Evolution of protective human antibodies against Plasmodium falciparum circumsporozoite protein repeat motifs
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99 GENERAL AND MISCELLANEOUS↗
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Self-Supervised Anomaly Detection With Neural Transformations
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Qiu, Chen [Bosch Center for AI, Pittsburgh, PA, US↗
The Event Detection System in the NEXT-White Detector
This article describes the event detection system of the NEXT-White detector, a 5 kg high pressure xenon TPC with electroluminescent amplification, located in the Laboratorio Subterráneo de Canfranc (LSC), Spain. The detector is based on a plane of photomultipliers (PMTs) for energy measurements and a silicon photomultiplier (SiPM) tracking plane for offline topological event filtering. The event detection system, based on the SRS-ATCA data acquisition system developed in the framework of the CERN RD51 collaboration, has been designed to detect multiple events based on online PMT signal energy measurements and a coincidence-detection algorithm. Implemented on FPGA, the system has been successfully running and evolving during NEXT-White operation. The event detection system brings some relevant and new functionalities in the field. A distributed double event processor has been implemented to detect simultaneously two different types of events thus allowing simultaneous calibration and physics runs. This special feature provides constant monitoring of the detector conditions, being especially relevant to the lifetime and geometrical map computations which are needed to correct high-energy physics events. Other features, like primary scintillation event rejection, or a double buffer associated with the type of event being searched, help reduce the unnecessary data throughput thus minimizing dead time and improving trigger efficiency.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Data Compression in the NEXT-100 Data Acquisition System
NEXT collaboration detectors are based on energy measured by an array of photomultipliers (PMT) and topological event filtering based on an array of silicon photomultipliers (SiPMs). The readout of the PMT sensors for low-frequency noise effects and detector safety issues requires a grounded cathode connection that makes the readout AC-couple with variations in the signal baseline. Strict detector requirements of energy resolution better than 1% FWHM require a precise baseline reconstruction that is performed offline for data analysis and detector performance characterization. Baseline variations make it inefficient to apply traditional lossy data compression techniques, such as zero-suppression, that help to minimize data throughput and, therefore, the dead time of the system. However, for the readout of the SiPM sensors with less demanding requirements in terms of accuracy, a traditional zero-suppression is currently applied with a configuration that allows for a compression ratio of around 71%. The third stage in the NEXT detectors program, the NEXT-100 detector, is a 100 kg detector that instruments approximately five times more PMT sensors and twice the number of SiPM sensors than its predecessor, the NEXT-White detector, putting more pressure in the DAQ throughput, expected to be over 900 MB/s with the current configuration, which will worsen the dead time of the acquisition data system. This paper describes the data compression techniques applied to the sensor data in the NEXT-100 detector, which reduces data throughput and minimizes dead time while maintaining the event rate to the level of its predecessor, around 50 Hz.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Quantification of Native Lignin Structural Features with Gel–Phase 2D–HSQC 0 Reveals Lignin Structural Changes During Extraction
Our ability to study and valorize the lignin fraction of biomass is hampered by the fundamental and still unmet challenge of precisely quantifying native lignin's structural features. Here, we developed a rapid elevated-temperature 1 H– 13 C Heteronuclear Single-Quantum Coherence Zero (HSQC 0 ) NMR method that enables this precise quantification of native lignin structural characteristics even with whole plant cell wall (WPCW) NMR spectroscopy, overcoming fast spin relaxation in the gel phase. We also formulated a Gaussian fitting algorithm to perform automatic and reliable spectral integration. By combining HSQC 0 measurements with yield measurements following depolymerisation, we can confirm the combinatorial nature of radical coupling reactions during biosynthesis leading to a random sequential organization of linkages within a largely linear lignin chain. Such analyses illustrate how this analytical method can greatly facilitate the study of native lignin structure, which can then be used for fundamental studies or to understand lignin depolymerization methods like reductive catalytic fractionation or aldehyde-assisted fractionation.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Quantification of Native Lignin Structural Features with Gel–Phase 2D–HSQC 0 Reveals Lignin Structural Changes During Extraction
Our ability to study and valorize the lignin fraction of biomass is hampered by the fundamental and still unmet challenge of precisely quantifying native lignin's structural features. Here, we developed a rapid elevated-temperature 1 H– 13 C Heteronuclear Single-Quantum Coherence Zero (HSQC 0 ) NMR method that enables this precise quantification of native lignin structural characteristics even with whole plant cell wall (WPCW) NMR spectroscopy, overcoming fast spin relaxation in the gel phase. We also formulated a Gaussian fitting algorithm to perform automatic and reliable spectral integration. By combining HSQC 0 measurements with yield measurements following depolymerisation, we can confirm the combinatorial nature of radical coupling reactions during biosynthesis leading to a random sequential organization of linkages within a largely linear lignin chain. Such analyses illustrate how this analytical method can greatly facilitate the study of native lignin structure, which can then be used for fundamental studies or to understand lignin depolymerization methods like reductive catalytic fractionation or aldehyde-assisted fractionation.
