bluuebunny/crossref_metadata_2025 huggingface dataset:
A Clinicopathological Analysis of Molecular Subtypes of Breast Cancer using Immunohistochemical Surrogates: A 6-Year Institutional Experience from a Tertiary Cancer Center in North India
Authors: Somal Puneet Kaur , Sancheti Sankalp , Sharma Aishwarya , Sali Akash Pramod , Chaudhary Debashish , Goel Alok , Dora Tapas Kumar , Brar Rahat , Gulia Ashish , Divatia Jigeeshu
Published: March 2023

Objective Classification of breast cancer into different molecular subtypes has important prognostic and therapeutic implications. The immunohistochemistry surrogate classification has been advocated for this purpose. The primary objective of the present study was to assess the prevalence of the different molecular subtypes of invasive breast carcinoma and study the clinicopathological parameters in a tertiary care cancer center in rural North India.

Materials and Methods All female patients diagnosed with invasive breast cancer and registered between January 1, 2015, and December 31, 2020, were included. Patients with bilateral cancer, missing information on HER2/ER/PR receptor status, absence of reflex FISH testing after an equivocal score on Her 2 IHC were excluded. The tumors were classified into different molecular subtypes based on IHC expression as follows-luminal A-like (ER- and PR-positive, Her2-negative, Ki67 < 20%), luminal B-like Her2-negative (ER-positive, Her2-negative and any one of the following Ki67% ≥ 20% or PR-negative/low, luminal B-like Her2-positive (ER- and HER2-positive, any Ki67, any PR), Her2-positive (ER- and PR-negative, Her2-positive) and TNBC (ER, PR, Her2-negative). Chi square test was used to compare the clinicopathological parameters between these subtypes.

Results A total of 1,625 cases were included. Luminal B-like subtype was the most common (41.72%). The proportion of each subtype was luminal A (15.69%), luminal B Her2-negative (23.93%), luminal B Her2-positive (17.78%), Her2-positive (15.26%), TNBC (27.32%). Majority of the tumors were Grade 3 (75.81%). Nodal metastases were present in 59%. On subanalysis of the luminal type tumors without Her2 expression (luminal A-like and luminal B-like (Her2-negative), luminal A-like tumors presented significantly with a lower grade (p < 0.001) and more frequent node-negative disease in comparison to luminal B-like (Her2-negative) tumors. In comparison to other subtypes, TNBC tumors were more frequently seen in the premenopausal age group (p < 0.001) and presented with node-negative disease (p < 0.001).

Conclusion This is one of the largest studies that enumerates the prevalence of various molecular subtypes of breast cancer in North India. Luminal B-like tumors were the most common followed by TNBC. TNBC tumors presented more commonly in premenopausal age group and with node negative disease in comparison to other subtypes.
Moving Beyond Movement: Diagnosing Functional Movement Disorder
Authors: Gilmour Gabriela S. , Lidstone Sarah C.
Published: March 2023

Functional movement disorder (FMD) is a complex neuropsychiatric syndrome, encompassing abnormal movements and weakness, and is a common cause of potentially disabling neurological symptoms. It is vital to recognize that FMD is a syndrome, with nonmotor manifestations negatively affecting a patient's quality of life. This review highlights a diagnostic algorithm, where a history suggestive of FMD is combined with the presence of positive signs on examination and appropriate investigations to make the diagnosis. Positive signs indicate internal inconsistency such as variability and distractibility, and clinical findings that are incongruent with other known neurological disease. Importantly, the clinical assessment acts as the first opportunity to allow patients to understand FMD as the cause for their symptoms. Accurate and early diagnosis of FMD is necessary given that it is a treatable and potentially reversible cause of disability, with significant risk of iatrogenic harm associated with misdiagnosis.
Global Epidemiology of Movement Disorders: Rare or Underdiagnosed?
Authors: O'Shea Sarah A. , Shih Ludy C.
Published: March 2023

In this manuscript, we review the epidemiology of movement disorders including Parkinson's disease (PD), atypical parkinsonism, essential tremor, dystonia, functional movement disorders, tic disorders, chorea, and ataxias. We emphasize age-, sex-, and geography-based incidence and prevalence, as well as notable trends including the rising incidence and prevalence of PD. Given the growing global interest in refining clinical diagnostic skills in recognizing movement disorders, we highlight some key epidemiological findings that may be of interest to clinicians and health systems tasked with diagnosing and managing the health of patients with movement disorders.
Not just mind reading: improving the stability and scalability of brain-machine interfaces
Authors: Lim Alane
Published: March 2023

Research on smart, flexible electronics can pave the way for higher-resolution and highly stable brain-machine devices.
Quasi-localized charge approximation approach for the nonlinear structures in strongly coupled Yukawa systems
Authors: Kumar Prince , Sharma Devendra
Published: March 2023

