Miracle-dz/UniFAR-FTUs huggingface dataset:
Delay of Social Search on Small-World Graphs

This article introduces an analytical framework for two small-world network models and studies the delay of targeted social search by considering messages traveling between source and target individuals in these networks. In particular, by considering graphs constructed on different network domains, such as rectangular, circular, and spherical network domains, analytical solutions for the average social search delay and the delay distribution are obtained as functions of source–target separation, distribution of the number of long-range connections and geometrical properties of network domains. Derived analytical formulas are first verified by agent-based simulations and then compared with empirical observations in small-world experiments. These formulas indicate that individuals tend to communicate with one another only through their short-range contacts and the average social search delay rises linearly, when the separation between the source and target is small. As this separation increases long-range connections are more commonly used, and the average social search delay rapidly saturates to a constant value and stays almost the same for all large values of the separation. These results do not require the dimensionality of the social space to be identical to the decay exponent of long-range social connections and are qualitatively consistent with experimental observations made by Travers and Milgram in 1969 as well as by others. Moreover, analytical distributions for the delay of social search predicted by the models introduced in this article are also compared with corresponding empirical distributions, and good statistical matches between them are observed. Other somewhat surprising conclusions of the article are that hubs have limited effect in reducing the delay of social search and variation in node degree distribution adversely affects this delay.
Effect of sympathetic denervation on the rate of protein synthesis in rat skeletal muscle.

Rates of protein synthesis were investigated in skeletal muscles from rats submitted to chemical and surgical sympathectomy. Three models of sympathetic denervation were used: 1) treatment with guanethidine (100 mg.kg(-1). day(-1) sc); 2) lumbar sympathetic denervation (surgical excision of the second and third lumbar ganglia of the sympathetic chain, from which arises the postganglionic fibers to the skeletal muscles of rat hindlimb); and 3) adrenodemedullation. Protein synthesis was estimated in isolated soleus muscle by the rate of incorporation of [(14)C]tyrosine (0.1 mM, 0.05 microCi/ml) into total protein. Soleus isolated after 2 and 4 days of chemical sympathectomy or after 3 days of lumbar denervation showed a 17-20% statistically significant decrease in in vitro rates of protein synthesis. These effects were reverted by addition of 10(-5) M isoproterenol or epinephrine in vitro. Neither clenbuterol nor isoproterenol (10(-7), 10(-6), or 10(-5) M) in vitro affected the rate of protein synthesis in soleus from normal rats. On the other hand, clenbuterol or epinephrine (10(-5) M) increased by 20% the rate of protein synthesis in soleus muscles from adrenodemedullated rats and prevented its decrease in muscles from fasted rats. The data suggest that the sympathetic nervous system stimulates protein synthesis in oxidative muscles, probably through the activation of beta(2)-adrenoceptors, especially in situations of hormonal or nutritional deficiency.
Differential Effects of Domoic Acid and E. coli Lipopolysaccharide on Tumor Necrosis Factor-α, Transforming Growth Factor-β1 and Matrix Metalloproteinase-9 Release by Rat Neonatal Microglia: Evaluation of the Direct Activation Hypothesis

The excitatory amino acid domoic acid is the causative agent of amnesic shellfish poisoning in humans. The in vitro effects of domoic acid on rat neonatal brain microglia were compared with E. coli lipopolysaccharide (LPS), a known activator of microglia mediator release over a 4 to 24 hour observation period. LPS [3 ng/mL] but not domoic acid [1mM] stimulated a statistically significant increase in TNF-α mRNA and protein generation. Furthermore, both LPS and domoic acid did not significantly affect TGF-β1 gene expression and protein release. Finally, an in vitro exposure of microglia to LPS resulted in statistically significant MMP-9 expression and release, thus extending and confirming our previous observations. However, in contrast, no statistically significant increase in MMP-9 expression and release was observed after domoic acid treatment. Taken together our observations do not support the hypothesis that a short term (4 to 24 hours) in vitro exposure to domoic acid, at a concentration toxic to neuronal cells, activates rat neonatal microglia and the concomitant release of the pro-inflammatory mediators tumor necrosis factor-α (TNF-α) and matrix metalloproteinases-9 (MMP-9), as well as the anti-inflammatory cytokine transforming growth factor β1 (TGF-β1).
Dynamics of Apis mellifera Filamentous Virus (AmFV) Infections in Honey Bees and Relationships with Other Parasites