09 BIOMASS FUELS↗
Emigration and Survival of Hatchery‐Reared Coho Salmon Released as Parr and Smolts in a Reintroduction Program
ABSTRACT Releasing fish at varied life stages is an underutilized hatchery‐rearing practice. Columbia River Treaty tribes have been working to reintroduce extirpated Coho Salmon to historical habitats in upper watersheds. This effort has included the release of hatchery‐origin fish at both the parr and smolt life stages in the Yakima River Basin (Washington State USA), a tributary to the Columbia River. We evaluated releases of parr and smolts tagged with passive integrated transponders over 11 brood years. We assessed emigration timing, fish survival, and age‐at‐return for the two release groups. Emigrating juveniles released as smolts had higher survival and arrived downstream earlier than fish released as parr. Survival from release locations to adult return did not significantly differ for the two release groups. However, we observed a difference in apparent marine survival as fish released as parr had mean juvenile‐to‐adult return rates greater than fish released as smolts. Parr releases also tended to return at older age than smolt releases. Our results indicate that implementing practices to reduce homogenization of hatchery releases may produce survival and diversity benefits as fish mature to later life stages. Given the rapid ecosystem changes Pacific Salmon are experiencing throughout their life cycles, practices such as this may have increasing utility and import.
Bosch, William J. [Yakama Nation Fisheries Toppeni↗
Effects of Supplementation in Upper Yakima River Chinook Salmon
Abstract To promote recovery of natural salmonid populations, managers are utilizing hatchery supplementation programs to increase abundance of spawners on the spawning grounds. However, studies have provided evidence that captive breeding can result in domestication, demonstrated by lower fitness of hatchery‐origin compared with natural‐origin fish. Supplementation programs, therefore, typically use natural‐origin broodstock in an effort to minimize long‐term negative fitness impacts. Here we evaluated the upper Yakima River spring supplementation program for Chinook Salmon Oncorhynchus tshawytscha , which has broodstock comprised exclusively of unmarked fish presumed to be of natural‐origin. Using 5 years of spawner data, we tested for effects of hatchery breeding and rearing on total adult returns and their individual reproductive success when spawning naturally. Our study revealed that supplementation increased overall abundance of fish spawning naturally on the spawning grounds. However, on average, compared with natural‐origin spawners, hatchery‐origin fish had reduced reproductive success, which also translated to reduced reproductive success in three out of five return years for natural‐origin fish that spawned with hatchery‐origin fish. As expected, body length and return timing were also significant predictors of reproductive success. However, more generations of data are needed to establish the extent to which reduced reproductive success is passed on to naturally produced progeny.
