Determinants of Histone H3K4 Methylation Patterns

Soares, Luis M.,He, P. Cody,Chun, Yujin,Suh, Hyunsuk,Kim, TaeSoo,Buratowski, Stephen Cell Press 2017 Molecular cell Vol.68 No.4

<P><B>Summary</B></P> <P>Various factors differentially recognize trimethylated histone H3 lysine 4 (H3K4me3) near promoters, H3K4me2 just downstream, and promoter-distal H3K4me1 to modulate gene expression. This methylation “gradient” is thought to result from preferential binding of the H3K4 methyltransferase Set1/complex associated with Set1 (COMPASS) to promoter-proximal RNA polymerase II. However, other studies have suggested that location-specific cues allosterically activate Set1. Chromatin immunoprecipitation sequencing (ChIP-seq) experiments show that H3K4 methylation patterns on active genes are not universal or fixed and change in response to both transcription elongation rate and frequency as well as reduced COMPASS activity. Fusing Set1 to RNA polymerase II results in H3K4me2 throughout transcribed regions and similarly extended H3K4me3 on highly transcribed genes. Tethered Set1 still requires histone H2B ubiquitylation for activity. These results show that higher-level methylations reflect not only Set1/COMPASS recruitment but also multiple rounds of transcription. This model provides a simple explanation for non-canonical methylation patterns at some loci or in certain COMPASS mutants.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Many genes do not show the canonical H3K4 methylation gradient pattern </LI> <LI> H3K4 methylation levels are determined by the time Set1 spends near the nucleosome </LI> <LI> Multiple rounds of transcription contribute to H3K4 trimethylation levels </LI> <LI> Set1 fused to RNA pol II places H3K4me2 and H3K4me3 throughout transcribed regions </LI> </UL> </P> <P><B>Graphical Abstract</B></P> <P>[DISPLAY OMISSION]</P>

O-JMeSH: creating a bilingual English-Japanese controlled vocabulary of MeSH UIDs through machine translation and mutual information

Soares, Felipe,Tateisi, Yuka,Takatsuki, Terue,Yamaguchi, Atsuko Korea Genome Organization 2021 Genomics & informatics Vol.19 No.3

Previous approaches to create a controlled vocabulary for Japanese have resorted to existing bilingual dictionary and transformation rules to allow such mappings. However, given the possible new terms introduced due to coronavirus disease 2019 (COVID-19) and the emphasis on respiratory and infection-related terms, coverage might not be guaranteed. We propose creating a Japanese bilingual controlled vocabulary based on MeSH terms assigned to COVID-19 related publications in this work. For such, we resorted to manual curation of several bilingual dictionaries and a computational approach based on machine translation of sentences containing such terms and the ranking of possible translations for the individual terms by mutual information. Our results show that we achieved nearly 99% occurrence coverage in LitCovid, while our computational approach presented average accuracy of 63.33% for all terms, and 84.51% for drugs and chemicals.

A Body Condition Scoring System for Bali Cattle

Soares, F.S.,Dryden, G. McL. Asian Australasian Association of Animal Productio 2011 Animal Bioscience Vol.24 No.11

Live weight, body length, hip and shoulder heights, heart girth, and metatarsal length were measured on 100 one to two years old Bali (Bos javanicus) bulls. Multiple regression of these measurements on live weight gave a prediction equation involving heart girth and body length (prediction $R^2$ = 0.845). These measurements were also used to derive several frame scores (FS). Live weight (Lwt) divided by FS was used as an index of body condition. Lwt/(length+hip height) was normally distributed and highly correlated with other normally-distributed condition indexes. This index was used to define five body condition scores. These were used to develop a five-point body condition scoring system in which the amount of fleshing over the vertebral processes, ribs, hindquarters, tail head, hooks, at the top of the neck, and the shoulders, the development of wrinkles in the skin above the hock and the neck, and the size of the dewlap, were used to describe the different body condition scores. Animals of score 1 had prominent hooks, shoulders, vertebrae and ribs, and hollow hindquarters and flat tailhead. Score 5 animals had rounded hindquarters, well-filled upper hind legs, small mounds of soft tissue were apparent on the tailhead, their hooks, necks, shoulders, vertebrae and ribs were well covered, and the dewlap was prominent.

