bluuebunny/crossref_metadata_2025 huggingface dataset:
Numerical study of equilibrium radial positions of neutrally buoyant balls in circular Poiseuille flows
Authors: Pan Tsorng-Whay , Li Ang , Glowinski Roland
Published: March 2021

In this article, we have studied, via direct numerical simulations, the equilibrium radial positions of neutrally buoyant balls moving in circular Poiseuille flows. For the one ball case, the Segre–Silberberg effect takes place at low Reynolds numbers (Re) as expected. However, at higher Re, the ball moves to one of two equilibrium positions. At even higher Re, the ball is pinched to a radial position closer to the central axis. For the case of two neutrally buoyant balls placed on a line parallel with the central axis initially, this two-ball train is stable at low Re and its mass center moves to the outer Segre–Silberberg equilibrium position like the migration of a single neutrally buoyant ball. Moreover, for Re values greater than the critical value, Rec = 435, the two-ball train is unstable. The two balls interact periodically, suggesting a (kind of) Hopf bifurcation phenomenon. Nevertheless, the averaged mass center of the two balls is located at the inner equilibrium radial position.
Deep learning virtual colorization overcoming chromatic aberrations in singlet lens microscopy
Authors: Bian Yinxu , Jiang Yannan , Huang Yuran , Yang Xiaofei , Deng Weijie , Shen Hua , Shen Renbing , Kuang Cuifang
Published: March 2021

Singlet lenses are free from precise assembling, aligning, and testing, which are helpful for the development of portable and low-cost microscopes. However, balancing the spectrum dispersion or chromatic aberrations using a singlet lens made of one material is difficult. Here, a novel method combining singlet lens microscopy and computational imaging, which is based on deep learning image-style-transfer algorithms, is proposed to overcome this problem in clinical pathological slide microscopy. In this manuscript, a singlet aspheric lens is used, which has a high cut-off frequency and linear signal properties. Enhanced by a trained deep learning network, it is easy to transfer the monochromatic gray-scale microscopy picture to a colorful microscopy picture, with only one single-shot recording by a monochromatic CMOS image sensor. By experiments, data analysis, and discussions, it is proved that our proposed virtual colorization microscope imaging method is effective for H&E stained tumor tissue slides in singlet microscopy. It is believable that the computational virtual colorization method for singlet microscopes would promote the low-cost and portable singlet microscopy development in medical pathological label staining observing (e.g., H&E staining, Gram staining, and fluorescent labeling) biomedical research.
Investigation on the effect of the reference supply voltage on the micro-rectangular-columned Ti3SiC2 surface by wire electrical discharge machining
Authors: Zhou Chaolan , Liu Kaige , Wu Xiaoyu , Kong Lingbing
Published: March 2021

In this paper, an isotropous hydrophobic Ti3SiC2 surface with a micro-rectangular-columned structure can be machined by wire electrical discharge machining (WEDM) by different reference supply voltages. To optimize the WEDM processing parameters, the influence of the reference supply voltage on the topographies and phase constitutions of the micro-rectangular-columned Ti3SiC2 surface was studied. The relation between the phase constitution of the machined Ti3SiC2 surfaces and the different reference supply voltages was analyzed. The influences of the different reference supply voltages on the wetting behaviors of the textured Ti3SiC2 surfaces were characterized by the variation in the water contact angles on the textured surfaces. It was found that increasing the reference supply voltage would increase the surface roughness of the textured surface and aggravate the decomposition of Ti3SiC2 on the surfaces. The textured Ti3SiC2 surface had a maximum contact angle of 147.8°, which was increased by about 67% compared with the contact angle on the untextured Ti3SiC2 surface.
Data-driven subgrid-scale modeling of forced Burgers turbulence using deep learning with generalization to higher Reynolds numbers via transfer learning
Authors: Subel Adam , Chattopadhyay Ashesh , Guan Yifei , Hassanzadeh Pedram
Published: March 2021

