Renormalization group approach to multiscale modelling in materials science

Dendritic growth, and the formation of material microstructure in general, necessarily involves a wide range of length scales from the atomic up to sample dimensions. The phase field approach of Langer, enhanced by optimal asymptotic methods and adaptive mesh refinement, copes with this range of scales, and provides an effective way to move phase boundaries. However, it fails to preserve memory of the underlying crystallographic anisotropy, and thus is ill-suited for problems involving defects or elasticity. The phase field crystal (PFC) equation-- a conserving analogue of the Hohenberg-Swift equation --is a phase field equation with periodic solutions that represent the atomic density. It can natively model elasticity, the formation of solid phases, and accurately reproduces the nonequilibrium dynamics of phase transitions in real materials. However, the PFC models matter at the atomic scale, rendering it unsuitable for coping with the range of length scales in problems of serious interest. Here, we show that a computationally-efficient multiscale approach to the PFC can be developed systematically by using the renormalization group or equivalent techniques to derive appropriate coarse-grained coupled phase and amplitude equations, which are suitable for solution by adaptive mesh refinement algorithms

Energetic synchrony throughout the non-breeding season in common guillemots from four colonies

The non‐breeding season presents significant energetic challenges to birds that breed in temperate or polar regions, with clear implications for population dynamics. In seabirds, the environmental conditions at non‐breeding sites drive food availability and the energetic cost of regulatory processes, resulting in variation in diet, behaviour and energetics; however, very few studies have attempted to understand if and how these aspects vary between populations. We investigated whether non‐breeding location influenced diet, behaviour and energetics in the common guillemot Uria aalge. We studied guillemots from four UK breeding colonies, two located on the west coast of Scotland and two on the east. We quantified non‐breeding distribution, foraging behaviour and activity budgets of 39 individuals from July to March, using geolocation–immersion loggers and time‐depth recorders, and used feather stable isotope signatures to infer diet during the post‐breeding moult. We calculated energy expenditure and investigated whether the peak (an indicator of the potential vulnerability to marine threats) varied between colonies. Individuals were spatially segregated according to the coastline they breed on, with west coast guillemots distributed off the west coast of the UK and east coast guillemots distributed off the east coast. Diet and behaviour were more similar in guillemots that shared a breeding coastline than those that did not, as west coast guillemots foraged at a lower trophic level, spent less time diving and engaged in more pelagic foraging than east coast guillemots. However, energy expenditure was remarkably similar between colonies, peaking during late February/early March, indicating that, during our study period, there was high synchrony between colonies in the timing of potential vulnerability to marine threats. Therefore, any anthropogenic changes that result in decreased food availability or increased energy expenditure during late winter may have greater impacts on energy balance, with consequences for population dynamics.</jats:p

Reproductive Intentions and Outcomes among Women on Antiretroviral Therapy in Rural Uganda: A Prospective Cohort Study

Background: Antiretroviral therapy (ART) may influence the biological, social and behavioral determinants of pregnancy in HIV-infected women. However, there are limited longitudinal data on the reproductive intentions and outcomes among women on ART in Africa. Methodology /Principal Findings: Using a prospective cohort design, we analyzed trends in desire for children and predictors of pregnancy among a cohort of 733 HIV-infected women in rural Uganda who initiated ART between May 2003 and May 2004 and were followed up in their homes until June 2006. Women answered in-depth social and behavioral questionnaires administered every quarter in year 1 after initiating ART, and every 6 to 12 months thereafter. Use of family planning methods was assessed at 18 and 24 months after starting ART. We tested for non-constant pregnancy incidence by using a shape parameter test from the Weibull distribution. We modeled repeated measurements of all variables related to the women’s desire for children over time using a generalized estimating equation (GEE) extension to the logistic regression model. Risk factors for pregnancy were examined using Cox proportional hazards model. 711 women eligible for the study were followed-up for a median time of 2.4 years after starting ART. During this time, less than 7 % of women reported wanting more children at any time point yet 120 (16.9%) women experienced 140 pregnancies and pregnancy incidence increased from 3.46 per 100 women-years (WY) in the first quarter to 9.5 per 100 WY at 24 months (p,0.0001). This wa

Leveraging Spatial Variation in Tumor Purity for Improved Somatic Variant Calling of Archival Tumor Only Samples

