bluuebunny/crossref_metadata_2025 huggingface dataset:
Hippocampal gamma and sharp wave/ripples mediate bidirectional interactions with cortical networks during sleep
Authors: Pedrosa Rafael , Nazari Mojtaba , Mohajerani Majid H. , Knöpfel Thomas , Stella Federico , Battaglia Francesco P.
Published: October 2022

Hippocampus–neocortex interactions during sleep are critical for memory processes: Hippocampally initiated replay contributes to memory consolidation in the neocortex and hippocampal sharp wave/ripples modulate cortical activity. Yet, the spatial and temporal patterns of this interaction are unknown. With voltage imaging, electrocorticography, and laminarly resolved hippocampal potentials, we characterized cortico-hippocampal signaling during anesthesia and nonrapid eye movement sleep. We observed neocortical activation transients, with statistics suggesting a quasi-critical regime, may be helpful for communication across remote brain areas. From activity transients, we identified, in a data-driven fashion, three functional networks. A network overlapping with the default mode network and centered on retrosplenial cortex was the most associated with hippocampal activity. Hippocampal slow gamma rhythms were strongly associated to neocortical transients, even more than ripples. In fact, neocortical activity predicted hippocampal slow gamma and followed ripples, suggesting that consolidation processes rely on bidirectional signaling between hippocampus and neocortex.
Mechanism of voltage gating in the voltage-sensing phosphatase Ci-VSP
Authors: Shen Rong , Meng Yilin , Roux Benoît , Perozo Eduardo
Published: October 2022

Conformational changes in voltage-sensing domains (VSDs) are driven by the transmembrane electric field acting on the protein charges. Yet, the overall energetics and detailed mechanism of this process are not fully understood. Here, we determined free energy and displacement charge landscapes as well as the major conformations visited during a complete functional gating cycle in the isolated VSD of the phosphatase Ci-VSP (Ci-VSD) comprising four transmembrane helices (segments S1 to S4). Molecular dynamics simulations highlight the extent of S4 movements. In addition to the crystallographically determined activated “Up” and resting “Down” states, the simulations predict two Ci-VSD conformations: a deeper resting state (“down-minus”) and an extended activated (“up-plus”) state. These additional conformations were experimentally probed via systematic cysteine mutagenesis with metal-ion bridges and the engineering of proton conducting mutants at hyperpolarizing voltages. The present results show that these four states are visited sequentially in a stepwise manner during voltage activation, each step translocating one arginine or the equivalent of ∼1
e
0
across the membrane electric field, yielding a transfer of ∼3
e
0
charges in total for the complete process.
Energy-efficient network activity from disparate circuit parameters
Authors: Deistler Michael , Macke Jakob H. , Gonçalves Pedro J.
Published: October 2022

Neural circuits can produce similar activity patterns from vastly different combinations of channel and synaptic conductances. These conductances are tuned for specific activity patterns but might also reflect additional constraints, such as metabolic cost or robustness to perturbations. How do such constraints influence the range of permissible conductances? Here we investigate how metabolic cost affects the parameters of neural circuits with similar activity in a model of the pyloric network of the crab
Cancer borealis
. We present a machine learning method that can identify a range of network models that generate activity patterns matching experimental data and find that neural circuits can consume largely different amounts of energy despite similar circuit activity. Furthermore, a reduced but still significant range of circuit parameters gives rise to energy-efficient circuits. We then examine the space of parameters of energy-efficient circuits and identify potential tuning strategies for low metabolic cost. Finally, we investigate the interaction between metabolic cost and temperature robustness. We show that metabolic cost can vary across temperatures but that robustness to temperature changes does not necessarily incur an increased metabolic cost. Our analyses show that despite metabolic efficiency and temperature robustness constraining circuit parameters, neural systems can generate functional, efficient, and robust network activity with widely disparate sets of conductances.
Topological gelation of reconnecting polymers
Authors: Bonato Andrea , Marenduzzo Davide , Michieletto Davide , Orlandini Enzo
Published: October 2022

DNA recombination is a ubiquitous process that ensures genetic diversity. Contrary to textbook pictures, DNA recombination, as well as generic DNA translocations, occurs in a confined and highly entangled environment. Inspired by this observation, here, we investigate a solution of semiflexible polymer rings undergoing generic cutting and reconnection operations under spherical confinement. Our setup may be realized using engineered DNA in the presence of recombinase proteins or by considering micelle-like components able to form living (or reversibly breakable) polymer rings. We find that in such systems, there is a topological gelation transition, which can be triggered by increasing either the stiffness or the concentration of the rings. Flexible or dilute polymers break into an ensemble of short, unlinked, and segregated rings, whereas sufficiently stiff or dense polymers self-assemble into a network of long, linked, and mixed loops, many of which are knotted. We predict that the two phases should behave qualitatively differently in elution experiments monitoring the escape dynamics from a permeabilized container. Besides shedding some light on the biophysics and topology of genomes undergoing DNA reconnection in vivo, our findings could be leveraged in vitro to design polymeric complex fluids—e.g., DNA-based complex fluids or living polymer networks—with desired topologies.
Yin and yang regulation of stress granules by Caprin-1
Authors: Song Dan , Kuang Lisha , Yang Lin , Wang Lei , Li Hao , Li Xiu , Zhu Zhimin , Shi Chaowei , Zhu Haining , Gong Weimin
Published: October 2022