Strongly coupled systems occupying the transitional range between the Wigner crystal and fluid phases are the most dynamic constituents of the nature. Highly localized but strongly interacting elements in this phase possess enough thermal energy to trigger the transition between a variety of short to long range order phases. Nonlinear excitations are often carriers of proliferating structural modifications in the strongly coupled Yukawa systems. Well represented by laboratory dusty plasmas, these systems show explicit propagation of nonlinear shocks and solitary structures both in experiments and first principles simulations. The shorter scale length contributions remain absent at strong screening in the present approximate models, which nevertheless prescribe nonlinear solitary solutions that consequently lose their coherence in a numerical evolution of the system under the special implementation of a quasi-localized charge approximation (QLCA) formulation. The stable coherent structures self-consistently emerge following an initial transient in the numerical evolution that adapts QLCA approach to spatiotemporal domain for accessing the nonlinear excitations in the strong screening limit. The present κ∼1 limit of the existing Yukawa fluid models to show agreement with the experiment and molecular dynamical simulations has, therefore, been overcome, and the coherent nonlinear excitations have become characterizable up to κ∼2.7, before they become computationally challenging in the present implementation.
Semi Active Control of sinusoidal shock waveform on drop test machine (DTM) using non-linear dynamic model of hybrid wave generator (HWG) consisting of rubber and electroMagnet
Authors: Iqbal Muhammad Zahid , Israr Asif , Abbas Tanveer
Published: March 2023

Sinusoidal shock waveforms are the classical type of waveforms generated in Drop Test Machines (DTMs) using Rubber Wave Generators (RWGs). For different specifications of pulse, different RWGs are used, leading to the laborious work of replacing RWGs in DTMs. In this study, a novel technique is developed to predict a shock pulse of variable height and time using a Hybrid Wave Generator (HWG) that yields variable stiffness. This variable stiffness is a combination of the fixed stiffness of rubber and the variable stiffness of magnet. A mathematical nonlinear model has developed, consisting of a polynomial model of RWG and an integral approach of magnetic force. The designed HWG is capable enough to produce a strong magnetic force as a result of a high magnetic field generated in the solenoid. This magnetic force combines with rubber to give a variable stiffness effect. This way, a semi-active control of the stiffness and pulse shape is achieved. Two sets of HWGs are tested to study the control over the shock pulse. An average hybrid stiffness from 32 to 74 kN/m is observed by varying voltage from 0 to 1000 VDC, resulting in a change of height of pulse from 18 to 56 g (net change 38 g) and a change of shock pulse width from 17 to 12 ms (net change 5 ms). From experimental results, it is concluded that the developed technique gives satisfactory results for the control/prediction of variable shape shock pulse.
Femtosecond laser fabrication of large-core fiber Bragg gratings for high-power fiber oscillators
Authors: Li Hao , Yang Baolai , Wang Meng , Gao Chenhui , Wu Baiyi , Zeng Lingfa , Xi Xiaoming , Chen Zilun , Wang Xiaolin , Wang Zefeng , Chen Jinbao
Published: March 2023

In this paper, a fs-laser phase mask inscription system based on a galvanometer scanning strategy is designed and set up for the fabrication of large-core fiber Bragg gratings (FBGs). Based on this setup, a homogeneous cross-sectional refractive index modulation can be achieved in the core of a large-mode-area fiber, and a pair of FBGs are fabricated in fibers with a core diameter of 30 µm. To investigate the performance of the fabricated FBGs, a high power all-fiber oscillator is built using a pure backward pumping structure. The FBGs work well, and the maximum output power of 7920 W is achieved with an optical–optical conversion efficiency of 77.3%. To the best of our knowledge, this is the highest power of all-fiber oscillators based on fs-written FBGs. This work provides a flexible, stable, and economic scanning strategy for large-core FBG inscription and exhibits excellent performance for high power fiber lasers.
Studies on plasma transport processes in the cathode sheath of atmospheric direct-current arc discharge with particle-in-cell and Monte Carlo collision simulation
Authors: Sun Li , Sun Xian-Pin , Zhou Wen , Li Zeng-Yao
Published: March 2023

A voltage-driven cathode sheath model in an atmospheric-pressure argon arc discharge is developed in the framework of an implicit particle-in-cell Monte Carlo collision (PIC–MCC) method. Plasma transport processes are solved numerically in one dimension without any local-equilibrium hypotheses, in particular, without explicitly dividing sheath and a quasi-neutral plasma region. The right boundary of the computational domain located at the pre-sheath is determined first by observing the variation in typical parameters. A comparison of results is given with different positions of the right boundary to study the plasma transport processes in the cathode sheath. Number densities, spatially averaged energies, electric field and potential, collision frequency, heating rate of electrons, as well as the spatially averaged electron energy probability function inside the sheath, are predicted self-consistently based on this newly developed kinetic model. It is shown that both excitation collisions and ionization collisions occur inside the sheath, and collision frequency of the former is larger than the latter. The collision frequency of charge exchange is higher than that of elastic collision for ions. In addition, the effects of different electron emission processes are described. It is indicated that the thermionic emission on the hot cathode surface is not the only significant emission mechanism to sustain the arc discharges.
Drift-ordered fluid vorticity equation with energy consistency
Authors: Halpern Federico D. , Waltz Ronald E. , Bernard Tess N.
Published: March 2023

