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CRISPR-COPIES: an in silico platform for discovery of neutral integration sites for CRISPR/Cas-facilitated gene integration
Abstract The CRISPR/Cas system has emerged as a powerful tool for genome editing in metabolic engineering and human gene therapy. However, locating the optimal site on the chromosome to integrate heterologous genes using the CRISPR/Cas system remains an open question. Selecting a suitable site for gene integration involves considering multiple complex criteria, including factors related to CRISPR/Cas-mediated integration, genetic stability, and gene expression. Consequently, identifying such sites on specific or different chromosomal locations typically requires extensive characterization efforts. To address these challenges, we have developed CRISPR-COPIES, a COmputational Pipeline for the Identification of CRISPR/Cas-facilitated intEgration Sites. This tool leverages ScaNN, a state-of-the-art model on the embedding-based nearest neighbor search for fast and accurate off-target search, and can identify genome-wide intergenic sites for most bacterial and fungal genomes within minutes. As a proof of concept, we utilized CRISPR-COPIES to characterize neutral integration sites in three diverse species: Saccharomyces cerevisiae, Cupriavidus necator, and HEK293T cells. In addition, we developed a user-friendly web interface for CRISPR-COPIES (https://biofoundry.web.illinois.edu/copies/). We anticipate that CRISPR-COPIES will serve as a valuable tool for targeted DNA integration and aid in the characterization of synthetic biology toolkits, enable rapid strain construction to produce valuable biochemicals, and support human gene and cell therapy applications.
On Distribution Grid Optimal Power Flow Development and Integration
Due to changes in electric distribution grid operation, new operation regimes have been recommended. Distribution grid optimal power flow (DOPF) has received tremendous attention in the research community, yet it has not been fully adopted across the utility industry. Our paper recognizes this problem and suggests a development and integration procedure for DOPF. We propose development of DOPF as a three step procedure of 1) processing the grid, 2) obtaining a tractable solution, and 3) implementing multiple solution algorithms and benchmarking them to improve application reliability. For the integration of DOPF, we demonstrate how a DOPF federate may be developed that can be integrated in a co-simulation environment to mimic the real-world conditions and hence improve its practicality to be deployed in the field. To demonstrate the efficacy of the proposed methods, tests on IEEE 123 bus system are performed where the usage of tractable formulation in DOPF algorithm development and its comparison to the benchmark solution are demonstrated.
Integrating 5G Technology for Improved Process Monitoring and Network Slicing in ICS
Industrial Control Systems (ICS) are crucial for monitoring physical processes that support essential cyber-enabled services like power generation. The use of proprietary communication and lack of effective intrusion detection mechanisms pose constraints for efficient operation. Therefore, there is a need to modernize these systems with decentralized technologies like Edge Computing and 5G. However, integrating 5G and Edge Computing into large-scale ICS networks presents implementation and performance challenges. To address these challenges, this paper proposes an integrated ICS architecture that combines 5G and Edge Computing technologies with traditional ICS protocols. The objective is to minimize implementation and operational difficulties while improving the monitoring of physical processes and enabling robust intrusion detection. The proposed architecture outlines the necessary components, services, and communication protocols required for the integration of 5G and Edge Computing.
Data for "Discovery, Characterization, and Application of Chromosomal Integration Sites in the Hyperthermophilic Archaeon Sulfolobus islandicus"
Sulfolobus islandicus , an emerging archaeal model organism, offers unique advantages for metabolic engineering and synthetic biology applications owing to its ability to thrive in extreme environments. Although several genetic tools have been established for this organism, the lack of well-characterized chromosomal integration sites has limited its potential as a cellular factory. Here, we systematically identified and characterized 13 artificial CRISPR RNAs targeting eight integration sites in S. islandicus using the CRISPR-COPIES pipeline and a multi-omics-informed computational workflow. We leveraged the endogenous CRISPR-Cas system to integrate the reporter gene lacS and validated heterologous expression through a β-galactosidase assay, revealing significant positional effects. As a proof of concept, we utilized these sites to genetically manipulate lipid ether composition by overexpressing glycerol dibiphytanyl glycerol tetraether (GDGT) ring synthase B (GrsB). This study expands the genetic toolbox for S. islandicus and advances its potential as a robust platform for archaeal synthetic biology and industrial biotechnology.
