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At least 1,261 records · Page 70

Ceiling art in a radiation therapy department: its effect on patient treatment experience

A new initiative has been implemented at the Sunshine Hospital Radiation Therapy Centre, to provide a calming and comforting environment for patients attending radiation therapy treatment. As part of this initiative, the department's computed tomography (CT) room and radiation therapy bunkers were designed to incorporate ceiling art that replicates a number of different visual scenes. The study was undertaken to determine if ceiling art in the radiation therapy treatment CT and treatment bunkers had an effect on a patient's experience during treatment at the department. Additionally, the study aimed to identify which of the visuals in the ceiling art were most preferred by patients. Patients were requested to complete a 12-question survey. The survey solicited a patient's opinion/perception on the unit's unique ceiling display with emphasis on aesthetic appeal, patient treatment experience and the patient's engagement due to the ceiling display. The responses were dichotomised to ‘positive’ or ‘negative’. Every sixth patient who completed the survey was invited to have a general face-to-face discussion to provide further information about their thoughts on the displays. The results demonstrate that the ceiling artwork solicited a positive reaction in 89.8% of patients surveyed. This score indicates that ceiling artwork contributed positively to patients’ experiences during radiation therapy treatment. The study suggests that ceiling artwork in the department has a positive effect on patient experience during their radiation therapy treatment at the department.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

White‐tailed deer carrying capacity, intercropping switchgrass, and pine plantations

ABSTRACT Switchgrass ( Panicum virgatum ) is a cellulosic feedstock for alternative energy production that can be grown between rows of planted pines ( Pinus spp.) within intensively managed forests. Southeastern planted pine occupies 15.8 million ha and thus, switchgrass intercropping could have far‐ranging effects on plant communities and biomass production within these forests if broadly implemented. Such intercropping could lead to alterations to plant communities that may cause bottom‐up ecological changes affecting ecologically, economically, and socially important wildlife, such as white‐tailed deer ( Odocoileus virginianus ; deer). Therefore, we tested whether intercropping switchgrass in loblolly pine ( P. taeda ) plantations would cause switchgrass to dominate vegetative biomass thereby decreasing biomass of forages and reducing white‐tailed deer nutritional carrying capacity (NCC), or whether disturbance associated with establishment and harvest of switchgrass would facilitate ruderal forbs, and thereby increase biomass of preferred deer forages and increase NCC. In a randomized complete block design, we assigned 2 treatments (intercropped switchgrass and a standard pine management control) to 4 replicates of 10‐ha experimental units in Kemper County, Mississippi during summers of 2011−2015. We detected 323 plant species. Intercropping switchgrass had little effect on plant biomass production, and did not affect white‐tailed deer NCC at a maintenance diet of 6% crude protein. Intercropping provided additional disturbance allowing high‐protein content ruderal plants to colonize, and temporarily increased (3 yr) deer NCC at the 14% crude protein diet considered necessary to support lactation. However, concomitant with a sharp increase in switchgrass biomass in the third year of the study, NCC dropped to levels similar to traditionally managed pine stands. Switchgrass intercropping is not a reliable means of increasing deer NCC as a management strategy but does not appear to reduce carrying capacity in the short‐term relative to standard intensive pine management. © 2017 The Wildlife Society.

Loman, Zachary G.↗

Data‐Driven Engineering of Thermostable Collagen‐Mimetic Peptoid Triple Helices

Collagen-mimetic peptides (CMPs) are engineered molecules designed to replicate the triple-helical structure of natural collagen. A repeating x–y-Gly sequence is the defining motif of CMPs and is critical to their triple-helical structure and stability. Substitutions to the residues occupying the x and y positions present a means to modulate the CMP structure and properties. Peptoid residues—N-substituted glycine derivatives—present an attractive potential substitution due to their thermal stability, proteolytic resistance, biocompatibility, and diverse palette of non-natural side chains, but also tend to introduce a high degree of backbone flexibility that can diminish the stability of the triple helix. In this work, we report a computational active learning cycle comprising molecular dynamics simulation, Gaussian process regression, and Bayesian optimization to computationally identify a number of promising peptoid substitutions predicted to stabilize the desired quaternary structure through side chain interactions and produce stable peptoid-based collagen-like triple helices. To experimentally test the computational predictions, a top candidate identified by the screen was synthesized and imaged using scanning electron microscopy to resolve fibril-like bundles consistent with collagen-like triple helices. This work predicts a number of CMP peptoid substitutions capable of forming stable triple-helical structures, presents a generalizable design strategy for engineering desired peptoid structures, and opens new avenues for the design of peptoid-based biomimetic materials.

