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At least 361 records · Page 20

Making Corgis Important for Honeycomb Classification: Adversarial Attacks on Concept-based Explainability Tools

Methods for model explainability have become increasingly critical for testing the fairness and soundness of deep learning. Concept-based interpretability techniques, which use a small set of human-interpretable concept exemplars in order to measure the influence of a concept on a model's internal representation of input, are an important thread in this line of research. In this work we show that these explainability methods can suffer the same vulnerability to adversarial attacks as the models they are meant to analyze. We demonstrate this phenomenon on two well-known concept-based interpretability methods: TCAV and faceted feature visualization. We show that by leveraging the geometry of the problem and carefully perturbing the examples of the concept that is being investigated, we can radically change the output of the interpretability method. The attacks that we propose can either induce positive interpretations (polka dots are an important concept for a model when classifying zebras) or negative interpretations (stripes are not an important factor in identifying images of a zebra). Our work highlights the fact that in safety-critical applications, there is need for security around not only the machine learning pipeline but also the model interpretation process.

Brown, Davis R.↗

Thermomechanical Degradation of Sintered Copper Under High-Temperature Thermal Shock

The need for reliable bonded interface materials is critical to realize the performance benefits of wide-bandgap devices in power electronics modules, especially in operating temperatures greater than 150 degrees C. In this paper, we investigate the thermomechanical performance of sintered copper (Cu) as a large-area attachment, bonded between Cu baseplates and active-metal-bonded substrates, under accelerated thermal shock (-40 degrees C to 200 degrees C) conditions. In the fabrication phase of the samples, we used different stencil patterns and found that the grid and stripe patterns resulted in a better outgassing of the residual organics during the sintering process, thereby ensuring a substantially improved bond quality compared to a full-area print. The paste consisted of Cu microflakes, and we performed sintering using a Budatec SP300 sintering press at 275 degrees C with 15 MPa of bonding pressure for 5 minutes in a nitrogen atmosphere. Under accelerated experiments, we monitored the degradation of the sintered Cu bond in the samples through C-mode scanning acoustic microscope (C-SAM) images. To quantify the defect percentage in C-SAM images, we investigated image denoising techniques to exclude the pattern prints. Finally, we cross-sectioned a sample and obtained scanning electron microscope images, which revealed adhesive fracture as the dominant failure mechanism.

ADVANCED PROPULSION SYSTEMS,INORGANIC, ORGANIC, PH↗

An FPGA-Based Neuromorphic Processor with All-to-All Connectivity

Neuromorphic computing is a promising paradigm for future energy-efficient computing. At present, however, it is in its nascent stages—most hardware implementations are research-grade, commercial products are not available, and the software tools are not production-ready. The lack of hardware and software tools makes neuromorphic computing inaccessible to researchers around the globe. To this extent, we intend to build a low-cost, open-source, FPGA-based digital neuromorphic processor that can be used by researchers worldwide. In this paper, we present a preliminary implementation of the processor on a Xilinx Artix-7 FPGA using SystemVerilog. Our implementation supports the integrate-and-fire neuron with two parameters each for neurons and synapses. It also features all-to-all connectivity among neurons on the hardware. We test our implementation on four cases: bars and stripes datasets, shortest path algorithm, logic gates, and 8-3 encoder. We also perform a scalability study to understand the resource utilization of the FPGA as the number of all-to-all connected neurons increases. With our implementation, the Artix- 7 supports 65 neurons with all-to-all connectivity. Moreover, all the test cases mentioned above achieve 100% accuracy.

Maheshwari, Disha↗

Harnessing Chemical Short‐Range Disorder to Improve Lithium Retention in Epitaxial LLTO Solid‐Electrolyte Thin Films

Lithium lanthanum titanate Li 3x La 2/3-x TiO 3 (LLTO) is a promising perovskite-based solid-state electrolyte for next-generation lithium-ion batteries, but controlling crystallinity and Li stoichiometry in thin-film form is challenging because high growth temperatures are required to achieve good crystallinity while Li remains strongly volatile. Here, we systematically investigate the effect of substrate temperature on epitaxial LLTO thin films grown by pulsed laser deposition. We identify a narrow growth window (750–800°C) in which LLTO films grow as c-axis oriented with atomically flat surfaces. Lower growth temperatures (<750°C) stabilize laterally extended, chemically disordered stripe domains that coexist with ordered LLTO regions, whereas higher temperatures (≥825°C) suppress these defects but promote island morphologies and Al/Ti interdiffusion. While spectroscopy measurements show that Ti remains in the 4+ oxidation state and Li is globally deficient for all films, our depth-resolved time-of-flight secondary ion mass spectrometry studies reveal that the 700°C film retains the highest Li content across its thickness. These results clarify how growth temperature controls crystallinity, chemical short-range disorder, and Li retention, and highlight moderate growth temperatures (∼700°C) as a route to mitigate Li loss in epitaxial solid-electrolyte films.

