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At least 343 records · Page 19

Torsional Eye Movements Evoked by Unilateral Labyrinthine Galvanic Polarizations in the Squirrel Monkey

Electrical stimulation of vestibular-nerve afferents innervating the semicircular canals has been used to identify the extraocular muscles receiving activation or inhibition by individual ampullary nerves. This technique was originally developed by Szentagothai (1950) and led to the description of three neuron reflex arcs that connect each semicircular canal through an interneuron traversing in the region of the medial longitudinal fasciculus to one ipsilateral and one contralateral eye muscle. Selective ampullary nerve stimulation was subsequently used by Cohen and colleagues (Cohen and Suzuki, 1963; Cohen et al., 1964; Suzuki et al., 1964; Cohen et al., 1966) to study movements of the eyes and activation of individual extraocular muscles in response to stimulation of combinations of ampullary nerves. This work led to a description of the now familiar relationships between activation of a semicircular canal ampullary nerves and the anticipated movement in each eye. Disconjugacy of eye movements induced by individual vertical canal stimulation and dependence of the pulling direction of vertical recti and oblique muscles on eye position were also defined in these experiments. Subsequent studies have defined the mechanisms by which externally applied galvanic currents result in a change in vestibular-nerve afferent discharge. The currents appear to act at the spike trigger site. Perilymphatic cathodal currents depolarize the trigger site and lead to excitation whereas anodal currents hyperpolarize and result in inhibition. Afferents innervating all five vestibular endorgans appear to be affected equally by the currents (Goldberg et al., 1984). Irregularly discharging afferents are about 5-10 times more sensitive than regularly discharging ones because of the steeper slope of the former's faster postspike recovery of excitability in encoder sensitivity (Smith and Goldberg, 1986). Response adaptation similar to that noted during acceleration steps is apparent for longer periods of current administration. This adaptation is manifested as a perstimulus return toward resting discharge and poststimulus after-response in the opposite direction (Goldberg et al., 1984; Minor and Goldberg, l991). Cathodal currents (with respect to the perilymphatic space of the vestibule) are excitatory whereas anodal currents are inhibitory. Horizontal eye movements evoked by unilateral galvanic polarizations administered through chronically implanted labyrinthine stimulating electrodes have been studied in alert squirrel monkeys (Minor and Goldberg, 1991). We sought to extend this analysis by recording three-dimensional eye movements during galvanic stimulation. As predicted based upon roughly equal stimulation of ampullary nerves innervating the vertical canals, a substantial torsional component to the nystagmus is noted. The trajectory of torsional slow phases and nystagmus profile after the polarization provide insight into the central mechanisms that influence these responses.

Minor, Lloyd B.↗

Stroboscopic x-ray diffraction microscopy of dynamic strain in diamond thin-film bulk acoustic resonators for quantum control of nitrogen-vacancy centers

Bulk-mode acoustic waves in a crystalline material exert lattice strain through the thickness of the sample, which couples to the spin Hamiltonian of defect-based qubits such as the nitrogen-vacancy (N-V) center defect in diamond. This mechanism has previously been harnessed for unconventional quantum spin control, spin decoherence protection, and quantum sensing. Bulk-mode acoustic wave devices are also important in the microelectronics industry as microwave filters. A key challenge in both applications is a lack of appropriate operando microscopy tools for quantifying and visualizing gigahertz-frequency dynamic strain. Here, in this work, we directly image acoustic strain within N-V center-coupled diamond thin-film bulk acoustic wave resonators using stroboscopic scanning hard x-ray diffraction microscopy at the Advanced Photon Source. The far-field scattering patterns of the nanofocused x-ray diffraction encode strain information entirely through the illuminated thickness of the resonator. These patterns have a real-space spatial variation that is consistent with the bulk strain’s expected modal distribution and a momentum-space angular variation from which the strain amplitude can be quantitatively deduced. We also perform optical measurements of strain-driven Rabi precession of of the N-V center spin ensemble, providing an additional quantitative measurement of the strain amplitude. As a result, we directly measure one of the six N-V spin-stress coupling parameters, 𝑏 =2.73⁢(2) MHz/GPa, by correlating these measurements at the same spatial position and applied microwave power. Our results demonstrate a unique technique for directly imaging ac lattice strain in micromechanical structures and provide a direct measurement of a fundamental constant for the N-V center defect spin Hamiltonian.

