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At least 595 records · Page 33

Fluorescent amplification for next generation sequencing (FA-NGS) library preparation

BACKGROUND: Next generation sequencing (NGS) has become a universal practice in modern molecular biology. As the throughput of sequencing experiments increases, the preparation of conventional multiplexed libraries becomes more labor intensive. Conventional library preparation typically requires quality control (QC) testing for individual libraries such as amplification success evaluation and quantification, none of which occur until the end of the library preparation process. RESULTS: In this study, we address the need for a more streamlined high-throughput NGS workflow by tethering real-time quantitative PCR (qPCR) to conventional workflows to save time and implement single tube and single reagent QC. We modified two distinct library preparation workflows by replacing PCR and quantification with qPCR using SYBR Green I. qPCR enabled individual library quantification for pooling in a single tube without the need for additional reagents. Additionally, a melting curve analysis was implemented as an intermediate QC test to confirm successful amplification. Sequencing analysis showed comparable percent reads for each indexed library, demonstrating that pooling calculations based on qPCR allow for an even representation of sequencing reads. To aid the modified workflow, a software toolkit was developed and used to generate pooling instructions and analyze qPCR and melting curve data. CONCLUSIONS: We successfully applied fluorescent amplification for next generation sequencing (FA-NGS) library preparation to both plasmids and bacterial genomes. As a result of using qPCR for quantification and proceeding directly to library pooling, the modified library preparation workflow has fewer overall steps. Therefore, we speculate that the FA-NGS workflow has less risk of user error. The melting curve analysis provides the necessary QC test to identify and troubleshoot library failures prior to sequencing. While this study demonstrates the value of FA-NGS for plasmid or gDNA libraries, we speculate that its versatility could lead to successful application across other library types.

59 BASIC BIOLOGICAL SCIENCES↗

Vapor deposition and condensate flow on combustion turbine blades - Theoretical model to predict/understand some corrosion rate consequences of molten alkali sulfate deposition in the field or laboratory

An analysis is undertaken of aerodynamically- and centrifugally-driven liquid condensate layers on nonisothermal combustion turbines' stator vanes and rotor blades. Attention is given to the quantitative consequences of one possible mechanism for the initiation of 'hot corrosion' in the underlying blade material through a 'fluxing' of the protective oxide coating by the molten salt of the Newtonian condensate film. Illustrative calculations are presented for the condensate streamline pattern and the distributions of the steady-state condensate layer thickness, together with the corresponding oxide dissolution rate, for a test turbine blade.

Rosner, Daniel E.↗

Hypersonic Boundary-Layer Transition on Blunted Cones at Angle of Attack

Experimental studies of cones at several high-speed facilities have demonstrated that, for small nosetip bluntness, transition onset over a circular cone moves upstream along the leeward side and downstream along the windward side, but this trend may be reversed at large bluntness values, where transition onset moves downstream along the leeward side and upstream along the windward side. A theoretical and numerical investigation is performed to characterize the effects of nose bluntness on disturbance amplification over the circular cone for several angles of attack, with the goal of understanding the potential physical mechanisms behind the experimental observations. The three-dimensional laminar basic states over a 1.5 m long, 7-degree half-angle cone with 9.525 mm nosetip radius are computed for selected angles of attack values and freestream conditions that are selected to match the Mach 10 experiments conducted within the Hypervelocity Wind Tunnel 9 at the Arnold Engineering Development Complex (AEDC). The solutions at a freestream unit Reynolds number of 17.1 million per meter are used to perform detailed instability analyses for angles of attack equal to 0, 1, 3, and 5 degrees. Results indicate that the linear amplification of stationary crossflow waves along inflection lines may begin to influence transition along the acreage of the cone for angles of attack equal to or larger than 5 degrees. The measured trend in transition front with respect to increasing angle of attack is found to be consistent with the predicted increase in the amplification factors for Mack mode disturbances along the streamline trajectories. The increase in Mack mode amplification along the windward ray for higher angles of attack is shown to be the result of a progressively earlier entropy-layer swallowing. Computations also indicate that the transition amplification factor along the windward ray is not constant and increases with the angle of attack and that the transition #-factors along the leeward ray are rather small. The nonmodal analysis for zero degrees angle of attack shows that entropy-layer disturbances with appreciably strong energy growth can coexist with Mack mode instabilities at the measured transition location.