chemical short-range disorder↗

Local adaptation of both plant and pathogen: an arms‐race compromise in switchgrass rust

In coevolving species, parasites locally adapt to host populations as hosts locally adapt to resist parasites. Parasites often outpace host local adaptation since they have rapid life cycles, but host diversity, the strength of selection, and external environmental influence can result in complex outcomes. To better understand local adaptation in host–parasite systems, we examined locally adapted switchgrass (Panicum virgatum), and its leaf rust pathogen (Puccinia novopanici) across a latitudinal range in North America. We grew switchgrass genotypes in 10 replicated multiyear common gardens, measuring rust severity from natural infection in a ‘host reciprocal transplant’ framework for testing local adaptation. We conducted genome-wide association mapping to identify genetic loci associated with rust severity. Genetically differentiated rust populations were locally adapted to northern and southern switchgrass, despite host local adaptation to environmental conditions in the same regions. Rust resistance was polygenic, and distinct loci were associated with rust severity in the north and south. We narrowed a previously identified large-effect quantitative trait locus for rust severity to a candidate YELLOW STRIPE-LIKE gene and linked numerous other loci to defense-related genes. Overall, our results suggest that both hosts and parasites can be simultaneously locally adapted, especially when parasites impose less selection than other environmental factors.

59 BASIC BIOLOGICAL SCIENCES↗

Rapid and efficient in planta genome editing in sorghum using foxtail mosaic virus‐mediated sgRNA delivery

SUMMARY The requirement of in vitro tissue culture for the delivery of gene editing reagents limits the application of gene editing to commercially relevant varieties of many crop species. To overcome this bottleneck, plant RNA viruses have been deployed as versatile tools for in planta delivery of recombinant RNA. Viral delivery of single‐guide RNAs (sgRNAs) to transgenic plants that stably express CRISPR‐associated (Cas) endonuclease has been successfully used for targeted mutagenesis in several dicotyledonous and few monocotyledonous plants. Progress with this approach in monocotyledonous plants is limited so far by the availability of effective viral vectors. We engineered a set of foxtail mosaic virus (FoMV) and barley stripe mosaic virus (BSMV) vectors to deliver the fluorescent protein AmCyan to track viral infection and movement in Sorghum bicolor . We further used these viruses to deliver and express sgRNAs to Cas9 and Green Fluorescent Protein (GFP) expressing transgenic sorghum lines, targeting Phytoene desaturase ( PDS ), Magnesium‐chelatase subunit I ( MgCh ), 4‐hydroxy‐3‐methylbut‐2‐enyl diphosphate reductase , orthologs of maize Lemon white1 ( Lw1 ) or GFP . The recombinant BSMV did neither infect sorghum nor deliver or express AmCyan and sgRNAs. In contrast, the recombinant FoMV systemically spread throughout sorghum plants and induced somatic mutations with frequencies reaching up to 60%. This mutagenesis led to visible phenotypic changes, demonstrating the potential of FoMV for in planta gene editing and functional genomics studies in sorghum.

54 ENVIRONMENTAL SCIENCES↗

Two-dimensional superconductivity and anisotropic transport at KTaO 3 (111) interfaces

The distinctive electronic structure found at interfaces between materials can allow unconventional quantum states to emerge. Here we report on the discovery of superconductivity in electron gases formed at interfaces between (111)-oriented KTaO 3 and insulating overlayers of either EuO or LaAlO 3 . The superconducting transition temperature, as high as 2.2 kelvin, is about one order of magnitude higher than that of the LaAlO 3 /SrTiO 3 system. Notably, similar electron gases at KTaO 3 (001) interfaces remain normal down to 25 millikelvin. The critical field and current-voltage measurements indicate that the superconductivity is two-dimensional. In EuO/KTaO 3 (111) samples, a spontaneous in-plane transport anisotropy is observed before the onset of superconductivity, suggesting the emergence of a distinct “stripe”-like phase, which is also revealed near the critical field.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Atomic-scale visualization of topological spin textures in the chiral magnet MnGe

Peeking into magnetic textures Topological spin textures hold promise as robust carriers of information and have been observed in bulk materials with a specific crystal structure. One of these materials, manganese germanide (MnGe), exhibits unusual textures in bulk form. Repicky et al . used spin-polarized scanning tunneling microscopy to study surface magnetism in thin films of MnGe. Achieving high spatial resolution, the researchers observed stripe-like features consistent with a helical state. In regions where the film was slightly curved due to strain, the intersection of domain walls led to characteristic closed patterns that could be manipulated with current/voltage pulses. —JS

