ProbFAST: Probabilistic Functional Analysis System Tool

Background: The post-genomic era has brought new challenges regarding the understanding of the organization and function of the human genome. Many of these challenges are centered on the meaning of differential gene regulation under distinct biological conditions and can be performed by analyzing the Multiple Differential Expression (MDE) of genes associated with normal and abnormal biological processes. Currently MDE analyses are limited to usual methods of differential expression initially designed for paired analysis. Results: We proposed a web platform named ProbFAST for MDE analysis which uses Bayesian inference to identify key genes that are intuitively prioritized by means of probabilities. A simulated study revealed that our method gives a better performance when compared to other approaches and when applied to public expression data, we demonstrated its flexibility to obtain relevant genes biologically associated with normal and abnormal biological processes. Conclusions: ProbFAST is a free accessible web-based application that enables MDE analysis on a global scale. It offers an efficient methodological approach for MDE analysis of a set of genes that are turned on and off related to functional information during the evolution of a tumor or tissue differentiation. ProbFAST server can be accessed at http://gdm.fmrp.usp.br/probfast.

A score system for quality evaluation of RNA sequence tags: an improvement for gene expression profiling

Background: High-throughput molecular approaches for gene expression profiling, such as Serial Analysis of Gene Expression (SAGE), Massively Parallel Signature Sequencing (MPSS) or Sequencing-by-Synthesis (SBS) represent powerful techniques that provide global transcription profiles of different cell types through sequencing of short fragments of transcripts, denominated sequence tags. These techniques have improved our understanding about the relationships between these expression profiles and cellular phenotypes. Despite this, more reliable datasets are still necessary. In this work, we present a web-based tool named S3T: Score System for Sequence Tags, to index sequenced tags in accordance with their reliability. This is made through a series of evaluations based on a defined rule set. S3T allows the identification/selection of tags, considered more reliable for further gene expression analysis. Results: This methodology was applied to a public SAGE dataset. In order to compare data before and after filtering, a hierarchical clustering analysis was performed in samples from the same type of tissue, in distinct biological conditions, using these two datasets. Our results provide evidences suggesting that it is possible to find more congruous clusters after using S3T scoring system. Conclusion: These results substantiate the proposed application to generate more reliable data. This is a significant contribution for determination of global gene expression profiles. The library analysis with S3T is freely available at http://gdm.fmrp.usp.br/s3t/.S3T source code and datasets can also be downloaded from the aforementioned website.

Identification of COL6A1 as a differentially expressed gene in human astrocytomas

Diffuse infiltrating gliomas are the most common tumors of the central nervous system. Gliomas are classified by the WHO according to their histopathological and clinical characteristics into four classes: grade I (pilocytic astrocytoma), grade II (diffuse astrocytoma), grade III (anaplastic astrocytoma), and grade IV (glioblastoma multiforme). Several genes have already been correlated with astrocytomas, but many others are yet to be uncovered. By analyzing the public SAGE data from 21 patients, comprising low malignant grade astrocytomas and glioblastomas, we found COL6A1 to be differentially expressed, confirming this finding by real time RT-PCR in 66 surgical samples. To the best of our knowledge, COL6A1 has never been described in gliomas. The expression of this gene has significantly different means when normal glia is compared with low-grade astrocytomas (grades I and II) and high-grade astrocytomas (grades III and IV), with a tendency to be greater in higher grade samples, thus rendering it a powerful tumor marker.

Dignified death: Concept development involving nurses and doctors in Pediatric Intensive Care Units

The aim of this study was to develop the concept of the dignified death of children in Brazilian pediatric intensive care units (PICUs). The Hybrid Model for Concept Development was used to develop a conceptual structure of dignified death in PICUs in an attempt to define the concept. The fieldwork study was carried out by means of in-depth interviews with nine nurses and seven physicians working in PICUs. Not unexpectedly, the concept of dignified death was found to be a complex phenomenon involving aspects related to decisions made by the multidisciplinary team as well as those related to care of the child and the family. Knowledge of the concept`s dimensions can promote reflection on the part of healthcare professionals regarding the values and beliefs underlying their conduct in end-of-life situations. Our hope is that this study may contribute to theoretic and methodological development in the area of end-of-life care.

