Prior knowledge transfer across transcriptional data sets and technologies using compositional statistics yields new mislabelled ovarian cell line

Here, we describe gene expression compositional assignment (GECA), a powerful, yet simple method based on compositional statistics that can validate the transfer of prior knowledge, such as gene lists, into independent data sets, platforms and technologies. Transcriptional profiling has been used to derive gene lists that stratify patients into prognostic molecular subgroups and assess biomarker performance in the pre-clinical setting. Archived public data sets are an invaluable resource for subsequent in silico validation, though their use can lead to data integration issues. We show that GECA can be used without the need for normalising expression levels between data sets and can outperform rank-based correlation methods. To validate GECA, we demonstrate its success in the cross-platform transfer of gene lists in different domains including: bladder cancer staging, tumour site of origin and mislabelled cell lines. We also show its effectiveness in transferring an epithelial ovarian cancer prognostic gene signature across technologies, from a microarray to a next-generation sequencing setting. In a final case study, we predict the tumour site of origin and histopathology of epithelial ovarian cancer cell lines. In particular, we identify and validate the commonly-used cell line OVCAR-5 as non-ovarian, being gastrointestinal in origin. GECA is available as an open-source R package.

Positive narratives: the stories young people with Social, Emotional and Behavioural Difficulties (SEBD) tell about their futures

This research drew on positive psychology in order to offer an optimistic way of conceptualising the lives of young people who are often described as having ‘SEBD’ (Social, emotional, behaviour difficulties), now SEMH (Social, emotional, mental health) in the new SEND Code of Practice (2014). Positive psychology places emphasis on: the future, strengths, resources and potential, and suggests that negative experiences can build positive qualities. A life path tool was used in order to hear the stories that eight young people tell about themselves in the future. Narrative Oriented Inquiry (NOI) was used to analyse the themes of potential and growth in their stories. The young people in this research identified a range of strengths and resources in their lives that they had built as a result of earlier negative experiences. Their stories reveal their hopes and aspirations for the future. By giving these young people the opportunity to tell their stories this research permitted them to focus on where they were going, rather than where they had been.

Concussion: Examining the Effect of Neuronal Oxidative Stress on the Pathophysiology of Brain and Blood Brain Barrier Cells

Neuronal stretching during concussion alters glucose transport and reduces neuronal viability, also affecting other cells in the brain and the Blood Brain Barrier (BBB). Our hypothesis is that oxidative stress (OS) generated in neurons during concussions contributes to this outcome. To validate this, we investigated: (1) whether OS independently causes alterations in brain and BBB cells, namely human neuron-like, neuroblastoma cells (NCs), astrocyte cells (ACs) and brain microvascular endothelial cells (ECs), and (2) whether OS originated in NCs (as in concussion) is responsible for causing the subsequent alterations observed in ACs and ECs. We used H2O2 treatment to mimic OS, validated by examining the resulting reactive oxygen species, and evaluated alterations in cell morphology, expression and localization of the glucose transporter GLUT1, and the overall cell viability. Our results showed that OS, either directly affecting each cell type or originally affecting NCs, caused changes in several morphological parameters (surface area, Feret diameter, circularity, inter-cellular distance), slightly varied GLUT1 expression and lowered the overall cell viability of all NCs, ACs, and ECs. Therefore, we can conclude that oxidative stress, which is known to be generated during concussion, caused alterations in NCs, ACs, and ECs whether independently originated in each cell or when originated in the NCs and could further propagate the ACs and ECs.

O uso de filme como recurso pedagógico no estudo das epidemias: possibilidades na aprendizagem significativa

Acompanha: Epidemias na escola? Só em filmes: possibilidades de contaminação na aprendizagem significativa

Disseminated Cerebral and Intradural Extramedullary Spinal Nocardiosis in an Immunocompetent Patient

Disseminated nocardiosis of the central nervous system (CNS) has been rarely reported, especially in the immunocompetent patient. We report a case of cerebral and cervical intradural extramedullary nocardiosis likely to have been the result of disseminated spread from a pulmonary infective focus. Attempts at tissue biopsy and culture of the initial cerebral and pulmonary lesions both failed to yield the diagnosis. Interval development of a symptomatic intradural extramedullary cervical lesion resulted in open biopsy and an eventual diagnosis of nocardiosis was made. We highlight the diagnostic dilemma and rarity of spinal nocardial dissemination in an immunocompetent individual.

