VISOR: a versatile haplotype-aware structural variant simulator for short- and long-read sequencing.

Abstract Summary VISOR is a tool for haplotype-specific simulations of simple and complex structural variants (SVs). The method is applicable to haploid, diploid or higher ploidy simulations for bulk or single-cell sequencing data. SVs are implanted into FASTA haplotypes at single-basepair resolution, optionally with nearby single-nucleotide variants. Short or long reads are drawn at random from these haplotypes using standard error profiles. Double- or single-stranded data can be simulated and VISOR supports the generation of haplotype-tagged BAM files. The tool further includes methods to interactively visualize simulated variants in single-stranded data. The versatility of VISOR is unmet by comparable tools and it lays the foundation to simulate haplotype-resolved cancer heterogeneity data in bulk or at single-cell resolution. Availability and implementation VISOR is implemented in python 3.6, open-source and freely available at https://github.com/davidebolo1993/VISOR. Documentation is available at https://davidebolo1993.github.io/visordoc/. Supplementary information Supplementary data are available at Bioinformatics online

Analysis of enhanced-performance fibre Brillouin ring laser for Brillouin sensing applications

In this work, we present an enhanced design for a Brillouin ring laser (BRL), which employs a double resonant cavity (DRC) with short fiber length, paired with a heterodyne-based wavelength-locking system, to be employed as a pump-probe source for Brillouin sensing. The enhanced source is compared to traditional long-cavity pump-probe source, showing a significantly lower relative intensity noise (~-145 dB/Hz in the whole 0\u2013800 MHz range), a narrow linewidth (10 kHz), and large tunability features, resulting in an effective pump-probe source in BOTDA systems, with an excellent pump-probe frequency stability (~200 Hz), which is uncommon for fiber lasers. The enhanced source showed an improved signal-to-noise ratio (SNR) of about 22 dB with respect to standard BRL schemes, resulting in an improved temperature/strain resolution in BOTDA applications up to 5.5 dB, with respect to previous high-noise BRL designs

A single extracellular amino acid in Free Fatty Acid Receptor 2 defines antagonist species selectivity and G protein selection bias

Free Fatty Acid Receptor 2 is a GPCR activated by short chain fatty acids produced in high levels in the lower gut by microbial fermentation of non-digestible carbohydrates. A major challenge in studying this receptor is that the mouse ortholog does not have significant affinity for antagonists that are able to block the human receptor. Docking of exemplar antagonists from two chemical series to homology models of both human and mouse Free Fatty Acid Receptor 2 suggested that a single lysine - arginine variation at the extracellular face of the receptor might provide the basis for antagonist selectivity and mutational swap studies confirmed this hypothesis. Extending these studies to agonist function indicated that although the lysine - arginine variation between human and mouse orthologs had limited effect on G protein-mediated signal transduction, removal of positive charge from this residue produced a signalling-biased variant of Free Fatty Acid Receptor 2 in which Gi-mediated signalling by both short chain fatty acids and synthetic agonists was maintained whilst there was marked loss of agonist potency for signalling via Gq/11 and G12/13 G proteins. A single residue at the extracellular face of the receptor thus plays key roles in both agonist and antagonist function

Optical fiber sensing cables for brillouin-based distributed measurements

Brillouin distributed optical fiber sensing (Brillouin D-FOS) is a powerful technology for real-time in situ monitoring of various physical quantities, such as strain, temperature, and pressure. Compared to local or multi-point fiber optic sensing techniques, in Brillouin-based sensing, the optical fiber is interrogated along its complete length with a resolution down to decimeters and with a frequency encoding of the measure information that is not affected by changes in the optical attenuation. The fiber sensing cable plays a significant role since it must ensure a low optical loss and optimal transfer of the measured parameters for a long time and in harsh conditions, e.g., the presence of moisture, corrosion, and relevant mechanical or thermal stresses. In this paper, research and application regarding optical fiber cables for Brillouin distributed sensing are reviewed, connected, and extended. It is shown how appropriate cable design can give a significant contribution toward the successful exploitation of the Brillouin D-FOS technique

