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At least 37 records · Page 2

Stage-resolved gene regulatory network analysis reveals developmental reprogramming and genes with robust stem-preferred expression in sorghum

Sorghum bicolor is a deep-rooted, heat- and drought-tolerant crop that thrives on marginal lands and is increasingly valued for its applications in biofuel, bioenergy, and biopolymer production. The sorghum stem, which can reach 4–5 m in length, serves as the primary reservoir of both lignocellulosic biomass and soluble sugars, making it a promising bioenergy feedstock. Although recent advances in genetic, genomic, and transcriptomic resources have improved our understanding of sorghum biology, comprehensive genome-wide analyses of functional dynamics across diverse organ types and developmental stages remain limited. In particular, candidate genes with stem preferred expression pattern or their associated cis-regulatory elements, which may program key stem-related functions and enable organ- or tissue-specific engineering, have not yet been identified.

59 BASIC BIOLOGICAL SCIENCES↗

Growth reponses of eggplant and soybean seedlings to mechanical stress in greenhouse and outdoor environments

Eggplant (Solanum melongena L. var. esculentum 'Burpee's Black Beauty') and soybean [Glycine max (L.) Merr. 'Wells II'] seedlings were assigned to a greenhouse or a windless or windy outdoor environment. Plants within each environment received either periodic seismic (shaking) or thigmic (flexing or rubbing) treatment, or were left undisturbed. Productivity (dry weight) and dimensional (leaf area and stem length) growth parameters generally were reduced more by mechanical stress in the greenhouse (soybean) or outdoor-windless environment (eggplant) than in the outdoor windy environment. Outdoor exposure enhanced both stem and leaf specific weights, whereas mechanical stress enhanced only leaf specific weight. Although both forms of controlled mechanical stress tended to reduce node and internode diameters of soybean, outdoor exposure increased stem diameter.

NASA Discipline Number 61-10↗

Importance of Tree- and Species-Level Interactions With Wildfire, Climate, and Soils in Interior Alaska: Implications for Forest Change Under A Warming Climate

The boreal zone of Alaska is dominated by interactions between disturbances, vegetation, and soils. These interactions are likely to change in the future through increasing permafrost thaw, more frequent and intense wildfires, and vegetation change from drought and competition. We utilize an individual tree-based vegetation model, the University of Virginia Forest Model Enhanced (UVAFME), to estimate current and future forest conditions across sites within interior Alaska. We updated UVAFME for application within interior Alaska, including improved simulation of permafrost dynamics, litter decay, nutrient dynamics, fire mortality, and post-fire regrowth. Following these updates, UVAFME output on species-specific biomass and stem density was comparable to inventory measurements at various forest types within interior Alaska. We then simulated forest response to climate change at specific inventory locations and across the Tanana Valley River Basin on a 2 × 2 km2 grid. We derived projected temperature and precipitation from a five-model average taken from the CMIP5 archive under the RCP 4.5 and 8.5 scenarios. Results suggest that climate change and the concomitant impacts on wildfire and permafrost dynamics will result in overall decreases in biomass (particularly for spruce (Picea spp.)) within the interior Tanana Valley, despite increases in quaking aspen (Populus tremuloides) biomass, and a resulting shift towards higher deciduous fraction. Simulation results also predict increases in biomass at cold, wet locations and at high elevations, and decreases in biomass in dry locations, under both moderate (RCP 4.5) and extreme (RCP 8.5) climate change scenarios. These simulations demonstrate that a highly detailed, species interactive model can be used across a large region within Alaska to investigate interactions between vegetation, climate, wildfire, and permafrost. The vegetation changes predicted here have the capacity to feed back to broader scale climate-forest interactions in the North American boreal forest, a region which contributes significantly to the global carbon and energy budgets.

forest modeling↗

Cell‐type‐specific transcriptomics uncovers spatial regulatory networks in bioenergy sorghum stems