Science & Technology - Other Topics↗

Ordered and disordered skyrmion states on a square substrate

We examine the ordering of skyrmions interacting with a square substrate created from a modulation of anisotropy using atomistic simulations. We consider fillings of ƒ = 1.5, 2.0, 2.5, 3.0, and 3.5 skyrmions per potential minimum as a function of magnetic field and sample size. For a filling of ƒ = 2.0, we find various dimer orderings, such as tilted dimer states, as well as antiferromagnetic ordering that is similar to the colloidal dimer ordering seen on square substrates. Furthermore, the ability of the skyrmions to change shape or annihilate produces additional states that do not occur in the colloidal systems. For certain parameters at ƒ = 2.0, half of the skyrmions can annihilate to form a square lattice, or a superlattice of trimers and monomers containing skyrmions of different sizes can form. At lower fields, ordered stretched skyrmion states can appear, and for zero field, there can be ordered stripe states. For ƒ = 3.0, we find ferromagnetic ordered trimers, tilted lattices, columnar lattices, and stretched phases. For fillings of ƒ = 1.5 and 2.5, we find bipartite lattices, different ordered and disordered states, and several extended disordered regions produced by frustration effects.

36 MATERIALS SCIENCE↗

BSMV-mediated genome editing exhibits host-specific heritability: germline transmission in barley and somatic edits in Nicotiana benthamiana

Plant RNA virus–mediated guide RNA (gRNA) delivery represents a transformative advance in genome editing technologies. Unlike conventional transformation methods that rely on labor-intensive tissue culture and regeneration for each individual gRNA delivery, viral vectors can rapidly and systemically transmit gRNAs into pre-established Cas-expressing plants, providing an accelerated route for functional genomics and trait discovery directly in planta . However, key design parameters, including subgenomic promoter choice, transcript architecture, and their effects on viral fitness and editing outcomes, remain to be elucidated for most viral platforms. We developed five Barley stripe mosaic virus (BSMV) vectors, each with distinct subgenomic promoter elements to drive single gRNA expression. These were initially evaluated in Cas9-expressing transgenic Nicotiana benthamiana plants targeting the Phytoene desaturase ( PDS ) gene to compare their editing efficiencies. Single gRNAs expressed under the duplicated γb subgenomic promoter or when fused directly to the γb genome achieved the highest mutation frequencies (up to 90% at 60 days post-inoculation), whereas β1- and β2-driven sgRNAs produced delayed and reduced editing. Thus, promoter selection critically determines gRNA accumulation and the efficacy of BSMV-mediated genome editing. The top-performing design was then applied to Cas9-expressing barley ( Hordeum vulgare ) targeting HvCMF7 (conferring green-white variegation) and HvGW2.1 (impacts grain width and weight). BSMV spread systemically throughout barley, inducing somatic and heritable mutations at frequencies up to 100%, with virus-free edited progeny. In contrast, despite robust somatic editing in N. benthamiana, no heritable mutations were detected indicating species-dependent limitations in germline transmission. Our systematic comparison of subgenomic promoter architectures establishes clear design principles for optimizing viral vector–mediated delivery. Promoter choice and transcript structure critically shape editing efficiency and viral stability. The host-specific boundary for germline editing, defined by efficient heritable editing in barley but not N. benthamiana , highlights where BSMV offers advantages and where alternative vectors or hybrid strategies are required, guiding rational platform selection for diverse crop species and applications. Collectively, these findings establish BSMV as a promising next-generation vector for rapid, tissue culture–free, and transformation-independent genome editing in cereals and other recalcitrant monocots.

