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At least 1,747 records · Page 97

The first ensemble of kilometer-scale simulations of a hydrological year over the third pole

An accurate understanding of the current and future water cycle over the Third Pole is of great societal importance, given the role this region plays as a water tower for densely populated areas downstream. An emerging and promising approach for skillful climate assessments over regions of complex terrain is kilometer-scale climate modeling. As a foundational step towards such simulations over the Third Pole, we present a multi-model and multi-physics ensemble of kilometer-scale regional simulations for the hydrological year of October 2019 to September 2020. The ensemble consists of 13 simulations performed by an international consortium of 10 research groups, configured with a horizontal grid spacing ranging from 2.2 to 4 km covering all of the Third Pole region. These simulations are driven by ERA5 and are part of a Coordinated Regional Climate Downscaling EXperiment Flagship Pilot Study on Convection-Permitting Third Pole. The simulations are compared against available gridded and in-situ observations and remote-sensing data, to assess the performance and spread of the model ensemble compared to the driving reanalysis during the cold and warm seasons. Although ensemble evaluation is hindered by large differences between the gridded precipitation datasets used as a reference over this region, we show that the ensemble improves on many warm-season precipitation metrics compared with ERA5, including most wet-day and hour statistics, and also adds value in the representation of wet spells in both seasons. As such, the ensemble will provide an invaluable resource for future improvements in the process understanding of the hydroclimate of this remote but important region.

54 ENVIRONMENTAL SCIENCES↗

MeMoVolc report on classification and dynamics of volcanic explosive eruptions

Classifications of volcanic eruptions were first introduced in the early twentieth century mostly based on qualitative observations of eruptive activity, and over time, they have gradually been developed to incorporate more quantitative descriptions of the eruptive products from both deposits and observations of active volcanoes. Progress in physical volcanology, and increased capability in monitoring, measuring and modelling of explosive eruptions, has highlighted shortcomings in the way we classify eruptions and triggered a debate around the need for eruption classification and the advantages and disadvantages of existing classification schemes. Here, we (i) review and assess existing classification schemes, focussing on subaerial eruptions; (ii) summarize the fundamental processes that drive and parameters that characterize explosive volcanism; (iii) identify and prioritize the main research that will improve the understanding, characterization and classification of volcanic eruptions and (iv) provide a roadmap for producing a rational and comprehensive classification scheme. In particular, classification schemes need to be objective-driven and simple enough to permit scientific exchange and promote transfer of knowledge beyond the scientific community. Schemes should be comprehensive and encompass a variety of products, eruptive styles and processes, including for example, lava flows, pyroclastic density currents, gas emissions and cinder cone or caldera formation. Furthermore open questions, processes and parameters that need to be addressed and better characterized in order to develop more comprehensive classification schemes and to advance our understanding of volcanic eruptions include conduit processes and dynamics, abrupt transitions in eruption regime, unsteadiness, eruption energy and energy balance.

58 GEOSCIENCES↗

A modified moment-fitted integration scheme for X-FEM applications with history-dependent material data

Here, we present a strategy for the numerical integration of partial elements with the eXtended finite element method (X-FEM). The new strategy is specifically designed for problems with propagating cracks through a bulk material that exhibits inelasticity. Following a standard approach with the X-FEM, as the crack propagates into new regions of the domain, elements are split into several copies that contain pieces of the domain on either side of the crack. We examine quadrature rules that have sufficient accuracy to calculate stiffness matrices regardless of the orientation of the crack with respect to the element. This permits the number of integration points within elements to remain constant as a crack propagates, and for state data to be easily transferred between successive discretizations. In order to maintain weights that are strictly positive, we propose an approach that blends moment-fitted weights with volume-fraction based weights. To demonstrate the efficacy of this simple approach, we present results from numerical tests and examples with both elastic and plastic material response.