Stress granules (SGs) are cytoplasmic biomolecular condensates containing proteins and RNAs in response to stress. Ras-GTPase–activating protein binding protein 1 (G3BP1) is a core SG protein. Caprin-1 and ubiquitin specific peptidase 10 (USP10) interact with G3BP1, facilitating and suppressing SG formation, respectively. The crystal structures of the nuclear transport factor 2-like (NTF2L) domain of G3BP1 in complex with the G3BP1-interacting motif (GIM) of Caprin-1 and USP10 show that both GIMs bind to the same hydrophobic pocket of G3BP1. Moreover, both GIMs suppressed the liquid–liquid phase separation (LLPS) of G3BP1, suggesting that Caprin-1 likely facilitates SG formation via other mechanisms. Thus, we dissected various domains of Caprin-1 and investigated their role in LLPS in vitro and SG formation in cells. The C-terminal domain of Caprin-1 underwent spontaneous LLPS, whereas the N-terminal domain and GIM of Caprin-1 suppressed LLPS of G3BP1. The opposing effect of the N- and C-terminal domains of Caprin-1 on SG formation were demonstrated in cells with or without the endogenous Caprin-1. We propose that the N- and C-terminal domains of Caprin-1 regulate SG formation in a “yin and yang” fashion, mediating the dynamic and reversible assembly of SGs.
Bovine and human endometrium-derived hydrogels support organoid culture from healthy and cancerous tissues
Authors: Jamaluddin M. Fairuz B. , Ghosh Arnab , Ingle Aviraj , Mohammed Riazuddin , Ali Ayesha , Bahrami Mohammad , Kaiko Gerard , Gibb Zamira , Filipe Elysse C. , Cox Thomas R. , Boulton Angela , O’Sullivan Rachel , Ius Yvette , Karakoti Ajay , Vinu Ajayan , Nahar Pravin , Jaaback Kenneth , Bansal Vipul , Tanwar Pradeep S.
Published: October 2022

Organoid technology has provided unique insights into human organ development, function, and diseases. Patient-derived organoids are increasingly used for drug screening, modeling rare disorders, designing regenerative therapies, and understanding disease pathogenesis. However, the use of Matrigel to grow organoids represents a major challenge in the clinical translation of organoid technology. Matrigel is a poorly defined mixture of extracellular matrix proteins and growth factors extracted from the Engelbreth–Holm–Swarm mouse tumor. The extracellular matrix is a major driver of multiple cellular processes and differs significantly between tissues as well as in healthy and disease states of the same tissue. Therefore, we envisioned that the extracellular matrix derived from a native healthy tissue would be able to support organoid growth akin to organogenesis in vivo. Here, we have developed hydrogels from decellularized human and bovine endometrium. These hydrogels supported the growth of mouse and human endometrial organoids, which was comparable to Matrigel. Organoids grown in endometrial hydrogels were proteomically more similar to the native tissue than those cultured in Matrigel. Proteomic and Raman microspectroscopy analyses showed that the method of decellularization affects the biochemical composition of hydrogels and, subsequently, their ability to support organoid growth. The amount of laminin in hydrogels correlated with the number and shape of organoids. We also demonstrated the utility of endometrial hydrogels in developing solid scaffolds for supporting high-throughput, cell culture–based applications. In summary, endometrial hydrogels overcome a major limitation of organoid technology and greatly expand the applicability of organoids to understand endometrial biology and associated pathologies.
Mercury isotopic evidence for the importance of particles as a source of mercury to marine organisms
Authors: Motta Laura C. , Blum Joel D. , Popp Brian N. , Umhau Blaire P. , Benitez-Nelson Claudia R. , Close Hilary G. , Washburn Spencer J. , Drazen Jeffrey C.
Published: October 2022

The origin of methylmercury in pelagic fish remains unclear, with many unanswered questions regarding the production and degradation of this neurotoxin in the water column. We used mercury (Hg) stable isotope ratios of marine particles and biota to elucidate the cycling of methylmercury prior to incorporation into the marine food web. The Hg isotopic composition of particles, zooplankton, and fish reveals preferential methylation of Hg within small (< 53 µm) marine particles in the upper 400 m of the North Pacific Ocean. Mass-dependent Hg isotope ratios (δ
202
Hg) recorded in small particles overlap with previously estimated δ
202
Hg values for methylmercury sources to Pacific and Atlantic Ocean food webs. Particulate compound specific isotope analysis of amino acids (CSIA-AA) yield δ
15
N values that indicate more-significant microbial decomposition in small particles compared to larger particles. CSIA-AA and Hg isotope data also suggest that large particles (> 53 µm) collected in the equatorial ocean are distinct from small particles and resemble fecal pellets. Additional evidence for Hg methylation within small particles is provided by a statistical mixing model of even mass–independent (Δ
200
Hg and Δ
204
Hg) isotope values, which demonstrates that Hg within near-surface marine organisms (0–150 m) originates from a combination of rainfall and marine particles. In contrast, in meso- and upper bathypelagic organisms (200–1,400 m), the majority of Hg originates from marine particles with little input from wet deposition. The occurrence of methylation within marine particles is supported further by a correlation between Δ
200
Hg and Δ
199
Hg values, demonstrating greater overlap in the Hg isotopic composition of marine organisms with marine particles than with total gaseous Hg or wet deposition.
In vitro evolution of ribonucleases from expanded genetic alphabets
Authors: Jerome Craig A. , Hoshika Shuichi , Bradley Kevin M. , Benner Steven A. , Biondi Elisa
Published: October 2022

