A robust prognostic signature for hormone-positive node-negative breast cancer

BACKGROUND: Systemic chemotherapy in the adjuvant setting can cure breast cancer in some patients that would otherwise recur with incurable, metastatic disease. However, since only a fraction of patients would have recurrence after surgery alone, the challenge is to stratify high-risk patients (who stand to benefit from systemic chemotherapy) from low-risk patients (who can safely be spared treatment related toxicities and costs). METHODS: We focus here on risk stratification in node-negative, ER-positive, HER2-negative breast cancer. We use a large database of publicly available microarray datasets to build a random forests classifier and develop a robust multi-gene mRNA transcription-based predictor of relapse free survival at 10 years, which we call the Random Forests Relapse Score (RFRS). Performance was assessed by internal cross-validation, multiple independent data sets, and comparison to existing algorithms using receiver-operating characteristic and Kaplan-Meier survival analysis. Internal redundancy of features was determined using k-means clustering to define optimal signatures with smaller numbers of primary genes, each with multiple alternates. RESULTS: Internal OOB cross-validation for the initial (full-gene-set) model on training data reported an ROC AUC of 0.704, which was comparable to or better than those reported previously or obtained by applying existing methods to our dataset. Three risk groups with probability cutoffs for low, intermediate, and high-risk were defined. Survival analysis determined a highly significant difference in relapse rate between these risk groups. Validation of the models against independent test datasets showed highly similar results. Smaller 17-gene and 8-gene optimized models were also developed with minimal reduction in performance. Furthermore, the signature was shown to be almost equally effective on both hormone-treated and untreated patients. CONCLUSIONS: RFRS allows flexibility in both the number and identity of genes utilized from thousands to as few as 17 or eight genes, each with multiple alternatives. The RFRS reports a probability score strongly correlated with risk of relapse. This score could therefore be used to assign systemic chemotherapy specifically to those high-risk patients most likely to benefit from further treatment

Research on the reduction of SO2 doses in winemaking using lysozyme and oenological tannin

The effect of reducing the dose of sulfur dioxide on the physico-chemical and organoleptic properties of wines with Murfatlar controlled designation of origin was studied in this paper, experimenting with different prefermentative oenological treatments. For this purpose, a series of experimental variants was carried out on two Romanian grape cultivars for white wines ('Fetească regală') and red wines ('Fetească neagră'), using two yeast strains that produce low amounts of SO2 (Saccharomyces cerevisiae var. bayanus and Metschnikowia pulcherrima, a Non-Saccharomyces strain) and four prefermentative treatments with different doses of sulfur dioxide, lysozyme and oenological tannin. The obtained results highlighted the fact that reducing the dose of sulfur dioxide using lysozyme and oenological tannin can provide oxidative protection during the alcoholic fermentation stage, improving the organoleptic characteristics of white and red wines. From the physico-chemical point of view, the wines did not show statistically significant differences, except for the color intensity, which was higher in the case of the variants supplemented with 500 mg/L lysozymes, for both of the yeast strains used for fermentation. This study encourages the continuation of research regarding the experimentation of alternative products, to reduce the sulfur dioxide normally used in the winemaking process, in order to obtain healthy products, in accordance with current consumer requirements

Understanding the stigma of psychosis in ethnic minority groups: A qualitative exploration

Psychosis is a mental health difficulty which is widely stigmatized. The stigma of psychosis can lead to detrimental consequences and cause further distress. The aim of this study was to explore the experience of stigma and discrimination of psychosis from the perspective of service users from ethnic minority backgrounds. A total of 21 semistructured interviews were conducted with service users with psychosis from ethnic minority backgrounds examining their experiences of stigma from psychosis. Qualitative data were analyzed using thematic analysis. Five superordinate themes were identified, “social and cultural context of stigma,” “stigma is a family problem,” “stigma and discrimination within mental health services,” “intrapersonal impacts,” and “managing stigma within relationships.” Stigma is a significant concern for people with psychosis from an ethnic minority background. It is important that stigma and discrimination are appropriately assessed and considered within the care of people from ethnic minority backgrounds

