RNA extraction from ten year old formalin-fixed paraffin-embedded breast cancer samples: a comparison of column purification and magnetic bead-based technologies

Abstract Background The development of protocols for RNA extraction from paraffin-embedded samples facilitates gene expression studies on archival samples with known clinical outcome. Older samples are particularly valuable because they are associated with longer clinical follow up. RNA extracted from formalin-fixed paraffin-embedded (FFPE) tissue is problematic due to chemical modifications and continued degradation over time. We compared quantity and quality of RNA extracted by four different protocols from 14 ten year old and 14 recently archived (three to ten months old) FFPE breast cancer tissues. Using three spin column purification-based protocols and one magnetic bead-based protocol, total RNA was extracted in triplicate, generating 336 RNA extraction experiments. RNA fragment size was assayed by reverse transcription-polymerase chain reaction (RT-PCR) for the housekeeping gene glucose-6-phosphate dehydrogenase (G6PD), testing primer sets designed to target RNA fragment sizes of 67 bp, 151 bp, and 242 bp. Results Biologically useful RNA (minimum RNA integrity number, RIN, 1.4) was extracted in at least one of three attempts of each protocol in 86–100% of older and 100% of recently archived ("months old") samples. Short RNA fragments up to 151 bp were assayable by RT-PCR for G6PD in all ten year old and months old tissues tested, but none of the ten year old and only 43% of months old samples showed amplification if the targeted fragment was 242 bp. Conclusion All protocols extracted RNA from ten year old FFPE samples with a minimum RIN of 1.4. Gene expression of G6PD could be measured in all samples, old and recent, using RT-PCR primers designed for RNA fragments up to 151 bp. RNA quality from ten year old FFPE samples was similar to that extracted from months old samples, but quantity and success rate were generally higher for the months old group. We preferred the magnetic bead-based protocol because of its speed and higher quantity of extracted RNA, although it produced similar quality RNA to other protocols. If a chosen protocol fails to extract biologically useful RNA from a given sample in a first attempt, another attempt and then another protocol should be tried before excluding the case from molecular analysis.

Dentoskeletal changes induced by the Jasper jumper and the activator-headgear combination appliances followed by fixed orthodontic treatment

Introduction: The aim of this study was to compare the dentoskeletal changes of patients with Class II Division 1 malocclusion treated with either the Jasper jumper appliance or the activator-headgear combination, both associated with fixed appliances. Methods: The sample comprised 72 subjects with Class II Division 1 malocclusion divided into 3 groups: group 1 included 25 subjects treated with fixed appliances and the force modules of the Jasper jumper at an initial mean age of 12.72 years, group 2 included 25 subjects treated with the activator-headgear combination followed by fixed appliances at an initial mean age of 11.07 years, and group 3 included 22 untreated subjects at an initial mean age of 12.67 years. Initial cephalometric characteristics and dentoskeletal changes were compared with analysis of variance. Results: Both experimental groups had similar dentoskeletal changes: restrictive effect on the maxilla, clockwise mandibular rotation and a slight increase in anterior face height, retrusion of the maxillary incisors, distalization of the maxillary molars, protrusion of the mandibular incisors, extrusion of the mandibular molars, and significant improvements of the maxillomandibular relationship, overjet, overbite, and the molar relationship. Conclusions: The effects of the Jasper jumper and the activator-headgear combination followed by fixed orthodontic appliances were similar in Class II malocclusion treatment.

Estabilidade em longo prazo do tratamento da má oclusão de classe II, divisão 1, com a utilização de um aparelho funcional propulsor mandibular fixo: relato de caso

O tratamento da má oclusão de Classe II sem extrações dentárias vem ganhando popularidade na comunidade ortodôntica já há três décadas. Aparelhos funcionais fixos vêm sendo utilizados por profissionais, de maneira crescente, para promover compensações dentoalveolares e corrigir a má oclusão de Classe II. Os efeitos mais significativos são observados em pacientes com padrão de crescimento horizontal. Um caso clínico será relatado com o uso do aparelho fixo Twin Force Bite Corrector em uma paciente do sexo feminino, para a correção da Classe II. Esse dispositivo de ancoragem fixa dispensa o uso de aparelhos funcionais removíveis e não necessita da cooperação do paciente.

