bluuebunny/crossref_metadata_2025 huggingface dataset:
Objective molecular dynamics investigation of dissociation and recombination kinetics in high-temperature nitrogen
Authors: Pahlani Gunjan , Torres Erik , Schwartzentruber Thomas , James Richard D.
Published: June 2023

In this study, we propose the use of the novel approach of objective molecular dynamics (OMD) simulating far-from-equilibrium gas dynamics problems with chemical reactions. The OMD method has an exact relation to models in continuum mechanics and can be used to improve those models. We provide a detailed molecular dynamics investigation of chemically reacting nitrogen gas in a space-homogeneous adiabatic reactor. The analysis is based on a first-principles derived reactive ReaxFF potential energy surface, which captures the relevant processes of rovibrational relaxation, dissociation, and exchange as well as recombination in a gas evolving under non-equilibrium conditions. We examine the evolution of the internal mode population distribution of all the molecules as well as the rovibrational probability distribution of the pre-collision dissociating and post-collision recombined N2 molecules to investigate the microscopic selectivity of various reactive processes. Subsequently, we make comparisons with results obtained by means of an alternative modeling approach called direct molecular simulation. The current work illustrates the application of the method of OMD to study the compression and expansion kinetics of dissociation-recombination nitrogen mixture relevant to normal shock wave and nozzle expansion.
Adsorption of melting deoxyribonucleic acid
Authors: Majumdar Debjyoti
Published: June 2023

The melting of a homopolymer double-stranded (ds) deoxyribonucleic acid (DNA) in the dilute limit is studied numerically in the presence of an attractive and impenetrable surface on a simple cubic lattice. The two strands of the DNA are modeled using two self-avoiding walks, capable of interacting at complementary sites, thereby mimicking the base pairing. The impenetrable surface is modeled by restricting the DNA configurations at the z≥0 plane, with attractive interactions for monomers at z = 0. Further, we consider two variants for z = 0 occupations by ds segments, where one or two surface interactions are counted. This consideration has significant consequences, to the extent of changing the stability of the bound phase in the adsorbed state. Interestingly, adsorption changes from critical to first-order with a modified exponent on coinciding with the melting transition. For simulations, we use the pruned and enriched Rosenbluth algorithm.
Simultaneous refinement of molecular dynamics ensembles and forward models using experimental data
Authors: Fröhlking Thorben , Bernetti Mattia , Bussi Giovanni
Published: June 2023

A novel method combining the maximum entropy principle, the Bayesian-inference of ensembles approach, and the optimization of empirical forward models is presented. Here, we focus on the Karplus parameters for RNA systems, which relate the dihedral angles of γ, β, and the dihedrals in the sugar ring to the corresponding 3J-coupling signal between coupling protons. Extensive molecular simulations are performed on a set of RNA tetramers and hexamers and combined with available nucleic-magnetic-resonance data. Within the new framework, the sampled structural dynamics can be reweighted to match experimental data while the error arising from inaccuracies in the forward models can be corrected simultaneously and consequently does not leak into the reweighted ensemble. Carefully crafted cross-validation procedure and regularization terms enable obtaining transferable Karplus parameters. Our approach identifies the optimal regularization strength and new sets of Karplus parameters balancing good agreement between simulations and experiments with minimal changes to the original ensemble.
Memory properties and short-range order in silicon oxynitride-based memristors
Authors: Novikov Yu. N. , Kamaev G. N. , Prosvirin I. P. , Gritsenko V. A.
Published: June 2023

Silicon oxynitride films of various compositions were grown by the plasma-enhanced chemical deposition method using a setup with remote plasma and an inductive excitation from a gas mixture of 10% monosilane (diluted with argon) and nitrogen in the presence of residual oxygen in working gas mixtures. The high-frequency generator power (13.56 MHz) was varied in the range of 50–150 W. The samples composition was studied using x-ray photoelectron spectroscopy. A comparison of the experimental Si 2p photoelectron spectrum with the calculation showed that, at a low generator power (50 W), the short-range order in silicon oxynitride films is better described by the “random mixture” model. As the generator power is increased (100 W and higher), the excess silicon content in a silicon oxynitride film is decreased, and the short-range order is better described by the “random bonding” model. On metal–insulator–semiconductor-structures based on the silicon oxynitride films obtained, measurements of current–voltage characteristics were carried out, and the resistive switching of the obtained structures is studied in the present contribution. It is found that, in films in which the short-range order is described by the random bonding model, a stable switching in the bipolar regime is observed.
Facilitating the formation of SnO2 film via HfO2-modified FTO electrode for efficient perovskite solar cells
Authors: Lv Jiancong , Li Hongxing , Chen Hanyue , Ke Lili , Du Wenjuan , Xiong Jian , Zhou Conghua , Liu Gang
Published: June 2023

