Hierarchical non‐negative matrix factorization to characterize brain tumor heterogeneity using multi‐parametric MRI

Tissue characterization in brain tumors and, in particular, in high‐grade gliomas is challenging as a result of the co‐existence of several intra‐tumoral tissue types within the same region and the high spatial heterogeneity. This study presents a method for the detection of the relevant tumor substructures (i.e. viable tumor, necrosis and edema), which could be of added value for the diagnosis, treatment planning and follow‐up of individual patients. Twenty‐four patients with glioma [10 low‐grade gliomas (LGGs), 14 high‐grade gliomas (HGGs)] underwent a multi‐parametric MRI (MP‐MRI) scheme, including conventional MRI (cMRI), perfusion‐weighted imaging (PWI), diffusion kurtosis imaging (DKI) and short‐TE ¹H MRSI. MP‐MRI parameters were derived: T₂, T₁ + contrast, fluid‐attenuated inversion recovery (FLAIR), relative cerebral blood volume (rCBV), mean diffusivity (MD), fractional anisotropy (FA), mean kurtosis (MK) and the principal metabolites lipids (Lip), lactate (Lac), N‐acetyl‐aspartate (NAA), total choline (Cho), etc. Hierarchical non‐negative matrix factorization (hNMF) was applied to the MP‐MRI parameters, providing tissue characterization on a patient‐by‐patient and voxel‐by‐voxel basis. Tissue‐specific patterns were obtained and the spatial distribution of each tissue type was visualized by means of abundance maps. Dice scores were calculated by comparing tissue segmentation derived from hNMF with the manual segmentation by a radiologist. Correlation coefficients were calculated between each pathologic tissue source and the average feature vector within the corresponding tissue region. For the patients with HGG, mean Dice scores of 78%, 85% and 83% were obtained for viable tumor, the tumor core and the complete tumor region. The mean correlation coefficients were 0.91 for tumor, 0.97 for necrosis and 0.96 for edema. For the patients with LGG, a mean Dice score of 85% and mean correlation coefficient of 0.95 were found for the tumor region. hNMF was also applied to reduced MRI datasets, showing the added value of individual MRI modalities. Copyright © 2015 John Wiley & Sons, Ltd.     

How to evaluate PCR assays for the detection of low‐level DNA

High sensitivity of PCR‐based detection of very low copy number DNA targets is crucial. Much focus has been on design of PCR primers and optimization of the amplification conditions. Very important are also the criteria used for determining the outcome of a PCR assay, e.g. how many replicates are needed and how many of these should be positive or what amount of template should be used? We developed a mathematical model to obtain a simple tool for quick PCR assay evaluation before laboratory optimization and validation procedures . The model was based on the Poisson distribution and the Binomial distribution describing parameters for singleplex real‐time PCR‐based detection of low‐level DNA. The model was tested against experimental data of diluted cell‐free foetal DNA. Also, the model was compared with a simplified formula to enable easy predictions. The model predicted outcomes that were not significantly different from experimental data generated by testing of cell‐free foetal DNA. Also, the simplified formula was applicable for fast and accurate assay evaluation. In conclusion, the model can be applied for evaluation of sensitivity of real‐time PCR‐based detection of low‐level DNA, and may also assist in design of new assays before standard laboratory optimization and validation is initiated.     

Impact of surgical aortic valve replacement on global and regional longitudinal strain across four flow gradient patterns of severe aortic stenosis

The International Journal of Cardiovascular Imaging - To evaluate the impact of surgical aortic valve replacement (SAVR) on global (GLS) and regional longitudinal strain (RLS) across four...     

‘You need to know in order to help’: how HIV-related stigma obstructs pastoral care in Kenyan primary schools

ABSTRACT

In low-resource and high HIV prevalence settings, schools are increasingly called upon as sites of care and support for vulnerable children. It is therefore crucial to understand the processes through which teachers take on pastoral care roles in response to the needs of vulnerable learners. As pastoral care is often contingent on teacher’s being aware of learner’s vulnerabilities and needs, we examine information-sharing between learners, their parents, and teachers. We draw on eight individual interviews conducted with teachers from three rural primary schools located in high HIV prevalence settings of the Siaya district of Western Kenya. The interviews were recorded, transcribed, and analysed using thematic network analysis. Our analysis revealed that HIV-related stigma made it difficult for vulnerable learners to disclose their vulnerabilities to teachers, fearing the repercussions of what might happen if other members of the school community would become aware of their association with HIV. When teachers sought out parents for more information, they were often met with denial of their vulnerabilities. This paper provides valuable insights into some of the difficulties primary school teachers face in ascertaining the pastoral care needs of vulnerable learners. It highlights that HIV-related stigma is a critical barrier for teachers to adopt a pastoral care role in high HIV prevalence communities of western Kenya.     

