bluuebunny/crossref_metadata_2025 huggingface dataset:
A combat game model with inter-network confrontation and intra-network cooperation
Authors: Chen Hao , Wang Lin , Wang Xiaofan
Published: March 2023

Inter-network combat and intra-network cooperation among structured systems are likely to have been recurrent features of human evolutionary history; however, little research has investigated the combat mechanism between structured systems that the adversarial interactions will cause the disability of agents and agents are prone to seek cooperation with neighbors. Hence, the current study has proposed a two-network combat game model and designed the corresponding rules of how to attack, how to be disabled, how to cooperate, and how to win. First, within the framework of our model, we have simulated the combat among four common network structures—the Erdős–Rényi (ER) random network, the grid graph, the small-world network, and the scale-free network. We found that the grid network always holds the highest winning percentage, while the ER random graph is most likely to lose when combating with the other three network structures. For each structure, we have also simulated the combat between the same network structures with different generating parameters. The simulations reveal that the small-world property and heterogeneity can promote winning a combat. Besides, by broadening and deepening cooperation, we have found that broader cooperation helps defeat the opposite system on grid and scale-free networks, yet hinders it on ER and Watts–Strogatz (WS) networks, while deeper cooperation can benefit to winning except on scale-free networks. These findings inform our understanding of the effects of structure and cooperation in a combat.
Thickness-tuned magnetotransport properties of topological semimetal trigonal PtBi2
Authors: Zhu Ankang , Wang Huanhuan , Chen Zheng , Han Yuyan , Zhu Mengcheng , Han Minglong , Zhu Xiangde , Gao Wenshuai , Tian Mingliang
Published: March 2023

Here, we report systematic studies on thickness-dependent magnetotransport properties of trigonal layered PtBi2. When the thickness decreases, the metallicity is gradually suppressed, and it ultimately displays a semiconductor-like behavior when the thickness is reduced to 22 nm. Interestingly, the magnetoresistance (MR) decreases gradually as well as the thickness decreases, followed by an abrupt increase in the 22 nm nanoflake. The Hall resistance demonstrates the distinct evolution of an electronic state on thickness, revealing that the carrier compensation mechanism may play a role on the large MR in the 22 nm PtBi2 nanoflake. The scanning transmission electron microscopy image clearly uncovers the surface reconstruction of trigonal PtBi2, and qualitative interpretation is proposed for understanding the thickness-dependent transport properties. Our results provide insight into the electronic properties in the low-dimensional limit of topological semimetal trigonal PtBi2.
Wavelength-modulated photoacoustic spectroscopy sensor for multi-gas measurement of acetone, methane, and water vapor based on a differential acoustic resonator
Authors: Huang Yan , Zhang Tie , Wang Gao-Xuan , Xing Yu-Xin , He Sai-Ling
Published: March 2023

Precise assessment of breath acetone and methane is significant to the medical diagnosis process. A multi-gas sensing system based on wavelength-modulated differential photoacoustic spectroscopy was developed for simultaneous measurement of acetone and methane. A distributed feedback diode laser emitting in the range from 3363 to 3371 nm was employed to scan the absorption lines of acetone and methane. The cross sensitivities in terms of spectral interference among acetone, methane, and water vapor are effectively eliminated by using a linear combination method of reference spectra for accurately determining the concentration of acetone and methane. The positive effect of water vapor on photoacoustic signal resulting from the light absorption of acetone and methane was precisely evaluated. To improve the instrument performance, a differential PA cell companying with a differential amplifier circuit is experimentally demonstrated in providing a better performance of noise suppression compared with a single acoustic resonator. With a low detection limit down to 0.43 ppm and 12 ppb (integration time of 10 s) for acetone and methane, the sensor shows a great potential for medical diagnosis in simultaneous measurement of acetone and methane.
Power-grid vulnerability and its relation with network structure
Authors: Dias Jussara , Montanari Arthur N. , Macau Elbert E. N.
Published: March 2023

Interconnected systems with critical infrastructures can be affected by small failures that may trigger a large-scale cascade of failures, such as blackouts in power grids. Vulnerability indices provide quantitative measures of a network resilience to component failures, assessing the break of information or energy flow in a system. Here, we focus on a network vulnerability analysis, that is, indices based solely on the network structure and its static characteristics, which are reliably available for most complex networks. This work studies the structural connectivity of power grids, assessing the main centrality measures in network science to identify vulnerable components (transmission lines or edges) to attacks and failures. Specifically, we consider centrality measures that implicitly model the power flow distribution in power systems. This framework allow us to show that the efficiency of the power flow in a grid can be highly sensitive to attacks on specific (central) edges. Numerical results are presented for randomly generated power-grid models and established power-grid benchmarks, where we demonstrate that the system’s energy efficiency is more vulnerable to attacks on edges that are central to the power flow distribution. We expect that the vulnerability indices investigated in our work can be used to guide the design of structurally resilient power grids.
Ordinal analysis of lexical patterns
Authors: Sánchez David , Zunino Luciano , De Gregorio Juan , Toral Raúl , Mirasso Claudio
Published: March 2023

