L-Grassf: A New Model for Simulating the Genetic Environment Interactions on the Reproductive Phenology of Grasses

Predicting the reproductive phenology in perennial grasses is a major concern because it determines the quantity and quality of forage. It varies a lot depending on site, year and cultivar. Projections of future climates suggest significant changes in seasonal temperature pattern, with new combinations of temperature and photoperiod, whose consequences on the floral induction of perennial grasses are unknown. L-GrassF is a new Functional Structural Plant Model simulating genetic variability of the phenology of perennial ryegrass in order to better understand the perenniality of grasslands and better anticipate the effects of climate change. L-GrassF stems from a previous model (L-Grass) and now simulates the reproductive stages by integrating the interactions between vegetative growth, floral induction and reproductive organ development. The sensitivity analysis of a set of parameters was studied in the range of oceanic temperate climate conditions, on several European cultivars. It was further calibrated and validated on two independent datasets from the French Variety and Seed Study and Control Group (GEVES), which include the observations of heading dates for seven cultivars of Lolium perenne grown in six French locations between 2001 and 2017

Nulling interferometry: performance comparison between Antarctica and other ground-based sites

Detecting the presence of circumstellar dust around nearby solar-type main sequence stars is an important pre-requisite for the design of future life-finding space missions such as ESA's Darwin or NASA's Terrestrial Planet Finder (TPF). The high Antarctic plateau may provide appropriate conditions to perform such a survey from the ground. We investigate the performance of a nulling interferometer optimised for the detection of exozodiacal discs at Dome C, on the high Antarctic plateau, and compare it to the expected performance of similar instruments at temperate sites. Based on the currently available measurements of the turbulence characteristics at Dome C, we adapt the GENIEsim software (Absil et al. 2006, A&A 448) to simulate the performance of a nulling interferometer on the high Antarctic plateau. To feed a realistic instrumental configuration into the simulator, we propose a conceptual design for ALADDIN, the Antarctic L-band Astrophysics Discovery Demonstrator for Interferometric Nulling. We assume that this instrument can be placed above the 30-m high boundary layer, where most of the atmospheric turbulence originates. We show that an optimised nulling interferometer operating on a pair of 1-m class telescopes located 30 m above the ground could achieve a better sensitivity than a similar instrument working with two 8-m class telescopes at a temperate site such as Cerro Paranal. The detection of circumstellar discs about 20 times as dense as our local zodiacal cloud seems within reach for typical Darwin/TPF targets in a integration time of a few hours. Moreover, the exceptional turbulence conditions significantly relax the requirements on real-time control loops, which has favourable consequences on the feasibility of the nulling instrument.Comment: 10 pages, accepted for publication in A&

Jahn-Teller effects in initial and final states: high-resolution X-ray absorption, photoelectron and Auger spectroscopy of allene

Carbon K-edge resonant Auger spectra of gas-phase allene following excitation of the pre-edge 1s → π* transitions are presented and analysed with the support of EOM-CCSD/cc-pVTZ calculations. X-Ray absorption (XAS), X-ray photoelectron (XPS), valence band and non-resonant Auger spectra are also reanalysed with a series of computational approaches. The results presented demonstrate the importance of including nuclear ensemble effects for simulating X-ray observables and as an effective strategy for capturing Jahn-Teller effects in spectra

Digital correction of residual straylight in FLEX images

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The value of prognostic factors for uterine cervical cancer patients treated with irradiation alone

<p>Abstract</p> <p>Background</p> <p>The aim of our study was to investigate and evaluate the prognostic value of and correlations between preclinical and clinical factors such as the stage of the disease, blood Hb level before treatment, size of cervix and lymph nodes evaluated by CT, age, dose of irradiation and duration of radiotherapy related to overall survival, disease-free survival, local control and metastases-free survival in cervical cancer patients receiving radiotherapy alone.</p> <p>Methods</p> <p>162 patients with International Federation of Gynecology and Obstetrics (FIGO) stage IIA-IIIB cervical carcinoma treated with irradiation were analysed. Univariate and multivariate analyses using the Cox regression model were performed to determine statistical significance of some tumor-related factors.</p> <p>Results</p> <p>The Hb level before treatment showed significant influence on overall survival (p = 0.001), desease free survival (p = 0.040) and local control (p = 0.038). The lymph node status (>10 mm) assessed on CT had impact on overall survival (p = 0,030) and local control (p = 0,036). The dose at point A had impact on disease free survival (p = 0,028) and local control (p = 0,021) and the radiotherapy duration had showed significant influence on overall survival (p = 0,045), disease free survival (p = 0,006) and local control (p = 0,033).</p> <p>Conclusion</p> <p>Anemia is a significant and independent prognostic factor of overall survival, disease-free survival and local control in cervical cancer patients treated with irradiation. The size of lymph nodes in CT is an independent prognostic factor for overall survival and local control in cervical cancer patients. The size of cervix uteri evaluated by CT has no prognostic significance in cervical cancer patients treated with radiotherapy. The prognostic value of FIGO stage of cervical cancer is influenced by other factors, analyzed in this study and is not an independent prognostic factor.</p

