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At least 451 records · Page 25

Population genomic analysis reveals differential evolutionary histories and patterns of diversity across subgenomes and subpopulations of Brassica napus L.

The allotetraploid species Brassica napus L. is a global crop of major economic importance, providing canola oil (seed) and vegetables for human consumption and fodder and meal for livestock feed. Characterizing the genetic diversity present in the extant germplasm pool of B. napus is fundamental to better conserve, manage and utilize the genetic resources of this species. We used sequence-based genotyping to identify and genotype 30,881 SNPs in a diversity panel of 782 B. napus accessions, representing samples of winter and spring growth habits originating from 33 countries across Europe, Asia, and America. We detected strong population structure broadly concordant with growth habit and geography, and identified three major genetic groups: spring (SP), winter Europe (WE), and winter Asia (WA). Subpopulation-specific polymorphism patterns suggest enriched genetic diversity within the WA group and a smaller effective breeding population for the SP group compared to WE. Interestingly, the two subgenomes of B. napus appear to have different geographic origins, with phylogenetic analysis placing WE and WA as basal clades for the other subpopulations in the C and A subgenomes, respectively. Finally, we identified 16 genomic regions where the patterns of diversity differed markedly from the genome-wide average, several of which are suggestive of genomic inversions. The results obtained in this study constitute a valuable resource for worldwide breeding efforts and the genetic dissection and prediction of complex B. napus traits.

58 GEOSCIENCES↗

Impact of Drought on Ecohydrology of Southern California Grassland and Shrubland

Abstract Through their rooting profiles and water demands, plants affect the distribution of water in the soil profile. Simultaneously, soil water content controls plant development and interactions within and between plant communities. These plant-soil water feedbacks might vary across plant communities with different rooting depths and species composition. In semiarid environments, understanding these differences will be essential to predict how ecosystems will respond to drought, which may become more frequent and severe with climate change. In this study, we tested how plant-soil water feedbacks responded to drought in two contrasting ecosystem types—grassland and shrubland—in the coastal foothills of southern California. During years 5–8 of an ongoing precipitation manipulation experiment, we measured changes in plant communities and soil moisture up to 2 m depth. We observed different water use patterns in grassland and shrubland communities with distinct plant functional types and water use strategies. Drought treatment did not affect perennial, deep-rooted shrubs because they could access deep soil water pools. However, mid-rooted shrubs were sensitive to drought and experienced decreased productivity and die-off. As a result, water content actually increased with drought at soil depths from 50–150 cm. In grassland, biomass production by annual species, including annual grasses and forbs, declined with drought, resulting in lower water uptake from the surface soil layer. An opportunistic “live fast, die young“ life strategy allowed these species to recover quickly once water availability increased. Our results show how drought interacts with plant community composition to affect the soil water balance of semiarid ecosystems, information that could be integrated into global scale models.

54 ENVIRONMENTAL SCIENCES↗

Zooming in on virtual commutes: Telecommuting impacts on mobility and sustainability

Motivated by a societal shift towards remote work and rapid advancement in information and communication technologies, this study examines the impact of telecommuting on urban mobility across the nine counties of the San Francisco Bay Area, California. Utilizing a behaviorally realistic integrated agent-based transportation model and recent data on telecommuting patterns, we simulate the impact of multiple telecommuting scenarios on transportation system outcomes. This provides a comprehensive picture of the impact of remote work on travel costs and accessibility of all travelers, factoring in changes in mode use and congestion. We analyze how telecommuting influences broader societal factors such as transportation energy consumption. Our findings indicate that increased telecommuting reduces overall person miles traveled and transportation energy consumption. Furthermore, telecommuting results in externality benefits by improving accessibility and reducing commute times for non-telecommuters.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Ab Initio Flexible Force Field for Metal–Organic Frameworks Using Dummy Model Coordination Bonds

