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All sources NASA NTRS DOE OSTI

DOE OSTI2021

Analysis of Completion Design Impact on Cluster Efficiency and Pressure-Based Well Communication in HFTS-2 Delaware Basin

The Hydraulic Fracturing Test Site 2 (HFTS-2) is a joint industry project in the Delaware basin to advance hydraulic fracturing understanding and improve productivity in shale reservoirs. The project integrates multi-disciplinary approaches to evaluate different completion designs, well spacing, inter-well communication, and stimulated rock volume, among other factors. This paper focused on two major areas related to hydraulic fracture performance. First, an analysis of different completion designs on cluster efficiency based on near well Distributed Acoustic Sensing (DAS). Second, an evaluation of well and completion designs on inter-well fracture driven interactions (FDIs) based on downhole pressure monitoring. Fluid/sand distribution and cluster efficiency analyses were based on near wellbore DAS data collected from two adjacent horizontal wells completed in two different landing zones in the Wolfcamp formation. These wells had different completion designs aiming to evaluate the effect of normal vs. extended stage lengths, perforation hole tapering and limited entry. Standard deviation from ideal fluid/sand distribution and waterfall plots were used to evaluate cluster efficiency for each design and stage. Inter-well FDIs analysis was conducted among the horizontal wells and a vertical monitor well. One horizontal well served as the monitor well while the other horizontal well was being treated. The vertical well was instrumented with downhole pressure and temperature gauges to aid monitoring fracture height growth. The pressure response during and after fracturing was characterized based on maximum pressure increase value and slope. Pressure response vs. FDIs trigger factors such distance, cluster efficiency and stage fluid volume were also analyzed. Based on the different completion and perforation designs tested, DAS analysis suggests that limited entry design worked best. Extreme limited entry showed the potential of high perforation erosion and reduced cluster efficiency. Here, the limited entry and tapered perforation design demonstrated potential to improve the cluster efficiency for extended stage lengths. Pressure monitoring across formation units proved to be critical to understand fracture interactions and fracture vertical growth. Pressure communication across different formation units during hydraulic fracturing operation indicate fractures grew upwards during Wolfcamp wells fracturing. However, this pressure communication dissipated over time. High intensity FDIs were recorded when the frac stages Downloaded from http://onepetro.org/URTECONF/proceedings-pdf/21URTC/1-21URTC/D011S018R001/2477607/urtec-2021-5289-ms.pdf/1 by Carol Worster on 28 February 2022 URTeC 5289 were closer to the pressure gauge location in the monitor wells. Some of these stages that produced high intensity FDIs also had high fluid volume per cluster and low cluster efficiency. The multi-disciplinary and high-quality data collected from HFTS-2 helped to further understand why completion approaches such as limited entry and tapered perforation design are successful in improving cluster efficiency. The DAS data combined with downhole high-resolution pressure measurements also helped to quantify the effect of lower cluster efficiency data on the incidence and intensity of FDIs.

58 GEOSCIENCES↗

DOE OSTI2015

Completion Design Considerations for a Horizontal Enhanced Geothermal System

The petroleum industry has had considerable success in recent decades in developing unconventional shale plays using horizontal drilling and multi-zonal isolation and stimulation techniques to fracture tight formations to enable the commercial production of oil and gas. Similar well completions could be used in Enhanced Geothermal Systems (EGS) to create multiple fractures from horizontal wells. This study assesses whether well completion techniques used in the unconventional shale industry to create multi-stage fractures can be applied to an enhanced geothermal system, with a focus on the completion of the EGS injection well. This study assumes an Enhanced Geothermal System (EGS) consisting of a central horizontal injection well flanked on each side by horizontal production wells, connected to the injection well by multiple fractures. The focus is on the design and completion of the horizontal well. For the purpose of developing design criteria, a reservoir temperature of 200 degrees C (392 degrees F) and an injection well flow rate of 87,000 barrels per day (160 kg/s), corresponding to production well flow rates of 43,500 barrels per day (80 kg/s) is assumed. The analysis found that 9-5/8 inches 53.5 pounds per foot (ppf) P110 casing string with premium connections meets all design criteria for the horizontal section of injection well. A P110 grade is fairly common and is often used in horizontal sections of shale development wells in petroleum operations. Next, several zonal isolation systems commonly used in the shale gas industry were evaluated. Three techniques were evaluated -- a 'plug and perf' design, a 'sand and perf' design, and a 'packer and port' design. A plug and perf system utilizes a cemented casing throughout the length of the injector wellbore. The sand and perf system is identical to the plug and perf system, but replaces packers with sand placed in the casing after stimulation to screen out the stimulated perforated zones and provide zonal isolation. The packer and port completion approach utilizes an open horizontal hole that zonally isolates areas through the use of external packers and a liner. A review of technologies used in these systems was performed to determine if commercially available equipment from the petroleum industry could be used at the temperatures, pressures, and sizes encountered in geothermal settings. The study found no major technical barriers to employing shale gas multi-zonal completion techniques in a horizontal well in a geothermal setting for EGS development. For all techniques considered, temperature limitations of equipment are a concern. Commercially available equipment designed to operate at the high temperatures encountered in geothermal systems are available, but is generally unproven for geothermal applications. Based on the study, further evaluation of adapting oil and gas completion techniques to EGS is warranted.