Words are fundamental linguistic units that connect thoughts and things through meaning. However, words do not appear independently in a text sequence. The existence of syntactic rules induces correlations among neighboring words. Using an ordinal pattern approach, we present an analysis of lexical statistical connections for 11 major languages. We find that the diverse manners that languages utilize to express word relations give rise to unique pattern structural distributions. Furthermore, fluctuations of these pattern distributions for a given language can allow us to determine both the historical period when the text was written and its author. Taken together, our results emphasize the relevance of ordinal time series analysis in linguistic typology, historical linguistics, and stylometry.
Uncovering the path to low-field colossal magnetoresistance: A microscopic view of field driven percolative insulator-to-metal transition in manganites
Authors: Xiang Lifen , Shi Yang , Chao Wei , Zhang Huanyu , Li Qiang , Hu Wenjie , Wang Wenbin , Guo Hangwen , Zheng Changlin , Etheridge Joanne , Yin Lifeng , Zhu Yinyan , Zhou Xiaodong , Shen Jian
Published: March 2023

For perovskite manganites, their colossal magnetoresistance (CMR) requires a large field, which limits their potential applications. In order to uncover the path to achieve low-field CMR, it is crucial to understand the microscopic process of the field driven insulator-to-metal transition (IMT) in manganites. This is particularly true considering the fact that the IMT is of a percolative type, in which the interplay between nucleation and growth of the electronic phase separation domains under magnetic field is not well investigated. In this work, we investigate the magnetic field driven percolative IMT in a model system of La1−x−yPrxCayMnO3 in real space via magnetic force microscopy (MFM). Our experimental observations show unambiguously three stages of the IMT phase transition where domain nucleation and domain growth exhibit distinctly different features in the global initial magnetization measurements. Moreover, MFM reveals that domain growth requires a much lower field than domain nucleation, which provides critical information on how to achieve low-field CMR. It is believed that the exchange field provided by ferromagnetic metallic domains at the boundary with antiferromagnetic insulating domains plays a critical role in assisting the domain growth process. Optimizing such internal exchange fields in manganites is a potential route to achieve CMR without the need of a large external field.
Volumetric measurement of a Newtonian fluid flow through three-dimensional porous media using Lagrangian particle tracking (Shake-the-Box) technique
Authors: Bagheri Maryam , Mirbod Parisa
Published: March 2023

This work experimentally investigates the pressure-driven flow of a pure Newtonian fluid through three-dimensional (3D) porous media models. The porous media model consists of square arrays of rods that also could be interpreted as a periodic tandem rod arrangement. We employed a time-resolved three-dimensional particle tracking velocimetry (3D Shake-the-Box) technique for a range of Reynolds numbers 111 ≤ R e ≤ 890 to observe flow structures and vortex formation between the rods in porous media structures with different porosities of ε = 0.7 ,   0.8 ,   and   0.9 , which corresponds to the spacing ratio of L D = 1.75 ,   2 ,   and   3, where L is the distance between the centers of the rods, and D is the diameter of the rods. For all the examined cases, we further analyzed the effect of the Reynolds number and the spacing ratio on the instantaneous and averaged patterns of velocity, vorticity, and the other flow parameters after obtaining the two-dimensional velocity fields using the bin-averaging method. We observed both symmetrical and asymmetrical patterns of structure and recirculation regions between the rods depending on the Reynolds number and spacing ratio. Increasing the Reynolds number reduced the symmetrical patterns of flow structures with respect to the centerline of the gap region, while the spacing ratio was randomly affecting the symmetry degree. Vortex shedding was considerable for the two examined high Reynolds numbers of Re = 444 and Re = 890 behind the upstream rod as the porosity increased. The backward movement of the reattachment point has been observed by increasing the Reynolds number.
Effects of proton irradiation-induced point defects on Shockley–Read–Hall recombination lifetimes in homoepitaxial GaN p–n junctions
Authors: Narita Tetsuo , Kanechika Masakazu , Tomita Kazuyoshi , Nagasato Yoshitaka , Kondo Takeshi , Uesugi Tsutomu , Ikeda Satoshi , Kosaki Masayoshi , Oka Tohru , Suda Jun
Published: March 2023

This work examined the intentional generation of recombination centers in GaN p–n junctions on freestanding GaN substrates. Irradiation with a 4.2 MeV proton beam was used to create a uniform distribution of vacancies and interstitials across GaN p+/n− and p−/n+ junctions through anode electrodes. With increasing proton dose, the effective doping concentrations were found to be reduced. Because the reduction in the doping concentration was much higher than the hydrogen atom concentration, this decrease could not be attributed solely to carrier compensation resulting from interstitial hydrogen atoms. In fact, more than half of the electron and hole compensation was caused by the presence of point defects. These defects evidently served as Shockley–Read–Hall (SRH) recombination centers such that the SRH lifetimes were reduced to several picoseconds from several hundred picoseconds prior to irradiation. The compensation for holes in the p−/n+ junctions was almost double that for electrons in the p+/n− junctions. Furthermore, the SRH lifetimes associated with p−/n+ junctions were shorter than those for p+/n− junctions for a given proton dose. These differences can be explained by variations in the charge state and/or the formation energy of intrinsic point defects in the p-type and n-type GaN layers. The results of the present work indicate the asymmetry of defect formation in GaN based on the fact that intrinsic point defects in p-type GaN readily compensate for holes.
Data-driven modal decomposition methods as feature detection techniques for flow problems: A critical assessment
Authors: Begiashvili B. , Groun N. , Garicano-Mena J. , Le Clainche S. , Valero E.
Published: March 2023