The ability of nucleic acids to catalyze reactions (as well as store and transmit information) is important for both basic and applied science, the first in the context of molecular evolution and the origin of life and the second for biomedical applications. However, the catalytic power of standard nucleic acids (NAs) assembled from just four nucleotide building blocks is limited when compared with that of proteins. Here, we assess the evolutionary potential of libraries of nucleic acids with six nucleotide building blocks as reservoirs for catalysis. We compare the outcomes of in vitro selection experiments toward RNA-cleavage activity of two nucleic acid libraries: one built from the standard four independently replicable nucleotides and the other from six, with the two added nucleotides coming from an artificially expanded genetic information system (AEGIS). Results from comparative experiments suggest that DNA libraries with increased chemical diversity, higher information density, and larger searchable sequence spaces are one order of magnitude richer reservoirs of molecules that catalyze the cleavage of a phosphodiester bond in RNA than DNA libraries built from a standard four-nucleotide alphabet. Evolved AEGISzymes with nitro-carrying nucleobase Z appear to exploit a general acid–base catalytic mechanism to cleave that bond, analogous to the mechanism of the ribonuclease A family of protein enzymes and heavily modified DNAzymes. The AEGISzyme described here represents a new type of catalysts evolved from libraries built from expanded genetic alphabets.
Rheology of debris flow materials is controlled by the distance from jamming
Authors: Kostynick Robert , Matinpour Hadis , Pradeep Shravan , Haber Sarah , Sauret Alban , Meiburg Eckart , Dunne Thomas , Arratia Paulo , Jerolmack Douglas
Published: October 2022

Debris flows are dense and fast-moving complex suspensions of soil and water that threaten lives and infrastructure. Assessing the hazard potential of debris flows requires predicting yield and flow behavior. Reported measurements of rheology for debris flow slurries are highly variable and sometimes contradictory due to heterogeneity in particle composition and volume fraction (ϕ) and also inconsistent measurement methods. Here we examine the composition and flow behavior of source materials that formed the postwildfire debris flows in Montecito, CA, in 2018, for a wide range ofϕthat encapsulates debris flow formation by overland flow. We find that shear viscosity and yield stress are controlled by the distance from jamming,Δϕ=ϕm−ϕ, where the jamming fractionϕmis a material parameter that depends on grain size polydispersity and friction. By rescaling shear and viscous stresses to account for these effects, the data collapse onto a simple nondimensional flow curve indicative of a Bingham plastic (viscoplastic) fluid. Given the highly nonlinear dependence of rheology onΔϕ, our findings suggest that determining the jamming fraction for natural materials will significantly improve flow models for geophysical suspensions such as hyperconcentrated flows and debris flows.
Biochronology of South African hominin-bearing sites: A reassessment using cercopithecid primates
Authors: Frost Stephen R. , White Frances J. , Reda Hailay G. , Gilbert Christopher C.
Published: October 2022

Despite recent advances in chronometric techniques (e.g., Uranium-Lead [U-Pb], cosmogenic nuclides, electron spin resonance spectroscopy [ESR]), considerable uncertainty remains regarding the age of many Plio-Pleistocene hominin sites, including several in South Africa. Consequently, biochronology remains important in assessments of Plio-Pleistocene geochronology and provides direct age estimates of the fossils themselves. Historically, cercopithecid monkeys have been among the most useful taxa for biochronology of early hominins because they are widely present and abundant in the African Plio-Pleistocene record. The last major studies using cercopithecids were published over 30 y ago. Since then, new hominin sites have been discovered, radiometric age estimates have been refined, and many changes have occurred in cercopithecid taxonomy and systematics. Thus, a biochronological reassessment using cercopithecids is long overdue. Here, we provide just such a revision based on our recent study of every major cercopithecid collection from African Plio-Pleistocene sites. In addition to correlations based on shared faunal elements, we present an analysis based on the dentition of the abundant cercopithecid
Theropithecus oswaldi
, which increases in size in a manner that is strongly correlated with geological age (
r
2
∼0.83), thereby providing a highly accurate age-estimation tool not previously utilized. In combination with paleomagnetic and U-Pb data, our results provide revised age estimates and suggest that there are no hominin sites in South Africa significantly older than ∼2.8 Ma. Where conflicting age estimates exist, we suggest that additional data are needed and recall that faunal estimates have ultimately proved reliable in the past (e.g., the age of the KBS Tuff).
Neuronal signature of spatial decision-making during navigation by freely moving rats by using calcium imaging
Authors: Gobbo Francesco , Mitchell-Heggs Rufus , Tse Dorothy , Al Omrani Meera , Spooner Patrick A. , Schultz Simon R. , Morris Richard G. M.
Published: October 2022