Fabricating a dense and crystalline SnO2 film has been an important step for efficient SnO2-based perovskite solar cells (PSCs). Herein, a wide bandgap material, HfO2, was deposited on the surface of FTO to facilitate the formation of an SnO2 film. It was found that the HfO2 modification on FTO could significantly improve the crystallization of the upper SnO2 film and passivate the trap states within the SnO2 layer. Moreover, the high conduction band level of HfO2 can block the backflow of electrons and suppress the nonradiative recombination of carriers. Eventually, the best PSC with HfO2 interlayer presented a power conversion efficiency (PCE) of 21.13% with a VOC of 1.13 V, which are higher than those of the reference device. This study provides a meaningful strategy for ETL optimization to further increase the efficiency of the SnO2-based PSCs.
Effect of passive strut angle on the vortical structures and mixing characteristics of scramjet combustor
Authors: Nair Prasanth P. , Suryan Abhilash , Narayanan Vinod
Published: June 2023

Scramjet is considered as the future of high-speed transportation and reusable launch vehicle for satellite placement. However, the combustion of fuel at supersonic speeds is a challenge. Since combustion takes place at high velocities, analyzing the mixing of air and fuel in the engine is important for enhancing performance. The current study focuses on two passive struts that are placed at a short distance downstream of the fuel injection strut. Diverging angles of these passive struts are varied to assess the effect of the mixing and corresponding acoustic behavior. The computational study is conducted using an improved delayed detached-eddy simulation turbulence model. The single strut scramjet configuration is taken as a benchmark to compare it with different strut configurations. The mixing efficiency is highly affected by the divergent angle of the passive strut. Mixing performance enhances as the back-pressure increases due to the passive strut. If the back-pressure becomes too high due to the divergence of the passive strut angle, then the unstart phenomenon is observed. Pressure loss is observed to decrease with a decrease in the divergence angle of the passive strut. As the divergence angle of the passive strut configuration increases, low-frequency vortices are generated. The modal analysis shows the low-frequency modes responsible for the enhanced mixing performance. Overall sound pressure level increases with an increase in the divergence angle of the passive strut.
Experimental observation of the combustion modes based on a novel multistage pre-chamber turbulent jet ignition (TJI) system
Authors: Zhou Lei , Zhong Lijia , Liu Peilin , Feng Zhonghui , Wei Haiqiao
Published: June 2023

Transient jet flame propagation under newly proposed multistage pre-chambers is studied in a constant-volume combustion chamber with a high-speed schlieren photography system. Various combustion behaviors, including the flame tip velocity, jet emergence timing, projected flame area, pressure, and heat release rate, are investigated under different pre-chamber structures. The present work will provide constructive insight into the design, manufacture, and application of turbulent jet ignition engines. It is shown that the pre-chamber structure determines the main chamber flame development by influencing the flame development inside the pre-chamber. As the flame is accelerated by an obstacle in the pre-chamber, faster exit velocity of hot jet and intense turbulence are observed in the main chamber. In addition, the overall development of the jet flame in the main chamber can be separated into two stages, the former of which is dominated by jet flows, while the latter stage is controlled by the chemical reaction under different excess air coefficients, presenting turbulent combustion characteristics. In this work, six ignition modes under ultra-lean conditions are observed, including (1) jet ignition occurrence on the entire jet surface due to the sufficiently high reactivity; (2) local ignition in the middle of the hot jet; (3) local multipoint ignition and ignition at the jet tip; (4) ignition induced by delayed burning at the jet root; (5) jet tip ignition with backward flame propagation; and (6) global extinction. For the effect of initial pressure, it is found that under stoichiometric conditions, the initial pressure has a minor influence on flame tip propagation, while it significantly influences pressure evolution and heat release rate. However, the increase in initial pressure can improve flame propagation and pressure evolution under lean conditions. Under near-extinction conditions, the ignition mode could be switched from unstable ignition to stable ignition. A numerical simulation is also conducted to reveal the flame development inside the pre-chamber under different pre-chamber structures.
Impact of bending stiffness on ground-state conformations for semiflexible polymers
Authors: Aierken Dilimulati , Bachmann Michael
Published: June 2023

Many variants of RNA, DNA, and even proteins can be considered semiflexible polymers, where bending stiffness, as a type of energetic penalty, competes with attractive van der Waals forces in structure formation processes. Here, we systematically investigate the effect of the bending stiffness on ground-state conformations of a generic coarse-grained model for semiflexible polymers. This model possesses multiple transition barriers. Therefore, we employ advanced generalized-ensemble Monte Carlo methods to search for the lowest-energy conformations. As the formation of distinct versatile ground-state conformations, including compact globules, rod-like bundles, and toroids, strongly depends on the strength of the bending restraint, we also performed a detailed analysis of contact and distance maps.
Process-dependent reconfigurability in a gradient ferroelectric field-effect transistor
Authors: Wen Jiaxuan , Yao Songyou , Zhang Xiaoyue , Zheng Yue
Published: June 2023

In this paper, we demonstrate reconfigurable ferroelectric field-effect transistors (Fe-FETs) exhibiting process dependence based on poly(vinylidene fluoride-trifluoroethylene)/molybdenum telluride[P(VDF-TrFE)/MoTe2] heterostructures. By introducing a thickness gradient to a ferroelectric polymer, we constructed a gradient distribution of coercive voltage. This enables programmable configuration of the device (n–p, p–n, p–p, or n–n) depending on the input voltage sequence. Our Fe-FETs exhibit multilevel storage capacity and logic ability, including an on/off ratio of 106, an adjustable rectification ratio from 1 to 45, and a reversible rectification direction. The use of such a structure-gradient design in an Fe-FET provides a valuable strategy for realizing process-dependent reconfigurability and the creation of intelligent devices.
Alternating current polarization to enhance piezoelectric performance of single crystal composites
Authors: Jia Nanxiang , Li ChunChun , Qiu Chaorui , Wang Ting , Ning Li , Du Hongliang , Li Fei , Xu Zhuo
Published: June 2023

