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At least 649 records · Page 36

Knowledge-matching based computational framework for genome-scale metabolic model refinement

Genome-scale metabolic models (GEMs) are mathematically structured knowledge base reconstructed from annotated genome of different organisms. With the advancement of next-generation sequencing technology, many organisms have had their genomes sequenced. However, obtaining a high-quality GEM is highly time-consuming, even with the introduction of several genome-scale reconstruction tools that offer automated draft network generation and gap filling. It has been recognized that the iterative process of manual curation and refinement is the limiting step of GEM development, and how to expedite the GEM refinement is still an open question. As cellular metabolism is a complex system with very high degree of freedom and redundancy, the principles and techniques developed in process systems engineering can be adapted to expedite GEM refinement. In this paper we present a knowledge-matching based computation framework for GEM refinement, and demonstrate the effectiveness of the proposed solution using the refinement of a GEM for Clostridium tyrobutyricum.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Anomalous elasticity, fluctuations and disorder in elastic membranes

Motivated by freely suspended graphene and polymerized membranes in soft and biological matter we present a detailed study of a tensionless elastic sheet in the presence of thermal fluctuations and quenched disorder. The manuscript is based on an extensive draft dating back to 1993, that was circulated privately. It presents the general theoretical framework and calculational details of numerous results, partial forms of which have been published in brief Letters (Le Doussal and Radzihovsky, 1992; 1993). The experimental realization atom-thin graphene sheets (Novoselov et al., 2004) have driven a resurgence in this fascinating subject, making our dated predictions and their detailed derivations timely. To this end we analyze the statistical mechanics of a generalized D-dimensional elastic “membrane” embedded in d dimensions using a self-consistent screening approximation (SCSA), that has proved to be unprecedentedly accurate in this system, exact in three complementary limits: (i) d→∞, (ii) D→4, and (iii) D=d. Focusing on the critical “flat” phase, for a homogeneous two-dimensional (D=2) membrane embedded in three dimensions (d=3), we predict its universal roughness exponent ζ=0.590, length-scale dependent elastic moduli exponents η=0.821 and η{sub u}=0.358, and an anomalous Poisson ratio, σ = - 1/3. In the presence of random uncorrelated heterogeneity the membrane exhibits a glassy wrinkled ground state, characterized by ζ'=0.775,η' = 0.449,η{sub u}'=1.101 and a Poisson ratio σ ' = - 1/3. Motivated by a number of physical realizations (charged impurities, disclinations and dislocations) we also study power-law correlated quenched disorder that leads to a variety of distinct glassy wrinkled phases. Finally, neglecting self-avoiding interaction we demonstrate that at high temperature a “phantom” sheet undergoes a continuous crumpling transition, characterized by a radius of gyration exponent, ν=0.732 and η=0.535. Many of these universal predictions have received considerable support from simulations. We hope that this detailed presentation of the SCSA theory will be useful to further theoretical developments and corresponding experimental investigations on freely suspended graphene.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

In situ characterization of the biological performance of a Francis turbine retrofitted with a modular guide vane

There are two strategies to lower overall project costs to an extent that will make many potential sustainable hydropower sites economically viable: (1) design standardized/modular components; (2) use advanced tools to reduce environmental evaluation costs. In this study an autonomous sensor device (Sensor Fish) was used to study a Francis turbine retrofitted with a modular guide vane. The median nadir pressures measured were 74.7, 66.6, and 56.6 kPaA for 90-, 190-, and 380-kW operating conditions respectively. These nadir pressures were compared to other Francis turbines studied using Sensor Fish and were found to be within the same range. The proportion of Sensor Fish releases with severe acceleration events (acceleration = 95G) was also investigated. The proportion ranged from 73 to 80% (runner region), 50 to 64% (guide vane region), and 9 to 28% (draft tube region), which was within the range of the other turbines used for comparison. The Sensor Fish testing that was conducted at Hurley Dam demonstrates that the modular guide vane that was retrofitted to the existing Francis turbine is potentially a suitable replacement that can provide biological performance similar to the guide vane used with other existing Francis turbines, but with the benefit of reduced fabrication costs.

