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Libra is a Python package that extends support of its parent package, SQLAlchemy. Libra’s primary functionality supports the dynamic creation of object-oriented analogs of SQL tables from a variety of user-defined, text-based schema definition formats and provides quality control and analysis tools and methods
Elucidation of the functional properties and structural organization of membrane protein complexes is one of the central objectives of current biochemical investigation. One of the most intriguing aspects of membrane protein function is its role in the mediation of energy transduction in photosynthetic organisms. Light energy, which is the product of a most violent physical process, fusion, is transformed into biological energy equivalents utilized by the photosynthetic cell. This photosynthetic process provides both the carbohydrate that lies at the base of virtually all food chains and, as a byproduct, all of the atmospheric oxygen utilized by heterotrophic organisms. The photosynthetic apparatus, however, is quite susceptible to damage by Reactive Oxygen Species (ROS). These species include O2 ·– , ·OH, H 2 O 2 and 1 O 2 . The production of ROS is an unavoidable byproduct of electron transport under aerobic conditions and these can damage lipids, nucleic acids and proteins. Our research has centered on the identification of amino acid oxidative damage which occurs in the vicinity of photosynthetic energy transfer cofactors. These cofactors participate in excitation energy transfer and linear electron transport within Photosystem II, the Cytochrome b 6 ƒ complex and Photosystem I. Additionally, we have participated in a number of productive collaborations leveraging our expertise in photosynthetic measurements and mass spectrometry to assist other investigators in their research.
Ga2O3 is a wide-bandgap semiconducting material known for its high breakdown electric field and thermal stability. Its various crystalline forms have shown great potential in power electronics, optoelectronics, and high-temperature applications. Specifically, ß-Ga2O3 has been recognized for its suitability in neutron and gamma radiation detection, making it ideal for sensor and detector applications [1]. Notably, ß-Ga2O3 exhibits anisotropic thermal conductivity, meaning that the magnitude of thermal conductivity varies with the crystallographic direction [2]. Under neutron irradiation, Ga2O3 undergoes a significant phenomenon, resulting in the formation of Helium bubbles within its crystalline matrix. The presence of Helium in Ga2O3 has been found to influence the material's anisotropic thermal conductivity. In this study, the objectives were twofold: firstly, to employ Density Functional Theory (DFT) to determine the most probable sites of Helium occupation in ß-Ga2O3, and secondly, to investigate the anisotropic variation in thermal conductivity when Helium is present in the crystalline matrix of ß-Ga2O3. These ab-initio DFT studies provide crucial insights into understanding the behavior of Helium in Ga2O3 and its impact on thermal conductivity, which can contribute to further advancements in sensor and detector applications based on this wide-bandgap semiconductor.
Historically, Savannah River Nuclear Solutions LLC (SRNS) tracked environmental regulatory commitments and the requirements from hundreds of permits at the Savannah River Site (SRS) using several separate methods, making integrated compliance assurance cumbersome and labor-intensive. When SRNS experienced an increase in environmental issues in 2017, SRNS management and U.S. Department of Energy - Savannah River (DOE-SR) management decided a single, proactive approach was needed to capture environmental permit information (including regulations, Consent Orders, DOE Orders, and any other state or federally issued statement of requirements), track the tasks necessary to ensure compliance with these requirements, and thereby mitigate the risk of noncompliance. SRNS developed a list of mandatory objectives that the tool must meet to function as a Comprehensive Environmental Permits Linking Tool (CEPLT). A key requirement was the ability to map Site permits to their governed locations and display the associated requirements at the compliance point (e.g., outfall, stack, waste unit, etc.). Several options included modifying existing onsite resources, building a custom onsite solution, purchasing an off-the-shelf solution, and contracting an offsite developer to build a custom solution. SRNS concluded an off-the-shelf solution with configuration and customization options would provide the flexibility to fit the unique needs of Savannah River Site (SRS) while taking advantage of industry-tested software and providing a reduced deployment timeline. SRNS chose Gensuite{sup R} a, a cloud-based solution that offers numerous a la carte applications in the environmental, health, and safety arenas, as the best candidate. SRNS selected three (3) integrated applications (Compliance Calendar, Permit Manager, and Mapper) to function as the CEPLT. The Compliance Calendar module allows for