acoustic techniques↗

Real time pressure signal system for a rotary engine

A real-time IMEP signal which is a composite of those produced in any one chamber of a three-lobed rotary engine is developed by processing the signals of four transducers positioned in a Wankel engine housing such that the rotor overlaps two of the transducers for a brief period during each cycle. During the overlap period of any two transducers, their output is compared and sampled for 10 microseconds per 0.18 degree of rotation by a sampling switch and capacitive circuit. When the switch is closed, the instantaneous difference between the value of the transducer signals is provided while with the switch open the average difference is produced. This combined signal, along with the original signal of the second transducer, is fed through a multiplexer to a pressure output terminal. Timing circuits, controlled by a crank angle encoder on the engine, determine which compared transducer signals are applied to the output terminal and when, as well as the open and closed periods of the switches.

Rice, W. J.↗

Investigating permafrost carbon dynamics in Alaska with artificial intelligence

Abstract Positive feedbacks between permafrost degradation and the release of soil carbon into the atmosphere impact land–atmosphere interactions, disrupt the global carbon cycle, and accelerate climate change. The widespread distribution of thawing permafrost is causing a cascade of geophysical and biochemical disturbances with global impacts. Currently, few earth system models account for permafrost carbon feedback (PCF) mechanisms. This research study integrates artificial intelligence (AI) tools and information derived from field-scale surveys across the tundra and boreal landscapes in Alaska. We identify and interpret the permafrost carbon cycling links and feedback sensitivities with GeoCryoAI, a hybridized multimodal deep learning (DL) architecture of stacked convolutionally layered, memory-encoded recurrent neural networks (NN). This framework integratesin-situmeasurements and flux tower observations for teacher forcing and model training. Preliminary experiments to quantify, validate, and forecast permafrost degradation and carbon efflux across Alaska demonstrate the fidelity of this data-driven architecture. More specifically, GeoCryoAI logs the ecological memory and effectively learns covariate dynamics while demonstrating an aptitude to simulate and forecast PCF dynamics—active layer thickness (ALT), carbon dioxide flux (CO 2 ), and methane flux (CH 4 )—with high precision and minimal loss (i.e. ALT RMSE : 1.327 cm [1969–2022]; CO 2 RMSE : 0.697µmolCO 2 m −2 s −1 [2003–2021]; CH 4 RMSE : 0.715 nmolCH 4 m −2 s −1 [2011–2022]). ALT variability is a sensitive harbinger of change, a unique signal characterizing the PCF, and our model is the first characterization of these dynamics across space and time.

Environmental Sciences & Ecology↗

Genes encoding calmodulin-binding proteins in the Arabidopsis genome

Analysis of the recently completed Arabidopsis genome sequence indicates that approximately 31% of the predicted genes could not be assigned to functional categories, as they do not show any sequence similarity with proteins of known function from other organisms. Calmodulin (CaM), a ubiquitous and multifunctional Ca(2+) sensor, interacts with a wide variety of cellular proteins and modulates their activity/function in regulating diverse cellular processes. However, the primary amino acid sequence of the CaM-binding domain in different CaM-binding proteins (CBPs) is not conserved. One way to identify most of the CBPs in the Arabidopsis genome is by protein-protein interaction-based screening of expression libraries with CaM. Here, using a mixture of radiolabeled CaM isoforms from Arabidopsis, we screened several expression libraries prepared from flower meristem, seedlings, or tissues treated with hormones, an elicitor, or a pathogen. Sequence analysis of 77 positive clones that interact with CaM in a Ca(2+)-dependent manner revealed 20 CBPs, including 14 previously unknown CBPs. In addition, by searching the Arabidopsis genome sequence with the newly identified and known plant or animal CBPs, we identified a total of 27 CBPs. Among these, 16 CBPs are represented by families with 2-20 members in each family. Gene expression analysis revealed that CBPs and CBP paralogs are expressed differentially. Our data suggest that Arabidopsis has a large number of CBPs including several plant-specific ones. Although CaM is highly conserved between plants and animals, only a few CBPs are common to both plants and animals. Analysis of Arabidopsis CBPs revealed the presence of a variety of interesting domains. Our analyses identified several hypothetical proteins in the Arabidopsis genome as CaM targets, suggesting their involvement in Ca(2+)-mediated signaling networks.