Pb-based relaxor piezoelectric single crystal composites (PSCCs) have attracted widespread attention for improving the bandwidth and sensitivity performance of acoustic transducers due to their excellent electromechanical and piezoelectric properties. Alternating current polarization (ACP) has been proven as an effective method for enhancing the dielectric and piezoelectric properties of relaxor-PbTiO3 single crystals. Herein, we investigated the effects of the amplitude, frequency, and cycle number of the poling electric field on the piezoelectric and dielectric performances of PSCCs and obtained the optimum poling condition of ACP. Compared with the traditional direct current poling method, both the dielectric permittivity (ε33T/ε0) and piezoelectric coefficient (d33) of the AC-poled PSCCs were both increased by up to 20%. Notably, the ACP PSCC with a volume fraction of 60% exhibited a high d33 of 1610 pC/N, which is superior to values previously reported for PSCCs. This work provides an alternative strategy for enhancing the properties of PSCCs and may contribute to the further development of piezoelectric applications.
On melting of Boltzmann system of quantum hard spheres
Authors: Stishov S. M.
Published: June 2023

Melting of a quantum system of hard spheres has been considered in the case when the effects of Bose and Fermi statistics can be neglected. It has been found that the quantum melting line always differs from the classical line except for T = 0, P = 0, where the both lines cross. It is shown that the classical limit is not reachable at any finite temperature.
Modeling of drag coefficient under emergent and submerged flexible vegetated flow
Authors: Hussain Awesar A. , Al-Obaidi Mudhar A. , Rashid Farhan Lafta
Published: June 2023

In an open-channel flow, vegetation study is crucial to be investigated with any type of plants including trees, shrubs, and grasses, which are growing within or near the channel banks and beds in natural or artificial waterways, such as rivers, streams, and canals. These plants are different in height, size, shape, and arrangements, which have a big impact on the turbulence and flow resistance structures. In this paper, a regression analysis has been used based on collected experimental data to improve a specific equation for the drag coefficient for rigid vegetation stems and expanded to flexible stem types under emergent and submerged flow conditions. The equation suggests a length scale metric that, by analogy with the log wake law, normalizes velocity profiles of the depth-limited open channel flow with submerged, rigid vegetation. It has been formulated by drawing regression analysis for each parameter including (Re) Reynolds number, (h*) submergence ratio, and (λ) vegetation density by considering the (Fr) Froude number ranges for the water flows and vegetated channel flows. Using the Reynolds number, which is determined by the height and diameter of the vegetation, the results demonstrate an increase and decrease in the drag coefficient. For assessing the impact of vegetation on flow resistance at the surface layer, the notion of the drag coefficient is introduced. It shows better performance than other length scales in collapsing resistance data gathered under a variety of vegetation circumstances. The proposed scaling is more accurate than those based on the logarithmic, velocity-defect, and power laws in collapsing regression analysis for the studied parameters.
Mode specificity of water dissociating on Ni(100): An approximate full-dimensional quantum dynamics study
Authors: Liu Tianhui , Fu Bina , Zhang Dong H.
Published: June 2023

The mode-specific dynamics for the dissociative chemisorption of H2O on rigid Ni(100) is investigated by approximate nine-dimensional (9D) quantum dynamics calculations. The vibrational state-specific 9D dissociation probabilities are obtained by site-averaging the site-specific seven-dimensional results based on an accurate full-dimensional potential energy surface newly developed by neural network fitting to density functional theory energy points with the revised version of the Perdew, Burke, and Ernzerhof functional. The mode specificity of H2O/Ni(100) is very different from that of H2O/Ni(111) or H2O/Cu(111) whose reactivity enhancement by vibrational excitations is quite efficient. For H2O/Ni(100), it is found that the excitation in the symmetric stretching mode is more efficacious than increasing the translational energy in promoting the reaction, while the excitations in the asymmetric stretching mode and bending mode are less efficacious than the translational energy at low collision energies. These interesting observations can be attributed to the near central-barrier reaction for H2O/Ni(100), as well as large discrepancies between the site-specific mode specificities at different impact sites. The mode-specific dynamics obtained in this study is different from that obtained with the reaction path Hamiltonian approach, indicating the importance of full-dimensional quantum dynamics for gas–surface reactions.
Indicators of functional integrity in production animals
Authors: Colditz I. G. , Smith E. G. , Ingham A. B. , Dominik S.
Published: June 2023