42 ENGINEERING↗

D-Band EPR and ENDOR Spectroscopy of 15 N-Labeled Photosystem I

For billions of years, nature has optimized the photosynthetic machinery that converts light energy into chemical energy. Key primary reactions of photosynthesis occur in large membrane protein-cofactor complexes. The light-induced sequential electron transfer reactions occur through a chain of donor/acceptor cofactors embedded in the protein matrix resulting in a long-lived transmembrane charge-separated state. EPR is the method of choice to study electron transfer and the interaction of protein environment with redox-active cofactors. However, the spectra of organic cofactor radicals typically are not fully resolved and severely overlap at conventional X-band EPR. Even at Q-band EPR, this overlap is present and often a serious problem. As a result, there is a large variation of the reported EPR data and limited understanding of electronic structures of several redox-active cofactors. These serious problems can often be overcome by the excellent spectral resolution provided by high-frequency EPR (HF EPR). In this work, we study the electronic structure of the primary electron donor P 700 and the secondary electron acceptor A 1 of Photosystem I (PSI) using 130 GHz (D-band) EPR and Electron-Nuclear-Double-Resonance (ENDOR) spectroscopy. PSI was isotopically labeled with 15 N (I = $\frac{1/2}$) to avoid quadrupolar interactions in the most abundant nitrogen isotope 14 N (I = 1) and simplify the ENDOR spectra. ENDOR spectroscopy is central for determining the hyperfine coupling of nitrogen atoms of the two chlorophyll molecules comprising oxidized P 700 and the involvement of protein nitrogen atoms with reduced A 1 . While HF ENDOR of A 1 - allows identification of two nitrogen atoms, HF ENDOR of P 700 + still does not permit unique assignment of the recorded hyperfine couplings.

15N↗

A multi-method approach for groundwater resource assessment in coastal carbonate (karst) aquifers: the case study of Sierra Almijara (southern Spain)

Understanding the transference of water resources within hydrogeological systems, particularly in coastal aquifers, in which groundwater discharge may occur through multiple pathways (through springs, into rivers and streams, towards the sea, etc.), is crucial for sustainable groundwater use. This research aims to demonstrate the usefulness of the application of conventional recharge assessment methods coupled to isotopic techniques for accurately quantifying the hydrogeological balance and submarine groundwater discharge (SGD) from coastal carbonate aquifers. Sierra Almijara (Southern Spain), a carbonate aquifer formed of Triassic marbles, is considered as representative of Mediterranean coastal karst formations. The use of a multi-method approach has permitted the computation of a wide range of groundwater infiltration rates (17–60%) by means of direct application of hydrometeorological methods (Thornthwaite and Kessler) and spatially distributed information (modified APLIS method). A spatially weighted recharge rate of 42% results from the most coherent information on physiographic and hydrogeological characteristics of the studied system. Natural aquifer discharge and groundwater abstraction have been volumetrically quantified, based on flow and water-level data, while the relevance of SGD was estimated from the spatial analysis of salinity, {sup 222}Rn and the short-lived radium isotope {sup 224}Ra in coastal seawater. The total mean aquifer discharge (44.9–45.9 hm{sup 3} year{sup −1}) is in agreement with the average recharged groundwater (44.7 hm{sup 3} year{sup −1}), given that the system is volumetrically equilibrated during the study period. Besides the groundwater resources assessment, the methodological aspects of this research may be interesting for groundwater management and protection strategies in coastal areas, particularly karst environments.

58 GEOSCIENCES↗

3D Histopathology—a Lung Tissue Segmentation Workflow for Microfocus X-ray-Computed Tomography Scans

Lung histopathology is currently based on the analysis of 2D sections of tissue samples. The use of microfocus X-ray-computed tomography imaging of unstained soft tissue can provide high-resolution 3D image datasets in the range of 2–10 μm without affecting the current diagnostic workflow. Important details of structural features such as the tubular networks of airways and blood vessels are contained in these datasets but are difficult and time-consuming to identify by manual image segmentation. Providing 3D structures permits a better understanding of tissue functions and structural interrelationships. It also provides a more complete picture of heterogeneous samples. In addition, 3D analysis of tissue structure provides the potential for an entirely new level of quantitative measurements of this structure that have previously been based only on extrapolation from 2D sections. In this paper, a workflow for segmenting such 3D images semi-automatically has been created using and extending the ImageJ open-source software and key steps of the workflow have been integrated into a new ImageJ plug-in called LungJ. Results indicate an improved workflow with a modular organization of steps facilitating the optimization for different sample and scan properties with expert input as required. This allows for incremental and independent optimization of algorithms leading to faster segmentation. Representation of the tubular networks in samples of human lung, building on those segmentations, has been demonstrated using this approach.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Special Radwaste Management Prospects