Modeling precision treatment of breast cancer

Background: First-generation molecular profiles for human breast cancers have enabled the identification of features that can predict therapeutic response; however, little is known about how the various data types can best be combined to yield optimal predictors. Collections of breast cancer cell lines mirror many aspects of breast cancer molecular pathobiology, and measurements of their omic and biological therapeutic responses are well-suited for development of strategies to identify the most predictive molecular feature sets. Results: We used least squares-support vector machines and random forest algorithms to identify molecular features associated with responses of a collection of 70 breast cancer cell lines to 90 experimental or approved therapeutic agents. The datasets analyzed included measurements of copy number aberrations, mutations, gene and isoform expression, promoter methylation and protein expression. Transcriptional subtype contributed strongly to response predictors for 25% of compounds, and adding other molecular data types improved prediction for 65%. No single molecular dataset consistently out-performed the others, suggesting that therapeutic response is mediated at multiple levels in the genome. Response predictors were developed and applied to TCGA data, and were found to be present in subsets of those patient samples. Conclusions: These results suggest that matching patients to treatments based on transcriptional subtype will improve response rates, and inclusion of additional features from other profiling data types may provide additional benefit. Further, we suggest a systems biology strategy for guiding clinical trials so that patient cohorts most likely to respond to new therapies may be more efficiently identified

Expression variability of co-regulated genes differentiates Saccharomyces cerevisiae strains

Background: Saccharomyces cerevisiae (Baker’s yeast) is found in diverse ecological niches and is characterized by high adaptive potential under challenging environments. In spite of recent advances on the study of yeast genome diversity, little is known about the underlying gene expression plasticity. In order to shed new light onto this biological question, we have compared transcriptome profiles of five environmental isolates, clinical and laboratorial strains at different time points of fermentation in synthetic must medium, during exponential and stationary growth phases. Results: Our data unveiled diversity in both intensity and timing of gene expression. Genes involved in glucose metabolism and in the stress response elicited during fermentation were among the most variable. This gene expression diversity increased at the onset of stationary phase (diauxic shift). Environmental isolates showed lower average transcript abundance of genes involved in the stress response, assimilation of nitrogen and vitamins, and sulphur metabolism, than other strains. Nitrogen metabolism genes showed significant variation in expression among the environmental isolates. Conclusions: Wild type yeast strains respond differentially to the stress imposed by nutrient depletion, ethanol accumulation and cell density increase, during fermentation of glucose in synthetic must medium. Our results support previous data showing that gene expression variability is a source of phenotypic diversity among closely related organisms.Fundação para a Ciência e TecnologiaThe authors wish to thank Adega Cooperativa da Bairrada, Cantanhede, Portugal, for providing the commercial strains

The violent youth of bright and massive cluster galaxies and their maturation over 7 billion years

In this study, we investigate the formation and evolution mechanisms of the brightest cluster galaxies (BCGs) over cosmic time. At high redshift (z ∼ 0.9), we selected BCGs and most massive cluster galaxies (MMCGs) from the Cl1604 supercluster and compared them to low-redshift (z ∼ 0.1) counterparts drawn from the MCXC meta-catalogue, supplemented by Sloan Digital Sky Survey imaging and spectroscopy. We observed striking differences in the morphological, colour, spectral, and stellar mass properties of the BCGs/MMCGs in the two samples. High-redshift BCGs/MMCGs were, in many cases, star-forming, late-type galaxies, with blue broad-band colours, properties largely absent amongst the low-redshift BCGs/MMCGs. The stellar mass of BCGs was found to increase by an average factor of 2.51 ± 0.71 from z ∼ 0.9 to z ∼ 0.1. Through this and other comparisons, we conclude that a combination of major merging (mainly wet or mixed) and in situ star formation are the main mechanisms which build stellar mass in BCGs/MMCGs. The stellar mass growth of the BCGs/MMCGs also appears to grow in lockstep with both the stellar baryonic and total mass of the cluster. Additionally, BCGs/MMCGs were found to grow in size, on average, a factor of ∼3, while their average Sérsic index increased by ∼0.45 from z ∼ 0.9 to z ∼ 0.1, also supporting a scenario involving major merging, though some adiabatic expansion is required. These observational results are compared to both models and simulations to further explore the implications on processes which shape and evolve BCGs/MMCGs over the past ∼7 Gyr