NASA Discipline Plant Biology↗

The cosmological bootstrap: inflationary correlators from symmetries and singularities

Scattering amplitudes at weak coupling are highly constrained by Lorentz invariance, locality and unitarity, and depend on model details only through coupling constants and the particle content of the theory. For example, four-particle amplitudes are analytic for contact interactions and have simple poles with appropriately positive residues for tree-level exchange. In this paper, we develop an understanding of inflationary correlators which parallels that of flat-space scattering amplitudes. Specifically, we study slow-roll inflation with weak couplings to extra massive particles, for which all correlation functions are controlled by an approximate conformal symmetry on the boundary of the spacetime. After systematically classifying all possible contact terms in de Sitter space, we derive an analytic expression for the four-point function of conformally coupled scalars mediated by the tree-level exchange of massive scalars. Conformal symmetry implies that the correlator satisfies a pair of differential equations with respect to spatial momenta, encoding bulk time evolution in purely boundary terms. The absence of unphysical singularities (and the correct normalization of physical ones) completely fixes this correlator. Moreover, a “spin-raising” operator relates it to the correlators associated with the exchange of particles with spin, while “weight-shifting” operators map it to the four-point function of massless scalars. We explain how these de Sitter four-point functions can be perturbed to obtain inflationary three-point functions. Using our formalism, we reproduce many classic results in the literature, such as the three-point function of slow-roll inflation, and provide a complete classification of all inflationary three- and four-point functions arising from weakly broken conformal symmetry. Remarkably, the inflationary bispectrum associated with the exchange of particles with arbitrary spin is completely characterized by the soft limit of the simplest scalar-exchange four-point function of conformally coupled scalars and a series of contact terms. Finally, we demonstrate that the inflationary correlators contain flat-space scattering amplitudes via a suitable analytic continuation of the external momenta, which can also be directly connected with the signals for particle production seen in the squeezed limit.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Demonstration of a High-Efficiency Free-Space Optical Communications Link

In this paper we discuss recent progress on the implementation of a hardware free-space optical communications test-bed. The test-bed implements an end-to-end communications system comprising a data encoder, modulator, laser-transmitter, telescope, detector, receiver and error-correction-code decoder. Implementation of each of the component systems is discussed, with an emphasis on 'real-world' system performance degradation and limitations. We have demonstrated real-time data rates of 44 Mbps and photon efficiencies of approximately 1.8 bits/photon over a 100m free-space optical link.

pulse-position-modulation↗

Molecular genetics of root gravitropism and waving in Arabidopsis thaliana

When Arabidopsis thaliana seedlings grow embedded in an agar-based medium, their roots grow vertically downward. This reflects their ability to sense the gravity vector and to position their tip parallel to it (gravitropism). We have isolated a number of mutations affecting root gravitropism in Arabidopsis thaliana. One of these mutations, named arg1, affects root and hypocotyl gravitropism without promoting defects in starch content or in the ability of seedlings' organs to respond to plant hormones. The ARG1 gene was cloned and shown to code for a protein with a J domain at its amino terminus and a second sequence motif found in several cytoskeleton binding proteins. Mutations in the AGR1 locus promote a strong defect in root gravitropism. Some alleles also confer an increased root resistance to exogenous ethylene and an increased sensitivity to auxin. AGR1 was cloned and found to encode a putative transmembrane protein which might be involved in polar auxin transport, or in regulating the differential growth response to gravistimulation. When Arabidopsis seedlings grow on the surface of agar-based media tilted backward, their roots wave. That wavy pattern of root growth derives from a combined response to gravity, touch and other surface-derived stimuli. It is accompanied by a reversible rotation of the root tip about its axis. A number of mutations affect the presence or the shape of root waves on tilted agar-based surfaces. One of them, wvc1, promotes the formation of compressed root waves under these conditions. The physiological and molecular analyses of this mutant suggest that a tryptophan-derived molecule other than IAA might be an important regulator of the curvature responsible for root waving.