A challenge in spatial memory is understanding how place cell firing contributes to decision-making in navigation. A spatial recency task was created in which freely moving rats first became familiar with a spatial context over several days and thereafter were required to encode and then selectively recall one of three specific locations within it that was chosen to be rewarded that day. Calcium imaging was used to record from more than 1,000 cells in area CA1 of the hippocampus of five rats during the exploration, sample, and choice phases of the daily task. The key finding was that neural activity in the startbox rose steadily in the short period prior to entry to the arena and that this selective population cell firing was predictive of the daily changing goal on correct trials but not on trials in which the animals made errors. Single-cell and population activity measures converged on the idea that prospective coding of neural activity can be involved in navigational decision-making.
A neural signature of the vividness of prospective thought is modulated by temporal proximity during intertemporal decision making
Authors: Lee Sangil , Parthasarathi Trishala , Cooper Nicole , Zauberman Gal , Lerman Caryn , Kable Joseph W.
Published: October 2022

Why do people discount future rewards? Multiple theories in psychology argue that one reason is that future events are imagined less vividly than immediate events, thereby diminishing their perceived value. Here we provide neuroscientific evidence for this proposal. First, we construct a neural signature of the vividness of prospective thought, using an fMRI dataset where the vividness of imagined future events is orthogonal to their valence by design. Then, we apply this neural signature in two additional fMRI datasets, each using a different delay-discounting task, to show that neural measures of vividness decline as rewards are delayed farther into the future.
HOIP modulates the stability of GPx4 by linear ubiquitination
Authors: Dong Kangyun , Wei Ran , Jin Taijie , Zhang Mengmeng , Shen Jiali , Xiang Huaijiang , Shan Bing , Yuan Junying , Li Ying
Published: October 2022

LUBAC-mediated linear ubiquitination plays a pivotal role in regulation of cell death and inflammatory pathways. Genetic deficiency in LUBAC components leads to severe immune dysfunction or embryonic lethality. LUBAC has been extensively studied for its role in mediating TNF signaling. However,
Tnfr1
knockout is not able to fully rescue the embryonic lethality of LUBAC deficiency, suggesting that LUBAC may modify additional key cellular substrates in promoting cell survival. GPx4 is an important selenoprotein involved in regulating cellular redox homeostasis in defense against lipid peroxidation-mediated cell death known as ferroptosis. Here we demonstrate that LUBAC deficiency sensitizes to ferroptosis by promoting GPx4 degradation and downstream lipid peroxidation. LUBAC binds and stabilizes GPx4 by modulating its linear ubiquitination both in normal condition and under oxidative stress. Our findings identify GPx4 as a key substrate of LUBAC and a previously unrecognized role of LUBAC-mediated linear ubiquitination in regulating cellular redox status and cell death.
GABA signaling enforces intestinal germinal center B cell differentiation
Authors: Liao Yuexia , Fan Lijuan , Bin Peng , Zhu Congrui , Chen Qingyi , Cai Yepeng , Duan Jielin , Cai Qian , Han Wei , Ding Shizhen , Hu Xiangyu , Zhang Yiran , Yin Yulong , Ren Wenkai
Published: October 2022

Recent compelling results indicate possible links between neurotransmitters, intestinal mucosal IgA
+
B cell responses, and immunoglobulin A nephropathy (IgAN) pathogenesis. Here, we demonstrated that γ-amino butyric acid (GABA) transporter-2 (GAT-2) deficiency induces intestinal germinal center (GC) B cell differentiation and worsens the symptoms of IgAN in a mouse model. Mechanistically, GAT-2 deficiency enhances GC B cell differentiation through activation of GABA–mammalian target of rapamycin complex 1 (mTORC1) signaling. In addition, IgAN patients have lower GAT-2 expression but higher activation of mTORC1 in blood B cells, and both are correlated with kidney function in IgAN patients. Collectively, this study describes GABA signaling–mediated intestinal mucosal immunity as a previously unstudied pathogenesis mechanism of IgAN and challenges the current paradigms of IgAN.
The rubber brick’s story: A cultural sociology of policing protest in Europe
Authors: Kretschmann Andrea
Published: October 2022

This ethnographically based article investigates the simulated enactments European police forces undergo in mock cities in order to train for protest policing. From a perspective grounded in cultural sociology, the analysis focuses on the rubber brick used in these simulations as a substitute for the stones that protesters sometimes hurl at police. It looks at the brick as a cultural materialisation that marks a specific form of police training, as well as policing more generally. By following the stone’s trace, the article argues that the brick acts as a medium that reflects police action: It derives its meaning from the imaginary of the demonstrators and protesters as violent, and sometimes even as hostile, in the sense of forces which should be met with a combative police reaction. Thus, the stone creates a self-image of the police characterised by toughness, courage, and strength. The thorough article adds to the research about protest policing by offering the first investigation of the meaning of simulated training for police forces.
Upon the horizon’s verge: Thermal particle creation between and approaching horizons
Authors: Fernández-Silvestre Diego , Good Michael R R , Linder Eric V
Published: October 2022