15 GEOTHERMAL ENERGY↗

NASA NTRS1992

Completable scheduling: An integrated approach to planning and scheduling

The planning problem has traditionally been treated separately from the scheduling problem. However, as more realistic domains are tackled, it becomes evident that the problem of deciding on an ordered set of tasks to achieve a set of goals cannot be treated independently of the problem of actually allocating resources to the tasks. Doing so would result in losing the robustness and flexibility needed to deal with imperfectly modeled domains. Completable scheduling is an approach which integrates the two problems by allowing an a priori planning module to defer particular planning decisions, and consequently the associated scheduling decisions, until execution time. This allows a completable scheduling system to maximize plan flexibility by allowing runtime information to be taken into consideration when making planning and scheduling decision. Furthermore, through the criteria of achievability placed on deferred decision, a completable scheduling system is able to retain much of the goal-directedness and guarantees of achievement afforded by a priori planning. The completable scheduling approach is further enhanced by the use of contingent explanation-based learning, which enables a completable scheduling system to learn general completable plans from example and improve its performance through experience. Initial experimental results show that completable scheduling outperforms classical scheduling as well as pure reactive scheduling in a simple scheduling domain.

Gervasio, Melinda T.↗

DOE OSTI2021

HFTS-2 Completions Design and State-of-the-Art Diagnostics Results

Various completion schemes were tested as part of the Hydraulic Fracture Test Site-2 (HFTS-2) project. The wells were instrumented with permanent fiber optic (FO) cable, and unique near-wellbore and far-field region surveys were acquired to evaluate spatial and temporal hydraulic fracture characteristics. The state-of-the-art diagnostics included substantial monitoring of both the well stimulation and longer-term production performance. The objective was to evaluate and improve stimulation distribution effectiveness (SDE) for different completion designs based on the diagnostics results. A hydraulic fracturing (HF) profile (i.e., proppant/fluid allocation among clusters) was obtained using near-wellbore Distributed Acoustic Sensing (DAS) data acquired during stimulation. Statistical analysis provided a quantitative assessment of SDE for the different completion designs. A novel workflow was developed to assess time-lapse fracture property changes at the cluster and stage levels based on Distributed Strain Sensing (DSS) data acquired during the production phase. These time-lapse fracture property changes were compared with the HF profile. Based on the statistical analysis, Rate Per Cluster (RPC) during proppant slurry placement appears to be a primary completion design variable, rather than the typical Rate Per Perf (RPP). If RPC was not maintained at a certain level, the likelihood of uneven distribution increased dramatically. The stage configurations that created low RPC while maintaining high RPP did not show improved SDE. The strain change results based on DSS data during the production phase indicated near-wellbore fracture property changes (e.g., aperture changes during well shut-in and flow periods) and aligned well with near-wellbore DAS signals acquired during stimulation. More importantly, fracture property changes based on DSS data acquired during two tests over a 7-month period show high consistency and good alignment with the near-wellbore HF profile. This workflow quantitatively evaluates SDE for different completion designs using diagnostic results and could help optimize completion strategy for future development projects. Here, the analysis and interpretation of results demonstrate the technical feasibility of using permanent fiber optic cable for stimulation and production monitoring and indic