The Emergence of Family Nursing in Brazil

A family perspective has been influencing Brazilian nursing practice and research, in particular in the past decade. Despite this development, there is evidence from research and from nurses` narratives that nurses still experience serious challenges in providing nursing care to families in Brazil. These challenges are analyzed and strategies are offered to support nurses in Brazil to ""think family"" and stimulate advanced practice in family nursing.

The ethical component of professional competence in nursing: An analysis

The purpose of this article is to initiate a philosophical discussion about the ethical component of professional competence in nursing from the perspective of Brazilian nurses. Specifically, this article discusses professional competence in nursing practice in the Brazilian health context, based on two different conceptual frameworks. The first framework is derived from the idealistic and traditional approach while the second views professional competence through the lens of historical and dialectical materialism theory. The philosophical analyses show that the idealistic view of professional competence differs greatly from practice. Combining nursing professional competence with philosophical perspectives becomes a challenge when ideals are opposed by the reality and implications of everyday nursing practice.

Images of a `good nurse` presented by teaching staff

Nursing is at the same time a vocation, a profession and a job. By nature, nursing is a moral endeavor, and being a `good nurse` is an issue and an aspiration for professionals. The aim of our qualitative research project carried out with 18 nurse teachers at a university nursing school in Brazil was to identify the ethical image of nursing. In semistructured interviews the participants were asked to choose one of several pictures, to justify their choice and explain what they meant by an ethical nurse. Five different perspectives were revealed: good nurses fulfill their duties correctly; they are proactive patient advocates; they are prepared and available to welcome others as persons; they are talented, competent, and carry out professional duties excellently; and they combine authority with power sharing in patient care. The results point to a transition phase from a historical introjection of religious values of obedience and service to a new sense of a secular, proactive, scientific and professional identity.

Composite materials obtained from textile fiber residue

This article presents the use of fibers residue from textile industry to minimize environmental problems associated with material accumulation. Composite materials utilizing textile fiber residues and high density polyethylene were prepared. Effect of treatment with hot water on fibers to prepare composites was studied to provide an improvement in mechanical properties of these materials. This treatment on fibers was evaluated by X-ray diffraction and scanning electron microscopy techniques. Experimental results of mechanical properties indicated higher mechanical strength for treated fiber composites compared to the untreated fiber composites.

Quality of life after coronary artery bypass surgery

This study assessed the quality of life (QoL) of 124 people with coronary artery disease who had coronary artery bypass surgery in a hospital in Brazil, by using the Modified Flanagan`s QoL instrument as the outcome measure. In addition, we studied the association between QoL and demographic, clinical, and perceived health status (using SF-36 Health Survey) measures. The mean for the Modified Flanagan`s QoL was high (M = 84.8, SD = 13.6) when compared to similar studies in the United States. In a linear regression analysis, the SF-36 subscales of vitality, and general and mental health were statistically significant (p < .01 for all), after adjusting for other demographic and clinical variables. Increasing values of those SF-36 subscales corresponded to increasing Modified Flanagan`s QoL. Despite the limitations of the study, this result suggests that future clinical interventions aimed to improve QoL in this population could focus on the patient`s psychological conditions after the surgery.

The effect of additional strengthening of hip abductor and lateral rotator muscles in patellofemoral pain syndrome: a randomized controlled pilot study

Objectives: To study the effect of additional strengthening of hip abductor and lateral rotator muscles in a strengthening quadriceps exercise rehabilitation programme for patients with the patellofemoral pain syndrome. Design: Randomized controlled pilot trial. Setting: Clinical setting with home programme. Participants: Fourteen patients with patellofemoral pain syndrome. Intervention: The subjects were randomly assigned to the intervention group (strengthening of quadriceps plus strengthening of hip abductor and lateral rotator muscles) or to the control group (strengthening of quadriceps). Both groups participated in a six-week home exercise protocol. Main outcome measures: The perceived pain symptoms, isokinetic eccentric knee extensor, hip abductor and lateral rotator torques and the gluteus medius electromyographic activity were assessed before and after treatment. Parametric and non-parametric tests were used to compare the groups before and after treatment with alpha = 0.05. Results: Only the intervention group improved perceived pain symptoms during functional activities (P=0.02-0.04) and also increased their gluteus medius electromyographic activity during isometric voluntary contraction (P=0.03), Eccentric knee extensors torque increased in both groups (P=0.04 and P=0.02). There was no statistically significant difference in the hip muscles torque in either group. Conclusion: Supplementation of strengthening of hip abductor and lateral rotator muscles in a strengthening quadriceps exercise programme provided additional benefits with respect to the perceived pain symptoms during functional activities in patients with patellofemoral pain syndrome after six weeks of treatment.