SUMMARY Bioenergy sorghum is a low‐input, drought‐resilient, deep‐rooting annual crop that has high biomass yield potential enabling the sustainable production of biofuels, biopower, and bioproducts. Bioenergy sorghum's 4–5 m stems account for ~80% of the harvested biomass. Stems accumulate high levels of sucrose that could be used to synthesize bioethanol and useful biopolymers if information about cell‐type gene expression and regulation in stems was available to enable engineering. To obtain this information, laser capture microdissection was used to isolate and collect transcriptome profiles from five major cell types that are present in stems of the sweet sorghum Wray. Transcriptome analysis identified genes with cell‐type‐specific and cell‐preferred expression patterns that reflect the distinct metabolic, transport, and regulatory functions of each cell type. Analysis of cell‐type‐specific gene regulatory networks (GRNs) revealed that unique transcription factor families contribute to distinct regulatory landscapes, where regulation is organized through various modes and identifiable network motifs. Cell‐specific transcriptome data was combined with known secondary cell wall (SCW) networks to identify the GRNs that differentially activate SCW formation in vascular sclerenchyma and epidermal cells. The spatial transcriptomic dataset provides a valuable source of information about the function of different sorghum cell types and GRNs that will enable the engineering of bioenergy sorghum stems, and an interactive web application developed during this project will allow easy access and exploration of the data ( https://mc‐lab.shinyapps.io/lcm‐dataset/ ).

09 BIOMASS FUELS↗

Building a Diverse and Inclusive STEM Workforce: The JUMP into STEM Program: Preprint

The JUMP into STEM program is a DOE-funded initiative jointly run by the National Renewable Energy Laboratory and Oak Ridge National La-boratory. Through this program, students from historically underrepresented backgrounds are engaged in the science of building energy-efficient infrastruc-ture. Through program stages, students have opportunity to compete in chal-lenges, competitions, and internship opportunities. We have conducted a study of past participants in the program. We find that 1) the program has been effec-tive at engaging a diverse array of participants from a variety of backgrounds, including historically underrepresented backgrounds, and 2) the program has been effective at promoting career paths in STEM, and more specifically, in en-ergy efficiency.

DEI↗

Divergences in hydraulic conductance and anatomical traits of stems and leaves in three temperate tree species coping with drought, N addition and their interactions

Drought and N addition have been shown to affect tree hydraulic traits, but few studies have been made on their interactions across species with different wood types or leaf forms. We examined the responses of hydraulic conductance and xylem anatomical traits of Quercus mongolica (ring-porous with simple-leaves), Fraxinus mandshurica (ring-porous with compound-leaves), and Tilia amurensis (diffuse-porous with simple-leaves) to drought, N addition and their interactions. Drought stress decreased current-year xylem-specific conductivity in stems (Ksx) and leaf hydraulic conductance (Kleaf), but N addition affected Ksx and Kleaf differently among species and watering regimes. These divergent effects were associated with different responses of anatomical traits and leaf forms. Higher mean vessel diameter in stems (Dstem) and lower vessel density in leaves (VDvein) were observed with N addition. The three-way interactive effects of drought, N addition and tree species were significant for most values of anatomical traits. These results were also reflected in large differences in vessel diameter and density among species with different wood types or leaf forms. The two-way interactive effects of drought and N addition were significant on Kleaf and predawn water potential (?pd), but not Ksx, indicating that leaves were more sensitive than stems to a combination of drought stress and N addition. Our results provide mechanistic insight into the variable responses of xylem water transport to the interactions of drought and N availability.

Hydraulic conductance, hydraulic architecture, N f↗

Parallelized Screening of Characterized and DFT-Modeled Bimetallic Colloidal Cocatalysts for Photocatalytic Hydrogen Evolution

Using a newly designed and developed parallelized photoreactor and colorimetric detection method, a large sampling of bimetallic co-catalysts (Pd/Sn, Pd/Mo, Pd/Ru, Pd/Pb, Pd/Ni, Ni/Sn, Mo/Sn and Pt/Sn) for photocatalytic water reduction have been tested in this work. Of these co-catalysts, the combination of palladium and tin showed the highest synergistic behavior and peak hydrogen gas production at a low relative fraction of palladium. The resulting Pd/Sn bimetallic co-catalysts were characterized using high-angle annular dark-field (HAADF) and scanning transmission electron microscopy energy dispersive X-ray spectroscopy (STEM-EDS), and specifically, investigation of the palladium/tin mixture indicated that palladium and tin elements reside within the same particle. The experimental catalytic activity for the palladium/tin mixture was compared to density functional theory-derived energy values associated with the adsorption of hydrogen onto a surface. This comparison demonstrated that the typical peak found in electrochemical Sabatier volcano plots at ΔG H* = ~0 eV was replicated in the experimental photocatalytic system with a peak activity observed at ΔG H* = -0.036 eV. Computational confirmation of the results expressed here demonstrates the efficacy of colorimetric detection of hydrogen in parallel and presents a model for increasingly rapid catalyst screening.