NASA Discipline Plant Biology↗

The White Dwarfs of the Old, Solar-metallicity Open Star Cluster Messier 67: Properties and Progenitors

The old, solar-metallicity open cluster Messier 67 has long been considered a lynchpin in the study and understanding of the structure and evolution of solar-type stars. The same is arguably true for stellar remnants; the white dwarf population of M67 provides crucial observational data for understanding and interpreting white dwarf populations and evolution. In this work, we determine the white dwarf masses and derive their progenitor star masses using high signal-to-noise spectroscopy of warm (≳10,000 K) DA white dwarfs in the cluster. From this, we are able to derive each white dwarf’s position on the initial–final mass relation (IFMR), with an average M {sub WD} = 0.60 ± 0.01 M {sub ⊙} and progenitor mass M {sub i} = 1.52 ± 0.04 M {sub ⊙}. These values are fully consistent with recently published linear and piecewise linear fits to the semiempirical IFMR and provide a crucial, precise anchor point for the IFMR for solar-metallicity, low-mass stars. The mean mass of M67 white dwarfs is also consistent with the sharp narrow peak in the local field white dwarf mass distribution, indicating that a majority of recently formed field white dwarfs come from stars with progenitor masses of ≈1.5 M {sub ⊙}. Our results enable more precise modeling of the Galactic star formation rate encoded in the field white dwarf mass distribution.

47 OTHER INSTRUMENTATION↗

The Design of a Flexible, Interoperable Navigation Signal for Future Lunar Missions

The LunaNet Interoperability Specification (LNIS) is a set of standards currently under development by NASA, ESA, and JAXA, which define a common, interoperable set of services and interfaces for lunar communication and navigation. The LNIS includes specifications for the GNSS-like Augmented Forward Signal (AFS). The LANS (Lunar Augmented Navigation Service) will be comprised of Multiple LunaNet Service Provider (LNSP) nodes broadcasting the AFS, such as NASA’s LCRNS (Lunar Communications Relay and Navigation Systems), ESA’s Moonlight LCNS (Lunar Communication and Navigation Services) and the Japan LNSS (Lunar Navigation Satellite System). The LANS will provide a GNSS-like capability enabling orbiting and surface users in lunar space (such as Artemis) to estimate their position, velocity and time as described in Giordano et al., (2023). Initial capabilities will focus on providing service to the lunar South pole region. The specification of AFS defines two orthogonal signal components on a single carrier, with the in-phase component (AFS-I) being a lower-chip-rate data channel tailored for applications where low SWaP is critical (e.g., IoT devices or search and rescue), and the quadrature component (AFS-Q) being a high-chip-rate data-less pilot signal for high-precision, robust lunar navigation and positioning applications. An initial description of AFS was provided in the LNIS, (2023), and initial analysis results were shown in Dafesh, et al., (2024). In this work, we provide rationale for updates to the LNIS that define key aspects of the signal including the primary spreading code designs for the data and pilot channels, and a three-tiered overlay code approach for the pilot channel that provides flexible signal acquisition alternatives, rapid time dissemination and robust frame Sync. The paper also describes a robust data sync word that is designed to enable frame Sync. for low-SWaP receivers that only use the I channel, as well as a low-density parity check code (LDPC) data message encoding design and interleaving definition. The work further describes the impact of the updated AFS design in terms of improved acquisition performance, interference resistance, navigation message capabilities and rapid absolute time dissemination for users able to access clock and ephemeris data over an external network. The cross-correlation and synchronization performance of the AFS design is also compared to potential alternatives, further providing rationale for the final signal design configuration.

LANS↗

The Design of a Flexible, Interoperable Navigation Signal for Future Lunar Missions