Quantum particle creation from spacetime horizons, or accelerating boundaries in the dynamical Casimir effect, can have an equilibrium, or thermal, distribution. Using an accelerating boundary in flat spacetime (moving mirror), we investigate the production of thermal energy flux despite non-equilibrium accelerations, the evolution between equilibrium states, and the ‘interference’ between horizons. In particular, this allows us to give a complete solution to the particle spectrum of the accelerated boundary correspondence with Schwarzschild–de Sitter spacetime.
Emergence of smooth distance and apparent magnitude in a lumpy Universe
Authors: Umeh Obinna
Published: October 2022

The standard interpretation of observations such as the peak apparent magnitude of Type Ia supernova made from one location in a lumpy Universe is based on the idealised Friedmann–Lemaître–Robertson–Walker (FLRW) spacetime. All possible corrections to this model due to inhomogeneities are usually neglected. Here, we use the result from the recent concise derivation of the area distance in an inhomogeneous Universe to study the monopole and Hubble residual of the apparent magnitude of Type Ia supernovae. We find that at low redshifts, the background FLRW spacetime model of the apparent magnitude receives corrections due to relative velocity perturbation in the observed redshift. We show how this velocity perturbation could contribute to a variance in the Hubble residual and how it could impact the calibration of the absolute magnitude of the Type Ia supernova in the Hubble flow. We also show that it could resolve the tension in the determination of the Hubble rate from the baryon acoustic oscillation and local measurements.
Numerical simulation of non-central collisions of spherical magnets
Authors: Bartz Sean P , Shaw Jacob
Published: October 2022

We present a computational model of non-central collisions of two spherical neodymium-iron-boron magnets, suggested as a demonstration of angular momentum conservation. Our program uses an attractive dipole–dipole force and a repulsive contact force to solve the Newtonian equations of motion for the magnets. We confirm the conservation of angular momentum and study the changes in energy throughout the interaction. Using the exact expression for the dipole–dipole force, including non-central terms, we correctly model the final rotational frequencies, which is not possible with a simple power-law approximation.
The properties of perovskite solar cells with novel MAPbBr3/CsPbBr3 double absorber
Authors: He Bolong , Liu Linlin , Hu Jialong , Nie Shu , Chen Yihui , Chen Yonsheng
Published: October 2022

Perovskite solar cells (PSCs) based on CsPbBr3 have garnered considerable attention due to their high stability and all-inorganic components. Although thermal annealing is a conventional and effective method to improve the quality of CsPbBr3 films, property improvement strategies are still scarce, especially for the vapor deposition process. In this work, a MAPbBr3 layer is introduced at the TiO2 and CsPbBr3 interface to construct a double-absorber heterojunction structure. It is found that the cubic phase of CsPbBr3 is formed directly on the MAPbBr3 underlayer due to the epitaxial growth. Furthermore, the heterojunction formed at the MAPbBr3/CsPbBr3 interface contributes to the superior extraction of the light-generated carriers. A power conversion efficiency (PCE) of 6.53% is obtained for the PSC with a double-absorber design. Despite the thickness of the epitaxial layer being shrunken after annealing at 150 °C for 30 min, a PCE of 5.90% is achieved, indicating the high thermal stability of the double-absorber device. Our work provides a new insight into quality engineering for the perovskite deposited by the vapor deposition process.
Inverse design of a topological phononic beam with interface modes
Authors: Muhammad  , Ogun Oluwaseyi , Kennedy John
Published: October 2022

Inspired by the idea of topological mechanics and geometric phase, the topological phononic beam governed by topological invariants has seen growing research interest due to generation of a topologically protected interface state that can be characterized by geometric Zak phase. The interface mode has maximum amount of wave energy concentration at the interface of topologically variant beams with minimal losses and decaying wave energy fields away from it. The present study has developed a deep learning based autoencoder (AE) to inversely design topological phononic beam with invariants. By applying the transfer matrix method, a rigorous analytical model is developed to solve the wave dispersion relation for longitudinal and bending elastic waves. By determining the phase of the reflected wave, the geometric Zak phase is determined. The developed analytical models are used for input data generation to train the AE. Upon successful training, the network prediction is validated by finite element numerical simulations and experimental test on the manufactured prototype. The developed AE successfully predicts the interface modes for the combination of topologically variant phononic beams. The study findings may provide a new perspective for the inverse design of metamaterial beam and plate structures in solid and computational mechanics. The work is a step towards deep learning networks suitable for the inverse design of phononic crystals and metamaterials enabling design optimization and performance enhancements.
A reference-free MEAM potential for α-Fe and γ-Fe
Authors: Slooter Rutger J , Sluiter Marcel H F , Kranendonk Winfried G T , Bos Cornelis
Published: October 2022

