The CCD and readout electronics for the OMC instrument on Integral

The Optical Monitoring Camera (OMC) on ESA's Integral gamma-ray astronomy satellite is devoted to optical wavelength observations simultaneously covering the same field-of-view as the gamma-ray and X-ray instruments. The OMC consists of a refracting telescope with a CCD as the imaging device in the focal plane. Here we describe the CCD and its associated readout electronics, in particular pointing out features of interest to users of the OMC instrument and its data

Modeling chemistry in and above snow at Summit, Greenland – Part 1: Model description and results

Sun-lit snow is increasingly recognized as a chemical reactor that plays an active role in uptake, transformation, and release of atmospheric trace gases. Snow is known to influence boundary layer air on a local scale, and given the large global surface coverage of snow may also be significant on regional and global scales. We present a new detailed one-dimensional snow chemistry module that has been coupled to the 1-D atmospheric boundary layer model MISTRA. The new 1-D snow module, which is dynamically coupled to the overlaying atmospheric model, includes heat transport in the snowpack, molecular diffusion, and wind pumping of gases in the interstitial air. The model includes gas phase chemical reactions both in the interstitial air and the atmosphere. Heterogeneous and multiphase chemistry on atmospheric aerosol is considered explicitly. The chemical interaction of interstitial air with snow grains is simulated assuming chemistry in a liquid-like layer (LLL) on the grain surface. The coupled model, referred to as MISTRA-SNOW, was used to investigate snow as the source of nitrogen oxides (NOx) and gas phase reactive bromine in the atmospheric boundary layer in the remote snow covered Arctic (over the Greenland ice sheet) as well as to investigate the link between halogen cycling and ozone depletion that has been observed in interstitial air. The model is validated using data taken 10 June–13 June, 2008 as part of the Greenland Summit Halogen-HOx experiment (GSHOX). The model predicts that reactions involving bromide and nitrate impurities in the surface snow can sustain atmospheric NO and BrO mixing ratios measured at Summit, Greenland during this period

Eave tubes for malaria control in Africa: a modelling assessment of potential impact on transmission.

BACKGROUND: Novel interventions for malaria control are necessary in the face of problems such as increasing insecticide resistance and residual malaria transmission. One way to assess performance prior to deployment in the field is through mathematical modelling. Modelled here are a range of potential outcomes for eave tubes, a novel mosquito control tool combining house screening and targeted use of insecticides to provide both physical protection and turn the house into a lethal mosquito killing device. METHODS: The effect of eave tubes was modelled by estimating the reduction of infectious mosquito bites relative to no intervention (a transmission metric defined as relative transmission potential, RTP). The model was used to assess how RTP varied with coverage when eave tubes were used as a stand-alone intervention, or in combination with either bed nets (LLINs) or indoor residual spraying (IRS). RESULTS: The model indicated the impact of eave tubes on transmission increases non-linearly as coverage increases, suggesting a community level benefit. For example, based on realistic assumptions, just 30 % coverage resulted in around 70 % reduction in overall RTP (i.e. there was a benefit for those houses without eave tubes). Increasing coverage to around 70 % reduced overall RTP by >90 %. Eave tubes exhibited some redundancy with existing interventions, such that combining interventions within properties did not give reductions in RTP equal to the sum of those provided by deploying each intervention singly. However, combining eave tubes and either LLINs or IRS could be extremely effective if the technologies were deployed in a non-overlapping way. CONCLUSION: Using predictive models to assess the benefit of new technologies has great value, and is especially pertinent prior to conducting expensive, large scale, randomized controlled trials. The current modelling study indicates eave tubes have considerable potential to impact malaria transmission if deployed at scale and can be used effectively with existing tools, especially if they are combined strategically with, for example, IRS and eave tubes targeting different houses.This work was supported by European Union Seventh Framework Programme Grant 306105, FP7-HEALTH-2012-INNOVATION-1

Observation of a single-beam gradient force acoustical trap for elastic particles: acoustical tweezers

We demonstrate the trapping of elastic particles by the large gradient force of a single acoustical beam in three dimensions. Acoustical tweezers can push, pull and accurately control both the position and the forces exerted on a unique particle. Forces in excess of 1 micronewton were exerted on polystyrene beads in the submillimeter range. A beam intensity less than 50  W/cm^{2} was required, ensuring damage-free trapping conditions. The large spectrum of frequencies covered by coherent ultrasonic sources provides a wide variety of manipulation possibilities from macroscopic to microscopic length scales. Our observations could open the way to important applications, in particular, in biology and biophysics at the cellular scale and for the design of acoustical machines in microfluidic environments

