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At least 541 records · Page 30

Nucleation of stoichiometric compounds from liquid: Role of the kinetic factor

The nucleation rate depends on the free-energy barrier and the kinetic factor. While the role of the free energy barrier is a text-book subject, the importance of the kinetic factor is frequently underestimated. Here in this study, we applied the mean first-passage time method, to obtain the free-energy landscape and kinetic factor directly from the molecular dynamics (MD) simulations of the nucleation of the face-centered cubic (fcc) phase in the pure Ni and the B2 phases in the Ni 50 Al 50 and Cu 50 Zr 50 alloys. The obtained data show that while the free-energy barrier for nucleation is higher in pure Ni the nucleation rate is considerably lower in the Ni 50 Al 50 alloy. This result can be explained by the slow attachment kinetics in the N i 50 A l 50 alloy, which was related to the ordered nature of the B2 phase. Even smaller fraction of the antisite defects in the C u 50 Z r 50 alloy leads to such a slow attachment kinetics that the nucleation is never observed for this alloy in the course of the MD simulation. Finally, this is consistent with the experimental facts that the Cu 50 Zr 50 alloy is a good glass forming alloy and the Ni 50 Al 50 alloy is not. Thus the present study demonstrates that the atom attachment rate can be the critical factor that controls the nucleation process under certain conditions.

36 MATERIALS SCIENCE↗

Beyond integration: modeling every pixel to obtain better structure factors from stills

Most crystallographic data processing methods use pixel integration. In serial femtosecond crystallography (SFX), the intricate interaction between the reciprocal lattice point and the Ewald sphere is integrated out by averaging symmetrically equivalent observations recorded across a large number (10 4 -10 6 ) of exposures. Although sufficient for generating biological insights, this approach converges slowly, and using it to accurately measure anomalous differences has proved difficult. This report presents a novel approach for increasing the accuracy of structure factors obtained from SFX data. A physical model describing all observed pixels is defined to a degree of complexity such that it can decouple the various contributions to the pixel intensities. Model dependencies include lattice orientation, unit-cell dimensions, mosaic structure, incident photon spectra and structure factor amplitudes. Maximum likelihood estimation is used to optimize all model parameters. The application of prior knowledge that structure factor amplitudes are positive quantities is included in the form of a reparameterization. The method is tested using a synthesized SFX dataset of ytterbium(III) lysozyme, where each X-ray laser pulse energy is centered at 9034 eV. This energy is 100 eV above the Yb 3+ L -III absorption edge, so the anomalous difference signal is stable at 10 electrons despite the inherent energy jitter of each femtosecond X-ray laser pulse. This work demonstrates that this approach allows the determination of anomalous structure factors with very high accuracy while requiring an order-of-magnitude fewer shots than conventional integration-based methods would require to achieve similar results.

59 BASIC BIOLOGICAL SCIENCES↗

Power Factor revisited

Power factor is a term whose value can be found by dividing the power in a load to the product of the voltage and the current. It has been used as a rule of thumb to estimate the cost of the losses incurred in delivering reactive power. But it has been extremely troublesome. The same load might be penalized by some definitions, and might not by others. That is still the situation today. There have been two efforts at solution. In 1919 a committee of experts was formed to solve the problem of its definition. The effort did not succeed at producing a definition; two alternatives were recommended in the committee’s final report, but both were adopted. In 2010, IEEE issued Standard 1459 to give definitions. In this standard, definitions of power factor appear under no less than seven different headings. The problem demands solution. The matter is of considerable economic importance to power producers, consumers, and instrument makers. This paper examines the history of the topic, and explores reasons for the difficulty of definition in terms of measurement theory. It is shown that power factor is not suited to purpose. In fact, no definition can exist that will define power factor usefully for its intended economic purpose. Two alternatives are proposed.