Developing data-driven subgrid-scale (SGS) models for large eddy simulations (LESs) has received substantial attention recently. Despite some success, particularly in a priori (offline) tests, challenges have been identified that include numerical instabilities in a posteriori (online) tests and generalization (i.e., extrapolation) of trained data-driven SGS models, for example, to higher Reynolds numbers. Here, using the stochastically forced Burgers turbulence as the test-bed, we show that deep neural networks trained using properly pre-conditioned (augmented) data yield stable and accurate a posteriori LES models. Furthermore, we show that transfer learning enables accurate/stable generalization to a flow with 10× higher Reynolds number.
Preparation, structure, and luminescent properties of Dy3+-doped borate Ca3La3(BO3)5: Dy3+ for potential application in UV-LEDs
Authors: Dai Wubin , Fan Yeming , Xu Man , Shen Fan
Published: March 2021

A single-phase white light-emitting phosphor Ca3La3(BO3)5: Dy3+ (CLBD) was prepared via a solid-state reaction. The introduction of Dy3+ in Ca3La3(BO3)5 with a preferred location on La3+ was confirmed by x-ray diffraction and Rietveld structural refinement studies. The micrograph observed by scanning electron microscopy reveals an inhomogeneous and uneven dense morphology in the micrometer range. The optical spectra analysis shows that the CLBD can be efficiently excited by ultraviolet (UV) light and emitted intense white light due to the combination of blue 4F9/2 → 6H15/2 (∼485 nm) and yellow 4F9/2 → 6H13/2 (∼575 nm) emissions originated from 4f–4f transitions of Dy3+. The critical concentration is determined to be ∼12 mol. %, and the dipole–dipole (d–d) interaction is responsible for the quenching mechanism. In additional, the CLBD has high thermal stability. By incorporating the CLBD with a phosphor-capping method on AlInGaN LED, we obtain the white light that meets the spectral and efficiency requirements for high-efficacy solid-state white lighting lamps. The Commission Internationale de I'Eclairage chromaticity coordinates and color correlated temperature with optimal electroluminescence intensity are calculated to be ∼(0.338, 0.342) and 5950 K, respectively. All results indicate the CLBD could serve as a promising candidate for white UV-LEDs.
Superalkali NLi4 anchored on BN sheets for reversible hydrogen storage
Authors: Wang Xiang , Qi Hao , Ma Li , Chen Hongshan
Published: March 2021

Developing an efficient storage medium is a substantial challenge for the utilization of hydrogen as an energy carrier, and designing materials with intermediate holding strength for hydrogen is the key to the solution. In this paper, we decorate h-BN using superalkali NLi4 and investigate the hydrogen storage properties by density functional theory. NLi4 clusters can be anchored stably on BN sheets with a binding energy −1.43 eV. As the NLi4 species has enhanced stability, decoration using the superalkali effectively improves the aggregation of the metal atoms on a substrate. Replacing alkali metal atoms by superalkalis also offers more spaces for H2 adsorption. The H2 molecules adsorbed on the bottom Li+ cations are strongly polarized due to the small radius of Li+, and the H2 molecules attached to the top Li+ are adsorbed by feeding back the excess electron up to the antibonding σ* orbitals of the H2 molecules. Each NLi4 can absorb nine H2 molecules with adsorption energies about −0.20 eV/H2. The adsorption strengths fall in the ideal window for reversible uptake-release at ambient temperatures. The hydrogen storage capacity at the decoration density of NLi4/BN = 1:6 reaches 9.40 wt. %. The present study suggests that NLi4 decorated 2D materials can be potential candidates for hydrogen storage at room temperature.
Quantum bath effects on nonequilibrium heat transport in model molecular junctions
Authors: Carpio-Martínez Pablo , Hanna Gabriel
Published: March 2021