boundary layer transition↗

Hypersonic Boundary-Layer Transition on Blunted Cones at Angle of Attack

Experimental studies of cones at several high-speed facilities have demonstrated that, for small nosetip bluntness, transition onset over a circular cone moves upstream along the leeward side and downstream along the windward side, but this trend may be reversed at large bluntness values, where transition onset moves downstream along the leeward side and upstream along the windward side. A theoretical and numerical investigation is performed to characterize the effects of nose bluntness on disturbance amplification over the circular cone for several angles of attack, with the goal of understanding the potential physical mechanisms behind the experimental observations. The three-dimensional laminar basic states over a 1.5 m long, 7-degree half-angle cone with 9.525 mm nosetip radius are computed for selected angles of attack values and freestream conditions that are selected to match the Mach 10 experiments conducted within the Hypervelocity Wind Tunnel 9 at the Arnold Engineering Development Complex (AEDC). The solutions at a freestream unit Reynolds number of 17.1 million per meter are used to perform detailed instability analyses for angles of attack equal to 0, 1, 3, and 5 degrees. Results indicate that the linear amplification of stationary crossflow waves along inflection lines may begin to influence transition along the acreage of the cone for angles of attack equal to or larger than 5 degrees. The measured trend in transition front with respect to increasing angle of attack is found to be consistent with the predicted increase in the amplification factors for Mack mode disturbances along the streamline trajectories. The increase in Mack mode amplification along the windward ray for higher angles of attack is shown to be the result of a progressively earlier entropy-layer swallowing. Computations also indicate that the transition amplification factor along the windward ray is not constant and increases with the angle of attack and that the transition #-factors along the leeward ray are rather small. The nonmodal analysis for zero degrees angle of attack shows that entropy-layer disturbances with appreciably strong energy growth can coexist with Mack mode instabilities at the measured transition location.

Boundary Layer Transition↗

Analysis of Validating and Verifying OpenACC Compilers 3.0 and Above

OpenACC is a high-level directive-based parallel programming model that can manage the sophistication of heterogeneity in architectures and abstract it from the users. The portability of the model across CPUs and accelerators has gained the model a wide variety of users. This means it is also crucial to analyze the reliability of the compilers’ implementations. To address this challenge, the OpenACC Validation and Verification team has proposed a validation testsuite to verify the OpenACC implementations across various compilers with an infrastructure for a more streamlined execution. This paper will cover the following aspects: (a) the new developments since the last publication on the testsuite, (b) outline the use of the infrastructure, (c) discuss tests that highlight our workflow process, (d) analyze the results from executing the testsuite on various systems, and (e) outline future developments.

Jarmusch, Aaron↗

Modification and analysis of context-specific genome-scale metabolic models: methane-utilizing microbial chassis as a case study