The LunaNet Interoperability Specification (LNIS) is a set of standards currently under development by NASA, ESA, and JAXA, which define a common, interoperable set of services and interfaces for lunar communication and navigation. The LNIS includes specifications for the GNSS-like Augmented Forward Signal (AFS). The LANS (Lunar Augmented Navigation Service) will be comprised of Multiple LunaNet Service Provider (LNSP) nodes broadcasting the AFS, such as NASA’s LCRNS (Lunar Communications Relay and Navigation Systems), ESA’s Moonlight LCNS (Lunar Communication and Navigation Services) and the Japan LNSS (Lunar Navigation Satellite System). The LANS will provide a GNSS-like capability enabling orbiting and surface users in lunar space (such as Artemis) to estimate their position, velocity and time as described in Giordano et al., (2023). Initial capabilities will focus on providing service to the lunar South pole region. The specification of AFS defines two orthogonal signal components on a single carrier, with the in-phase component (AFS-I) being a lower-chip-rate data channel tailored for applications where low SWaP is critical (e.g., IoT devices or search and rescue), and the quadrature component (AFS-Q) being a high-chip-rate data-less pilot signal for high-precision, robust lunar navigation and positioning applications. An initial description of AFS was provided in the LNIS, (2023), and initial analysis results were shown in Dafesh, et al., (2024). In this work, we provide rationale for updates to the LNIS that define key aspects of the signal including the primary spreading code designs for the data and pilot channels, and a three-tiered overlay code approach for the pilot channel that provides flexible signal acquisition alternatives, rapid time dissemination and robust frame Sync. The paper also describes a robust data sync word that is designed to enable frame Sync. for low-SWaP receivers that only use the I channel, as well as a low-density parity check code (LDPC) data message encoding design and interleaving definition. The work further describes the impact of the updated AFS design in terms of improved acquisition performance, interference resistance, navigation message capabilities and rapid absolute time dissemination for users able to access clock and ephemeris data over an external network. The cross-correlation and synchronization performance of the AFS design is also compared to potential alternatives, further providing rationale for the final signal design configuration.

LunaNet↗

tRNA shape is an identity element for an archaeal pyrrolysyl-tRNA synthetase from the human gut

Protein translation is orchestrated through tRNA aminoacylation and ribosomal elongation. Among the highly conserved structure of tRNAs, they have distinguishing features which promote interaction with their cognate aminoacyl tRNA synthetase (aaRS). These key features are referred to as identity elements. In our study, we investigated the tRNA:aaRS pair that installs the 22nd amino acid, pyrrolysine (tRNAPyl:PylRS). Pyrrolysyl-tRNA synthetases (PylRSs) are naturally encoded in some archaeal and bacterial genomes to acylate tRNAPyl with pyrrolysine. Their large amino acid binding pocket and poor recognition of the tRNA anticodon have been instrumental in incorporating > 200 noncanonical amino acids. PylRS enzymes can be divided into three classes based on their genomic structure. Two classes contain both an N-terminal and C-terminal domain, however the third class (ΔpylSn) lacks the N-terminal domain. In this study we explored the tRNA identity elements for a ΔpylSn tRNAPyl from Candidatus Methanomethylophilus alvus which drives the orthogonality seen with its cognate PylRS (MaPylRS). From aminoacylation and translation assays we identified five key elements in ΔpylSn tRNAPyl necessary for MaPylRS activity. The absence of a base (position 8) and a G–U wobble pair (G28:U42) were found to affect the high-resolution structure of the tRNA, while molecular dynamic simulations led us to acknowledge the rigidity imparted from the G–C base pairs (G3:C70 and G5:C68).

