Defect loops in gauged Wess-Zumino-Witten models

We consider loop observables in gauged Wess-Zumino-Witten models, and study the action of renormalization group flows on them. In the WZW model based on a compact Lie group G, we analyze at the classical level how the space of renormalizable defects is reduced upon the imposition of global and affine symmetries. We identify families of loop observables which are invariant with respect to an affine symmetry corresponding to a subgroup H of G, and show that they descend to gauge-invariant defects in the gauged model based on G/H. We study the flows acting on these families perturbatively, and quantize the fixed points of the flows exactly. From their action on boundary states, we present a derivation of the "generalized Affleck-Ludwig rule, which describes a large class of boundary renormalization group flows in rational conformal field theories.Comment: 43 pages, 2 figures. v2: a few typos corrected, version to be published in JHE

Non-invasive scoring of cellular atypia in keratinocyte cancers in 3D LC-OCT images using Deep Learning

Diagnosis based on histopathology for skin cancer detection is today's gold standard and relies on the presence or absence of biomarkers and cellular atypia. However it suffers drawbacks: it requires a strong expertise and is time-consuming. Moreover the notion of atypia or dysplasia of the visible cells used for diagnosis is very subjective, with poor inter-rater agreement reported in the literature. Lastly, histology requires a biopsy which is an invasive procedure and only captures a small sample of the lesion, which is insufficient in the context of large fields of cancerization. Here we demonstrate that the notion of cellular atypia can be objectively defined and quantified with a non-invasive in-vivo approach in three dimensions (3D). A Deep Learning (DL) algorithm is trained to segment keratinocyte (KC) nuclei from Line-field Confocal Optical Coherence Tomography (LC-OCT) 3D images. Based on these segmentations, a series of quantitative, reproducible and biologically relevant metrics is derived to describe KC nuclei individually. We show that, using those metrics, simple and more complex definitions of atypia can be derived to discriminate between healthy and pathological skins, achieving Area Under the ROC Curve (AUC) scores superior than 0.965, largely outperforming medical experts on the same task with an AUC of 0.766. All together, our approach and findings open the door to a precise quantitative monitoring of skin lesions and treatments, offering a promising non-invasive tool for clinical studies to demonstrate the effects of a treatment and for clinicians to assess the severity of a lesion and follow the evolution of pre-cancerous lesions over time.© 2022. The Author(s)

SNPLims: a data management system for genome wide association studies

<p>Abstract</p> <p>Background</p> <p>Recent progresses in genotyping technologies allow the generation high-density genetic maps using hundreds of thousands of genetic markers for each DNA sample. The availability of this large amount of genotypic data facilitates the whole genome search for genetic basis of diseases.</p> <p>We need a suitable information management system to efficiently manage the data flow produced by whole genome genotyping and to make it available for further analyses.</p> <p>Results</p> <p>We have developed an information system mainly devoted to the storage and management of SNP genotype data produced by the Illumina platform from the raw outputs of genotyping into a relational database.</p> <p>The relational database can be accessed in order to import any existing data and export user-defined formats compatible with many different genetic analysis programs.</p> <p>After calculating family-based or case-control association study data, the results can be imported in SNPLims. One of the main features is to allow the user to rapidly identify and annotate statistically relevant polymorphisms from the large volume of data analyzed. Results can be easily visualized either graphically or creating ASCII comma separated format output files, which can be used as input to further analyses.</p> <p>Conclusions</p> <p>The proposed infrastructure allows to manage a relatively large amount of genotypes for each sample and an arbitrary number of samples and phenotypes. Moreover, it enables the users to control the quality of the data and to perform the most common screening analyses and identify genes that become “candidate” for the disease under consideration.</p

Identification of the Neogenin-Binding Site on the Repulsive Guidance Molecule A

Repulsive guidance molecule (RGM) is a membrane-bound protein that was originally identified as an axon guidance molecule in the chick retinotectal system. RGMa, one of the 3 isoforms found in mammals, is involved in laminar patterning, cephalic neural tube closure, axon guidance, and inhibition of axonal regeneration. In addition to its roles in the nervous system, RGMa plays a role in enhancing helper T-cell activation. Binding of RGM to its receptor, neogenin, is considered necessary to transduce these signals; however, information on the binding of RGM to neogenin is limited. Using co-immunoprecipitation studies, we have identified that the RGMa region required for binding to neogenin contains amino acids (aa) 259–295. Synthesized peptide consisting of aa 284–293 directly binds to the extracellular domain (ECD) of recombinant neogenin, and addition of this peptide inhibits RGMa-induced growth cone collapse in mouse cortical neurons. Thus, we propose that this peptide is a promising lead in finding reagents capable of inhibiting RGMa signaling