Quantum–classical dynamics simulations enable the study of nonequilibrium heat transport in realistic models of molecules coupled to thermal baths. In these simulations, the initial conditions of the bath degrees of freedom are typically sampled from classical distributions. Herein, we investigate the effects of sampling the initial conditions of the thermal baths from quantum and classical distributions on the steady-state heat current in the nonequilibrium spin-boson model—a prototypical model of a single-molecule junction—in different parameter regimes. For a broad range of parameter regimes considered, we find that the steady-state heat currents are ∼1.3–4.5 times larger with the classical bath sampling than with the quantum bath sampling. Using both types of sampling, the steady-state heat currents exhibit turnovers as a function of the bath reorganization energy, with sharper turnovers in the classical case than in the quantum case and different temperature dependencies of the turnover maxima. As the temperature gap between the hot and cold baths increases, we observe an increasing difference in the steady-state heat currents obtained with the classical and quantum bath sampling. In general, as the bath temperatures are increased, the differences between the results of the classical and quantum bath sampling decrease but remain non-negligible at the high bath temperatures. The differences are attributed to the more pronounced temperature dependence of the classical distribution compared to the quantum one. Moreover, we find that the steady-state fluctuation theorem only holds for this model in the Markovian regime when quantum bath sampling is used. Altogether, our results highlight the importance of quantum bath sampling in quantum–classical dynamics simulations of quantum heat transport.
The role of plasmalogens, Forssman lipids, and sphingolipid hydroxylation in modulating the biophysical properties of the epithelial plasma membrane
Authors: Wilson Katie A. , Fairweather Stephen J. , MacDermott-Opeskin Hugo I. , Wang Lily , Morris Richard A. , O’Mara Megan L.
Published: March 2021

A coarse-grain model of the epithelial plasma membrane was developed from high-resolution lipidomic data and simulated using the MARTINI force field to characterize its biophysical properties. Plasmalogen lipids, Forssman glycosphingolipids, and hydroxylated Forssman glycosphingolipids and sphingomyelin were systematically added to determine their structural effects. Plasmalogen lipids have a minimal effect on the overall biophysical properties of the epithelial plasma membrane. In line with the hypothesized role of Forssman lipids in the epithelial apical membrane, the introduction of Forssman lipids initiates the formation of glycosphingolipid-rich nanoscale lipid domains, which also include phosphatidylethanolamine (PE), sphingomyelin (SM), and cholesterol (CHOL). This decreases the lateral diffusion in the extracellular leaflet, as well as the area per lipid of domain forming lipids, most notably PE. Finally, hydroxylation of the Forssman glycosphingolipids and sphingomyelin further modulates the lateral organization of the membrane. Through comparison to the previously studied average and neuronal plasma membranes, the impact of membrane lipid composition on membrane properties was characterized. Overall, this study furthers our understanding of the biophysical properties of complex membranes and the impact of lipid diversity in modulating membrane properties.
Exploring and enhancing the accuracy of interior-scaled Perdew–Zunger self-interaction correction
Authors: Bhattarai Puskar , Santra Biswajit , Wagle Kamal , Yamamoto Yoh , Zope Rajendra R. , Ruzsinszky Adrienn , Jackson Koblar A. , Perdew John P.
Published: March 2021