A reference-free modified embedded atom method (RF-MEAM) potential for iron has been constructed. The new potential is made to predict both bcc and fcc (α-Fe and γ-Fe) lattice properties, with a special interest in modelling in the 800–1300 K temperature range. This is the range in which transformations and key processes in steel occur. RF-MEAM potentials can be used directly in commonly used molecular dynamics simulation software (e.g. LAMMPS). The new potential is compared to several other (M)EAM potentials which are commonly used. It is demonstrated that the new potential combines good characteristics for point defect energies with free surface and stacking fault energies. Also the Nishiyama–Wassermann and Kurdjumov–Sachs orientation relation ratios and interface energies are reproduced, allowing for simulations of α-Fe and γ-Fe interphases.
Comparing wire-mesh sensor with neutron radiography for measurement of liquid fraction in foam
Authors: Ziauddin M , Schleicher E , Trtik P , Knüpfer L , Skrypnik A , Lappan T , Eckert K , Heitkam S
Published: October 2022

The liquid fraction of foam is an important quantity in engineering process control and essential to interpret foam rheology. Established measurement tools for the liquid fraction of foam, such as optical measurement or radiography techniques as well as weighing the foam, are mostly laboratory-based, whereas conductivity-based measurements are limited to the global measurement without detailed spatial information of liquid fraction. In this work, which combines both types of measurement techniques, the conductivity-based wire-mesh sensor is compared with neutron radiography. We found a linear dependency between the liquid fraction of the foam and the wire-mesh readings with a statistical deviation less than 15%. However, the wire-mesh sensor systematically overestimates the liquid fraction, which we attribute to liquid bridge formation between the wires.
Selective triggering in-plane and out-of-plane dipolar modes of hexagonal Au nanoplate with the polarization of excitation beam
Authors: Zhang Hanmou , Wang Qifa , Hou Liping , Xiao Fajun , Zhao Jianlin
Published: October 2022

The dipolar responses of a single hexagonal Au nanoplate are investigated under the illuminations of linearly polarized beam and tightly focused radially polarized beam (RPB). It is found from the scattering spectra that the in-plane and out-of-plane electric dipole modes can be selectively triggered with a linearly polarized beam and tightly focused RPB, respectively. The features of these two dipolar modes are further confirmed in terms of electrical field and charge maps by the finite-difference time-domain simulation. Additionally, using the multipole expansion method, the existence of the out-of-plane dipole mode is further verified by the fact that the z-component of electric dipole response has a dominant contribution to the scattered power. Moreover, by combining the back focal plane imaging technique with the simulation, the appearance of in-plane and out-of-plane dipoles in the scattering pattern are clearly discerned. Our results provide an efficient method for selectively exciting the in-plane and out-of-plane dipolar modes of the nanoplate. We envision that the ease of tuning the dipolar momentum may facilitate the enhancement of the interaction between the plasmon and emitters at single-particle level.
The PRISM semantic cohort builder: a novel tool to search and access clinical data in TCIA imaging collections
Authors: Bona Jonathan P , Utecht Joseph , Bost Sarah , Brochhausen Mathias , Prior Fred
Published: October 2022

The cancer imaging archive (TICA) receives and manages an ever-increasing quantity of clinical (non-image) data containing valuable information about subjects in imaging collections. To harmonize and integrate these data, we have first cataloged the types of information occurring across public TCIA collections. We then produced mappings for these diverse instance data using ontology-based representation patterns and transformed the data into a knowledge graph in a semantic database. This repository combined the transformed instance data with relevant background knowledge from domain ontologies. The resulting repository of semantically integrated data is a rich source of information about subjects that can be queried across imaging collections. Building on this work we have implemented and deployed a REST API and a user-facing semantic cohort builder tool. This tool allows allow researchers and other users to search and identify groups of subject-level records based on non-image data that were not queryable prior to this work. The search results produced by this interface link to images, allowing users to quickly identify and view images matching the selection criteria, as well as allowing users to export the harmonized clinical data.
Recent advances in psychoradiology
Authors: Luo Lekai , You Wanfang , DelBello Melissa P , Gong Qiyong , Li Fei
Published: October 2022

Psychiatry, as a field, lacks objective markers for diagnosis, progression, treatment planning, and prognosis, in part due to difficulties studying the brain in vivo, and diagnoses are based on self-reported symptoms and observation of patient behavior and cognition. Rapid advances in brain imaging techniques allow clinical investigators to noninvasively quantify brain features at the structural, functional, and molecular levels. Psychoradiology is an emerging discipline at the intersection of psychiatry and radiology. Psychoradiology applies medical imaging technologies to psychiatry and promises not only to improve insight into structural and functional brain abnormalities in patients with psychiatric disorders but also to have potential clinical utility. We searched for representative studies related to recent advances in psychoradiology through May 1, 2022, and conducted a selective review of 165 references, including 75 research articles. We summarize the novel dynamic imaging processing methods to model brain networks and present imaging genetics studies that reveal the relationship between various neuroimaging endophenotypes and genetic markers in psychiatric disorders. Furthermore, we survey recent advances in psychoradiology, with a focus on future psychiatric diagnostic approaches with dimensional analysis and a shift from group-level to individualized analysis. Finally, we examine the application of machine learning in psychoradiology studies and the potential of a novel option for brain stimulation treatment based on psychoradiological findings in precision medicine. Here, we provide a summary of recent advances in psychoradiology research, and we hope this review will help guide the practice of psychoradiology in the scientific and clinical fields.
Optimizing breakdown voltage and on-state resistance by modulating the barrier height along 2DEG channel for power p-GaN HEMTs
Authors: Xin Yajie , Chen Wanjun , Sun Ruize , Liu Chao , Xia Yun , Wang Fangzhou , Deng Xiaochuan , Li Zhaoji , Zhang Bo
Published: October 2022