Radio & Optical Interferometry: Basic Observing Techniques and Data Analysis

Astronomers usually need the highest angular resolution possible, but the blurring effect of diffraction imposes a fundamental limit on the image quality from any single telescope. Interferometry allows light collected at widely-separated telescopes to be combined in order to synthesize an aperture much larger than an individual telescope thereby improving angular resolution by orders of magnitude. Radio and millimeter wave astronomers depend on interferometry to achieve image quality on par with conventional visible and infrared telescopes. Interferometers at visible and infrared wavelengths extend angular resolution below the milli-arcsecond level to open up unique research areas in imaging stellar surfaces and circumstellar environments. In this chapter the basic principles of interferometry are reviewed with an emphasis on the common features for radio and optical observing. While many techniques are common to interferometers of all wavelengths, crucial differences are identified that will help new practitioners avoid unnecessary confusion and common pitfalls. Concepts essential for writing observing proposals and for planning observations are described, depending on the science wavelength, angular resolution, and field of view required. Atmospheric and ionospheric turbulence degrades the longest-baseline observations by significantly reducing the stability of interference fringes. Such instabilities represent a persistent challenge, and the basic techniques of phase-referencing and phase closure have been developed to deal with them. Synthesis imaging with large observing datasets has become a routine and straightforward process at radio observatories, but remains challenging for optical facilities. In this context the commonly-used image reconstruction algorithms CLEAN and MEM are presented. Lastly, a concise overview of current facilities is included as an appendix.Comment: 45 pages, 14 Figures; an abridged version of a chapter to appear in Volume 2 of Planets, Stars and Stellar Systems, to be published in 2011 by Springe

Determinants of patient satisfaction in ambulatory oncology: a cross sectional study based on the OUT-PATSAT35 questionnaire

<p>Abstract</p> <p>Background</p> <p>The aim of this study was to identify factors associated with satisfaction with care in cancer patients undergoing ambulatory treatment. We investigated associations between patients' baseline clinical and socio-demographic characteristics, as well as self-reported quality of life, and satisfaction with care.</p> <p>Methods</p> <p>Patients undergoing ambulatory chemotherapy or radiotherapy in 2 centres in France were invited, at the beginning of their treatment, to complete the OUT-PATSAT35, a 35 item and 13 scale questionnaire evaluating perception of doctors, nurses and aspects of care organisation. Additionally, for each patient, socio-demographic variables, clinical characteristics and self-reported quality of life using the EORTC QLQ-C30 questionnaire were recorded.</p> <p>Results</p> <p>Among 692 patients included between January 2005 and December 2006, only 6 were non-responders. By multivariate analysis, poor perceived global health strongly predicted dissatisfaction with care (<it>p </it>< 0.0001). Patients treated by radiotherapy (vs patients treated by chemotherapy) reported lower levels of satisfaction with doctors' technical and interpersonal skills, information provided by caregivers, and waiting times. Patients with primary head and neck cancer (vs other localisations), and those living alone were less satisfied with information provided by doctors, and younger patients (< 55 years) were less satisfied with doctors' availability.</p> <p>Conclusions</p> <p>A number of clinical of socio-demographic factors were significantly associated with different scales of the satisfaction questionnaire. However, the main determinant was the patient's global health status, underlining the importance of measuring and adjusting for self-perceived health status when evaluating satisfaction. Further analyses are currently ongoing to determine the responsiveness of the OUT-PATSAT35 questionnaire to changes over time.</p

Glucose variability measures and their effect on mortality: a systematic review

Objective: To systematically review the medical literature on the association between glucose variability measures and mortality in critically ill patients. Methods: Studies assessing the association between a measure of glucose variability and mortality that reported original data from a clinical trial or observational study on critically ill adult patients were searched in Ovid MEDLINE (R) and Ovid EMBASE (R). Data on patient populations, study designs, glucose regulations, statistical approaches, outcome measures, and glucose variability indicators (their definition and applicability) were extracted. Result: Twelve studies met the inclusion criteria; 13 different indicators were used to measure glucose variability. Standard deviation and the presence of both hypo-and hyperglycemia were the most common indicators. All studies reported a statistically significant association between mortality and at least one glucose variability indicator. In four studies both blood glucose levels and severity of illness were considered as confounders, but only one of them checked model assumptions to assert inference validity. Conclusions: Glucose variability has been quantified in many different ways, and in each study at least one of them appeared to be associated with mortality. Because of methodological limitations and the possibility of reporting bias, it is still unsettled whether and in which quantification this association is independent of other confounders. Future research will benefit from using an indicator reference subset for glucose variability, metrics that are linked more directly to negative physiological effects, more methodological rigor, and/or better reportin