58 GEOSCIENCES↗

DOE OSTI2013

EFFECTS OF DIFFUSE BACKGROUND EMISSION AND SOURCE CROWDING ON PHOTOMETRIC COMPLETENESS IN SPITZER SPACE TELESCOPE IRAC SURVEYS: THE GLIMPSE CATALOGS AND ARCHIVES

We characterize the completeness of point source lists from Spitzer Space Telescope surveys in the four Infrared Array Camera (IRAC) bandpasses, emphasizing the Galactic Legacy Infrared Mid-Plane Survey Extraordinaire (GLIMPSE) programs (GLIMPSE I, II, 3D, 360; Deep GLIMPSE) and their resulting point source Catalogs and Archives. The analysis separately addresses effects of incompleteness resulting from high diffuse background emission and incompleteness resulting from point source confusion (i.e., crowding). An artificial star addition and extraction analysis demonstrates that completeness is strongly dependent on local background brightness and structure, with high-surface-brightness regions suffering up to five magnitudes of reduced sensitivity to point sources. This effect is most pronounced at the IRAC 5.8 and 8.0 {mu}m bands where UV-excited polycyclic aromatic hydrocarbon emission produces bright, complex structures (photodissociation regions). With regard to diffuse background effects, we provide the completeness as a function of stellar magnitude and diffuse background level in graphical and tabular formats. These data are suitable for estimating completeness in the low-source-density limit in any of the four IRAC bands in GLIMPSE Catalogs and Archives and some other Spitzer IRAC programs that employ similar observational strategies and are processed by the GLIMPSE pipeline. By performing the same analysis on smoothed images we show that the point source incompleteness is primarily a consequence of structure in the diffuse background emission rather than photon noise. With regard to source confusion in the high-source-density regions of the Galactic Plane, we provide figures illustrating the 90% completeness levels as a function of point source density at each band. We caution that completeness of the GLIMPSE 360/Deep GLIMPSE Catalogs is suppressed relative to the corresponding Archives as a consequence of rejecting stars that lie in the point-spread function wings of saturated sources. This effect is minor in regions of low saturated star density, such as toward the Outer Galaxy; this effect is significant along sightlines having a high density of saturated sources, especially for Deep GLIMPSE and other programs observing closer to the Galactic center using 12 s or longer exposure times.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2021

Low-rank Tensor Completion for PMU Data Recovery

This paper proposes a tensor completion method for the recovery of missing phasor measurement unit (PMU) measurements. Tensor completion as the general case of matrix completion has attracted increasing attention in recent years. The imputation accuracy for the existing matrix completion methods may be significantly reduced when there are consecutive data losses across multiple data channels. To tackle this issue, we explore the multi-way characteristics of PMU measurements by using a tensor model. We leverage the low-rank property of the PMU measurements and formulate the missing PMU data recovery problem as a low-rank tensor completion problem. An efficient algorithm based on alternating direction method of multipliers (ADMM) is developed to solve the tensor completion problem. The experiments using the real PMU dataset show that the proposed method exhibits better imputation accuracy compared with the conventional data recovery methods.

Ghasemkhani, Amir↗

DOE OSTI2018

Application of Horizontal Well Completion Techniques to Enhanced Geothermal Systems: Final Report October 2015 - September 2016

The petroleum industry has had success in developing unconventional shale plays using horizontal drilling and multi-zonal isolation and stimulation techniques to fracture tight formations, thus enabling the commercial production of oil and gas. Wellbore similarity exists with enhanced geothermal system (EGS) proposals. The technologies and techniques from the petroleum industry are being stretched to accommodate the higher temperatures, high water flow rates, and large-diameter completions encountered in geothermal settings. In this study, we assess whether well completion techniques used in the unconventional shale industry to create multi-stage fractures can be applied to an enhanced geothermal system, focusing on the fracture construction and completion of the EGS production well. We reviewed technologies used in these systems to determine if commercially available equipment from the petroleum industry could be used at the temperatures, pressures, and sizes encountered in geothermal settings. Our study found no major technical barriers to employing shale gas multi-zonal completion techniques in a horizontal well in a geothermal setting for EGS development. Temperature limitations of equipment are a concern for all techniques considered. Equipment designed to operate at high temperatures encountered in geothermal systems is commercially available, but is generally unproven for geothermal applications. Based on our study, further evaluation is warranted on adapting oil and gas completion techniques to EGS. This project is a continuation of the FY14 Horizontal Geothermal Completion project sponsored by the U.S. Department of Energy through the National Renewable Energy Laboratory and the Colorado School of Mines.