active learning↗

Deterministic direct aperture optimization using multiphase piecewise constant segmentation

Purpose Direct aperture optimization (DAO) attempts to incorporate machine constraints in the inverse optimization to eliminate the post‐processing steps in fluence map optimization (FMO) that degrade plan quality. Current commercial DAO methods utilize a stochastic or greedy approach to search a small aperture solution space. In this study, we propose a novel deterministic direct aperture optimization that integrates the segmentation of fluence map in the optimization problem using the multiphase piecewise constant Mumford‐Shah formulation. Methods The Mumford‐Shah based direct aperture optimization problem was formulated to include an L2‐norm dose fidelity term to penalize differences between the projected dose and the prescribed dose, an anisotropic total variation term to promote piecewise continuity in the fluence maps, and the multiphase piecewise constant Mumford‐Shah function to partition the fluence into pairwise discrete segments. A proximal‐class, first‐order primal‐dual solver was implemented to solve the large scale optimization problem, and an alternating module strategy was implemented to update fluence and delivery segments. Three patients of varying complexity—one glioblastoma multiforme (GBM) patient, one lung (LNG) patient, and one bilateral head and neck (H&N) patient with 3 PTVs—were selected to test the new DAO method. For each patient, 20 non‐coplanar beams were first selected using column generation, followed by the Mumford‐Shah based DAO (DAO MS ). For comparison, a popular and successful approach to DAO known as simulated annealing—a stochastic approach—was replicated. The simulated annealing DAO (DAO SA ) plans were then created using the same beam angles and maximum number of segments per beam. PTV coverage, PTV homogeneity , and OAR sparing were assessed for each plan. In addition, high dose spillage, defined as the 50% isodose volume divided by the tumor volume, as well as conformity, defined as the van't Riet conformation number, were evaluated. Results DAO MS achieved essentially the same OAR doses compared with the DAO SA plans for the GBM case. The average difference of OAR D max and D mean between the two plans were within 0.05% of the plan prescription dose. The lung case showed slightly improved critical structure sparing using the DAO MS approach, where the average OAR D max and D mean were reduced by 3.67% and 1.08%, respectively, of the prescription dose. The DAO MS plan substantially improved OAR dose sparing for the H&N patient, where the average OAR D max and D mean were reduced by over 10% of the prescription dose. The DAO MS and DAO SA plans were comparable for the GBM and LNG PTV coverage, while the DAO MS plan substantially improved the H&N PTV coverage, increasing D99 by 6.98% of the prescription dose. For the GBM and LNG patients, the DAO MS and DAO SA plans had comparable high dose spillage but slightly worse conformity with the DAO MS approach. For the H&N plan, DAO MS was considerably superior in high dose spillage and conformity to the DAO SA . The deterministic approach is able to solve the DAO problem substantially faster than the simulated annealing approach, with a 9.5‐ to 40‐fold decrease in total solve time, depending on the patient case. Conclusions A novel deterministic direct aperture optimization formulation was developed and evaluated. It combines fluence map optimization and the multiphase piecewise constant Mumford‐Shah segmentation into a unified framework, and the resulting optimization problem can be solved efficiently. Compared to the widely and commercially used simulated annealing DAO approach, it showed comparable dosimetry behavior for simple plans, and substantially improved OAR sparing, PTV coverage, PTV homogeneity, high dose spillage, and conformity for the more complex head and neck plan.

Nguyen, Dan↗

Capturing the two-way hydromechanical coupling effect on fluid-driven fracture in a dual-graph lattice beam model

Fluid-driven fractures of brittle rock is simulated via a dual-graph lattice model. The new discrete hydromechanical model incorporates a two-way coupling mechanism between the discrete element model and the flow network. Through adopting an operator-split algorithm, the coupling model is able to replicate the transient poroelasticity coupling mechanism and the resultant Mandel-Cryer hydromechanical coupling effect in a discrete mechanics framework. As crack propagation, coalescence and branching are all path-dependent and irreversible processes, capturing this transient coupling effect is important for capturing the essence of the fluid-driven fracture in simulations. Injection simulations suggest that the onset and propagation of fractures is highly sensitive to the ratio between the injection rate and the effective permeability. Moreover, we show that in a permeable rock, the borehole breakdown pressure, the pressure at which fractures start to grow from the borehole, depends on both the given ratio between injection rate and permeability and the Biot coefficient.