We present force fields developed from periodic density functional theory (DFT) calculations that can be used in classical molecular simulations to model M–MOF-74 (M = Co, Fe, Mg, Mn, Ni, Zn) and its extended linker analogs. Our force fields are based on cationic dummy models (CDMs). These dummy models simplify the methodology required to tune the parameters and improve the accuracy of the force fields. We used our force fields to compare mechanical properties across the M–MOF-74 series and determine that increasing the size of the linker decreases the framework rigidity. In addition, we applied our force fields to an extended linker analog of Mg–MOF-74 and characterized the free energy of a previously reported deformation pattern in which the one-dimensional hexagonal channels of the framework become irregular. The free energy profiles confirm that the deformation is adsorbate induced and impossible to access solely by a pressure stimulus. On the basis of our results, we conclude that the force fields presented here and others that may be developed using our methodology are transferable across metal–organic framework series that share a metal center topology. Lastly, we believe that these force fields have the potential to be adapted for the study of complex problems in MOF chemistry, including defects and crystal growth, that have thus far been beyond the scope of classical molecular simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Ultrafast optical melting of trimer superstructure in layered 1T′-TaTe2

Abstract Quasi-two-dimensional transition-metal dichalcogenides are a key platform for exploring emergent nanoscale phenomena arising from complex interactions. Access to the underlying degrees-of-freedom on their natural time scales motivates the use of advanced ultrafast probes sensitive to self-organised atomic-scale patterns. Here, we report the ultrafast investigation of TaTe 2 , which exhibits unique charge and lattice trimer order characterised by a transition upon cooling from stripe-like chains into a (3 × 3) superstructure of trimer clusters. Utilising MeV-scale ultrafast electron diffraction, we capture the photo-induced TaTe 2 structural dynamics – exposing a rapid ≈ 1.4 ps melting of its low-temperature ordered state followed by recovery via thermalisation into a hot cluster superstructure. Density-functional calculations indicate that the initial quench is triggered by intra-trimer Ta charge transfer which destabilises the clusters, unlike melting of charge density waves in other TaX 2 compounds. Our work paves the way for further exploration and ultimately rapid optical and electronic manipulation of trimer superstructures.

36 MATERIALS SCIENCE↗

Selection of dietary protein and carbohydrate by rats: Changes with maturation

Weaning (21-day-old; 40-50 g) male rats given simultaneous access to foods, containing 18 percent casein and 15 or 70 percent carbohydrate (dextrin), tended to consume only 29-35 percent as much protein as carbohydrate (i.e., protein/carbohydrate ratios were 0.29-0.35). With maturation, when animals weighed 100 g or more, about half continued this pattern of nutrient choice, but the others abruptly began to consume considerably larger proportions of protein, exhibiting protein/carbohydrate ratios as high as 0.80-1.00. Each adult animal's protein/carbohydrate ratio tended to vary only slightly (s.e. = 3 percent of means). Adult protein/carbohydrate ratios were not correlated with fasting brain 5-HT or 5-HIAA levels. These marked differences among rats in eating behavior would not be observed when--as is usually the case--animals are given access to only one diet.

Yokogoshi, Hidehiko↗

HPC Campaign Management: Remote data access with user-defined error bound using ADIOS and ZFP

Remote access to large-scale scientific datasets, like those generated by combustion simulations or other high-performance computing (HPC) applications, presents a significant challenge. Downloading entire datasets is often impractical due to their size and the bandwidth limitations of typical networks. To address this challenge, we propose a novel approach that enables efficient remote access to large datasets distributed across multiple facilities. Our method enables technologies to download only the data values of a select variable, in a select region of interest, to a user-defined accuracy. For this purpose, we extended the ADIOS IO library to provide read functions with user-defined accuracy, a remote data server that understands multidimensional selections of specific variables, steps and accuracy from an ADIOS dataset, and which uses lossy compression on the remote site to reduce the data to be transferred back to the client. In addition, our extension of the ADIOS library collects metadata from multiple datasets in small files called Campaign Archives, which can be shared among project participants on any HPC, cloud or laptop, and which can easily facilitate the discovery of content and pointers to the data location as well as remote access to the data by local tools as if data was local. This feature called Campaign Management, enables a group of scientists to manage related datasets stored in multiple files, across multiple facilities as if it was in a single file/database. We demonstrate the effectiveness of our approach using a 1.5 TB dataset from the S3D combustion simulation on Frontier at the Oak Ridge Leadership Facility. Even a single variable from this dataset, at 64 GB, is too large to be processed on a standard laptop. We show two different reading patterns for 2D plots and 3D visualization, with careful settings that a scientist studying combustion data would do and show that running the same Python scripts on Frontier directly takes comparable time than running them on the local laptop with remote access to the data on Frontier.