Performance of fixed-pressure valve with antisiphon device SPHERA® in hydrocephalus treatment and overdrainage prevention

Patients with hydrocephalus and risk factors for overdrainage may be submitted to ventricular shunt (VS) implant with antisiphon device. The objective of this study was to prospectively evaluate for two years the clinical and tomographic results of the implant of fixed-pressure valves with antisiphon device SPHERA® in 35 adult patients, with hydrocephalus and risk factors for overdrainage. Of these, 3 had congenital hydrocephalus in adult patients with very dilated ventricles (Evans index >50%), 3 had symptomatic overdrainage after previous VS implant (subdural hematoma, hygroma or slit ventricle syndrome), 1 had previous chronic subdural hematoma, 15 had normal pressure hydrocephalus with final lumbar pressure <5 cm H2O after tap test (40 mL), 6 had pseudotumor cerebri, and 7 had hydrocephalus due to other causes. Clinical improvement was observed and sustained in 94.3% of the patients during the two-year period with no computed tomography (CT) evidence of hypo or overdrainage, and no immediate early or late significant complications.

Computational simulation of the flow-induced vibration of a circular cylinder subjected to wake interference

In this work, we considered the flow around two circular cylinders of equal diameter placed in tandem with respect to the incident uniform flow. The upstream cylinder was fixed and the downstream cylinder was completely free to move in the cross-stream direction, with no spring or damper attached to it. The centre-to-centre distance between the cylinders was four diameters, and the Reynolds number was varied from 100 to 645. We performed two- and three-dimensional simulations of this flow using a Spectral/hp element method to discretise the flow equations, coupled to a simple Newmark integration routine that solves the equation of the dynamics of the cylinder. The differences of the behaviours observed in the two- and three-dimensional simulations are highlighted and the data is analysed under the light of previously published experimental results obtained for higher Reynolds numbers.

A fixed point theorem for Meir-Keeler contractions in ordered metric spaces

[EN] The purpose of this paper is to present some fixed point theorems for Meir-Keeler contractions in a complete metric space endowed with a partial order. MSC: 47H10.

On some Banach space constants arising in nonlinear fixed point and eigenvalue theory

[EN] As is well known, in any infinite-dimensional Banach space one may find fixed point free self-maps of the unit ball, retractions of the unit ball onto its boundary, contractions of the unit sphere, and nonzero maps without positive eigenvalues and normalized eigenvectors. In this paper, we give upper and lower estimates, or even explicit formulas, for the minimal Lipschitz constant and measure of noncompactness of such maps.

Fixed point theorems in partially ordered spaces and aplications

[ES]Recientemente, en la Teoría del punto fijo, han aparecido muchos resultados que obtienen condiciones suficientes para la existencia de un punto fijo si trabajamos con aplicaciones en un conjunto dotado de un orden parcial. Generalmente, estos resultados combinan dos teoremas del punto fijo fundamentales: el Teorema de la contracción de Banach y el Teorema de Knaster-Tarski.

Intrinsic ordering, combinatorial numbers and reliability engineering

[EN]A new algorithm for evaluating the top event probability of large fault trees (FTs) is presented. This algorithm does not require any previous qualitative analysis of the FT. Indeed, its efficiency is independent of the FT logic, and it only depends on the number n of basic system components and on their failure probabilities. Our method provides exact lower and upper bounds on the top event probability by using new properties of the intrinsic order relation between binary strings. The intrinsic order enables one to select binary n-tuples with large occurrence probabilities without necessity to evaluate them. This drastically reduces the complexity of the problem from exponential (2n binary n-tuples) to linear (n Boolean variables)...

Estimating persistent Betti numbers for discrete shape analysis

Persistent Topology is an innovative way of matching topology and geometry, and it proves to be an effective mathematical tool in shape analysis. In order to express its full potential for applications, it has to interface with the typical environment of Computer Science: It must be possible to deal with a finite sampling of the object of interest, and with combinatorial representations of it. Following that idea, the main result claims that it is possible to construct a relation between the persistent Betti numbers (PBNs; also called rank invariant) of a compact, Riemannian submanifold X of R^m and the ones of an approximation U of X itself, where U is generated by a ball covering centered in the points of the sampling. Moreover we can state a further result in which, this time, we relate X with a finite simplicial complex S generated, thanks to a particular construction, by the sampling points. To be more precise, strict inequalities hold only in "blind strips'', i.e narrow areas around the discontinuity sets of the PBNs of U (or S). Out of the blind strips, the values of the PBNs of the original object, of the ball covering of it, and of the simplicial complex coincide, respectively.