power factror, definitions, measurement theory, IE↗

A Communication-Avoiding 3D LU Factorization Algorithm for Sparse Matrices

We propose a new algorithm to improve the strong scalability of right-looking sparse LU factorization on distributed memory systems. Our 3D sparse LU algorithm uses a three-dimensional MPI process grid, aggressively exploits elimination tree parallelism and trades off increased memory for reduced per-process communication. We also analyze the asymptotic improvements for planar graphs (e.g., from 2D grid or mesh domains) and certain non-planar graphs (specifically for 3D grids and meshes). For planar graphs with n vertices, our algorithm reduces communication volume asymptotically in n by a factor of O{log n} and latency by a factor of O{log n}. For non-planar cases, our algorithm can reduce the per-process communication volume by 3× and latency by O{n^1/3} times. In all cases, the memory needed to achieve these gains is a constant factor. We implemented our algorithm by extending the 2D data structure used in superLU. Our new 3D code achieves speedups up to 27× for planar graphs and up to 3.3× for non-planar graphs over the baseline 2D superLU when run on 24,000 cores of a Cray XC30.

Sao, Piyush↗

COM1 , a factor of alternative non‐homologous end joining, lagging behind the classic non‐homologous end joining pathway in rice somatic cells

SUMMARY The role of rice ( Oryza sativa ) COM1 in meiotic homologous recombination (HR) is well understood, but its part in somatic double‐stranded break (DSB) repair remains unclear. Here, we show that for rice plants COM1 conferred tolerance against DNA damage caused by the chemicals bleomycin and mitomycin C, while the COM1 mutation did not compromise HR efficiencies and HR factor (RAD51 and RAD51 paralogues) localization to irradiation‐induced DSBs. Similar retarded growth at the post‐germination stage was observed in the com1‐2 mre11 double mutant and the mre11 single mutant, while combined mutations in COM1 with the HR pathway gene ( RAD51C ) or classic non‐homologous end joining (NHEJ) pathway genes ( KU70 , KU80 , and LIG4 ) caused more phenotypic defects. In response to γ‐irradiation, COM1 was loaded normally onto DSBs in the ku70 mutant, but could not be properly loaded in the MRE11 RNAi plant and in the wortmannin‐treated wild‐type plant. Under non‐irradiated conditions, more DSB sites were occupied by factors (MRE11, COM1, and LIG4) than RAD51 paralogues (RAD51B, RAD51C, and XRCC3) in the nucleus of wild‐type; protein loading of COM1 and XRCC3 was increased in the ku70 mutant. Therefore, quite differently to its role for HR in meiocytes, rice COM1 specifically acts in an alternative NHEJ pathway in somatic cells, based on the Mre11–Rad50–Nbs1 (MRN) complex and facilitated by PI3K‐like kinases. NHEJ factors, not HR factors, preferentially load onto endogenous DSBs, with KU70 restricting DSB localization of COM1 and XRCC3 in plant somatic cells.

Xu, Zhan↗

A Discussion of Strength Reduction Factor Development for Thermal Aging Effect on Nuclear Structural Alloys

In consideration of structural alloy property deterioration during long-term exposure to elevated temperatures, the yield and ultimate tensile strength reduction factors are provided in the Boiler and Pressure Vessel Code Section III for nuclear reactor component design and operation analysis. Because the Gen IV reactor requirement of 40 ~ 60 years of service life makes it difficult to acquire such long exposure test data for developing the reduction factors, they must be derived from test data with relatively short exposure by predictive methods considered to be reasonably reliable. A novel approach with a physically-based model has recently been proposed for application to development of reduction factors for 9Cr-1Mo-V. In the model, contributors to the tensile strength are first identified and related to definite microstructural features of the alloy, then some physically-based methods are employed to simulate the microstructural evolution, and finally the model is assembled with test-data-calibrated parameters to generate the yield and ultimate tensile strength reduction factors covering elevated temperature exposure for up to 57 years. The approach is undoubtedly a trailblazing development that will, if proven reliable, lead to a paradigm shift in predicting thermal aging behavior of many other alloys. Its debut application to Section III, however, concerns nuclear safety and naturally warrants objective, impartial, and thorough technical scrutiny. In the present paper, the novel and conventional approaches are discussed. Necessary improvements to the novel approach are recommended for its application to nuclear structural component design and analysis, and for its potential expanded use to other alloys.