Modal decomposition techniques are showing a fast growth in popularity for their wide range of applications and their various properties, especially as data-driven tools. There are many modal decomposition techniques, yet Proper Orthogonal Decomposition (POD) and Dynamic Mode Decomposition (DMD) are the most widespread methods, especially in the field of fluid dynamics. Following their highly competent performance on various applications in several fields, numerous extensions of these techniques have been developed. In this work, we present an ambitious review comparing eight different modal decomposition techniques, including most established methods, i.e., POD, DMD, and Fast Fourier Transform; extensions of these classical methods: based either on time embedding systems, Spectral POD and Higher Order DMD, or based on scales separation, multi-scale POD (mPOD) and multi-resolution DMD (mrDMD); and also a method based on the properties of the resolvent operator, the data-driven Resolvent Analysis. The performance of all these techniques will be evaluated on four different test cases: the laminar wake around cylinder, a turbulent jet flow, the three-dimensional wake around a cylinder in transient regime, and a transient and turbulent wake around a cylinder. All these mentioned datasets are publicly available. First, we show a comparison between the performance of the eight modal decomposition techniques when the datasets are shortened. Next, all the results obtained will be explained in detail, showing both the conveniences and inconveniences of all the methods under investigation depending on the type of application and the final goal (reconstruction or identification of the flow physics). In this contribution, we aim at giving a—as fair as possible—comparison of all the techniques investigated. To the authors' knowledge, this is the first time a review paper gathering all these techniques have been produced, clarifying to the community what is the best technique to use for each application.
Numerical study of microjet and heat flux effects on flow separation and heat transfer over a ramp
Authors: Pour Razzaghi Mohammad Javad , Masoumi Yasin , Rezaei Sani Seyed Mojtaba
Published: March 2023

The control of flow and heat transfer has recently been of great interest to engineering researchers in light of computational technology advances. Microjets are used as control solutions to avoid flow separation and increase heat transfer. The present study evaluates a microjet over a ramp at microjet velocity ratios (jet to inflow velocity) of V jet / U 0 = 1, 2, and 4 and heat flux ratios (heat flux to based heat flux) of q s / q 0 = 1, 2, and 3 to examine the flow separation area and heat transfer improvement numerically. The numerical velocity and temperature gradients were compared to earlier numerical and experimental works. Then, the flow over the ramp was analyzed at the aforementioned microjet velocity and heat flux ratios. Moreover, streamlines, bed pressure, fluid temperature, and bed Nusselt number were evaluated. It was found that a microjet with the optimal velocity could not only diminish the separation bubble but also improve heat transfer. A rise in the velocity ratio from 2 to 4 led to a nearly 33% decrease in the separation bubble and an approximately 20% rise in the Nusselt number. In addition, the microjets enhanced heat transfer by up to 50%.
An efficient optical diffuser fabricated from fungal mycelium
Authors: Carrillo-Acuña Isaac , Villanueva-Tiburcio Juan Edson , Gutiérrez-Medina Braulio
Published: March 2023

Scattering of light from randomly textured materials is ubiquitous and of great interest in biology and for diverse applications—including filtering, light trapping in solar cells, and speckle photography. One attractive means to build these materials is by harnessing the complexity present in structures of biological origin. Here, we report on the development of a random phase diffuser based on intertwined filamentous cells (hyphae) of the fungus Trichoderma atroviride. A fungal colony (mycelium) is grown on the surface of a gel medium, and then removed, fixated, and dehydrated, resulting in a free-standing, two-dimensional random mesh (1 cm × 1 cm × 5 μm) composed of rigid hyphae separated by air gaps. A laser beam incident on the bioplate results in speckle patterns of nearly equal intensity in transmission and reflection. By modeling the bioplate as composed of optical phase elements and computing Fraunhofer diffraction, we recover the overall shape of the observed diffuse light spot. As the hyphal density composing the sample is increased, all optical power is in the speckle pattern, and approximate Lambertian transmissivity is reached. Altogether, our observations suggest that a planar fungal colony can scatter light efficiently by imparting a random phase. These results underscore the potential of a biological structure to develop optical elements and to use light scattering to evaluate morphology in complex structures—such as filamentous mycelia.
First Principles Modeling of Strain Induced Effects in Functional Materials
Authors: Raghunathan Rajamani
Published: March 2023

Functional materials that show a response to an external perturbation such as temperature, photons, pressure, and electric or magnetic field are technologically important for applications such as spintronics, opto-electronics and photovoltaics. However, in many materials the response is inadequate for any practical use. Traditionally, strain has been a very useful degree of freedom that has been leveraged to tailor properties and also provides opportunities for understanding the mechanism behind such properties. Theoretical modeling is a very useful tool to gain insights into the origin of material properties at the nanoscale and further use that understanding to tailor existing properties. This chapter will introduce some of the basic concepts of density functional theory, one of the most powerful and widely used techniques to model properties of solids, nanostructures, and molecules. An overview of recent research directions focused on strain-induced effects on electronic structure, transport, optical, thermal, and ferroelectric properties will be presented. Properties of some of the exciting materials like the transition metal oxides, two-dimensional materials including their heterostructures will be covered in this chapter. Finally, we conclude the chapter and present our outlook.
Strain Engineering in 2-2 Multilayered Magneto-Electric (ME) Nanocomposites
Authors: Bhat Anantha P. , Ramadurai Ranjith
Published: March 2023

