Accelerated Calder\'on preconditioning for Maxwell transmission problems

We investigate a range of techniques for the acceleration of Calder\'on (operator) preconditioning in the context of boundary integral equation methods for electromagnetic transmission problems. Our objective is to mitigate as far as possible the high computational cost of the barycentrically-refined meshes necessary for the stable discretisation of operator products. Our focus is on the well-known PMCHWT formulation, but the techniques we introduce can be applied generically. By using barycentric meshes only for the preconditioner and not for the original boundary integral operator, we achieve significant reductions in computational cost by (i) using "reduced" Calder\'on preconditioners obtained by discarding constituent boundary integral operators that are not essential for regularisation, and (ii) adopting a ``bi-parametric'' approach in which we use a lower quality (cheaper) $\mathcal{H}$-matrix assembly routine for the preconditioner than for the original operator, including a novel approach of discarding far-field interactions in the preconditioner. Using the boundary element software Bempp (www.bempp.com), we compare the performance of different combinations of these techniques in the context of scattering by multiple dielectric particles. Applying our accelerated implementation to 3D electromagnetic scattering by an aggregate consisting of 8 monomer ice crystals of overall diameter 1cm at 664GHz leads to a 99% reduction in memory cost and at least a 75% reduction in total computation time compared to a non-accelerated implementation

A new machine learning based approach to predict Freezing of Gait

Freezing of gait (FoG) is a motor symptom of Parkinson’s disease (PD) that frequently occurs in the long-term sufferers of the disease. FoG may result to nursing home admission as it can lead to falls, and therefore, it impacts negatively on the quality of life. The focus of this study is the systematic evaluation of machine learning techniques in conjunction with varying size time windows and time/frequency domain feature sets in predicting a FoG event before its onset. In the experiments, the Daphnet FoG dataset is used to benchmark performance. This consists of accelerometer signals obtained from sensors mounted on the ankle, thigh and trunk of the PD patients. The dataset is annotated with instances of normal activity events, and FoG events. To predict the onset of FoG, the dataset is augmented with an additional class, termed ‘transition’, which relates to a manually defined period prior to the occurrence of a FoG episode. In this research, five machine learning models are used, namely, Random Forest, Extreme Gradient Boosting, Gradient Boosting, Support Vector Machines using Radial Basis Functions, and Neural Networks. Support Vector Machines with Radial Basis kernels provided the best performance achieving sensitivity values of 72.34%, 91.49%, 75.00%, and specificity values of 87.36%, 88.51% and 93.62%, for the FoG, transition and normal activity classes, respectivel

Tunable force transduction through the Escherichia coli cell envelope

The outer membrane (OM) of Gram-negative bacteria is not energised and so processes requiring a driving force must connect to energy-transduction systems in the inner membrane (IM). Tol (Tol-Pal) and Ton are related, proton motive force- (PMF-) coupled assemblies that stabilise the OM and import essential nutrients, respectively. Both rely on proton-harvesting IM motor (stator) complexes, which are homologues of the flagellar stator unit Mot, to transduce force to the OM through elongated IM force transducer proteins, TolA and TonB, respectively. How PMF-driven motors in the IM generate mechanical work at the OM via force transducers is unknown. Here, using cryoelectron microscopy, we report the 4.3Å structure of the Escherichia coli TolQR motor complex. The structure reaffirms the 5:2 stoichiometry seen in Ton and Mot and, with motor subunits related to each other by 10 to 16° rotation, supports rotary motion as the default for these complexes. We probed the mechanism of force transduction to the OM through in vivo assays of chimeric TolA/TonB proteins where sections of their structurally divergent, periplasm-spanning domains were swapped or replaced by an intrinsically disordered sequence. We find that TolA mutants exhibit a spectrum of force output, which is reflected in their respective abilities to both stabilise the OM and import cytotoxic colicins across the OM. Our studies demonstrate that structural rigidity of force transducer proteins, rather than any particular structural form, drives the efficient conversion of PMF-driven rotary motions of 5:2 motor complexes into physiologically relevant force at the OM

Rapid and Sensitive Assessment of Globin Chains for Gene and Cell Therapy of Hemoglobinopathies

The β-hemoglobinopathies sickle cell anemia and β-thalassemia are the focus of many gene-therapy studies. A key disease parameter is the abundance of globin chains because it indicates the level of anemia, likely toxicity of excess or aberrant globins, and therapeutic potential of induced or exogenous β-like globins. Reversed-phase high-performance liquid chromatography (HPLC) allows versatile and inexpensive globin quantification, but commonly applied protocols suffer from long run times, high sample requirements, or inability to separate murine from human β-globin chains. The latter point is problematic for in vivo studies with gene-addition vectors in murine disease models and mouse/human chimeras. This study demonstrates HPLC-based measurements of globin expression (1) after differentiation of the commonly applied human umbilical cord blood-derived erythroid progenitor-2 cell line, (2) in erythroid progeny of CD34+ cells for the analysis of clustered regularly interspaced short palindromic repeats/Cas9-mediated disruption of the globin regulator BCL11A, and (3) of transgenic mice holding the human β-globin locus. At run times of 8 min for separation of murine and human β-globin chains as well as of human γ-globin chains, and with routine measurement of globin-chain ratios for 12 nL of blood (tested for down to 0.75 nL) or of 300,000 in vitro differentiated cells, the methods presented here and any variant-specific adaptations thereof will greatly facilitate evaluation of novel therapy applications for β-hemoglobinopathies