Apis mellifera filamentous virus (AmFV) is a large double stranded DNA virus of honey bees, but its relationship with other parasites and prevalence are poorly known. We analyzed individual honey bees from three colonies at different times post emergence in order to monitor the dynamics of the AmFV gut colonization under natural conditions. Prevalence and loads of microsporidia and trypanosomes were also recorded, as well as five common honey bee RNA viruses. The results show that a high proportion of bees get infected with AmFV during the first week post-emergence (75%) and that AmFV DNA levels remained constant. A similar pattern was observed for microsporidia while trypanosomes seem to require more time to colonize the gut. No significant associations between these three infections were found, but significant positive correlations were observed between AmFV and RNA viruses. In parallel, the prevalence of AmFV in France and Sweden was assessed from pooled honey bee workers. The data indicate that AmFV is almost ubiquitous, and does not seem to follow seasonal patterns, although higher viral loads were significantly detected in spring. A high prevalence of AmFV was also found in winter bees, without obvious impact on overwintering of the colonies.
Active Learning to Understand Infectious Disease Models and Improve Policy Making

Modeling plays a major role in policy making, especially for infectious disease interventions but such models can be complex and computationally intensive. A more systematic exploration is needed to gain a thorough systems understanding. We present an active learning approach based on machine learning techniques as iterative surrogate modeling and model-guided experimentation to systematically analyze both common and edge manifestations of complex model runs. Symbolic regression is used for nonlinear response surface modeling with automatic feature selection. First, we illustrate our approach using an individual-based model for influenza vaccination. After optimizing the parameter space, we observe an inverse relationship between vaccination coverage and cumulative attack rate reinforced by herd immunity. Second, we demonstrate the use of surrogate modeling techniques on input-response data from a deterministic dynamic model, which was designed to explore the cost-effectiveness of varicella-zoster virus vaccination. We use symbolic regression to handle high dimensionality and correlated inputs and to identify the most influential variables. Provided insight is used to focus research, reduce dimensionality and decrease decision uncertainty. We conclude that active learning is needed to fully understand complex systems behavior. Surrogate models can be readily explored at no computational expense, and can also be used as emulator to improve rapid policy making in various settings.
Nuclear congression and membrane fusion: two distinct events in the yeast karyogamy pathway

Karyogamy is the process where haploid nuclei fuse to form a diploid nucleus during yeast mating. We devised a novel genetic screen that identified five new karyogamy (KAR) genes and three new cell fusion (FUS) genes. The kar mutants fell into two classes that represent distinct events in the yeast karyogamy pathway. Class I mutations blocked congression of the nuclei due to cytoplasmic microtubule defects. In Class II mutants, nuclear congression proceeded and the membranes of apposed nuclei were closely aligned but unfused. In vitro, Class II mutant membranes were defective in a homotypic ER/nuclear membrane fusion assay. We propose that Class II mutants define components of a novel membrane fusion complex which functions during vegetative growth and is recruited for karyogamy.
The contribution of mast cells to bacterial and fungal infection immunity