This article proposes a novel step-type gate p-GaN HEMT (STG-HEMT) to optimize breakdown voltage (BV) and on-state resistance (R
ON) by modulating the barrier height along the two-dimensional electron gas (2DEG) channel. The step-type gate consists of thicker and thinner p-GaN layers. At off-state, the barrier height is higher due to the clamping potential effect induced by the thinner p-GaN layer, which contributes to improving BV. At on-state, the barrier height under the thinner p-GaN layer is lower, which contributes to improving 2DEG density under the gate (namely reducing R
ON). Verified by the calibrated simulation, the results show STG-HEMT’s BV is increased by 55% and STG-HEMT’s R
ON is decreased by 20% compared with the conventional power p-GaN HEMT (C-HEMT). At transient behavior, the total switching loss keeps nearly unchanged, while the gate driver loss is increased by about 19%. Furthermore, the impact of the gate length and p-GaN layer’s parameters (including thickness, length, activated Mg doping density) on R
ON, BV, and threshold voltage are discussed.
Design and performance analysis of GaN vertical JFETs with ion-implanted gates
Authors: Stein Shane R , Khachariya Dolar , Pavlidis Spyridon
Published: October 2022

We present a comprehensive performance analysis of vertical GaN JFETs via TCAD simulation with unique considerations for gates formed by Mg ion implantation into GaN. The dependence of the specific ON-resistance and pinch-off voltage on the gate and channel design parameters is first evaluated for a JFET with abrupt gate-channel junctions. Then, the influence of the gate acceptor concentration and distribution is studied to elucidate the consequences of incomplete acceptor activation or acceptor diffusion resulting from specialized post-implantation annealing techniques necessary for the activation of p-GaN. Examples of normally-ON and normally-OFF designs with 1.7 kV breakdown voltage for 1.2 kV applications are chosen for the activation and diffusion studies to demonstrate how the pinch-off and conduction characteristics are affected for different channel widths and doping concentrations conducive to each type of operation. Record low specific ON-resistance below 1 mΩ cm2 is predicted for both, but gate acceptor diffusion increases the channel resistance, especially for JFETs designed to be normally-OFF.
Large-scale phase retrieval from coded diffraction patterns with electrically tunable lens
Authors: Zhang Cheng , Zhang Liru , Wang Meiqin , Zhang Ru , Chen Mingsheng , Wei Sui
Published: October 2022

General optical detection devices rely on converting photons to electrons (current), and do not allow for direct recording of the phase due to the high oscillation frequency. As so, the missing phase can only be recovered from the intensity measurements. The emerging non-convex phase retrieval algorithm, represented by the Wirtinger Flow (WF) algorithm requires multiple-shot coded diffraction patterns (CDPs) for accurate recovery. To achieve the real-time acquisition for multiple CDPs, this paper proposes a 4f imaging system based on an electrically tunable lens (ETL), which can be used for real-time acquisition of multiple-shot CDPs, and can take the advantages of highspeed, high-resolution, extended depth-of-field, high-sensitivity and low-cost imaging. In this paper, the performance of 4f-ETL based imaging system for phase retrieval with multiple CDPs is compared under different iteration times, different object size, different numbers of masks and different noise levels. Numerical experiments demonstrate the effectiveness and superiority of our proposed ETL-based imaging system, and ETL allows variable-distance focusing of imaging and display systems without mechanical structures, which reduces the mechanical complexity and power consumption, improves acquisition speed.
Unveiling dark fifth forces with linear cosmology
Authors: Archidiacono Maria , Castorina Emanuele , Redigolo Diego , Salvioni Ennio
Published: October 2022

We initiate the exploration of the cosmology of dark fifth forces: new forces acting
solely on Dark Matter. We focus on long range interactions which lead to an effective violation of
the Equivalence Principle on cosmological scales today. At the microscopic level, the dark fifth
force can be realized by a light scalar with mass smaller than the Hubble constant today
(≲ 10-33 eV) coupled to Dark Matter. We study the behavior of the background
cosmology and linear perturbations in such a Universe. At the background level, the new force
modifies the evolution of the Dark Matter energy density and thus the Hubble flow. At linear
order, it modifies the growth of matter perturbations and generates relative density and velocity
perturbations between Dark Matter and baryons that grow over time. We derive constraints from
current CMB and BAO data, bounding the strength of the dark fifth force to be less than a percent
of gravity. These are the strongest constraints to date. We present potential implications of this
scenario for the Hubble tension and discuss how our results are modified if the light scalar
mediator accounts for the observed density of the Dark Energy. Finally, we comment on the
interplay between our constraints and searches for violations of the Equivalence Principle in the
visible sector.
Palatini R
2 quintessential inflation
Authors: Dimopoulos Konstantinos , Karam Alexandros , Sánchez López Samuel , Tomberg Eemeli
Published: October 2022

