A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study

Background: Expressed Sequence Tags (ESTs) are a source of simple sequence repeats (SSRs) that can be used to develop molecular markers for genetic studies. The availability of ESTs for Quercus robur and Quercus petraea provided a unique opportunity to develop microsatellite markers to accelerate research aimed at studying adaptation of these long-lived species to their environment. As a first step toward the construction of a SSR-based linkage map of oak for quantitative trait locus (QTL) mapping, we describe the mining and survey of EST-SSRs as well as a fast and cost-effective approach (bin mapping) to assign these markers to an approximate map position. We also compared the level of polymorphism between genomic and EST-derived SSRs and address the transferability of EST-SSRs in Castanea sativa (chestnut). Results: A catalogue of 103,000 Sanger ESTs was assembled into 28,024 unigenes from which 18.6% presented one or more SSR motifs. More than 42% of these SSRs corresponded to trinucleotides. Primer pairs were designed for 748 putative unigenes. Overall 37.7% (283) were found to amplify a single polymorphic locus in a reference fullsib pedigree of Quercus robur. The usefulness of these loci for establishing a genetic map was assessed using a bin mapping approach. Bin maps were constructed for the male and female parental tree for which framework linkage maps based on AFLP markers were available. The bin set consisting of 14 highly informative offspring selected based on the number and position of crossover sites. The female and male maps comprised 44 and 37 bins, with an average bin length of 16.5 cM and 20.99 cM, respectively. A total of 256 EST-SSRs were assigned to bins and their map position was further validated by linkage mapping. EST-SSRs were found to be less polymorphic than genomic SSRs, but their transferability rate to chestnut, a phylogenetically related species to oak, was higher. Conclusion: We have generated a bin map for oak comprising 256 EST-SSRs. This resource constitutes a first step toward the establishment of a gene-based map for this genus that will facilitate the dissection of QTLs affecting complex traits of ecological importance

Ge-rich graded-index SiGe alloys: exploring a versatile platform for mid-IR photonics

International audienceIn this paper, the recent progress on a new Ge-rich SiGe platform for mid-IR integrated photonics is presented. Low-loss spiral waveguides working over a broadband wavelength range are discussed, followed by a sensing proof-of-concept using a standalone photoresist with a known spectral absorption pattern. In addition, the development of new mid-IR interferometric devices for wavelength filtering and enhancement of the light-matter interaction are presented. Finally, efficient designs to exploit the third-order nonlinearities in these Ge-rich SiGe waveguides at mid-IR wavelengths are shown. The demonstration of these key building blocks will pave the way towards the implementation of new mid-IR photonic integrated systems with multiple functionalities

Quantum Fluctuation Relations for the Lindblad Master Equation

An open quantum system interacting with its environment can be modeled under suitable assumptions as a Markov process, described by a Lindblad master equation. In this work, we derive a general set of fluctuation relations for systems governed by a Lindblad equation. These identities provide quantum versions of Jarzynski-Hatano-Sasa and Crooks relations. In the linear response regime, these fluctuation relations yield a fluctuation-dissipation theorem (FDT) valid for a stationary state arbitrarily far from equilibrium. For a closed system, this FDT reduces to the celebrated Callen-Welton-Kubo formula

Delivery of hepato-pancreato-biliary surgery during the COVID-19 pandemic: an European-African Hepato-Pancreato-Biliary Association (E-AHPBA) cross-sectional survey

Background: The extent of the COVID-19 pandemic and the resulting response has varied globally. The European and African Hepato-Pancreato-Biliary Association (E-AHPBA), the premier representative body for practicing HPB surgeons in Europe and Africa, conducted this survey to assess the impact of COVID-19 on HPB surgery. Methods: An online survey was disseminated to all E-AHPBA members to assess the effects of the pandemic on unit capacity, management of HPB cancers, use of COVID-19 screening and other aspects of service delivery. Results: Overall, 145 (25%) members responded. Most units, particularly in COVID-high countries (>100,000 cases) reported insufficient critical care capacity and reduced HPB operating sessions compared to COVID-low countries. Delayed access to cancer surgery necessitated alternatives including increased neoadjuvant chemotherapy for pancreatic cancer and colorectal liver metastases, and locoregional treatments for hepatocellular carcinoma. Other aspects of service delivery including COVID-19 screening and personal protective equipment varied between units and countries. Conclusion: This study demonstrates that the COVID-19 pandemic has had a profound adverse impact on the delivery of HPB cancer care across the continents of Europe and Africa. The findings illustrate the need for safe resumption of cancer surgery in a “new” normal world with screening of patients and staff for COVID-19

