Counting the changes of random Δ20 sets

We study the number of changes of the initial segment Zs ↾n for computable approximations of a Martin-Löf random Δ02Δ20 set Z. We establish connections between this number of changes and various notions of computability theoretic lowness, as well as the fundamental thesis that, among random sets, randomness is antithetical to computational power. We introduce a new randomness notion, called balanced randomness, which implies that for each computable approximation and each constant c, there are infinitely many n such that Zs ↾n changes more than c2n times. We establish various connections with ω-c.e. tracing and omega;-c.e. jump domination, a new lowness property. We also examine some relationships to randomness theoretic notions of highness, and give applications to the study of (weak) Demuth cuppability.Fil: Figueira, Santiago. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Computación; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Hirschfeldt, Denis R.. University of Chicago; Estados UnidosFil: Miller, Joseph S.. University of Wisconsin; Estados UnidosFil: Ng, Keng Meng. Nanyang Technological University; SingapurFil: Nies, André. The University Of Auckland; Nueva Zeland

Miniature implantable antennas for biomedical telemetry: from simulation to realization

WOS:000310154700019 (Nº de Acesso Web of Science)“Prémio Científico ISCTE-IUL 2013”We address numerical versus experimental design and testing of miniature implantable antennas for biomedical telemetry in the medical implant communications service band (402-405 MHz). A model of a novel miniature antenna is initially proposed for skin implantation, which includes varying parameters to deal with fabrication-specific details. An iterative design-and-testing methodology is further suggested to determine the parameter values that minimize deviations between numerical and experimental results. To assist in vitro testing, a low-cost technique is proposed for reliably measuring the electric properties of liquids without requiring commercial equipment. Validation is performed within a specific prototype fabrication/testing approach for miniature antennas. To speed up design while providing an antenna for generic skin implantation, investigations are performed inside a canonical skin-tissue model. Resonance, radiation, and safety performance of the proposed antenna is finally evaluated inside an anatomical head model. This study provides valuable insight into the design of implantable antennas, assessing the significance of fabrication-specific details in numerical simulations and uncertainties in experimental testing for miniature structures. The proposed methodology can be applied to optimize antennas for several fabrication/testing approaches and biotelemetry applications

Cyclooxygenase-2 Expression in Bladder Cancer and Patient Prognosis: Results from a Large Clinical Cohort and Meta-Analysis

Aberrant overexpression of cyclooxygenase-2 (COX2) is observed in urothelial carcinoma of the bladder (UCB). Studies evaluating COX2 as a prognostic marker in UCB report contradictory results. We determined the prognostic potential of COX2 expression in UCB and quantitatively summarize the results with those of the literature through a meta-analysis. Newly diagnosed UCB patients recruited between 1998–2001 in 18 Spanish hospitals were prospectively included in the study and followed-up (median, 70.7 months). Diagnostic slides were reviewed and uniformly classified by expert pathologists. Clinical data was retrieved from hospital charts. Tissue microarrays containing non-muscle invasive (n = 557) and muscle invasive (n = 216) tumours were analyzed by immunohistochemistry using quantitative image analysis. Expression was evaluated in Cox regression models to assess the risk of recurrence, progression and disease-specific mortality. Meta-hazard ratios were estimated using our results and those from 11 additional evaluable studies. COX2 expression was observed in 38% (211/557) of non-muscle invasive and 63% (137/216) of muscle invasive tumors. Expression was associated with advanced pathological stage and grade (p<0.0001). In the univariable analyses, COX2 expression - as a categorical variable - was not associated with any of the outcomes analyzed. As a continuous variable, a weak association with recurrence in non-muscle invasive tumors was observed (p-value = 0.048). In the multivariable analyses, COX2 expression did not independently predict any of the considered outcomes. The meta-analysis confirmed these results. We did not find evidence that COX2 expression is an independent prognostic marker of recurrence, progression or survival in patients with UCB.The work was partially supported by the Fondo de Investigaciones Sanitarias, Instituto de Salud Carlos III, Ministry of Science and Innovation, Spain (G03/174, 00/0745, PI051436, PI061614 and G03/174); Red Temática de Investigación Cooperativa en Cáncer- RD06/0020-RTICC; Consolider ONCOBIO; EU-FP6-STREP-37739-DRoP-ToP; EU-FP7-HEALTH-F2-2008-201663-UROMOL; EU-FP7-HEALTH-F2-2008-201333-DECanBio; USA-NIH-RO1-CA089715; and a PhD fellowship awarded to MJC from the ‘‘la Caixa’’ foundation, Spain, and a postdoctoral fellowship awarded to AFSA from the Fundación Científica de la AEC