An ability to describe the quality of lived experience across the course of an animal’s life is of increasing interest in studies on wellbeing in farm animals. Integrity of physical functions is an important aspect of the tripartite model of wellbeing: feeling, functioning and interacting well. This review examines measures of functional integrity as potential indicators of functional (eudaimonic) wellbeing. Copious literature shows that coping with day-to-day fluctuations in the environment influences (1) periodicity of biorhythms, (2) allocation of resources to growth, defence and repair, and (3) rate of biological aging. Here we review opportunities for assessing functional integrity through analysis of (1) the dynamic status of physiological and behavioural variables, (2) the accretion of resources in production tissues (milk, eggs, body mass, offspring) and physical structures (fibre, hoof, bone, tooth, placoid scale, otolith, beak), and (3) biological age. A reduction in periodicity of biorhythms, complexity of behaviours, or uniformity of trajectories of growth and production is often associated with poorer current and future health outcomes and shorter functional longevity. These analytical approaches are grounded in statistical measures of stability in complex dynamic systems. Additionally, the cumulative effect of wear and tear on biological age can be assessed via telomere length, DNA methylation, biomarkers of allostatic load, hair cortisol, and physiological functional capacity. Timeseries of behaviour, physiology and accretion provide a richer record of functional integrity than do cumulative indicators of biological age. Indicators of integrity are needed for each phase of the animal’s life course including attainment of developmental competencies, stability of mature performance, and rate of decline with advancing age, to provide a comprehensive record across the whole of the animal’s life. The utility of measures may differ between real-time and retrospective assessments and between application to every individual versus sentinels. Further validation is required for interpretating measures of functional integrity as indicators of the functional aspect of wellbeing, together with determining their practicality and reliability before translation to commercial settings is feasible. A single type of indicator of functional wellbeing (e.g. DNA methylation) is unlikely to have utility for all life stages, species, production systems, and environments.
Understanding the health care needs of transgender and gender diverse people engaging with rural Australian sexual health centres: a qualitative interview study
Authors: Del Tufo Ava , Foster Rosalind , Haire Bridget , Newman Christy E. , Smith Anthony K. J. , Crowley Margaret , Burn Donna , McNulty Anna
Published: June 2023

Background Although there is a presumption that LGBTQ+ people living in rural Australia will have poorer health outcomes than those living in metropolitan areas, minimal research has focused specifically on the perspectives of transgender and gender diverse (henceforth referred to as ‘trans’) people living in these regions. The purpose of this study was to understand what health and wellbeing means to trans people in a regional or rural community and identify their health needs and experiences. Methods A total of 21 trans people were recruited through two regional sexual health centres (SHC) and interviewed between April and August 2021. Data were analysed via reflexive thematic analysis. This paper focuses on participants’ accounts of health and wellbeing regarding gender affirmation, the experience of rural living, respectful holistic care, safety in rural communities, isolation, loneliness, and employment. Results The experience of living rurally can have both positive and negative impacts on the experiences of trans people. Participants reported experiences of stigma and discrimination, reduced employment opportunities and limited social interactions, which led to feelings of isolation and loneliness; however, they also reported high quality of care, particularly with the specific SHCs which supported this research. Conclusion Living rurally can impact both positively and negatively on the health and wellbeing of trans peoples, and the experiences of living in this environment are diverse. Our findings challenge the perception that rural trans people experience only poor health outcomes and shows the difference that key health services such as SHCs can make in supporting trans health.
The application of catch–effort models to estimate the efficacy of aerial shooting operations on sambar deer (Cervus unicolor)
Authors: Ramsey David S. L. , McMaster Damien , Thomas Elaine
Published: June 2023

Context Aerial shooting from a helicopter targeting introduced sambar deer (Cervus unicolor) is a key activity being undertaken on public land in the North East and East Gippsland regions of Victoria. However, there is currently little published information on the efficacy of aerial shooting for reducing sambar deer populations in Australia. Aims The aims of this study were to analyse the operational data collected during an aerial shooting program in eastern Victoria, to assess the efficacy of aerial shooting at reducing sambar deer density and to inform management decisions on the required intensity of aerial shooting to achieve target densities. Methods Operational data (locations of all shot animals as well as aerial search effort) were analysed from 10 sites using a Bayesian generalised catch–effort model, which allowed for population changes between five periods of intensive control. The model allowed estimates of initial and residual abundance for each site to be made from the catch–effort data, which were used to estimate the efficacy of aerial shooting. Estimates of the detection rate of deer, which were allowed to vary with removal occasion and site, were then used to estimate the amount of aerial search effort required to reduce population densities by various proportional amounts. Key results Aerial shooting resulted in population reductions of 50–70% of sambar deer at four sites where aerial search intensities per unit area were highest. However, results at the remaining sites suggest that sambar deer densities have either remained static or increased over the five periods of aerial control. Recruitment of sambar deer between control periods, which was strongly influenced by study site elevation and season, was largely responsible for eroding reductions achieved by aerial shooting. Conclusions Catch–effort models applied to operational data collected during aerial shooting programs can be used to estimate control efficacy without the need for additional monitoring. Our analysis suggests that sufficiently high search intensities, around 1.4 km of search effort per km2 of habitat in each of five removal occasions, would need to be applied to achieve at least a 50% reduction in sambar deer densities.
3D surface reconstruction of cellular cryo-soft X-ray microscopy tomograms using semisupervised deep learning
Authors: Dyhr Michael C. A. , Sadeghi Mohsen , Moynova Ralitsa , Knappe Carolin , Kepsutlu Çakmak Burcu , Werner Stephan , Schneider Gerd , McNally James , Noé Frank , Ewers Helge
Published: June 2023

