Multiclass cancer diagnosis using tumor gene expression signatures

The optimal treatment of patients with cancer depends on establishing accurate diagnoses by using a complex combination of clinical and histopathological data. In some instances, this task is difficult or impossible because of atypical clinical presentation or histopathology. To determine whether the diagnosis of multiple common adult malignancies could be achieved purely by molecular classification, we subjected 218 tumor samples, spanning 14 common tumor types, and 90 normal tissue samples to oligonucleotide microarray gene expression analysis. The expression levels of 16,063 genes and expressed sequence tags were used to evaluate the accuracy of a multiclass classifier based on a support vector machine algorithm. Overall classification accuracy was 78%, far exceeding the accuracy of random classification (9%). Poorly differentiated cancers resulted in low-confidence predictions and could not be accurately classified according to their tissue of origin, indicating that they are molecularly distinct entities with dramatically different gene expression patterns compared with their well differentiated counterparts. Taken together, these results demonstrate the feasibility of accurate, multiclass molecular cancer classification and suggest a strategy for future clinical implementation of molecular cancer diagnostics.

Molecular classification of multiple tumor types

Using gene expression data to classify tumor types is a very promising tool in cancer diagnosis. Previous works show several pairs of tumor types can be successfully distinguished by their gene expression patterns (Golub et al. 1999, Ben-Dor et al. 2000, Alizadeh et al. 2000). However, the simultaneous classification across a heterogeneous set of tumor types has not been well studied yet. We obtained 190 samples from 14 tumor classes and generated a combined expression dataset containing 16063 genes for each of those samples. We performed multi-class classification by combining the outputs of binary classifiers. Three binary classifiers (k-nearest neighbors, weighted voting, and support vector machines) were applied in conjunction with three combination scenarios (one-vs-all, all-pairs, hierarchical partitioning). We achieved the best cross validation error rate of 18.75% and the best test error rate of 21.74% by using the one-vs-all support vector machine algorithm. The results demonstrate the feasibility of performing clinically useful classification from samples of multiple tumor types.

GeneCluster 2.0: an advanced toolset for bioarray analysis

SUMMARY

GeneCluster 2.0 is a software package for analyzing gene expression and other bioarray data, giving users a variety of methods to build and evaluate class predictors, visualize marker lists, cluster data and validate results. GeneCluster 2.0 greatly expands the data analysis capabilities of GeneCluster 1.0 by adding classification, class discovery and permutation test methods. It includes algorithms for building and testing supervised models using weighted voting and k-nearest neighbor algorithms, a module for systematically finding and evaluating clustering via self-organizing maps, and modules for marker gene selection and heat map visualization that allow users to view and sort samples and genes by many criteria. GeneCluster 2.0 is a stand-alone Java application and runs on any platform that supports the Java Runtime Environment version 1.3.1 or greater.