08 HYDROGEN↗

Investigations of a turbulence-driven solar wind model

This work presents an investigation of the properties of the one-dimensional, two-fluid turbulence-driven solar wind model introduced by Hollweg and Johnson (1988). It is found that the model has serious difficulties in reproducing the observed high-speed wind at 1 AU. In particular, the model proton temperatures are lower than those observed by a factor of 2 or more, and the highest temperature models yield excessive wave intensities at 1 AU. It appears that the problem stems from the specific spatial distribution of heat deposition in the model. Thus this study does not rule out a turbulence-driven fast solar wind, since other forms of the turbulent evolution could probably achieve better results. A three-fluid version of the model is also presented to show that the addition of alpha particles does not significantly reduce the extreme proton temperatures displayed near the sun by the Hollweg and Johnson work. Finally, it is suggested that the additional heating needs to be located well beyond the critical point, implying that the heating mechanism for the fast solar wind is likely not the same as that heating the solar corona.

Isenberg, Philip A.↗

Induced compression wood formation in Douglas fir (Pseudotsuga menziesii) in microgravity

In the microgravity environment of the Space Shuttle Columbia (Life and Microgravity Mission STS-78), were grown 1-year-old Douglas fir and loblolly pine plants in a NASA plant growth facility. Several plants were harnessed (at 45 degrees ) to establish if compression wood biosynthesis, involving altered cellulose and lignin deposition and cell wall structure would occur under those conditions of induced mechanical stress. Selected plants were harnessed at day 2 in orbit, with stem sections of specific plants harvested and fixed for subsequent microscopic analyses on days 8, 10 and 15. At the end of the total space mission period (17 days), the remaining healthy harnessed plants and their vertical (upright) controls were harvested and fixed on earth. All harnessed (at 45 degrees ) plant specimens, whether grown at 1 g or in microgravity, formed compression wood. Moreover, not only the cambial cells but also the developing tracheid cells underwent significant morphological changes. This indicated that the developing tracheids from the primary cell wall expansion stage to the fully lignified maturation stage are involved in the perception and transduction of the stimuli stipulating the need for alteration of cell wall architecture. It is thus apparent that, even in a microgravity environment, woody plants can make appropriate corrections to compensate for stress gradients introduced by mechanical bending, thereby enabling compression wood to be formed. The evolutionary implications of these findings are discussed in terms of "variability" in cell wall biosynthesis.

manned↗

Differences in the response of wheat, soybean and lettuce to reduced blue radiation

Although many fundamental blue light responses have been identified, blue light dose-response curves are not well characterized. We studied the growth and development of soybean, wheat and lettuce plants under high-pressure sodium (HPS) and metal halide (MH) lamps with yellow filters creating five fractions of blue light. The blue light fractions obtained were < 0.1, 2 and 6% under HPS lamps, and 6, 12 and 26% under MH lamps. Studies utilizing both lamp types were done at two photosynthetic photon flux levels, 200 and 500 mumol m-2 s-1 under a 16 h photoperiod. Phytochrome photoequilibria was nearly identical among treatments. The blue light effect on dry mass, stem length, leaf area, specific leaf area and tillering/branching was species dependent. For these parameters, wheat did not respond to blue light, but lettuce was highly sensitive to blue light fraction between 0 and 6% blue. Soybean stem length decreased and leaf area increased up to 6% blue, but total dry mass was unchanged. The blue light fraction determined the stem elongation response in soybean, whereas the absolute amount of blue light determined the stem elongation response in lettuce. The data indicate that lettuce growth and development requires blue light, but soybean and wheat may not.