Koch, Ilana J.↗
Effects of volitional emigration timing and smolt size on survival and age-at-return in a Pacific salmon hatchery population
Abstract Many Pacific salmon populations are returning from sea at younger ages and smaller sizes. Hatchery culture, management practices, and environmental factors influence juvenile release size and emigration timing, which in turn affect important demographic characteristics in returning adults. We analyzed data from approximately 345,000 tagged spring Chinook Salmon juveniles exiting Cle Elum Supplementation and Research Facility (Yakima River, Washington, USA) acclimation sites over thirteen brood years (2002–2014), evaluating smolt size, emigration timing, river flow, juvenile survival, and age-at-return. We observed a relationship between size and volitional exit timing of smolts from acclimation sites, with larger fish tending to emigrate earlier than smaller fish. Early emigration was also coincident with lower river flows near acclimation sites. Later emigration timing was correlated with an increase in apparent survival of juveniles to Bonneville Dam (500–530 km downstream of acclimation sites), but also with a lower rate of survival to return from sea. In general, for juveniles successfully emigrating downstream of Bonneville Dam, age-at-return increased with decreasing juvenile fish size and later emigration timing. Our results support a growing body of evidence that hatchery practices may result in larger smolts that tend to return at younger ages. Given the biological and economic consequences of younger age-at-maturation, methods to reverse this trend should be further explored and implemented.
Bosch, William J. (ORCID:0000000300447390)↗
Dissecting the Shared Genetic Architecture of Suicide Attempt, Psychiatric Disorders, and Known Risk Factors
Suicide is a leading cause of death worldwide, and non-fatal suicide attempts, which occur far more frequently, are a major source of disability and social and economic burden. Both have substantial genetic etiology, which is partially shared and partially distinct from that of related psychiatric disorders. Methods: We conducted a genome-wide association study (GWAS) of 29,782 suicide attempt (SA) cases and 519,961 controls in the International Suicide Genetics Consortium. The GWAS of SA was conditioned on psychiatric disorders using GWAS summary statistics via mtCOJO, to remove genetic effects on SA mediated by psychiatric disorders. We investigated the shared and divergent genetic architectures of SA, psychiatric disorders and other known risk factors. Results: Two loci reached genome-wide significance for SA: the major histocompatibility complex and an intergenic locus on chromosome 7, which remained associated with SA after conditioning on psychiatric disorders and replicated in an independent cohort from the Million Veteran Program. This locus has been implicated in risk-taking, smoking, and insomnia. SA showed strong genetic correlation with psychiatric disorders, particularly major depression, and also with smoking, pain, risk-taking, sleep disturbances, lower educational attainment, reproductive traits, lower socioeconomic status and poorer general health. After conditioning on psychiatric disorders, the genetic correlations between SA and psychiatric disorders decreased, whereas those with non-psychiatric traits remained largely unchanged. Conclusions: Our results identify a risk locus that contributes more strongly to SA than other phenotypes and suggest a shared underlying biology between SA and known risk factors that is not mediated by psychiatric disorders.
60 APPLIED LIFE SCIENCES↗
Monitoring agroecosystem productivity and phenology at a national scale: A metric assessment framework
Effective measurement of seasonal variations in the timing and amount of production is critical to managing spatially heterogeneous agroecosystems in a changing climate. Although numerous technologies for such measurements are available, their relationships to one another at a continental extent are unknown. Using data collected from across the Long-Term Agroecosystem Research (LTAR) network and other networks, we investigated correlations among key metrics representing primary production, phenology, and carbon fluxes in croplands, grazing lands, and crop-grazing integrated systems across the continental U.S. Metrics we examined included gross primary productivity (GPP) estimated from eddy covariance (EC) towers and modelled from the Landsat satellite, Landsat NDVI, and vegetation greenness (Green Chromatic Coordinate, GCC) from tower-mounted PhenoCams for 2017 and 2018. Overall, our analysis compared production dynamics estimated from three independent ground and remote platforms using data for 34 agricultural sites constituting 51 site-years of co-located time series. Pairwise sensor comparisons across all four metrics revealed stronger correlation and lower root mean square error (RMSE) between end of season (EOS) dates (Pearson R ranged from 0.6 to 0.7 and RMSE from 32.5 to 67.8) than start of season (SOS) dates (0.46 to 0.69 and 40.4 to 66.2). Overall, moderate to high correlations between SOS and EOS metrics complemented one another except at some lower productivity grazing land sites where estimating SOS can be challenging. Growing season length estimates derived from 16-day satellite GPP (179.1 days) were significantly longer than those from PhenoCam G CC (70.4 days, p adj < 0.0001) and EC GPP (79.6 days, p adj < 0.0001). Landscape heterogeneity did not explain differences in SOS and EOS estimates. Annual integrated estimates of productivity from EC GPP and PhenoCam G CC diverged from those estimated by Landsat GPP and NDVI at sites where annual production exceeds 1000 gC/m –2 yr –1 . Based on our results, we developed a “metric assessment framework” that articulates where and how metrics from satellite, eddy covariance and PhenoCams complement, diverge from, or are redundant with one another. The framework was designed to optimize instrumentation selection for monitoring, modeling, and forecasting ecosystem functioning with the ultimate goal of informing decision-making by land managers, policy-makers, and industry leaders working at multiple scales.