The initial registration brought to light the characteristics and disposition of wastes that should be disposed of on-site (special radioactive wastes). The criteria for validating the classification of radwastes as special are presented. The established criteria for the origin of wastes and the location of an object and its sanitaryprotective zone do not permit classifying the radwastes of certain large objects as special even though their removal is unjustified both in terms of dose loads and the risk of potential radiation as well as in terms of financial cost. Criteria are proposed for storage sites for special radwastes for inclusion in the developed regulatory documents, regulating their safe operation and transfer to accommodation and storage sites.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

CONV-3D Code Application for CFD-Modeling of Lead-Bismuth Coolant

The results of testing the three-dimensional CFD-code on problems very close to real processes for lead–bismuth eutectic are presented: flow in a 19-fuel element assembly with three spacing lattices and convection in the ‘tumbler’ model. The results of convergence on a sequence of grids permit drawing the conclusion that for a 19-fuel element assembly the error in the calculation of the friction coefficient on a more finely divided grid does not exceed 10% with two-fold smaller grid step in each direction. Similar arguments are valid for the calculation of the hydraulic resistance coefficient.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Modelling climate analogue regions for a central European city

In this study, we describe a methodology to derive climate analogue cities for spatially highly resolved future climate scenarios. For the computation, a reduced and in hindsight bias-adjusted EURO-CORDEX EUR-11 dataset is used based on two climate scenarios (RCP4.5 and RCP8.5). A total of 389 European cities are processed by the algorithm, which uses five statistical climate variables (2-m air temperature average and amplitude, precipitation sum and amplitude, correlation between 2-m air temperature average and precipitation sum). Additionally, extreme weather events (hot days, summer days, tropical nights, extreme precipitation events) are calculated for further comparison and validation. Finding an appropriate analogue permits a more accurate derivation and depiction of necessary climate adaptation efforts and therefore assist decision-making in city planning. As an example of our method, we searched for plausible climate twins for the mid-sized city of Aachen (Germany) at the end of the twenty-first century. Our results show that the French city of Dijon is highly likely to become Aachen’s climate twin by the end of the century for RCP4.5. As for the scenario RCP8.5, no clear European analogue city could be determined, indicating that the city might enter a novel climate. The nearest match suggests the cities of Florence and Prato in Tuscany. However, considering climate indices, the encompassing region of the French–Spanish city triangle Bordeaux–Toulouse–Bilbao is a better fit. The developed algorithm can be applied to any of the cities included in the dataset.

54 ENVIRONMENTAL SCIENCES↗

A soft X-ray beam-splitting multilayer optic for the NASA GEMS Bragg Reflection Polarimeter

A soft X-ray, beam-splitting, multilayer optic has been developed for the Bragg Reflection Polarimeter (BRP) on the NASA Gravity and Extreme Magnetism Small Explorer Mission (GEMS). The optic is designed to reflect 0.5 keV X-rays through a 90° angle to the BRP detector, and transmit 2–10 keV X-rays to the primary polarimeter. The transmission requirement prevents the use of a thick substrate, so a 2 μm thick polyimide membrane was used. Atomic force microscopy has shown the membrane to possess high spatial frequency roughness less than 0.2 nm rms, permitting adequate X-ray reflectance. A multilayer thin film was especially developed and deposited via magnetron sputtering with reflectance and transmission properties that satisfy the BRP requirements and with near-zero stress. Furthermore, reflectance and transmission measurements of BRP prototype elements closely match theoretical predictions, both before and after rigorous environmental testing.

