Comprehensive validation of published immunohistochemical prognostic biomarkers of prostate cancer-what has gone wrong? A blueprint for the way forward in biomarker studies

BACKGROUND Treatment planning of localised prostate cancer remains challenging. Besides conventional parameters, a wealth of prognostic biomarkers has been proposed so far. None of which, however, have successfully been implemented in a routine setting so far. The aim of our study was to systematically verify a set of published prognostic markers for prostate cancer. METHODS Following an in-depth PubMed search, 28 markers were selected that have been proposed as multivariate prognostic markers for primary prostate cancer. Their prognostic validity was examined in a radical prostatectomy cohort of 238 patients with a median follow-up of 60 months and biochemical progression as endpoint of the analysis. Immunohistochemical evaluation was performed using previously published cut-off values, but allowing for optimisation if necessary. Univariate and multivariate Cox regression were used to determine the prognostic value of biomarkers included in this study. RESULTS Despite the application of various cut-offs in the analysis, only four (14%) markers were verified as independently prognostic (AKT1, stromal AR, EZH2, and PSMA) for PSA relapse following radical prostatectomy. CONCLUSIONS Apparently, many immunohistochemistry-based studies on prognostic markers seem to be over-optimistic. Codes of best practice, such as the REMARK guidelines, may facilitate the performance of conclusive and transparent future studies.

A comment on the article “A collinearity diagnosis of the GNSS geocenter determination” by P. Rebischung, Z. Altamimi, and T. Springer

Meindl et al. (Adv Space Res 51(7):1047–1064, 2013) showed that the geocenter z -component estimated from observations of global navigation satellite systems (GNSS) is strongly correlated to a particular parameter of the solar radiation pressure (SRP) model developed by Beutler et al. (Manuscr Geod 19:367–386, 1994). They analyzed the forces caused by SRP and the impact on the satellites’ orbits. The authors achieved their results using perturbation theory and celestial mechanics. Rebischung et al. (J Geod doi:10.1016/j.asr.2012.10.026, 2013) also deal with the geocenter determination with GNSS. The authors carried out a collinearity diagnosis of the associated parameter estimation problem. They conclude “without much exaggerating that current GNSS are insensitive to any component of geocenter motion”. They explain this inability by the high degree of collinearity of the geocenter coordinates mainly with satellite clock corrections. Based on these results and additional experiments, they state that the conclusions drawn by Meindl et al. (Adv Space Res 51(7):1047–1064, 2013) are questionable. We do not agree with these conclusions and present our arguments in this article. In the first part, we review and highlight the main characteristics of the studies performed by Meindl et al. (Adv Space Res 51(7):1047–1064, 2013) to show that the experiments are quite different from those performed by Rebischung et al. (J Geod doi:10.1016/j.asr.2012.10.026,2013) . In the second part, we show that normal equation (NEQ) systems are regular when estimating geocenter coordinates, implying that the covariance matrices associated with the NEQ systems may be used to assess the sensitivity to geocenter coordinates in a standard way. The sensitivity of GNSS to the components of the geocenter is discussed. Finally, we comment on the arguments raised by Rebischung et al. (J Geod doi:10.1016/j.asr.2012.10.026, 2013) against the results of Meindl et al. (Adv Space Res 51(7):1047–1064, 2013).

Processing 20 years of SLR observations to GNSS satellites

We process 20 years of SLR observations to GPS and GLONASS satellites using the reprocessed 3-day and 1-day microwave orbits provided by the Center for Orbit Determination in Europe (CODE) for the period 1994-2013. We study the dependency of the SLR residuals on the type, size, and a number of corner cubes in satellite laser reflector arrays (LRA). We show that the mean SLR residuals and the RMS of residuals depend on the coating of LRA and the block or type of GNSS satellites. The SLR mean residuals are also a function of the equipment used at SLR stations including detector types and detecting modes.

The eukaryotic way to defend and edit genomes by sRNA-targeted DNA deletion

While there is currently burgeoning interest in the application of the CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated genes) to genome editing, it is perhaps not widely appreciated that this is the second discovery of a small RNA (sRNA)-targeted DNA-deletion system. The first sRNA-targeted DNA-deletion system to be discovered, which we call IES/Ias (internal eliminated sequence/IES-associated genes) to contrast with CRISPR/Cas, is found in ciliates, and, like CRISPR/Cas, is thought to serve as a form of immune defense against invasive DNAs. The manner in which the ciliate IES/Ias system functions is distinct from that of the CRISPR/Cas system in archaea and bacteria, and arose independently through a synthesis of RNA interference-derived and DNA-specific molecular components. Despite the major differences between CRISPR/Cas and IES/Ias, both systems face similar conceptual challenges in targeting invasive DNAs. In this review, we focus on the discovery, effects, function, and evolutionary consequences of the IES/Ias system.

Downward Causation – The Way How Mind and Matter Interact?