58 GEOSCIENCES↗

Experimental study of compaction localization in carbonate rock and constitutive modeling of mechanical anisotropy

Abstract Sedimentary rocks are inherently anisotropic and prone to strain localization. While the influence of rock anisotropy on the brittle/dilative regime has been studied extensively, its influence on the ductile/compactive regime is much less explored. This paper discusses the anisotropic behavior of a high‐porosity carbonate rock from central Europe (the Maastricht Tuffeau). A set of triaxial tests with concurrent x‐ray tomography has been performed at different confining pressures. The anisotropic characteristics of this rock have been investigated by testing samples cored at different inclinations of the bedding, thus revealing non‐negligible effects of the coring direction on yielding and compaction behavior. Specifically, samples cored perpendicular to bedding display higher strength and longer stages of post‐yielding deformation before manifesting re‐hardening. Despite such alterations of the inelastic response, Digital Image Correlation has revealed that the strain localization mode is independent of the coring direction, thus being primarily affected by the confinement level. To capture the observed interaction between material anisotropy and compaction behavior at the continuum‐scale, an elastoplastic constitutive law has been proposed. For this purpose, a set of tensorial bases has been introduced to replicate how the oriented rock fabric modulates the yielding and plastic flow characteristics of the material. The analyses show that the impact of the coring direction on yield function and plastic flow rule is fundamentally different, thus requiring the use of distinct projection strategies (a strategy here defined heterotopic mapping). The performance of the model, studied through parametric analyses and by calibrating the experimental results, illustrates the improved capability of the proposed constitutive approach when applied to strongly anisotropic porous rocks.

Shahin, Ghassan↗

Degradation in photovoltaic encapsulant transmittance: Results of the first PVQAT TG5 artificial weathering study

Reduced optical transmittance of encapsulants resulting from ultraviolet (UV) degradation is frequently identified as a cause of decreased performance through the service life of photovoltaic modules. However, the present module safety and qualification standards apply short UV doses, only capable of examining design robustness and 'infant mortality' failures. Furthermore, essential information remains unknown that might be used to screen encapsulants through product lifetime. We conducted an interlaboratory study to provide the understanding that will be used toward developing a higher-fidelity, more-rigorous UV weathering test. Five representative known formulations of poly (ethylene-co-vinyl acetate) were studied, in addition to one thermoplastic polyurethane material. Replicate laminated silica/polymer/silica specimens were examined at seven institutions using a variety of indoor chambers (including xenon, UVA-340, and metal-halide light sources). Specimens were artificially weathered for 180 cumulative days at steady-state accelerated test conditions, predesignated relative to the default irradiance of 1.0 W m-2 nm-1 at 340 nm, chamber temperature of 60 degrees C, and chamber relative humidity of 30%. The solar-weighted transmittance, yellowness index, and the UV cut-off wavelength - each determined from the measured hemispherical transmittance - are examined to provide understanding and guidance for the UV light source (type lamp and filters), temperature, and humidity used in accelerated UV aging tests. The relative efficacy of xenon-arc and UVA-340 fluorescent sources and the typical range of activation energy for degradation is quantified from the experiments.

14 SOLAR ENERGY↗

Light and temperature effects on miR156 transgenic switchgrass flowering: A simulated latitudinal study

The control of flowering in perennial grasses is an important trait, especially among biofuel feedstocks. Lignocellulosic biomass may be increased commensurate with decreased or delayed flowering as the plant allocates energy for stems and leaves harvested for bioenergy at the end of the growing season. For transgenic feedstocks, such as switchgrass ( Panicum virgatum L. ) grown in its geographic center of distribution, it is foreseeable that regulators may require greatly decreased gene flow frequencies to enable commercialization. Transgenic switchgrass with various overexpression levels of a rice microRNA gene, miR156, when grown in field conditions, holds promise for decreased flowering, yielding high biomass, and altered cell wall traits, which renders it as a potential crossing partner for further breeding with switchgrass lines for decreased recalcitrance. In the current research, we simulated a latitudinal cline in controlled growth chamber experiments for various individual sites from the tropics to cool-temperate conditions which included weekly average high and low temperatures and day lengths over the switchgrass growing season for each simulated site: Guayaquil, Ecuador; Laredo, Texas, USA; and Brattleboro, Vermont, USA. Flowering and reproduction among transgenic lines with low (T-14 and T-35)--tomoderate (T-27 and T-37) overexpression of miR156 were assessed. Lower simulated latitudes (higher temperatures with low-variant day length) and long growing seasons promoted flowering of the miR156 transgenic switchgrass lines. Tropical conditions rescued the flowering phenotype in all transgenic lines except T-27. Higher numbers of plants in lines T-35 and T-37 and the controls produced panicles, which also occurred earlier in the study as temperatures increased and day length decreased. Line T-14 was the exception as more clonal replicates flowered in the cool-temperate (Vermont) conditions. Increased biomass was found in transgenic lines T-35 and T-37 in tropical conditions. No difference in biomass was found in subtropical (Texas) chambers, and two lines (T-14 and T-35) produced less biomass than the control in cool-emperate conditions. Our findings suggest that switchgrass plants engineered to overexpress miR156 for delayed flowering to promote bioconfinement and biomass production may be used for plant breeding at tropical sites.

