Pattern matching and pattern discovery algorithms for protein topologies

We describe algorithms for pattern matching and pattern learning in TOPS diagrams (formal descriptions of protein topologies). These problems can be reduced to checking for subgraph isomorphism and finding maximal common subgraphs in a restricted class of ordered graphs. We have developed a subgraph isomorphism algorithm for ordered graphs, which performs well on the given set of data. The maximal common subgraph problem then is solved by repeated subgraph extension and checking for isomorphisms. Despite the apparent inefficiency such approach gives an algorithm with time complexity proportional to the number of graphs in the input set and is still practical on the given set of data. As a result we obtain fast methods which can be used for building a database of protein topological motifs, and for the comparison of a given protein of known secondary structure against a motif database

Airy processes and variational problems

We review the Airy processes; their formulation and how they are conjectured to govern the large time, large distance spatial fluctuations of one dimensional random growth models. We also describe formulas which express the probabilities that they lie below a given curve as Fredholm determinants of certain boundary value operators, and the several applications of these formulas to variational problems involving Airy processes that arise in physical problems, as well as to their local behaviour.Comment: Minor corrections. 41 pages, 4 figures. To appear as chapter in "PASI Proceedings: Topics in percolative and disordered systems

The Medical Oncology resident mentor: situation and workload

Purpose: The Spanish Society for Medical Oncology (SEOM, for its acronym in Spanish) and the National Commission for the Specialty of Medical Oncology seek to highlight the important workload and unrecognized dedication entailed in working as a Medical Oncology (MO) resident mentor, as well as its relevance for the quality of teaching units and the future of the specialty. Materials and methods: The current situation and opinion regarding the activity of MO resident mentors was analyzed by reviewing the standing national and autonomic community regulations and via an online survey targeting mentors, residents, and physicians who are not MO mentors. The project was supervised by a specially designated group that agreed on a proposal containing recommendations for improvement. Results: Of the MO mentors, 90% stated that they did not have enough time to perform their mentoring duties. An estimated 172 h/year on average was dedicated to mentoring, which represents 10.1% of the total time. MO mentors dedicate an average of 6.9 h/month to these duties outside their workday. Forty-five percent of the mentors feel that their role is scantly recognized, if at all. Conclusions: The study reveals the substantial dedication and growing complexity of MO resident mentoring. A series of recommendations are issued to improve the conditions in which it is carried out, including the design of systems that adapt to the professional activity in those departments that have time set aside for mentoring tasks

Dynamically Induced Spontaneous Symmetry Breaking in 3-3-1 Models

We show that in SU(3)_C X SU(3)_L X U(1)_N (3-3-1) models embedded with a singlet scalar playing the role of the axion, after imposing scale invariance, dynamical symmetry breaking of Peccei-Quinn symmetry occurs through the one-loop effective potential for the singlet field. We, then, analyze the structure of spontaneous symmetry breaking by studying the new scalar potential for the model, and verify that electroweak symmetry breaking is tightly connected to the 3-3-1 breaking by the strong constraints among their vacuum expectation values. This offers a valuable guide to write down the correct pattern of symmetry breaking for multi-scalar theories. We also obtained that the accompanying massive pseudo-scalar, instead of acquiring mass of order of Peccei-Quinn scale as we would expect, develops a mass at a much lower scale, a consequence solely of the dynamical breaking.Comment: 12 pages, typos corrected, improved text, conclusions unchange

Constituents of Quercus eduardii leaf infusion: Their interaction with gut microbiota communities and therapeutic role in colorectal cancer.

The infusion of Q. eduardii leaves has been used ancestrally for medicinal purposes. We investigated the effect of Q. eduardii infusion intake on inflammatory and oncogenic biomarkers in animals induced to have colorectal cancer with DMH. We also investigated its influence on the microbiota, establishing the main microbial metabolites in the intestinal content of the experimental animals. The microbial metabolites associated with greater anti-inflammatory and anticarcinogenic activity were 3́-hydroxyphenylacetic acid (3HPA) and €-3-(3,4,5-trimethoxyphenyl) prop-2-enoic acid (TMCA). Finally, the intake of the Q. eduardii infusion significantly increased the abundance of the Erysipelotrichaceae and Lachnospiraceae families, that seems to have a great influence on the antitumor responses detected in the study.post-print4648 K

Durability assessment of external thermal insulation composite systems in urban and maritime environments