Cryo-soft X-ray tomography (cryo-SXT) is a powerful method to investigate the ultrastructure of cells, offering resolution in the tens of nanometer range and strong contrast for membranous structures without requiring labeling or chemical fixation. The short acquisition time and the relatively large field of view leads to fast acquisition of large amounts of tomographic image data. Segmentation of these data into accessible features is a necessary step in gaining biologically relevant information from cryo-soft X-ray tomograms. However, manual image segmentation still requires several orders of magnitude more time than data acquisition. To address this challenge, we have here developed an end-to-end automated 3D segmentation pipeline based on semisupervised deep learning. Our approach is suitable for high-throughput analysis of large amounts of tomographic data, while being robust when faced with limited manual annotations and variations in the tomographic conditions. We validate our approach by extracting three-dimensional information on cellular ultrastructure and by quantifying nanoscopic morphological parameters of filopodia in mammalian cells.
A molecular rotor FLIM probe reveals dynamic coupling between mitochondrial inner membrane fluidity and cellular respiration
Authors: Singh Gaurav , George Geen , Raja Sufi O. , Kandaswamy Ponnuvel , Kumar Manoj , Thutupalli Shashi , Laxman Sunil , Gulyani Akash
Published: June 2023

The inner mitochondrial membrane (IMM), housing components of the electron transport chain (ETC), is the site for respiration. The ETC relies on mobile carriers; therefore, it has long been argued that the fluidity of the densely packed IMM can potentially influence ETC flux and cell physiology. However, it is unclear if cells temporally modulate IMM fluidity upon metabolic or other stimulation. Using a photostable, red-shifted, cell-permeable molecular-rotor, Mitorotor-1, we present a multiplexed approach for quantitatively mapping IMM fluidity in living cells. This reveals IMM fluidity to be linked to cellular-respiration and responsive to stimuli. Multiple approaches combining in vitro experiments and live-cell fluorescence (FLIM) lifetime imaging microscopy (FLIM) show Mitorotor-1 to robustly report IMM ‘microviscosity’/fluidity through changes in molecular free volume. Interestingly, external osmotic stimuli cause controlled swelling/compaction of mitochondria, thereby revealing a graded Mitorotor-1 response to IMM microviscosity. Lateral diffusion measurements of IMM correlate with microviscosity reported via Mitorotor-1 FLIM-lifetime, showing convergence of independent approaches for measuring IMM local-order. Mitorotor-1 FLIM reveals mitochondrial heterogeneity in IMM fluidity; between-and-within cells and across single mitochondrion. Multiplexed FLIM lifetime imaging of Mitorotor-1 and NADH autofluorescence reveals that IMM fluidity positively correlates with respiration, across individual cells. Remarkably, we find that stimulating respiration, through nutrient deprivation or chemically, also leads to increase in IMM fluidity. These data suggest that modulating IMM fluidity supports enhanced respiratory flux. Our study presents a robust method for measuring IMM fluidity and suggests a dynamic regulatory paradigm of modulating IMM local order on changing metabolic demand.
Disrupting hate: The effect of deplatforming hate organizations on their online audience
Authors: Thomas Daniel Robert , Wahedi Laila A.
Published: June 2023

How does removing the leadership of online hate organizations from online platforms change behavior in their target audience? We study the effects of six network disruptions of designated and banned hate-based organizations on Facebook, in which known members of the organizations were removed from the platform, by examining the online engagements of the audience of the organization. Using a differences-in-differences approach, we show that on average the network disruptions reduced the consumption and production of hateful content, along with engagement within the network among periphery members. Members of the audience closest to the core members exhibit signs of backlash in the short term, but reduce their engagement within the network and with hateful content over time. The results suggest that strategies of targeted removals, such as leadership removal and network degradation efforts, can reduce the ability of hate organizations to successfully operate online.
Capturing patterns of evolutionary relatedness with reflectance spectra to model and monitor biodiversity
Authors: Griffith Daniel M. , Byrd Kristin B. , Anderegg Leander D. L. , Allan Elijah , Gatziolis Demetrios , Roberts Dar , Yacoub Rosie , Nemani Ramakrishna R.
Published: June 2023

Biogeographic history can set initial conditions for vegetation community assemblages that determine their climate responses at broad extents that land surface models attempt to forecast. Numerous studies have indicated that evolutionarily conserved biochemical, structural, and other functional attributes of plant species are captured in visible-to-short wavelength infrared, 400 to 2,500 nm, reflectance properties of vegetation. Here, we present a remotely sensed phylogenetic clustering and an evolutionary framework to accommodate spectra, distributions, and traits. Spectral properties evolutionarily conserved in plants provide the opportunity to spatially aggregate species into lineages (interpreted as “lineage functional types” or LFT) with improved classification accuracy. In this study, we use Airborne Visible/Infrared Imaging Spectrometer data from the 2013 Hyperspectral Infrared Imager campaign over the southern Sierra Nevada, California flight box, to investigate the potential for incorporating evolutionary thinking into landcover classification. We link the airborne hyperspectral data with vegetation plot data from 1372 surveys and a phylogeny representing 1,572 species. Despite temporal and spatial differences in our training data, we classified plant lineages with moderate reliability (Kappa = 0.76) and overall classification accuracy of 80.9%. We present an assessment of classification error and detail study limitations to facilitate future LFT development. This work demonstrates that lineage-based methods may be a promising way to leverage the new-generation high-resolution and high return-interval hyperspectral data planned for the forthcoming satellite missions with sparsely sampled existing ground-based ecological data.
Scavenger receptor B2, a type III membrane pattern recognition receptor, senses LPS and activates the IMD pathway in crustaceans
Authors: Shi Xiu-Zhen , Yang Ming-Chong , Kang Xin-Le , Li Yan-Xue , Hong Pan-Pan , Zhao Xiao-Fan , Vasta Gerardo R. , Wang Jin-Xing
Published: June 2023

