Excretion of S- and O-methyl esters and other volatile compounds by Ochromonas danica

The formation of volatile excretion products was studied in axenic cultures of Ochromonas danica. Under microaerobic conditions in the light, an ac     

Morphological changes in external and internal feeding structures during the transition phyllosoma-puerulus-juvenile in the Western Rock Lobster (Panulirus cygnus,Decapoda: Palinuridae)

External and internal feeding structures of the pelagic final phyllosoma, the transitional puerulus, and the benthic juvenile Western Rock Lobster, Panulirus cygnus, were studied by means of scanning electron microscopy. The study revealed that the external feeding structures of phyllosomata are well equipped for capture and mastication of food. The foregut, however, is not clearly divided into pyloric and cardiac regions and a gastric mill is absent, although a comb row and gland filter are present. Juveniles, on the other hand, have a well-developed gastric mill and gastric teeth, and a cardiopyloric valve separates the foregut into cardiac and pyloric regions. External mouthparts of juveniles are suitable for mastication of solid food particles and bear numerous setae. In contrast, external mouthparts of pueruli are largely non-setose. Furthermore, although the foregut is differentiated into pyloric and gastric regions and a gland filter and comb row are present, a functional gastric mill is absent during the puerulus stage. Absence of such structures indicates that the puerulus may be a non-feeding stage. It is postulated that absence of (or reduced) feeding may be a response to an increased risk of predation rather than a result of the considerable morphological changes taking place during the transition from a planktonic to a benthic lifestyle, as has been previously proposed. © 1994 Wiley-Liss, Inc.     

Detection and correction of probe-level artefacts on microarrays

ABSTRACT: BACKGROUND: A recent large-scale analysis of Gene Expression Omnibus (GEO) data found frequent evidence for spatial defects in a substantial fraction of Affymetrix microarrays in the GEO. Nevertheless, in contrast to quality assessment, artefact detection is not widely used in standard gene expression analysis pipelines. Furthermore, although approaches have been proposed to detect diverse types of spatial noise on arrays, the correction of these artefacts is mostly left to either summarization methods or the corresponding arrays are completely discarded. RESULTS: We show that state-of-the-art robust summarization procedures are vulnerable to artefacts on arrays and cannot appropriately correct for these. To address this problem, we present a simple approach to detect artefacts with high recall and precision, which we further improve by taking into account the spatial layout of arrays. Finally, we propose two correction methods for these artefacts that either substitute values of defective probes using probeset information or filter corrupted probes. We show that our approach can identify and correct defective probe measurements appropriately and outperforms existing tools. CONCLUSIONS: While summarization is insufficient to correct for defective probes, this problem can be addressed in a straightforward way by the methods we present for identification and correction of defective probes. As these methods output CEL files with corrected probe values that serve as input to standard normalization and summarization procedures, they can be easily integrated into existing microarray analysis pipelines as an additional pre-processing step. An R package is freely available from http://www.bio.ifi.lmu.de/artefact-correction.     

Oesophageal cancer survival in Europe: A EUROCARE-4 study

Oesophageal cancer survival is poor with variation across Europe. No pan-European studies of survival differences by oesophageal cancer subtype exist. This study investigates rates and trends in oesophageal cancer survival across Europe. Data for primary malignant oesophageal cancer diagnosed in 1995–1999 and followed up to the end of 2003 was obtained from 66 cancer registries in 24 European countries. Relative survival was calculated using the Hakulinen approach. Staging data were available from 19 registries. Survival by region, gender, age, morphology and stage was investigated. Cohort analysis and the period approach were applied to investigate survival trends from 1988 to 2002 for 31 registries in 17 countries. In total 51,499 cases of oesophageal cancer diagnosed 1995–1999 were analysed. Overall, European 1- and 5-year survival rates were 33.4% (95% CI 32.9–33.9%) and 9.8% (95% CI 9.4–10.1%), respectively. Males, older patients and patients with late stage disease had poorer 1- and 5-year relative survival. Patients with squamous cell carcinoma had poorer 1-year relative survival. Regional variation in survival was observed with Central Europe above and Eastern Europe below the European pool. Survival for distant stage disease was similar across Europe while survival rates for localised disease were below the European pool in Eastern and Southern Europe. Improvement in European 1-year relative survival was reported (p = 0.016). Oesophageal cancer survival was poor across Europe. Persistent regional variations in 1-year survival point to a need for a high resolution study of diagnostic and treatment practices of oesophageal cancer.     

Predicting Optimal Outcomes in Cognitive Therapy or Interpersonal Psychotherapy for Depressed Individuals Using the Personalized Advantage Index Approach

IntroductionAlthough psychotherapies for depression produce equivalent outcomes, individual patients respond differently to different therapies. Predictors of outcome have been identified in the context of randomized trials, but this information has not been used to predict which treatment works best for the depressed individual. In this paper, we aim to replicate a recently developed treatment selection method, using data from an RCT comparing the effects of cognitive therapy (CT) and interpersonal psychotherapy (IPT).Methods134 depressed patients completed the pre- and post-treatment BDI-II assessment. First, we identified baseline predictors and moderators. Second, individual treatment recommendations were generated by combining the identified predictors and moderators in an algorithm that produces the Personalized Advantage Index (PAI), a measure of the predicted advantage in one therapy compared to the other, using standard regression analyses and the leave-one-out cross-validation approach.ResultsWe found five predictors (gender, employment status, anxiety, personality disorder and quality of life) and six moderators (somatic complaints, cognitive problems, paranoid symptoms, interpersonal self-sacrificing, attributional style and number of life events) of treatment outcome. The mean average PAI value was 8.9 BDI points, and 63% of the sample was predicted to have a clinically meaningful advantage in one of the therapies. Those who were randomized to their predicted optimal treatment (either CT or IPT) had an observed mean end-BDI of 11.8, while those who received their predicted non-optimal treatment had an end-BDI of 17.8 (effect size for the difference = 0.51).DiscussionDepressed patients who were randomized to their predicted optimal treatment fared much better than those randomized to their predicted non-optimal treatment. The PAI provides a great opportunity for formal decision-making to improve individual patient outcomes in depression. Although the utility of the PAI approach will need to be evaluated in prospective research, this study promotes the development of a treatment selection approach that can be used in regular mental health care, advancing the goals of personalized medicine.