The paper analyzes Karl Popper’s and John Eccles’ account of mind-matter interaction and compares their use of the concept of downward causation with other more recent accounts of it, especially those of Nancey Murphy and George Ellis. The argument includes John Polkinghorne’s take on Divine action, as it provides an interesting version of downward mind/matter-interaction. It will be argued that while downward causation is a speculative concept, it nevertheless remains the best approximation to a scientific perspective on mind/matter interaction that we can obtain. As a result, Popper’s and Eccles’ account seems to be more interesting in these regards than usually assumed, and should not continue to be overlooked in the debate.

Doppler Orbit Determination of Deep Space Probes by the Bernese GNSS Software: First Results of the Combined Orbit Determination from DSN and Inter-Satellite Ka-Band Data from the Grail Mission

Navigation of deep space probes is most commonly operated using the spacecraft Doppler tracking technique. Orbital parameters are determined from a series of repeated measurements of the frequency shift of a microwave carrier over a given integration time. Currently, both ESA and NASA operate antennas at several sites around the world to ensure the tracking of deep space probes. Just a small number of software packages are nowadays used to process Doppler observations. The Astronomical Institute of the University of Bern (AIUB) has recently started the development of Doppler data processing capabilities within the Bernese GNSS Software. This software has been extensively used for Precise Orbit Determination of Earth orbiting satellites using GPS data collected by on-board receivers and for subsequent determination of the Earth gravity field. In this paper, we present the currently achieved status of the Doppler data modeling and orbit determination capabilities in the Bernese GNSS Software using GRAIL data. In particular we will focus on the implemented orbit determination procedure used for the combined analysis of Doppler and intersatellite Ka-band data. We show that even at this earlier stage of the development we can achieve an accuracy of few mHz on two-way S-band Doppler observation and of 2 µm/s on KBRR data from the GRAIL primary mission phase.

Sublimation of water ice mixed with silicates and tholins: Evolution of surface texture and reflectance spectra, with implications for comets

The surfaces of many objects in the Solar System comprise substantial quantities of water ice sometimes mixed with minerals and/or organic molecules. The sublimation of the ice changes the structural and optical properties of these objects. We present laboratory data on the evolution of the structure and the visible and near-infrared spectral reflectance of icy surface analogues of cometary ices, made of water ice, complex organic matter (tholins) and silicates, as they undergo sublimation under low temperature (<-70°C) and pressure (10-⁵mbar) conditions inside the SCITEAS simulation chamber. As the water ice sublimated, we observed in situ the formation of a porous sublimation lag deposit, or sublimation mantle, at the top of the ice. This mantle is a network of filaments made of the non-volatile particles. Organics or phyllosilicates grains, able to interact via stronger inter-particulate forces than olivine grains, can form a foam-like structure having internal cohesiveness, holding olivine grains together. As this mantle builds-up, the band depths of the sub-surface water ice are attenuated until complete extinction under only few millimeters of mantle. Optically thick sublimation mantles are mainly featureless in the near infrared. The absorption bands of the minerals present in the mantle are weak, or even totally absent if minerals are mixed with organics which largely dominate the VIS–NIR reflectance spectrum. During sublimation, ejections of large fragments of mantle, triggered by the gas flow, expose ice particles to the surface. The contrast of brightness between mantled and ice-exposed areas depends on the wavelength range and the dust/ice ratio considered. We describe how the chemical nature of the non-volatiles, the size of their particles, the way they are mixed with the ice and the dust/ice mass ratio influence the texture, activity and spectro-photometric properties of the sublimation mantles. These data provide useful references for interpreting remote-sensing observations of comets and also icy satellites or trans-neptunian objects.

Quality of Life in Swiss Paediatric Inflammatory Bowel Disease Patients: Do Patients and Their Parents Experience Disease in the Same Way?

BACKGROUND AND AIMS Inflammatory bowel diseases (IBDs) may impair quality of life (QoL) in paediatric patients. We aimed to evaluate in a nationwide cohort whether patients experience QoL in a different way when compared with their parents. METHODS Sociodemographic and psychosocial characteristics were prospectively acquired from paediatric patients and their parents included in the Swiss IBD Cohort Study. Disease activity was evaluated by the Paediatric Crohn's Disease Activity Index (PCDAI) and the Paediatric Ulcerative Colitis Activity Index (PUCAI). We assessed QoL using the KIDSCREEN questionnaire. The QoL domains were analysed and compared between children and parents according to type of disease, parents' age, origin, education and marital status. RESULTS We included 110 children and parents (59 Crohn's disease [CD], 45 ulcerative colitis [UC], 6 IBD unclassified [IBDU]). There was no significant difference in QoL between CD and UC/IBDU, whether the disease was active or in remission. Parents perceived overall QoL, as well as 'mood', 'family' and 'friends' domains, lower than the children themselves, independently of their place of birth and education. However, better concordance was found on 'school performance' and 'physical activity' domains. Marital status and age of parents significantly influenced the evaluation of QoL. Mothers and fathers being married or cohabiting perceived significantly lower mood, family and friends domains than their children, whereas mothers living alone had a lower perception of the friends domain; fathers living alone had a lower perception of family and mood subscores. CONCLUSION Parents of Swiss paediatric IBD patients significantly underestimate overall QoL and domains of QoL of their children independently of origin and education.