creation and tracking of regulatory commitment tasks assigned to responsible environmental professionals. Permit Manager organizes permits and other requirement documents, linking the commitments in each to Compliance Calendar tasks and/or implementing procedures. Mapper provides GIS capability for mapping the data from the other two modules to their physical onsite locations. The CEPLT was configured to allow for other SRS Site Tenants to eventually utilize the applications. Additionally, DOE-SR uses the CEPLT to provide an overview of contractor environmental compliance activities and to organize DOE-specific documents and tasks. The CEPLT fulfilled the requirement of meeting current compliance needs as well as providing the ability to grow as new organizations are incorporated and functionality is expanded. SRNS now uses the CEPLT to more effectively manage permit requirements, improve knowledge transfer, and increase the Site's overall protection of the environment, the Site worker, and the public. Possible future uses of the system include integration of mobile applications for timely communication of potential non-compliant conditions and DOE complex-wide deployment allowing for enhanced DOE site and Head Quarters oversight. Implementation of CEPLT will result in cost savings, both in terms of dollars and man-hours. (authors)
Passive remediation can be appropriate where natural processes and actions such as institutional controls mitigate exposure to contaminated groundwater, achieving remedial action objectives and protectiveness of human health and the environment. Monitored natural attenuation (MNA) is a prevalent passive remediation strategy supported by a regulatory framework and monitoring design guidance. However, long-term passive remedies are usually selected in combination with at least one active remedy, such as source removal, in situ treatment, or pump-and-treat, functioning as a complementary method for achieving remediation objectives and meeting the applicable statutory and regulatory requirements. However, MNA and existing monitoring guidance primarily target situations where the remedial action objectives are met within a few decades. When time scales for passive remediation extend to many decades (50 years or more), a corresponding change in monitoring strategy is needed to adapt to the extended time scale. This document provides guidance for implementing an extended-scale monitoring (ESM) approach appropriate for long-duration passive remediation. Extended-scale is defined in this document with respect to time (i.e., a long duration of remediation) and a large enough physical scale such that downstream receptors will not be impacted within the remediation timeframe. ESM applies to slow-moving groundwater contaminant plumes and emphasizes monitoring primarily for potential exposure pathways. For this approach, the primary monitoring objective is to demonstrate that the plume diminishes before reaching the receptor zone or point of compliance and/or a receptor does not receive concentrations above the compliance limit. While the overall objectives of protecting human health and the environment are the same as for plumes where remediation can occur over a shorter time period, the time scales between decisions are longer and the dynamics of plume evolution are slower. To this end, a scenario-based strategy is described for different plume and source conditions, defining a containment and receptor zones. The containment zone is the area where the risk of exposure to groundwater contamination can be mitigated (e.g., through institutional controls) during the remediation time period. The receptor zone is defined as the area where exposure to groundwater contamination cannot be mitigated and compliance concentration standards must be met. Within the containment zone, slow plume migration may occur, leading to concentrations that exceed compliance standards. However, where distance to the receptor zone is large relative to plume migration and attenuation rate, this approach can be protective of the receptor zone. Selection of a long-duration passive remedy needs to be based on sufficient understanding of contaminant sources, hydrogeology, and contaminant plumes. A strong technical basis, supported by predictive analysis, is recommended to substantiate that contamination is expected to stay within the containment zone during the active remediation and attainment phase of the remedy, and diminish to meet compliance standards within the extended timeframe prior to reaching the receptor zone (e.g., many decades or even centuries). The ESM approach is based on verification of plume behavior and not on detailed plume dynamics. Monitoring is conducted to confirm expected behavior with an emphasis on exposure pathways to verify that plumes remain contained in areas where the protectiveness objectives can be met. ESM should not be adopted if there is significant risk of the plume extending beyond the containment zone. Given the slow movement within the containment zone, less frequent sampling is required relative to approaches used for conventional-scale remediation.