13 HYDRO ENERGY↗

A review of EIAs on trade policy in China: Exploring the way for economic policy EIAs

During the discussion on the “Environmental Protection Law Amendment (draft)” in 2011, it was decided to drop the proposed clauses related to environmental impact assessments (EIAs) on policy, which means that there remained no provisions for policy EIAs, and China's strategic environmental assessment system stayed limited to the planning level. However, considering that economic policy making is causing significant direct and indirect environmental problems and that almost every aspect of governmental policy has an economic aspect, EIAs on economic policies are of the utmost urgency. The purpose of this study is to review the EIA work that has been carried out on trade policy in China through four case studies, and illustrate how trade policy EIAs can be helpful in achieving better environmental outcomes in the area of trade. Through the trade policy EIA case studies we try to argue for the feasibility of conducting EIAs on economic policies in China. We also discuss the implications of the case studies from the point of view of how to proceed with EIAs on economic policy and how to promote their practice. - Highlights: • SEA system is incomplete and stays limited to the plan EIA level in China. • EIA on economic policy is of utmost importance for all the developing countries. • Four case studies of trade policy EIA in China are reviewed for policy implications. • Departmental competition for political power impedes economic policy EIAs in China. • Legislative regulation on policy EIA is the first thing needed to overcome barrier.

54 ENVIRONMENTAL SCIENCES↗

Assessment of external costs for transport project evaluation: Guidelines in some European countries

Many studies about the external costs generated by the transport system have been developed in the last twenty years. To standardize methodologies and assessment procedures to be used in the evaluation of the projects, some European countries recently have adopted specific guidelines that differ from each other in some aspects even sensibly. This paper presents a critical analysis of the British, Italian and German guidelines and is aimed at cataloguing the external cost types regarded and the assessment methods indicated as well as to highlight the differences of the results, in terms of applicability and reliability. The goal is to contribute to a European standardization process that would lead to the drafting of guidelines suited for all EU countries. - Highlights: • The analyzed guidelines agree on the methods to evaluate costs from air pollution, greenhouse gases and accidents. • They recommend respectively: dose-resp. approach; costs to reduce/permit emissions; whole direct, indirect and social costs. • For noise, DE guide indicates defensive expenditure or SP methods; IT guide, SP method; UK guide, the hedonic prices one. • For on territory impact, DE guide regards only the barrier effect; the IT one, also the soil consumption and system effects. • British guide proposes a qualitative methodology to estimate the impact on various landscapes and environments.

54 ENVIRONMENTAL SCIENCES↗

Strategic health assessment for large scale industry development activities: An introduction

Attention to the determinants of health and health equity in impact assessment remains under-utilised at the project, Environmental Impact Assessment, level. Determinants focussed health impact assessment has developed at an upstream, policy level, but tends to assess draft proposals rather than form the basis of policies and plans. Project level health (risk) impact assessment tends to focus on a project by project basis, and generally eschews a broad model of health. One answer to this ‘health and impact assessment’ problem is to shift attention to the strategic level, in a similar manner to, and learning from, the development of Strategic Environmental Assessment and its theoretical and practical derivatives. In this article we explain the need for this shift both conceptually and practically by navigating the literature. Our analysis derives specifically from developing the Strategic Health Impact Assessment section of new international industry HIA guidance, coupled with work in and around health impact assessment and policy analysis for the past decade. We develop characteristics of conducting strategic health assessments for multiple industry development activities at the supra national, national or regional level. Our intended audience are public administrators, industry planners and financial sector investors. A particular focus is low and middle income countries, now seen by industry as emerging markets.