AVAILABILITY

http://www.broad.mit.edu/cancer/software

Hyperhomocyst(e)inemia induces multiorgan damage

Hyperhomocyst(e)inemia has been associated with the development of hypertension, stroke, and cardiovascular, cerebral/neuronal, renal, and liver diseases. To test the hypothesis that homocyst(e)ine plays an integrated role in multiorgan injury in hypertension, we employed: (1) spontaneously hypertensive rats (SHR) in which endogenous homocyst(e)ine levels are moderately high (18.1 +/- ().5 microM); (2) control age- and sex-matched Wistar Kyoto (WKY) rats in which homocyst(e)ine levels are normal (3.7 +/- 0.3 microM). To create the pathophysiological condition of hyperhomocyst(e)inemia, 20 mg/day homocyst(e)ine was administered for 12 weeks in (3) SHR (SHR-H) and in (4) WKY (WKY-H) rats. (5) Endogenous homocyst(e)ine levels were reduced slightly but not significantly from 18.1 +/- 0.5 microM to 12.5 +/- 0.7 microM in SHR by folic acid administration (SHR-F). Plasma and tissue levels of homocyst(e)ine were determined by HPLC and spectrophotometric methods. Plasma and sympathetic ganglion (neuronal) matrix metalloproteinase (MMP) activity was measured by zymography. Activity of neuronal MMP was increased in hyperhomocyst(e)inemic rats as compared with controls. Mean arterial pressure (mmHg) was 95 +/- 5, 126 +/- 8,157 +/- 10, 188 +/- 5, and 165 +/- 12 in WKY, WKY-H, SHR, SHR-H, and SHR-F, respectively. Urinary protein (mg/day) was 0.11 +/- 0.03, 0.88 +/- 0.22, 0.47 +/- 0.10, 0.89 +/- 0.21, and 0.81 +/- 0.21 in WKY, WKY-H. SHR, SHR-H, and SHR-F, respectively, as measured by the Bio-Rad dye binding assay. The relationships between increased arterial pressure, plasma homocyst(e)ine, and urinary protein were delineated. Plasma and neuronal creatinine phosphokinase (CK) isoenzymes were measured by agarose gel electrophoresis. All three CK isoenzymes, i.e., MM, MB, and BB, specific for skeletal, cardiac, and nerve tissue, respectively, were induced following 12 weeks' hyperhomocyst(e)inemia, suggesting multiorgan injury by homocyst(e)ine. Homocyst(e)ine induces endocardial endothelial cell (capillary) apoptosis and may reduce capillary cell density. Structural damage to aorta, myocardium, kidney, and renalureter was analyzed by histology. Results suggested an integrated physiological role of homocyst(e)ine in injury to the endothelial/epithelial cell lining in the respective organs.

Sexual dimorphisms in the effect of low-level p25 expression on synaptic plasticity and memory

p25, a degradation product of p35, has been reported to accumulate in the forebrain of patients with Alzheimer's disease. p25 as well as p35 are activators of cyclin-dependent kinase 5 (Cdk5) although p25/Cdk5 and p35/Cdk5 complexes have distinct properties. Several mouse models with high levels of p25 expression exhibit signs of neurodegeneration. On the contrary, we have shown that low levels of p25 expression do not cause neurodegeneration and are even beneficial for particular types of learning and memory [Angelo et al., (2003) Eur J. Neurosci., 18, 423-431]. Here, we have studied the influence of low-level p25 expression in hippocampal synaptic plasticity and in learning and memory for each sex separately in two different genetic backgrounds (129B6F1 and C57BL/6). Surprisingly, we found that low-level p25 expression had different consequences in male and female mutants. In the two genetic backgrounds LTP induced by a strong stimulation of the Schaffer's collaterals (four trains, 1-s duration, 5-min interval) was severely impaired in male, but not in female, p25 mutants. Furthermore, in the two genetic backgrounds spatial learning in the Morris water maze was faster in female p25 mutants than in male transgenic mice. These results suggest that, in women, the production of p25 in Alzheimer's disease could be a compensation for some early learning and memory deficits.

Basically substituted ellipticine analogues as potential antitumor agents

Installation of a basic side chain on the ring nitrogen of ellipticine did, as expected, improve the DNA binding properties of these molecules as measured by an ethidium displacement assay. In vivo antitumor activity was not, however, improved.

Family caregivers: what do they need? An integrative review

OBJECTIVE

Aimed to identify the main needs expressed by family caregivers in caring for adependent person.

METHOD

An integrative review of the literature in the period between 2010 and 2015 using specific search engine tools in the EBSCO and SCOPUSdatabases.

RESULTS

11 articles were selected, and the analysis of the scientific evidence obtained allowed for organizing the results into five thematic areas:transition into care, being responsible for everything, the importance of support, access to formal support, communication and informationprocesses.

CONCLUSION

The results showed that caregivers have many needs in different areas, which should be addressed in nursing interventions.

OBJETIVO

Este estudo teve como objetivo identificar quais as principais necessidades manifestadas pelo cuidador familiar no cuidado à pessoa dependente.