The immune deficiency (IMD) pathway is critical for elevating host immunity in both insects and crustaceans. The IMD pathway activation in insects is mediated by peptidoglycan recognition proteins, which do not exist in crustaceans, suggesting a previously unidentified mechanism involved in crustacean IMD pathway activation. In this study, we identified a
Marsupenaeus japonicus
B class type III scavenger receptor, SRB2, as a receptor for activation of the IMD pathway. SRB2 is up-regulated upon bacterial challenge, while its depletion exacerbates bacterial proliferation and shrimp mortality via abolishing the expression of antimicrobial peptides. The extracellular domain of SRB2 recognizes bacterial lipopolysaccharide (LPS), while its C-terminal intracellular region containing a cryptic RHIM-like motif interacts with IMD, and activates the pathway by promoting nuclear translocation of RELISH. Overexpressing shrimp SRB2 in
Drosophila melanogaster
S2 cells potentiates LPS-induced IMD pathway activation and
diptericin
expression. These results unveil a previously unrecognized SRB2-IMD axis responsible for antimicrobial peptide induction and restriction of bacterial infection in crustaceans and provide evidence of biological diversity of IMD signaling in animals. A better understanding of the innate immunity of crustaceans will permit the optimization of prevention and treatment strategies against the arising shrimp diseases.
Membrane vesicle delivery of a streptococcal M protein disrupts the blood–brain barrier by inducing autophagic endothelial cell death
Authors: Pan Fei , Zhu Mingli , Liang Ying , Yuan Chen , Zhang Yu , Wang Yuchang , Fan Hongjie , Waldor Matthew K. , Ma Zhe
Published: June 2023

M family proteins are critical virulence determinants of Streptococci.
Streptococcus equi
subsp.
zooepidemicus
(SEZ) are Group C streptococci that cause meningitis in animals and humans. SzM, the M protein of SEZ, has been linked to SEZ brain invasion. Here, we demonstrate that SzM is important in SEZ disruption of the blood–brain barrier (BBB). SEZ release SzM-bound membrane vesicles (MVs), and endocytosis of these vesicles by human brain endothelial microvascular cells (hBMECs) results in SzM-dependent cytotoxicity. Furthermore, administration of SzM-bound MVs disrupted the murine BBB. A CRISPR screen revealed that SzM cytotoxicity in hBMECs depends on PTEN-related activation of autophagic cell death. Pharmacologic inhibition of PTEN activity prevented SEZ disruption of the murine BBB and delayed mortality. Our data show that MV delivery of SzM to host cells plays a key role in SEZ pathogenicity and suggests that MV delivery of streptococcal M family proteins is likely a common streptococcal virulence mechanism.
Selective permeation up a chemical potential gradient to enable an unusual solvent purification modality
Authors: White Haley D. , Yoon Young Hee , Ren Yi , Roos Conrad J. , Wang Yuxiang , Koros William J. , Lively Ryan P.
Published: June 2023

The need for energy-efficient recovery of organic solutes from aqueous streams is becoming more urgent as chemical manufacturing transitions toward nonconventional and bio-based feedstocks and processes. In addition to this, many aqueous waste streams contain recalcitrant organic contaminants, such as pharmaceuticals, industrial solvents, and personal care products, that must be removed prior to reuse. We observe that rigid carbon membrane materials can remove and concentrate organic contaminants via an unusual liquid-phase membrane permeation modality. Surprisingly, detailed thermodynamic calculations on the chemical potential of the organic contaminant reveal that the organic species has a higher chemical potential on the permeate side of the membrane than on the feed side of the membrane. This unusual observation challenges conventional membrane transport theory that posits that all permeating species move from high chemical potential states to lower chemical potential states. Based on experimental measurements, we hypothesize that the organic is concentrated in the membrane relative to water via favorable binding interactions between the organic and the carbon membrane. The concentrated organic is then swept through the membrane via the bulk flow of water in a modality known as “sorp-vection.” We highlight via simplified nonequilibrium thermodynamic models that this “uphill” chemical potential permeation of the organic does not result in second-law violations and can be deduced via measurements of the organic and water sorption and diffusion rates into the carbon membrane. Moreover, this work identifies the need to consider such nonidealities when incorporating unique, rigid materials for the separations of aqueous waste streams.
Sensory and motor representations of internalized rhythms in the cerebellum and basal ganglia
Authors: Kameda Masashi , Niikawa Koichiro , Uematsu Akiko , Tanaka Masaki
Published: June 2023