barley↗

Transformation and gene editing in the bioenergy grass Miscanthus

Miscanthus, a C4 member of Poaceae, is a promising perennial crop for bioenergy, renewable bioproducts, and carbon sequestration. Species of interest include nothospecies M. x giganteus and its parental species M. sacchariflorus and M. sinensis. Use of biotechnology-based procedures to genetically improve Miscanthus, to date, have only included plant transformation procedures for introduction of exogenous genes into the host genome at random, non-targeted sites. We developed gene editing procedures for Miscanthus using CRISPR/Cas9 that enabled the mutation of a specific (targeted) endogenous gene to knock out its function. Classified as paleo-allopolyploids (duplicated ancient Sorghum-like DNA plus chromosome fusion event), design of guide RNAs (gRNAs) for Miscanthus needed to target both homeologs and their alleles to account for functional redundancy. Prior research in Zea mays demonstrated that editing the lemon white1 (lw1) gene, involved in chlorophyll and carotenoid biosynthesis, via CRISPR/Cas9 yielded pale green/yellow, striped or white leaf phenotypes making lw1 a promising target for visual confirmation of editing in other species. Using sequence information from both Miscanthus and sorghum, orthologs of maize lw1 were identified; a multi-step screening approach was used to select three gRNAs that could target homeologs of lw1. Embryogenic calli of M. sacchariflorus, M. sinensis and M. x giganteus were transformed via particle bombardment (biolistics) or Agrobacterium tumefaciens introducing the Cas9 gene and three gRNAs to edit lw1. Leaves on edited Miscanthus plants displayed the same phenotypes noted in maize. Sanger sequencing confirmed editing; deletions in lw1 ranged from 1 to 26 bp in length, and one deletion (433 bp) encompassed two target sites. Confocal microscopy verified lack of autofluorescence (chlorophyll) in edited leaves/sectors. We developed procedures for gene editing via CRISPR/Cas9 in Miscanthus and, to the best of our knowledge, are the first to do so. This included five genotypes representing three Miscanthus species. Designed gRNAs targeted all copies of lw1 (homeologous copies and their alleles); results also confirmed lw1 made a good editing target in species other than Z. mays. The ability to target specific loci to enable endogenous gene editing presents a new avenue for genetic improvement of this important biomass crop.

09 BIOMASS FUELS↗

Pattern formation and transport for externally driven active matter on periodic substrates (a)

Abstract We investigate the transport of interacting active run-and-tumble particles moving under an external drift force through a periodic array of obstacles for increasing drive amplitudes. For high activity where the system forms a motility-induced phase-separated state, there are several distinct dynamic phases including a low drive pinned cluster phase, an intermediate uniform fluid, and a higher drive stripe crystal state. The transitions between the phases are correlated with signatures in the transport curves, differential mobility, and power spectra of the velocity fluctuations. In contrast, in the low activity regime the transport curves and power spectra undergo little change as a function of drive. We argue that in the high activity limit, the behavior is similar to that of driven solids on periodic substrates, while in the low activity limit the system behaves like a driven fluid.

36 MATERIALS SCIENCE↗

Advancing stem cell technologies for conservation of wildlife biodiversity

ABSTRACT Wildlife biodiversity is essential for healthy, resilient and sustainable ecosystems. For biologists, this diversity also represents a treasure trove of genetic, molecular and developmental mechanisms that deepen our understanding of the origins and rules of life. However, the rapid decline in biodiversity reported recently foreshadows a potentially catastrophic collapse of many important ecosystems and the associated irreversible loss of many forms of life on our planet. Immediate action by conservationists of all stripes is required to avert this disaster. In this Spotlight, we draw together insights and proposals discussed at a recent workshop hosted by Revive & Restore, which gathered experts to discuss how stem cell technologies can support traditional conservation techniques and help protect animal biodiversity. We discuss reprogramming, in vitro gametogenesis, disease modelling and embryo modelling, and we highlight the prospects for leveraging stem cell technologies beyond mammalian species.

Developmental Biology↗

Data for Rapid and Efficient in planta Genome Editing in Sorghum Using Foxtail Mosaic Virus-mediated sgRNA Delivery

The requirement of in vitro tissue culture for the delivery of gene editing reagents limits the application of gene editing to commercially relevant varieties of many crop species. To overcome this bottleneck, plant RNA viruses have been deployed as versatile tools for in planta delivery of recombinant RNA. Viral delivery of single-guide RNAs (sgRNAs) to transgenic plants that stably express CRISPR-associated (Cas) endonuclease has been successfully used for targeted mutagenesis in several dicotyledonous and few monocotyledonous plants. Progress with this approach in monocotyledonous plants is limited so far by the availability of effective viral vectors. We engineered a set of foxtail mosaic virus (FoMV) and barley stripe mosaic virus (BSMV) vectors to deliver the fluorescent protein AmCyan to track viral infection and movement in Sorghum bicolor . We further used these viruses to deliver and express sgRNAs to Cas9 and Green Fluorescent Protein (GFP) expressing transgenic sorghum lines, targeting Phytoene desaturase (PDS), Magnesium-chelatase subunit I (MgCh), 4-hydroxy-3-methylbut-2-enyl diphosphate reductase, orthologs of maize Lemon white1 (Lw1) or GFP. The recombinant BSMV did neither infect sorghum nor deliver or express AmCyan and sgRNAs. In contrast, the recombinant FoMV systemically spread throughout sorghum plants and induced somatic mutations with frequencies reaching up to 60%. This mutagenesis led to visible phenotypic changes, demonstrating the potential of FoMV for in planta gene editing and functional genomics studies in sorghum.