Magnetoelectric (ME) nano composites, facilitates realization of various ME devices due to the rarity of the phenomenon existing in single-phase material. These composites primarily consists of a ferroelectric material and an antiferro/ferromagnetic material. Though it is known that the ME property exhibited by these composites are strain mediated across the interface, composites with 2-2 connectivity offers superior properties. Hence, in this chapter theoretical models that details the factors that affect the coupling between the layers and experimental methods that facilitate realization of atomically sharp interface are discussed. Multilayered structures with a columnar growth feature ensures maximum strain transfer across the layers and an approach to estimate the size of the strain gradient present across the interface is discussed. Samples that are specifically prepared to estimate the strain gradient is discussed and the obtained spatial operational range of strain is used for further optimization of nanostructures. Thus strain optimized multilayers with specific periodicities are shown to exhibit superior strain coupling between the piezoelectric and magnetostrictive layers. Thus the morphologically coherent columnar structure of both the phases and the epitaxial registry like behavior across the individual grains at the interface of the composite significantly enhances the coupling between the ferroelectric/ferromagnetic phases. Such strain-mediated size optimization offers nanocomposites with superior ME effects.
Integrating dual-purpose crops mitigates feedbase risk and facilitates improved lamb production systems across environments: a whole-farm modelling analysis
Authors: Watt Lucinda J. , Bell Lindsay W. , Herrmann Neville I. , Hunt Peter W.
Published: March 2023

Context The winter feed gap is a common problem for livestock grazing systems worldwide, and changes to climate have made these deficits more unpredictable and extreme. Dual-purpose crops are an important tool in many southern Australian mixed crop–livestock systems to help fill the winter feed gap. Providing more reliable feed over winter can remove feed constraints and allow for earlier lambing in autumn with potential whole-farm system benefits. Aims We simulated a whole-farm livestock enterprise in the Agricultural Production Systems Simulator (APSIM) to examine the implications of spring- and autumn-lambing systems relying on a standard pasture-only feedbase compared with a farm where 25% of its grazed area is allocated to dual-purpose crops. Methods Twelve simulations were run across four locations in New South Wales, Australia, that varied in climatic conditions (both rainfall total and distribution) including two lambing systems (spring vs autumn) × two feedbase types (100% pasture vs 75% pasture and 25% dual-purpose crops) × three stocking densities. Key results For autumn-lambing systems, integrating dual-purpose crops helped to fill the winter feed gap and reduced supplement demand on average by ~28% compared with a pasture-only system. Compared with the standard pasture-only spring-lambing system, integrating dual-purpose crops into spring- and autumn-lambing systems more than doubled gross margin returns due to economic grain yield and lower supplement demand. A shift from spring- to autumn-lambing facilitated by dual-purpose crops also led to better reproductive performance of ewes in the subsequent year. In higher-rainfall, cooler environments, autumn-lambing systems with dual-purpose crops had the highest system gross margins, lowest economic risk and allowed for a safe increase in stocking density. In lower-rainfall, warmer environments, integration of dual-purpose crops into spring-lambing systems returned marginally higher gross margins than for the autumn-lambing system, but differences were less apparent at high stocking density. In lower-rainfall environments, dual-purpose crops helped to mitigate some of the economic risk, but the benefits were less clear. Conclusions We show dual-purpose crops can help fill the winter feed gap and support earlier lambing in autumn across a range of environments, especially in higher-rainfall cooler environments, with significant improvements in total farm gross margins. Implications Integrating dual-purpose crops will enable farmers to change their livestock system to mitigate their risks, reduce supplementary feeding and capitalise on other potential benefits, such as improved marketing and avoiding animal health problems.
Mechanical analysis of bovid horns and cervid antlers: a possible ultimate cause for antler casting
Authors: Liu Yaxin , Li Chunwang
Published: March 2023

Context Cervids and bovids have antlers and horns respectively, which serve important functions. Bovids horns grow continuously, while almost all cervids cast antlers annually. Aims We compared some measurements of the cervid antlers with the bovid horns to show the possible morphological and mechanical reasons for antler casting. Methods We measured the weight and the length of 59 cervid antlers and 35 bovid horns. Then, we calculated the ratio of antler (or horn) weight to bodyweight, as well as the torque of the antler and horns. We used general linear model to test the difference of these four variables between cervids and bovids. Key results Our results showed that (1) the weight of cervid antlers was significantly higher than that of bovid horns, (2) the ratio of antler (or horn) weight to bodyweight showed no significant difference between cervids and bovids, (3) the distance from the centre of gravity to the base of the antler or horn differed significantly between bovids and cervids, and (4) the torque of cervid antlers was significantly greater than that of bovid horns. Conclusions We assumed that the antlers exert more burden on the head of cervids than do horns on the head of bovids. Antler casting could be the evolutionary strategy of deer to relieve the burden of antlers. Implications Unpacking the burden of antler could be one of the ultimate causes for antler casting in cervids.
The age estimation of an extremely old Silver Drummer Kyphosus sydneyanus (Günther 1886) from southern Western Australia
Authors: Coulson Peter Graham
Published: March 2023