Podhorszki, Norbert [ORNL] (ORCID:000000019647542X↗

Cancer Incidence Trends in Successive Social Generations in the US

Importance: The incidence of some cancers in the US is increasing in younger age groups, but underlying trends in cancer patterns by birth year remain unclear. Objective: To estimate cancer incidence trends in successive social generations. Design, Setting, and Participants: In this cohort study, incident invasive cancers were ascertained from the Surveillance, Epidemiology, and End Results (SEER) program’s 13-registry database (November 2020 submission, accessed August 14, 2023). Invasive cancers diagnosed at ages 35 to 84 years during 1992 to 2018 within 152 strata were defined by cancer site, sex, and race and ethnicity. Exposure: Invasive cancer. Main Outcome and Measures: Stratum-specific semiparametric age-period-cohort (SAGE) models were fitted and incidence per 100 000 person-years at the reference age of 60 years was calculated for single-year birth cohorts from 1908 through 1983 (fitted cohort patterns [FCPs]). The FCPs and FCP incidence rate ratios (IRRs) were compared by site for Generation X (born between 1965 and 1980) and Baby Boomers (born between 1946 and 1964). Results: A total of 3.8 million individuals with invasive cancer (51.0% male; 8.6% Asian or Pacific Islander, 9.5% Hispanic, 10.4% non-Hispanic Black, and 71.5% non-Hispanic White) were included in the analysis. In Generation X vs Baby Boomers, FCP IRRs among women increased significantly for thyroid (2.76; 95% CI, 2.41-3.15), kidney (1.99; 95% CI, 1.70-2.32), rectal (1.84; 95% CI, 1.52-2.22), corpus uterine (1.75; 95% CI, 1.40-2.18), colon (1.56; 95% CI, 1.27-1.92), and pancreatic (1.39; 95% CI, 1.07-1.80) cancers; non-Hodgkins lymphoma (1.40; 95% CI, 1.08-1.82); and leukemia (1.27; 95% CI, 1.03-1.58). Among men, IRRs increased for thyroid (2.16; 95% CI, 1.87-2.50), kidney (2.14; 95% CI, 1.86-2.46), rectal (1.80; 95% CI, 1.52-2.12), colon (1.60; 95% CI, 1.32-1.94), and prostate (1.25; 95% CI, 1.03-1.52) cancers and leukemia (1.34; 95% CI, 1.08-1.66). Lung (IRR, 0.60; 95% CI, 0.50-0.72) and cervical (IRR, 0.71; 95% CI, 0.57-0.89) cancer incidence decreased among women, and lung (IRR, 0.51; 95% CI, 0.43-0.60), liver (IRR, 0.76; 95% CI, 0.63-0.91), and gallbladder (IRR, 0.85; 95% CI, 0.72-1.00) cancer and non-Hodgkins lymphoma (IRR, 0.75; 95% CI, 0.61-0.93) incidence decreased among men. For all cancers combined, FCPs were higher in Generation X than for Baby Boomers because gaining cancers numerically overtook falling cancers in all groups except Asian or Pacific Islander men. Conclusions and Relevance: In this model-based cohort analysis of incident invasive cancer in the general population, decreases in lung and cervical cancers in Generation X may be offset by gains at other sites. Generation X may be experiencing larger per-capita increases in the incidence of leading cancers than any prior generation born in 1908 through 1964. On current trajectories, cancer incidence could remain high for decades.

60 APPLIED LIFE SCIENCES↗

Author Correction: A universal language for finding mass spectrometry data patterns

Correction to: Nature Methodshttps://doi.org/10.1038/s41592-025-02660-z, published online 12 May 2025. This article was originally published under standard Springer Nature license (© The Author(s), under exclusive licence to Springer Nature America, Inc.). It is now available as an open-access paper under a Creative Commons Attribution 4.0 International license, © The Author(s). The error has been corrected in the HTML and PDF versions of the article.

