Atomic matter wave scanner

We report on the experimental realization of an atom optical device, that allows scanning of an atomic beam. We used a time-modulated evanescent wave field above a glass surface to diffract a continuous beam of metastable Neon atoms at grazing incidence. The diffraction angles and efficiencies were controlled by the frequency and form of modulation, respectively. With an optimized shape, obtained from a numerical simulation, we were able to transfer more than 50% of the atoms into the first order beam, which we were able to move over a range of 8 mrad.Comment: 4 pages, 4 figure

Distribution of mutational fitness effects and of epistasis in the 5' untranslated region of a plant RNA virus

[Background[ Understanding the causes and consequences of phenotypic variability is a central topic of evolutionary biology. Mutations within non-coding cis-regulatory regions are thought to be of major effect since they affect the expression of downstream genes. To address the evolutionary potential of mutations affecting such regions in RNA viruses, we explored the fitness properties of mutations affecting the 5’-untranslated region (UTR) of a prototypical member of the picorna-like superfamily, tobacco etch virus (TEV). This 5’ UTR acts as an internal ribosomal entry site (IRES) and is essential for expression of all viral genes.[Results] We determined in vitro the folding of 5’ UTR using the selective 2’-hydroxyl acylation analyzed by primer extension (SHAPE) technique. Then, we created a collection of single-nucleotide substitutions on this region and evaluated the statistical properties of their fitness effects in vivo. We found that, compared to random mutations affecting coding sequences, mutations at the 5’ UTR were of weaker effect. We also created double mutants by combining pairs of these single mutations and found variation in the magnitude and sign of epistatic interactions, with an enrichment of cases of positive epistasis. A correlation exists between the magnitude of fitness effects and the size of the perturbation made in the RNA folding structure, suggesting that the larger the departure from the predicted fold, the more negative impact in viral fitness.[Conclusions] Evidence that mutational fitness effects on the short 5’ UTR regulatory sequence of TEV are weaker than those affecting its coding sequences have been found. Epistasis among pairs of mutations on the 5’ UTR ranged between the extreme cases of synthetic lethal and compensatory. A plausible hypothesis to explain all these observations is that the interaction between the 5’ UTR and the host translational machinery was shaped by natural selection to be robust to mutations, thus ensuring the homeostatic expression of viral genes even at high mutation rates.This work was supported by grant BFU2012-30805 from the Spanish Ministry of Economy and Competitiveness (MINECO), grant PROMETEOII/2014/021 from Generalitat Valenciana and the EvoEvo (ICT610427) project from the European Commission 7th Framework Program. Publication fees have been partially paid by the CSIC Open Access Publication Support Initiative through its Unit of Information Resources for Research (URICI).Peer reviewe

Implementation of mean-timing and subsequent logic functions on an FPGA

This article describes the implementation of a mean-timer and coincidence logic on a Virtex-5 FPGA for trigger purposes in a particle physics experiment. The novel feature is that the mean-timing and the coincidence logic are not synchronized with a clock which allows for a higher resolution of approximately 400 ps, not limited by a clock frequency.Comment: 15 pages, 11 figure

Focal modulation using rotating phase filters

We describe a simple method of refocusing optical systems that is based on the use of two identical phase filters. These filters are divided in annuli and each annulus is divided into sectors with a particular phase value. A controlled focus displacement is achieved by rotating one filter with respect to the other. This displacement is related with the filter parameters. Transverse responses are studied as a function of filters relative position. Furthermore, the experimental set up shows that theoretical prediction fit well with experimental results. The main advantage of this system is the ease of fabrication so that it could be useful in different applications requiring small size, light weight or thin systems, like mobile phone cameras, microscopy tomography, and others

Urine Fetuin-A is a biomarker of autosomal dominant polycystic kidney disease progression.

BACKGROUND: Autosomal dominant polycystic kidney disease (ADPKD) is a genetic disorder characterized by numerous fluid-filled cysts that frequently result in end-stage renal disease. While promising treatment options are in advanced clinical development, early diagnosis and follow-up remain a major challenge. We therefore evaluated the diagnostic value of Fetuin-A as a new biomarker of ADPKD in human urine. RESULTS: We found that renal Fetuin-A levels are upregulated in both Pkd1 and Bicc1 mouse models of ADPKD. Measurement by ELISA revealed that urinary Fetuin-A levels were significantly higher in 66 ADPKD patients (17.5 ± 12.5 μg/mmol creatinine) compared to 17 healthy volunteers (8.5 ± 3.8 μg/mmol creatinine) or 50 control patients with renal diseases of other causes (6.2 ± 2.9 μg/mmol creatinine). Receiver operating characteristics (ROC) analysis of urinary Fetuin-A levels for ADPKD rendered an optimum cut-off value of 12.2 μg/mmol creatinine, corresponding to 94% of sensitivity and 60% of specificity (area under the curve 0.74 ; p = 0.0019). Furthermore, urinary Fetuin-A levels in ADPKD patients correlated with the degree of renal insufficiency and showed a significant increase in patients with preserved renal function followed for two years. CONCLUSIONS: Our findings establish urinary Fetuin-A as a sensitive biomarker of the progression of ADPKD. Further studies are required to examine the pathogenic mechanisms of elevated renal and urinary Fetuin-A in ADPKD

Familial risk for depressive and anxiety disorders:associations with genetic, clinical, and psychosocial vulnerabilities

BACKGROUND: In research and clinical practice, familial risk for depression and anxiety is often constructed as a simple Yes/No dichotomous family history (FH) indicator. However, this measure may not fully capture the liability to these conditions. This study investigated whether a continuous familial loading score (FLS), incorporating family- and disorder-specific characteristics (e.g. family size, prevalence of depression/anxiety), (i) is associated with a polygenic risk score (PRS) for major depression and with clinical/psychosocial vulnerabilities and (ii) still captures variation in clinical/psychosocial vulnerabilities after information on FH has been taken into account. METHODS: Data came from 1425 participants with lifetime depression and/or anxiety from the Netherlands Study of Depression and Anxiety. The Family Tree Inventory was used to determine FLS/FH indicators for depression and/or anxiety. RESULTS: Persons with higher FLS had higher PRS for major depression, more severe depression and anxiety symptoms, higher disease burden, younger age of onset, and more neuroticism, rumination, and childhood trauma. Among these variables, FH was not associated with PRS, severity of symptoms, and neuroticism. After regression out the effect of FH from the FLS, the resulting residualized measure of FLS was still associated with severity of symptoms of depression and anxiety, rumination, and childhood trauma. CONCLUSIONS: Familial risk for depression and anxiety deserves clinical attention due to its associated genetic vulnerability and more unfavorable disease profile, and seems to be better captured by a continuous score that incorporates family- and disorder-specific characteristics than by a dichotomous FH measure