Archival tumor samples represent a rich resource of annotated specimens for translational genomics research. However, standard variant calling approaches require a matched normal sample from the same individual, which is often not available in the retrospective setting, making it difficult to distinguish between true somatic variants and individual-specific germline variants. Archival sections often contain adjacent normal tissue, but this tissue can include infiltrating tumor cells. As existing comparative somatic variant callers are designed to exclude variants present in the normal sample, a novel approach is required to leverage adjacent normal tissue with infiltrating tumor cells for somatic variant calling. Here we present lumosVar 2.0, a software package designed to jointly analyze multiple samples from the same patient, built upon our previous single sample tumor only variant caller lumosVar 1.0. The approach assumes that the allelic fraction of somatic variants and germline variants follow different patterns as tumor content and copy number state change. lumosVar 2.0 estimates allele specific copy number and tumor sample fractions from the data, and uses a to model to determine expected allelic fractions for somatic and germline variants and to classify variants accordingly. To evaluate the utility of lumosVar 2.0 to jointly call somatic variants with tumor and adjacent normal samples, we used a glioblastoma dataset with matched high and low tumor content and germline whole exome sequencing data (for true somatic variants) available for each patient. Both sensitivity and positive predictive value were improved when analyzing the high tumor and low tumor samples jointly compared to analyzing the samples individually or in-silico pooling of the two samples. Finally, we applied this approach to a set of breast and prostate archival tumor samples for which tumor blocks containing adjacent normal tissue were available for sequencing. Joint analysis using lumosVar 2.0 detected several variants, including known cancer hotspot mutations that were not detected by standard somatic variant calling tools using the adjacent tissue as presumed normal reference. Together, these results demonstrate the utility of leveraging paired tissue samples to improve somatic variant calling when a constitutional sample is not available

Constraints on perception of information from obstacles during foot clearance in people with chronic stroke

The aim of this study was to examine effects of different types of task constraints on coupling of perception and action in people with chronic stroke when crossing obstacles during a walking task. Ten participants with hemiplegic chronic stroke volunteered to walk over a static obstacle under two distinct task constraints: simple and dual task. Under simple task constraints, without specific instructions, participants walked at their preferred speed and crossed over an obstacle. Under dual task constraints the same individuals were required to subtract numbers whilst walking. Under both distinct task constraints, we examined emergent values of foot distance when clearing a static obstacle in both affected and unaffected legs, measured by a 3D motion tracking system. Principal Component Analysis was used to quantify task performance and discriminant analysis was used to compare gait performance between task constraints. Results suggested that patients, regardless of affected body side, demonstrated differences in perception of distance information from the obstacle, which constrained gait differences in initial swing, mid-swing and crossing phases. Further, dual task constraints, rather than hemiplegic body side, was a significant discriminator in patients' perceptions of distance and height information to the obstacle. These findings suggested how performance of additional cognitive tasks might constrain perception of information from an obstacle in people with chronic stroke during different phases of obstacle crossing, and thus may impair their adaptive ability to successfully manoeuvre around objects

The Supercam Instrument Suite on the NASA Mars 2020 Rover: Body Unit and Combined System Tests

The SuperCam instrument suite provides the Mars 2020 rover, Perseverance, with a number of versatile remote-sensing techniques that can be used at long distance as well as within the robotic-arm workspace. These include laser-induced breakdown spectroscopy (LIBS), remote time-resolved Raman and luminescence spectroscopies, and visible and infrared (VISIR; separately referred to as VIS and IR) reflectance spectroscopy. A remote micro-imager (RMI) provides high-resolution color context imaging, and a microphone can be used as a stand-alone tool for environmental studies or to determine physical properties of rocks and soils from shock waves of laser-produced plasmas. SuperCam is built in three parts: The mast unit (MU), consisting of the laser, telescope, RMI, IR spectrometer, and associated electronics, is described in a companion paper. The on-board calibration targets are described in another companion paper. Here we describe SuperCam’s body unit (BU) and testing of the integrated instrument. The BU, mounted inside the rover body, receives light from the MU via a 5.8 m optical fiber. The light is split into three wavelength bands by a demultiplexer, and is routed via fiber bundles to three optical spectrometers, two of which (UV and violet; 245–340 and 385–465 nm) are crossed Czerny-Turner reflection spectrometers, nearly identical to their counterparts on ChemCam. The third is a high-efficiency transmission spectrometer containing an optical intensifier capable of gating exposures to 100 ns or longer, with variable delay times relative to the laser pulse. This spectrometer covers 535–853 nm (105–7070 cm−1 Raman shift relative to the 532 nm green laser beam) with 12 cm−1 full-width at half-maximum peak resolution in the Raman fingerprint region. The BU electronics boards interface with the rover and control the instrument, returning data to the rover. Thermal systems maintain a warm temperature during cruise to Mars to avoid contamination on the optics, and cool the detectors during operations on Mars. Results obtained with the integrated instrument demonstrate its capabilities for LIBS, for which a library of 332 standards was developed. Examples of Raman and VISIR spectroscopy are shown, demonstrating clear mineral identification with both techniques. Luminescence spectra demonstrate the utility of having both spectral and temporal dimensions. Finally, RMI and microphone tests on the rover demonstrate the capabilities of these subsystems as well