54 ENVIRONMENTAL SCIENCES↗
Supporting cost-effective watershed management strategies for Chesapeake Bay using a modeling and optimization framework
Extensive efforts to adaptively manage nutrient pollution rely on Chesapeake Bay Program’s (Phase 6) Watershed Model, called Chesapeake Assessment Scenario Tool (CAST), which helps decision-makers plan and track implementation of Best Management Practices (BMPs). We describe mathematical characteristics of CAST and develop a constrained nonlinear BMP-subset model, software, and visualization framework. This represents the first publicly available optimization framework for exploring least-cost strategies of pollutant load control for the United States’ largest estuary. The optimization identifies implementation options for a BMP subset modeled with load reduction effectiveness factors, and the web interface facilitates interactive exploration of >30,000 solutions organized by objective, nutrient control level, and for ~200 counties. We assess framework performance and demonstrate modeled cost improvements when comparing optimization-suggested proposals with proposals inspired by jurisdiction plans. Stakeholder feedback highlights the framework’s current utility for investigating cost-effective tradeoffs and its usefulness as a foundation for future analysis of restoration strategies.
54 ENVIRONMENTAL SCIENCES↗
Development of simplified model for injection rate prediction of diesel injectors during transient and steady operation
Determining the injection rate of the diesel injector during the transient short injection operations is a critical matter to enhance the combustion process by improving air/fuel mixture formation. In this regard, numerous injection models have been suggested in the literature to predict the injection rate accurately. However, such algorithms have not precisely predicted the rate of injection (ROI) in transient short injection events. In addition, most of those models require many input parameters to characterize hydraulic and mechanical subsystems in the injector, which can make them inconvenient to tune for different injector specifications, in other words not suitable for universal usage. Therefore, our study aims to develop a simple injection model that can predict injection rate precisely in the short and long injection durations considering relatively fewer input parameters. The model traces the pressure variation inside the sac based on the bulk modulus theory to predict nozzle exit velocity, thus the injection rate of the injector. In the algorithm, the bulk modulus of fuel (E) and discharge coefficients of the nozzle hole and needle seat (C d,H and C d,N ) have been considered to vary rather than set constant during the injection process since such flow parameters would have a critical impact on the flow development at the transient stage, thus affecting the injection rate of diesel injectors. Here with this modelling strategy, the accuracy of the new model on ROI prediction was confirmed with acceptable model error for both short and long injection durations by validating against experimental results. To understand the effect of the new model scheme on ROI prediction, ROI results with the new model have been discussed by comparing it with the ROI results predicted with constant flow parameters.
42 ENGINEERING↗
NRG Oncology/RTOG Consensus Guidelines for Delineation of Clinical Target Volume for Intensity Modulated Pelvic Radiation Therapy in Postoperative Treatment of Endometrial and Cervical Cancer: An Update
Accurate target definition is critical for the appropriate application of radiation therapy. In 2008, the Radiation Therapy Oncology Group (RTOG) published an international collaborative atlas to define the clinical target volume (CTV) for intensity modulated pelvic radiation therapy in the postoperative treatment of endometrial and cervical cancer. The current project is an updated consensus of CTV definitions, with removal of all references to bony landmarks and inclusion of the para-aortic and inferior obturator nodal regions.