Photoproduction of electron-positron pairs in bent single crystals

The process of photoproduction of electron-positron pairs in bent single crystals is considered in this paper. In particular, it is shown that the probability of the process for gamma-quanta with energies from 100 GeV on is significantly higher than the one in an amorphous medium. A possible scenario for the experimental validation of the process is discussed and the positive features of the photoproduction in bent crystals compared to straight ones are underlined from the point of view of possible applications.Comment: 13 pages, 6 figure

Shear Strength of Precast Prestressed Concrete Hollow Core Slabs

Since early eighties, the precast prestressed concrete hollow core slab cross sections with non-circular voids became gradually popular, first in 400 mm thick slabs, then in 500 mm thick slabs. However, it is evidenced that this type of deeper slab sections have subjected to initial web shear cracking when they are provided longer supports and resist for higher line loads acting close to supports. Therefore, the objective of this study is to review the equations specified in American Concrete Institute (ACI), Eurocode 2 (EC2) and Canadian Standards Association (CSA) specifications to evaluate the shear strength of a member having no transverse reinforcement as in the case of hollow core slabs. For this purpose, the experimental test data on hollow core slabs are collected from past experimental programs and detailed finite element analyses are performed. Based on experimental and numerical results, it could be concluded that the evaluation of shear strength by the equations specified in ACI, EC2 and CSA specifications are conservative for the slab cross sections with circular voids while ACI and EC2 predictions are not conservative for deeper slab sections with flat webs. However, CSA predictions for all types of hollow core slab sections are more conservative than ACI and EC2 predictions

Multiplexing of encrypted data using fractal masks

This paper was published in OPTICS LETTERS and is made available as an electronic reprint with the permission of OSA. The paper can be found at the following URL on the OSA website: http://dx.doi.org/10.1364/OL.37.002895. Systematic or multiple reproduction or distribution to multiple locations via electronic or other means is prohibited and is subject to penalties under lawIn this Letter, we present to the best of our knowledge a new all-optical technique for multiple-image encryption and multiplexing, based on fractal encrypting masks. The optical architecture is a joint transform correlator. The multiplexed encrypted data are stored in a photorefractive crystal. The fractal parameters of the key can be easily tuned to lead to a multiplexing operation without cross talk effects. Experimental results that support the potential of the method are presented.This research was performed under grants TWAS-UNESCO Associateship Scheme at Centres of Excellence in the South, CONICET No. 0863 (Argentina), ANCYT PICT 1167 (Argentina), and Facultad de Ingenieria, Universidad Nacional de La Plata No. 11/I125 (Argentina), Sostenibilidad 2011-2012, and CODI (Universidad de Antioquia-Colombia). W. D. Furlan and J. A. Monsoriua acknowledge financial support from Ministerio de Economia y Competitividad (grant FIS2011-23175), Generalitat Valenciana (grant PROMETEO2009-077), and Universitat Politecnica de Valencia (grants PAID-05-11 and PAID-02-11), Spain.Barrera, J.; Tebaldi, M.; Amaya, D.; Furlan, W.; Monsoriu Serra, JA.; Bolognini, NA.; Torroba, RD.... (2012). Multiplexing of encrypted data using fractal masks. Optics Letters. 37(14):2895-2897. doi:10.1364/OL.37.002895S289528973714Refregier, P., & Javidi, B. (1995). Optical image encryption based on input plane and Fourier plane random encoding. Optics Letters, 20(7), 767. doi:10.1364/ol.20.000767Matoba, O., & Javidi, B. (1999). Encrypted optical memory system using three-dimensional keys in the Fresnel domain. Optics Letters, 24(11), 762. doi:10.1364/ol.24.000762Unnikrishnan, G., Joseph, J., & Singh, K. (2000). Optical encryption by double-random phase encoding in the fractional Fourier domain. Optics Letters, 25(12), 887. doi:10.1364/ol.25.000887Nomura, T. (2000). Polarization encoding for optical security systems. Optical Engineering, 39(9), 2439. doi:10.1117/1.1288369Tebaldi, M., Furlan, W. D., Torroba, R., & Bolognini, N. (2009). Optical-data storage-readout technique based on fractal encrypting masks. Optics Letters, 34(3), 316. doi:10.1364/ol.34.000316Situ, G., & Zhang, J. (2005). Multiple-image encryption by wavelength multiplexing. Optics Letters, 30(11), 1306. doi:10.1364/ol.30.001306Liu, Z., & Liu, S. (2007). Double image encryption based on iterative fractional Fourier transform. Optics Communications, 275(2), 324-329. doi:10.1016/j.optcom.2007.03.039Hwang, H.-E., Chang, H. T., & Lie, W.-N. (2009). Multiple-image encryption and multiplexing using a modified Gerchberg-Saxton algorithm and phase modulation in Fresnel-transform domain. Optics Letters, 34(24), 3917. doi:10.1364/ol.34.003917Matoba, O., & Javidi, B. (1999). Encrypted optical storage with angular multiplexing. Applied Optics, 38(35), 7288. doi:10.1364/ao.38.007288Fredy Barrera, J., Henao, R., Tebaldi, M., Torroba, R., & Bolognini, N. (2006). Multiplexing encryption–decryption via lateral shifting of a random phase mask. Optics Communications, 259(2), 532-536. doi:10.1016/j.optcom.2005.09.027Henao, R., Rueda, E., Barrera, J. F., & Torroba, R. (2010). Noise-free recovery of optodigital encrypted and multiplexed images. Optics Letters, 35(3), 333. doi:10.1364/ol.35.000333Barrera, J. F., Henao, R., Tebaldi, M., Torroba, R., & Bolognini, N. (2006). Multiple image encryption using an aperture-modulated optical system. Optics Communications, 261(1), 29-33. doi:10.1016/j.optcom.2005.11.055Mosso, F., Barrera, J. F., Tebaldi, M., Bolognini, N., & Torroba, R. (2011). All-optical encrypted movie. Optics Express, 19(6), 5706. doi:10.1364/oe.19.005706Monsoriu, J. A., Saavedra, G., & Furlan, W. D. (2004). Fractal zone plates with variable lacunarity. Optics Express, 12(18), 4227. doi:10.1364/opex.12.00422