Ren, Weiju↗

Factor analysis in automated face detection: gender, occlusion, eyewear, brightness, contrast, and focus measure

Computer-based facial recognition algorithms exploit the unique characteristics of faces in images. However, in non-cooperative situations these unique characteristics are often disturbed. In this study, we examine the effect of six different factors on face detection in an unconstrained imaging environment: image brightness, image contrast, focus measure, eyewear, gender, and occlusion. The aim of this study is twofold: first, to quantify detection rates of conventional Haar cascade algorithms across these six factors; and second, to propose methods for automatically labeling datasets whose size prohibits manual labeling. First, we manually classify a uniquely challenging dataset comprising 9,688 images of passengers in vehicles acquired from a roadside camera system. Next, we quantify how each of the aforementioned factors affect face detection on this dataset. Of the six factors studied, occlusion had the most significant impact, resulting in a 54% decrease in detection rate between unoccluded and severely occluded faces in our unique dataset. Finally, we provide a methodology for data analytics of large datasets where manual labeling of the whole dataset is not possible.

Jafek, Benjamin↗

Xylanolytic metabolism is regulated by coordination of transcription factors XynR and XylR in extremely thermophilic Caldicellulosiruptorales

ABSTRACT Global transcription factors (TFs) control metabolic processes in bacteria to efficiently utilize available carbon. The orderCaldicellulosiruptoraleshas drawn interest due to the ability of its members to degrade components of lignocellulosic biomass. Regulatory reconstruction ofAnaerocellum (f. Caldicellulosiruptor) besciiidentified two major global transcription factors for xylan utilization, XynR and XylR, and the corresponding putative transcription factor binding sites. Recombinant versions of XynR (LacI family) and XylR (ROK family) were subjected to fluorescence polarization (FP) and biolayer interferometry (BLI) analysis to confirm the predicted binding sites. Four XynR sites and two XylR sites were validated, accounting for 20 of 26 genes regulated by XynR and six of seven genes regulated by XylR. Bioinformatic analysis of the individual genes controlled by the two regulators showed an inter-dependent scheme for xylan conversion; the transport of xylooligosaccharides (XOS) is dependent on XylR, while enzymes responsible for hydrolysis are controlled by both regulators. For xylose catabolism by the xylose isomerase-xylulose kinase pathway, regulation is also split, with XylR controlling xylose isomerase and XynR controlling xylokinase. The XynR/XylR regulator pair withinA. besciiis conserved in all sequenced species ofCaldicellulosiruptorales, suggesting similarities in regulating linear xylan conversion. In other xylanolytic thermophiles, XylR homologs control xylan degradation, compared to just 6 out of 26 genes forA. bescii. These results show that two separate regulatory schemes (dual repression) are coordinated byA. besciito effectively regulate the hemicellulose inventory and xylan catabolism. IMPORTANCE To take full advantage of extreme thermophiles as platform metabolic engineering microorganisms, the tools for genetic manipulation must be further developed, and strategies that exploit a better understanding of metabolic regulation need to be discerned.Anaerocellum bescii, the most studied of the extremely thermophilic fermentative anaerobic bacteria that can utilize microcrystalline cellulose, can degrade microcrystalline cellulose and hemicellulose and has been metabolically engineered to convert the resulting sugars to products such as ethanol and acetone. For xylan, in particular, two major global transcription factors (TFs), XynR and XylR, play a role in sugar metabolism, although their predicted regulatory interdependence from bioinformatics analysis has not been elucidated experimentally. Here, fluorescence polarization (FP) and biolayer interferometry (BLI) were used to explore this issue to support metabolic engineering efforts aimed at improving carbohydrate processing to industrial chemicals.

Biotechnology & Applied Microbiology↗

The electromagnetic Sigma-to-Lambda hyperon transition form factors at low energies

Using dispersion theory the low-energy electromagnetic form factors for the transition of a Sigma to a Lambda hyperon are related to the pion vector form factor. The additionally required input, i.e. the two-pion-Sigma-Lambda amplitudes are determined from relativistic next-to-leading-order (NLO) baryon chiral perturbation theory including the baryons from the octet and optionally from the decuplet. Pion rescattering is again taken into account by dispersion theory. It turns out that the inclusion of decuplet baryons is not an option but a necessity to obtain reasonable results. The electric transition form factor remains very small in the whole low-energy region. The magnetic transition form factor depends strongly on one not very well determined low-energy constant of the NLO Lagrangian. Furthermore, one obtains reasonable predictive power if this low-energy constant is determined from a measurement of the magnetic transition radius. Such a measurement can be performed at the future Facility for Antiproton and Ion Research (FAIR).

