CAncer bioMarker Prediction Pipeline (CAMPP) - A standardized framework for the analysis of quantitative biological data

With the improvement of -omics and next-generation sequencing (NGS) methodologies, along with the lowered cost of generating these types of data, the analysis of high-throughput biological data has become standard both for forming and testing biomedical hypotheses. Our knowledge of how to normalize datasets to remove latent undesirable variances has grown extensively, making for standardized data that are easily compared between studies. Here we present the CAncer bioMarker Prediction Pipeline (CAMPP), an open-source R-based wrapper (https://github.com/ELELAB/CAncer-bioMarker-Prediction-Pipeline -CAMPP) intended to aid bioinformatic software-users with data analyses. CAMPP is called from a terminal command line and is supported by a user-friendly manual. The pipeline may be run on a local computer and requires little or no knowledge of programming. To avoid issues relating to R-package updates, a renv .lock file is provided to ensure R-package stability. Data-management includes missing value imputation, data normalization, and distributional checks. CAMPP performs (I) k-means clustering, (II) differential expression/abundance analysis, (III) elastic-net regression, (IV) correlation and co-expression network analyses, (V) survival analysis, and (VI) protein-protein/miRNA-gene interaction networks. The pipeline returns tabular files and graphical representations of the results. We hope that CAMPP will assist in streamlining bioinformatic analysis of quantitative biological data, whilst ensuring an appropriate bio-statistical framework

Å bli overvåket gjennom en radiosender - hvordan psykotiske uttryk forstås og kontrolleres i en psykiatrisk avdeling

Artikkelen handler om, hvordan psykotiske tanker, forestillinger og uttrykk blir forstått og håndtert av personalet og pasienter i en psykiatrisk avdeling. Pasienter, som blir diagnostisert som schizofrene, forteller ofte om spesielle erfaringer som for eksempel å bli overvåket av en radiosender eller å bli utsatt for et komplott. Artikkelen har bakgrunn i et åtte måneders feltarbeid ved en norsk psykiatrisk rehabiliteringsavdeling. Utgangspunktet er en enkelt pasient, som er overbevist om at en lege har lagt inn en radiosender i kroppen hans. Gjennom empiriske eksempler settes fokus på, hvordan disiplin og kontroll av psykotiske tanker utspiller seg. Materialet viser en asymmetri i maktforholdet mellom pasientenes og personalets ulike kunnskapsregimer. Dette forholdet analyseres i lys av bla. Michel Foucaults arbeider om makt, kontroll og selvteknologier. Det argumenteres for et mer åpent og dialogpreget møte med psykotiske uttrykk, der det gis større rom for ulike perspektiver påpsykotiske erfaringer

Er sykepleiediagnoser relevant i psykisk helsearbeid?

Akseptert versjon av en artikkel som er publisert i tidsskriftet: Tidsskrift for psykisk helsearbeid Forlagets publiserte versjon på Idunn: http://www.idunn.no/ts/tph/2009/01/er_sykepleiediagnoser_relevant_i_psykisk_helsearbeidI denne artikkelen, som baserer seg et på et åtte måneders feltarbeid i en psykiatrisk rehabiliteringsavdeling, retter jeg et kritisk søkelys på anvendelse av sykepleiediagnoser i psykisk helsearbeid. Jeg tar utgangspunkt i det amerikanske sykepleiediagnostiske klassifikasjonssystemet NANDA-NOC-NIC og vurderer relevansen av slike systemer på bakgrunn av erfaringer fra mitt feltarbeid. Jeg fant at såkalte tegn på psykisk lidelse ikke var statiske størrelser, men endret seg gjennom relasjoner, tid, læring og kontekst. Mine observasjoner tyder på at sykepleiediagnoser ikke egner seg i psykisk helsearbeid, fordi de ikke forholder seg til at mennesker forandrer seg. Klassifikasjonene slås fast som uforanderlige fakta, de problematiseres ikke og innbyr ikke til dialog eller utforsking av ulike perspektiver. De fanger ikke opp det komplekse og dynamiske mangfoldet av menneskelige følelser, tanker og atferd som jeg erfarte i mitt forskningsarbeid. Are Nursing Diagnoses Relevant in the Mental Health Field? In this article, which is based upon eight months of ethnographic fieldwork in a psychiatric rehabilitation unit, I critically view the application of nursing diagnoses in the mental health field. I focus on the American classification system NANDA-NOC-NIC and consider the relevance of this system in the light of my field experiences. I learned that so-called signs of mental illness were not static, but that they changed according to relations, contexts, time and learning. My observations therefore indicate that nursing diagnoses are not relevant in the mental health field, because they do not consider the fact that people change. Diagnoses are stated as unchangeable facts; they are not discussed or scrutinized. Moreover, they do not encourage dialogue or the exploration of different perspectives. They do not absorb the dynamic complexity of human emotions, thinking and demeanour, as observed during my field experiences

A Multi-Parametric Imaging Investigation of the Response of C6 Glioma Xenografts to MLN0518 (Tandutinib) Treatment.

Angiogenesis, the development of new blood vessels, is essential for tumour growth; this process is stimulated by the secretion of numerous growth factors including platelet derived growth factor (PDGF). PDGF signalling, through its receptor platelet derived growth factor receptor (PDGFR), is involved in vessel maturation, stimulation of angiogenesis and upregulation of other angiogenic factors, including vascular endothelial growth factor (VEGF). PDGFR is a promising target for anti-cancer therapy because it is expressed on both tumour cells and stromal cells associated with the vasculature. MLN0518 (tandutinib) is a potent inhibitor of type III receptor tyrosine kinases that demonstrates activity against PDGFRα/β, FLT3 and c-KIT. In this study a multi-parametric MRI and histopathological approach was used to interrogate changes in vascular haemodynamics, structural response and hypoxia in C6 glioma xenografts in response to treatment with MLN0518. The doubling time of tumours in mice treated with MLN0518 was significantly longer than tumours in vehicle treated mice. The perfused vessel area, number of alpha smooth muscle actin positive vessels and hypoxic area in MLN0518 treated tumours were also significantly lower after 10 days treatment. These changes were not accompanied by alterations in vessel calibre or fractional blood volume as assessed using susceptibility contrast MRI. Histological assessment of vessel size and total perfused area did not demonstrate any change with treatment. Intrinsic susceptibility MRI did not reveal any difference in baseline R2* or carbogen-induced change in R2*. Dynamic contrast-enhanced MRI revealed anti-vascular effects of MLN0518 following 3 days treatment. Hypoxia confers chemo- and radio-resistance, and alongside PDGF, is implicated in evasive resistance to agents targeted against VEGF signalling. PDGFR antagonists may improve potency and efficacy of other therapeutics in combination. This study highlights the challenges of identifying appropriate quantitative imaging response biomarkers in heterogeneous models, particularly considering the multifaceted roles of angiogenic growth factors

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Negotiating experience in patient involvement: Challenges of practicing storytelling in health care conversations

This paper investigates the challenges of integrating patient experiences in patient involving health care interventions. Experience occupying a central importance is often perceived to be something inherent to the patient to be communicated to the health professional during conversations. Yet drawing on empirical material from an ‘Intercultural Health Conversation’ and by departing in anthropological debates seeing experience as something socially expressed and negotiated this article demonstrates how boundaries and constraints emerge when experiences become socially expressed through the practice of storytelling in conversations in health care