In vitro determination of extracellular proteins from xylella fastidiosa

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)The phytopathogen Xylella fastidiosa causes economic losses in important agricultural crops. Xylem vessel occlusion caused by biofilm formation is the major mechanism underlying the pathogenicity of distinct strains of X. fastidiosa. Here, we provide a detailed in vitro characterization of the extracellular proteins of X. fastidiosa. Based on the results, we performed a comparison with a strain J1a12, which cannot induce citrus variegated chlorosis symptoms when inoculated into citrus plants. We then extend this approach to analyze the extracellular proteins of X. fastidiosa in media supplemented with calcium. We verified increases in extracellular proteins concomitant with the days of growth and, consequently, biofilm development (330 days). Outer membrane vesicles carrying toxins were identified beginning at 10 days of growth in the 9a5c strain. In addition, a decrease in extracellular proteins in media supplemented with calcium was observed in both strains. Using mass spectrometry, 71 different proteins were identified during 30 days of X. fastidiosa biofilm development, including proteases, quorum-sensing proteins, biofilm formation proteins, hypothetical proteins, phage-related proteins, chaperones, toxins, antitoxins, and extracellular vesicle membrane components.The phytopathogen Xylella fastidiosa causes economic losses in important agricultural crops. Xylem vessel occlusion caused by biofilm formation is the major mechanism underlying the pathogenicity of distinct strains of X. fastidiosa. Here, we provide a de7Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP) [2001/07533-7, 2012/51580-4]Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior (CAPES, Computational Biology Program)CAPESFAPESP [2011/50268-4]CAPES (Computational Biology Program)Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq

Phase transitions in a frustrated XY model with zig-zag couplings

We study a new generalized version of the square-lattice frustrated XY model where unequal ferromagnetic and antiferromagnetic couplings are arranged in a zig-zag pattern. The ratio between the couplings $\rho$ can be used to tune the system, continuously, from the isotropic square-lattice to the triangular-lattice frustrated XY model. The model can be physically realized as a Josephson-junction array with two different couplings, in a magnetic field corresponding to half-flux quanta per plaquette. Mean-field approximation, Ginzburg-Landau expansion and finite-size scaling of Monte Carlo simulations are used to study the phase diagram and critical behavior. Depending on the value of $\rho$, two separate transitions or a transition line in the universality class of the XY-Ising model, with combined $Z_2$ and U(1) symmetries, takes place. In particular, the phase transitions of the standard square-lattice and triangular-lattice frustrated XY models correspond to two different cuts through the same transition line. Estimates of the chiral ($Z_2$) critical exponents on this transition line deviate significantly from the pure Ising values, consistent with that along the critical line of the XY-Ising model. This suggests that a frustrated XY model or Josephson-junction array with a zig-zag coupling modulation can provide a physical realization of the XY-Ising model critical line.Comment: 11 pages, 9 figures, RevTex, to appear in Phys. Rev.

Vapd In Xylella Fastidiosa Is A Thermostable Protein With Ribonuclease Activity.