Mixture models for distance sampling detection functions

Funding: EPSRC DTGWe present a new class of models for the detection function in distance sampling surveys of wildlife populations, based on finite mixtures of simple parametric key functions such as the half-normal. The models share many of the features of the widely-used “key function plus series adjustment” (K+A) formulation: they are flexible, produce plausible shapes with a small number of parameters, allow incorporation of covariates in addition to distance and can be fitted using maximum likelihood. One important advantage over the K+A approach is that the mixtures are automatically monotonic non-increasing and non-negative, so constrained optimization is not required to ensure distance sampling assumptions are honoured. We compare the mixture formulation to the K+A approach using simulations to evaluate its applicability in a wide set of challenging situations. We also re-analyze four previously problematic real-world case studies. We find mixtures outperform K+A methods in many cases, particularly spiked line transect data (i.e., where detectability drops rapidly at small distances) and larger sample sizes. We recommend that current standard model selection methods for distance sampling detection functions are extended to include mixture models in the candidate set.Publisher PDFPeer reviewe

A Newly Developed Web-Based Resource on Genetic Eye Disorders for Users With Visual Impairment (Gene.Vision): Usability Study

Background: Despite the introduction of the Web Content Accessibility Guidelines and legislations, many websites remain poorly accessible to users with disability, especially those with visual impairment, as the internet has become a more visually complex environment. With increasing reliance on the internet and almost 2 million people in the United Kingdom being affected by vision loss, it is important that they are not overlooked when developing web-based materials. A significant proportion of those affected have irreversible vision loss due to rare genetic eye disorders, and many of them use the internet as a primary source of information for their conditions. However, access to high-quality web-based health information with an inclusive design remains a challenge for many. We have developed a new web-based resource for genetic eye disorders called Gene.Vision that aims to provide a holistic guide for patients, relatives, and health care professionals. Objective: Through a usability testing session of our website prototype, this study aims to identify key web-based accessibility features for internet users with vision impairment and to explore whether the contents provided in Gene.Vision are relevant and comprehensible. Methods: A face-to-face testing session with 8 participants (5 patients, 2 family members, and 1 member of the public) and 8 facilitators was conducted on a prototype website. Remote testing was performed with another patient due to COVID-19 restrictions. Home page design, navigation, content layout and quality, language, and readability were explored through direct observation and task completion using the think-aloud method. A patient focus group was organized to elicit further feedback. Qualitative data were gathered and analyzed to identify core themes through open and axial coding. Results: All participants had good computer literacy; 6 patients with visual impairment used visual aid software including iOS VoiceOver and Speak Screen, iOS Classic Invert, ZoomText 2020, Job Access With Speech, and Nonvisual Desktop Access. The features identified by the participants that will enhance accessibility and usability for users with visual impairment were a consistent website layout, a structured information hierarchy with a clear description of links, good chromatic and luminance contrast, a simple home page with predictable and easy navigation, adaptability to various assistive software, and readable and relevant content. They reported that dynamic content (such as carousels) and large empty spaces reduced accessibility. Information on research, support available, practical advice, and links to charities were incentives for repeated website visits. Conclusions: We demonstrated the importance of developing a website with a user-based approach. Through end user testing, we identified several key web-based accessibility features for people with visual impairment. Target end users should always be involved early and throughout the design process to ensure their needs are met. Many of these steps can be implemented easily and will aid in search engine optimization

Bats Use Magnetite to Detect the Earth's Magnetic Field

While the role of magnetic cues for compass orientation has been confirmed in numerous animals, the mechanism of detection is still debated. Two hypotheses have been proposed, one based on a light dependent mechanism, apparently used by birds and another based on a “compass organelle” containing the iron oxide particles magnetite (Fe3O4). Bats have recently been shown to use magnetic cues for compass orientation but the method by which they detect the Earth's magnetic field remains unknown. Here we use the classic “Kalmijn-Blakemore” pulse re-magnetization experiment, whereby the polarity of cellular magnetite is reversed. The results demonstrate that the big brown bat Eptesicus fuscus uses single domain magnetite to detect the Earths magnetic field and the response indicates a polarity based receptor. Polarity detection is a prerequisite for the use of magnetite as a compass and suggests that big brown bats use magnetite to detect the magnetic field as a compass. Our results indicate the possibility that sensory cells in bats contain freely rotating magnetite particles, which appears not to be the case in birds. It is crucial that the ultrastructure of the magnetite containing magnetoreceptors is described for our understanding of magnetoreception in animals

Genomic and experimental evidence for multiple metabolic functions in the RidA/YjgF/YER057c/UK114 (Rid) protein family.