59 BASIC BIOLOGICAL SCIENCES↗

Metabolomic, photoprotective, and photosynthetic acclimatory responses to post‐flowering drought in sorghum

Abstract Climate change is globally affecting rainfall patterns, necessitating the improvement of drought tolerance in crops. Sorghum bicolor is a relatively drought‐tolerant cereal. Functional stay‐green sorghum genotypes can maintain green leaf area and efficient grain filling during terminal post‐flowering water deprivation, a period of ~10 weeks. To obtain molecular insights into these characteristics, two drought‐tolerant genotypes, BTx642 and RTx430, were grown in replicated control and terminal post‐flowering drought field plots in California's Central Valley. Photosynthetic, photoprotective, and water dynamics traits were quantified and correlated with metabolomic data collected from leaves, stems, and roots at multiple timepoints during control and drought conditions. Physiological and metabolomic data were then compared to longitudinal RNA sequencing data collected from these two genotypes. The unique metabolic and transcriptomic response to post‐flowering drought in sorghum supports a role for the metabolite galactinol in controlling photosynthetic activity through regulating stomatal closure in post‐flowering drought. Additionally, in the functional stay‐green genotype BTx642, photoprotective responses were specifically induced in post‐flowering drought, supporting a role for photoprotection in the molecular response associated with the functional stay‐green trait. From these insights, new pathways are identified that can be targeted to maximize yields under growth conditions with limited water.

54 ENVIRONMENTAL SCIENCES↗

Expression of a mammalian RNA demethylase increases flower number and floral stem branching in Arabidopsis thaliana

Abstract RNA methylation plays a central regulatory role in plant biology and is a relatively new target for plant improvement efforts. In nearly all cases, perturbation of the RNA methylation machinery results in deleterious phenotypes. However, a recent landmark paper reported that transcriptome‐wide use of the human RNA demethylase FTO substantially increased the yield of rice and potatoes. Here, we have performed the first independent replication of those results and demonstrated broader transferability of the trait, finding increased flower and fruit count in the model species Arabidopsis thaliana . We also performed RNA‐seq of our FTO‐transgenic plants, which we analyzed in conjunction with previously published datasets to detect several previously unrecognized patterns in the functional and structural classification of the upregulated and downregulated genes. From these, we present mechanistic hypotheses to explain these surprising results with the goal of spurring more widespread interest in this promising new approach to plant engineering.

59 BASIC BIOLOGICAL SCIENCES↗

An Algal Nutrient‐Replete, Optimized Medium for Fast Growth and High Triacylglycerol Accumulation

Microalgae are promising sources to sustainably meet the global needs for energy and products. Algae grow under different trophic conditions, where nutritional status regulates biosynthetic pathways, energy production, and growth. The green alga Chromochloris zofingiensis has strong economic potential because it co-produces biofuel precursors and the high-value antioxidant astaxanthin while accumulating biomass when grown mixotrophically. As an emerging reference alga for photosynthesis, metabolism, and bioproduction, C. zofingiensis needs a defined, optimized medium to standardize experiments during fast growth for batch cultivation. Because the interplay of glucose treatment (+Glc) and mineral deficiency influences photosynthesis, growth, and the production of lipids and astaxanthin, we designed a replete nutrient medium tailored to the C. zofingiensis cellular ionome. We combined inductively coupled plasma mass spectrometry (ICP-MS) and +Glc growth curves to determine a medium that is nutrient replete for at least 5 days of +Glc logarithmic growth. We found that there are high nutritional needs for phosphorus and sulfur during mixotrophy. Iron was the only element measured for which the cellular concentration correlated with exogenous concentration and was iteratively adjusted until the cellular ionome was consistent through the logarithmic growth phase. This Chromochloris-Optimized Ratio of Elements (CORE) medium supports fast growth and high biomass and lipid accumulation without causing excess nutrient toxicity. This defined, nutrient-replete standard is important for future C. zofingiensis investigations and can be adapted for other species to support high biomass for batch cultivation. The method used to develop CORE medium shows how ionomics informs replicable media design and may be applied in industrial settings to inform cost-effective biofuel production.