Feedstock Production↗

Rotational symmetry relation for efficient response function generation in the coarse mesh transport method COMET

The coarse mesh transport code COMET is a continuous energy hybrid stochastic-deterministic neutronics solver with high fidelity and formidable computation speed in solving reactor core problems. Its method is based on the incident flux expansion theory. In this work, we take advantage of the local geometric symmetry in many reactor cores lattices (e.g., fuel lattices and reflector blocks) to develop relations among the flux response expansion coefficients for symmetric surfaces to further improve the computational efficiency of the COMET response function generation tool (method). This is done by a rigorous derivation of the transformation matrices for the angular and spatial expansion moments resulting from a rotation of a coarse mesh by an arbitrary angle. The relations for the response coefficients for the symmetric surfaces can be then written as the Kronecker product of those transformation matrices. The method is implemented into COMET and tested on two advanced high temperature reactor (AHTR) full-length single assembly benchmark problems. The COMET results using the response function library based on the symmetry relations were compared to those using the library directly generated by continuous energy Monte Carlo for all surfaces. It was found that the eigenvalues and stripe-wise fission densities using the two libraries are in statistical agreement as expected. This indicates that the new method maintains the high fidelity of the original COMET method while improving the computational efficiency in the response function generation by 270% to 400%, depending on the local geometric symmetry. This method also reduces the size of the response function library by the same magnitude (270% to 400%). (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Green edge emitting lasers with porous GaN cladding

GaN lasers with green emission wavelength at λ = 510 nm have been fabricated using novel nano-porous GaN cladding under pulsed electrical injection. The low slope efficiency of 0.13 W/A and high threshold current density of 14 kA/cm 2 are related to a combination of poor injection efficiency and high loss, analyzed by the independent characterization methods of variable stripe length and segmented contacts. Continuous wave operation showed narrowed spectra and augmented spontaneous emission.

47 OTHER INSTRUMENTATION↗

III-nitride m-plane violet narrow ridge edge-emitting laser diodes with sidewall passivation using atomic layer deposition

A novel deep-ridge laser structure with atomic-layer deposition (ALD) sidewall passivation was proposed that enhances the optical characteristics of 8-µm ridge width III-nitride violet lasers on freestanding m -plane GaN substrates. The internal loss was determined using the variable stripe length method, where the laser structure with ALD sidewall passivation showed lower internal loss compared to the conventional shallow-ridge laser design. ALD sidewall passivation plays a critical role in device improvements; compared to the lasers without ALD sidewall passivation, the lasers with ALD sidewall passivation yield improved optoelectrical performance and longer lifetime under continuous-wave operation at high current density. This work demonstrates the importance of ALD sidewall passivation to laser performance, which enables high energy efficiency.

Wong, Matthew S.↗

A User’s Guide to the PLTEMP/ANL Code

PLTEMP/ANL V4.3 is a program that obtains a steady-state flow and temperature solution for a nuclear reactor core, or for a single fuel assembly. It is based on an evolutionary sequence of codes originally used for plate temperatures, hence “PLTEMP”, developed at Argonne National Laboratory over several decades. Fueled and non-fueled regions are modeled. Each fuel assembly consists of one or more plates or tubes separated by coolant channels. The fuel plates may have one to five layers of different materials, each with heat generation. The width of a fuel plate may be divided into multiple longitudinal stripes, each with its own axial power shape. Depending upon the heat transfer method selected, the temperature solution is effectively 2-dimensional or 3-dimensional (Appendix XV). It begins with a solution across all coolant channels and fuel plates or tubes within a given fuel assembly, at the entrance to the assembly. The temperature solution is repeated for each axial node along the length of the fuel assembly. The geometry may be either slab or radial, corresponding to fuel assemblies made of a series of flat (or slightly curved) plates, or of nested tubes. A variety of thermal-hydraulic correlations are available to determine safety margins such as onset-of-nucleate boiling ratio(ONBR), departure from nucleate boiling ratio (DNBR), and onset of flow instability ratio (OFIR). Coolant properties for either light or heavy water are obtained from FORTRAN functions rather than from tables. The code is intended for thermal-hydraulic analysis of research reactor performance in the sub-cooled boiling regime. Both turbulent and laminar flow regimes can be modeled. Options to calculate both forced flow and natural circulation are available. A general search capability is available (Appendix XII) to greatly reduce the reactor analyst’s time.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