Contribution à la détermination de la structure électronique d'alliages métalliques amorphes Cu50Zr50 par spectroscopie optique

Amorphous Cu50Zr50 samples were prepared by sputtering from an alloy target. The film thicknesses are ranging from a few hundred of angströms to several micrometers. The thickness homogeneity is very good, even for very thin films. The complex dielectric constant is determined from reflectance and transmittance measurements for semi-transparent films, from reflectance measurements only using Kramers-Kronig analysis for opaque samples. The optical results concern Cu50Zr50 alloys between 50 μm and 0.2 μm. The optical spectra show in particular, an absorption peak around 3.5 eV, which could be due to transitions starting from the Cu partial d-band, shifted towards higher binding energies with respect to its position in pure Cu. These results are in good agreement with U.P.S. measurements by Oelhafen et al.Les échantillons de Cu50Zr50 amorphes sont préparés par pulvérisation cathodique triode d'une cible d'alliage de composition déterminée. L'épaisseur des dépôts étudiés varie de quelques centaines d'angströms à plusieurs microns. L'homogénéité en épaisseur est très bonne, même pour les échantillons très minces. La constante diélectrique est déterminée soit à partir des mesures de réflexion et de transmission en incidence normale pour les échantillons semi-transparents, soit à partir des mesures de réflexion en utilisant la transformation de Kramers-Kronig pour les échantillons opaques. Le domaine spectral étudié va de 50 μ à 0,2 μ. Les spectres optiques montrent en particulier un pic d'absorption vers 3,5 eV, qui doit être dû à des transitions entre la sous-bande d du cuivre (déplacée vers les grandes énergies de liaison par rapport à sa position dans le métal pur) et le niveau de Fermi. Ces résultats sont en bon accord avec les mesures de photoémission de Oelhafen et al

Photonic bandtail in 1D randomly-perturbed periodic systems

The results of a detailed numerical study of the optical bandtail in a 1D randomly-perturbed periodic system are reported. It is found that the width of the optical bandtail grows proportionally to the magnitude of the random perturbations, and the states in the bandtail regime, which are tightly localized, are separated from the more extended states in the pass band by a quasi mobility edge. Frequency dependence of the localization length and its relation to the distribution of the random perturbations are also examined. © 1993

Characterization of inhomogeneous weakly absorbing thin films by photothermal deflection spectroscopy, applications to hydrogenated amorphous silicon films

We explore the possibilities offered by transverse photothermal deflection spectroscopy at low modulation frequencies for studying variations of the optical absorption coefficient of hydrogenated amorphous silicon thin films across their thickness, with a special emphasis on the low energy range

Perception of facial expressions of emotion in bipolar disorder

Objectives: Some studies have reported deficits in the perception of facial expressions among depressed individuals compared with healthy controls, while others have reported negative biases in expression perception. We examined whether altered perception of emotion reflects an underlying trait-like effect in affective disorder by examining facial expression perception in euthymic bipolar patients.Methods: Sensitivity to six different facial expressions, as well as accuracy of emotion recognition, was examined among 17 euthymic bipolar patients and 17 healthy controls using an interactive computer program.Results: No differences were found between euthymic bipolar patients and controls in terms of sensitivity to any particular emotion. Although initial analysis of the data suggested impairment in the recognition of fear among the patients, identification of this emotion was not relatively impaired compared with that of the other emotions.Conclusions: The study did not find any conclusive evidence for trait-like deficits in the perception of facially conveyed emotions in bipolar disorder. Altered perception of facial expressions that has been found to accompany depressed mood may instead reflect mood-congruent biases.</p