Abstract Context An association of thyroid function with mood disorders has been widely suggested, but very few studies have examined this association longitudinally. Objective We assessed the cross-sectional and longitudinal association between thyroid function and depression in a population-based cohort. Methods A total of 9471 individuals were included in cross-sectional analyses, of whom 8366 had longitudinal data. At baseline, we assessed thyroid function using serum samples (thyrotropin [TSH], free thyroxine (FT4), and thyroid peroxidase antibodies) and depressive symptoms using the Centre for Epidemiologic Studies Depression (CES-D) scale. Incident depressive events (n = 1366) were continuously followed up with the CES-D and clinical interviews. We analyzed the cross-sectional association of thyroid function and thyroid disease with depressive symptoms using linear and logistic regression, and the longitudinal association with Cox proportional hazard models for depressive events. Results Lower TSH levels and lower and higher FT4 levels were cross-sectionally associated with more depressive symptoms with a B value of −0.07 per 1 unit increase of natural log-transformed TSH (95% CI −0.11; −0.04). Furthermore, hypothyroidism was cross-sectionally associated with less depressive symptoms and hyperthyroidism with more depressive symptoms. Longitudinally, there was a U-shaped association between FT4 and incident depressive events but only in euthyroid participants. Conclusion We show a cross-sectional association between thyroid (dys)function with depressive symptoms, and a U-shaped association between FT4 and incident depressive events in euthyroid individuals. Our findings suggest an association of thyroid function with the risk of developing depression, albeit small. Reverse causation and additional underlying factors may also contribute to the association.
The main objective of this study was the dynamic rupture modeling of the M7.3 1999 Chi-Chi, Taiwan earthquake. The purpose of the numerical modeling was two folded. First, using models of rupture dynamics, derive kinematic rupture characteristics, including spatial and temporal variations of the slip rate time history and rupture speed, in the long-period ground motion generation area (LMGA), strong motion generation areas (SMGAs) and background fault area for a thrust shallow rupture. Second, investigate the sensitivity of source time function characteristics in the LMGA and SMGA areas to model parameterization of low-velocity weak zone, such as thickness and shear wave velocity.
The proposed research developed the zentropy theory through applications to complex magnetic materials and superconductors under the hypothesis that the emergent properties of complex magnetic materials and superconductors can be predicted by statistical mechanics of ergodic microstates with their partition functions computed from DFT-predicted free energies. The key objective is to develop approaches to systematically determine the types and number of microstates and the supercell size in DFT-based calculations through convergency of macroscopic functionalities, with the incorporation of our mixed-space approach accounting for the interactions between periodic supercells. In addition to use scientific intuitions to guide the design of important microstates, the key innovation of the proposed research is to integrate the domain knowledge and the material-property-descriptor database (MPDD) with 4 million microstates, which is supported by our deep neural network machine learning models (SIPFENN: structure-informed prediction of formation energy using neural networks) and integrated with our high throughput DFT Tool Kit (DFTTK). For complex magnetic materials, one of the objectives is to develop approaches to calculate short-range ordering from the statistical distribution of each microstate. For superconductors, the divergency of quasiparticle effective mass at a quantum critical point will be investigated, and the superconducting and non-superconducting microstates will be delineated through analysis of electronic band structure, density of states, charge density, and Fermi surface.
The hydrated electron, an excess electron in liquid water, plays a crucial role in a plethora of chemical processes, motivating extensive research efforts to characterize its structure, dynamics, and reactivity in solution. Recent theoretical approaches to understanding this intriguing object have involved ab initio simulations based on density functional theory (DFT). Although DFT allows for the study of hydrated electron reactivity and quantum mechanical behavior, it is well-known that anionic systems can suffer from significant density-driven errors (DDEs). Density-corrected DFT (DC-DFT) provides a framework to mitigate such errors; the method reduces DDEs by replacing the self-consistent (SC) density associated with a given density functional with the Hartree–Fock (HF) density. Since HF densities tend to be more localized than DFT SC densities, the DC-DFT scheme significantly improves errors in calculations where the SC density is spuriously delocalized. Here, we investigate how the use of density correction affects the calculated properties of the DFT-simulated (PBEh) hydrated electron, a particularly challenging diffuse anionic system to simulate. First, we analyze charge delocalization in a system consisting of a model octahedral hydrated electron water cluster (the so-called Kevan structure) along with a spatially separated sulfur atom. We show that the use of density correction indeed reduces DDEs in comparison to a standard DFT global hybrid functional. We then propagate molecular dynamics trajectories of the hydrated electron using DC-DFT, where we find that DC further localizes electron density in the cavity region, a signature of reduced charge delocalization. Unfortunately, the decreased radius of gyration of the spin density and corresponding tightening of the local solvation structure from density correction causes predicted observables to deviate further from experimental measurements than when density correction is not employed. Here, we argue that DC’s worse agreement with experiment results from the removal of a fortuitous cancellation of errors that is intrinsic to the PBEh functional. This indicates that the difficulties with DFT to simulate hydrated electrons are primarily due to the inherent approximations in DFT rather than to density-driven errors.