Although drift-ordered fluid models are widely applied in tokamak edge turbulence simulations, the models used are acknowledged not to conserve energy or even electrical charge. The present paper aims to remove many of the existing pitfalls in drift-fluid models, however, with the objective of finding a solution simple enough to be implemented in numerical applications. Our main result is an improved version of the drift-Braginskii equations involving a generalized vorticity function. In the new drift-Braginskii system, the quasi-neutrality condition translates into a transport equation for a generalized vorticity, expressed in conservation form, and related to the total mass-weighted circulation. It is found that kinetic energy conservation can be achieved if the polarization flow is defined recursively. The resulting model conserves the kinetic energy associated with E×B and diamagnetic flows and retains the associated perpendicular kinetic energy flux.
Variational theory of angulons and their rotational spectroscopy
Authors: Zeng Zhongda , Yakaboylu Enderalp , Lemeshko Mikhail , Shi Tao , Schmidt Richard
Published: March 2023

The angulon, a quasiparticle formed by a quantum rotor dressed by the excitations of a many-body bath, can be used to describe an impurity rotating in a fluid or solid environment. Here, we propose a coherent state ansatz in the co-rotating frame, which provides a comprehensive theoretical description of angulons. We reveal the quasiparticle properties, such as energies, quasiparticle weights, and spectral functions, and show that our ansatz yields a persistent decrease in the impurity’s rotational constant due to many-body dressing, which is consistent with experimental observations. From our study, a picture of the angulon emerges as an effective spin interacting with a magnetic field that is self-consistently generated by the molecule’s rotation. Moreover, we discuss rotational spectroscopy, which focuses on the response of rotating molecules to a laser perturbation in the linear response regime. Importantly, we take into account initial-state interactions that have been neglected in prior studies and reveal their impact on the excitation spectrum. To examine the angulon instability regime, we use a single-excitation ansatz and obtain results consistent with experiments, in which a broadening of spectral lines is observed while phonon wings remain highly suppressed due to initial-state interactions.
A direct liquid sampling interface for photoelectron photoion coincidence spectroscopy
Authors: Wu Xiangkun , Pan Zeyou , Steglich Mathias , Ascher Patrick , Bodi Andras , Bjelić Saša , Hemberger Patrick
Published: March 2023

We introduce an effective and flexible high vacuum interface to probe the liquid phase with photoelectron photoion coincidence (liq-PEPICO) spectroscopy at the vacuum ultraviolet (VUV) beamline of the Swiss Light Source. The interface comprises a high-temperature sheath gas-driven vaporizer, which initially produces aerosols. The particles evaporate and form a molecular beam, which is skimmed and ionized by VUV radiation. The molecular beam is characterized using ion velocity map imaging, and the vaporization parameters of the liq-PEPICO source have been optimized to improve the detection sensitivity. Time-of-flight mass spectra and photoion mass-selected threshold photoelectron spectra (ms-TPES) were recorded for an ethanolic solution of 4-propylguaiacol, vanillin, and 4-hydroxybenzaldehyde (1 g/l of each). The ground state ms-TPES band of vanillin reproduces the reference, room-temperature spectrum well. The ms-TPES for 4-propylguaiacol and 4-hydroxybenzaldehyde are reported for the first time. Vertical ionization energies obtained by equation-of-motion calculations reproduce the photoelectron spectral features. We also investigated the aldol condensation dynamics of benzaldehyde with acetone using liq-PEPICO. Our direct sampling approach, thus, enables probing reactions at ambient pressure during classical synthesis procedures and microfluidic chip devices.
Disentangling the magneto-optic Kerr effect of manganite epitaxial heterostructures
Authors: Schöpf Jörg , van Loosdrecht Paul H. M. , Lindfors-Vrejoiu Ionela
Published: March 2023

The magneto-optic Kerr effect can probe the process of magnetization reversal in ferromagnetic thin films and can, thus, be used as an alternative to magnetometry. The Kerr effect is wavelength-dependent and the Kerr rotation can reverse sign, vanishing at particular wavelengths. We investigate the epitaxial heterostructures of ferromagnetic manganite, La0.7Sr0.3Mn0.9Ru0.1O3, by using the polar Kerr effect and magnetometry. The manganite layers are separated by or interfaced with a layer of nickelate, NdNiO3. The Kerr rotation hysteresis loops of trilayers, with two manganite layers of different thicknesses separated by a nickelate layer, have intriguing humplike features when measured with light of 400 nm wavelength. By investigating additional reference samples, we disentangle the contributions of the individual layers to the loops: we show that the humps originate from the opposite sense of the Kerr rotation of the two different ferromagnetic layers, combined with the additive behavior of the Kerr signal. The change of sign of the Kerr rotation for the thinner manganite layer is most likely caused by optical interference.
Quantum electrodynamics of non-demolition detection of single microwave photon by superconducting qubit array
Authors: Navez P. , Balanov A. G. , Savel’ev S. E. , Zagoskin A. M.
Published: March 2023