15 GEOTHERMAL ENERGY↗

DOE OSTI2023

Completeness of the NASA/IPAC Extragalactic Database (NED) Local Volume Sample

We introduce the NASA/IPAC Extragalactic Database (NED) Local Volume Sample (NED-LVS), a subset of ~1.9 million objects with distances out to 1000 Mpc. We use UV and IR fluxes available in NED from all-sky surveys to derive physical properties, and estimate the completeness relative to the expected local luminosity density. The completeness relative to near-IR luminosities (which traces a galaxy's stellar mass) is roughly 100% at D < 30 Mpc and remains moderate (70%) out to 300 Mpc. For brighter galaxies (≳L * ), NED-LVS is ~100% complete out to ~400 Mpc. When compared to other local Universe samples (GLADE and HECATE), all three are ~100% complete below 30 Mpc. At distances beyond ~80 Mpc, NED-LVS is more complete than both GLADE and HECATE by ~10%–20%. NED-LVS is the underlying sample for the NED gravitational-wave follow-up service (NED-GWF), which provides prioritized lists of host candidates for GW events within minutes of alerts issued by the LIGO–Virgo–KAGRA collaboration. We test the prioritization of galaxies in the volume of GW170817 by three physical properties, where we find that both stellar mass and inverse specific star formation rate place the correct host galaxy in the top 10. In addition, NED-LVS can be used for a wide variety of other astrophysical studies: galaxy evolution, star formation, large-scale structure, galaxy environments, and more. The data in NED are updated regularly, and NED-LVS will be updated concurrently. Consequently, NED-LVS will continue to provide an increasingly complete sample of galaxies for a multitude of astrophysical research areas for years to come.

79 ASTRONOMY AND ASTROPHYSICS↗

NASA NTRS2019

Completeness Index for Earthquake-Induced Landslide Inventories

Understanding the global relation between Earthquake-Induced Landslides (EQILs) and the factors contributing to their initiation is still an open topic within the geomorphological community. Accessing EQIL inventories and analyzing them concerning their potential causes is the key to explore such relation. However, each of the existing EQIL inventories has its level of completeness and associated uncertainty which makes any unified relationship which is challenging to obtain. So far, the completeness of EQIL inventories has never been clearly defined. As a result, it has never been accounted for in global EQIL predictive models. In this technical note, we propose a simple definition for the completeness of EQIL inventories. We analyze 30 digital EQIL for 21 earthquakes and develop a semi-quantitative method to estimate the completeness level, which we refer to as Completeness Index (CI). The CI results from a combination of topographic factors, ground shaking parameters, and a measure derived from landslide size statistics. The proposed CI consists of Low, Moderate, and High completeness classes which can be used to evaluate any landslide inventory. We made the whole procedure to compute the CI accessible in an ArcGIS toolbox together with a test dataset.

Hakan Tanyas↗

DOE OSTI2016

Completing the Cleanup of the US Department of Energy's East Tennessee Technology Park - Four Years Early - 16067