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Sel1-like proteins and peptides are the major Oxalobacter formigenes -derived factors stimulating oxalate transport by human intestinal epithelial cells

Kidney stones (KSs) are very common, excruciating, and associated with tremendous healthcare cost, chronic kidney disease (CKD), and kidney failure (KF). Most KSs are composed of calcium oxalate and small increases in urinary oxalate concentration significantly enhance the stone risk. Oxalate also potentially contributes to CKD progression, kidney disease-associated cardiovascular diseases, and poor renal allograft survival. This emphasizes the urgent need for plasma and urinary oxalate lowering therapies, which can be achieved by enhancing enteric oxalate secretion. We previously identified Oxalobacter formigenes (O. formigenes)-derived factors secreted in its culture-conditioned medium (CM), which stimulate oxalate transport by human intestinal Caco2-BBE (C2) cells and reduce urinary oxalate excretion in hyperoxaluric mice by enhancing colonic oxalate secretion. Given their remarkable therapeutic potential, we now identified Sel1-like proteins as the major O. formigenes-derived secreted factors using mass spectrometry and functional assays. Crystal structures for six proteins were determined to confirm structures and better understand functions. OxBSel1-14-derived small peptides P8 and P9 were identified as the major factors, with P8 + 9 closely recapitulating the CM’s effects, acting through the oxalate transporters SLC26A2 and SLC26A6 and PKA activation. Besides C2 cells, P8 + 9 also stimulate oxalate transport by human ileal and colonic organoids, confirming that they work in human tissues. Finally, P8 and P9 peptides are identified as the major O. formigenes-derived secreted factors and they have significant therapeutic potential for hyperoxalemia, hyperoxaluria, and related disorders, impacting the outcomes of patients suffering from KSs, enteric hyperoxaluria, primary hyperoxaluria, CKD, KF, and renal transplant recipients.

59 BASIC BIOLOGICAL SCIENCES↗

Assessment of Electric Grid Transmission System Simulator for Human Factors Research

Over the past decades, various technologies have been developed for electric grid operations to support clean energy, meet rising electricity demands, and address infrastructure concerns. However, the human factors aspect is often overlooked during rapid integration. Questions persist about how these technologies impact human performance. Simulators play a critical role in supporting investigation of human factors design concepts and conducting comprehensive usability testing to evaluate human performance and assess human reliability. This paper aims to address human factors research simulator requirements and conduct a comparative study of six different simulators. A detailed evaluation reveals that the evaluated simulators lack the ability to customize user interfaces. Additionally, their user interface designs do not fulfill the basic human factors design principles, potentially leading to increased response variability and reduced statistical power when conducting controlled experimental research. In the future, it is essential to develop scripting tools to integrate customizable user interfaces and simulation models, ensuring meeting research requirements.

Li, Ruixuan↗

The examination of the spatial and contextual disparities of determinant factors of adult obesity among communities in Chicago

The issue of adult obesity has multiple complexes contributing factors and is becoming a significant public health concern worldwide, including in the neighborhoods of Chicago. This study utilized data on nineteen demographic, environmental, socioeconomic, and behavioral characteristics of community neighborhoods in Chicago to analyze the interplay and impact of these complex factors, which is essential for understanding and addressing the issue. The analysis revealed significant geographic variations in the prevalence of adult obesity across Chicago neighborhoods, with associations of these patterns found significant in 17 out of 19 determinant factors studied. Notably, strong associations were found between obesity and the percentage of the White population, the quality of sidewalks and walkability, the economic hardship index, and the unemployment rate. Identifying high-risk adult obesity communities and understanding the multifaceted contributing factors is crucial for developing evidence-based interventions and policy initiatives to reduce obesity and create healthier, more equitable urban neighborhoods for a city such as Chicago and beyond.