By consistently applying the formalism of quantum electrodynamics, we developed a comprehensive theoretical framework describing the interaction of single microwave photons with an array of superconducting transmon qubits in a waveguide cavity resonator. In particular, we analyze the effects of microwave photons on the array’s response to a weak probe signal exciting the resonator. The study reveals that high quality factor cavities provide a better spectral resolution of the response, while cavities with moderate quality factors allow better sensitivity for a single-photon detection. Remarkably, our analysis showed that a single-photon signal can be detected by even a sole qubit in a cavity under the realistic range of system parameters. We also discuss how the quantum properties of the microwave radiation and electrodynamical properties of resonators affect the response of qubits’ array. Our results provide an efficient theoretical background for informing the development and design of quantum devices consisting of arrays of qubits, especially for those using a cavity where an explicit expression for the transmission or reflection is required.
A perspective on Faraday isolators for advanced lasers
Authors: Mironov E. A. , Snetkov I. L. , Starobor A. V. , Palashov O. V.
Published: March 2023

Advances in the development of lasers with high output power raise the problem of increasing the operating power of Faraday isolators, since these devices can be indispensable in a number of applications. Due to the relatively high absorption of laser radiation in magneto-active media that are the basis of isolators, their use in laser systems is limited. In this Perspective, we overview the approaches that can be used to develop Faraday isolators with a high level of operating power and summarize the related achievements made in recent years, which have become possible due to the production of a wide range of new magneto-active media and the study of their properties. The issues and challenges on the path of further progress, as well as promising directions for it, are discussed.
Dust acoustic wave properties in varying discharge volumes
Authors: Knapek C. A. , Schwabe M. , Yaroshenko V. , Huber P. , Mohr D. P. , Konopka U.
Published: March 2023

Properties of self-excited dust acoustic waves under the influence of active compression of the dust particle system were experimentally studied in the laboratory and under microgravity conditions (parabolic flight). Ground based laboratory experiments clearly show that wave properties can be manipulated by changing the discharge volume, its aspect ratio, and thus the dust particle density. Complementary experiments under microgravity conditions, performed to exclude the effects of gravity inflicted sedimentation and anisotropic behavior, were less conclusive due to residual fluctuations in the planes acceleration indicating the need for a better microgravity environment. A theoretical model, using plasma parameters obtained from particle-in-cell simulations as input, supports the experimental findings. It shows that the waves can be described as a new observation of the dust acoustic mode, which demonstrates their generic character.
Recommended Correlations for the Surface Tension of Ethers
Authors: Mulero A. , Cachadiña I. , Becerra A.
Published: March 2023

Surface tension values for 82 ethers have been compiled from databases, books, and papers in the literature. The data were carefully screened, and finally, 2122 values were selected. Each fluid dataset has been fitted with the Guggenheim–Katayama correlation with two, four, or six adjustable parameters, except diphenyl ether, for which the data taken from different sources clearly disagree. Thus, recommended correlations are proposed for 81 ethers. The proposed correlations provide mean absolute deviations equal to or below 0.5 mN/m and mean absolute percentage deviations below 2.6% for 79 ethers. Moreover, percentage deviations below 9.5% are obtained for all the selected data of 78 ethers. The highest deviations found are due to the disagreement between the data obtained from different sources and not to an inadequate mathematical form of the correlation model. These correlations are added to the collection of those previously proposed for different fluids, including common substances, alcohols, refrigerants, organic acids, n-alkanes, and esters.
A comprehensive modeling approach for polymorph selection in Lennard-Jones crystallization
Authors: Bulutoglu Pelin S. , Zalte Akshat S. , Nere Nandkishor K. , Ramkrishna Doraiswami , Corti David S.
Published: March 2023

Computational predictions of the polymorphic outcomes of a crystallization process, referred to as polymorph selection, can accelerate the process development for manufacturing solid products with targeted properties. Polymorph selection requires understanding the interplay between the thermodynamic and kinetic factors that drive nucleation. Moreover, post-nucleation events, such as crystal growth and polymorphic transformation, can affect the resulting crystal structures. Here, the nucleation kinetics of the Lennard-Jones (LJ) fluid from the melt is investigated with a focus on the competition between FCC and HCP crystal structures. Both molecular dynamics (MD) simulations and 2D free energy calculations reveal that polymorph selection occurs not during nucleation but when the cluster sizes exceed the critical cluster size. This result contrasts with the classical nucleation mechanism, where each polymorph is assumed to nucleate independently as an ideal bulk-like cluster, comprised only of its given structure. Using the 2D free energy surface and the MD simulation-derived diffusion coefficients, a structure-dependent nucleation rate is estimated, which agrees with the rate obtained from brute force MD simulations. Furthermore, a comprehensive population balance modeling (PBM) approach for polymorph selection is proposed. The PBM combines the calculated nucleation rate with post-nucleation kinetics while accounting for the structural changes of the clusters after nucleation. When applied to the LJ system, the PBM predicts with high accuracy the polymorphic distribution found in a population of crystals generated from MD simulations. Due to the non-classical nucleation mechanism of the LJ system, post-nucleation kinetic events are crucial in determining the structures of the grown crystals.
Single-molecule tracking of dye diffusion in synthetic polymers: A tutorial review
Authors: Tran-Ba Khanh-Hoa , Foreman Kathryn
Published: March 2023