Mast cells are hematopoietic progenitor‐derived, granule‐containing immune cells that are widely distributed in tissues that interact with the external environment, such as the skin and mucosal tissues. It is well‐known that mast cells are significantly involved in IgE‐mediated allergic reactions, but because of their location, it has also been long hypothesized that mast cells can act as sentinel cells that sense pathogens and initiate protective immune responses. Using mast cell or mast cell protease‐deficient murine models, recent studies by our groups and others indicate that mast cells have pleiotropic regulatory roles in immunological responses against pathogens. In this review, we discuss studies that demonstrate that mast cells can either promote host resistance to infections caused by bacteria and fungi or contribute to dysregulated immune responses that can increase host morbidity and mortality. Overall, these studies indicate that mast cells can influence innate immune responses against bacterial and fungal infections via multiple mechanisms. Importantly, the contribution of mast cells to infection outcomes depends in part on the infection model, including the genetic approach used to assess the influence of mast cells on host immunity, hence highlighting the complexity of mast cell biology in the context of innate immune responses.
The expression of SR calcium transport ATPase and the Na(+)/Ca(2+)Exchanger are antithetically regulated during mouse cardiac development and in Hypo/hyperthyroidism.

The mouse has been used extensively for generating transgenic animal models to study cardiovascular disease. Recently, a number of transgenic mouse models have been created to investigate the importance of sarcoplasmic reticulum (SR) Ca(2+)transport proteins in cardiac pathophysiology. However, the expression and regulation of cardiac SR Ca(2+)ATPase and other Ca(2+)transport proteins have not been studied in detail in the mouse. In this study, we used multiplex RNase mapping analysis to determine SERCA2, phospholamban (PLB), and Na(+)/Ca(2+)-exchanger (NCX-1) gene expression throughout mouse heart development and in hypo/hyperthyroid animals. Our results demonstrate that the expression of SERCA2 and PLB mRNA increase eight-fold from fetal to adult stages, indicating that SR function increases with heart development. In contrast, the expression of the Na(+)/Ca(2+)-exchanger gene is two-fold higher in fetal heart compared to adult. Our study also makes the important observation that in hypothyroidic hearts the NCX-1 mRNA and protein levels were upregulated, whereas the SERCA2 mRNA/protein levels were downregulated. In hyperthyroidic hearts, however, an opposite response was identified. These findings are important and point out that the expression of NCX-1 is regulated antithetically to that of SERCA2 during heart development and in response to alterations in thyroid hormone levels.
The Relationship between Displaying and Perceiving Nonverbal Cues of Affect: A Meta-Analysis to Solve an Old Mystery

The authors address the decades-old mystery of the association between individual differences in the expression and perception of nonverbal cues of affect. Prior theories predicted positive, negative, and zero correlations in performance-given empirical results ranging from r = -. 80 to r = +. 64. A meta-analysis of 40 effects showed a positive correlation for nonverbal behaviors elicited as intentional communication displays but zero for spontaneous, naturalistic, or a combination of display types. There was greater variation in the results of studies having round robin designs and analyzed with statistics that do not account for the interdependence of data. The authors discuss implications for theorists to distinguish emotional skills in terms of what people are capable of doing versus what people actually do.
Strong Invariants for the Efficient Construction of Machine-Checked Protocol Security Proofs

We embed an operational semantics for security protocols in the interactive theorem prover Isabelle/HOL and derive two strong protocol-independent invariants. These invariants allow us to reason about the possible origin of messages and justify a local typing assumption for the otherwise untyped protocol variables. The two rules form the core of a theory that is well-suited for interactively constructing natural, human-readable, correctness proofs. Moreover, we develop an algorithm that automatically generates proof scripts based on these invariants. Both interactive and automatic proof construction are faster than competing approaches. Moreover, we have strong correctness guarantees since all proofs, including those deriving the underlying theory from the semantics, are machine checked.
Etiology of Invasive Bacterial Infections in Immunocompetent Children in Korea (2006–2010): a Retrospective Multicenter Study