Damiani, Tito↗

How cell wall complexity influences saccharification efficiency in Miscanthus sinensis

The production of bioenergy from grasses has been developing quickly during the last decade, with Miscanthus being among the most important choices for production of bioethanol. However, one of the key barriers to producing bioethanol is the lack of information about cell wall structure. Cell walls are thought to display compositional differences that lead to emergence of a very high level of complexity, resulting in great diversity in cell wall architectures. In this work, a set of different techniques was used to access the complexity of cell walls of different genotypes of Miscanthus sinensis in order to understand how they interfere with saccharification efficiency. Three genotypes of M. sinensis displaying different patterns of correlation between lignin content and saccharification efficiency were subjected to cell wall analysis by quantitative/qualitative analytical techniques such as monosaccharide composition, oligosaccharide profiling, and glycome profiling. When saccharification efficiency was correlated negatively with lignin, the structural features of arabinoxylan and xyloglucan were found to contribute positively to hydrolysis. In the absence of such correlation, different types of pectins, and some mannans contributed to saccharification efficiency. In conclusion, different genotypes of M. sinensis were shown to display distinct interactions among their cell wall components, which seem to influence cell wall hydrolysis.

09 BIOMASS FUELS↗

Clustering and statistical analyses of air-conditioning intensity and use patterns in residential buildings

Energy conservation in residential buildings has gained increased attention due to its large portion of global energy use and potential of energy savings. Occupant behavior has been recognized as a key factor influencing the energy use and load diversity in buildings, therefore more realistic and accurate air-conditioning (AC) operating schedules are imperative for load estimation in equipment design and operation optimization. With the development of sensor technology, it became easier to access an increasing amount of heating/cooling data from thermal energy metering systems in residential buildings, which provides another possible way to understand building energy usage and occupant behaviors. However, except for cooling energy consumption benchmarking, there currently lacks effective and easy approaches to analyze AC usage and provide actionable insights for occupants. To fill this gap, this study proposes clustering analysis to identify AC use patterns of residential buildings, and develops new key performance indicators (KPIs) and data analytics to explore the AC operation characteristics using the long-term metered cooling energy use data, which is of great importance for inhabitants to understand their thermal energy use and save energy cost through adjustment of their AC use behavior. We demonstrate the proposed approaches in a residential district comprising 300 apartments, located in Zhengzhou, China. Main outcomes include: Representative AC use patterns are developed for three room types of residential buildings in the cold climate zone of China, which can be used as more realistic AC schedules to improve accuracy of energy simulation; Distributions of KPIs on household cooling energy usage are established, which can be used for household AC use intensity benchmarking and performance diagnoses.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Fluorescence In Situ mRNA Hybridization for Gene Expression Detection in a Wood Decay Fungus

Wood-degrading fungi efficiently decompose wood using a series of steps that are regulated across time and space. RNA sequencing with “bulk” sampling method has indicated processes controlled at the transcription level at different decay stages and locations along hyphal networks. To further understand these regulatory mechanisms, a high-resolution technique for gene expression determination is required. In this work, Fluorescence In Situ Hybridization (FISH) of mRNA was tested and optimized in the ‘brown rot’-type (carbohydrate-selective; lignin-rich residues) model fungus Postia (Rhodonia) placenta to image gene expression at the hyphal scale, <10 micrometers. The mRNA of one housekeeping gene Tef1a and three wood-decaying genes Cel28a, Cel5b and Qrd1 were tested in hyphae grown in liquid nutrients and wood substrate. The 20 bp-long DNA probes were successfully delivered intracellularly to give sufficient hybridization signal for imaging. Ahead of hybridization, permeabilization by lyticase and proteinase K treatments proved to be the critical step to increase probe and mRNA accessibility. Tyramide signal amplification was used after hybridization to enhance signal. This gave qualitative measures of mRNA of the four target genes, which were generally in line with previous expression patterns generated from coarser-scale RNA-seq and qRT-PCR studies. These techniques were not without challenges, and future optimization using multiple probe fragments for each mRNA molecule is proposed.