Jeffers, Tim L. [University of California, Berkele↗

Proteome profile of the endomembrane of developing coleoptiles from switchgrass ( Panicum virgatum )

The cost-effective production of biofuels from lignocellulosic material will likely require manipulation of plant biomass, specifically cell walls. The North American native prairie grass Panicum virgatum (switchgrass) is seen as a potential biofuel crop with an array of genetic resources currently being developed. We have characterized the endomembrane proteome of switchgrass coleoptiles to provide additional information to the switchgrass community. In total, we identified 1750 unique proteins from two biological replicates. These data have been deposited in the ProteomeXchange with the identifier PXD001351 (http://proteomecentral.proteomexchange.org/dataset/PXD001351).

59 BASIC BIOLOGICAL SCIENCES↗

A fast and sensitive size-exclusion chromatography method for plasma extracellular vesicle proteomic analysis

Extracellular vesicles (EVs) carry diverse biomolecules derived from their parental cells, making their components excellent biomarker candidates. However, purifying EVs is a major hurdle in biomarker discovery since current methods require large amounts of samples, are time-consuming and typically have poor reproducibility. Here we describe a simple, fast, and sensitive EV fractionation method using size exclusion chromatography (SEC) on a fast protein liquid chromatography (FPLC) system. Our method uses a Superose 6 Increase 5/150, which has a bed volume of 2.9 mL. The FPLC system and small column size enable reproducible separation of only 50 µL of human plasma in 15 min. To demonstrate the utility of our method, we used longitudinal samples from a group of individuals who underwent intense exercise. A total of 838 proteins were identified, of which, 261 were previously characterized as EV proteins, including classical markers, such as cluster of differentiation (CD)9 and CD81. Quantitative analysis showed low technical variability with correlation coefficients greater than 0.9 between replicates. The analysis captured differences in relevant EV proteins involved in response to physical activity. Our method enables fast and sensitive fractionation of plasma EVs with low variability, which will facilitate biomarker studies in large clinical cohorts.

59 BASIC BIOLOGICAL SCIENCES↗

Comparison of open‐source three‐dimensional reconstruction pipelines for maize‐root phenotyping

Abstract Understanding three‐dimensional (3D) root traits is essential to improve water uptake, increase nitrogen capture, and raise carbon sequestration from the atmosphere. However, quantifying 3D root traits by reconstructing 3D root models for deeper field‐grown roots remains a challenge due to the unknown tradeoff between 3D root‐model quality and 3D root‐trait accuracy. Therefore, we performed two computational experiments. We first compared the 3D model quality generated by five state‐of‐the‐art open‐source 3D model reconstruction pipelines on 12 contrasting genotypes of field‐grown maize roots. These pipelines included COLMAP, COLMAP+PMVS (Patch‐based Multi‐View Stereo), VisualSFM, Meshroom, and OpenMVG+MVE (Multi‐View Environment). The COLMAP pipeline achieved the best performance regarding 3D model quality versus computational time and image number needed. In the second test, we compared the accuracy of 3D root‐trait measurement generated by the Digital Imaging of Root Traits 3D pipeline (DIRT/3D) using COLMAP‐based 3D reconstruction with our current DIRT/3D pipeline that uses a VisualSFM‐based 3D reconstruction on the same dataset of 12 genotypes, with 5–10 replicates per genotype. The results revealed that (1) the average number of images needed to build a denser 3D model was reduced from 3000 to 3600 (DIRT/3D [VisualSFM‐based 3D reconstruction]) to around 360 for computational test 1, and around 600 for computational test 2 (DIRT/3D [COLMAP‐based 3D reconstruction]); (2) denser 3D models helped improve the accuracy of the 3D root‐trait measurement; (3) reducing the number of images can help resolve data storage problems. The updated DIRT/3D (COLMAP‐based 3D reconstruction) pipeline enables quicker image collection without compromising the accuracy of 3D root‐trait measurements.