High-density integrated delay line using extreme skin-depth subwavelength grating waveguides
Optical delay lines control the flow of light in time, introducing phase and group delays for engineering interferences and ultrashort pulses. Photonic integration of such optical delay lines is essential for chip-scale lightwave signal processing and pulse control. However, typical photonic delay lines based on long spiral waveguides require extensively large chip footprints, ranging from mm 2 to cm 2 scales. Here we present a scalable, high-density integrated delay line using a skin-depth engineered subwavelength grating waveguide, i.e., an extreme skin-depth (eskid) waveguide. The eskid waveguide suppresses the crosstalk between closely spaced waveguides, significantly saving the chip footprint area. Our eskid-based photonic delay line is easily scalable by increasing the number of turns and should improve the photonic chip integration density.
The MIST /MIUS Integration and Subsystems Test/ laboratory - A testbed for the MIUS /Modular Integrated Utility System/ program
The MIUS (Modular Integrated Utility System) concept is to be an energy-conserving, economically feasible, integrated community utility system to provide five necessary services: electricity generation, space heating and air conditioning, solid waste processing, liquid waste processing, and residential water purification. The MIST (MIUS Integration and Subsystem Test) integrated system testbed constructed at the Johnson Space Center in Houston includes subsystems for power generation, heating, ventilation, and air conditioning (HVAC), wastewater management, solid waste management, and control and monitoring. The key design issues under study include thermal integration and distribution techniques, thermal storage, integration of subsystems controls and displays, incinerator performance, effluent characteristics, and odor control.
Improving the Accuracy of the Boundary Integral Method Based on the Helmholtz Integral
Several recent papers in the literature have been based on various forms of the Helmholtz integral to compute the radiation fields of vibrating bodies. The surface integral form is given. The symbols of P,R micron, rho,G,R,V, and S micron are acoustic pressure, source coordinate, angular frequency, fluid density, Green function, field coordinate, surface velocity and body surface respectively. A discretized form of the surface integral is also given. Solutions to the surface integral are complicated with the singularity of the Green function at R=R micron and with the uniqueness problem at interior eigen frequencies of the enclosed space. The use of the interior integral circumvents the singularity problem since the field points are chosen in the interior space of the vibrating body where a zero pressure condition exists. The interior integral form is given. The method to improve the accuracy is detailed. Examples of the method is presented for a variety of radiators.
The Vehicle Integrated Performance Analysis Experience: Reconnecting With Technical Integration
Very early in the Space Launch Initiative program, a small team of engineers at MSFC proposed a process for performing system-level assessments of a launch vehicle. Aimed primarily at providing insight and making NASA a smart buyer, the Vehicle Integrated Performance Analysis (VIPA) team was created. The difference between the VIPA effort and previous integration attempts is that VIPA a process using experienced people from various disciplines, which focuses them on a technically integrated assessment. The foundations of VIPA s process are described. The VIPA team also recognized the need to target early detailed analysis toward identifying significant systems issues. This process is driven by the T-model for technical integration. VIPA s approach to performing system-level technical integration is discussed in detail. The VIPA process significantly enhances the development and monitoring of realizable project requirements. VIPA s assessment validates the concept s stated performance, identifies significant issues either with the concept or the requirements, and then reintegrates these issues to determine impacts. This process is discussed along with a description of how it may be integrated into a program s insight and review process. The VIPA process has gained favor with both engineering and project organizations for being responsive and insightful
An Overview of Integration and Test of the James Webb Space Telescope Integrated Science Instrument Module
The James Webb Space Telescope (JWST) is a 6.6m diameter, segmented, deployable telescope for cryogenic IR space astronomy (approx.40K). The JWST Observatory architecture includes the Optical Telescope Element (OTE) and the Integrated Science Instrument Module (ISIM) element that contains four science instruments (SI) including a Guider. The SIs and Guider are mounted to a composite metering structure with outer dimensions of 2.1x2.2x1.9m. The SI and Guider units are integrated to the ISIM structure and optically tested at NASA/Goddard Space Flight Center as an instrument suite using a high-fidelity, cryogenic JWST telescope simulator that features a 1.5m diameter powered mirror. The SIs are integrated and aligned to the structure under ambient, clean room conditions. SI performance, including focus, pupil shear and wavefront error, is evaluated at the operating temperature. We present an overview of the ISIM integration within the context of Observatory-level construction. We describe the integration and verification plan for the ISIM element, including an overview of our incremental verification approach, ambient mechanical integration and test plans and optical alignment and cryogenic test plans. We describe key ground support equipment and facilities.