Adalimumab efficacy in enteropathic spondyloarthritis: A 12-mo observational multidisciplinary study

AIM To report adalimumab (Ada) efficacy on articulargastrointestinal disease and health-related quality of life (HRQoL) in patients with enteropathic spondyloarthritis (ES). METHODS A cohort of 52 patients with ES was evaluated in the departments of gastroenterology and internal medicine. At baseline, all patients underwent assessment by an integrated gastro-rheumatologic evaluation of articular and gastrointestinal activity, as well patient reported outcomes (PROs) of the HRQoL questionnaires. After this integrated evaluation and following a specific working flowchart, the Ada anti-tumor necrosis factor (TNF)-inhibitor was assigned to a cohort of 30 patients and its clinical efficacy was evaluated at baseline and after 6-mo and 12-mo treatment by the following tests: (1) Ankylosing Spondylitis Disease Activity Score- C-Reactive Protein (ASDAS-CRP); Bath Ankylosing Spondylitis Disease Activity Index (BASDAI), Bath Ankylosing Spondylitis Functional Index (BASFI) and Bath Ankylosing Spondylitis Metrology Index (BASMI) for articular activity; (2) Inflammatory Bowel Disease Questionnaire (IBDQ), Crohn's Disease Activity Index (CDAI) and partial Mayo (pMayo) score for gastrointestinal symptoms and activity; and (3) Health Assessment Questionnaire (HAQ), Patient Global Assessment (PGA) and Short Form-36 health survey (SF-36) questionnaires for PROs of the HRQoL. RESULTS Integrated evaluation and management of the patients affected by ES, carried out simultaneously by a gastroenterologist and a rheumatologist, allowed clinicians to choose the optimal therapeutic strategy. In a cohort of 30 ES patients affected by active articular and gastrointestinal disease, or axial active articular inflammation, Ada led to fast and sustained improvement of both articular and gastrointestinal disease activities. In fact, all the clinimetric evaluation tests exploring articular or gastrointestinal activity, as well as all the HRQoL scores, showed a significant improvement having been achieved at the earliest (6-mo) assessment. This important clinical improvement was maintained at the 12-mo follow-up. Importantly, global and gastrointestinal quality of life significantly correlated with articular disease activity, providing evidence to support that the integrated evaluation is the best option to manage patients with ES. CONCLUSION Ada treatment, upon multidisciplinary (gastrorheumatologic) evaluation, significantly improves both articular and gastrointestinal inflammation, thereby improving the HRQoL in patients affected by ES