On August 1, 2011, URS - CH2M Oak Ridge LLC (UCOR) began its $2.6 billion cleanup of the East Tennessee Technology Park (ETTP), the former Oak Ridge Gaseous Diffusion Plant, located on the U.S. Department of Energy's (DOE) Oak Ridge Reservation (ORR) in Tennessee. Under the contract, the scope of work to be completed includes demolition of all gaseous diffusion buildings, namely K-25, K-31 and K-27, as well as other facilities such as the Toxic Substance Control Act (TSCA) Incinerator, the K-1200 Centrifuge Complex and the K-1037 Barrier Plant. Additionally, UCOR will remove contaminated soils and treat contaminated groundwater. Waste generated by these cleanup activities will be disposed at onsite as well as offsite facilities. UCOR will also continue to manage hundreds of the DOE Oak Ridge Office of Environmental Management (OREM)-owned facilities across the ORR. Due largely to funding challenges early in the project, the DOE estimated in their October 2013 Program Plan 2014-2024 that ETTP cleanup would not be achieved until 2024, four years later than originally scheduled in UCOR's contract with the DOE. In November 2014, the DOE Manager for OREM, Susan Cange, publicly shared her 'vision' for ETTP cleanup by 2020, four years earlier than the DOE's current plan. As part of Vision 2020, all gaseous diffusion buildings would be demolished by the end of 2016. In response to Ms. Cange's vision, UCOR published a Strategic Plan describing how ETTP could be cleaned up by 2020, provided that a number of funding and programmatic and technical challenges could be overcome. UCOR is in the midst of implementing its Strategic Plan, and progress is being made to that end. Since assuming its responsibilities as the ETTP cleanup contractor, UCOR has completed its life-cycle Performance Measurement Baseline (PMB); received its Earned Value Management System (EVMS) certification; completed the D and D of the 44-acre K-25 and 17-acre K-31 gaseous diffusion buildings; completed the K-1070- B Burial Ground remediation project; completed RCRA closure of the TSCA Incinerator; and disposed of more than 541,411 cubic yards of cleanup waste while managing the on-site Environmental Management Waste Management Facility (EMWMF). In 2015, UCOR achieved safety 'Star Status' under the DOE's Voluntary Protection Program (VPP); completed the demolition of the K-31 gaseous diffusion building; advanced the characterization and deactivation of the K-27 gaseous diffusion building, readying the building for the start of demolition in 2016; and began characterization activities in the K-1037 Barrier Plant as well as a number of facilities in the Poplar Creek Area of the ETTP Site. Project performance through December 31, 2015, is as follows: Cost Performance Index - 1.12, Schedule Performance Index - 1.02. Since safety is the foundation of all cleanup work, UCOR's safety record goes hand-in-hand with its project performance. Through calendar year 2015, UCOR's recordable injury rate was 0.94 occurrences per 200,000 work hours, and the day away case rate was 0.31. These rates are both below the DOE and UCOR goals. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2022

Formal verification and validation of run-to-completion style state charts using Event-B

State chart notations with ‘run to completion’ semantics are popular with engineers for designing controllers that react to environment events with a sequence of state transitions but lack formal refinement and rigorous verification methods. State chart models are typically used to design complex control systems that respond to environmental triggers with a sequential process. The model is usually constructed at a concrete level and verified and validated using animation techniques relying on human judgement. Event-B, on the other hand, is based on refinement from an initial abstraction and is designed to make formal verification by automatic theorem provers feasible. Abstraction and formal verification provide greater assurance that critical (e.g. safety or security) properties are not violated by the control system. In this paper, we introduce a notion of refinement into a ‘run to completion’ state chart modelling notation and leverage Event-B’s tool support for theorem proving. We describe the difficulties in translating ‘run to completion’ semantics into Event-B refinements and suggest a solution. We illustrate our approach and show how models can be validated at different refinement levels using our scenario checker animation tools. We show how critical invariant properties can be verified by proof despite the reactive nature of the system and how behavioural aspects of the system can be verified by testing the expected reactions using a temporal logic, model checking approach. To verify liveness, we outline a proof that the run to completion is deadlock-free and converges to complete the run.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Enhanced Tensor Completion Based Approaches for State Estimation in Distribution Systems

Grid state estimation is essential for effective control and management of distribution systems. While weighted least squares has been the conventional method for state estimation, sparsity-aware methods have become popular due to their superior performance with limited data. Matrix completion and compressed sensing-based state estimation approaches exploit the underlying smoothness in the state variables. However, classic matrix completion methods do not take into account the temporal correlation of system states. Compressed sensing methods, on the other hand, require an appropriate choice of sparsifying basis that may not be easy to identify. This paper proposes a blocktensor completion based framework which uses an alternative approach to estimate voltage phasor, power injections and branch currents. This approach utilizes the temporal correlation of the system states in a tensor trace-norm minimization formulation with power flow equations as constraints. Herein, feature scaling is introduced in the problem formulation to benefit from the improved sensitivity of the tensor trace norm to the matrix columns in the scaled unfoldings of the tensor. Weighted tensor norm is utilized to exploit the structures of the different unfoldings of the state measurement tensor to improve the voltage estimation. The estimation accuracy is further improved by alternatively estimating the tensor columns and increasing the available data at each stage in the tensor completion process. The proposed methods are evaluated on the IEEE-33, 37 test systems and a 100- node test system. The proposed methods are shown to provide significant performance gains relative to the classic matrix and tensor completion based approaches.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2020