Control system design for flexible rotors supported by actively lubricated bearings

This article presents a methodology for calculating the gains of an output feedback controller for active vibration control of flexible rotors. The methodology is based on modal reduction. The proportional and derivative gains are obtained by adjusting the first two damping factors of the system and keeping the lengths of the two eigenvalues constant in the real-imaginary plane. The methodology is applied to an industrial gas compressor supported by active tilting-pad journal bearings. The unbalance response functions and mode shapes of the flexible rotor with and without active control are presented, showing significative improvement in damping reserve with the control. The importance of sensor location is emphasized, on the basis of the energy necessary to operate the active system over the entire frequency range studied. The best results are obtained by a decentralized controller, observing displacement and velocity of the shaft at the bearing positions.

Experimental analysis of active-passive vibration control using viscoelastic materials and extension and shear piezoelectric actuators

Hybrid active-passive damping treatments combine the reliability, low cost and robustness of viscoelastic damping treatments and the high-performance, modal selective and adaptive piezoelectric active control. Numerous hybrid damping treatments have been reported in the literature. They differ mainly by the relative positions of viscoelastic treatments, sensors and piezoelectric actuators. In this work we present an experimental analysis of three active-passive damping design configurations applied to a cantilever beam. In particular, two design configurations based on the extension mode of piezoelectric actuators combined with viscoelastic constrained layer damping treatments and one design configuration with shear piezoelectric actuators embedded in a sandwich beam with viscoelastic core are analyzed. For comparison purposes, a purely active design configuration with an extension piezoelectric actuator bonded to an elastic beam is also analyzed. The active-passive damping performance of the four design configurations is compared. Results show that active-passive design configurations provide more reliable and wider-range damping performance than the purely active configuration.

Macro-Fiber Composite Actuators for Flow Control of a Variable Camber Airfoil

This research employs solid-state actuators for delay of flow separation seen in airfoils at low Reynolds numbers. The flow control technique investigated here is aimed for a variable camber airfoil that employs two active surfaces and a single four-bar (box) mechanism as the internal structure. To reduce separation, periodic excitation to the flow around the leading edge of the airfoil is induced by a total of nine piezocomposite actuated clamped-free unimorph benders distributed in the spanwise direction. An electromechanical model is employed to design an actuator capable of high deformations at the desired frequency for lift improvement at post-stall angles. The optimum spanwise distribution of excitation for increasing lift coefficient is identified experimentally in the wind tunnel. A 3D (non-uniform) excitation distribution achieved higher lift enhancement in the post-stall region with lower power consumption when compared to the 2D (uniform) excitation distribution. A lift coefficient increase of 18.4% is achieved with the identified non-uniform excitation mode at the bender resonance frequency of 125 Hz, the flow velocity of 5 m/s and at the reduced frequency of 3.78. The maximum lift (Clmax) is increased 5.2% from the baseline. The total power consumption of the flow control technique is 639 mW(RMS).

Piezoceramic Composite Actuators for Flow Control in Low Reynolds Number Airflow

The research presented here employs solid-state actuators for flow separation delay or for forced attachment of separated flow seen in airfoils at low Reynolds numbers. To reduce separation, periodic excitation to the flow around the leading edge of the airfoil is induced by Macro-Fiber Composite actuated clamped-free unimorph benders. An electromechanical model of the unimorph is briefly presented and parametric study is conducted to aid the design of a unimorph to output high deformation at a desired frequency. The optimum frequency and amplitude for lift improvement at post-stall angles are identified experimentally. Along with aerodynamic force and structural displacement measurements, helium bubble flow visualization is used to verify existing separated flow, and the attached flow induced by flow control. The lift enhancement induced by several flow control techniques is compared. A symmetric and non-uniform (3D) flow excitation results in the maximum lift enhancement at post-stall region at the lowest power consumption level. A maximum lift coefficient increase of 27.5% (in the post-stall region) is achieved at 125 Hz periodic excitation, with the 3D symmetric actuation mode at 5 m/s and the reduced frequency of 3.78. C(l,max) is increased 7.6% from the baseline.