CATARINA 2012-Leg 1 - CTD-O2 Data report

The CATARINA Leg1 cruise was carried out from June 22 to July 24 2012 on board the B/O Sarmiento de Gamboa, under the scientific supervision of Aida Rios (CSIC-IIM). It included the occurrence of the OVIDE hydrological section that was performed in June 2002, 2004, 2006, 2008 and 2010, as part of the CLIVAR program (name A25) ), and under the supervision of Herlé Mercier (CNRSLPO). This section begins near Lisbon (Portugal), runs through the West European Basin and the Iceland Basin, crosses the Reykjanes Ridge (300 miles north of Charlie-Gibbs Fracture Zone, and ends at Cape Hoppe (southeast tip of Greenland). The objective of this repeated hydrological section is to monitor the variability of water mass properties and main current transports in the basin, complementing the international observation array relevant for climate studies. In addition, the Labrador Sea was partly sampled (stations 101-108) between Greenland and Newfoundland, but heavy weather conditions prevented the achievement of the section south of 53°40’N. The quality of CTD data is essential to reach the first objective of the CATARINA project, i.e. to quantify the Meridional Overturning Circulation and water mass ventilation changes and their effect on the changes in the anthropogenic carbon ocean uptake and storage capacity. The CATARINA project was mainly funded by the Spanish Ministry of Sciences and Innovation and co-funded by the Fondo Europeo de Desarrollo Regional. The hydrological OVIDE section includes 95 surface-bottom stations from coast to coast, collecting profiles of temperature, salinity, oxygen and currents, spaced by 2 to 25 Nm depending on the steepness of the topography. The position of the stations closely follows that of OVIDE 2002. In addition, 8 stations were carried out in the Labrador Sea. From the 24 bottles closed at various depth at each stations, samples of sea water are used for salinity and oxygen calibration, and for measurements of biogeochemical components that are not reported here. The data were acquired with a Seabird CTD (SBE911+) and an SBE43 for the dissolved oxygen, belonging to the Spanish UTM group. The software SBE data processing was used after decoding and cleaning the raw data. Then, the LPO matlab toolbox was used to calibrate and bin the data as it was done for the previous OVIDE cruises, using on the one hand pre and post-cruise calibration results for the pressure and temperature sensors (done at Ifremer) and on the other hand the water samples of the 24 bottles of the rosette at each station for the salinity and dissolved oxygen data. A final accuracy of 0.002°C, 0.002 psu and 0.04 ml/l (2.3 umol/kg) was obtained on final profiles of temperature, salinity and dissolved oxygen, compatible with international requirements issued from the WOCE program.

"A beleza é o grau mais elevado da verdade", "Os Memoráveis", de Lídia Jorge

Foi um prazer ler o último romance de Lídia Jorge, editado em março último, pela Dom Quixote. E as razões foram muitas. Porque fala de um dia da nossa história que me diz bastante: o 25 de abril de 1974. Apesar de ter dele apenas uma vaga ideia, foi sendo sempre falado na minha família e faz parte do meu presente. Porque reconheço grande parte da história ali contada, fazendo-me sentir cúmplice, quer do texto, quer dos acontecimentos. Porque o romance é um género que faz falta para contar a História. É um modo de chegar a muito mais gente que, depois de o ler (ou enquanto o vai lendo), vai ter vontade de ir procurar os outros livros – os de História não romanceada – para aprender sobre as horas daquela noite de 24 para 25 e sobre os seus protagonistas. Apesar da «transfiguração literária », como se lê na nota de edição, quem sabe se não os reconhecerá? E saltando muitas outras razões, porque é um livro muito bem escrito. As pontas que vão sendo soltas ao longo da narrativa juntam-se em outros momentos, completando quadros de sentido. Ana Maria Machada, a narradora, como participante da história, sabe tanto como nós sobre o que pensam as outras personagens, mas sabe um bocadinho mais do que, em certos momentos, conta. Por exemplo, quando a equipa de reportagem entrevista a viúva de um dos capitães de Abril (que percebemos ser Salgueiro Maia, apesar de apenas ser referido pela sua «alcunha doméstica», isto é, pelo nome que a mãe de Ana Maria lhe dera: Charlie 8) e tenta conseguir que esta diga quem queria mal ao marido, perante a relutância em acusar alguém, a «Machadinha» afirma «Nós sabíamos, mas não tão bem como ela, que as vinganças de que foram vítimas ele e os outros como ele, tinham tido autores concretos, nomeáveis, intérpretes e responsáveis, colocados no topo das estruturas criadas num país onde passara a haver liberdade para legitimar tudo e o seu contrário» (p. 249).