Energy Systems Integration Facility (ESIF): World-Class Systems Integration Capabilities and Research
The Energy Systems Integration Facility (ESIF), located at the National Renewable Energy Laboratory (NREL) South Table Mountain campus, is a world-renowned user facility for research and development of modern, advanced, and clean energy technologies. ESIF is distinguished by its continuously evolving, highly integrated systems that span throughout the building, connecting research capabilities across multiple laboratories and test areas. The primary ESIF research systems include: [1] data, cyber, and control networks, [2] research electrical distribution buses (REDB), [3] thermal integration infrastructure, and [4] hydrogen systems. The data, cyber, and control networks provide monitoring, control, communication, automation, visualization, and time series data storage and tagging capabilities for research projects and ESIF systems, including facility safety functions. The REDB system consists of four dedicated AC and DC electrical power networks that can connect devices located across the facility through versatile, automatic circuit configuration to support complex power electronics experiments up to the megawatt-scale. The thermal integration infrastructure consists of three temperature-conditioned water loops that provide heating and cooling interfaces and capabilities for thermal energy research. The hydrogen systems provide megawatt-scale hydrogen production, drying, compression, high-pressure storage, and delivery to laboratory end uses, including hydrogen fuel cell vehicle fueling. The ESIF research systems interconnect and extend throughout the various lab areas of the facility to create elaborate networks composed of diverse technologies for cutting-edge research. The ESIF capabilities are operated and stewarded by the ESIF Research Operations group, who also actively upgrade and advance the systems to ensure they remain ahead of anticipated research - enabling the success of many pioneering energy integration projects. The poster, created by members of the ESIF Research Operations team, highlights and summarizes the four core integrated systems at ESIF. The poster was first presented at the internal NREL Energize Forum on May 13th, 2024, and received the "Best Poster" award.
Integrated Thermal Energy Storage and Brayton Cycle Equipment Demonstration (Integrated TESTBED) Project Design Basis
The Integrated Thermal Energy Storage and Brayton cycle Equipment Demonstration (Integrated TESTBED) project seeks to retire commercial-scale risks associated with the design, integration,and operation of a supercritical carbon dioxide (sCO2) power cycle and concentrating solar power (CSP) thermal energy storage (TES) system. This requires an understanding of commercial-scale collector system transient impacts on the TES system, the dynamics of heat exchange from theTES to the power cycle, and the control and operation of the power cycle to accommodate various dispatch strategies. In order to retire these risks, Heliogen has proposed to construct a 5 MWe CSP demonstration facility based on directly heated particle and sCO2 technology. The receivers, primary heat exchanger, and power cycle will be deployed at a full commercial scale based on Heliogen’s modular plant architecture to ensure actual system integration risks are validated during design, construction, and operation. This work summarizes the design basis for the Integrated TESTBED project demonstration facility including a design target for capacity factor to support test operations, hours of storage, particle silo arrangement, centrifugal article receivers, a diffusion bonded particle-sCO2 heat exchanger, and a 5 MWe (net) integrally geared sCO2 recompression Brayton cycle.