Neoadjuvante Therapiekonzepte beim Zervixkarzinom

Bei vielen Organentitäten ist das neoadjuvante Konzept mittlerweile etablierter Bestandteil der Therapie. Die neoadjuvante Therapie scheint auch in speziellen Situationen für Zervixkarzinompatientinnen interessant. Dieser Artikel soll einen Überblick über die aktuell diskutierten Einsatzgebiete in der Neoadjuvanz beim Zervixkarzinom darlegen, die verschiedenen Optionen werden besprochen. Als Grundlage für diesen Artikel dient die S3-Leitlinie Diagnostik, Therapie und Nachsorge der Patientin mit Zervixkarzinom AWMF(Arbeitsgemeinschaft der Wissenschaftlichen Medizinischen Fachgesellschaften)-Registernummer 032/033OL in der Version von 2014. Diese wurde durch die Literatur zur Update-Recherche der Neufassung der Leitlinie erweitert. Die NACT(neoadjuvante Chemotherapie)-Ansprechrate liegt bei 84 %, das progressionsfreie Überleben (PFS) über 5 Jahre und das Gesamtüberleben (OS) betragen 61,9 und 72,8 %. Das Ansprechen auf eine NACT korreliert mit einem besseren Langzeitüberleben. In einer Cochrane-Analyse von 2012 wurde gezeigt, dass eine neoadjuvante Chemotherapie vor geplanter Operation zu einer Verbesserung des PFS (HR [Hazard Ratio] 0,75, 95 %-KI [Konfidenzintervall] 0,61–0,93, p = 0,008) und des Gesamtüberlebens (HR 0,77, 95 %-KI 0,62–0,96, p = 0,02) führt. Unter Berücksichtigung des Random-Effekt-Modells war der Effekt aber nicht mehr signifikant (OR [Odds Ratio] 0,60, 95 %-KI 0,32–1,12, p = 0,11). Bei makroinvasiven Karzinomen in der Schwangerschaft vor einer möglichen Entbindung ist die NACT fester Bestandteil der Therapie. Die Datenlage zum Einsatz der neoadjuvanten Therapie beim Zervixkarzinom ist unklar. Die neoadjuvante Therapie ist aktuell kein Standard in der Behandlung des Zervixkarzinoms. Ungeklärt ist auch die Rolle des operativen Stagings und positiver Lymphknoten nach der neoadjuvanten Therapie. In verschiedenen Metaanalysen konnte gezeigt werden, dass die neoadjuvante Therapie das PFS und das OS verbessert. Dies gilt insbesondere für Frauen, die auf die neoadjuvante Therapie angesprochen haben.     

Trends in cancer incidence by socioeconomic deprivation in Germany in 2007 to 2018: An ecological registry-based study

Age-standardized cancer incidence has decreased over the last years for many cancer sites in developed countries. Whether these trends led to narrowing or widening socioeconomic inequalities in cancer incidence is unknown. Using cancer registry data covering 48 million inhabitants in Germany, the ecological association between age-standardized total and site specific (colorectal, lung, prostate and breast) cancer incidence in 2007 to 2018 and a deprivation index on district level (aggregated to quintiles) was investigated. Incidence in the most and least deprived districts were compared using Poisson models. Average annual percentage changes (AAPCs) and differences in AAPCs between deprivation quintiles were assessed using Joinpoint regression analyses. Age-standardized incidence decreased strongly between 2007 and 2018 for total cancer and all cancer sites (except female lung cancer), irrespective of the level of deprivation. However, differences in the magnitude of trends across deprivation quintiles resulted in increasing inequalities over time for total cancer, colorectal and lung cancer. For total cancer, the incidence rate ratio between the most and least deprived quintile increased from 1.07 (95% confidence interval: 1.01-1.12) to 1.23 (1.12-1.32) in men and from 1.07 (1.01-1.13) to 1.20 (1.14-1.26) in women. Largest inequalities were observed for lung cancer with 82% (men) and 88% (women) higher incidence in the most vs the least deprived regions in 2018. The observed increase in inequalities in cancer incidence is in alignment with trends in inequalities in risk factor prevalence and partly utilization of screening. Intervention programs targeted at socioeconomically deprived and urban regions are highly needed.