Background Invasive bacterial infections in apparently immunocompetent children were retrospectively analyzed to figure causative bacterial organisms in Korea. Methods A total of 947 cases from 25 university hospitals were identified from 2006 to 2010 as a continuance of a previous 10-year period study from 1996 to 2005. Results Escherichia coli (41.3%), Streptococcus agalactiae (27.7%), and Staphylococcus aureus (27.1%) were the most common pathogens in infants < 3 months of age. S. agalactiae was the most prevalent cause of meningitis and pneumonia and E. coli was the major cause of bacteremia without localizing signs in this group. In children 3 to 59 months of age, Streptococcus pneumoniae (54.2%), S. aureus (20.5%), and Salmonella spp. (14.4%) were the most common pathogens. S. pneumoniae was the leading cause of pneumonia (86.0%), meningitis (65.0%), and bacteremia without localizing signs (49.0%) in this group. In children ≥ 5 years of age, S. aureus (62.8%) was the predominant pathogen, followed by Salmonella species (12.4%) and S. pneumoniae (11.5%). Salmonella species (43.0%) was the most common cause of bacteremia without localizing signs in this group. The relative proportion of S. aureus increased significantly over the 15-year period (1996–2010) in children ≥ 3 months of age (P < 0.001), while that of Haemophilus influenzae decreased significantly in both < 3 months of age group (P = 0.036) and ≥ 3 months of age groups (P < 0.001). Conclusion S. agalactiae, E. coli, S. pneumoniae, and S. aureus are common etiologic agents of invasive bacterial infections in Korean children.
FRACTURE PROPERTIES AND BRITTLENESSS OF HIGH-STRENGTH CONCRETE

The size effect method for determining material fracture characteristics, as previously proposed by Bazant is applied to typical high-strength concrete. Geometrically similar 3-point bending specimens are tested and the measured peak load values are used to obtain the fracture energy, the fracture toughness, the effective length of the fracture process zone, and the effective critical crack tip opening displacement. The brittleness of the material is shown to be objectively quantified through the size-effect method. Comparing the material fracture properties obtained with those of normal strength concrete shows that an increase of 16 % in compressive srength causes: (1) increase of fracture toughness; (2) decrease of effective fracture process zone length; (3) more than doubling of the brittleness number. The brittleness number, however, is still not high enough to permit the use of linear elastic fracture mechanics. The R-curves are demonstrated to derive according to the size effect law exclusively from the maximum loads of specimens of various sizes and yield remarkably good predictions of the load-deflection curves.
Non-singular solutions to Einstein-Klein-Gordon equations with a phantom scalar field

It is shown that the 4D Einstein-Klein-Gordon equations with a phantom scalar field (a scalar field with a negative sign in front of the kinetic energy term of its Lagrange density) has non-singular, spherically symmetry solutions. These solutions have a combination of features found in other spherically symmetric gravity plus field solutions. A stability analysis on these solutions indicates they are unstable.
Uptake of metal ions from solution by inactivated cells of cyanobacteria

Some species of cyanobacteria have the ability to grow under stress conditions that would kill many other bacteria. Solutions of 0.25 mM Cu were inoculated with the cyanobacteria Synechococcus sp . PCC 7942 and Synechocystis sp. PCC 6803 with the idea that these cyanobacteria may develop certain defense mechanisms allowing their survival in such stressed environments. Transmission electron microscopy showed that Synechocystis sp. g rown in 0.25 mM copper(II) developed a filamentous sheath around the cell wall, which could be responsible for binding copper ions on the cell surface. The presence of copper adsorbed by Synechocystis sp . was corroborated using environmental scanning electron microscopy equipped with an x-ray energy-dispersive spectrometer. Synechococcus has the ability to grow in mass quantity under ideal conditions, providing usable biomass at a minimal effort. Using lyophilized biomass grown under normal conditions, Synechococcus was tested for its potential to bind copper(II), lead(II), and nickel(II) ions from solution. Batch experiments were performed to determine the optimum binding pH, time dependency, and metal binding capacities for copper(II), lead(II), and nickel(II), along with desorption of the metal bound. The biomass studied showed a high affinity for all metal ions as the pH increased from two to six with optimum binding occurring at pH 5. Time dependency studies showed that this cyanobacterium had rapid binding to all three metals. Capacity experiments showed that this cyanobacterium bound 11.3 mg of copper(II) per gram of biomass, 30.4 mg of lead(II) per gram of biomass, and 3.2 mg of nickel(II) per gram of biomass. More than 98% of the copper(II), lead(II) and nickel(II) adsorbed by the biomass was recovered when treated with 0.1M HCl. Cyanobacterial biomass can eventually be used as the source for a novel approach in using biosystems to remediate contaminants from solution. K EYWORDS: Synechococcus , Synechocystis , cyanobacteria, heavy metal binding,
Transition-Based Parsing for Deep Dependency Structures