This report describes an efficient and robust voxel-based methodology for computing the medial axis, local thickness, and distance-to-skeleton of arbitrary three-dimensional geometries. It is assumed that the object can be represented by an exact or approximate signed distance function on a discrete grid. The gradient of such function is used to formulate a hyperbolic partial differential equation (PDE) that models the collapse of the position vector in space. By exploiting the causality property of the PDE, the Fast Sweeping Method is able to obtain the solution in a finite number of sweeps independent of the mesh resolution. The intersection of characteristic lines leads to the formation of shocks and a discrete bisector function is used to identify the medial axis. The same PDE approach is used to compute the local thickness inside the object and obtain the distance-to-skeleton field. Multiple examples are given in two and three dimensions along with a resolution study. The methodology has optimal complexity and yields subsecond computational times for geometries with over a million zones on a single core. The methodology is also capable of parallelization across shared and distributed memory architectures.
An optimization algorithm for a group of nonsmooth nonconvex problems inspired by two-stage stochastic programming problems is proposed. The main challenges for these problems include (1) the problems lack the popular lower-type properties such as prox-regularity assumed in many nonsmooth nonconvex optimization algorithms, (2) the objective can not be analytically expressed and (3) the evaluation of function values and subgradients are computationally expensive. To address these challenges, this report first examines the properties that exist in many two-stage problems, specifically upper-C 2 objectives. Then, we show that quadratic penalty method for securityconstrained alternating current optimal power flow (SCACOPF) contingency problems can make the contingency solution functions upper-C 2 . Based on these observations, a simplified bundle algorithm that bears similarity to sequential quadratic programming (SQP) method is proposed. It is more efficient in implementation and computation compared to conventional bundle methods. Global convergence analysis of the algorithm is presented under novel and reasonable assumptions. The proposed algorithm therefore fills the gap of theoretical convergence for smoothed SCACOPF problems. The inconsistency that might arise in our treatment of the constraints are addressed through a penalty algorithm whose convergence analysis is also provided. Finally, theoretical capabilities and numerical performance of the algorithm are demonstrated through numerical examples.
This paper presents a unified approach to unit testing and runtime assertion checking using Fortran 2023. The paper describes the support for our approach in the Julienne framework. Julienne leverages recent Fortran standards to implement object-oriented design patterns, support testing parallel programs, and implement functional programming patterns in order to craft idioms inspired by natural-language expressions. The presented idioms employ novel operators to write expressions that evaluate to a test-diagnosis object encapsulating two components: (1) the test outcome or assertion outcome and (2) an automatically generated diagnostic string. Two other novel aspects of the approach include (1) the ability to enforce assertions inside pure procedures and (2) the ability to output rich diagnostic information inside pure procedures during error termination when assertions fail. The latter capability mitigates against a reason that Fortran programmers commonly cite for not writing pure procedures: difficulty obtaining useful program output inside pure procedures when debugging code. This paper demonstrates how the adoption of the proposed idioms leads naturally to a unifying theme across two otherwise disparate technologies: unit testing and runtime assertion checking. Finally, this paper describes the usage of the Julienne testing framework for writing unit tests and assertions in the Matcha high-performance computing application and the Fiats deep learning library.
The Boston University component has focused on the algorithmic development of new Multigrid solver for the critical kernel for the Dirac propagators that dominated the both simulation require for lattice ensemble and the analysis of physical correlation functions. Progress on this has meet the above objects, even exceeding them a bit. The result is the beginning if multiscale lattice QCD applicable to future Exascale hardware and the development of the QUDA software for NVIDIA GPUs to give near optimal performance. As we approach exascale hardware and computation at that scale this provides the infrastructure for further advances.
