A closure for the Master Equation starting from the Dynamic Cavity Method

We consider classical spin systems evolving in continuous time with interactions given by a locally tree-like graph. Several approximate analysis methods have earlier been reported based on the idea of Belief Propagation / cavity method. We introduce a new such method which can be derived in a more systematic manner, and which performs better on several important classes of problems.Comment: arXiv admin note: text overlap with arXiv:2205.0075

Evaluation of a Large-Scale Biomedical Data Annotation Initiative

Background: This study describes a large-scale manual re-annotation of data samples in the Gene Expression Omnibus (GEO), using variables and values derived from the National Cancer Institute thesaurus. A framework is described for creating an annotation scheme for various diseases that is flexible, comprehensive, and scalable. The annotation structure is evaluated by measuring coverage and agreement between annotators. Results: There were 12,500 samples annotated with approximately 30 variables, in each of six disease categories – breast cancer, colon cancer, inflammatory bowel disease (IBD), rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), and Type 1 diabetes mellitus (DM). The annotators provided excellent variable coverage, with known values for over 98% of three critical variables: disease state, tissue, and sample type. There was 89% strict inter-annotator agreement and 92% agreement when using semantic and partial similarity measures. Conclusion: We show that it is possible to perform manual re-annotation of a large repository in a reliable manner

Decay of metastable phases in a model for the catalytic oxidation of CO

We study by kinetic Monte Carlo simulations the dynamic behavior of a Ziff-Gulari-Barshad model with CO desorption for the reaction CO + O $\to$ CO$_2$ on a catalytic surface. Finite-size scaling analysis of the fluctuations and the fourth-order order-parameter cumulant show that below a critical CO desorption rate, the model exhibits a nonequilibrium first-order phase transition between low and high CO coverage phases. We calculate several points on the coexistence curve. We also measure the metastable lifetimes associated with the transition from the low CO coverage phase to the high CO coverage phase, and {\it vice versa}. Our results indicate that the transition process follows a mechanism very similar to the decay of metastable phases associated with {\it equilibrium} first-order phase transitions and can be described by the classic Kolmogorov-Johnson-Mehl-Avrami theory of phase transformation by nucleation and growth. In the present case, the desorption parameter plays the role of temperature, and the distance to the coexistence curve plays the role of an external field or supersaturation. We identify two distinct regimes, depending on whether the system is far from or close to the coexistence curve, in which the statistical properties and the system-size dependence of the lifetimes are different, corresponding to multidroplet or single-droplet decay, respectively. The crossover between the two regimes approaches the coexistence curve logarithmically with system size, analogous to the behavior of the crossover between multidroplet and single-droplet metastable decay near an equilibrium first-order phase transition.Comment: 27 pages, 22 figures, accepted by Physical Review

Heat stress during the pre-slaughter on broiler chicken

A cadeia da carne de frango no Brasil é um importante setor do agronegócio, ocupando a terceira maior produção mundial e o primeiro lugar nas exportações. Para atender a demanda, é fundamental minimizar os problemas de manejo, que causam o aparecimento de problemas fisiológicos. A seleção genética intensiva, que é usada na obtenção de taxas de crescimento mais rápidas para frangos de corte, contribuiu para que as linhagens melhoradas atuais sejam muito susceptíveis ao estresse térmico. Quando a temperatura ambiente se eleva acima da zona de termoneutralidade, a ave é submetida a uma condição de estresse, podendo gerar hipertermia aguda, alcalose respiratória, desequilíbrio eletrolítico, redução no consumo de alimento, menor taxa de crescimento, aumento na mortalidade e/ou até mesmo efeitos negativos na qualidade da carne, pela incidência de carnes pálidas e, em outros casos, escuras, interferindo nas propriedades como rendimento industrial, capacidade de retenção de água, cor e maciez. Os resultados de avaliação dos parâmentros de qualidade observados na literatura evidenciam que o estresse térmico, crônico ou agudo sofrido por frangos de corte geram consequências negativas sobre as propriedades funcionais da carne. São necessários mais estudos sobre essa questão, principalmente em relação ao Brasil, por ser um país tropical, com elevadas temperaturas, especialmente, no verão, para compreender, prevenir e contornar a extensão ou intensidade do estresse, evitando problemas e prejuízos para a cadeia da carne.The chicken meat chain in Brazil is an important sector of agribusiness, accounting for the third largest world's production and first place in exports. To meet this demand, it is essential to minimize management problems, which cause the appearance of physiological problems. The intensive genetic selection used to obtain faster growth rates for broilers contributed for the current improved strains to become very susceptible to heat stress. When the environment temperature rises above the thermoneutrality zone, the bird is submitted to a stress condition, which can generate acute hyperthermia, respiratory alkalosis, electrolyte imbalance, reduction in food consumption, lower growth rate, increased mortality rate and even negative effects on meat quality due to the incidence of pale meat and dark in other cases, interfering in properties such as industrial yield, water holding capacity, color and tenderness. The results of the evaluation of quality parameters observed in literature showed that the heat stress, chronic or acute, suffered by broiler chickens, generates negative consequences on the functional properties of meat. Further studies with this research line should be conducted, mainly in Brazil, for being a tropical country with high temperatures in the summer in order to understand, prevent and overcome the extent or intensity of this stress, avoiding problems and damages to the meat chain