Brown rot fungi, decomposition, FISH, gene express↗

Direct Laser Writing Crystal Polymorphs of Organic Semiconductors for Phase Change Electronics

The many diverse polymorphic behaviors observed in organic electronic materials offer opportunities to modulate electronic properties through reversibly switching crystal structures. Here, we access the prolific polymorphism observed in two-dimensional quinoidal terthiophene via laser writing to locally heat and direct the phase transitions. We access a metastable polymorph IV through rapid cooling and observe distinct symmetry as well as packing through grazing incidence X-ray diffraction (GIXD). Using our open-source PolyChemPrint patterning platform, we direct laser heating to initiate the IV-I transition, switching the conductance by >2 orders of magnitude. Here, this is confirmed via a combination of GIXD and Raman spectroscopy. Finally, we demonstrate switching of transistor devices as well as discrete tuning of conductance via laser writing.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Comparative Uptake Patterns of Radioactive Iodine and [18F]-Fluorodeoxyglucose (FDG) in Metastatic Differentiated Thyroid Cancers

Background: Metastatic differentiated thyroid cancer (DTC) represents a molecularly heterogeneous group of cancers with varying radioactive iodine (RAI) and [ 18 F]-fluorodeoxyglucose (FDG) uptake patterns potentially correlated with the degree of de-differentiation through the so-called “flip-flop” phenomenon. However, it is unknown if RAI and FDG uptake patterns correlate with molecular status or metastatic site. Materials and Methods: A retrospective analysis of metastatic DTC patients (n = 46) with radioactive 131-iodine whole body scan (WBS) and FDG-PET imaging between 2008 and 2022 was performed. The inclusion criteria included accessible FDG-PET and WBS studies within 1 year of each other. Studies were interpreted by two blinded radiologists for iodine or FDG uptake in extrathyroidal sites including lungs, lymph nodes, and bone. Cases were stratified by BRAF V600E mutation status, histology, and a combination of tumor genotype and histology. The data were analyzed by McNemar’s Chi-square test. Results: Lung metastasis FDG uptake was significantly more common than iodine uptake (WBS: 52%, FDG: 84%, p = 0.04), but no significant differences were found for lymph or bone metastases. Lung metastasis FDG uptake was significantly more prevalent in the papillary pattern sub-cohort (WBS: 37%, FDG: 89%, p = 0.02) than the follicular pattern sub-cohort (WBS: 75%, FDG: 75%, p = 1.00). Similarly, BRAF V600E+ tumors with lung metastases also demonstrated a preponderance of FDG uptake (WBS: 29%, FDG: 93%, p = 0.02) than BRAF V600E- tumors (WBS: 83%, FDG: 83%, p = 1.00) with lung metastases. Papillary histology featured higher FDG uptake in lung metastasis (WBS: 39%, FDG: 89%, p = 0.03) compared with follicular histology (WBS: 69%, FDG: 77%, p = 1.00). Patients with papillary pattern disease, BRAF V600E+ mutation, or papillary histology had reduced agreement between both modalities in uptake at all metastatic sites compared with those with follicular pattern disease, BRAF V600E- mutation, or follicular histology. Low agreement in lymph node uptake was observed in all patients irrespective of molecular status or histology. Conclusions: The pattern of FDG-PET and radioiodine uptake is dependent on molecular status and metastatic site, with those with papillary histology or BRAF V600E+ mutation featuring increased FDG uptake in distant metastasis. Further study with an expanded cohort may identify which patients may benefit from specific imaging modalities to recognize and surveil metastases.

60 APPLIED LIFE SCIENCES↗

Influence of substitution pattern on the dynamics of internal conversion and intersystem crossing in thiopyridone isomers