Both the cerebellum and basal ganglia are involved in rhythm processing, but their specific roles remain unclear. During rhythm perception, these areas may be processing purely sensory information, or they may be involved in motor preparation, as periodic stimuli often induce synchronized movements. Previous studies have shown that neurons in the cerebellar dentate nucleus and the caudate nucleus exhibit periodic activity when the animals prepare to respond to the random omission of regularly repeated visual stimuli. To detect stimulus omission, the animals need to learn the stimulus tempo and predict the timing of the next stimulus. The present study demonstrates that neuronal activity in the cerebellum is modulated by the location of the repeated stimulus and that in the striatum (STR) by the direction of planned movement. However, in both brain regions, neuronal activity during movement and the effect of electrical stimulation immediately before stimulus omission were largely dependent on the direction of movement. These results suggest that, during rhythm processing, the cerebellum is involved in multiple stages from sensory prediction to motor control, while the STR consistently plays a role in motor preparation. Thus, internalized rhythms without movement are maintained as periodic neuronal activity, with the cerebellum and STR preferring sensory and motor representations, respectively.
Experimentally simulating the evolution-to-ecology connection: Divergent predator morphologies alter natural food webs
Authors: Kolbe Jason J. , Giery Sean T. , Lapiedra Oriol , Lyberger Kelsey P. , Pita-Aquino Jessica N. , Moniz Haley A. , Leal Manuel , Spiller David A. , Losos Jonathan B. , Schoener Thomas W. , Piovia-Scott Jonah
Published: June 2023

The idea that changing environmental conditions drive adaptive evolution is a pillar of evolutionary ecology. But, the opposite—that adaptive evolution alters ecological processes—has received far less attention yet is critical for eco-evolutionary dynamics. We assessed the ecological impact of divergent values in a key adaptive trait using 16 populations of the brown anole lizard (Anolis sagrei). Mirroring natural variation, we established islands with short- or long-limbed lizards at both low and high densities. We then monitored changes in lower trophic levels, finding that on islands with a high density of short-limbed lizards, web-spider densities decreased and plants grew more via an indirect positive effect, likely through an herbivore-mediated trophic cascade. Our experiment provides strong support for evolution-to-ecology connections in nature, likely closing an otherwise well-characterized eco-evolutionary feedback loop.
Perceptual specializations for processing species-specific vocalizations in the common marmoset (Callithrix jacchus)
Authors: Osmanski Michael S. , Wang Xiaoqin
Published: June 2023

How humans and animals segregate sensory information into discrete, behaviorally meaningful categories is one of the hallmark questions in neuroscience. Much of the research around this topic in the auditory system has centered around human speech perception, in which categorical processes result in an enhanced sensitivity for acoustically meaningful differences and a reduced sensitivity for nonmeaningful distinctions. Much less is known about whether nonhuman primates process their species-specific vocalizations in a similar manner. We address this question in the common marmoset, a small arboreal New World primate with a rich vocal repertoire produced across a range of behavioral contexts. We first show that marmosets perceptually categorize their vocalizations in ways that correspond to previously defined call types for this species. Next, we show that marmosets are differentially sensitive to changes in particular acoustic features of their most common call types and that these sensitivity differences are matched to the population statistics of their vocalizations in ways that likely maximize category formation. Finally, we show that marmosets are less sensitive to changes in these acoustic features when within the natural range of variability of their calls, which possibly reflects perceptual specializations which maintain existing call categories. These findings suggest specializations for categorical vocal perception in a New World primate species and pave the way for future studies examining their underlying neural mechanisms.
Adaptive and maladaptive introgression in grapevine domestication
Authors: Xiao Hua , Liu Zhongjie , Wang Nan , Long Qiming , Cao Shuo , Huang Guizhou , Liu Wenwen , Peng Yanling , Riaz Summaira , Walker Andrew M. , Gaut Brandon S. , Zhou Yongfeng
Published: June 2023

Domesticated grapevines spread to Europe around 3,000 years ago. Previous studies have revealed genomic signals of introgression from wild to cultivated grapes in Europe, but the time, mode, genomic pattern, and biological effects of these introgression events have not been investigated. Here, we studied resequencing data from 345 samples spanning the distributional range of wild (
Vitis vinifera
ssp.
sylvestris
) and cultivated (
V. vinifera
ssp.
vinifera
) grapes. Based on machine learning–based population genetic analyses, we detected evidence for a single domestication of grapevine, followed by continuous gene flow between European wild grapes (EU) and cultivated grapes over the past ~2,000 y, especially from EU to wine grapes. We also inferred that soft-selective sweeps were the dominant signals of artificial selection. Gene pathways associated with the synthesis of aromatic compounds were enriched in regions that were both selected and introgressed, suggesting EU wild grapes were an important resource for improving the flavor of cultivated grapes. Despite the potential benefits of introgression in grape improvement, the introgressed fragments introduced a higher deleterious burden, with most deleterious SNPs and structural variants hidden in a heterozygous state. Cultivated wine grapes have benefited from adaptive introgression with wild grapes, but introgression has also increased the genetic load. In general, our study of beneficial and harmful effects of introgression is critical for genomic breeding of grapevine to take advantage of wild resources.
Cross-talk between phospholipid synthesis and peptidoglycan expansion by a cell wall hydrolase
Authors: Som Nilanjan , Reddy Manjula
Published: June 2023

