matrix elements for a generalized spiked harmonic oscillator

Closed form expressions for the singular-potential integrals 〈m|x−α|n〉 are obtained with respect to the Gol’dman and Krivchenkov eigenfunctions for the singular potential Bx2+A/x2, B>0, A⩾0. The formulas obtained are generalizations of those found earlier by use of the odd solutions of the Schrodinger equation with the harmonic oscillator potential [Aguilera-Navarro et al., J. Math. Phys. 31, 99 (1990)].
Optimal Timing for an Asset Sale in an Incomplete Market

In this paper we investigate the pricing via utility indierence of the right to sell a non-traded asset. Consider an agent with power utility who owns a single unit of an indivisible, non-traded asset, and who wishes to choose the optimum time to sell this asset. Suppose that this right to sell forms just part of the wealth of the agent, and that other wealth can be invested in a complete frictionless market. We express the problem as a mixed stochastic control/optimal stopping problem. We analyse the problem of determining the optimal behaviour of the agent, including the optimal criteria for the timing of the sale. It turns out that the
Compensating for Missing Data from Longitudinal Studies Using WinBUGS

Missing data is a common problem in survey based research. There are many packages that compensate for missing data but few can easily compensate for missing longitudinal data. WinBUGS compensates for missing data using multiple imputation, and is able to incorporate longitudinal structure using random effects. We demonstrate the superiority of longitudinal imputation over cross-sectional imputation using WinBUGS. We use example data from the Australian Longitudinal Study on Women's Health. We give a SAS macro that uses WinBUGS to analyze longitudinal models with missing covariate date, and demonstrate its use in a longitudinal study of terminal cancer patients and their carers.
Benchmarking the generalization capabilities of a compiling genetic programming system using sparse data sets

Compiling Genetic Programming Systems ('CPGS') are advanced evolutionary algorithms that directly evolve RISC machine code. In this paper we compare the ability of CGPS to generalize with that of other machine learning ('ML') paradigms. This study presents our results on three classification problems. Our study involved 720 complete CGPS runs of population 3000 each, over 500 billion fitness evaluations and 480 neural network runs as benchmarks. Our results were as follows: 1. When CGPS was trained on data sets that were not too sparse, CGPS performed very well, equaling the generalization capability of other ML systems quickly and consistently. 2. When CGPS was trained on very sparse data sets, CGPS produced individuals that generalized almost as well other ML systems trained on much larger data sets. 3. As between CGPS and multilayer feedforward neural networks trained on the same sparse data sets, CGPS generalized as well (and often better) than the neural network.
The Interaction of Structures and Voter Behavior

Does institutional performance aVect people’s sense of whether their political system is legitimate? Does the economy inXuence voter support for incumbent governments? Do citizens’ policy preferences shape their vote choice? Do domestic institutions aVect whether citizens are willing to transfer authority to supranational and international institutions? These are all questions social scientists have asked for some time. As it turns out, more often than not the answer is a resounding ‘‘it depends. ’’ SpeciWcally, political scientists have come to realize that the answers to these questions depend on understanding the interaction of countries’ macrocharacteristics and individual diVerences among citizens. Relying on so-called multi-level models, which combine information about individuals and the contexts to which they are exposed, scholars of behavioral politics have started to comprehend more systematically than ever before the conditions under which the relations mentioned above exist or are strengthened and weakened (Kedar and Shively 2005). As I describe below, such models are a growth industry in the comparative study of behavioral politics because of advances in scholarly understandings of institutions and context as well as signiWcant advances in statistical
A Global Analysis of the Relationship between Farmed Seaweed Production and Herbivorous Fish Catch