Joint Optimization of Well Completions and Controls for CO 2 Enhanced Oil Recovery and Storage

CO 2 storage through CO 2 enhanced oil recovery (EOR) is considered as one of the technologies to help promote larger scale deployment of CO 2 storage because of associated economic benefits through oil recovery, 45Q tax credits and the utilization of existing infrastructure. The objective of this study is to demonstrate how optimal reservoir management and operation strategies (including well completions and controls) can be used to optimize both CO 2 storage and oil recovery. The optimization problem was focused on jointly estimating the well completions (i.e., fraction of injection/production well perforations in each reservoir layer) and CO 2 injection/oil production controls that maximize the net present value (NPV) in a CO 2 EOR and storage operation. We utilized the newly developed StoSAG algorithm, one of the most efficient optimization algorithms in the reservoir management community, to solve the optimization problem. The performance of joint optimization approach was compared with the performance of well control only optimization approach. In addition, the performance of co-optimization of CO 2 storage and oil recovery approach was compared with the performances of maximization of only CO 2 storage and maximization of only oil recovery approaches. The optimization results showed that a joint optimization of well completions and well controls can achieve an 8.84% higher final NPV than the one obtained from the optimization of only well controls. It was observed that the NPV incremental for joint optimization is mainly due to the fact that the optimal well completions and controls approach results in efficient CO 2 storage and oil production from different reservoir layers depending on the differences in individual layer properties. Comparison of co-optimization (i.e., maximization of NPV) and maximization of only CO 2 storage or only oil recovery showed that the co-optimization and maximization of only oil recovery result in significantly higher final NPV than that obtained through maximization of only CO 2 storage approach while maximization of only CO 2 storage can achieve significantly higher CO 2 storage in the reservoir compared to the other two scenarios. The similar results for co-optimization and maximization of oil production are obtained because of the difference in oil revenue compared to CO 2 storage tax credit. To the best of our knowledge, this is the first study in oil/gas industry and CO 2 storage community to perform joint optimization of well completions and well controls in the fields. We expect that the proposed optimization framework will be a useful and efficient tool for field engineers to optimally manage CO 2 EOR projects to maximize revenue through oil recovery as well as CO 2 storage by taking advantage of the new 45Q tax law.

Artificial intelligence↗

DOE OSTI2021

Non-invertible global symmetries and completeness of the spectrum

It is widely believed that consistent theories of quantum gravity satisfy two basic kinematic constraints: they are free from any global symmetry, and they contain a complete spectrum of gauge charges. For compact, abelian gauge groups, completeness follows from the absence of a 1-form global symmetry. However, this correspondence breaks down for more general gauge groups, where the breaking of the 1-form symmetry is insufficient to guarantee a complete spectrum. We show that the correspondence may be restored by broadening our notion of symmetry to include non-invertible topological operators, and prove that their absence is sufficient to guarantee a complete spectrum for any compact, possibly disconnected gauge group. In addition, we prove an analogous statement regarding the completeness of twist vortices: codimension-2 objects defined by a discrete holonomy around their worldvolume, such as cosmic strings in four dimensions. We discuss how this correspondence is modified in various, more general contexts, including non-compact gauge groups, Higgsing of gauge theories, and the addition of Chern-Simons terms. Finally, we discuss the implications of our results for the Swampland program, as well as the phenomenological implications of the existence of twist strings.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2013

Complete genome sequencing and evolutionary analysis of Indian isolates of Dengue virus type 2