Kyphosids are conspicuous members of temperate and tropical reef fish communities. Some species contribute to commercial and recreational fisheries but are vulnerable to capture in large numbers due to their schooling behaviour and site fidelity. Previous ageing studies of kyphosids have determined that some species are long-lived, with maximum ages >40 years, which is a trait often associated with low natural mortality rates. Kyphosus sydneyanus is one of the largest kyphosids and has historically been caught in large numbers as a bycatch species in the demersal gillnet fishery in southern Western Australia. A large K. sydneyanus specimen was collected from that fishery in March 2021. A count of the growth (opaque) zones in the sectioned otoliths were used to determine that the age of this individual was 93 years, more than double the previous maximum age of a Kyphosus species and the longest-lived coastal species in southern Australia.
A Toll pathway effector protects
Drosophila
specifically from distinct toxins secreted by a fungus or a bacterium
Authors: Huang Jianqiong , Lou Yanyan , Liu Jiyong , Bulet Philippe , Cai Chuping , Ma Kaiyu , Jiao Renjie , Hoffmann Jules A. , Liégeois Samuel , Li Zi , Ferrandon Dominique
Published: March 2023

The
Drosophila
systemic immune response against many Gram-positive bacteria and fungi is mediated by the Toll pathway. How Toll-regulated effectors actually fulfill this role remains poorly understood as the known Toll-regulated antimicrobial peptide (AMP) genes are active only against filamentous fungi and not against Gram-positive bacteria or yeasts. Besides AMPs, two families of peptides secreted in response to infectious stimuli that activate the Toll pathway have been identified, namely Bomanins and peptides derived from a polyprotein precursor known as Baramicin A (BaraA). Unexpectedly, the deletion of a cluster of 10 Bomanins phenocopies the Toll mutant phenotype of susceptibility to infections. Here, we demonstrate that
BaraA
is required specifically in the host defense against
Enterococcus faecalis
and against the entomopathogenic fungus
Metarhizium robertsii
, albeit the fungal burden is not altered in
BaraA
mutants. BaraA protects the fly from the action of distinct toxins secreted by these Gram-positive and fungal pathogens, respectively, Enterocin V and Destruxin A. The injection of Destruxin A leads to the rapid paralysis of flies, whether wild type (WT) or mutant. However, a larger fraction of wild-type than
BaraA
flies recovers from paralysis within 5 to 10 h. BaraAs' function in protecting the host from the deleterious action of Destruxin is required in glial cells, highlighting a resilience role for the Toll pathway in the nervous system against microbial virulence factors. Thus, in complement to the current paradigm, innate immunity can cope effectively with the effects of toxins secreted by pathogens through the secretion of dedicated peptides, independently of xenobiotics detoxification pathways.
Dysregulation of ribosome-associated quality control elicits cognitive disorders via overaccumulation of TTC3
Authors: Endo Ryo , Chen Yi-Kai , Burke John , Takashima Noriko , Suryawanshi Nayan , Hui Kelvin K. , Miyazaki Tatsuhiko , Tanaka Motomasa
Published: March 2023

Ribosome-associated quality control (RQC) pathway is responsible for degradation of nascent polypeptides in aberrantly stalled ribosomes, and its defects may lead to neurological diseases. However, the underlying molecular mechanism of how RQC dysfunction elicits neurological disorders remains poorly understood. Here we revealed that neurons with knockout (KO) of ubiquitin ligase LTN1, a key gene in the RQC pathway, show developmental defects in neurons via upregulation of TTC3 and UFMylation signaling proteins. The abnormally enhanced TTC3 protein in
Ltn1
KO neurons reduced further accumulation of translationally arrested products by preventing translation initiation of selective genes. However, the overaccumulated TTC3 protein in turn caused dendritic abnormalities and reduced surface-localized GABA
A
receptors during neuronal development.
Ltn1
KO mice showed behavioral deficits associated with cognitive disorders, a subset of which were restored by TTC3 knockdown in medial prefrontal cortex. Together, the overactivated cellular compensatory mechanism against defective RQC through TTC3 overaccumulation induced synaptic and cognitive deficits. More broadly, these findings represent a novel cellular mechanism underlying neuronal dysfunctions triggered by exaggerated cellular stress response to accumulated abnormal translation products in neurons.
Classification of domains in predicted structures of the human proteome
Authors: Schaeffer R. Dustin , Zhang Jing , Kinch Lisa N. , Pei Jimin , Cong Qian , Grishin Nick V.
Published: March 2023