Engineering long-range order in supramolecular assemblies on surfaces : the paramount role of internal double bonds in discrete long-chain naphthalenediimides

Achieving long-range order with surface-supported supramolecular assemblies is one of the pressing challenges in the prospering field of non-covalent surface functionalization. Having access to defect-free on-surface molecular assemblies will pave the way for various nanotechnology applications. Here we report the synthesis of two libraries of naphthalenediimides (NDIs) symmetrically functionalized with long aliphatic chains (C28 and C33) and their self-assembly at the 1-phenyloctane/highly oriented pyrolytic graphite (1-PO/HOPG) interface. The two NDI libraries differ by the presence/absence of an internal double bond in each aliphatic chain (unsaturated and saturated compounds, respectively). All molecules assemble into lamellar arrangements, with the NDI cores lying flat and forming 1D rows on the surface, while the carbon chains separate the 1D rows from each other. Importantly, the presence of the unsaturation plays a dominant role in the arrangement of the aliphatic chains, as it exclusively favors interdigitation. The fully saturated tails, instead, self-assemble into a combination of either interdigitated or non-interdigitated diagonal arrangements. This difference in packing is spectacularly amplified at the whole surface level and results in almost defect-free self-assembled monolayers for the unsaturated compounds. In contrast, the monolayers of the saturated counterparts are globally disordered, even though they locally preserve the lamellar arrangements. The experimental observations are supported by computational studies and are rationalized in terms of stronger van der Waals interactions in the case of the unsaturated compounds. Our investigation reveals the paramount role played by internal double bonds on the self-assembly of discrete large molecules at the liquid/solid interface

QUALITY CONTROL METHODS AND INDUSTRIAL APPLICATIONS

Paper presents four control methods widely used in quality control in industry and their applications. The three methods analyzed in this work are optical-visual control, control with penetrating liquids, control with magnetic powders and measuring the thickness of paint layers. To exemplify them, several images are presented that emphasize their practical importance in the case of several parts made by plastic deformation or by welding. The work can fit very well into the research regarding the current state of the application of the control methods used successfully in the industry

PET imaging shows no changes in TSPO brain density after IFN-α immune challenge in healthy human volunteers

Depression is associated with peripheral inflammation, but its link with brain microglial activity remains unclear. In seven healthy males, we used repeated translocator protein-Positron Emission Tomography (TSPO-PET) dynamic scans with [11C]PBR28 to image brain microglial activation before and 24 h after the immune challenge interferon (IFN)-α. We also investigated the association between changes in peripheral inflammation, changes in microglial activity, and changes in mood. IFN-α administration decreased [11C]PBR28 PET tissue volume of distribution (Vt) across the brain (−20 ± 4%; t6 = 4.1, p = 0.01), but after correction for radioligand free-plasma fraction there were no longer any changes (+23 ± 31%; t = 0.1, p = 0.91). IFN-α increased serum IL-6 (1826 ± 513%, t6 = −7.5, p &lt; 0.001), IL-7 (39 ± 12%, t6 = −3.6, p = 0.01), IL-10 (328 ± 48%, t6 = −12.8, p &lt; 0.001), and IFN-γ (272 ± 64%, t6 = −7.0, p &lt; 0.001) at 4–6 h, and increased serum TNF-α (49 ± 7.6%, t6 = −7.5, p &lt; 0.001), IL-8 (39 ± 12%, t6 = −3.5, p = 0.013), and C-reactive protein (1320 ± 459%, t6 = −7.2, p &lt; 0.001) at 24 h. IFN-α induced temporary mood changes and sickness symptoms after 4–6 h, measured as an increase in POMS-2 total mood score, confusion and fatigue, and a decrease in vigor and friendliness (all p ≤ 0.04). No association was found between changes in peripheral inflammation and changes in PET or mood measures. Our work suggests that brain TSPO-PET signal is highly dependent of inflammation-induced changes in ligand binding to plasma proteins. This limits its usefulness as a sensitive marker of neuroinflammation and consequently, data interpretation. Thus, our results can be interpreted as showing either that [11C]PBR28 is not sensitive enough under these conditions, or that there is simply no microglial activation in this model.</p