External Thermal Insulation Composite Systems (ETICS) are multilayer solutions which provide an enhanced thermal performance to the building envelope. However, significant anomalies can be detected on ETICS facades, in some cases shortly after the application of these systems. This study intends to evaluate and compare the durability of six commercially available ETICS after two years of outdoor exposure at both urban and maritime conditions in Portugal. The systems were characterized by means of non-destructive testing (i.e., visual and microscopic assessment, water transport properties, thermal conductivity, surface roughness), thus allowing to evaluate the performance loss throughout natural aging. The bio-susceptibility and aesthetic properties (color and gloss) were also investigated. Results showed that the performance and durability of the complete system is significantly affected by the rendering system formulation. The lime-based specimens obtained the highest rate of mold development after one year of aging in a maritime environment, becoming considerably darker and with lower surface gloss. Fungal analysis of this darkish stained area indicated the presence of mold species of the genera Alternaria, Didymella, Cladosporium and Epicoccum, and yeasts of the genera Vishniacozyma and Cystobasidium. An increase of both capillary water absorption and water vapor permeability was also registered for the aged lime-based specimens. Acrylic-based systems obtained lower capillary water absorption after aging and greater dirt deposition on their surfaces, especially in urban conditions. These systems had also higher color variation and surface gloss decrease and slightly higher mold growth, when compared with those aged in a maritime environment. Finally, no mold growth was detected on the silicate-based specimens after two years of aging. However, these specimens obtained higher capillary water absorption and lower vapor permeability after aging, possibly leading to moisture accumulation within the system. Results contribute towards the development of ETICS with enhanced performance and durability.info:eu-repo/semantics/publishedVersio

LMI-fuzzy control design for non-minimum-phase DC-DC converters: An application for output regulation

Indexación ScopusRobust control techniques for power converters are becoming more attractive because they can meet with most demanding control goals like uncertainties. In this sense, the Takagi-Sugeno (T-S) fuzzy controller based on linear matrix inequalities (LMI) is a linear control by intervals that has been relatively unexplored for the output-voltage regulation problem in switching converters. Through this technique it is possible to minimize the disturbance rejection level, satisfying constraints over the decay rate of state variables as well as the control effort. Therefore, it is possible to guarantee, a priori, the stability of the large-signal converters in a broad operation domain. This work presents the design of a fuzzy control synthesis based on a T-S fuzzy model for non-minimum phase dc-dc converters, such as boost and buck-boost. First, starting from the canonical bilinear converters expression, a Takagi-Sugeno (T-S) fuzzy model is obtained, allowing to define the fuzzy controller structure through the parallel distributed compensation technique (PDC). Finally, the fuzzy controller design based on LMIs is solved for the defined specification in close loop through MATLAB toolbox LMI. Simulations and experimental results of a 60 W prototype are presented to verify theoretical predictions. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.https://www.mdpi.com/2076-3417/11/5/228

Lubricated revolute joints in rigid multibody systems

The main purpose of this work is to present a general methodology for modeling lubricated revolute joints in constrained rigid multibody systems. In the dynamic analysis of journal-bearings, the hydrodynamic forces, which include both squeeze and wedge effects, generated by the lubricant fluid, oppose the journal motion. The hydrodynamic forces are obtained by integrating the pressure distribution evaluated with the aid of Reynolds’ equation, written for the dynamic regime. The hydrodynamic forces built up by the lubricant fluid are evaluated from the system state variables and included into the equations of motion of the multibody system. Numerical examples are presented in order to demonstrate the use of the methodologies and procedures described in this work.Fundação para a Ciência e a Tecnologia (FCT

DCC gene network in the prefrontal cortex is associated with total brain volume in childhood

BACKGROUND: Genetic variation in the guidance cue DCC gene is linked to psychopathologies involving dysfunction in the prefrontal cortex. We created an expression-based polygenic risk score (ePRS) based on the DCC coexpression gene network in the prefrontal cortex, hypothesizing that it would be associated with individual differences in total brain volume. METHODS: We filtered single nucleotide polymorphisms (SNPs) from genes coexpressed with DCC in the prefrontal cortex obtained from an adult postmortem donors database (BrainEAC) for genes enriched in children 1.5 to 11 years old (BrainSpan). The SNPs were weighted by their effect size in predicting gene expression in the prefrontal cortex, multiplied by their allele number based on an individual's genotype data, and then summarized into an ePRS. We evaluated associations between the DCC ePRS and total brain volume in children in 2 community-based cohorts: the Maternal Adversity, Vulnerability and Neurodevelopment (MAVAN) and University of California, Irvine (UCI) projects. For comparison, we calculated a conventional PRS based on a genome-wide association study of total brain volume. RESULTS: Higher ePRS was associated with higher total brain volume in children 8 to 10 years old (β = 0.212, p = 0.043; n = 88). The conventional PRS at several different thresholds did not predict total brain volume in this cohort. A replication analysis in an independent cohort of newborns from the UCI study showed an association between the ePRS and newborn total brain volume (β = 0.101, p = 0.048; n = 80). The genes included in the ePRS demonstrated high levels of coexpression throughout the lifespan and are primarily involved in regulating cellular function. LIMITATIONS: The relatively small sample size and age differences between the main and replication cohorts were limitations. CONCLUSION: Our findings suggest that the DCC coexpression network in the prefrontal cortex is critically involved in whole brain development during the first decade of life. Genes comprising the ePRS are involved in gene translation control and cell adhesion, and their expression in the prefrontal cortex at different stages of life provides a snapshot of their dynamic recruitment