Globally, farmed seaweed production is expanding rapidly in shallow marine habitats. While seaweed farming provides vital income to millions of artisanal farmers, it can negatively impact shallow coral reef and seagrass habitats. However, seaweed farming may also potentially provide food subsidies for herbivorous reef fish such as the Siganidae, a valuable target family, resulting in increased catch. Comparisons of reef fish landings across the central Philippines revealed that the catch of siganids was positively correlated to farmed seaweed production whilst negatively correlated to total reef fish catch over the same period of time. We tested the generality of this pattern by analysing seaweed production, siganid catch, and reef fish catch for six major seaweed-producing countries in the tropics. We hypothesized that increased seaweed production would correspond with increased catch of siganids but not other reef fish species. Analysis of the global data showed a positive correlation between farmed seaweeds and siganids in Southeast Asia (Indonesia, Malaysia, and the Philippines) but not Africa (Tanzania and Zanzibar), or the Western Pacific (Fiji). In Southeast Asia, siganid catch increased disproportionately faster with seaweed production than did reef fish catch. Low continuity, sporadic production and smaller volumes of seaweed farming may explain the differences.
INVITED REVIEW: Using genome scans of DNA polymorphism to infer adaptive population divergence

Elucidating the genetic basis of adaptive population divergence is a goal of central importance in evolutionary biology. In principle, it should be possible to identify chromosomal regions involved in adaptive divergence by screening genome‐wide patterns of DNA polymorphism to detect the locus‐specific signature of positive directional selection. In the case of spatially separated populations that inhabit different environments or sympatric populations that exploit different ecological niches, it is possible to identify loci that underlie divergently selected traits by comparing relative levels of differentiation among large numbers of unlinked markers. In this review I first address the question of whether diversifying selection on polygenic traits can be expected to produce predictable patterns of allelic variation at the underlying quantitative trait loci (QTL), and whether the locus‐specific effects of selection can be reliably detected against the genome‐wide backdrop of stochastic variability. I then review different approaches that have been developed to identify loci involved in adaptive population divergence and I discuss the relative merits of model‐based approaches that rely on assumptions about population structure vs. model‐free approaches that are based on empirical distributions of summary statistics. Finally, I consider the evolutionary and functional insights that might be gained by conducting genome scans for loci involved in adaptive population divergence.
The Broadband Spectrum and Infrared Variability of the Magnetar AXP 1E 1048.1–5937

We present photometry of the anomalous X-ray pulsar (AXP) 1E 1048.1-5937 in the infrared and optical, taken at Magellan and the VLT. The object is detected in the I, J, and Ks bands under excellent conditions. We find that the source has varied greatly in its infrared brightness and present these new magnitudes. No correlation is found between the infrared flux and spin-down rate, but the infrared flux and X-ray flux may be anticorrelated. Assuming nominal reddening values, the resultant spectral energy distribution (SED) is found to be inconsistent with the only other AXP SED available (for 4U 0142+61). We consider the effect of the uncertainty in the reddening to the source on its SED. We find that although both the X-ray and infrared fluxes have varied greatly for this source, the most recent flux ratio is remarkably consistent with what is found for other AXPs. Finally, we discuss the implications of our findings in the context of the magnetar model.
Preferences of Knowledge Users for Two Formats of Summarizing Results from Systematic Reviews: Infographics and Critical Appraisals

Objectives To examine and compare preferences of knowledge users for two different formats of summarizing results from systematic reviews: infographics and critical appraisals. Design Cross-sectional. Setting Annual members’ meeting of a Network of Centres of Excellence in Knowledge Mobilization called TREKK (Translating Emergency Knowledge for Kids). TREKK is a national network of researchers, clinicians, health consumers, and relevant organizations with the goal of mobilizing knowledge to improve emergency care for children. Participants Members of the TREKK Network attending the annual meeting in October 2013. Outcome Measures Overall preference for infographic vs. critical appraisal format. Members’ rating of each format on a 10-point Likert scale for clarity, comprehensibility, and aesthetic appeal. Members’ impressions of the appropriateness of the two formats for their professional role and for other audiences. Results Among 64 attendees, 58 members provided feedback (91%). Overall, their preferred format was divided with 24/47 (51%) preferring the infographic to the critical appraisal. Preference varied by professional role, with 15/22 (68%) of physicians preferring the critical appraisal and 8/12 (67%) of nurses preferring the infographic. The critical appraisal was rated higher for clarity (mean 7.8 vs. 7.0; p = 0.03), while the infographic was rated higher for aesthetic appeal (mean 7.2 vs. 5.0; p<0.001). There was no difference between formats for comprehensibility (mean 7.6 critical appraisal vs. 7.1 infographic; p = 0.09). Respondents indicated the infographic would be most useful for patients and their caregivers, while the critical appraisal would be most useful for their professional roles. Conclusions Infographics are considered more aesthetically appealing for summarizing evidence; however, critical appraisal formats are considered clearer and more comprehensible. Our findings show differences in terms of audience-specific preferences for presentation of research results. This study supports other research indicating that tools for knowledge dissemination and translation need to be targeted to specific end users’ preferences and needs.
Maintaining redundancy in the coordination of medical emergencies