NASA Discipline Life Support Systems↗

Data for The Stem Cell-Type Transcriptome of Bioenergy Sorghum Reveals the Spatial Regulation of Secondary Cell Wall Networks

Bioenergy sorghum is a low-input, drought-resilient, deep-rooting annual crop that has high biomass yield potential enabling the sustainable production of biofuels, biopower, and bioproducts. Bioenergy sorghum’s 4-5 m stems account for ~80% of the harvested biomass. Stems accumulate high levels of sucrose that could be used to synthesize bioethanol and useful biopolymers if information about stem cell-type gene expression and regulation was available to enable engineering. To obtain this information, Laser Capture Microdissection (LCM) was used to isolate and collect transcriptome profiles from five major cell types that are present in stems of the sweet sorghum Wray. Transcriptome analysis identified genes with cell-type specific and cell-preferred expression patterns that reflect the distinct metabolic, transport, and regulatory functions of each cell type. Analysis of cell-type specific gene regulatory networks (GRNs) revealed that unique TF families contribute to distinct regulatory landscapes, where regulation is organized through various modes and identifiable network motifs. Cell-specific transcriptome data was combined with a stem developmental transcriptome dataset to identify the GRN that differentially activates the secondary cell wall (SCW) formation in stem xylem sclerenchyma and epidermal cells. The cell-type transcriptomic dataset provides a valuable source of information about the function of sorghum stem cell types and GRNs that will enable the engineering of bioenergy sorghum stems.

Software↗

DYRK1A is required for maintenance of cancer stemness, contributing to tumorigenic potential in oral/oropharyngeal squamous cell carcinoma

Highlights: • DYRK1A is essential to maintain cancer stemness in OSCC. • DYRK1A regulates cancer stemness via FGF2 expression. • Levels of DYRK1A and FGF2 expression are positively correlated in OSCC cells. • DYRK1A-FGF2 is a novel molecular axis regulating cancer stemness in OSCC. DYRK1A, one of the dual-specificity tyrosine phosphorylation-regulated kinases (DYRKs), plays an important role in various biological processes by regulating downstream targets via kinase-dependent and independent mechanisms. Here, we report a novel role of DYRK1A in maintaining tumor growth and stemness of oral/oropharyngeal squamous cell carcinoma (OSCC) cells. Deletion of DYRK1A from OSCC cells abrogated their in vivo tumorigenicity and self-renewal capacity, the key features of cancer stem-like cells (CSCs; also referred to as tumor-initiating cells). The DYRK1A deletion also induced the suppression of CSC populations and properties, such as migration ability and chemoresistance. Conversely, ectopic expression of DYRK1A in OSCC cells augmented their CSC phenotype. Among five DYRK members (DYRK1A, 1B, 2, 3, and 4), DYRK1A is the most dominantly expressed kinase, and its expression is upregulated in OSCC compared to normal oral epithelial cells. More importantly, DYRK1A was highly enriched in various CSC-enriched OSCC populations compared to their corresponding non-CSC populations, indicating its pivotal role in cancer progression and stemness. Further, our study revealed that fibroblast growth factor 2 (FGF2) is a key regulator in the DYRK1A-mediated CSC regulation. Functional studies demonstrated that the loss of DYRK1A inhibits CSC phenotype via reduction of FGF2. Overexpression of DYRK1A promotes CSC phenotype via upregulation of FGF2. Our study delineates a novel mechanism of cancer stemness regulation by DYRK1A-FGF2 axis in OSCC. Thus, inhibition of DYRK1A would lead to a potential novel therapeutic option for targeting CSCs in OSCC.

60 APPLIED LIFE SCIENCES↗

Gibberellins promote polar auxin transport to regulate stem cell fate decisions in cambium

Vascular cambium contains bifacial stem cells, which produce secondary xylem to one side and secondary phloem to the other. However, how these fate decisions are regulated is unknown. Here we show that the positioning of an auxin signalling maximum within the cambium determines the fate of stem cell daughters. The position is modulated by gibberellin-regulated, PIN1-dependent polar auxin transport. Gibberellin treatment broadens auxin maximum from the xylem side of the cambium towards the phloem. As a result, xylem-side stem cell daughter preferentially differentiates into xylem, while phloem-side daughter retains stem cell identity. Occasionally, this broadening leads to direct specification of both daughters as xylem, and consequently, adjacent phloem-identity cell reverts to being stem cell. Conversely, reduced gibberellin levels favour specification of phloem-side stem cell daughter as phloem. Together, our data provide a mechanism by which gibberellin regulates the ratio of xylem and phloem production.