The principal objective of this project was to synthesize core-shell heterostructures for solid oxide fuel cell cathodes using a molten salt solvent. In doing so, the main goals were split into a) to elucidate and understand the influence of molten salt chemistries to expeditiously synthesize perovskite type oxides for solid oxide fuel cells, b) provide a chemical framework for future molten salt syntheses of energy relevant ceramic materials, c) demonstrate and investigate the required parameters for the optimal core-shell synthesis and yield of La 0.6 Sr 0.4 Co 0.2 Fe 0.8 O 3 (LSCF) – La 0.8 Sr 0.2 MnO 3 (shell), and d) demonstrate improved cathode performance of core-shell LSCF-LSM compared to an LSCF cathode on symmetric cells. The results clearly show that a) the influence of the molten salt cation outweighs the anion in regards to product stoichiometry, b) molten salts should be tailored to balance cationic and anionic acidity for high product yield, c) high yield of core-shell nanoparticles can be achieved by optimal mass ratio between core to shell, dwell time in the salt, size ratio between core to shell, and mass ratio between overall powder to salt, and d) the core-shell LSCF-LSM cathodes have lower polarization resistances than LSCF at higher temperatures. More work is required to optimize core-shell cathode performance at lower temperatures. However, this work thus provided justification for using the molten salt synthesis for SOFC cathodes and provided insights into future material modifications for improved performance.
In this series of papers, we employ several machine learning (ML) methods to classify the point-like sources from the miniJPAS catalogue, and identify quasar candidates. Since no representative sample of spectroscopically confirmed sources exists at present to train these ML algorithms, we rely on mock catalogues. In this first paper, we develop a pipeline to compute synthetic photometry of quasars, galaxies, and stars using spectra of objects targeted as quasars in the Sloan Digital Sky Survey . To match the same depths and signal-to-noise ratio distributions in all bands expected for miniJPAS point sources in the range 17.5 ≤ r < 24, we augment our sample of available spectra by shifting the original r-band magnitude distributions towards the faint end, ensure that the relative incidence rates of the different objects are distributed according to their respective luminosity functions, and perform a thorough modelling of the noise distribution in each filter, by sampling the flux variance either from Gaussian realizations with given widths, or from combinations of Gaussian functions. Finally, we also add in the mocks the patterns of non-detections which are present in all real observations. Although the mock catalogues presented in this work are a first step towards simulated data sets that match the properties of the miniJPAS observations, these mocks can be adapted to serve the purposes of other photometric surveys.
XtalCAMP is a software package based on the MATLAB platform, which is suitable for, but not limited to, the analysis and visualization of scanning Laue X-ray micro-/nanodiffraction data. The main objective of the software is to provide complementary functionalities to the Laue indexing software packages used at several synchrotron beamlines. Here, the graphical user interfaces allow the easy analysis of characteristic microstructure features, including real-time intensity mapping for a quick examination of phase, grain and defect distribution, 2D color-coded mapping of microstructural properties from the output of other Laue indexing software, crystal orientation visualization, grain boundary characterization based on orientation/misorientation calculation, principal strain/stress analysis, and strain ellipsoid representation, as well as a series of additional toolkits. As an example, XtalCAMP is applied to the microstructural investigation of a solution-heat-treated Ni-based superalloy manufactured using a laser 3D-printing technique, and a deformed natural quartzite from Val Bregaglia in the Central Alps.
Riparian and instream restorations are commonly implemented to improve ecosystem condition. However, very few restoration activities are monitored for multiple years to assess long-term effectiveness. At the Department of Defense’s Fort Benning Military Installation (FBMI) in west-central Georgia, two experimental restoration projects (ephemeral drainage revitalization and instream habitat augmentation [i.e., coarse woody debris (CWD) additions]) were implemented ~14 years ago with the goal of reducing environmental impacts of military training activities. A SERDP project found that instream restoration improved some aspects of ecosystem function and community structure but not others. The objective of the current study was to re-evaluate the effect of these restoration practices on stream ecosystem processes ~14 years after implementation.
Little data is available that quantifies IAQ or associates contaminant levels with air exchange in U.S. homes. To address this gap, the U.S. Department of Energy (DOE) Building America Program conducted a study to characterize IAQ in U.S. homes constructed since 2013, along with presence, functionality, and occupant use of control measures. Specific objectives of this study effort included: Measuring time-integrated concentrations and temporal profiles of established contaminants of concern; monitoring the use of ventilation equipment; and tracking activities that impact air pollutant emissions and removal processes in typical homes in various climate zones; Characterizing the prevalence, type, and installed performance of mechanical ventilation equipment in new homes; exploring regional variations in system designs and performance; Investigating associations between contaminant levels and the presence of control measures including whole-house mechanical ventilation (WHMV). The study engaged research teams to collect data at a regional level. This report introduces the study protocol and presents and discusses high-level results obtained from Florida Solar Energy Center (FSEC) data collection efforts in the southeastern U.S. states of Florida, Georgia, and South Carolina.