ABSTRACT Context-specific genome-scale model (CS-GSM) reconstruction is becoming an efficient strategy for integrating and cross-comparing experimental multi-scale data to explore the relationship between cellular genotypes, facilitating fundamental or applied research discoveries. However, the application of CS modeling for non-conventional microbes is still challenging. Here, we present a graphical user interface that integrates COBRApy, EscherPy, and RIPTiDe, Python-based tools within the BioUML platform, and streamlines the reconstruction and interrogation of the CS genome-scale metabolic frameworks via Jupyter Notebook. The approach was tested using -omics data collected for Methylotuvimicrobium alcaliphilum 20Z R , a prominent microbial chassis for methane capturing and valorization. We optimized the previously reconstructed whole genome-scale metabolic network by adjusting the flux distribution using gene expression data. The outputs of the automatically reconstructed CS metabolic network were comparable to manually optimized i IA409 models for Ca-growth conditions. However, the CS model questions the reversibility of the phosphoketolase pathway and suggests higher flux via primary oxidation pathways. The model also highlighted unresolved carbon partitioning between assimilatory and catabolic pathways at the formaldehyde-formate node. Only a very few genes and only one enzyme with a predicted function in C1 metabolism, a homolog of the formaldehyde oxidation enzyme ( fae1-2 ), showed a significant change in expression in La-growth conditions. The CS-GSM predictions agreed with the experimental measurements under the assumption that the Fae1-2 is a part of the tetrahydrofolate-linked pathway. The cellular roles of the tungsten (W)-dependent formate dehydrogenase ( fdhAB ) and fae homologs ( fae1-2 and fae3 ) were investigated via mutagenesis. The phenotype of the f dhAB mutant followed the model prediction. Furthermore, a more significant reduction of the biomass yield was observed during growth in La-supplemented media, confirming a higher flux through formate. M. alcaliphilum 20Z R mutants lacking fae1-2 did not display any significant defects in methane or methanol-dependent growth. However, contrary to fae1, the fae1-2 homolog failed to restore the formaldehyde-activating enzyme function in complementation tests. Overall, the presented data suggest that the developed computational workflow supports the reconstruction and validation of CS-GSM networks of non-model microbes. IMPORTANCE The interrogation of various types of data is a routine strategy to explore the relationship between genotype and phenotype. An efficient approach for integrating and cross-comparing experimental multi-scale data in the context of whole-genome-based metabolic network reconstruction becomes a powerful tool that facilitates fundamental and applied research discoveries. The present study describes the reconstruction of a context-specific (CS) model for the methane-utilizing bacterium, Methylotuvimicrobium alcaliphilum 20Z R . M. alcaliphilum 20Z R is becoming an attractive microbial platform for the production of biofuels, chemicals, pharmaceuticals, and bio-sorbents for capturing atmospheric methane. We demonstrate that this pipeline can help reconstruct metabolic models that are similar to manually curated networks. Furthermore, the model is able to highlight previously overlooked pathways, thus advancing fundamental knowledge of non-model microbial systems or promoting their development toward biotechnological or environmental implementations.

Kulyashov, M. A.↗

Integration of Structural Analysis and Manufacturing Process Planning for Global Optimization with Automated Fiber Placement

Design of mass-efficient composite structures intended for Automated Fiber Placement (AFP) requires close interaction between structural analysis and manufacturing process planning. Tools exist for each of these disciplines, but software interplay has been insufficient for rapid and efficient design iteration. Within the NASA Advanced Composites Consortium (ACC), the Design for Manufacturing (DFM) task has made significant progress towards linking these disciplines and respective software – HyperX (design), CAPP (process planning), and VCP (tool path generation). The initial focus in previous work was on data exchange between disciplines. The ability to both export and consume composite design and manufacturing data to and from each tool. This paper focuses on the effort to automate and streamline the connection between the tools listed above, with the goal of being able to automatically generate a composite AFP design that is mass-efficient and manufacturable. The optimization method being pursued is a bi-level approach, where each tool performs optimization within its discipline. The optimization in HyperX is focused on mass and laminate strength, while CAPP is focused on maximizing manufacturability. VCP is used to generate fiber paths for each design iteration. These sub-processes are wrapped with a global level optimization, driven by HyperX, used to converge the design. This paper describes the current state of this effort, which is a completed HyperX-VCP iteration loop and initial work on the HyperX-CAPP iteration loop. Additionally, example results are shown for a wind blade structure with double curvature.

Automated Fiber Placement↗

Reversible collisionless magnetic reconnection

Reversible magnetic reconnection is demonstrated for the first time by means of gyrokinetic numerical simulations of a collisionless magnetized plasma. Growth of a current-driven instability in a sheared magnetic field is accompanied by magnetic reconnection due to electron inertia effects. Following the instability growth, the collisionless reconnection is accelerated with development of a cross-shaped structure of current density, and then all field lines are reconnected. The fully reconnected state is followed by the secondary reconnection resulting in a weakly turbulent state. A time-reversed simulation starting from the turbulent state manifests that the collisionless reconnection process proceeds inversely leading to the initial state. During the reversed reconnection, the kinetic energy is reconverted into the original magnetic field energy. In order to understand the stability of reversed process, an external perturbation is added to the fully reconnected state, and it is found that the accelerated reconnection is reversible when the deviation of the E × B streamlines due to the perturbation is comparable with or smaller than a current layer width.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Mechanism-guided engineering of a minimal biological particle for genome editing