Path-Integrated X-Ray Images for Multi-Surface Digital Image Correlation (PI-DIC)
X-ray imaging offers unique possibilities for Digital Image Correlation (DIC), opening the door for full-field deformation measurements of a test article in complex environments where optical DIC suffers severe biases or is impossible. While X-ray DIC has been performed in the past with standard DIC codes designed for optical images, the path-integrated nature of X-ray images places constraints on the experimental setup, predominantly that only a single surface of interest moves/deforms. These requirements are difficult to realize for many practical situations and limit the amount of information that can be garnered in a single test. Other X-ray based diagnostics such as Digital Volume Correlation (DVC) and Projection DVC (P-DVC) overcome these obstacles, but DVC is limited to quasi-static tests, and both DVC and P-DVC necessitate high-resolution computed tomography (CT) scan(s) and often require a potentially invasive pattern throughout the volume of the specimen. Here this work presents a novel approach to measure time-resolved displacements and strains on multiple surfaces from a single series of 2D, path-integrated (PI) X-ray images, called PI-DIC. The principle of optical flow or conservation of intensity—the foundation of DIC—was reframed for path-integrated images, for an exemplar setup comprised of two plates moving and deforming independently. Synthetic images were generated for rigid translations, rigid rotations, and uniform stretches, where each plate underwent a unique motion/deformation. Experimental specimens were fabricated (either an aluminum plate with tantalum features or a plastic plate with steel features) and the two specimens were independently translated. PI-DIC was successfully demonstrated with the synthetic images and validated with the experimental images. Prescribed displacements were recovered for each plate from the single set of path-integrated, deformed images. Errors were approximately 0.02 px for the synthetic images with 1.5% image noise, and 0.05 px for the experimental images. These results provide the foundation for PI-DIC to measure motion and deformation of multiple, independent surfaces with subpixel accuracy from a single series of path-integrated X-ray images.
NASA's UAS Integration into the NAS: A Report on the Human Systems Integration Phase 1 Simulation Activities
In 2011 the National Aeronautics and Space Administration (NASA) began a five-year Project to address the technical barriers related to routine access of Unmanned Aerial Systems (UAS) in the National Airspace System (NAS). Planned in two phases, the goal of the first phase was to lay the foundations for the Project by identifying those barriers and key issues to be addressed to achieve integration. Phase 1 activities were completed two years into the five-year Project. The purpose of this paper is to review activities within the Human Systems Integration (HSI) subproject in Phase 1 toward its two objectives: 1) develop GCS guidelines for routine UAS access to the NAS, and 2) develop a prototype display suite within an existing Ground Control Station (GCS). The first objective directly addresses a critical barrier for UAS integration into the NAS - a lack of GCS design standards or requirements. First, the paper describes the initial development of a prototype GCS display suite and supporting simulation software capabilities. Then, three simulation experiments utilizing this simulation architecture are summarized. The first experiment sought to determine a baseline performance of UAS pilots operating in civil airspace under current instrument flight rules for manned aircraft. The second experiment examined the effect of currently employed UAS contingency procedures on Air Traffic Control (ATC) participants. The third experiment compared three GCS command and control interfaces on UAS pilot response times in compliance with ATC clearances. The authors discuss how the results of these and future simulation and flight-testing activities contribute to the development of GCS guidelines to support the safe integration of UAS into the NAS. Finally, the planned activities for Phase 2, including an integrated human-in-the-loop simulation and two flight tests are briefly described.
Engineering integration in elementary science classrooms: Effects of disciplinary language scaffolds on English learners' content learning and engineering identity
Abstract Background Limited research examines the effects of integrated science and engineering (SE) instruction emphasizing disciplinary literacy and language activities on engineering identity and content understanding. Far fewer studies target English learners (ELs). Purpose The impact of an SE intervention on the development of science, engineering, and technology knowledge as well as engineering identity was examined. To address ELs' learning needs, the curricular design was built on a validated SE model by integrating (1) developmental, (2) language scaffolds, and (3) culturally based accommodations. Design/Method Separate analysis of variance examined the effects of the intervention on science, engineering, and technology knowledge as well as engineering identity. The relationship among engineering identity and content outcomes was also examined. ELs from kindergarten to second grade classrooms were randomly assigned to the integrated SE group or control group. Results Integrated SE instruction significantly increased ELs' science, engineering, and technology knowledge as well as a substantially developed engineering identity. Overall, ELs' engineering identity is associated with an increase in science, engineering, and technology content knowledge. However, second grade girls' identity development was not associated with learning measures. These correlations suggest the context of the engineering activity may have reinforced gendered stereotypes and reduced the effects for girls' engineering attitudes. Conclusions Integrated SE instruction emphasizing disciplinary literacy and cultural accommodations increases early elementary ELs' learning and engineering identity. Future studies should examine the unique effects of language scaffolds and cultural modifications on student learning and the impact of gender stereotypes on girls' engineering attitudes.