54 ENVIRONMENTAL SCIENCES↗

Strategic Environmental Assessment, key issues of its effectiveness. The results of the Speedy Project

This paper describes the results of the European Speedy Project, concerning the application of cross-border SEA, a research that had two main objectives. The first has been the definition of cooperation modalities between various public body as well as private entity through the realization of a digital platform. The aims of this innovative platform include sharing of multidisciplinary knowledge, the training, the participation, etc. The second objective has been to draft a proposal for revision of Directive 2001/42/EC based on the criticalities of implementation in individual Member States emerged during the development of the project. This revision has taken, in the final research report, the form of problem areas and suggestions for amending the Directive. A particularly important result, in addition to those related to platform implementation and the SEA Directive revision, is the e-learning section of the same platform. The continuous training provision of the e-learning system, as well as providing a valuable support for professional upgrading, can provide a useful link between the experiences developed by territorial authorities or individual professionals and the construction of a disciplinary and technical corpus that meet new challenges arising from the changes in society and the evolution of the environmental system.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗

The flexibility gap: Socioeconomic and geographical factors driving residential flexibility

Residential consumers are moving to the center of electricity systems and their flexibility is seen as a key resource to integrate renewable energy sources and support the grid. However, residential flexibility capacities are not homogeneous, as they depend on household appliances, comfort patterns, occupancy, and climate conditions. In this work, we calculate the technical flexibility capacities of 45 consumer types in mainland Spain, organised according to income and regional criteria. We show that flexibility gaps exist at both regional and socioeconomic (income) levels with flexibility differences of up to 10 times more capacity between the household groups from the lowest to the highest capacities. These geographical and socioeconomic gaps in flexibility can lead to distortions in national markets and have the potential to exclude citizens from the provision of flexibility services. Our results show in quantitative terms that a consumer-centered approach without considering correcting measures nor these gaps in drafting energy policies may lead to increasing inequality levels in the residential sector. Under an economic competitive paradigm, households with lower income levels or located in regions with lower flexibility potential may be excluded from the provision of flexibility to the detriment of households with larger potential, raising justice concerns in a flexibility-based energy transition.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Greenhouse gas emissions from the enteric fermentation and manure storage of dairy and beef cattle in China during 1961–2010

Due to the expanding dairy and beef population in China and their contribution to global CH{sub 4} and N{sub 2}O budgets, a framework considering changes in feed, manure management and herd structure was established to indicate the trends of CH{sub 4} and N{sub 2}O emissions from the enteric formation and manure storage in China's beef and dairy production and the underlying driving forces during the period 1961–2010. From 1961 to 2010, annual CH{sub 4} and N{sub 2}O emissions from beef cattle in China increased from 2.18 Mt to 5.86 Mt and from 7.93 kt–29.56 kt, respectively, while those from dairy cattle increased from 0.023 to 1.09 Mt and 0.12 to 7.90 kt, respectively. These increases were attributed to the combined changes in cattle population and management practices in feeds and manure storage. Improvement in cattle genetics during the period increased the bodyweight, required dry matter intake and gross energy and thus resulted in increased enteric CH{sub 4} EFs for each category of beef and dairy cattle as well as the overall enteric EFs (i.e., Tier 1 in IPCC). However, for beef cattle, such an impact on the overall enteric EFs was largely offset by the herd structure transition from draft animal-oriented to meat animal-oriented during 1961–2010. Although the CO{sub 2}-eq of CH{sub 4} and N{sub 2}O from manure storage was less than the enteric emissions during 1961–2010 in China, it tended to increase both in beef and dairy cattle, which was mainly driven by the changes in manure management practices. - Highlights: • CH{sub 4} emissions dominated the CO{sub 2}-eq emissions from dairy and beef cattle in China. • Beef herd transition played an important role in CH{sub 4} emissions. • Changes of manure managements increased the manure EFs of CH{sub 4} and N{sub 2}O. • Manure contributed very less to the total CO{sub 2}-eq emissions but tended to grow.