Recent advances in protein structure prediction have generated accurate structures of previously uncharacterized human proteins. Identifying domains in these predicted structures and classifying them into an evolutionary hierarchy can reveal biological insights. Here, we describe the detection and classification of domains from the human proteome. Our classification indicates that only 62% of residues are located in globular domains. We further classify these globular domains and observe that the majority (65%) can be classified among known folds by sequence, with a smaller fraction (33%) requiring structural data to refine the domain boundaries and/or to support their homology. A relatively small number (966 domains) cannot be confidently assigned using our automatic pipelines, thus demanding manual inspection. We classify 47,576 domains, of which only 23% have been included in experimental structures. A portion (6.3%) of these classified globular domains lack sequence-based annotation in InterPro. A quarter (23%) have not been structurally modeled by homology, and they contain 2,540 known disease-causing single amino acid variations whose pathogenesis can now be inferred using AF models. A comparison of classified domains from a series of model organisms revealed expansions of several immune response-related domains in humans and a depletion of olfactory receptors. Finally, we use this classification to expand well-known protein families of biological significance. These classifications are presented on the ECOD website (
http://prodata.swmed.edu/ecod/index_human.php
).
An upper bound for extreme temperatures over midlatitude land
Authors: Zhang Yi , Boos William R.
Published: March 2023

Heatwaves damage societies worldwide and are intensifying with global warming. Several mechanistic drivers of heatwaves, such as atmospheric blocking and soil moisture-atmosphere feedback, are well-known for their ability to raise surface air temperature. However, what limits the maximum surface air temperature in heatwaves remains unclear; this became evident during recent Northern Hemisphere heatwaves which achieved temperatures far beyond the upper tail of the observed statistical distribution. Here, we present evidence for the hypothesis that convective instability limits annual maximum surface air temperatures (TXx) over midlatitude land. We provide a theory for the corresponding upper bound of midlatitude temperatures, which accurately describes the observed relationship between temperatures at the surface and in the midtroposphere. We show that known heatwave drivers shift the position of the atmospheric state in the phase space described by the theory, changing its proximity to the upper bound. This theory suggests that the upper bound for midlatitude TXx should increase 1.9 times as fast as 500-hPa temperatures at the time and location of TXx occurrences. Using empirical 500-hPa warming, we project that the upper bound of TXx over Northern Hemisphere midlatitude land (40°N to 65°N) will increase about twice as fast as global mean surface air temperature, and TXx will increase faster than this bound over regions that dry on the hottest days.
Heat shock potentiates aminoglycosides against gram-negative bacteria by enhancing antibiotic uptake, protein aggregation, and ROS
Authors: Lv Boyan , Huang Xuebing , Lijia Chenchen , Ma Yuelong , Bian Mengmeng , Li Zhongyan , Duan Juan , Zhou Fang , Yang Bin , Qie Xingwang , Song Yizhi , Wood Thomas K. , Fu Xinmiao
Published: March 2023

The potentiation of antibiotics is a promising strategy for combatting antibiotic-resistant/tolerant bacteria. Herein, we report that a 5-min sublethal heat shock enhances the bactericidal actions of aminoglycoside antibiotics by six orders of magnitude against both exponential- and stationary-phase
Escherichia coli
. This combined treatment also effectively kills various
E. coli
persisters,
E. coli
clinical isolates, and numerous gram-negative but not gram-positive bacteria and enables aminoglycosides at 5% of minimum inhibitory concentrations to eradicate multidrug-resistant pathogens
Acinetobacter baumannii
and
Klebsiella pneumoniae
. Mechanistically, the potentiation is achieved comprehensively by heat shock-enhanced proton motive force that thus promotes the bacterial uptake of aminoglycosides, as well as by increasing irreversible protein aggregation and reactive oxygen species that further augment the downstream lethality of aminoglycosides. Consistently, protonophores, chemical chaperones, antioxidants, and anaerobic culturing abolish heat shock-enhanced aminoglycoside lethality. We also demonstrate as a proof of concept that infrared irradiation- or photothermal nanosphere-induced thermal treatments potentiate aminoglycoside killing of
Pseudomonas aeruginosa
in a mouse acute skin wound model. Our study advances the understanding of the mechanism of actions of aminoglycosides and demonstrates a high potential for thermal ablation in curing bacterial infections when combined with aminoglycosides.
Experimental evidence for the functional importance and adaptive advantage of A-to-I RNA editing in fungi
Authors: Xin Kaiyun , Zhang Yang , Fan Ligang , Qi Zhaomei , Feng Chanjing , Wang Qinhu , Jiang Cong , Xu Jin-Rong , Liu Huiquan
Published: March 2023