60 APPLIED LIFE SCIENCES↗

The Composition and Spatial Patterns of Bacterial Virulence Factors and Antibiotic Resistance Genes in 19 Wastewater Treatment Plants

Bacterial pathogenicity and antibiotic resistance are of concern for environmental safety and public health. Accumulating evidence suggests that wastewater treatment plants (WWTPs) are as an important sink and source of pathogens and antibiotic resistance genes (ARGs). Virulence genes (encoding virulence factors) are good indicators for bacterial pathogenic potentials. To achieve a comprehensive understanding of bacterial pathogenic potentials and antibiotic resistance in WWTPs, bacterial virulence genes and ARGs in 19 WWTPs covering a majority of latitudinal zones of China were surveyed by using GeoChip 4.2. A total of 1610 genes covering 13 virulence factors and 1903 genes belonging to 11 ARG families were detected respectively. The bacterial virulence genes exhibited significant spatial distribution patterns of a latitudinal biodiversity gradient and a distance-decay relationship across China. Moreover, virulence genes tended to coexist with ARGs as shown by their strongly positive associations. In addition, key environmental factors shaping the overall virulence gene structure were identified. This study profiles the occurrence, composition and distribution of virulence genes and ARGs in current WWTPs in China, and uncovers spatial patterns and important environmental variables shaping their structure, which may provide the basis for further studies of bacterial virulence factors and antibiotic resistance in WWTPs.

54 ENVIRONMENTAL SCIENCES↗

Duality and form factors in the thermally deformed two-dimensional tricritical Ising model

The thermal deformation of the critical point action of the 2D tricritical Ising model gives rise to an exact scattering theory with seven massive excitations based on the exceptional E_7 E 7 Lie algebra. The high and low temperature phases of this model are related by duality. This duality guarantees that the leading and sub-leading magnetisation operators, \sigma(x) σ ( x ) and \sigma'(x) σ ′ ( x ) , in either phase are accompanied by associated disorder operators, \mu(x) μ ( x ) and \mu'(x) μ ′ ( x ) . Working specifically in the high temperature phase, we write down the sets of bootstrap equations for these four operators. For \sigma(x) σ ( x ) and \sigma'(x) σ ′ ( x ) , the equations are identical in form and are parameterised by the values of the one-particle form factors of the two lightest \mathbb{Z}_2 ℤ 2 odd particles. Similarly, the equations for \mu(x) μ ( x ) and \mu'(x) μ ′ ( x ) have identical form and are parameterised by two elementary form factors. Using the clustering property, we show that these four sets of solutions are eventually not independent; instead, the parameters of the solutions for \sigma(x)/\sigma'(x) σ ( x ) / σ ′ ( x ) are fixed in terms of those for \mu(x)/\mu'(x) μ ( x ) / μ ′ ( x ) . We use the truncated conformal space approach to confirm numerically the derived expressions of the matrix elements as well as the validity of the \Delta Δ -sum rule as applied to the off-critical correlators. We employ the derived form factors of the order and disorder operators to compute the exact dynamical structure factors of the theory, a set of quantities with a rich spectroscopy which may be directly tested in future inelastic neutron or Raman scattering experiments.

Cortes Cubero, Axel↗

Measurement of the proton form factor ratio at low momentum transfer

Experiment E08-007-II measured the proton elastic form factor ratio μG E =G M in the momentum transfer range of Q 2 ~ 0.02 - 0.08 GeV 2 , the lowest ever measured by polarization transfer techniques. The experiment was performed at the Thomas Jefferson National Accelerator Facility in Newport News, Virginia, USA during 2012. A polarized electron beam with energies of 1.1, 1.7, and 2.2 GeV was elastically scattered off a polarized solid NH 3 target. The asymmetries between the cross section of positive and negative helicity states of the beam were determined. These asymmetries can be used to determine the form factor ratio. In this thesis, we present the asymmetry analysis of the experiment, discuss the main challenges and show preliminary results for part of the data. Preliminary asymmetries indicate an increase in the form factor ratio above unity. However, a complete analysis is required before any conclusion can be made. Further analysis is ongoing, and final asymmetry results and form factor extraction is expected during 2017. We also present first results for 14 N asymmetries for elastic and quasi-elastic scattering. The measured asymmetries are in agreement with the shell model approximation, within the low accuracy of the measurement. A change in the asymmetry sign between the elastic and the quasi-elastic processes is seen, and should motivate further theoretical studies. These experimental asymmetries will also be useful for systematic studies of other experiments using polarized NH 3 targets.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

In-plane g factor of low-density two-dimensional holes in a Ge quantum well.