36 MATERIALS SCIENCE↗

The Bermuda Triangle: The Pragmatics, Policies, and Principles for Data Sharing in the History of the Human Genome Project

The Bermuda Principles for DNA sequence data sharing are an enduring legacy of the Human Genome Project (HGP). They were adopted by the HGP at a strategy meeting in Bermuda in February of 1996 and implemented in formal policies by early 1998, mandating daily release of HGP-funded DNA sequences into the public domain. The idea of daily sharing, we argue, emanated directly from strategies for large, goal-directed molecular biology projects first tested within the “community” of C. elegans researchers, and were introduced and defended for the HGP by the nematode biologists John Sulston and Robert Waterston. In the C. elegans community, and subsequently in the HGP, daily sharing served the pragmatic goals of quality control and project coordination. Yet in the HGP human genome, we also argue, the Bermuda Principles addressed concerns about gene patents impeding scientific advancement, and were aspirational and flexible in implementation and justification. They endured as an archetype for how rapid data sharing could be realized and rationalized, and permitted adaptation to the needs of various scientific communities. Yet in addition to the support of Sulston and Waterston, their adoption also depended on the clout of administrators at the US National Institutes of Health (NIH) and the UK nonprofit charity the Wellcome Trust, which together funded 90% of the HGP human sequencing effort. The other nations wishing to remain in the HGP consortium had to accommodate to the Bermuda Principles, requiring exceptions from incompatible existing or pending data access policies for publicly funded research in Germany, Japan, and France. We begin this story in 1963, with the biologist Sydney Brenner’s proposal for a nematode research program at the Laboratory of Molecular Biology (LMB) at the University of Cambridge. We continue through 2003, with the completion of the HGP human reference genome, and conclude with observations about policy and the historiography of molecular biology.

59 BASIC BIOLOGICAL SCIENCES↗

Suppression of Weakly-Damped Torsional Oscillations in Autonomous Power Systems

Variants are considered for suppression of weakly-damped vibration effects caused by the first critical frequency of torsional oscillations of a gas-turbine unit in the autonomous electric power system of an oil and gas field. It is shown that torsional oscillations can be suppressed with the aid both of a reactive power source installed at the field power system, consisting of a controlled shunt reactor (CSR) and a static capacitor battery, and of an auxiliary active RLC filter, when using in both cases auxiliary control loops of torsional deviation as well as its first and second derivatives. A methodology has been developed for simultaneous coordination of the settings of any regulation system based on a numerical optimization, which permits selecting the characteristics of control loops of the source of reactive power and active RLC filter that are optimal from the point of view of suppressing torsional oscillations.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Sonication-based isolation and enrichment of Chlorella protothecoides chloroplasts for illumina genome sequencing

With the increasing world demand for biofuel, a number of oleaginous algal species are being considered as renewable sources of oil. Chlorella protothecoides Krüger synthesizes triacylglycerols (TAGs) as storage compounds that can be converted into renewable fuel utilizing an anabolic pathway that is poorly understood. The paucity of algal chloroplast genome sequences has been an important constraint to chloroplast transformation and for studying gene expression in TAGs pathways. In this study, the intact chloroplasts were released from algal cells using sonication followed by sucrose gradient centrifugation, resulting in a 2.36-fold enrichment of chloroplasts from C. protothecoides, based on qPCR analysis. The C. protothecoides chloroplast genome (cpDNA) was determined using the Illumina HiSeq 2000 sequencing platform and found to be 84,576 Kb in size (8.57 Kb) in size, with a GC content of 30.8 %. This is the first report of an optimized protocol that uses a sonication step, followed by sucrose gradient centrifugation, to release and enrich intact chloroplasts from a microalga (C. prototheocoides) of sufficient quality to permit chloroplast genome sequencing with high coverage, while minimizing nuclear genome contamination. The approach is expected to guide chloroplast isolation from other oleaginous algal species for a variety of uses that benefit from enrichment of chloroplasts, ranging from biochemical analysis to genomics studies.

09 BIOMASS FUELS↗

Peptide nucleic acid Hoogsteen strand linker design for major groove recognition of DNA thymine bases