The Gram-negative bacterial cell envelope is a complex multilayered structure comprising a bilayered phospholipid (PL) membrane that surrounds the cytoplasm (inner membrane or IM) and an asymmetric outer membrane (OM) with PLs in the inner leaflet and lipopolysaccharides in the outer leaflet. Between these two layers is the periplasmic space, which contains a highly cross-linked mesh-like glycan polymer, peptidoglycan (PG). During cell expansion, coordinated synthesis of each of these components is required to maintain the integrity of the cell envelope; however, it is currently not clear how such coordination is achieved. In this study, we show that a cross-link-specific PG hydrolase couples the expansion of PG sacculus with that of PL synthesis in the Gram-negative model bacterium, 
Escherichia coli
. We find that unregulated activity of a PG hydrolytic enzyme, MepS is detrimental for growth of
E. coli
during fatty acid (FA)-limiting conditions. Further genetic and biochemical analyses revealed that cellular availability of FA or PL alters the post-translational stability of MepS by modulating the proteolytic activity of a periplasmic adaptor-protease complex, NlpI-Prc toward MepS. Our results indicate that loss of OM lipid asymmetry caused by alterations in PL abundance leads to the generation of a signal to the NlpI-Prc complex for the stabilization of MepS, which subsequently cleaves the cross-links to facilitate expansion of PG. In summary, our study shows the existence of a molecular cross-talk that enables coordinated expansion of the PG sacculus with that of membrane synthesis for balanced cell-envelope biogenesis.
Activator-induced conformational changes regulate division-associated peptidoglycan amidases
Authors: Cook Jonathan , Baverstock Tyler C. , McAndrew Martin B. L. , Roper David I. , Stansfeld Phillip J. , Crow Allister
Published: June 2023

AmiA and AmiB are peptidoglycan-hydrolyzing enzymes fromEscherichia coli that are required to break the peptidoglycan layer during bacterial cell division and maintain integrity of the cell envelope. In vivo, the activity of AmiA and AmiB is tightly controlled through their interactions with the membrane-bound FtsEX–EnvC complex. Activation of AmiA and AmiB requires access to a groove in the amidase-activating LytM domain of EnvC which is gated by ATP-driven conformational changes in FtsEX–EnvC complex. Here, we present a high-resolution structure of the isolated AmiA protein, confirming that it is autoinhibited in the same manner as AmiB and AmiC, and a complex of the AmiB enzymatic domain bound to the activating EnvC LytM domain. In isolation, the active site of AmiA is blocked by an autoinhibitory helix that binds directly to the catalytic zinc and fills the volume expected to accommodate peptidoglycan binding. In the complex, binding of the EnvC LytM domain induces a conformational change that displaces the amidase autoinhibitory helix and reorganizes the active site for activity. Our structures, together with complementary mutagenesis work, defines the conformational changes required to activate AmiA and/or AmiB through their interaction with their cognate activator EnvC.
Sugar status in preexisting leaves determines systemic stomatal development within newly developing leaves
Authors: Bao Qin-Xin , Mu Xin-Rong , Tong Chen , Li Cong , Tao Wen-Zhe , Zhao Sheng-Ting , Liu Yu-xin , Wang Wan-Ni , Wei Yu-ting , Yu Fu-Huan , Wang Jing-wen , Sun Zhi-Lan , Fan Bing-Ling , Sun Jia , Wang Chen , Loake Gary J. , Meng Lai-Sheng
Published: June 2023

Stomata are pores found in the epidermis of stems or leaves that modulate both plant gas exchange and water/nutrient uptake. The development and function of plant stomata are regulated by a diverse range of environmental cues. However, how carbohydrate status in preexisting leaves might determine systemic stomatal formation within newly developing leaves has remained obscure. The glucose (Glc) sensor HEXOKINASE1 (HXK1) has been reported to decrease the stability of an ethylene/Glc signaling transcriptional regulator, EIN3 (ETHYLENE INSENSITIVE3). EIN3 in turn directly represses the expression of
SUC2
(
sucrose transporter 2
), encoding a master transporter of sucrose (Suc). Further, KIN10, a nuclear regulator involved in energy homeostasis, has been reported to repress the transcription factor SPCH (SPEECHLESS), a master regulator of stomatal development. Here, we demonstrate that the Glc status of preexisting leaves determines systemic stomatal development within newly developing leaves by the HXK1—¦EIN3—¦SUC2 module. Further, increasing Glc levels in preexisting leaves results in a HXK1-dependent decrease of EIN3 and increase of SUC2, triggering the perception, amplification and relay of HXK1-dependent Glc signaling and thereby triggering Suc transport from mature to newly developing leaves. The HXK1—¦EIN3—¦SUC2 molecular module thereby drives systemic Suc transport from preexisting leaves to newly developing leaves. Subsequently, increasing Suc levels within newly developing leaves promotes stomatal formation through the established KIN10⟶ SPCH module. Our findings thus show how a carbohydrate signal in preexisting leaves is sensed, amplified and relayed to determine the extent of systemic stomatal development within newly developing leaves.