Towards a Virtual Fencing System: Training Domestic Sheep Using Audio Stimuli

Fencing in livestock management is essential for location and movement control yet with conventional methods to require close labour supervision, leading to increased costs and reduced flexibility. Consequently, virtual fencing systems (VF) have recently gained noticeable attention as an effective method for the maintenance and control of restricted areas for animals. Existing systems to control animal movement use audio followed by controversial electric shocks which are prohibited in various countries. Accordingly, the present work has investigated the sole application of audio signals in training and managing animal behaviour. Audio cues in the range of 125–17 kHz were used to prohibit the entrance of seven Hebridean ewes from a restricted area with a feed bowl. Two trials were performed over the period of a year which were video recorded. Sound signals were activated when the animal approached a feed bowl and a restricted area with no feed bowl present. Results from both trials demonstrated that white noise and sounds in the frequency ranges of 125–440 Hz to 10–17 kHz successfully discouraged animals from entering a specific area with an overall success rate of 89.88% (white noise: 92.28%, 10–14 kHz: 89.13%, 15–17 kHz: 88.48%, 125–440 Hz: 88.44%). The study demonstrated that unaided audio stimuli were effective at managing virtual fencing for sheep

Molecular understanding of the serum antibody repertoires after seasonal influenza vaccination among different age cohorts

Numerous influenza vaccination studies based on bulk serology have indicated that the antibody responses to the vaccine markedly decrease in the elderly. However, whether such decline results from the changes in the overall quantity or the quality of the circulating antibodies in serum remains unknown. Utilizing novel antibody repertoire profiling technologies, combining tandem mass spectrometry (LC-MS/MS) and high-throughput sequencing, we investigated the influenza-specific serological repertoires of 10 donors ranging from 26 to 70 years old vaccinated with Fluzone® 2013-2014 and/or 2014-2015. In particular, we determined the serum antibodies that are specific to the H1 or H3 component of the vaccine or cross-reactive between the two (H1+H3) and examined their relative quantitative distributions. Our data indicate that the proportion of H1+H3 antibodies significantly increases in the elderly and that the somatic hypermutation rates of the influenza-specific antibodies are higher in the elderly. These results suggest that the repeated exposure to the different virus subtypes could have led to the prolonged selection of H1+H3 antibodies targeting highly conserved epitopes. To evaluate the potency of the antibodies circulating in different age groups, we recombinantly expressed a number of representative monoclonal antibodies isolated from the donors in different age groups for further characterizations. Overall, our analysis suggests that the influenza-specific repertoire in the elderly may converge toward shared epitopes but the quality of the antibodies can be superior in terms of cross-reactivity. However, because the antibody repertoire “shrinks” as we age while targeting more conserved epitopes across different influenza subtypes, it is possible that the elderly is particularly susceptible to significantly altered strains. Collectively, profiling vaccine induced serological repertoires among different age cohorts can provide unprecedented insights regarding humoral immunity associated with age and a potential explanation for the vulnerability of the elderly

Discovery, characterization and in vivo activity of pyocin SD2, a protein antibiotic from Pseudomonas aeruginosa

Increasing rates of antibiotic resistance among Gram-negative pathogens such as Pseudomonas aeruginosa means alternative approaches to antibiotic development are urgently required. Pyocins, produced by P. aeruginosa for intraspecies competition, are highly potent protein antibiotics known to actively translocate across the outer membrane of P. aeruginosa. Understanding and exploiting the mechanisms by which pyocins target, penetrate and kill P. aeruginosa is a promising approach to antibiotic development. In this work we show the therapeutic potential of a newly identified tRNase pyocin, pyocin SD2, by demonstrating its activity in vivo in a murine model of P. aeruginosa lung infection. In addition, we propose a mechanism of cell targeting and translocation for pyocin SD2 across the P. aeruginosa outer membrane. Pyocin SD2 is concentrated at the cell surface, via binding to the common polysaccharide antigen (CPA) of P. aeruginosa lipopolysaccharide (LPS), from where it can efficiently locate its outer membrane receptor FpvAI. This strategy of utilizing both the CPA and a protein receptor for cell targeting is common among pyocins as we show that pyocins S2, S5 and SD3 also bind to the CPA. Additional data indicate a key role for an unstructured N-terminal region of pyocin SD2 in the subsequent translocation of the pyocin into the cell. These results greatly improve our understanding of how pyocins target and translocate across the outer membrane of P. aeruginosa. This knowledge could be useful for the development of novel anti-pseudomonal therapeutics and will also support the development of pyocin SD2 as a therapeutic in its own right

FINDbase: a relational database recording frequencies of genetic defects leading to inherited disorders worldwide

Frequency of INherited Disorders database (FINDbase) () is a relational database, derived from the ETHNOS software, recording frequencies of causative mutations leading to inherited disorders worldwide. Database records include the population and ethnic group, the disorder name and the related gene, accompanied by links to any corresponding locus-specific mutation database, to the respective Online Mendelian Inheritance in Man entries and the mutation together with its frequency in that population. The initial information is derived from the published literature, locus-specific databases and genetic disease consortia. FINDbase offers a user-friendly query interface, providing instant access to the list and frequencies of the different mutations. Query outputs can be either in a table or graphical format, accompanied by reference(s) on the data source. Registered users from three different groups, namely administrator, national coordinator and curator, are responsible for database curation and/or data entry/correction online via a password-protected interface. Databaseaccess is free of charge and there are no registration requirements for data querying. FINDbase provides a simple, web-based system for population-based mutation data collection and retrieval and can serve not only as a valuable online tool for molecular genetic testing of inherited disorders but also as a non-profit model for sustainable database funding, in the form of a ‘database-journal’