MÉTODO

Realizou-se uma revisão integrativa da literatura no período entre 2010 e 2015 com o recurso de instrumentos de busca específicos, nas bases de dados EBSCO e SCOPUS.

RESULTADOS

Foram selecionados 11 artigos A análise da evidência científica obtida permitiu organizar os resultados em cinco áreas temáticas: a transição para o cuidar, o ser responsável por tudo, a importância do suporte, o acesso aos apoios formais, a comunicação e a informação na tomada de decisão.

CONCLUSÃO

Os resultados demonstram que o cuidador apresenta inúmeras necessidades em áreas distintas,as quais devem ser abordadasnas intervenções de enfermagem.

The Caenorhabditis elegans dosage compensation machinery is recruited to X chromosome DNA attached to an autosome

The dosage compensation machinery of Caenorhabditis elegans is targeted specifically to the X chromosomes of hermaphrodites (XX) to reduce gene expression by half. Many of the trans-acting factors that direct the dosage compensation machinery to X have been identified, but none of the proposed cis-acting X chromosome-recognition elements needed to recruit dosage compensation components have been found. To study X chromosome recognition, we explored whether portions of an X chromosome attached to an autosome are competent to bind the C. elegans dosage compensation complex (DCC). To do so, we devised a three-dimensional in situ approach that allowed us to compare the volume, position, and number of chromosomal and subchromosomal bodies bound by the dosage compensation machinery in wild-type XX nuclei and XX nuclei carrying an X duplication. The dosage compensation complex was found to associate with a duplication of the right 30% of X, but the complex did not spread onto adjacent autosomal sequences. This result indicates that all the information required to specify X chromosome identity resides on the duplication and that the dosage compensation machinery can localize to a site distinct from the full-length hermaphrodite X chromosome. In contrast, smaller duplications of other regions of X appeared to not support localization of the DCC. In a separate effort to identify cis-acting X recognition elements, we used a computational approach to analyze genomic DNA sequences for the presence of short motifs that were abundant and overrepresented on X relative to autosomes. Fourteen families of X-enriched motifs were discovered and mapped onto the X chromosome.

Reflexões sobre o excesso de cesarianas no Brasil e a autonomia das mulheres

A medicalização do parto, como resultado da medicalização social, tem sido descrita como um processo sociocultural complexo que transforma em necessidades médicas, vivências, sofrimentos e dores antes administradas no próprio ambiente familiar ou comunitário. O objetivo é refletir sobre o excesso de cesarianas no Brasil, em uma perspectiva crítica e propositiva. Dados sobre taxas de cesariana e estudos sobre a preferência das mulheres sobre a via de parto são discutidos com a finalidade de contribuir para o debate sobre autonomia das usuárias do sistema de saúde. A medicalização é uma transformação cultural que influenciou a capacidade de enfrentamento autônomo da experiência de parir, visto que implica em dependência excessiva, heteronomia e consumo abusivo de cesarianas. Além disso, discutem-se as redes e os movimentos sociais como possíveis facilitadores da autonomia das mulheres, na medida em que possibilitam apoio mútuo e compartilhamento de experiências, contribuindo para a construção de relações mais igualitárias entre as mulheres e os profissionais de saúde. A participação nessas redes possibilita a mobilização coletiva das mulheres no sentido de reivindicarem seus direitos junto às diversas instâncias da sociedade.

Nurses’ attitudes regarding the importance of families in pediatric nursing care

Affective, cognitive and behavioral components affect nurses´ attitudes to include families in the care processes. The purpose of this study was to investigate the attitudes of nurses about the importance of including families in nursing care. Data collection was performed in pediatric and maternal-child unit of a Brazilian university hospital. A sample of 50 nurses completed the Portuguese version of the instrument Families’Importance in Nursing Care-Nurses’ Attitudes (FINC-NA). The results indicated that nurses have supportive attitudes regarding families participation in nursing care. Attitudes of lower support for involving families in nursing care were found among nurses with older age, more time in the profession and who had no previous contact with contents related to Family Nursing. The application of the instrument in other contexts of assistance may help to illuminate important aspects of the challenges to implementing a family-centered approach in clinical practice.