59 BASIC BIOLOGICAL SCIENCES↗

Radiation-Hard SpaceWire/Gigabit Ethernet-Compatible Transponder

A radiation-hard transponder was developed utilizing submicron/nanotechnology from IBM. The device consumes low power and has a low fabrication cost. This device utilizes a Plug-and-Play concept, and can be integrated into intra-satellite networks, supporting SpaceWire and Gigabit Ethernet I/O. A space-qualified, 100-pin package also was developed, allowing space-qualified (class K) transponders to be delivered within a six-month time frame. The novel, optical, radiation-tolerant transponder was implemented as a standalone board, containing the transponder ASIC (application specific integrated circuit) and optical module, with an FPGA (field-programmable gate array) friendly parallel interface. It features improved radiation tolerance; high-data-rate, low-power consumption; and advanced functionality. The transponder utilizes a patented current mode logic library of radiation-hardened-by-architecture cells. The transponder was developed, fabricated, and radhard tested up to 1 MRad. It was fabricated using 90-nm CMOS (complementary metal oxide semiconductor) 9 SF process from IBM, and incorporates full BIT circuitry, allowing a loop back test. The low-speed parallel LVCMOS (lowvoltage complementary metal oxide semiconductor) bus is compatible with Actel FPGA. The output LVDS (low-voltage differential signaling) interface operates up to 1.5 Gb/s. Built-in CDR (clock-data recovery) circuitry provides robust synchronization and incorporates two alarm signals such as synch loss and signal loss. The ultra-linear peak detector scheme allows on-line control of the amplitude of the input signal. Power consumption is less than 300 mW. The developed transponder with a 1.25 Gb/s serial data rate incorporates a 10-to-1 serializer with an internal clock multiplication unit and a 10-1 deserializer with internal clock and data recovery block, which can operate with 8B10B encoded signals. Three loop-back test modes are provided to facilitate the built-in-test functionality. The design is based on a proprietary library of differential current switching logic cells implemented in the standard 90-nm CMOS 9SF technology from IBM. The proprietary low-power LVDS physical interface is fully compatible with the SpaceWire standard, and can be directly connected to the SFP MSA (small form factor pluggable Multiple Source Agreement) optical transponder. The low-speed parallel interfaces are fully compatible with the standard 1.8 V CMOS input/output devices. The utilized proprietary annular CMOS layout structures provide TID tolerance above 1.2 MRad. The complete chip consumes less than 150 mW of power from a single 1.8-V positive supply source.

Katzman, Vladimir↗

Real-Time Interactive 4D-STEM Phase-Contrast Imaging From Electron Event Representation Data: Less computation with the right representation

The arrival of direct electron detectors (DED) with high frame-rates in the field of scanning transmission electron microscopy has enabled many experimental techniques that require collection of a full diffraction pattern at each scan position, a field which is subsumed under the name four dimensional-scanning transmission electron microscopy (4D-STEM). DED frame rates approaching 100 kHz require data transmission rates and data storage capabilities that exceed commonly available computing infrastructure. Current commercial DEDs allow the user to make compromises in pixel bit depth, detector binning or windowing to reduce the per-frame file size and allow higher frame rates. This change in detector specifications requires decisions to be made before data acquisition that may reduce or lose information that could have been advantageous during data analysis. The 4D Camera, a DED with 87 kHz frame-rate developed at Lawrence Berkeley National Laboratory, reduces the raw data to a linear-index encoded electron event representation (EER). Here we show with experimental data from the 4D Camera that linear-index encoded EER and its direct use in 4D-STEM phase contrast imaging methods enables real-time, interactive phase-contrast from large-area 4D-STEM datasets. Furthermore, we detail the computational complexity advantages of the EER and the necessary computational steps to achieve real-time interactive ptychography and center-of-mass differential phase contrast using commonly available hardware accelerators.

4D-STEM↗

A reference model for scientific information interchange

This paper presents an overview of an Information Interchange Reference Model (IIRM) currently being developed by individuals participating in the Consultative Committee for Space Data Systems (CCSDS) Panel 2, the Planetary Data Systems (PDS), and the Committee on Earth Observing Satellites (CEOS). This is an ongoing research activity and is not an official position by these bodies. This reference model provides a framework for describing and assessing current and proposed methodologies for information interchange within and among the space agencies. It is hoped that this model will improve interoperability between the various methodologies. As such, this model attempts to address key information interchange issues as seen by the producers and users of space-related data and to put them into a coherent framework. Information is understood as the knowledge (e.g., the scientific content) represented by data. Therefore, concern is not primarily on mechanisms for transferring data from user to user (e.g., compact disk read-only memory (CD-ROM), wide-area networks, optical tape, and so forth) but on how information is encoded as data and how the information content is maintained with minimal loss or distortion during transmittal. The model assumes open systems, which means that the protocols or methods used should be fully described and the descriptions publicly available. Ideally these protocols are promoted by recognized standards organizations using processes that permit involvement by those most likely to be affected, thereby enhancing the protocol's stability and the likelihood of wide support.