Reliability of Maintained Hull Girders of Two Bulk Carrier Designs Subjected to Fatigue and Corrosion

Soares, C.Guedes,Garbatov, Y. The Society of Naval Architects of Korea 1999 Journal of ship and ocean technology Vol.3 No.1

The objective of the paper is to study the impact of changing the traditional hull design of bulk carriers by providing them with a double hull while keeping the same deadweight. It is demonstrated that by introducing the double hull the structural reliability is increased throughout the entire life and also the extend of the needed repair is reduced. The results are obtained with recently developed mathematical tools for the reliability assessment of ship hulls subjected to the existence of multiple cracks both in the stiffeners and in the plating and it models the crack growth process. The effect of corrosion is represented as time dependent. The long-term stress range acting on the elements is defined as a function of the local transverse pressure of the internal cargo and outside sea water combined with the stresses resulting from the longitudinal bending of the hull, which is a combined with the stresses resulting from the longitudinal bending of the hull, which is a combineation of horizontal and vertical bending moments. The effect of maintenance actions is modelled as a stochastic process. The results show that a different design of the midship section improves the structural safety and also the economy with respect to structural repair of bulk carriers.

Cardiocirculatory, biochemical and hemostatic evaluation of dogs with hyperadrenocorticism at diagnosis and after treatment

Soares, Frederico Aecio Carvalho,Matheus, Juliana Pereira,Carvalho, Guilherme Luiz,Neuwald, Elisa Barp,Poppl, Alan Gomes,Valle, Stella Faria,Gonzalez, Felix Hilario Diaz The Korean Society of Veterinary Science 2016 大韓獸醫學會誌 Vol.56 No.3

Hyperadrenocorticism (HAC) is a common endocrinopathy among dogs that causes multisystemic signs. This study was conducted to evaluate cardiocirculatory, biochemical, and hemostatic parameters in dogs with HAC at diagnosis, in addition to verifying whether abnormal parameters could be controlled by initial treatment with trilostane. Fifteen dogs with HAC were assessed by systolic blood pressure measurement, electrocardiography, Doppler echocardiography, serum concentration of troponin I, and biochemical and hemostatic profile at diagnosis and after trilostane therapy. Unlike biochemical parameters, hemostatic and cardiocirculatory parameters were not significantly influenced by the onset of treatment. The authors believe that clinical treatment with trilostane for 3 to 4 months might not be sufficient for the stabilization of cardiocirculatory abnormalities such as hypertension. Therefore, dogs with HAC must receive cardiocirculatory monitoring at diagnosis and during drug treatment.

Unsteady Flow with Cavitation in Viscoelastic Pipes

Soares, Alexandre K.,Covas, Didia I.C.,Ramos, Helena M.,Reis, Luisa Fernanda R. Korean Society for Fluid machinery 2009 International journal of fluid machinery and syste Vol.2 No.4

The current paper focuses on the analysis of transient cavitating flow in pressurised polyethylene pipes, which are characterized by viscoelastic rheological behaviour. A hydraulic transient solver that describes fluid transients in plastic pipes has been developed. This solver incorporates the description of dynamic effects related to the energy dissipation (unsteady friction), the rheological mechanical behaviour of the viscoelastic pipe and the cavitating pipe flow. The Discrete Vapour Cavity Model (DVCM) and the Discrete Gas Cavity Model (DGCM) have been used to describe transient cavitating flow. Such models assume that discrete air cavities are formed in fixed sections of the pipeline and consider a constant wave speed in pipe reaches between these cavities. The cavity dimension (and pressure) is allowed to grow and collapse according to the mass conservation principle. An extensive experimental programme has been carried out in an experimental set-up composed of high-density polyethylene (HDPE) pipes, assembled at Instituto Superior T$\acute{e}$cnico of Lisbon, Portugal. The experimental facility is composed of a single pipeline with a total length of 203 m and inner diameter of 44 mm. The creep function of HDPE pipes was determined by using an inverse model based on transient pressure data collected during experimental runs without cavitating flow. Transient tests were carried out by the fast closure of the ball valves located at downstream end of the pipeline for the non-cavitating flow and at upstream for the cavitating flow. Once the rheological behaviour of HDPE pipes were known, computational simulations have been run in order to describe the hydraulic behaviour of the system for the cavitating pipe flow. The calibrated transient solver is capable of accurately describing the attenuation, dispersion and shape of observed transient pressures. The effects related to the viscoelasticity of HDPE pipes and to the occurrence of vapour pressures during the transient event are discussed.