We construct a model of quintessential inflation in Palatini R
2 gravity employing a
scalar field with a simple exponential potential and coupled to gravity with a running non-minimal
coupling. At early times, the field acts as the inflaton, while later on it becomes the current
dark energy. Combining the scalar sector with an ideal fluid, we study the cosmological evolution
of the model from inflation all the way to dark energy domination. We interpret the results in the
Einstein frame, where a coupling emerges between the fluid and the field, feeding energy from the
former to the latter during the matter-dominated era. We perform a numerical scan over the
parameter space and find points that align with observations for both the inflationary CMB data
and the late-time behaviour. The final dark energy density emerges from an interplay between the
model parameters, without requiring the extreme fine-tuning of the cosmological constant in
ΛCDM.
NiCo2O4@V2O5 nanobelts as electrode materials for efficient electrochemical charge storage
Authors: Mohapatra Dillip Kumar , Sahoo Malaya K , Praharaj Swetapadma , Rout Dibyaranjan
Published: October 2022

The development of novel nanostructured composites is of current interest for applications as electrode materials. In this regard, an attempt has been made to synthesize NiCo2O4@V2O5 nanocomposite and compare its charge storage performance with pristine NiCo2O4 nanoparticles. High-resolution scanning electron microscope micrographs reveal a mesoporous nanobelt like morphology of the nanocomposite with a Brunauer–Emmett–Teller surface area of ∼65 m2 g−1 and average mesopore size centered on ∼7.55 nm. Electrochemical measurements performed on both samples anticipate capacitive behavior with quasi-reversible redox reactions. However, NiCo2O4@V2O5 is found to demonstrate a strikingly high specific capacity of 194 mAh g−1 at 1 A g−1 along with a notable capacity retention of ∼90%, even after 3000 charge–discharge cycles, and a Coulombic efficiency >97% at 5 A g−1. These features are much superior to the properties of pristine NiCo2O4 nanoparticles. The results obtained in this work ascertain the functional robustness of NiCo2O4@V2O5 nanocomposites as electrode materials in supercapacitors.
Ripple formation with intense Gaussian femtosecond laser pulses close to the damage threshold
Authors: Teubner U , Andreev A , Makin V , Imgrunt J
Published: October 2022

The formation of laser-induced periodic surface structures (LIPSS or ripples) is a topic that has been investigated for almost 60 years. More recently with the advent of ultrashort laser pulses this subject has regained interest, in particular, due to interaction regimes that have not been present so far. Consequently a lot of work has been done in that field, especially with comprehensive experimental and theoretical investigations of the scaling of ripple parameters on laser pulse duration, wavelength, applied fluence, shot number and so on. However, there are still a lot of questions. The present work addresses an important issue on that subject. In particular, ripple formation is investigated at high laser intensity, namely at an intensity sufficiently large to generate a femtosecond-laser induced plasma. Thus ripple formation occurs close to damage threshold. Experimental results and theoretical discussion of ripple formation and the interrelation to laser pulse energy deposition, energy transport and sample damage originating from the optical interaction and additional thermal effects, respectively, are discussed. Most important, a reduction of ripple formation threshold with laser intensity and fluence, respectively, has been observed which is associated by a super-linear increase of the ripple area. The scaling of this reduction with laser fluence obtained from theoretical estimates is in good agreement with the experimental data.
GlycoEnzOnto: a GlycoEnzyme pathway and molecular function ontology
Authors: Groth Theodore , Diehl Alexander D , Gunawan Rudiyanto , Neelamegham Sriram
Published: October 2022

Motivation

The ‘glycoEnzymes’ include a set of proteins having related enzymatic, metabolic, transport, structural and cofactor functions. Currently, there is no established ontology to describe glycoEnzyme properties and to relate them to glycan biosynthesis pathways.

Results

We present GlycoEnzOnto, an ontology describing 403 human glycoEnzymes curated along 139 glycosylation pathways, 134 molecular functions and 22 cellular compartments. The pathways described regulate nucleotide-sugar metabolism, glycosyl-substrate/donor transport, glycan biosynthesis and degradation. The role of each enzyme in the glycosylation initiation, elongation/branching and capping/termination phases is described. IUPAC linear strings present systematic human/machine-readable descriptions of individual reaction steps and enable automated knowledge-based curation of biochemical networks. All GlycoEnzOnto knowledge is integrated with the Gene Ontology biological processes. GlycoEnzOnto enables improved transcript overrepresentation analyses and glycosylation pathway identification compared to other available schema, e.g. KEGG and Reactome. Overall, GlycoEnzOnto represents a holistic glycoinformatics resource for systems-level analyses.

Availability and implementation

https://github.com/neel-lab/GlycoEnzOnto.

Supplementary information

Supplementary data are available at Bioinformatics online.