BackgroundIt is now recognized that enzymatic or chemical side-reactions can convert normal metabolites to useless or toxic ones and that a suite of enzymes exists to mitigate such metabolite damage. Examples are the reactive imine/enamine intermediates produced by threonine dehydratase, which damage the pyridoxal 5'-phosphate cofactor of various enzymes causing inactivation. This damage is pre-empted by RidA proteins, which hydrolyze the imines before they do harm. RidA proteins belong to the YjgF/YER057c/UK114 family (here renamed the Rid family). Most other members of this diverse and ubiquitous family lack defined functions.ResultsPhylogenetic analysis divided the Rid family into a widely distributed, apparently archetypal RidA subfamily and seven other subfamilies (Rid1 to Rid7) that are largely confined to bacteria and often co-occur in the same organism with RidA and each other. The Rid1 to Rid3 subfamilies, but not the Rid4 to Rid7 subfamilies, have a conserved arginine residue that, in RidA proteins, is essential for imine-hydrolyzing activity. Analysis of the chromosomal context of bacterial RidA genes revealed clustering with genes for threonine dehydratase and other pyridoxal 5'-phosphate-dependent enzymes, which fits with the known RidA imine hydrolase activity. Clustering was also evident between Rid family genes and genes specifying FAD-dependent amine oxidases or enzymes of carbamoyl phosphate metabolism. Biochemical assays showed that Salmonella enterica RidA and Rid2, but not Rid7, can hydrolyze imines generated by amino acid oxidase. Genetic tests indicated that carbamoyl phosphate overproduction is toxic to S. enterica cells lacking RidA, and metabolomic profiling of Rid knockout strains showed ten-fold accumulation of the carbamoyl phosphate-related metabolite dihydroorotate.ConclusionsLike the archetypal RidA subfamily, the Rid2, and probably the Rid1 and Rid3 subfamilies, have imine-hydrolyzing activity and can pre-empt damage from imines formed by amine oxidases as well as by pyridoxal 5'-phosphate enzymes. The RidA subfamily has an additional damage pre-emption role in carbamoyl phosphate metabolism that has yet to be biochemically defined. Finally, the Rid4 to Rid7 subfamilies appear not to hydrolyze imines and thus remain mysterious

Silico identification, molecular characterization and expression analysis of the Trypanosoma brucei paraflagellar rod protein PFR3

En el presente artículo se describen la identificación y el aislamiento del gen codificante para la proteínaPFR3 del T. brucei. La secuencia deducida de aminoácidos produce una proteína de 592 residuos conun punto isoeléctrico de 5,14 y presenta una identidad de secuencia del 68,9% con la proteína PFR3 delT. cruzi. Sin embargo, el porcentaje de homología entre la proteína PFR3 de T. brucei y otras secuenciasdisponibles de PFRs de T. brucei y T. cruzi es inferior al 22%. En contraste con lo descrito para losmiembros de la familia de proteínas de filamento paraflagelar, la mayor divergencia entre las proteínasPFR3 de T. cruzi y T. brucei se encuentra en la región central de la proteína, con una similitud del 38%en 200 aminoácidos. Estimamos que existen dos copias de la proteína PFR3 de T. brucei por genomahaploide. El gen se transcribe como mARN de aproximadamente 3,6 kb de longitud, presente con lamisma abundancia en formas parasitarias procíclicas y del torrente sanguíneo.In the present paper we describe the identification and isolation of the gene coding for T. brucei PFR3protein. The deduced amino acid sequence produces a protein of 592 residues with an isoelectric pointof 5.14 and shows a 68.9% sequence identity with T. cruzi PFR3 protein. However, the percentage ofhomology among T. brucei PFR3 and other available PFRs sequences from T. brucei and T. cruzi islower than 22%. In contrast to that described for members of paraflagellar rod protein family, thehighest divergence between T. cruzi and T. brucei PFR3 proteins is located at the central region of theprotein with a 38% of similarity over 200 amino acid. We estimate that there exist two copies of theT. brucei PFR3 protein per haploid genome. The gene is transcribed as a mRNA of approximately 3.6kb in length, equally abundant in both procyclic and bloodstream parasite forms

Calculation of Volterra kernels for solutions of nonlinear differential equations

We consider vector-valued autonomous differential equations of the form x' = f(x) + phi with analytic f and investigate the nonanticipative solution operator phi bar right arrow A(phi) in terms of its Volterra series. We show that Volterra kernels of order > 1 occurring in the series expansion of the solution operator A are continuous functions, and establish recurrence relations between the kernels allowing their explicit calculation. A practical tensor calculus is provided for the finite-dimensional case. In addition to analytically calculating the kernels, we present an algorithm to numerically obtain them from the output x(t) through sampling the input space by linear combinations of delta functions. We call this "differential sampling". It is a nonlinear analogue of the classical method of impulse response. We prove a continuity theorem stating that, in the finite-dimensional case, approximate delta functions give rise to approximate Volterra kernels and that continuity holds in the sense of weak convergence. Finally, we discuss a practical implementation of differential sampling and relate it to the Wiener method