Synthesis and antifilarial activity of N-[4-[[4-alkoxy-3-[(dialkylamino)methyl]phenyl]amino]- 2-pyrimidinyl]-N'-phenylguanidines

A series of N-[4-[[4-alkoxy-3-[(dialkylamino)methyl]phenyl]amino]- 2-pyrimidinyl]-N'-phenylguanidines have been synthesized for antifilarial evaluation. Reaction of the appropriate benzenamines with N-cyanoguanidine, followed by condensation of the resultant N-phenylimidodicarbonimidic diamides (V) with ethyl 4,4,4-trifluoro-3-oxobutanoate provided the intermediate N-(4-hydroxy-2-pyrimidinyl)-N'-phenylguanidines VIa. Alternatively, compounds VIa were synthesized by reaction of the requisite beta-keto esters (VII) with N-cyanoguanidine to give the (4-hydroxy-2-pyrimidinyl)cyanamides (VIII), followed by treatment with the desired benzenamines. Chlorination with POCl3 and condensation with the appropriate benzenamines (IX) generated the desired guanidines (X). Antifilarial activity was confined to adult Litomosoides carinii infections, and a structure-activity relationship for this activity is discussed. Lack of activity against L. carinii microfilaria and adult Brugia pahangi infections preclude further work in this area pending evaluation in additional experimental models.

O significado da hospitalização para a criança pré-escolar: um modelo teórico

Este estudo teve como objetivo compreender o significado de estar hospitalizada, para a criança pré-escolar. Os referenciais teóricos foram o Interacionismo Simbólico e a teoria de Vygotsky sobre a brincadeira simbólica da criança e o referencial metodológico foi a Teoria Fundamentada nos Dados. Participaram do mesmo 11 crianças de três a seis anos de idade. As estratégias de coleta de dados foram: observação participante, entrevista com as crianças, mediada pelo Brinquedo Terapêutico e entrevista com as mães. A análise dos dados permitiu construir o modelo teórico Crescendo com a presença protetora da mãe, que evidencia a vulnerabilidade, a força da criança e a proteção recebida da mãe, para enfrentar o mistério e o terror da hospitalização.

Between freedom and reclusion: social support as a quality-of-life component in the family caregiver-dependent person binomial

This is a qualitative study which uses Grounded Theory as its methodological framework and Symbolic Interactionism as a theoretical base to understand the experience of family caregivers for Cerebrovascular Accident (CVA) patients with regard to social support during their rehabilitation process at home. The components (themes and categories) of the phenomenon assuming home care and specifically the themes assuming care with support and assuming care without support were inter-related for the purpose of comparison and analysis, in order to apprehend how the interaction between them occurred. It was observed that, in addition to the recovery of the patient's autonomy, social support is one of the intervenient components in the quality of life for the family caregiver-disabled person binomial, particularly with respect to the caregiver's freedom to resume his/her life plan.

Interação cuidador familiar-pessoa com AVC: autonomia compartilhada

Trata-se de um estudo qualitativo, utilizando-se como referencial metodológico a Grounded Theory e como referencial teórico o Interacionismo Simbólico, para compreender a experiência de cuidadores familiares de pessoas com AVC, acerca das modalidades de cuidado adotadas por eles, durante o processo de reabilitação de uma pessoa com AVC no domicílio. Tais modalidades podem ser exercidas: incentivando o doente a recuperar a sua autonomia; e não estimulando a autonomia do doente. Ao inter-relacionar os componentes relativos à experiência, evidenciamos que o próprio cuidador familiar percebe que os processos de retomada da autonomia - da pessoa vitimada pelo AVC e de sua própria - se configuram como interdependentes e condicionados ao nível de reabilitação alcançado pelo doente.