We report a combined experimental and theoretical investigation of the ultrafast internal conversion (IC) and intersystem crossing (ISC) dynamics of two thiopyridone (TP) isomers in solution. Our study used ultrafast transient X-ray absorption spectroscopy (XAS) at the sulfur K-edge, in conjunction with electronic excited state surface hopping molecular dynamics and simulations of the excited state XAS, to investigate the impact of the functional group substitution pattern and solvent on the dynamics of IC and ISC. The combination of the localized X-ray probe and the simulation results enables, in part, the differentiation between ππ* and nπ* character excited states, as well as singlet and triplet states. Access to nπ* character excitations has particular value since they often prove challenging to assess with optical spectroscopy. For 2-TP, the photoexcited S 2 (ππ*) state rapidly undergoes IC to the S 1 (nπ*) state below the instrument response time, followed by ISC to the T 1 (ππ*) state on a timescale of 600 fs in acetonitrile. For 4-TP, the timescale of S 2 to S 1 IC increases to 330 fs and the timescale of ISC increases to more than 10 ps. The differences between isomers are rationalized by considering the key role of the, nπ* intermediates in mediating the intersystem crossing of these systems. Varying the substitution pattern of the molecule can stabilize or destabilize these intermediates leading to the increase in ISC rate in the ortho isomer as compared to the para isomer, while changing the solvent from acetonitrile to water had minimal effect on the electronic excited state relaxation mechanism.

Garratt, Douglas [SLAC National Accelerator Labora↗

Influence of substrate quality on structural properties of AlGaN/GaN superlattices grown by molecular beam epitaxy

Short-period AlGaN/GaN superlattices were established as versatile test structures to investigate the structural properties of molecular beam epitaxy (MBE)-grown GaN and AlGaN layers and their dependence on the GaN substrate quality. X-ray diffractometry data of the investigated superlattices allow access to relevant structural parameters such as aluminum mole fraction and layer thicknesses. The occurrence of theoretically predicted intense high-order satellite peaks and pronounced interface fringes in the diffraction pattern reflects abrupt interfaces and perfect 2-dimensional growth resulting in smooth surfaces. The data unambiguously demonstrate that the structural quality of the MBE grown layers is limited by the structural properties of the GaN substrate.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Damsel: A Data Model Storage Library for Exascale Science

Computational science applications have been described as having one of seven motifs (the “seven dwarfs”), each having a particular pattern of computation and communication. From a storage and I/O perspective, these applications can also be grouped into a number of data model motifs describing the way data is organized and accessed during simulation, analysis, and visualization. Major storage data models developed in the 1990s, such as Network Common Data Format (netCDF) and Hierarchical Data Format (HDF) projects, created support for more complex data models. Development of both netCDF and HDF5 was influenced by multi-dimensional dataset storage requirements, but their access models and formats were designed with sequential storage in mind (e.g., a POSIX I/O model). Although these and other high-level I/O libraries have had a beneficial impact on large parallel applications, they do not always attain a high percentage of peak I/O performance due to fundamental design limitations, and they do not address the full range of current and future computational science data models. The goal of this project is to enable exascale computational science applications to interact conveniently and efficiently with storage through abstractions that match their data models. The project consists of three major activities: (1) identifying major data model motifs in computational science applications and developing representative benchmarks; (2) developing a data model storage library, called Damsel, that supports these motifs, provides efficient storage data layouts, incorporates optimizations to enable exascale operation, and is tolerant to failures; and (3) productizing Damsel and working with computational scientists to encourage adoption of this library by the scientific community. The product of this project, Damsel library, is openly available for download from http://cucis.ece.northwestern.edu/projects/DAMSEL. Several case studies and application programming interface reference are also available to assist new users to learn to use the library.

97 MATHEMATICS AND COMPUTING↗

Bubble domain technology for spacecraft onboard memory

Bubble device technologies for spacecraft onboard memory offer improved reliability and memory functional characteristics. Recent advances include Permalloy gap devices (commercially available) whose improved performance and higher density are attributable to an asymmetric chevron pattern. Secondly, an order of magnitude increase in density at less power than the Permalloy technology is possible with the ion implant technology. A third technology, the self-structured current access system, offers another order of magnitude improvement in density and data rate, and is being studied. Capacity estimates for Permalloy gap, ion implant, and self-structured current access systems are, respectively, 10 to the 8th, 10 to the 9th, and 10 to the 10th bits, and power per unit data rate efficiencies are 140, 60, and 2 W/Mbps. A flexible modular organization system, compatible with all of these device technologies, is analyzed, and, as the system is contained in a bubble, relatively simple retrofitting is foreseen.

Hayes, P. J.↗