Single-molecule tracking (SMT) methods have been widely employed to offer a high-resolution characterization of synthetic polymers under ambient conditions and, thus, have advanced our understanding of their unique material properties. SMT is based on the systematic monitoring of the diffusive motions of individual fluorescent dye molecules in the as-prepared polymer thin films or thicker monoliths. Quantitative assessment of the recorded SMT video data involves the systematic analysis of the generated diffusion trajectories of a single molecule using well-established and reported methods. The results have offered a wealth of new information on the structural alignment, orientational order, and long-range continuity of the polymer microdomains; the nanoscale material heterogeneities governed by defects, misalignment, and ill-controlled preparation conditions; as well as the various forms of probe–host interactions on the single-molecule level. In the first part of this Tutorial review, we describe the fundamental principles and instrumentation of SMT, before offering interested readers and potential future SMT users a practical guidance on the selection of fluorescent probe molecules, preparation of suitable samples, and optimization of experimental conditions and imaging parameters. Then, we highlight several representative SMT studies in microphase-separated block copolymers, and semicrystalline and amorphous homopolymers to further emphasize the usefulness of SMT methods for polymer characterization without neglecting some of their shortcomings. This Tutorial review is written with the motivation to attract new researchers to the fast-growing field and assist them in starting their own SMT research of synthetic polymers and other technologically useful soft matter systems.
Perspective on near-field radiative heat transfer
Authors: Pascale Mariano , Giteau Maxime , Papadakis Georgia T.
Published: March 2023

Although near-field radiative heat transfer was introduced in the 1950s, interest in the field has only recently revived, as the effect promises improved performance in various applications where contactless temperature regulation in the small-scale is a requirement. With progress in computational electromagnetics as well as in nanoinstrumentation, it has become possible to simulate the effect in complex configurations and to measure it with high precision. In this Perspective, we highlight key theoretical and experimental advances in the field, and we discuss important developments in tailoring and enhancing near-field thermal emission and heat transfer. We discuss opportunities in heat-to-electricity energy conversion with thermophotovoltaic systems, as well as non-reciprocal heat transfer, as two of many recent focus topics in the field. Finally, we highlight key experimental challenges and opportunities with emerging materials, for probing near-field heat transfer for relevant technologies in the large-scale.
Initial characterization of a dynamic hohlraum radiation source tailored for high-temperature opacity measurements at an 8-MA facility
Authors: Yi Qiang , Meng Shijian , Ye Fan , Lu Jian , Yan Xiaosong , Yang Ruihua , Jiang Shuqing , Ning Jiamin , Zhou Lin , Chen Faxin , Yang Jianlun , Xu Zeping , Li Zhenghong
Published: March 2023

This paper reports some important properties of a dynamic hohlraum radiation source intended to study the high-temperature opacity of medium-Z atoms. The time-resolved axial radiation power in two x-ray diodes gives the time-evolution of an equivalent black-body temperature that peaks at ∼260 eV at stagnation. Time-gated framing pinhole images show that the source comprises an intense high-temperature core that lasts for ∼2 ns preceded by a 10-ns-long lower-temperature implosion phase that emits mostly softer x rays. Combining pinhole images with soft x-ray power gives a time-resolved brightness radiation temperature that reaches 130 eV. Thus, the lower-temperature source could ionize an opacity sample, then the intense high-temperature radiation pulse could measure its opacity. Likewise, the time-integrated spectrum measured with a spherically bent crystal spectrometer is compatible with multiple blackbodies with different temperatures, from 176 to 185 eV. These characterizations suggest that this dynamic hohlraum can be used for high-temperature opacity measurements.
Using new solvatochromic parameters to investigate dye–solvent interactions
Authors: Akpe Victor , Biddle Timothy J. , Madu Christian , Kim Tak H. , Brown Christopher L. , Cock Ian E.
Published: March 2023

Solvatochromic behaviours of triazine substituted dyes were evaluated using a novel approach derived from the red shift index (RsI) and associated solvation energy (ASE). These parameters were used to describe the solvation trends of the dye–solvent interactions based on their polarity changes. The concept demonstrates the effect of substituent changes on the triazine scaffold and the induced solvent polarity changes as solvated dyes go through the HOMO–LUMO (highest occupied molecular orbital-lowest uncopied molecular orbital) phases. Primarily, these phases were characterised by evaluating the wavelength of the absorption and emission spectra in different solvents, which, in conjunction with the recently reported computational approaches, provides a well-adjusted model for predicting spectra polarity changes between the dye (solute) and the solvent. Based on the results from this study, predictive polarity changes on the triazine scaffold in different solvents can be empirically monitored both in ground and excited states. Moreover, the solvatochromic parameters can be extended to evaluate the predictive behaviours of different spectra dyes.
Friends to the rescue: using arbuscular mycorrhizal fungi to future-proof Australian agriculture
Authors: Heuck Meike Katharina , Birnbaum Christina , Frew Adam
Published: March 2023

With a rising global population and the challenges of climate change, there is an increasing need to find solutions to maintain crop yields in an ecologically sustainable way. Although many studies have focussed on this issue, comparatively few are conducted in the southern hemisphere. This is worrisome because the geographical and geomorphological conditions within Australia differ greatly from the northern hemisphere. To ensure food security, approaches can rely on conventional agricultural methods as well as commercial arbuscular mycorrhizal (AM) fungal inoculants. Both approaches lack the capacity to be successful in the long term or could have unknown negative effects on the naturally occurring microbial communities. We advocate for a sustainable and holistic approach that combines the effective management of functionally diverse AM fungal communities with precision farming techniques while integrating landscape elements into agricultural fields. In addition, landowners and scientists should collaborate and communicate their work with industry and government to take forward the shift to a more-sustainable agriculture. In this way, we will be better able to secure our food production while restoring our soil ecosystems.
Finding Ngabi (Hemiaspis damelii): factors affecting the use of modified floodplain wetlands by an endangered snake
Authors: Michael D. R. , Nimmo D. G. , Stevens E. , Schlen T. , Wassens S.
Published: March 2023

