Appearance of Saturn's F ring azimuthal channels for the anti-alignment configuration between the ring and Prometheus

In this article we explore the aspect of the F ring with respect to the anti-alignment configuration between the ring and Prometheus. We focus our attention on the shape of the F ring's azimuthal channels which were first reported by Porco et al. (2005) and numerically explored by Murray et al. (2005), who found excellent agreement between Cassini's ISS reprojected images and their numerical model via a direct comparison. We find that for anti-alignment the channels are wider and go deeper inside the ring material. From our numerical model we find a new feature, an island in the middle of the channel. This island is made up of the particles that have been perturbed the most by Prometheus and only appears when this satellite is close to apoapsis. In addition, plots of the anti-alignment configuration for different orbital stages of Prometheus are obtained and discussed here.Comment: Number of pages: 12, number of tables: 1, number of figures:

In silico evaluation of WHO-endorsed molecular methods to detect drug resistant tuberculosis

Universal drug susceptibility testing (DST) for tuberculosis is a major goal of the END TB strategy. PCR-based molecular diagnostic tests have been instrumental in increasing DST globally and several assays have now been endorsed by the World Health Organization (WHO) for use in the diagnosis of drug resistance. These endorsed assays, however, each interrogate a limited number of mutations associated with resistance, potentially limiting their sensitivity compared to sequencing-based methods. We applied an in silico method to compare the sensitivity and specificity of WHO-endorsed molecular based diagnostics to the mutation set identified by the WHO mutations catalogue using phenotypic DST as the reference. We found that, in silico, the mutation sets used by probe-based molecular diagnostic tests to identify rifampicin, isoniazid, pyrazinamide, levofloxacin, moxifloxacin, amikacin, capreomycin and kanamycin resistance produced similar sensitivities and specificities to the WHO mutation catalogue. PCR-based diagnostic tests were most sensitive for drugs where mechanisms of resistance are well established and localised to small genetic regions or a few prevalent mutations. Approaches using sequencing technologies can provide advantages for drugs where our knowledge of resistance is limited, or where complex resistance signatures exist

Codon-precise, synthetic, antibody fragment libraries built using automated hexamer codon additions and validated through next generation sequencing

We have previously described ProxiMAX, a technology that enables the fabrication of precise, combinatorial gene libraries via codon-by-codon saturation mutagenesis. ProxiMAX was originally performed using manual, enzymatic transfer of codons via blunt-end ligation. Here we present Colibra™: an automated, proprietary version of ProxiMAX used specifically for antibody library generation, in which double-codon hexamers are transferred during the saturation cycling process. The reduction in process complexity, resulting library quality and an unprecedented saturation of up to 24 contiguous codons are described. Utility of the method is demonstrated via fabrication of complementarity determining regions (CDR) in antibody fragment libraries and next generation sequencing (NGS) analysis of their quality and diversity

Modern Solutions for Ancient Pathogens: Direct Pathogen Sequencing for Diagnosis of Lepromatous Leprosy and Cerebral Coenurosis.

Microbes unculturable in vitro remain diagnostically challenging, dependent historically on clinical findings, histology, or targeted molecular detection. We applied whole-genome sequencing directly from tissue to diagnose infections with mycobacteria (leprosy) and parasites (coenurosis). Direct pathogen DNA sequencing provides flexible solutions to diagnosis of difficult pathogens in diverse contexts

Application of pharmacogenomics and bioinformatics to exemplify the utility of human <i>ex vivo</i> organoculture models in the field of precision medicine

Here we describe a collaboration between industry, the National Health Service (NHS) and academia that sought to demonstrate how early understanding of both pharmacology and genomics can improve strategies for the development of precision medicines. Diseased tissue ethically acquired from patients suffering from chronic obstructive pulmonary disease (COPD), was used to investigate inter-patient variability in drug efficacy using ex vivo organocultures of fresh lung tissue as the test system. The reduction in inflammatory cytokines in the presence of various test drugs was used as the measure of drug efficacy and the individual patient responses were then matched against genotype and microRNA profiles in an attempt to identify unique predictors of drug responsiveness. Our findings suggest that genetic variation in CYP2E1 and SMAD3 genes may partly explain the observed variation in drug response

Distasteful nectar deters floral robbery

Toxic nectar is an ecological paradox[1,2]. Plants divert substantial resources to produce nectar that attracts pollinators [3], but toxins in this reward could disrupt the mutualism and reduce plant fitness [4]. Alternatively, such compounds could protect nectar from robbers [2], provided they do not significantly alter pollinator visitation to the detriment of plant fitness [1,5–8]. Indeed, very few studies have investigated the role of plant toxins in nectar for defence against nectar robbers [4,9,10]. Here, we compared two Aconitum species (A. napellus and A. lycoctonum) that have flowers specialized for long-tongued bumblebee pollinators (Bombus hortorum) but are occasionally robbed by short-tongued bumblebees (B. terrestris) [6,11–13]. Pollinator visits to flowers were much more frequent than by robbers but visits correlated negatively with nectar alkaloid concentration and declined sharply between 200-380ppm. However, alkaloid concentrations of > 20ppm were deterrent to B. terrestris suggesting robbers were less tolerant of nectar alkaloids. Nectar of both plant species contained similar concentrations of carbohydrates and toxic alkaloids, but A. lycoctonum was more likely to secrete nectar in each flower and was also visited more frequently by pollinators and robbers.  We conclude that alkaloids in Aconitum sp. nectar affect rates of both pollinator visitation and robbery but may have co-evolved with nectar availability to maintain the fitness benefits of specialized plant-pollinator relationships. Chemical defence of nectar is, however, ultimately constrained by pollinator gustatory sensitivity

BINGO: A code for the efficient computation of the scalar bi-spectrum

We present a new and accurate Fortran code, the BI-spectra and Non-Gaussianity Operator (BINGO), for the efficient numerical computation of the scalar bi-spectrum and the non-Gaussianity parameter f_{NL} in single field inflationary models involving the canonical scalar field. The code can calculate all the different contributions to the bi-spectrum and the parameter f_{NL} for an arbitrary triangular configuration of the wavevectors. Focusing firstly on the equilateral limit, we illustrate the accuracy of BINGO by comparing the results from the code with the spectral dependence of the bi-spectrum expected in power law inflation. Then, considering an arbitrary triangular configuration, we contrast the numerical results with the analytical expression available in the slow roll limit, for, say, the case of the conventional quadratic potential. Considering a non-trivial scenario involving deviations from slow roll, we compare the results from the code with the analytical results that have recently been obtained in the case of the Starobinsky model in the equilateral limit. As an immediate application, we utilize BINGO to examine of the power of the non-Gaussianity parameter f_{NL} to discriminate between various inflationary models that admit departures from slow roll and lead to similar features in the scalar power spectrum. We close with a summary and discussion on the implications of the results we obtain.Comment: v1: 5 pages, 5 figures; v2: 35 pages, 11 figures, title changed, extensively revised; v3: 36 pages, 11 figures, to appear in JCAP. The BINGO code is available online at http://www.physics.iitm.ac.in/~sriram/bingo/bingo.htm