High-mobility two-dimensional (2D) holes residing in a Ge quantum well are a new electronic system with potentials in quantum computing and spintronics. Since for any electronic material, the effective mass and the g factor are two fundamental material parameters that determine the material response to electric and magnetic fields, measuring these two parameters in this material system is thus an important task that needs to be completed urgently. Because of the quantum confinement in the crystal growth direction (z), the biaxial strain of epitaxial Ge on SiGe, and the valance band nature, both the effective mass and the g factor can show very strong anisotropy. In particular, the in-plane g factor (g ip ) can be vanishingly small while the perpendicular g factor (g z ) can be much larger than 2. Here we report the measurement of g ip at very low hole densities using in-plane magneto-resistance measurement performed at the NHMFL.

36 MATERIALS SCIENCE↗

Electric Form Factor of the Neutron from Asymmetry Measurements

The overwhelming majority of visible mass in the universe is composed of protons and neutrons, collectively known as nucleons, which are arguably the most important strongly interacting systems to study. A nucleon may naively be thought of as a composite object built out of three non-interacting sub-objects, known as quarks, in the large energy limit; however, the structure of the nucleon is much more complicated, and consequently far richer, than a simple valence-quark picture. There are sea quarks in addition to valence quarks that interact strongly via the exchange of gluons resulting in a complex vacuum structure, and the collective system must give rise to the observed properties of the nucleon, e.g. the radius and mass. The nucleon is the most well-studied hadron and yet there are still unresolved complexities in the calculation of properties from first principles of QCD; this represents a central problem in nuclear physics. The theoretical difficulty with the nucleon requires experimentation, which is steadily increasing the knowledge of nucleon structure and the strong interaction. The subject of this thesis pertains to nucleon electromagnetic form factors which are fundamental quantities containing information on the spatial and momentum distributions of charge and current within the nucleon. Nucleon form factors may be accessed through well-understood leading order electromagnetic processes with a leptonic probe, and provide strong constraints on testing non-perturbative QCD and nuclear structure models. The form factor ratio of the neutron has been extracted via a beam-target helicity asymmetry measurement. The Jefferson Lab Hall A experiment E02-013 ran in 2006 utilizing the 6 GeV CEBAF for its high-duty, longitudinally polarized electron beam. The double-arm coincidence experiment detected the quasielastically scattered electrons in a large angular and momentum acceptance spectrometer. The recoiling nucleons were detected and momentum analyzed in a large scintillator-iron based neutron detector. The analysis of a previously unpublished extraction of the electric form factor of the neutron is presented.

Obrecht, Richard↗

FGR 13 Dose Conversion Factor Files

The purpose of this document is to discuss the construction of two MELCOR Accident Consequence Code System (MACCS) dose conversion factor (DCF) files in some detail, an older file created in 2007 named FGR13DCF.inp and a newer file created in 2018 called FGR13GyEquiv_RevAinp. Very briefly, the difference between the two files is that the older file follows the standard conventions of assigning a radiation weighting factor of 20 for alpha radiation for all tissues and organs; whereas, the newer file complies with the Federal Guidance Report (FGR) 13 health effects modeling and uses modified radiation weighting factors (referred to as relative biological effectiveness (RBE) factors) for alpha radiation of 10 for breast and of 1 for red bone marrow. During an intermediate period, a file called FGR13GyEquiv.inp was created and used for the State-of-the-Art Reactor Consequence Analysis (SOARCA) calculations. This file was not released to the MACCS user community, but it is also discussed briefly in this document.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