This paper reports from a study of Norwegian medical emergency call (AMK) centres, in which advanced radio and telephone communication technologies are handled by a team of nurses and ambulance personnel to coordinate medical emergency resources (ambulances, doctors, helicopters, and so on). The AMK centres have made use of a range of technologies since they were established 15-20 years ago. During the last 5 years, several of the centres have implemented an information system, AMIS to integrate several functions that before were handled by using separate specialised systems. By observation in seven medical emergency call centres and a survey covering 38 of 43 such centres in Norway in the period 1996-2002, this study focuses on collaboration and use of communication technologies in a teamwork setting. It is found that important aspects of the AMK centre teamwork include redundancy of communication, competence and technologies, as well as a well-developed overall attention from the operators. These aspects support a transparent social integration of technologies in use. The use of integrated systems, such as the AMIS, may challenge this transparency, by which one operator may follow the other operator's actions. It is concluded that serious care must be taken to introduce larger information systems, so that basic principles, which have emerged during the teamwork practice to secure high service reliability, are maintained.
Analysis of a fluid approximation to flow control dynamics

The authors consider a flow control mechanism that dynamically regulates the rate of data flow into a network based on feedback information about the network state. Such mechanisms have been introduced in a variety of networks, and have been advocated for future high-speed networks. The authors first model the flow control mechanism by a discrete-space stochastic process and define appropriate performance measures for transient and steady-state regimes. However, the model does not appear to be analytically tractable, and the authors study it through simulation. They then simplify it to a continuous-space deterministic (or fluid) model for which closed-form solutions can be derived easily. It is found that the analytical results for the fluid model agree well with the simulation results obtained using the discrete-space model. Both models explicitly consider delay of the feedback information, thus making them relevant for high-speed networks. <<ETX>>
Is the weighted z‐test the best method for combining probabilities from independent tests?

Through simulation, Whitlock showed that when all the alternatives have the same effect size, the weighted z‐test is superior to both unweighted z‐test and Fisher’s method when combining P‐values from independent studies. In this paper, we show that under the same situation, the generalized Fisher method due to Lancaster outperforms the weighted z‐test.
Preoperative CYFRA 21-1 and CEA as Prognostic Factors in Patients with Stage I Non-Small Cell Lung Cancer

Objective: To validate the prognostic value of preoperative levels of CYFRA 21-1, CEA and the corresponding tumor marker index (TMI) in patients with stage I non-small cell lung cancer (NSCLC). Methods: Two hundred forty stage I NSCLC patients (80 in pT1 and 160 in pT2; 100 squamous cell carcinomas, 91 adenocarcinomas, 32 large-cell carcinomas, 17 with other histologies; 171 males and 69 females) who had complete resection (R0) between 1986 and 2004 were included in the analysis. CYFRA 21-1 and CEA were measured using the Elecsys system (Roche) and AxSym-System (Abbott), respectively. Univariate analysis was performed using the Kaplan-Meier method to identify potential associations between survival and age, gender, CYFRA 21-1, CEA and TMI. Results: Overall 3- and 5-year survival rates were 74 and 64%, respectively. Male gender (p = 0.0009) and age >70 years (p = 0.0041) were associated with a worse prognosis; there were no differences between pT1 and pT2 nor between histological subtypes. Three-year survival was 72% for CYFRA 21-1 levels >3.3 ng/ml versus 75% for levels ≤3.3 ng/ml, 71% for CEA > 6.7 ng/ml versus 75% for CEA ≤6.7 ng/ml (both p values >0.05). Corresponding 5-year survival rates were near 64% both for patients with CYFRA 21-1 values above and below the cutoff (3.3 ng/ml), and 49 and 66% for patients with values above and below the CEA cutoff (6.7 ng/ml), respectively (both p values >0.05). Overall survival did not vary in the different TMI risk groups (p = 0.73). Conclusions: In this cohort of early-stage NSCLC patients, male gender and age >70 years were associated with a worse outcome, but elevated levels of CEA and CYFRA 21-1, and TMI risk were not.
No-excuses for character: A critique of character education in no-excuses charter schools