The widespread application of genome editing to treat and cure disease requires the delivery of genome editors into the nucleus of target cells. Enveloped delivery vehicles (EDVs) are engineered virally derived particles capable of packaging and delivering CRISPR-Cas9 ribonucleoproteins (RNPs). However, the presence of lentiviral genome encapsulation and replication proteins in EDVs has obscured the underlying delivery mechanism and precluded particle optimization. Here, we show that Cas9 RNP nuclear delivery is independent of the native lentiviral capsid structure. Instead, EDV-mediated genome editing activity corresponds directly to the number of nuclear localization sequences on the Cas9 enzyme. EDV structural analysis using cryo-electron tomography and small molecule inhibitors guided the removal of ~80% of viral residues, creating a minimal EDV (miniEDV) that retains full RNP delivery capability. MiniEDVs are 25% smaller yet package equivalent amounts of Cas9 RNPs relative to the original EDVs and demonstrated increased editing in cell lines and therapeutically relevant primary human T cells. These results show that virally derived particles can be streamlined to create efficacious genome editing delivery vehicles with simpler production and manufacturing.

59 BASIC BIOLOGICAL SCIENCES↗

Turbo‐charging crop improvement: harnessing multiplex editing for polygenic trait engineering and beyond

Multiplex CRISPR editing has emerged as a transformative platform for plant genome engineering, enabling the simultaneous targeting of multiple genes, regulatory elements, or chromosomal regions. This approach is effective for dissecting gene family functions, addressing genetic redundancy, engineering polygenic traits, and accelerating trait stacking and de novo domestication. Its applications now extend beyond standard gene knockouts to include epigenetic and transcriptional regulation, chromosomal engineering, and transgene‐free editing. These capabilities are advancing crop improvement not only in annual species but also in more complex systems such as polyploids, undomesticated wild relatives, and species with long generation times. At the same time, multiplex editing presents technical challenges, including complex construct design and the need for robust, scalable mutation detection. We discuss current toolkits and recent innovations in vector architecture, such as promoter and scaffold engineering, that streamline workflows and enhance editing efficiency. High‐throughput sequencing technologies, including long‐read platforms, are improving the resolution of complex editing outcomes such as structural rearrangements—often missed by standard genotyping—when targeting repetitive or tandemly spaced loci. To fully realize the potential of multiplex genome engineering, there is growing demand for user‐friendly, synthetic biology‐compatible, and scalable computational workflows for gRNA design, construct assembly, and mutation analysis. Experimentally validated inducible or tissue‐specific promoters are also highly desirable for achieving spatiotemporal control. As these tools continue to evolve, multiplex CRISPR editing is poised to become a foundational technology of next‐generation crop improvement to address challenges in agriculture, sustainability, and climate resilience.

59 BASIC BIOLOGICAL SCIENCES↗

Investigation of flow phenomena in a transonic fan rotor using laser anemometry

Several flow phenomena including flowfield periodicity, rotor shock oscillation, and rotor shock system geometry were investigated in a transonic low aspect ratio fan rotor using laser anemometry. Flow periodicity is found to increase with increasing rotor pressure rise, and to correlate with blade geometry variations. Analysis of time-accurate laser anemometer data indicates that the rotor shock oscillates about its mean location with an amplitude of 3 to 4 percent of rotor chord. The shock surface is nearly two-dimensional or levels of rotor pressure rise at and above the peak efficiency level but becomes more complex for lower levels of pressure rise. Spanwise shock lean generates radial flows due to streamline deflection in the hub-to-shroud streamsurface.

Strazisar, A. J.↗

Investigation of flow phenomena in a transonic fan rotor using laser anemometry

Several flow phenomena including flowfield periodicity, rotor shock oscillation, and rotor shock system geometry were investigated in a transonic low aspect ratio fan rotor using laser anemometry. Flow periodicity is found to increase with increasing rotor pressure rise, and to correlate with blade geometry variations. Analysis of time-accurate laser anemometer data indicates that the rotor shock oscillates about its mean location with an amplitude of 3 to 4 percent of rotor chord. The shock surface is nearly two-dimensional for levels of rotor pressure rise at and above the peak efficiency level but becomes more complex for lower levels of pressure rise. Spanwise shock lean generates radial flows due to streamline deflection in the hub-to-shroud streamsurface.