Context River regulation, coupled with climate change, has caused significant declines in global freshwater biodiversity. In Australia, water extraction within the Murray–Darling Basin (MDB) has reduced the frequency, extent and duration with which floodplains are inundated, resulting in widespread declines in wetland-dependent biodiversity, including reptiles. The endangered Ngabi (Hemiaspis damelii) is associated with floodplain systems in the MDB, yet its distribution and ecological requirements are poorly understood, hampering conservation actions. Aims We sought to validate an assumption that Ngabi is associated with wetland vegetation communities before investigating factors affecting its probability of detection in the lower Murrumbidgee catchment in southern New South Wales. We predicted Ngabi occurrence patterns would relate to frog abundance, wetland hydrology, microhabitat attributes and meteorological variables. Methods We compared Ngabi observations from 16 paired wetland and dryland vegetation transects to evaluate associations with vegetation type. We then used generalised linear mixed models to relate snake presence and absence to prey (frog abundance), microhabitat (logs and ground cover), wetland hydrology (water depth and inundation frequency) and meteorological conditions, using 12 repeat surveys between September 2018 and March 2021. Key results Fifty-eight snakes were observed at five of eight wetlands during the study. Ngabi was exclusively recorded in river red gum/spike rush or lignum vegetation communities, and was absent from sandhill woodland or chenopod communities. The probability of detecting Ngabi increased with ambient temperature and weakly with wetland inundation frequency, but not frog abundance, microhabitat attributes or year. Conclusions Ngabi is strongly associated with floodplain vegetation communities and, to some extent, frequently inundated wetlands in southern NSW, suggesting water management agencies should incorporate threatened floodplain snake species into future wetland management plans. The use of environmental water to restore aspects of flow regimes, improve wetland health and aquatic diversity is likely to benefit other wetland-dependent snake populations across the MDB. Implications The positive relationship between Ngabi detections and ambient temperature will be important for designing an effective monitoring program for the species across the MDB. Furthermore, our findings provide insight into the benefits of using environmental water to create wetland refuges to maintain floodplain snake populations during droughts.
Model misspecification misleads inference of the spatial dynamics of disease outbreaks
Authors: Gao Jiansi , May Michael R. , Rannala Bruce , Moore Brian R.
Published: March 2023

Epidemiology has been transformed by the advent of Bayesian phylodynamic models that allow researchers to infer the geographic history of pathogen dispersal over a set of discrete geographic areas [1, 2]. These models provide powerful tools for understanding the spatial dynamics of disease outbreaks, but contain many parameters that are inferred from minimal geographic information (i.e., the single area in which each pathogen was sampled). Consequently, inferences under these models are inherently sensitive to our prior assumptions about the model parameters. Here, we demonstrate that the default priors used in empirical phylodynamic studies make strong and biologically unrealistic assumptions about the underlying geographic process. We provide empirical evidence that these unrealistic priors strongly (and adversely) impact commonly reported aspects of epidemiological studies, including: 1) the relative rates of dispersal between areas; 2) the importance of dispersal routes for the spread of pathogens among areas; 3) the number of dispersal events between areas, and; 4) the ancestral area in which a given outbreak originated. We offer strategies to avoid these problems, and develop tools to help researchers specify more biologically reasonable prior models that will realize the full potential of phylodynamic methods to elucidate pathogen biology and, ultimately, inform surveillance and monitoring policies to mitigate the impacts of disease outbreaks.
Wheat
Ym2
originated from
Aegilops sharonensis
and confers resistance to soil-borne
Wheat yellow mosaic virus
infection to the roots
Authors: Mishina Kohei , Suzuki Takako , Oono Youko , Yamashita Yoko , Zhu Hongjing , Ogawa Taiichi , Ohta Masaru , Doman Kohei , Xu Wenjing , Takahashi Daichi , Miyazaki Taiga , Tagiri Akemi , Soma Chihiro , Horita Harukuni , Nasuda Shuhei , De Oliveira Romain , Paux Etienne , Chen Guoxiong , Pourkheirandish Mohammad , Wu Jianzhong , Liu Cheng , Komatsuda Takao
Published: March 2023