54 ENVIRONMENTAL SCIENCES↗

Convergent reductive evolution and host adaptation in Mycoavidus bacterial endosymbionts of Mortierellaceae fungi

Intimate associations between fungi and intracellular bacterial endosymbionts are becoming increasingly well understood. Phylogenetic analyses demonstrate that bacterial endosymbionts of Mucoromycota fungi are related either to free-living Burkholderia or Mollicutes species. The so-called Burkholderia-related endosymbionts or BRE comprise Mycoavidus, Mycetohabitans and Candidatus Glomeribacter gigasporarum. These endosymbionts are marked by genome contraction thought to be associated with intracellular selection. However, the conclusions drawn thus far are based on a very small subset of endosymbiont genomes, and the mechanisms leading to genome streamlining are not well understood. The purpose of this study was to better understand how intracellular existence shapes Mycoavidus and BRE functionally at the genome level. To this end we generated and analyzed 14 novel draft genomes for Mycoavidus living within the hyphae of Mortierellomycotina fungi. We found that our novel Mycoavidus genomes were significantly reduced compared to free-living Burkholderiales relatives. Using a genome-scale phylogenetic approach including the novel and available existing genomes of Mycoavidus, we show that the genus is an assemblage composed of two independently derived lineages including three well supported clades of Mycoavidus. Using a comparative genomic approach, we shed light on the functional implications of genome reduction, documenting shared and unique gene loss patterns between the three Mycoavidus clades. We found that many endosymbiont isolates demonstrate patterns of vertical transmission and host-specificity, but others are present in phylogenetically disparate hosts. We discuss how reductive evolution and host specificity reflect convergent adaptation to the intrahyphal selective landscape, and commonalities of eukaryotic endosymbiont genome evolution.

59 BASIC BIOLOGICAL SCIENCES↗

Mitigation of flow-induced pressure fluctuations in a Francis turbine operating at the design and partial load regimes-LES simulations

High-fidelity large eddy simulations (LES) were conducted to characterize the spatial and temporal structure of turbulent flows in an industrial-sized Francis turbine while the unit operated at the design point and partial load. A pressure surge with an amplitude of 8% of the turbine head was observed at partial load while the amplitude was<1% at the design point. The vortex rope precession observed in the draft tube correlated to the amplitude and frequency of the pressure surge. Central and peripheral water injections at various volumetric rates were considered to control the flow-induced pressure fluctuations. Central injection at the 4% and 6% flow rates attenuated high amplitude pressure fluctuations by 40% and 75% respectively at partial load. At the same operating conditions, peripheral injections did not have the same desired effect. Although power generation was not changed with water injection at the design point, it was reduced by about 2.5% by central injection and 0.5% by peripheral injection at partial load, showing a water injection mitigation strategy could be applied without any penalty.

Design and partial load regime↗

Expert Consensus Contouring Guidelines for Intensity Modulated Radiation Therapy in Esophageal and Gastroesophageal Junction Cancer

Purpose/Objective(s): Current guidelines for esophageal cancer contouring are derived from traditional 2-dimensional fields based on bony landmarks, and they do not provide sufficient anatomic detail to ensure consistent contouring for more conformal radiation therapy techniques such as intensity modulated radiation therapy (IMRT). Therefore, we convened an expert panel with the specific aim to derive contouring guidelines and generate an atlas for the clinical target volume (CTV) in esophageal or gastroesophageal junction (GEJ) cancer. Methods and Materials: Eight expert academically based gastrointestinal radiation oncologists participated. Three sample cases were chosen: a GEJ cancer, a distal esophageal cancer, and a mid-upper esophageal cancer. Uniform computed tomographic (CT) simulation datasets and accompanying diagnostic positron emission tomographic/CT images were distributed to each expert, and the expert was instructed to generate gross tumor volume (GTV) and CTV contours for each case. All contours were aggregated and subjected to quantitative analysis to assess the degree of concordance between experts and to generate draft consensus contours. The panel then refined these contours to generate the contouring atlas. Results: The κ statistics indicated substantial agreement between panelists for each of the 3 test cases. A consensus CTV atlas was generated for the 3 test cases, each representing common anatomic presentations of esophageal cancer. The panel agreed on guidelines and principles to facilitate the generalizability of the atlas to individual cases. Conclusions: This expert panel successfully reached agreement on contouring guidelines for esophageal and GEJ IMRT and generated a reference CTV atlas. This atlas will serve as a reference for IMRT contours for clinical practice and prospective trial design. Subsequent patterns of failure analyses of clinical datasets using these guidelines may require modification in the future.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Research-Driven Radiation Oncology: A Narrative on the Ongoing Legacy of Henry S. Kaplan