Adenosine-to-inosine (A-to-I) editing is the most prevalent type of RNA editing in animals, and it occurs in fungi specifically during sexual reproduction. However, it is debatable whether A-to-I RNA editing is adaptive. Deciphering the functional importance of individual editing sites is essential for the mechanistic understanding of the adaptive advantages of RNA editing. Here, by performing gene deletion for 17 genes with conserved missense editing (CME) sites and engineering underedited (ue) and overedited (oe) mutants for 10 CME sites using site-specific mutagenesis at the native locus in
Fusarium graminearum
, we demonstrated that two CME sites in
CME5
and
CME11
genes are functionally important for sexual reproduction. Although the overedited mutant was normal in sexual reproduction, the underedited mutant of
CME5
had severe defects in ascus and ascospore formation like the deletion mutant, suggesting that the CME site of
CME5
is co-opted for sexual development. The preediting residue of Cme5 is evolutionarily conserved across diverse classes of Ascomycota, while the postediting one is rarely hardwired into the genome, implying that editing at this site leads to higher fitness than a genomic A-to-G mutation. More importantly, mutants expressing only the underedited or the overedited allele of
CME11
are defective in ascosporogenesis, while those expressing both alleles displayed normal phenotypes, indicating that concurrently expressing edited and unedited versions of Cme11 is more advantageous than either. Our study provides convincing experimental evidence for the long-suspected adaptive advantages of RNA editing in fungi and likely in animals.
Functional SARS-CoV-2 cross-reactive CD4
+
T cells established in early childhood decline with age
Authors: Humbert Marion , Olofsson Anna , Wullimann David , Niessl Julia , Hodcroft Emma B. , Cai Curtis , Gao Yu , Sohlberg Ebba , Dyrdak Robert , Mikaeloff Flora , Neogi Ujjwal , Albert Jan , Malmberg Karl-Johan , Lund-Johansen Fridtjof , Aleman Soo , Björkhem-Bergman Linda , Jenmalm Maria C. , Ljunggren Hans-Gustaf , Buggert Marcus , Karlsson Annika C.
Published: March 2023

Pre-existing SARS-CoV-2-reactive T cells have been identified in SARS-CoV-2-unexposed individuals, potentially modulating COVID-19 and vaccination outcomes. Here, we provide evidence that functional cross-reactive memory CD4
+
T cell immunity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is established in early childhood, mirroring early seroconversion with seasonal human coronavirus OC43. Humoral and cellular immune responses against OC43 and SARS-CoV-2 were assessed in SARS-CoV-2-unexposed children (paired samples at age two and six) and adults (age 26 to 83). Pre-existing SARS-CoV-2-reactive CD4
+
T cell responses targeting spike, nucleocapsid, and membrane were closely linked to the frequency of OC43-specific memory CD4
+
T cells in childhood. The functional quality of the cross-reactive memory CD4
+
T cell responses targeting SARS-CoV-2 spike, but not nucleocapsid, paralleled OC43-specific T cell responses. OC43-specific antibodies were prevalent already at age two. However, they did not increase further with age, contrasting with the antibody magnitudes against HKU1 (β-coronavirus), 229E and NL63 (α-coronaviruses), rhinovirus, Epstein–Barr virus (EBV), and influenza virus, which increased after age two. The quality of the memory CD4
+
T cell responses peaked at age six and subsequently declined with age, with diminished expression of interferon (IFN)-γ, interleukin (IL)-2, tumor necrosis factor (TNF), and CD38 in late adulthood. Age-dependent qualitative differences in the pre-existing SARS-CoV-2-reactive T cell responses may reflect the ability of the host to control coronavirus infections and respond to vaccination.
In situ snapshots along a mammalian selective autophagy pathway
Authors: Li Meijing , Tripathi-Giesgen Ishita , Schulman Brenda A. , Baumeister Wolfgang , Wilfling Florian
Published: March 2023

Selective macroautophagy (hereafter referred to as autophagy) describes a process in which cytosolic material is engulfed in a double membrane organelle called an autophagosome. Autophagosomes are carriers responsible for delivering their content to a lytic compartment for destruction. The cargo can be of diverse origin, ranging from macromolecular complexes to protein aggregates, organelles, and even invading pathogens. Each cargo is unique in composition and size, presenting different challenges to autophagosome biogenesis. Among the largest cargoes targeted by the autophagy machinery are intracellular bacteria, which can, in the case of
Salmonella,
range from 2 to 5 μm in length and 0.5 to 1.5 μm in width. How phagophores form and expand on such a large cargo remains mechanistically unclear. Here, we used HeLa cells infected with an auxotrophic
Salmonella
to study the process of phagophore biogenesis using in situ correlative cryo-ET. We show that host cells generate multiple phagophores at the site of damaged
Salmonella
-containing vacuoles (SCVs). The observed double membrane structures range from disk-shaped to expanded cup-shaped phagophores, which have a thin intermembrane lumen with a dilating rim region and expand using the SCV, the outer membrane of
Salmonella
, or existing phagophores as templates. Phagophore rims establish different forms of contact with the endoplasmic reticulum (ER) via structurally distinct molecular entities for membrane formation and expansion. Early omegasomes correlated with the marker Double-FYVE domain-Containing Protein 1 (DFCP1) are observed in close association with the ER without apparent membrane continuity. Our study provides insights into the formation of phagophores around one of the largest selective cargoes.
Would you like a bag for that?
Authors: Kristiansen Elisabeth Dalby , Rasmussen Gitte
Published: March 2023

This article presents a study of participants’ practices for closing buying-selling encounters in retail shops. The study shows how the handing over of a shopping bag with the items purchased serves as a resource for organizing the closing of the encounter. Further, taking its point of departure in the growing societal awareness of the environmental impact of plastic waste, the study investigates how customers’ increasing avoidance of single-use shopping bags contributes to changing their practices for closing a buying-selling encounter, as the bags no longer provide a resource around which the closing can be organized.

The article uses ethnomethodological conversation analytic (EMCA) methods to describe how customers and sales assistants create and maintain the local order of the shop and how they, through their multimodal and embodied contributions, bring societal discourses into the buying-selling encounter.