Wheat yellow mosaic virus
(WYMV) is a pathogen transmitted into its host’s roots by the soil-borne vector
Polymyxa graminis
.
Ym1
and
Ym2
genes protect the host from the significant yield losses caused by the virus, but the mechanistic basis of these resistance genes remains poorly understood. Here, it has been shown that
Ym1
and
Ym2
act within the root either by hindering the initial movement of WYMV from the vector into the root and/or by suppressing viral multiplication. A mechanical inoculation experiment on the leaf revealed that the presence of
Ym1
reduced viral infection incidence, rather than viral titer, while that of
Ym2
was ineffective in the leaf. To understand the basis of the root specificity of the
Ym2
product, the gene was isolated from bread wheat using a positional cloning approach. The candidate gene encodes a CC-NBS-LRR protein and it correlated allelic variation with respect to its sequence with the host’s disease response.
Ym2
(B37500) and its paralog (B35800) are found in the near-relatives, respectively,
Aegilops sharonensi
s and 
Aegilops speltoides
(a close relative of the donor of bread wheat’s B genome), while both sequences, in a concatenated state, are present in several accessions of the latter species
.
Structural diversity in
Ym2
has been generated via translocation and recombination between the two genes and enhanced by the formation of a chimeric gene resulting from an intralocus recombination event. The analysis has revealed how the
Ym2
region has evolved during the polyploidization events leading to the creation of cultivated wheat.
Inflammation differentially controls transport of depolarizing Nav versus hyperpolarizing Kv channels to drive rat nociceptor activity
Authors: Higerd-Rusli Grant P. , Tyagi Sidharth , Baker Christopher A. , Liu Shujun , Dib-Hajj Fadia B. , Dib-Hajj Sulayman D. , Waxman Stephen G.
Published: March 2023

Inflammation causes pain by shifting the balance of ionic currents in nociceptors toward depolarization, leading to hyperexcitability. The ensemble of ion channels within the plasma membrane is regulated by processes including biogenesis, transport, and degradation. Thus, alterations in ion channel trafficking may influence excitability. Sodium channel NaV1.7 and potassium channel KV7.2 promote and oppose excitability in nociceptors, respectively. We used live-cell imaging to investigate mechanisms by which inflammatory mediators (IM) modulate the abundance of these channels at axonal surfaces through transcription, vesicular loading, axonal transport, exocytosis, and endocytosis. Inflammatory mediators induced a NaV1.7-dependent increase in activity in distal axons. Further, inflammation increased the abundance of NaV1.7, but not of KV7.2, at axonal surfaces by selectively increasing channel loading into anterograde transport vesicles and insertion at the membrane, without affecting retrograde transport. These results uncover a cell biological mechanism for inflammatory pain and suggest NaV1.7 trafficking as a potential therapeutic target.
Cross-sections of doubly curved sheets as confined elastica
Authors: He Mengfei , Démery Vincent , Paulsen Joseph D.
Published: March 2023

Although thin films are typically manufactured in planar sheets or rolls, they are often forced into three-dimensional (3D) shapes, producing a plethora of structures across multiple length scales. To understand this complex response, previous studies have either focused on the overall gross shape or the small-scale buckling that decorates it. A geometric model, which considers the sheet as inextensible yet free to compress, has been shown to capture the gross shape of the sheet. However, the precise meaning of such predictions, and how the gross shape constrains the fine features, remains unclear. Here, we study a thin-membraned balloon as a prototypical system that involves a doubly curved gross shape with large amplitude undulations. By probing its side profiles and horizontal cross-sections, we discover that the mean behavior of the film is the physical observable that is predicted by the geometric model, even when the buckled structures atop it are large. We then propose a minimal model for the horizontal cross-sections of the balloon, as independent elastic filaments subjected to an effective pinning potential around the mean shape. Despite the simplicity of our model, it reproduces a broad range of phenomena seen in the experiments, from how the morphology changes with pressure to the detailed shape of the wrinkles and folds. Our results establish a route to combine global and local features consistently over an enclosed surface, which could aid the design of inflatable structures, or provide insight into biological patterns.
Low-distortion information propagation with noise suppression in swarm networks
Authors: Tiwari Anuj , Devasia Santosh , Riley James J.
Published: March 2023

A method for low-distortion (low-dissipation, low-dispersion) information propagation in swarm-type networks with suppression of high-frequency noise is presented. Information propagation in current neighbor-based networks, where each agent seeks to achieve a consensus with its neighbors, is diffusion-like, dissipative, and dispersive and does not reflect the wave-like (superfluidic) behavior seen in nature. However, pure wave-like neighbor-based networks have two challenges: i) It requires additional communication for sharing information about time derivatives and ii) it can lead to information decoherence through noise at high frequencies. The main contribution of this work is to show that delayed self-reinforcement (DSR) by the agents using prior information (e.g., using short-term memory) can lead to the wave-like information propagation at low-frequencies as seen in nature without the need for additional information sharing between the agents. Moreover, it is shown that the DSR can be designed to enable suppression of high-frequency noise transmission while limiting the dissipation and dispersion of (lower-frequency) information content leading to similar (cohesive) behavior of agents. In addition to explaining noise-suppressed wave-like information transfer in natural systems, the result impacts the design of noise-suppressing cohesive algorithms for engineered networks.
A quantum information processing machine for computing by observables
Authors: Remacle F. , Levine R. D.
Published: March 2023