Vulnerabilidade da família: desenvolvimento do conceito

O objetivo deste estudo foi desenvolver o conceito vulnerabilidade da família. Os dados foram coletados utilizando-se a estratégia da Análise Qualitativa de Conceito que consta de duas etapas: na primeira, a fase teórica, utilizou-se dados da literatura e, na segunda, a fase de campo, entrevista e observação de 12 famílias vivenciando uma experiência de doença e hospitalização de um filho. O referencial teórico foi o Interacionismo Simbólico, dando sustentação à Teoria Fundamentada nos Dados, utilizada para guiar a coleta e análise dos dados na etapa de campo. Como resultado, construiu-se um modelo teórico cuja categoria central define a vulnerabilidade da família como SENTINDO-SE AMEAÇADA EM SUA AUTONOMIA, em razão das interações com a doença, família e equipe. A comparação das duas análises permitiu elaborar uma proposição teórica de vulnerabilidade da família e avançar em termos de conhecimento teórico para a área de enfermagem da família.

[Experiencing a difficult and revealing passage with her hospitalized child--a live-in mother's experience]

This study was conducted with live-in mother in university hospital. The objectives were as follows: to understand the experienced interactions, to identify the meanings that a family attribute to the experience of going through the child's hospitalization, to identify what the experience of hospitalization provokes in the family life and construct a model theory representative of the experience. Reference Theory the Symbolic Interactionism and Reference Methodology Grounded Theory had been utilized. From results appeared the phenomenon Going in search of solution and Going through a difficult situation. Through these phenomena, the main category Experiencing a difficult and revealing passage with her child was identified.

[The use of videotaping in qualitative research]

Considering advancements in data collection methods, we explore the use of videotaping in qualitative research. This bibliographical study aims at developing reflections on the possibilities of using videotapes in research and at providing material to researchers. The video is used as an instrument of data collection and generation. We mention technical aspects, such as the utilization of a mobile or fixed camera. By means of the latter, the authors report their experience, emphasizing compliance with the neutrality principle and the possibility of editing the images obtained as a means of generating new data. The authors highlight that it was possible to detect contradictions between discourse and behavior through the use of videotaping and interviews. The authors also discuss the ethical principles set by CNS Resolution 196/96 and other ethical questions, whose solutions should be based on the agreement between researchers and subjects.

[Trying to preserve the integrity of the family unit: the family living with the experience of having a child in the pediatric intensive care unit]

The purposes of this study were to: understand the dynamic functioning of the family with a child admitted to a pediatric intensive care unit (PICU) and to construct a theoretical model about the living experience of a family with a child admitted to the PICU. The study used as a theoretical reference the Symbolic Interactionism, and the Grounded theory methodology. The comparative analysis of the data permitted identify two phenomena: Having a family rupture and Living with the possibility of loosing a child. The relationship of these phenomena has permitted the identification of the core category TRYING TO PRESERVE THE INTEGRITY OF THE FAMILY UNIT based on which it was possible to propose a theoretical model to explain the experience.

[Family's presence in the pediatric emergency room: opinion of health's professionals]

OBJECTIVE

To learn the opinion of health professionals regarding the presence of family during pediatric emergency care.

METHODS

Cross-sectional study, performed with 46 health professionals, members of the medical and nursing team of a pediatric emergency service. The data were collected via the application of a questionnaire composed by variables related to the opinion of professionals about the studied subject, in line with the professional category and the vocational training time, as well as invasive procedures during which the presence of family is authorized by the professionals.

RESULTS

The medical staff and the professionals with shorter time after graduation (<10 years) were more favorable to the presence of family during emergency procedures. Regarding the complexity of the procedures, the nursing staff proved more favorable to the presence of family during less complex procedures-peripheral venous puncture and fluid sample-whereas the consent of the medical staff was similar, regardless the performed procedure-peripheral venous puncture, fluid sample, intraosseous puncture, tracheal intubation and cardiopulmonary resuscitation.

CONCLUSIONS

In order to allow the presence of family in the emergency room, it is necessary to sensitize health professionals, especially the nursing staff and the longer-term acting professionals, which are more resistant to allow the family to stay with the child during the emergency care.