Elastodynamic analysis by a frequency-domain FEM-BEM iterative coupling procedure

Soares, Delfim Jr.,Goncalves, Kleber A.,de Faria Telles, Jose Claudio Techno-Press 2015 Coupled systems mechanics Vol.4 No.3

This paper presents a coupled FEM-BEM strategy for the numerical analysis of elastodynamic problems where infinite-domain models and complex heterogeneous media are involved, rendering a configuration in which neither the Finite Element Method (FEM) nor the Boundary Element Method (BEM) is most appropriate for the numerical analysis. In this case, the coupling of these methodologies is recommended, allowing exploring their respective advantages. Here, frequency domain analyses are focused and an iterative FEM-BEM coupling technique is considered. In this iterative coupling, each sub-domain of the model is solved separately, and the variables at the common interfaces are iteratively updated, until convergence is achieved. A relaxation parameter is introduced into the coupling algorithm and an expression for its optimal value is deduced. The iterative FEM-BEM coupling technique allows independent discretizations to be efficiently employed for both finite and boundary element methods, without any requirement of matching nodes at the common interfaces. In addition, it leads to smaller and better-conditioned systems of equations (different solvers, suitable for each sub-domain, may be employed), which do not need to be treated (inverted, triangularized etc.) at each iterative step, providing an accurate and efficient methodology.

FEM-BEM iterative coupling procedures to analyze interacting wave propagation models: fluid-fluid, solid-solid and fluid-solid analyses

Soares, Delfim Jr. Techno-Press 2012 Coupled systems mechanics Vol.1 No.1

In this work, the iterative coupling of finite element and boundary element methods for the investigation of coupled fluid-fluid, solid-solid and fluid-solid wave propagation models is reviewed. In order to perform the coupling of the two numerical methods, a successive renewal of the variables on the common interface between the two sub-domains is performed through an iterative procedure until convergence is achieved. In the case of local nonlinearities within the finite element sub-domain, it is straightforward to perform the iterative coupling together with the iterations needed to solve the nonlinear system. In particular, a more efficient and stable performance of the coupling procedure is achieved by a special formulation that allows to use different time steps in each sub-domain. Optimized relaxation parameters are also considered in the analyses, in order to speed up and/or to ensure the convergence of the iterative process.

Fibre reinforcement in a structurally compromised endodontically treated molar: a case report

Soares, Renita,Ataide, Ida de Noronha de,Fernandes, Marina,Lambor, Rajan The Korean Academy of Conservative Dentistry 2016 Restorative Dentistry & Endodontics Vol.41 No.2

The reconstruction of structurally compromised posterior teeth is a rather challenging procedure. The tendency of endodontically treated teeth (ETT) to fracture is considerably higher than vital teeth. Although posts and core build-ups followed by conventional crowns have been generally employed for the purpose of reconstruction, this procedure entails sacrificing a considerable amount of residual sound enamel and dentin. This has drawn the attention of researchers to fibre reinforcement. Fibrereinforced composite (FRC), designed to replace dentin, enables the biomimetic restoration of teeth. Besides improving the strength of the restoration, the incorporation of glass fibres into composite resins leads to favorable fracture patterns because the fibre layer acts as a stress breaker and stops crack propagation. The following case report presents a technique for reinforcing a badly broken-down ETT with biomimetic materials and FRC. The proper utilization of FRC in structurally compromised teeth can be considered to be an economical and practical measure that may obviate the use of extensive prosthetic treatment.

Quality of biosafety guidelines for dental clinical practice throughout the world in the early COVID-19 pandemic: a systematic review

Soares Renata Cristina,Rocha Juliana Schaia,da Rosa Saulo Vinicius,Gonçalves Jéssica Rodrigues da Silva Noll,Perlas Condori Priscilla Lesly,Ribeiro Ana Elisa,Moysés Samuel Jorge,Baldani Márcia 한국역학회 2021 Epidemiology and Health Vol.43 No.-

OBJECTIVES: To conduct a systematic review of coronavirus disease 2019 (COVID-19)-related biosafety guidelines for dental clinical practice in the early stage of the pandemic, focusing on quality assessment. METHODS: Electronic (via PubMed, Scopus, Web of Science, Latin American and Caribbean Health Sciences Literature database, Brazilian Library in Dentistry, and Cochrane Library) and gray literature searches were performed for documents published up to May 12, 2020. Guidelines updated until April 17, 2021 were identified. Documents were included as guidelines if they (1) consisted of a set of statements, directions, or principles presenting current or future rules or policy; (2) were developed by government agencies, institutions, organizations, or expert panels; and (3) were related to the general conduct of health care activities rather a particular condition. Two researchers, using the Appraisal of Guidelines for Research & Evaluation II, independently extracted the recommendations and evaluated the quality of the guidelines. RESULTS: Twenty-seven documents from 19 countries were included in the review. These documents presented 122 recommendations related to (1) professional biosafety; (2) patients’/companions’ safety; (3) the organization and biosafety of the physical dental facility environment; and (4) the work process in dental care. Overall, the scientific quality of the guidelines was considered low. Some recommendations presented in these guidelines would require further research to establish their effectiveness. CONCLUSIONS: We found a wide variety of biosafety guidelines for dental practice regarding COVID-19