A quantum machine that accepts an input and processes it in parallel is described. The logic variables of the machine are not wavefunctions (qubits) but observables (i.e., operators) and its operation is described in the Heisenberg picture. The active core is a solid-state assembly of small nanosized colloidal quantum dots (QDs) or dimers of dots. The size dispersion of the QDs that causes fluctuations in their discrete electronic energies is a limiting factor. The input to the machine is provided by a train of very brief laser pulses, at least four in number. The coherent band width of each ultrashort pulse needs to span at least several and preferably all the single electron excited states of the dots. The spectrum of the QD assembly is measured as a function of the time delays between the input laser pulses. The dependence of the spectrum on the time delays can be Fourier transformed to a frequency spectrum. This spectrum of a finite range in time is made up of discrete pixels. These are the visible, raw, basic logic variables. The spectrum is analyzed to determine a possibly smaller number of principal components. A Lie-algebraic point of view is used to explore the use of the machine to emulate the dynamics of other quantum systems. An explicit example demonstrates the considerable quantum advantage of our scheme.
Dissecting the energetic architecture within an RNA tertiary structural motif via high-throughput thermodynamic measurements
Authors: Shin John H. , Bonilla Steve L. , Denny Sarah K. , Greenleaf William J. , Herschlag Daniel
Published: March 2023

Structured RNAs and RNA/protein complexes perform critical cellular functions. They often contain structurally conserved tertiary contact “motifs,” whose occurrence simplifies the RNA folding landscape. Prior studies have focused on the conformational and energetic modularity of intact motifs. Here, we turn to the dissection of one common motif, the 11nt receptor (11ntR), using quantitative analysis of RNA on a massively parallel array to measure the binding of all single and double 11ntR mutants to GAAA and GUAA tetraloops, thereby probing the energetic architecture of the motif. While the 11ntR behaves as a motif, its cooperativity is not absolute. Instead, we uncovered a gradient from high cooperativity amongst base-paired and neighboring residues to additivity between distant residues. As expected, substitutions at residues in direct contact with the GAAA tetraloop resulted in the largest decreases to binding, and energetic penalties of mutations were substantially smaller for binding to the alternate GUAA tetraloop, which lacks tertiary contacts present with the canonical GAAA tetraloop. However, we found that the energetic consequences of base partner substitutions are not, in general, simply described by base pair type or isostericity. We also found exceptions to the previously established stability–abundance relationship for 11ntR sequence variants. These findings of “exceptions to the rule” highlight the power of systematic high-throughput approaches to uncover novel variants for future study in addition to providing an energetic map of a functional RNA.
Endoplasmic reticulum–bound ANAC013 factor is cleaved by RHOMBOID-LIKE 2 during the initial response to hypoxia in
Arabidopsis thaliana
Authors: Eysholdt-Derzsó Emese , Renziehausen Tilo , Frings Stephanie , Frohn Stephanie , von Bongartz Kira , Igisch Clara P. , Mann Justina , Häger Lisa , Macholl Julia , Leisse David , Hoffmann Niels , Winkels Katharina , Wanner Pia , De Backer Jonas , Luo Xiaopeng , Sauter Margret , De Clercq Inge , van Dongen Joost T. , Schippers Jos H. M. , Schmidt-Schippers Romy R.
Published: March 2023

Aerobic reactions are essential to sustain plant growth and development. Impaired oxygen availability due to excessive water availability, e.g., during waterlogging or flooding, reduces plant productivity and survival. Consequently, plants monitor oxygen availability to adjust growth and metabolism accordingly. Despite the identification of central components in hypoxia adaptation in recent years, molecular pathways involved in the very early activation of low-oxygen responses are insufficiently understood. Here, we characterized three endoplasmic reticulum (ER)–anchored
Arabidopsis
ANAC transcription factors, namely ANAC013, ANAC016, and ANAC017, which bind to the promoters of a subset of hypoxia core genes (HCGs) and activate their expression. However, only ANAC013 translocates to the nucleus at the onset of hypoxia, i.e., after 1.5 h of stress. Upon hypoxia, nuclear ANAC013 associates with the promoters of multiple HCGs. Mechanistically, we identified residues in the transmembrane domain of ANAC013 to be essential for transcription factor release from the ER, and provide evidence that RHOMBOID-LIKE 2 (RBL2) protease mediates ANAC013 release under hypoxia. Release of ANAC013 by RBL2 also occurs upon mitochondrial dysfunction. Consistently, like
ANAC013
knockdown lines,
rbl
knockout mutants exhibit impaired low-oxygen tolerance. Taken together, we uncovered an ER-localized ANAC013-RBL2 module, which is active during the initial phase of hypoxia to enable fast transcriptional reprogramming.
Facetus and the birth of “European” politeness
Authors: Unceta Gómez Luis
Published: March 2023

This paper aims to contribute to the study of the first stages of the development of European politeness, through
the analysis of the metalanguage of politeness used in two Latin poems with the title Facetus (Facetus:
cum nihil utilius and Facetus: moribus et vita), both dating from the twelfth century. These two
texts established a fertile genre of behaviour manuals, developed during the Middle Ages both in Latin and in vernacular
languages, and illustrate an intermediary moment of transition from ancient conceptualisations of politeness (given that they
heavily draw on Roman ideas and literature) to early modern ones. The semantic analysis of the Latin politeness meta-terms used in
those poems, such as facetus, decorus, mos or decus, allows us to get a glimpse, through the
emic perspective offered by these meta-terms, of the moral order underlying the code of courtly behaviour.