Efficiently evaluating loop integrals in the EFTofLSS using QFT integrals with massive propagators
We develop a new way to analytically calculate loop integrals in the Effective Field Theory of Large Scale-Structure. Previous available methods show severe limitations beyond the one-loop power spectrum due to analytical challenges and computational and memory costs. Our new method is based on fitting the linear power spectrum with cosmology-independent functions that resemble integer powers of quantum field theory massive propagators with complex masses. A remarkably small number of them is sufficient to reach enough accuracy. Similarly to former approaches, the cosmology dependence is encoded in the coordinate vector of the expansion of the linear power spectrum in our basis. We first produce cosmology-independent tensors where each entry is the loop integral evaluated on a given combination of basis vectors. For each cosmology, the evaluation of a loop integral amounts to contracting this tensor with the coordinate vector of the linear power spectrum. The 3-dimensional loop integrals for our basis functions can be evaluated using techniques familiar to particle physics, such as recursion relations and Feynman parametrization. We apply our formalism to evaluate the one-loop bispectrum of galaxies in redshift space. The final analytical expressions are quite simple and can be evaluated with little computational and memory cost. We show that the same expressions resolve the integration of all one-loop N-point function in the EFTofLSS. This method, which is originally presented here, has already been applied in the first one-loop bispectrum analysis of the BOSS data to constraint ΛCDM parameters and primordial non-Gaussianities [1, 2].
An integrated integral projection model ( IPM 2 ) to disentangle size‐structured harvest and natural mortality
Abstract Body size is one of the most important traits governing individual‐level demographic rates and modulating population‐level processes. Multiple size‐dependent demographic rates can simultaneously change population structure, so distinguishing their individual contributions to overall population dynamics remains a challenge. Disentangling size‐dependent harvest rates from other demographic rates is critical for assessing the impact of removal on populations of invasive species. Inference about invasive populations can be difficult, however, as observations are often collected opportunistically as part of removal programs, rather than experimentally designed. Yet accurate inference is essential for understanding the feasibility of population suppression and optimising management decisions. We develop an integrated integral projection model (IPM 2 ) that leverages the strengths of the integrated population model and integral projection model to enable inference about complex, size‐structured demographic rates from imperfect observations. We apply the IPM 2 in the context of invasive European green crab ( Carcinus maenas ), a species for which individual body size strongly regulates both the observation‐generating process and latent, population dynamics. The IPM 2 facilitates the distinct estimation of green crab size‐structured harvest and natural mortality rates, parameters for which no explicit data is collected and that are unidentifiable in component datasets of the integrated population model. The model represents how the green crab population changes over time, providing the first estimates of size‐structured abundance of this high‐priority species. By forecasting the stable size distribution and equilibrium population size under varying removal efforts, we demonstrate that extremely high levels of removal effort can reduce the equilibrium green crab population size. Yet these high mortality rates also shift the stable size distribution and increase the equilibrium abundance of smaller crabs, since size‐selective removal alters intraspecific interactions. The ecological outcome of this shift in size structure will be variable, as green crab size modulates only some of its interactions with other species. These results highlight the value of the IPM 2 framework for inferring complex population dynamics with information needs that outpace information in individual observational datasets, providing a path forward for accurate assessment of conservation programs.
Multistep integration formulas for the numerical integration of the satellite problem
The use of two Class 2/fixed mesh/fixed order/multistep integration packages of the PECE type for the numerical integration of the second order, nonlinear, ordinary differential equation of the satellite orbit problem. These two methods are referred to as the general and the second sum formulations. The derivation of the basic equations which characterize each formulation and the role of the basic equations in the PECE algorithm are discussed. Possible starting procedures are examined which may be used to supply the initial set of values required by the fixed mesh/multistep integrators. The results of the general and second sum integrators are compared to the results of various fixed step and variable step integrators.