Derivations under different grammar formalisms allow extraction of various dependency structures. Particularly, bilexical deep dependency structures beyond surface tree representation can be derived from linguistic analysis grounded by CCG, LFG, and HPSG. Traditionally, these dependency structures are obtained as a by-product of grammar-guided parsers. In this article, we study the alternative data-driven, transition-based approach, which has achieved great success for tree parsing, to build general dependency graphs. We integrate existing tree parsing techniques and present two new transition systems that can generate arbitrary directed graphs in an incremental manner. Statistical parsers that are competitive in both accuracy and efficiency can be built upon these transition systems. Furthermore, the heterogeneous design of transition systems yields diversity of the corresponding parsing models and thus greatly benefits parser ensemble. Concerning the disambiguation problem, we introduce two new techniques, namely, transition combination and tree approximation, to improve parsing quality. Transition combination makes every action performed by a parser significantly change configurations. Therefore, more distinct features can be extracted for statistical disambiguation. With the same goal of extracting informative features, tree approximation induces tree backbones from dependency graphs and re-uses tree parsing techniques to produce tree-related features. We conduct experiments on CCG-grounded functor–argument analysis, LFG-grounded grammatical relation analysis, and HPSG-grounded semantic dependency analysis for English and Chinese. Experiments demonstrate that data-driven models with appropriate transition systems can produce high-quality deep dependency analysis, comparable to more complex grammar-driven models. Experiments also indicate the effectiveness of the heterogeneous design of transition systems for parser ensemble, transition combination, as well as tree approximation for statistical disambiguation.
Systematic review on the association between employee worktime control and work-non-work balance, health and well-being, and job-related outcomes.

OBJECTIVES The aim of this review was to assess systematically the empirical evidence for associations between employee worktime control (WTC) and work-non-work balance, health/well-being, and job-related outcomes (eg, job satisfaction, job performance). METHOD A systematic search of empirical studies published between 1995-2011 resulted in 63 relevant papers from 53 studies. Five different categories of WTC measurements were distinguished (global WTC, multidimensional WTC, flextime, leave control, and "other subdimensions of WTC"). For each WTC category, we examined the strength of evidence for an association with (i) work-non-work balance, (ii) health/well-being, and (iii) job-related outcomes. We distinguished between cross-sectional, longitudinal, and intervention studies. Evidence strength was assessed based on the number of studies and their convergence in terms of study findings. RESULTS (Moderately) strong cross-sectional evidence was found for positive associations between global WTC and both work-non-work balance and job-related outcomes, whereas no consistent evidence was found regarding health/well-being. Intervention studies on global WTC found moderately strong evidence for a positive causal association with work-non-work balance and no or insufficient evidence for health/well-being and job-related outcomes. Limited to moderately strong cross-sectional evidence was found for positive associations between multidimensional WTC and our outcome categories. Moderately strong cross-sectional evidence was found for positive associations between flextime and all outcome categories. The lack of intervention or longitudinal studies restricts clear causal inferences. CONCLUSIONS This review has shown that there are theoretical and empirical reasons to view WTC as a promising tool for the maintenance of employees' work-non-work balance, health and well-being, and job-related outcomes. At the same time, however, the current state of evidence allows only very limited causal inferences to be made regarding the impact of enhanced WTC.