09 BIOMASS FUELS↗

HopBox: An image analysis pipeline to characterize hop cone morphology

Abstract Hop cone morphology can influence picking and drying ability, and color can impact consumer preference and may be indicative of quality. However, these characteristics are not generally evaluated in hop breeding programs due to the tedious nature of trait quantification and the extensive variation among cones within a genotype. We developed the HopBox, which is a simply constructed light box with a camera mount, and a publicly available image processing pipeline that identifies hop cones within color‐corrected images, reads a QR code within the image, and outputs data on hop cone length, width, area, perimeter, openness, weight, color, and density. The trained model was applied to images of 500 cones each from 15 replicated advanced hop genotypes from the USDA‐ARS breeding program in Prosser, Washington. Analysis of variance revealed significant ( p < 0.001) differences between genotypes for all traits measured, enabling breeders to discriminate between genotypes for selection purposes. Broad sense heritability for all traits ranged from 0.23 to 0.59. A random sampling of hop cones from the complete dataset revealed that imaging only 5–10 cones adequately captured genotypic variation and provided acceptable rank correlations ( r s > 0.75); however, increasing the sample size to 30 provided optimal precision. Instructions for constructing a HopBox and the code for the analysis pipeline are publicly available online and have wide applicability for hop breeding and research.

Altendorf, Kayla R.↗

Data driven discovery and quantification of hyperspectral leaf reflectance phenotypes across a maize diversity panel

Abstract Estimates of plant traits derived from hyperspectral reflectance data have the potential to efficiently substitute for traits, which are time or labor intensive to manually score. Typical workflows for estimating plant traits from hyperspectral reflectance data employ supervised classification models that can require substantial ground truth datasets for training. We explore the potential of an unsupervised approach, autoencoders, to extract meaningful traits from plant hyperspectral reflectance data using measurements of the reflectance of 2151 individual wavelengths of light from the leaves of maize ( Zea mays ) plants harvested from 1658 field plots in a replicated field trial. A subset of autoencoder‐derived variables exhibited significant repeatability, indicating that a substantial proportion of the total variance in these variables was explained by difference between maize genotypes, while other autoencoder variables appear to capture variation resulting from changes in leaf reflectance between different batches of data collection. Several of the repeatable latent variables were significantly correlated with other traits scored from the same maize field experiment, including one autoencoder‐derived latent variable (LV8) that predicted plant chlorophyll content modestly better than a supervised model trained on the same data. In at least one case, genome‐wide association study hits for variation in autoencoder‐derived variables were proximal to genes with known or plausible links to leaf phenotypes expected to alter hyperspectral reflectance. In aggregate, these results suggest that an unsupervised, autoencoder‐based approach can identify meaningful and genetically controlled variation in high‐dimensional, high‐throughput phenotyping data and link identified variables back to known plant traits of interest.

Tross, Michael C.↗

Structure and specificity of FEN-1 from Methanopyrus kandleri

DNA repair is fundamental to genome stability and is found in all three domains of life. However, many archaeal species, such as Methanopyrus kandleri, contain only a subset of the eukaryotic nucleotide excision repair (NER) homologues, and those present often contain significant differences compared to their eukaryotic homologues. To clarify the role of the NER XPG-like protein Mk0566 from M. kandleri, its biochemical activity and three dimensional structure were investigated. Ultimately, we found both to be more similar to human FEN-1 than human XPG, suggesting a biological role in replication and long-patch base excision repair rather than in NER.

59 BASIC BIOLOGICAL SCIENCES↗

BCL::SAXS: GPU accelerated Debye method for computation of small angle X-ray scattering profiles

Small angle X-ray scattering (SAXS) is an experimental technique used for structural characterization of macromolecules in solution. In this work, we present BCL::SAXS--an algorithm designed to replicate SAXS profiles from rigid protein models at different levels of detail. We first show our derivation of BCL::SAXS and compare our results with the experimental scattering profile of hen egg white lysozyme. Using this protein we show how to generate SAXS profiles representing: (1) complete models, (2) models with approximated side chain coordinates, and (3) models with approximated side chain and loop region coordinates. We evaluated the ability of SAXS profiles to identify a correct protein topology from a non-redundant benchmark set of proteins. We find that complete SAXS profiles can be used to identify the correct protein by receiver operating characteristic (ROC) analysis with an area under the curve (AUC)>99%. We demonstrate how our approximation of loop coordinates between secondary structure elements improves protein recognition by SAχS for protein models without loop regions and side chains. Agreement with SAXS data is a necessary but not sufficient condition for structure determination. We conclude that experimental SAXS data can be used as a filter to exclude protein models with large structural differences from the native.

59 BASIC BIOLOGICAL SCIENCES↗