Highlights: •Complete genome of Indian DENV-2 was deciphered for the first time in this study. •The recent Indian DENV-2 revealed presence of many unique amino acid residues. •Genotype shift (American to Cosmopolitan) characterizes evolution of DENV-2 in India. •Circulation of a unique clade of DENV-2 in South Asia was identified. -- Abstract: Dengue is the most important arboviral infection of global public health significance. It is now endemic in most parts of the South East Asia including India. Though Dengue virus type 2 (DENV-2) is predominantly associated with major outbreaks in India, complete genome information of Indian DENV-2 is not available. In this study, the full-length genome of five DENV-2 isolates (four from 2001 to 2011 and one from 1960), from different parts of India was determined. The complete genome of the Indian DENV-2 was found to be 10,670 bases long with an open reading frame coding for 3391 amino acids. The recent Indian DENV-2 (2001–2011) revealed a nucleotide sequence identity of around 90% and 97% with an older Indian DENV-2 (1960) and closely related Sri Lankan and Chinese DENV-2 respectively. Presence of unique amino acid residues and non-conservative substitutions in critical amino acid residues of major structural and non-structural proteins was observed in recent Indian DENV-2. Selection pressure analysis revealed positive selection in few amino acid sites of the genes encoding for structural and non-structural proteins. The molecular phylogenetic analysis based on comparison of both complete coding region and envelope protein gene with globally diverse DENV-2 viruses classified the recent Indian isolates into a unique South Asian clade within Cosmopolitan genotype. A shift of genotype from American to Cosmopolitan in 1970s characterized the evolution of DENV-2 in India. Present study is the first report on complete genome characterization of emerging DENV-2 isolates from India and highlights the circulation of a unique clade in South Asia.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

CheckV assesses the quality and completeness of metagenome-assembled viral genomes

Abstract Millions of new viral sequences have been identified from metagenomes, but the quality and completeness of these sequences vary considerably. Here we present CheckV, an automated pipeline for identifying closed viral genomes, estimating the completeness of genome fragments and removing flanking host regions from integrated proviruses. CheckV estimates completeness by comparing sequences with a large database of complete viral genomes, including 76,262 identified from a systematic search of publicly available metagenomes, metatranscriptomes and metaviromes. After validation on mock datasets and comparison to existing methods, we applied CheckV to large and diverse collections of metagenome-assembled viral sequences, including IMG/VR and the Global Ocean Virome. This revealed 44,652 high-quality viral genomes (that is, >90% complete), although the vast majority of sequences were small fragments, which highlights the challenge of assembling viral genomes from short-read metagenomes. Additionally, we found that removal of host contamination substantially improved the accurate identification of auxiliary metabolic genes and interpretation of viral-encoded functions.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

Accuracy and Usefulness of Select Methods for Assessing Complete Collection of 24‐Hour Urine: A Systematic Review

Twenty‐four–hour urine collection is the recommended method for estimating sodium intake. To investigate the strengths and limitations of methods used to assess completion of 24‐hour urine collection, the authors systematically reviewed the literature on the accuracy and usefulness of methods vs para‐aminobenzoic acid ( PABA ) recovery (referent). The percentage of incomplete collections, based on PABA , was 6% to 47% (n=8 studies). The sensitivity and specificity for identifying incomplete collection using creatinine criteria (n=4 studies) was 6% to 63% and 57% to 99.7%, respectively. The most sensitive method for removing incomplete collections was a creatinine index <0.7. In pooled analysis (≥2 studies), mean urine creatinine excretion and volume were higher among participants with complete collection ( P <.05); whereas, self‐reported collection time did not differ by completion status. Compared with participants with incomplete collection, mean 24‐hour sodium excretion was 19.6 mmol higher (n=1781 specimens, 5 studies) in patients with complete collection. Sodium excretion may be underestimated by inclusion of incomplete 24‐hour urine collections. None of the current approaches reliably assess completion of 24‐hour urine collection.

John, Katherine A.↗

DOE OSTI2021

On completeness and generalized symmetries in quantum field theory

We review a notion of completeness in QFT arising from the analysis of basic properties of the set of operator algebras attached to regions. In words, this completeness asserts that the physical observable algebras produced by local degrees of freedom are the maximal ones compatible with causality. We elaborate on equivalent statements to this completeness principle such as the non-existence of generalized symmetries and the uniqueness of the net of algebras. We clarify that for non-complete theories, the existence of generalized symmetries is unavoidable and further that they always come in dual pairs with precisely the same “size”. Moreover, the dual symmetries are always broken together, be it explicitly or effectively. Finally, we comment on several issues raised in recent literature, such as the relationship between completeness and modular invariance, dense sets of charges, and absence of generalized symmetries in the bulk of holographic theories.

Astronomy & Astrophysics↗