In this rapidly evolving time of precision medicine and scientifically based cancer care, how radiation oncology became a strong research-based scientific discipline in the United States after its separation from diagnostic radiology might be lost. The importance of generational mentorship, “family trees,” and interpersonal relationships can be difficult or impossible to trace absent personal narrative recollections of those involved. Henry S. Kaplan is a central figure and the focal point for 3 generations of research-based academic department chairs. This report establishes a first draft of a living record of the radiation oncology history of the Kaplan legacy to serve as an example of how knowledge networks grow and flourish and as an impetus for others to trace the legacy of other radiation oncology academic “trees.”.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

A Framework for Patient-Centered Pathways of Care for Radiopharmaceutical Therapy: An ASTRO Consensus Document

Radiopharmaceutical therapy (RPT) is an area of projected growth and importance with several agents in clinical use, new agents in late-phase clinical trials, and many others under testing and development. This article proposes a framework for developing pathways of care that can be broadly applied to all RPTs, representing the current status of RPT. It suggests foundational elements for many pathways of care for patients with cancer and concludes with areas in active development and the future horizon for RPT treatment centers. Developing a framework for patient-centered pathways of care is a critical step in establishing RPT as standard therapy for patients with a diverse spectrum of cancers. This expected increase in RPT treatment options will affect a much larger population of patients with complex cancer. It will also require enhanced coordination and collaboration among appropriately qualified personnel with diverse expertise in image acquisition, image interpretation, quantitative imaging, dosimetry calculation, radiation quality assurance and safety as well as oncology care and RPT-induced sequelae and response assessment. The essential role of this evolving RPT care team within multidisciplinary oncology care is a cornerstone of this framework for a patient-centered pathway of care for RPT. Given the status of current RPT practice and the horizon for future applications, this patient-centered pathway of care guidance is timely and should help inform future clinical RPT practice paradigms. A task force was recruited from the Theranostic Working Group of the American Society for Radiation Oncology (ASTRO) in May 2019 with equal representation from the nuclear medicine community. The task force expanded on a framework that was originally conceived by the Working Group for patient-centered care. This framework was developed to incorporate the strengths of both radiation oncologists and nuclear medicine physicians. The manuscript was then developed by the task force and posted on the ASTRO website for a 6-week public comment period ending in July 2020. Comments were adjudicated, and the draft was sent to external organizations for potential endorsement. This document was sent to the ASTRO Board of Directors in October 2020 for approval.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Real-time optimization of multi-cell industrial evaporative cooling towers using machine learning and particle swarm optimization

Existing electrical generating stations must operate with greater flexibility due to increasing renewable energy penetration on the electrical grid, and many coal-fired power stations have transitioned away from baseload operation to load-following operation to aid in grid stability. In cases where multiple independently controlled cooling tower cells are used in parallel for the cooling purposes of such stations, there is an opportunity to increase plant efficiency through data-driven optimization across their full load ranges. This work presents a novel application of real-time optimization using machine learning and particle swarm optimization on a multi-cell induced-draft cooling tower servicing a coal-fired power station under variable load. This is the first work to demonstrate simultaneous optimization of a multi-cell cooling tower, in addition to using machine learning for closed-loop control on a cooling tower. A novel control configuration is presented that ensures original control logic is not adversely affected and that the overall plant process is not disrupted using only existing hardware and operational data. To verify this methodology, the 12 independent cooling tower cells are simulated in parallel using historic operating data to demonstrate the effectiveness of real-time optimization compared to current practice. An artificial neural network is trained to predict overall cooling tower power consumption using only operational data and ambient conditions with an R2 value of greater than 0.96. The real-time optimization using particle swarm yields 6.7% annual energy usage savings compared to current practices, although the extent of the real-time savings varies greatly with both plant load and environmental conditions. This is particularly significant for a variable load situation because frequent ramping typically results in reduced overall efficiency. Furthermore, this proposed AI-based solution presents an opportunity to improve the overall heat rate of a load-following coal-fired power plant without the need to perform extensive first-principles modeling or add additional hardware to the cooling tower, resulting in more resources conserved and less overall emissions per unit of electricity generated.