Sequence-specific targeting of double-stranded DNA and non-coding RNA via triple-helix-forming peptide nucleic acids (PNAs) has attracted considerable attention in therapeutic, diagnostic and nanotechnological fields. An E-base (3-oxo-2,3-dihydropyridazine), attached to the polyamide backbone of a PNA Hoogsteen strand by a side-chain linker molecule, is typically used in the hydrogen bond recognition of the 4-oxo group of thymine and uracil nucleic acid bases in the major groove. We report on the application of quantum chemical computational methods, in conjunction with spatial constraints derived from the experimental structure of a homopyrimidine PNA·DNA-PNA hetero-triplex, to investigate the influence of linker flexibility on binding interactions of the E-base with thymine and uracil bases in geometry-optimised model systems. Hydrogen bond formation between the N2 E-base atom and target pyrimidine base 4-oxo groups in model systems containing a β-alanine linker (J Am Chem Soc 119:11116, 1997) was found to incur significant internal strain energy and the potential disruption of intra-stand aromatic base stacking interactions in an oligomeric context. Additionally, in geometry-optimised model systems containing a 3-trans olefin linker (Bioorg Med Chem Lett 14:1551, 2004) the E-base swung out away from the target pyrimidine bases into the solvent. These findings are in qualitative agreement with calorimetric measurements in hybridisation experiments at T–A and U–A inversion sites. In contrast, calculations on a novel 2-cis olefin linker design indicate that it could permit simultaneous E-base hydrogen bonding with the thymine 4-oxo group, circumvention and solvent screening of the thymine 5-methyl group, and maintenance of triplex intra-stand base stacking interactions.

59 BASIC BIOLOGICAL SCIENCES↗

Estimates of Equivalent Heat Conductivity Coefficients of Carbon Nanotubes

We have obtained estimates of equivalent heat conductivity coefficients of nanostructured elements on the basis of the constructed mathematical model of the thermal energy transfer in a single-layer and a multilayer nanotube surrounded by a homogeneous material in the composite matrix. The values of such coefficients permit conditional replacement of nanotubes by solid anisotropic fibers, which makes it possible, in predicting the effective heat conductivity coefficient of a composite modified by carbon nanotubes, to use the known methods developed in detail to fit fibrous composites.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Furthering Precision in Sentinel Node Navigational Surgery for Oral Cancer: a Novel Triple Targeting System

To describe an innovative sentinel lymph node (SLN) guidance approach using a radionuclide tracer, 3D augmented reality-guided imaging, and near infrared (NIR) fluorescence over-lay imaging with hand-held probes to optimize accuracy, efficiency, and precise navigation for sentinel node (SN) localization in head and neck cancer. In a cT1N0M0 squamous cell carcinoma of the tongue, pre-operative radionuclide lymphoscintigraphy was performed with a sentinel node-specific radiolabeled tracer. Intraoperatively, a 3D hand-held augmented reality (AR) scanning SPECT probe assessed concordance of the SN with pre-operative SPECT-CT images. The real-time optical video was linked to the SPECT-CT images for added precision. Final guidance to the SN was performed using ICG fluorescence imaging. Dynamic and SPECT-CT showed bilateral lymphatic drainage from the tumor. The 3D hand-held AR SPECT probe SN localization was concordant with pre-operative imaging. The optical video successfully demonstrated the lymphatic drainage in real-time through a unique overlay fluorescence image. The ICG localized to the same nodes identified by both the SPECT-CT and hand-held SPECT images. The use of dual radiation and fluorescence tracers improved SN detection, especially for SN close to the injection site. The hand-held probes allowed the surgeon to dissect continuously, without needing to change tools. The combination of augmented reality, nuclear medicine, and over-lay fluorescence imaging allowed greater accuracy for matching the preoperative imaging with intraoperative identification and precisely guiding the dissection. This method uniquely permitted the surgeon to efficiently dissect the SN with accurate visualization and optimal precision.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Performance of a low-parasitic frequency-domain multiplexing readout

Frequency-domain multiplexing is a readout technique for transition-edge sensor bolometer arrays used on modern cosmic microwave background experiments, including the SPT-3G receiver. Here, we present design details and performance measurements for a low-parasitic frequency-domain multiplexing readout. Reducing the parasitic impedance of the connections between cryogenic components provides a path to improve both the crosstalk and noise performance of the readout. Reduced crosstalk will in turn allow higher-multiplexing factors. We have demonstrated a factor of two improvement in parasitic resistance compared to SPT-3G hardware. Reduced parasitics also permits operation of lower-resistance bolometers optimized for improved readout noise performance. We demonstrate that a module in the prototype system has comparable readout noise performance to an SPT-3G module when operated with dark TES bolometers in the laboratory.

frequency-domain multiplexing↗