62 RADIOLOGY AND NUCLEAR MEDICINE↗
Partial-Brain Radiation-Induced Microvascular Cognitive Impairment in Juvenile Murine Unilateral Hippocampal Synaptic Plasticity
Radiation-induced cognitive deficits have a severe negative impact on pediatric brain tumor patients. The severity of cognitive symptoms is related to the age of the child when radiation was applied, with the most severe effects seen in the youngest. Previous studies using whole-brain irradiation in mice confirmed these findings. To understand ipsilateral and contralateral changes in the hippocampus after partial-brain radiation therapy (PBRT) of the left hemisphere, we assessed the neuroplasticity and changes in the microvasculature of the irradiated and nonirradiated hippocampus in juvenile mice.
62 RADIOLOGY AND NUCLEAR MEDICINE↗
Synthesis of Na + -gated nanochannel membranes for the ammonia (NH 3 ) separation
Na + -gated nanochannel membranes were synthesized on α-Al 2 O 3 supports by secondary growth for ammonia (NH 3 ) separation from a mixture gas containing NH 3 , hydrogen (H 2 ) and nitrogen (N 2 ) at high temperature and pressure. Here, the effects of synthesis parameters (number of seeding steps, aging time, synthesis time, and Si/Al ratio) on membrane properties were investigated by characterization and gas permeation testing. Under the optimized condition (two-time seeding, 8 h aging time, 5 h synthesis time, and gel composition of 1.05 Al 2 O 3 : 5 SiO 2 : 50 Na 2 O: 100 H 2 O), the best membranes achieved NH 3 /H 2 and NH 3 /N 2 selectivities of 328 ± 60 and 1106 ± 207, respectively at 200 °C and 21 bar. Separation performance of the membrane was shown to be highly dependent on the permeances of N 2 and H 2 , which were greatly influenced by the membrane quality.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Grand Challenges and Opportunities in Stimulated Dynamic and Resonant Catalysis
Traditional heterogeneous catalysis is constrained by kinetic and thermodynamic limits, such as the Sabatier principle and reaction equilibrium. Dynamic and resonant catalysts hold promise to overcome these limitations by actively oscillating a catalyst’s physical or electronic structure at the time scale of the catalytic cycle, allowing programmable control over reaction pathways, and leading to improved rate and selectivity. External stimuli such as temperature swing, mechanical strain, electric charge, and light can perturb catalyst surfaces in different ways, altering adsorbate coverage, binding energies, and transition states beyond what steady-state catalysis allows. This work surveys the current state of dynamic catalysis, introduces the concept of “ stimulando ” characterization for observing transient dynamics, and outlines key modeling, mechanistic, and benchmarking strategies to advance the field toward improved chemical transformation.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Synergistic Multisites Fe 2 Mo 6 S 8 Electrocatalysts for Ambient Nitrogen Conversion to Ammonia
Electrochemical hydrogenation of N 2 under ambient conditions is attractive for sustainable and distributable NH 3 production but is limited by the lack of selective electrocatalysts. In this work, we describe active site motifs based on the Chevrel phase chalcogenide Fe 2 Mo 6 S 8 that exhibit intrinsic activities for converting N 2 to NH 3 in aqueous electrolytes. Despite having a very low specific surface area of ~2 m 2 /g, this catalyst exhibited a Faradaic efficiency of 12.5% and an average rate of 70 μg h –1 mg cat –1 for NH 3 production at -0.20 V vs RHE. Such activities were attributed to the unique composition and structure of Fe 2 Mo 6 S 8 that provide synergistic multisites for activating and associating key reaction intermediates. Specifically, Fe/Mo sites assist adsorption and activation of N 2 , whereas S sites stabilize hydrogen intermediate H ad * for N 2 hydrogenation. Fe in Fe 2 Mo 6 S 8 enhances binding of S with H ad * and thus inhibits the competing hydrogen evolution reaction. The spatial geometry of Fe, Mo, and S sites in Fe 2 Mo 6 S 8 promotes conversion of N 2 –H ad * association intermediates, reaching a turnover frequency of ~0.23 s –1 for NH 3 production.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