Xylella fastidiosa strain 9a5c is a gram-negative phytopathogen that is the causal agent of citrus variegated chlorosis (CVC), a disease that is responsible for economic losses in Brazilian agriculture. The most well-known mechanism of pathogenicity for this bacterial pathogen is xylem vessel occlusion, which results from bacterial movement and the formation of biofilms. The molecular mechanisms underlying the virulence caused by biofilm formation are unknown. Here, we provide evidence showing that virulence-associated protein D in X. fastidiosa (Xf-VapD) is a thermostable protein with ribonuclease activity. Moreover, protein expression analyses in two X. fastidiosa strains, including virulent (Xf9a5c) and nonpathogenic (XfJ1a12) strains, showed that Xf-VapD was expressed during all phases of development in both strains and that increased expression was observed in Xf9a5c during biofilm growth. This study is an important step toward characterizing and improving our understanding of the biological significance of Xf-VapD and its potential functions in the CVC pathosystem.10e014576

Location of chlorogenic acid biosynthesis pathway and polyphenol oxidase genes in a new interspecific anchored linkage map of eggplant

© Gramazio et al.; licensee BioMed Central. 2014. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated

An empirical evaluation of camera trap study design: How many, how long and when?

Abstract Camera traps deployed in grids or stratified random designs are a well‐established survey tool for wildlife but there has been little evaluation of study design parameters. We used an empirical subsampling approach involving 2,225 camera deployments run at 41 study areas around the world to evaluate three aspects of camera trap study design (number of sites, duration and season of sampling) and their influence on the estimation of three ecological metrics (species richness, occupancy and detection rate) for mammals. We found that 25–35 camera sites were needed for precise estimates of species richness, depending on scale of the study. The precision of species‐level estimates of occupancy (ψ) was highly sensitive to occupancy level, with 0.75) species, but more than 150 camera sites likely needed for rare (ψ < 0.25) species. Species detection rates were more difficult to estimate precisely at the grid level due to spatial heterogeneity, presumably driven by unaccounted habitat variability factors within the study area. Running a camera at a site for 2 weeks was most efficient for detecting new species, but 3–4 weeks were needed for precise estimates of local detection rate, with no gains in precision observed after 1 month. Metrics for all mammal communities were sensitive to seasonality, with 37%–50% of the species at the sites we examined fluctuating significantly in their occupancy or detection rates over the year. This effect was more pronounced in temperate sites, where seasonally sensitive species varied in relative abundance by an average factor of 4–5, and some species were completely absent in one season due to hibernation or migration. We recommend the following guidelines to efficiently obtain precise estimates of species richness, occupancy and detection rates with camera trap arrays: run each camera for 3–5 weeks across 40–60 sites per array. We recommend comparisons of detection rates be model based and include local covariates to help account for small‐scale variation. Furthermore, comparisons across study areas or times must account for seasonality, which could have strong impacts on mammal communities in both tropical and temperate sites

A new sensitive molecular marker for Aspergillus’ Calmodulin gene detection in biological samples, used as a supplementary diagnosis for invasive Aspergillosis (IA)/ Um novo marcador molecular sensível para a detecção do gene Calmodulin em amostras biológicas do Aspergillus, utilizado como diagnóstico suplementar para a Aspergilose invasiva (IA)

Introduction: Aspergillosis is caused by the fungi of Aspergillus genus. After inhalation, Aspergillus’ conidia can invade the tracheal bronchus and lungs, resulting in airway colonization, inflammatory granuloma and invasive aspergillosis (IA), which is most likely to occur in neutropenic and immunosuppressed patients. Presently, IA has been associated with COVID-19 in patients admitted to intensive care units (ICU) for longer periods of time. Objective: The objective of this is to design a new molecular marker for detection of Aspergillus spp. in biological samples, in order to develop a new technique for IA diagnosis which is faster, more efficient and safer. Methodology: The primer was designed in silico using conserved sequences of the Calmodulin gene. After confirming the results in silico, in vitro evaluation was performed using the PCR technique. Results: The designed primer showed high specificity for the Aspergillus species. Conclusion: In this study the standardized PCR reaction with the designed marker proved to be safely utilized as a diagnostic method for IA.  The development of a test to aid in the diagnosis of IA is of great importance, since traditional methods are in turn time consuming and generally confused with other diseases. Early diagnosis contributes to faster treatment initiation and increasing the patient's chance of survival. We can conclude that the standardized PCR with the designed primer can be used safely in the development of a diagnostic test for IA, being of low cost, and accessible to patients treated by the public health system. A Patent application for this molecular marker has been submitted, with the number BR1020190281294