Composition of objectively measured physical activity and sedentary behaviour participation across the school-day, influence of gender and weight status: cross-sectional analyses among disadvantaged Victorian school children

BACKGROUND: The after-school period has been described as the 'critical window' for physical activity (PA) participation. However, little is known about the importance of this window compared with the before and during-school period among socioeconomically disadvantaged children, and influence of gender and weight status.

METHODS: 39 out of 156 (RR=25%) invited primary schools across 26 local government areas in Victoria, Australia, consented to participate with 856 children (RR=36%) participating in the wider study. The analysis sample included 298 Grade 4 and Grade 6 children (mean age: 11.2±1.1; 44% male) whom met minimum accelerometry wear-time criteria and had complete height, weight and health-behaviours questionnaire data. Accelerometry measured duration in daily light-intensity PA (LPA), moderate-to-vigorous PA (MVPA) and sedentary time (ST) was calculated for before-school=8-8:59, during-school=9:00-15:29 and after-school=15:30-18:00. Bivariate and multivariable linear regression analyses were conducted.

RESULTS: During-school represented the greatest accumulation of LPA and MVPA compared with the before and after-school periods. Boys engaged in 102 min/day of LPA (95% CI 98.5 to 104.9) and 62 min/day of MVPA (95% CI 58.9 to 64.7) during-school; girls engaged in 103 min/day of LPA (95% CI 99.7 to 106.5) and 45 min/day of MVPA (95% CI 42.9 to 47.4). Linear regression models indicated that girls with overweight or obesity engaged in significantly less LPA, MVPA and more time in ST during-school.

CONCLUSIONS: This study highlights the importance of in-school PA compared with after-school PA among socioeconomically disadvantage children whom may have fewer resources to participate in after-school PA.

The Amplifier - v. 12, no. 4

In this issue...Butte Symphony, Dr. Adam Smith, NASA, Petroleum Engineering Scholarship, Charlie Brown, Peanuts Cartoon, Glee club, Library-Museum Building

The Amplifier - v. 13, no. 4

In this issue...NASA, College Business Symposium, Marcus Daly, Charlie Brown, Caterpillar Company, Copper Lounge, Student Union Building

The Amplifier - v. 15, no. 5

In this issue...Coach Charlie Armey, Veterans, Marcus Daly, Campus Pollution, Satellites, Campus Parking, Elks National Foundation, Kieth Strom, International Club

The Amplifier - v. 17, no. 9

In this issue...Peace Corps, National Wildlife Federation, Powder Puff Football, Geological Map, Arnold Olsen, Seventeen Magazine, Frozen Daiquiri

The Documentary Take

Documentary photography and contemporary art are existentially quite distinct practices. Occasionally, with the passing of time, great documentary lifts from the contact sheet, the magazine page or the short print run book and finds its way onto gallery walls as art.Presented within the context of Walker Evans: the magazine work, curated by David Campany, The documentary take invites the question, what aspects of documentary practice are seeping into contemporary art now? In his commentary and practice, Evans distinguished between documentary as a forensic practice and the 'documentary style', which he saw as art making.With the exception of work presented by Ponch Hawkes and David Wadelton, the artists here—Destiny Deacon and Virginia Fraser; Simryn Gill; Sonia Leber and David Chesworth; Louis Porter; Patrick Pound and Charlie Sofo—are far from documentarians, yet all benefit from proximity to the foundational practice of Walker Evans.While Walker Evans may or may not be influential on these artists, his work forms a language that is now background knowledge for the making of images about the world where, artifice aside, truth is at least relevant. Perhaps documentary practice enables contemporary art to "attend to the real" [i], without binding it to a utilitarian or forensic intention.In attending to the real, the quest for the documentarian is to reveal something of the world, while that of the contemporary artist is to make meaning in and of the world.