Brachytherapy for cervix cancer: low-dose rate or high-dose rate brachytherapy – a meta-analysis of clinical trials

<p>Abstract</p> <p>Background</p> <p>The literature supporting high-dose rate brachytherapy (HDR) in the treatment of cervical carcinoma derives primarily from retrospective series. However, controversy still persists regarding the efficacy and safety of HDR brachytherapy compared to low-dose rate (LDR) brachytherapy, in particular, due to inadequate tumor coverage for stage III patients. Whether LDR or HDR brachytherapy produces better results for these patients in terms of survival rate, local control rate and the treatment complications remain controversial.</p> <p>Methods</p> <p>A meta-analysis of RCT was performed comparing LDR to HDR brachytherapy for cervix cancer treated for radiotherapy alone. The MEDLINE, EMBASE, CANCERLIT and Cochrane Library databases, as well as abstracts published in the annual proceedings were systematically searched. We assessed methodological quality for each outcome by grading the quality of evidence using the Grading of Recommendations Assessment, Development and Evaluation (GRADE) methodology. We used "recommend" for strong recommendations, and "suggest" for weak recommendations.</p> <p>Results</p> <p>Pooled results from five randomized trials (2,065 patients) of HDR brachytherapy in cervix cancer showed no significant increase of mortality (p = 0.52), local recurrence (p = 0.68), or late complications (rectal; p = 0.7, bladder; p = 0.95 or small intestine; p = 0.06) rates as compared to LDR brachytherapy. In the subgroup analysis no difference was observed for overall mortality and local recurrence in patients with clinical stages I, II and III. The quality of evidence was low for mortality and local recurrence in patients with clinical stage I, and moderate for other clinical stages.</p> <p>Conclusion</p> <p>Our meta-analysis shows that there are no differences between HDR and LDR for overall survival, local recurrence and late complications for clinical stages I, II and III. By means of the GRADE system, we recommend the use of HDR for all clinical stages of cervix cancer.</p

The Biological Connection Markup Language: a SBGN-compliant format for visualization, filtering and analysis of biological pathways

Motivation: Many models and analysis of signaling pathways have been proposed. However, neither of them takes into account that a biological pathway is not a fixed system, but instead it depends on the organism, tissue and cell type as well as on physiological, pathological and experimental conditions

EMA - A R package for Easy Microarray data analysis

<p>Abstract</p> <p>Background</p> <p>The increasing number of methodologies and tools currently available to analyse gene expression microarray data can be confusing for non specialist users.</p> <p>Findings</p> <p>Based on the experience of biostatisticians of Institut Curie, we propose both a clear analysis strategy and a selection of tools to investigate microarray gene expression data. The most usual and relevant existing R functions were discussed, validated and gathered in an easy-to-use R package (EMA) devoted to gene expression microarray analysis. These functions were improved for ease of use, enhanced visualisation and better interpretation of results.</p> <p>Conclusions</p> <p>Strategy and tools proposed in the EMA R package could provide a useful starting point for many microarrays users. EMA is part of Comprehensive R Archive Network and is freely available at <url>http://bioinfo.curie.fr/projects/ema/</url>.</p

Classification of microarray data using gene networks

BACKGROUND: Microarrays have become extremely useful for analysing genetic phenomena, but establishing a relation between microarray analysis results (typically a list of genes) and their biological significance is often difficult. Currently, the standard approach is to map a posteriori the results onto gene networks in order to elucidate the functions perturbed at the level of pathways. However, integrating a priori knowledge of the gene networks could help in the statistical analysis of gene expression data and in their biological interpretation. RESULTS: We propose a method to integrate a priori the knowledge of a gene network in the analysis of gene expression data. The approach is based on the spectral decomposition of gene expression profiles with respect to the eigenfunctions of the graph, resulting in an attenuation of the high-frequency components of the expression profiles with respect to the topology of the graph. We show how to derive unsupervised and supervised classification algorithms of expression profiles, resulting in classifiers with biological relevance. We illustrate the method with the analysis of a set of expression profiles from irradiated and non-irradiated yeast strains. CONCLUSION: Including a priori knowledge of a gene network for the analysis of gene expression data leads to good classification performance and improved interpretability of the results

Objective Evaluation of Multiple Sclerosis Lesion Segmentation using a Data Management and Processing Infrastructure

We present a study of multiple sclerosis segmentation algorithms conducted at the international MICCAI 2016 challenge. This challenge was operated using a new open-science computing infrastructure. This allowed for the automatic and independent evaluation of a large range of algorithms in a fair and completely automatic manner. This computing infrastructure was used to evaluate thirteen methods of MS lesions segmentation, exploring a broad range of state-of-theart algorithms, against a high-quality database of 53 MS cases coming from four centers following a common definition of the acquisition protocol. Each case was annotated manually by an unprecedented number of seven different experts. Results of the challenge highlighted that automatic algorithms, including the recent machine learning methods (random forests, deep learning, …), are still trailing human expertise on both detection and delineation criteria. In addition, we demonstrate that computing a statistically robust consensus of the algorithms performs closer to human expertise on one score (segmentation) although still trailing on detection scores