The ‘no-excuses’ model of education has become one of the most prominent educational alternatives for urban youth. Recently, notable no-excuses charter schools have begun a concerted effort to develop students’ character strengths, striving to increase their chances of future success. In this article, we situate the no-excuses approach in the context of two prototypical positions in the history of character education: the ‘Traditional’ approach, stressing habit formation and the inculcation of virtuous character traits, and the ‘Progressive’ approach, dedicated to autonomous reasoning in determining moral codes. We identify two central limitations of the no-excuses approach. First, it combines incompatible components from both positions: the Traditional emphasis on a meticulous management of student conduct, together with the Progressive aspiration to cultivate autonomous decision-making. Second, while both Traditionalists and Progressives strive to develop character in light of moral values or principles, the no-excuses model is characterized by an instrumentalist conceptualization of character strengths as means towards achieving the goal of college completion. Consequently, this approach compromises the two central mechanisms that support the internalization of character strengths – practice in autonomous decision-making, and habituation in the service of principles. These shortcomings are further accentuated by the vast divergences between the no-excuses setting and future contexts in which character strengths are to be applied.
The Aesthetics of Heat: Guiding Awareness with Thermal Stimuli

In this paper we discuss the design process and results from a design exploration on the use of thermal stimuli in body awareness exercises. A user-study was performed on an interactive prototype in the form of an interactive heat mat. The paper brings forth an alternative understanding of heat as a design material that extends the common understanding of thermal stimuli in HCI as a communication modality to instead bring the aesthetic and experiential properties to the fore. Findings account for felt body experiences of thermal stimuli and a number of design qualities related to heat as a design material are formulated, pointing to experiential qualities concerning the felt body, subjectivity and subtleness as well as material qualities concerning materiality, inertia and heat transfer.
Predicting loyalty in clubs through motivation, perceived value, satisfaction, and place attachment

Club members are the lifeblood of the private club business, and yet member research is lacking in literature because of the private nature of the business and lack of recognition of studying members’ behaviors in clubs. The research investigated the relationship between motivation of joining factors of members in clubs, perceived value, satisfaction, place attachment of members to the club, and member loyalty. The study hypothesized that motivation of joining factors positively influences members' perceived value in a club. The perceived value of the club as described by members positively influences satisfaction. Satisfaction in the club positively influences place attachment of members to the club. Finally, members' place attachment positively influences member loyalty. The study produces a model that predicts 64% of member loyalty. It is critical for clubs to be sustainable by recruiting and retaining club members. By identifying the relationships among members' motivation of joining factors, perceived value, satisfaction, place attachment, and member loyalty to the club, the study will help the club business to understand members and predict their loyalty. A typical club replaces 5-10% of its members each year, and thus recruiting new members is important for clubs to be sustainable. The study identified a second order construct for motivation and satisfaction, while perceived value, place attachment, and loyalty used existing constructs modified for the club business. The sample for the research was members who belong to CMAA managed clubs in the United States. Through a collaboration with club research companies, a web-based survey using Qualtrics was conducted. Data collection occurred over a two week period in September of 2015. This study included over 900 valid responses from nine clubs in
Hierarchical Cooperative Control for Multiagent Systems With Switching Directed Topologies

The hierarchical cooperative control problem is concerned for a two-layer networked multiagent system under switching directed topologies. The group cooperative objective is to achieve finite-time formation control for the upper layer of leaders and containment control for the lower layer of followers. Two kinds of cooperative strategies, including centralized-distributed control and distributed-distributed control, are proposed for two types of switching laws: 1) random switching law with the dwell time and 2) Markov switching law with stationary distribution. Utilizing the state transition matrix methods and matrix measure techniques, some sufficient conditions are derived for asymptotical containment control and exponential almost sure containment control, respectively. Finally, some numerical examples are provided to demonstrate the effectiveness of the proposed control schemes.