42 ENGINEERING↗

A panel analysis of groundwater use in California

We report groundwater is a relevant source of drinking and agricultural water in many regions of the world, but many aquifers have been unsustainably over-drafted and polluted. This has significant environmental, health, and economic implications. We rely on panel analysis, with small-sample corrections for cluster-robust variance estimation and hypothesis testing, to investigate the dynamics of groundwater extraction. We focus on California, yet our approach could be helpful to analyze the dynamics of groundwater extraction in other groundwater-reliant regions of the world. In California, over-reliance on groundwater has led to significant overdraft, affecting long-term water supply reliability and groundwater pumping costs. It further caused subsidence and infrastructure damage, harmed groundwater-dependent ecosystems, and threatened the sustainability of groundwater resources in the state. We use panel data of the 56 California Water Plan planning areas over the 1998–2015 period. We concentrate on agricultural and urban water use and the major water projects in the state, to provide a better understanding of the relationships between groundwater extraction and water use and supply. Results suggest that reducing agricultural water in Central California and urban water in Southern California could reduce groundwater extraction in these regions by approximately the same amount of the reduced water. Other opportunities to reduce the stress on the groundwater resources in the state are available for other regions, yet with lower benefits. Results also suggest that a decrease in deliveries from the Central Valley Project to the southern part of the Central Valley would increase groundwater extraction by approximately the same proportion. Changes in deliveries from the major water projects in the state, as well as from other sources of surface water, would also have some, yet lower impacts on groundwater extraction in the Central and Southern California.

54 ENVIRONMENTAL SCIENCES↗

Pairwise-interaction extended point-particle model for particle-laden flows

In this work we consider the pairwise interaction extended point-particle (PIEP) model for Euler–Lagrange simulations of particle-laden flows. By accounting for the precise location of neighbors the PIEP model goes beyond local particle volume fraction, and distinguishes the influence of upstream, downstream and laterally located neighbors. The two main ingredients of the PIEP model are (i) the undisturbed flow at any particle is evaluated as a superposition of the macroscale flow and a microscale flow that is approximated as a pairwise superposition of perturbation fields induced by each of the neighboring particles, and (ii) the forces and torque on the particle are then calculated from the undisturbed flow using the Faxén form of the force relation. The computational efficiency of the standard Euler–Lagrange approach is retained, since the microscale perturbation fields induced by a neighbor are pre-computed and stored as PIEP maps. Here we extend the PIEP force model of Akiki et al. with a corresponding torque model to systematically include the effect of perturbation fields induced by the neighbors in evaluating the net torque. Also, we use DNS results from a uniform flow over two stationary spheres to further improve the PIEP force and torque models. We then test the PIEP model in three different sedimentation problems and compare the results against corresponding DNS to assess the accuracy of the PIEP model and improvement over the standard point-particle approach. In the case of two sedimenting spheres in a quiescent ambient the PIEP model is shown to capture the drafting-kissing-tumbling process. In cases of 5 and 80 sedimenting spheres a good agreement is obtained between the PIEP simulation and the DNS. For all three simulations, the DEM-PIEP was able to recreate, to a good extent, the results from the DNS, while requiring only a negligible fraction of the numerical resources required by the fully-resolved DNS.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