59 BASIC BIOLOGICAL SCIENCES↗

Carbon Fiber and Syntactic Foam Hybrid Materials via Core–Shell Material Extrusion Additive Manufacturing

Abstract Biological materials often employ hybrid architectures, such as the core–shell (C–S) motif present in porcupine quills and plant stems, to achieve unique specific properties and performance. Drawing inspiration from these natural materials, a new method to fabricate lightweight and stiff C–S architected filaments is reported. Specifically, a C–S printhead conducive to printing highly loaded fiber‐filled inks, as well as a new low‐density syntactic foam ink, are utilized to 3D‐print C–S architectures consisting of a syntactic epoxy foam core surrounded by a stiff carbon fiber‐reinforced epoxy composite shell. Effective printing of test specimens and structures with controlled geometry, composition, and architecture is demonstrated. The new foam ink exhibits density as low as 0.68 g cm −3 and C–S structures exhibit up to 25% higher specific flexural stiffness ( E 1/3 /ρ) than either constituent alone. Finally, a new mechanical model is presented to predict this performance improvement while accounting for potential eccentricity of the core.

Pack, Robert C.↗

Leveraging hyperspectral imaging to identify drought tolerant Populus species and genotypes within species

The aim of this study was to identity variation in drought tolerance across genotypes of Populus deltoides, Populus trichocarpa, and hybrids of the two species. A panel of 102 Populus genotypes, comprising 37 genotypes of P. trichocarpa, 37 of P. deltoides and 28 unique hybrid genotypes (P. trichocarpa x P. deltoides and P. deltoides x P. trichocarpa) were evaluated in the greenhouse under two treatments, well-watered (WW) and drought (DS). Plant physiological data were collected throughout the experiment once the drought treatment began. Throughout the experiment, we tracked soil volumetric water content, pot weight, stomatal conductance, quantum yield of photosystem II, and electron transport rate. In addition to those measurements, upon completion of the experiment, we assessed above and belowground plant biomass, plant height and stem diameter, leaf number, specific leaf area, relative water content, total protein, and total chlorophyll. We obtained hyperspectral signatures of one leaf from each plant at the end of the experiment. Columns BC – LL are hyperspectral averages for one leaf from each plant at each wavelength as described in the column header.

Hyper-spectral imaging, Populus, plant stress tole↗

Plant Roots: The Hidden Half: Calcium and Gravitropism - Chapter 16

Environmental signals such as light and gravity control many aspects of plant growth and development. In higher plants, the directional growth of an organ in response to stimuli such as gravity and light is considered a tropic movement. Such movement could be either positive or negative with respect to a specific stimulus. In general, stems show a positive response to light and negative response to gravity. In contrast, most roots show a positive response to gravity and a negative response to light. Investigations on plant tropism date back a century when Darwin studied the phototropic responses of maize seedlings (Darwin). Although the precise mechanism of signal perception and transduction in roots is not understood, Darwin recognized over 100 years ago that the root cap is the probable site of signal perception. He discovered that the removal of the root cap eliminates the ability of roots to respond to gravity. Other investigators have since confirmed Darwin's observation (Konings; Evans et al.). In recent years, especially with the advent of the U.S. Space Program, there has been a renewed interest in understanding how plants respond to extracellular signals such as gravity (Halstead and Dutcher). Studies on the mechanisms involved in perception and transduction of gravity signal by roots would ultimately help us to better understand gravitropism and also to grow plants under microgravity conditions as in space. In this chapter, we restrict ourselves to the role of calcium in transduction of the gravity signal. In doing so, emphasis is given to the role of calcium-modulated proteins and their role in signal transduction in gravitropism. Detailed reviews on various other aspects of gravitropism (Scott, Torrey, Wilkins, Fim and Digby, Feldman, Pickard, Moore and Evans, Halstead and Dutcher, Poovaiah et al.) and on the role of calcium as a messenger in signal transduction in general have been published (Helper and Wayne, Poovaiah and Reddy, Roberts and Hartnon, Bowler and Chua, Gilroy and Trewavas). Plant roots have been widely used to study the transduction of gravity and light signals (Poovaiah et al., Roux and Serlin). Most roots show positive gravitropic response in either dark or light. However, roots of some varieties of plants (e.g., Zea mays L., cv Merit, and Zea rwvs L., cv Golden Cross Bantam 70) show positive gravitropic response only in light (Feldman, Miyazaki et al.). Investigations from various laboratories indicate that calcium acts as a messenger in transducing gravity and light signals in plant roots(Pickard, Evans et al., Pooviah et al.).