Strazisar, A. J.↗

Systems Maintenance Automated Repair Tasks (SMART)

SMART is an interactive decision analysis and refinement software system that uses evaluation criteria for discrepant conditions to automatically provide and populate a document/procedure with predefined steps necessary to repair a discrepancy safely, effectively, and efficiently. SMART can store the tacit (corporate) knowledge merging the hardware specification requirements with the actual "how to" repair methods, sequences, and required equipment, all within a user-friendly interface. Besides helping organizations retain repair knowledge in streamlined procedures and sequences, SMART can also help them in saving processing time and expense, increasing productivity, improving quality, and adhering more closely to safety and other guidelines. Though SMART was developed for Space Shuttle applications, its interface is easily adaptable to any hardware that can be broken down by component, subcomponent, discrepancy, and repair.

Source record↗

Reforming EIA systems: A critical review of proposals in Brazil

Environmental Impact Assessment (EIA) systems are under pressure in many countries, driven by a call for efficiency and streamlining. Such a phenomenon is particularly clear in Brazil, where, in the past few years, a number of influential associations put forward documents proposing significant changes to environmental licensing and impact assessment regulations. So far, there is no publicly available information about any initiative towards scrutinizing those proposals. The objective of this study was to critically review the merits and drawbacks of the changes proposed in those documents. The analysis triangulated content analysis, focus group and online survey data. The focus group included ten seasoned Brazilian EIA specialists; the survey, based on Likert-scale and open-ended questions, resulted in 322 valid responses from EIA professionals. Results show that the proposals generally agree that the current EIA system, while playing a key role in mitigating impacts and enhancing project design, needs many changes. Nonetheless, the proposals neither offered solutions to overcome political, technical and budget barriers, nor established a sense of priority of the most urgent issues. Findings from the focus group and the survey signaled that a number of proposed actions might face public outcry, and that those changes that do not depend on legislative action are more likely to be implementable. Previous studies about EIA reform focused mostly on the context of developed countries after changes had taken place. This study, while addressing the perspective of a large developing country in a “before-reform” stage, shows that capacity-building is a key requirement in EIA reform. - Highlights: • Brazil's EIA system is under strong pressure for change. • Findings corroborate ineffectiveness in current system. • There are tensions as to the best approaches to overcome problems. • Exact effects of proposals are uncertain. • Low institutional capacity can play strong role in driving EIA reform.

54 ENVIRONMENTAL SCIENCES↗

BuildingSync® v.2.5.0 2024 [SWR-18-28]

BuildingSync® is a building data exchange schema to better enable integration between software tools and building data workflows. The schema's original use case was focused on commercial building energy audits; however, several additional use cases have been realized including building energy modeling and more high-level generic building data exchange. BuildingSync helps streamline the data exchange process, improving the value of the data, minimizing duplication of effort for subsequent building data collection efforts (including audits), and facilitating the achievement of greater energy efficiency. This in done in part by standardizing on (a) reporting audits in an electronic format, (b) tracking proposed, implemented, and discarded energy conservation measures, and (c) storing building characteristics (at multiple levels) for audits, benchmarking, and building energy analysis. BuildingSync has several documents and tools available to help users understand how to best leverage BuildingSync. The list below are only a subset of the resources available. If new resources are discovered, then feel free to create a new pull request with the additions. Generic BuildingSync information is available on the DOE website and the project website. BuildingSync Examples - These examples are kept up to date and show a wide range of implementations. Any new update to BuildingSync is required to pass validation on these example files. BuildingSync Use Case Validator allows for users to determine if their instance complies with a specific use case for BuildingSync by checking if the required elements are implemented in an uploaded instance. An API is also provided for automated integration into other tools. Also, the website contains an easy way to view the entirety of the schema and how elements relate to the Building Exchange Data Exchange Specification. The Validator is open sourced here Use Case TestSuite provides a Python package for easier generation of BuildingSync use cases. BuildingSync use cases depend on the generation of schematron documents, which is time-consuming and difficult to implement well. The TestSuite allows users to define a use case using a more palatable CSV template, which it then turns into a Schematron document. The source code is available here. BuildingSync to OpenStudio/EnergyPlus. The translator is open sourced here. This project will translate a Level 1 (and partial Level 2) ASHRAE Energy Audit to a fully defined OpenStudio and EnergyPlus model. This project is in early Beta testing and any feedback is welcome!