Clinical role of the nurse: concept analysis

AIMS AND OBJECTIVES

To identify the attributes of the concept 'clinical role of the nurse' in the literature.

BACKGROUND

The concept of nurses' clinical role is frequently mentioned in literature, but hardly explored in conceptual terms. This has implications for nursing practice and education.

DESIGN

Qualitative and descriptive study, which corresponds to the first phase in the concept development of the qualitative concept analysis method - identification of concept attributes.

METHODS

The critical literature analysis method was used to identify the antecedents, defining attributes and consequences of the nurse's clinical role. A systematic literature search was undertaken in International Literature in Health Sciences, Cumulative Index to Nursing and Allied Health Literature and Latin American and Caribbean Health Sciences.

RESULTS

The clinical role was shown to be a process of complex interaction between nurse and patient, with critical thinking, informed experience and a sense of clinical autonomy as its antecedents. Consequences of nurses' clinical role include transformations in the organisation and process of nursing practice. A theoretical proposal was elaborated for the concept of the clinical role of the nurse, identifying the defining attributes, antecedents and consequences.

CONCLUSIONS

The clinical role of the nurse concept that was developed represents innovative evidence on the theme. Nevertheless, a deeper understanding of nurses' clinical role is needed, as well as refinement of its conceptual components. This study should be integrated into a field research project, designed to illuminate how nurses manifest and articulate the concept in clinical practice.

RELEVANCE TO CLINICAL PRACTICE

Knowledge of clinical role attributes, associated with nursing competencies, can contribute to reflection on the dimensions involved in nursing practice and inform not only teaching and professional practice, but also health policies.

A organização familiar para o cuidado dos filhos: percepção das mães em uma comunidade de baixa renda

Este estudo teve como objetivos compreender a percepção que mães de uma comunidade de baixa renda da cidade de São Paulo, têm sobre o significado do seu papel na estrutura familiar, em relação ao cuidado dos filhos e as estratégias utilizadas para desempenhar esse cuidado. A análise etnográfica nos possibilitou reconhecer 6 domínios culturais e resultados reveladores de que a mãe ocupa lugar central na família e é responsável pela educação, criação e socialização dos filhos. A adaptação do seu papel caracteriza-se pelo atendimento às necessidades de sobrevivência dos filhos, entretanto com o crescimento das crianças, demonstra insegurança frente à isso.

BRINQUEDO: UM CAMINHO PARA A COMPREENSÃO DA CRIANÇA HOSPITALIZADA

A utilização de brinquedos, em hospitais, é um dos recursos que facilitam a experiência da hospitalizarão para a criança Além disso, é um valioso instrumento de informação para a equipe de saúde. A autora apresenta um estudo, onde, através da utilização do "brinquedo terapêutico", pode obter elementos para a compreensão das necessidades da criança hospitalizada.

Identificação da vulnerabilidade da família na prática clínica

Neste trabalho apresentamos o relato de uma situação clínica em que identificamos a vulnerabilidade da família, propiciando ao enfermeiro pediatra a utilização deste conceito na sua prática e intervenção com famílias. O estudo foi realizado com uma família que experienciava uma situação de doença e hospitalização de um filho. A vulnerabilidade foi identificada nas interações da família com a doença, a própria família e a equipe de saúde, e serviu de guia para o planejamento da assistência de enfermagem. As intervenções realizadas permitiram o fortalecimento da família para enfrentar a situação e o reconhecimento da importância para o enfermeiro pediatra utilizar resultados de pesquisa teórica em sua prática profissional.

[Approaching the family: presenting a new definition of family and care]

Identifying the need to comprehend how nurses 'move' to the family, with the intention of caring for them, the present study obtained twelve biographical narratives of pediatric nurses. The theoretical approach adopted was the Symbolic Interactionism and the methodological one was the Interpretative Interactionism. The analysis of the data allowed the reconstruction of a story which showed that through modifying the concept of caring and family is the process that approximate the pediatric nurses progressively to the family, to a being with them, reaching the freedom to act.