Poovaiah, B. W.↗

Microgravity-Enhanced Stem Cell Selection

Stem cells, both embryonic and adult, promise to revolutionize the practice of medicine in the future. In order to realize this potential, a number of hurdles must be overcome. Most importantly, the signaling mechanisms necessary to control the differentiation of stem cells into tissues of interest remain to be elucidated, and much of the present research on stem cells is focused on this goal. Nevertheless, it will also be essential to achieve large-scale expansion and, in many cases, assemble cells in 3D as transplantable tissues. To this end, microgravity analog bioreactors can play a significant role. Microgravity bioreactors were originally conceived as a tool to study the cellular responses to microgravity. However, the technology can address some of the shortcomings of conventional cell culture systems; namely, the deficiency of mass transport in static culture and high mechanical shear forces in stirred systems. Unexpectedly, the conditions created in the vessel were ideal for 3D cell culture. Recently, investigators have demonstrated the capability of the microgravity bioreactors to expand hematopoietic stem cells compared to static culture, and facilitate the differentiation of umbilical cord stem cells into 3D liver aggregates. Stem cells are capable of differentiating into functional cells. However, there are no reliable methods to induce the stem cells to form specific cells or to gain enough cells for transplantation, which limits their application in clinical therapy. The aim of this study is to select the best experimental setup to reach high proliferation levels by culturing these cells in a microgravity-based bioreactor. In typical cell culture, the cells sediment to the bottom surface of their container and propagate as a one-cell-layer sheet. Prevention of such sedimentation affords the freedom for self-assembly and the propagation of 3D tissue arrays. Suspension of cells is easily achievable using stirred technologies. Unfortunately, in conventional bioreactors, stirring invokes deleterious forces that disrupt cell aggregation and results in cell death. First-generation rotating bioreactors provided rotation on the horizontal axis, which resulted in the suspension of cells without stirring, thus providing a suitable environment to propagate cells without sedimentation to a surface. The rotating wall bioreactors did not provide a way to remove air bubbles that were causing shear and disrupting 3D cultures. Johnson Space Center successfully engineered the hydrofocusing bioreactor (HFB) that resolved the problem of removing the air bubbles from the fluid medium of NASA's rotating-wall space bioreactors. The HFB uses the principle of hydrodynamic focusing that simultaneously produces a low-shear fluid culture environment and a variable hydrofocusing force that can control the movement, location, and removal of suspended cells, tissues, and air bubbles from the bioreactor. The HFB is a rotating, domeshaped cell culture vessel with a centrally located sampling port and an internal viscous spinner. The vessel and spinner can rotate at different speeds either in the same or opposite directions. Rotation of the vessel and viscous interaction at the spinner generate a hydrofocusing force. Adjusting the differential rotation rate between vessel and spinner controls the magnitude of the force.

Claudio, Pier Paolo↗

Airfoil Selection for Mars Rotor Applications

This short white paper is aimed at providing an overview of design considerations for airfoil choices for rotor applications in the Martian atmosphere, at very low chord-based Reynolds number flows, around Rec = O (103 -104). The low Reynolds number typical of rotorcraft operation in the Martian atmosphere reduces the rotor lifting force and efficiency, which is only partially compensated for by a lower gravity on Mars. Additionally, the low temperature and largely CO2 based atmosphere of Mars compound the overall aerodynamic problem by resulting in a lower speed of sound, further constraining rotor operation in the Martian atmosphere by limiting the maximum rotor tip speed possible so as not to exceed an acceptable tip Mach number. In light of the expected reduced rotor efficiency, evaluating airfoils for compressible, low-Reynolds number Mars rotor applications is key. Prior research on airfoil optimization and performance evaluation at low Reynolds numbers, especially in the compressible regime, is scarce and deserves further understanding. Specifically, the proposed goal stemming from this overview is to develop airfoils tailored to the unique demands of the second generation of Mars rotorcraft, i.e. the Mars Science Helicopter (MSH). This research focuses on the airfoil performance at low Reynolds numbers and hopes to add to the work performed by, amongst others, Kroo et al., Kunz and Kroo, Oyama and Fujii, Anyoji et al.

Koning, Witold J. F.↗