Long, Nicholas↗

BuildingSync® v.2.7.0 (released 9.11.2025) [SWR-18-28]

BuildingSync® is a building data exchange schema to better enable integration between software tools and building data workflows. The schema's original use case was focused on commercial building energy audits; however, several additional use cases have been realized including building energy modeling and more high-level generic building data exchange. Version 2.7.0 adds new elements for file attachment feature and FederalBuilding, and generalizes usage of Optional Elements (e.g. EquipmentCondition, EquipmentID) to all assets/systems. BuildingSync helps streamline the data exchange process, improving the value of the data, minimizing duplication of effort for subsequent building data collection efforts (including audits), and facilitating the achievement of greater energy efficiency. This in done in part by standardizing on (a) reporting audits in an electronic format, (b) tracking proposed, implemented, and discarded energy conservation measures, and (c) storing building characteristics (at multiple levels) for audits, benchmarking, and building energy analysis. BuildingSync has several documents and tools available to help users understand how to best leverage BuildingSync. The list below are only a subset of the resources available. If new resources are discovered, then feel free to create a new pull request with the additions. Generic BuildingSync information is available on the DOE website and the project website. BuildingSync Examples - These examples are kept up to date and show a wide range of implementations. Any new update to BuildingSync is required to pass validation on these example files. BuildingSync Use Case Validator allows for users to determine if their instance complies with a specific use case for BuildingSync by checking if the required elements are implemented in an uploaded instance. An API is also provided for automated integration into other tools. Also, the website contains an easy way to view the entirety of the schema and how elements relate to the Building Exchange Data Exchange Specification. The Validator is open sourced here Use Case TestSuite provides a Python package for easier generation of BuildingSync use cases. BuildingSync use cases depend on the generation of schematron documents, which is time-consuming and difficult to implement well. The TestSuite allows users to define a use case using a more palatable CSV template, which it then turns into a Schematron document. The source code is available here. BuildingSync to OpenStudio/EnergyPlus. The translator is open sourced here. This project will translate a Level 1 (and partial Level 2) ASHRAE Energy Audit to a fully defined OpenStudio and EnergyPlus model. This project is in early Beta testing and any feedback is welcome!

Long, Nicholas [National Renewable Energy Lab. (NR↗

Aerodynamic heating and surface temperatures on vehicles for computer-aided design studies

A computer subprogram has been developed to calculate aerodynamic and radiative heating rates and to determine surface temperatures by integrating the heating rates along the trajectory of a vehicle. Convective heating rates are calculated by applying the axisymmetric analogue to inviscid surface streamlines and using relatively simple techniques to calculate laminar, transitional, or turbulent heating rates. Options are provided for the selection of gas model, transition criterion, turbulent heating method, Reynolds Analogy factor, and entropy-layer swallowing effects. Heating rates are compared to experimental data, and the time history of surface temperatures are given for a high-speed trajectory. The computer subprogram is developed for preliminary design and mission analysis where parametric studies are needed at all speeds.

Dejarnette, F. R.↗

Laser velocimetry measurements in non-isothermal CVD systems

Researchers at the NASA Langley Research Center are applying laser velocimetry (LV) techniques to characterize the fluid dynamics of non-isothermal flows inside fused silica chambers designed for chemical vapor deposition (CVD). Experimental issues involved in the application of LV techniques to this task include thermophoretic effects on the LV seed particles, seeding the hazardous gases, index of refraction gradients in the flow field and surrounding media, optical access, relatively low flow velocities, and analysis and presentation of sparse data. An overview of the practical difficulties these issues represent to the use of laser velocimetry instrumentation for CVD applications is given. A fundamental limitation on the application of LV techniques in non-isothermal systems is addressed which involves a measurement bias due to the presence of thermal gradients. This bias results from thermophoretic effects which cause seed particle trajectories to deviate from gas streamlines. Data from a research CVD reactor are presented which indicate that current models for the interaction of forces such as Stokes drag, inertia, gravity, and thermophoresis are not adequate to predict thermophoretic effects on particle-based velocimetry measurements in arbitrary flow configurations.

Johnson, E. J.↗