The data consists of 22 shopping sequences, recorded in Danish shops in 2018.
Effect of heat treatments on Inconel 625 fabricated by wire and arc additive manufacturing: An in situ synchrotron X-ray diffraction analysis
Authors: Rodrigues Tiago A. , Cipriano Farias Francisco Werley , Avila Julian A. , Maawad Emad , Schell Norbert , Santos Telmo G. , Oliveira J. P.
Published: March 2023

The effect of heat treatments on wire and arc additively manufactured Inconel 625 parts was investigated using in situ synchrotron X-ray diffraction and hardness testing. As-built samples revealed the presence of a γ-matrix with precipitation of γ′, γ′′ and MC carbides. When heat treated at 750°C for 4 h, γ′′ phase precipitated increasing the hardness by 5%. In situ X-ray observations revealed that heat treating at 870°C for 1 h resulted in δ-phase precipitation. Two different second-stage temperatures were tested (1050°C and 1150°C), which dissolved the δ-phase while MC carbides formed upon cooling. The second stage at 1150°C had a higher deleterious effect than the one performed at 1050°C due to extensive grain growth.
Uniqueness in determining rectangular grating profiles with a single incoming wave (Part I): TE polarization case
Authors: Xiang Jianli , Hu Guanghui
Published: March 2023

We investigate inverse diffraction problems for penetrable gratings in a piecewise constant medium. In the TE polarization case, it is proved that a rectangular grating profile together with the refractive index beneath it can be uniquely determined by the near-field observation data incited by a single plane wave and measured on a line segment above the grating. Our approach relies on the expansion of solutions to the Helmholtz equation and the corner singularity analysis of solutions to the inhomogeneous Laplace equation with a piecewise continuous source term in a sector. This paper also contributes to corner scattering theory for the Helmholtz equation in a special non-convex domain.
Sub-picosecond timing jitter between optically synchronized femtosecond and picosecond laser systems
Authors: Jiang Zhenfei , Strycker Benjamin , Hand Lucian , Adamonis Jonas , Yi Zhenhuan , Sokolov Alexei , Scully Marlan
Published: March 2023

Synchronized optical pulses are widely used. We report here characterization and measurement of synchronized femtosecond and picosecond pulses from a Ti:Sapphire laser (nominally 800 nm) and a Nd:YAG laser (1064 nm), respectively. Synchronization is achieved by utilizing soliton self-frequency shift in a photonic-crystal fiber that allows the 800 nm femtosecond oscillator to seed the third-harmonic generation (355 nm) of picosecond regenerative amplifier. The relative timing jitter between the amplified femtosecond and the third-harmonic generation of picosecond pulses is (710 ± 160) fs, which is only (1.17 ± 0.26)% of the picosecond pulse duration. This work paves way for applications in stimulated Raman scattering spectroscopy and amplification.
Structural and thermodynamic properties of quasi-2D Mo(1–x)W
x
(S, Se, Te)2 monolayer alloys: a statistical first principle study
Authors: de Carvalho Luiz Cláudio , da Lapa Rodrigo Santos , Alexandre Simone Silva , Nunes Ricardo Wagner
Published: March 2023

In this work, we report an ab initio study of the structural and thermodynamic properties of two-dimensional transition-metal dichalcogenides (2D-TMDC) alloys, Mo(1–x)W
x
(S, Se, Te)2, using the cluster expansion framework to compute the Helmholtz free energy of alloys as a function of alloy composition and temperature, in the framework of the generalized quasi-chemical approximation. We consider alloying only on the metal sublayer. Our results indicate a weak dependence of the structural properties (lattice constants, nearest-neighbor bond lengths, and layer width) on the alloy composition (i.e. concentrations of W and Mo atoms), in line with the very similar values of the atomic radii of Mo and W atoms. A stronger dependence on the chalcogen is obtained, a trend that reflects the larger variations in atomic radii among the three chalcogen species. As a function of composition, the structural parameters we examined show similar trends, with negligible bowing (i.e. deviations from a Vegard’s law interpolation between end compounds), for the three alloys. Moreover, already at 300 K the behavior of these structural features as a function of composition is very similar to that of the standard-regular-solution (SRS) high-temperature limit. In contrast, the electronic band gaps of the the three alloys as a function of composition show small but significant bowing, as high as −1% to −2% near the x = 0.5 alloy composition. Similarly to the structural features, the band gaps attain the high-temperature SRS limit already at 300 K. Regarding thermodynamic properties, we obtain negative values of the internal energy of mixing for the three alloys over the full range of compositions. Therefore, the theoretical alloying phase diagram for the three alloys is featureless, with stability of a fully-mixed alloy at all temperatures and compositions, with no miscibility gap (hence no bimodal nor spinodal decomposition lines). The thermodynamic potentials (mixing internal energy, mixing entropy, and mixing free energy) reach the high-temperature limit at ∼1000 K, the temperature range of synthesis of 2D-TMDC alloys. These trends of structural and electronic properties of the 2D-TMDC alloys are due to the very similar atomic radii and the nearly identical coordination chemistry of Mo and W. Our results are in agreement with experimental work on the alloying of Mo and W atoms, for samples of Mo(1–x)W
x
S2 monolayer alloys, that found that the random mixed alloy is the thermodynamically stable state for this alloy, with no segregation or phase separation.