Reich, Lou↗

Major Revisions in Arthropod Phylogeny Through Improved Supermatrix, With Support for Two Possible Waves of Land Invasion by Chelicerates

Deep phylogeny involving arthropod lineages is difficult to recover because the erosion of phylogenetic signals over time leads to unreliable multiple sequence alignment (MSA) and subsequent phylogenetic reconstruction. One way to alleviate the problem is to assemble a large number of gene sequences to compensate for the weakness in each individual gene. Such an approach has led to many robustly supported but contradictory phylogenies. A close examination shows that the supermatrix approach often suffers from two shortcomings. The first is that MSA is rarely checked for reliability and, as will be illustrated, can be poor. The second is that, to alleviate the problem of homoplasy at the third codon position of protein-coding genes due to convergent evolution of nucleotide frequencies, phylogeneticists may remove or degenerate the third codon position but may do it improperly and introduce new biases. We performed extensive reanalysis of one of such “big data” sets to highlight these two problems, and demonstrated the power and benefits of correcting or alleviating these problems. Our results support a new group with Xiphosura and Arachnopulmonata (Tetrapulmonata + Scorpiones) as sister taxa. This favors a new hypothesis in which the ancestor of Xiphosura and the extinct Eurypterida (sea scorpions, of which many later forms lived in brackish or freshwater) returned to the sea after the initial chelicerate invasion of land. Our phylogeny is supported even with the original data but processed with a new “principled” codon degeneration. We also show that removing the 1673 codon sites with both AGN and UCN codons (encoding serine) in our alignment can partially reconcile discrepancies between nucleotide-based and AA-based tree, partly because two sequences, one with AGN and the other with UCN, would be identical at the amino acid level but quite different at the nucleotide level.

59 BASIC BIOLOGICAL SCIENCES↗

Calmodulin Gene Family in Potato: Developmental and Touch-Induced Expression of the mRNA Encoding a Novel Isoform

Eight genomic clones of potato calmodulin (PCM1 to 8) were isolated and characterized. Sequence comparisons of different genes revealed that the deduced amino acid sequence of PCM1 had several unique substitutions, especially in the fourth Ca(2+)-binding area. The expression patterns of different genes were studied by northern analysis using the 3'-untranslated regions as probes. The expression of PCM1, 5, and 8 was highest in the stolon tip and it decreased during tuber development. The expression of PCM6 did not vary much in the tissues tested, except in the leaves, where the expression was lower; whereas, the expression of PCM4 was very low in all the tissues. The expression of PCM2 and PCM3 was not detected in any of the tissues tested. Among these genes, only PCM1 showed increased expression following touch stimulation. To study the regulation of PCM1, transgenic potato plants carrying the PCM1 promoter fused to the beta-glucuronidase (GUS) reporter gene were produced. GUS expression was found to be developmentally regulated and touch-responsive, indicating a positive correlation between the expression of PCM1 and GUS mRNAs. These results suggest that the 5'-flanking region of PCM1 controls developmental and touch-induced expression. X-Gluc staining patterns revealed that GUS localization is high in meristematic tissues such as the stem apex, stolon tip, and vascular regions.

Takezawa, D.↗

Accurate and uncertainty-aware multi-task prediction of HEA properties using prior-guided deep Gaussian processes

Surrogate modeling techniques have become indispensable in accelerating the discovery and optimization of high-entropy alloys (HEAs), especially when integrating computational predictions with sparse experimental observations. This study systematically evaluates the training and testing performance of four prominent surrogate models—conventional Gaussian processes (cGP), Deep Gaussian processes (DGP), encoder-decoder neural networks for multi-output regression and eXtreme Gradient Boosting (XGBoost)—applied to a hybrid dataset of experimental and computational properties of the 8-component HEA system Al-Co-Cr-Cu-Fe-Mn-Ni-V. We specifically assess their capabilities in predicting correlated material properties, including yield strength, hardness, modulus, ultimate tensile strength, elongation, and average hardness under dynamic/quasi-static conditions, alongside auxiliary computational properties. The comparison highlights the strengths of hierarchical deep modeling approaches in handling heteroscedastic, heterotopic, and incomplete data commonly encountered in materials science. Our findings illustrate that combined surrogate models such as DGPs infused with machine-learned priors outperform other surrogates by effectively capturing inter-property correlations and by assimilating prior knowledge. This enhanced predictive accuracy positions the combined surrogate models as powerful tools for robust and data-efficient materials design.

36 MATERIALS SCIENCE↗