The Perdew–Zunger self-interaction correction (PZ-SIC) improves the performance of density functional approximations for the properties that involve significant self-interaction error (SIE), as in stretched bond situations, but overcorrects for equilibrium properties where SIE is insignificant. This overcorrection is often reduced by local scaling self-interaction correction (LSIC) of the PZ-SIC to the local spin density approximation (LSDA). Here, we propose a new scaling factor to use in an LSIC-like approach that satisfies an additional important constraint: the correct coefficient of the atomic number Z in the asymptotic expansion of the exchange–correlation (xc) energy for atoms. LSIC and LSIC+ are scaled by functions of the iso-orbital indicator zσ, which distinguishes one-electron regions from many-electron regions. LSIC+ applied to the LSDA works better for many equilibrium properties than LSDA-LSIC and the Perdew, Burke, and Ernzerhof generalized gradient approximation (GGA), and almost close to the strongly constrained and appropriately normed (SCAN) meta-GGA. LSDA-LSIC and LSDA-LSIC+, however, fail to predict interaction energies involving weaker bonds, in sharp contrast to their earlier successes. It is found that more than one set of localized SIC orbitals can yield a nearly degenerate energetic description of the same multiple covalent bond, suggesting that a consistent chemical interpretation of the localized orbitals requires a new way to choose their Fermi orbital descriptors. To make a locally scaled down SIC to functionals beyond the LSDA requires a gauge transformation of the functional’s energy density. The resulting SCAN-sdSIC, evaluated on SCAN-SIC total and localized orbital densities, leads to an acceptable description of many equilibrium properties including the dissociation energies of weak bonds.
Evolutionary insights into shape-shifting proteins
Authors: Berkowitz Rachel
Published: March 2021

Over millions of years a protein that now folds into two stable structures likely favored first one configuration, then the other, before settling on both.
Topological phases emerge in an ecological model
Authors: Hill Heather
Published: March 2021

An exotic phenomenon in condensed-matter systems illuminates the behavior of a one-dimensional model akin to the game rock-paper-scissors.
Chemical lean determination of boneless beef and lamb using a halogen moisture analyser
Authors: Watkins Peter
Published: March 2021

Context Chemical lean (CL) is an important metric used by the Australian meat industry to describe fat content of meat product. It is a minimum meat specification included in contracts between Australian vendors of bulk packed boneless manufacturing meat and overseas or domestic buyers and can be regarded as the complement of chemically determined fat in meat (% fat, CL = 100-% fat). The microwave moisture method is commonly used for measuring CL content of meat in Australian abattoirs, relying on a relationship between CL and moisture content of boneless meat. It is regarded as a quick and easy method to use. More recently, newer methods for moisture analysis have become available which may also be suitable for CL determination, including commercial halogen moisture analysers (HMAs). HMAs use a halogen lamp as a source of infrared radiation that is absorbed by a sample, which then results in moisture loss. Aims This study aimed to compare the use of HMAs for CL determination of beef and lamb to that obtained from Soxhlet extraction technique, which is the AOAC Final Action Method for determining fat in meat and accepted as the reference method for fat determination. Additionally, the study sought to validate the use of HMAs as a method for CL determination in the Australian meat industry. Methods HMAs were used to determine the moisture content of six beef and one lamb samples, which were used to calculate the CL content. The fat content of the samples was also determined using Soxhlet fat extraction. Passing-Bablok regression and Bland-Altman plot analysis were used to identify any differences and bias between the methods, respectively. Key results Passing-Bablok regression showed that there was no difference between methods, while Bland-Altman plot analysis indicated no bias was evident between the methods. While some differences were apparent between approaches either due to using moisture as a proxy for fat/CL compared with continual solvent extraction or sample heterogeneity, sufficient agreement existed between results to lie within an acceptance criterion of 1.2 CL units. Conclusion The use of HMAs was substantiated as a method for CL determination in the Australian meat industry and has been accredited by AUS-MEAT Ltd as a method for boneless beef and lamb. Implications HMAs can be used in the Australian meat industry for CL determination and represent a relatively simpler and easier approach for this important industry metric.
NF-κB–induced R-loop accumulation and DNA damage select for nucleotide excision repair deficiencies in adult T cell leukemia
Authors: He Yunlong , Pasupala Nagesh , Zhi Huijun , Dorjbal Batsuhk , Hussain Imran , Shih Hsiu-Ming , Bhattacharyya Sharmistha , Biswas Roopa , Miljkovic Milos , Semmes Oliver John , Waldmann Thomas A. , Snow Andrew L. , Giam Chou-Zen
Published: March 2021

Significance

Cellular NF-κB activity is stringently regulated. Constitutive NF-κB activation (NF-κB
CA
), however, frequently occurs in T/B cell malignancies including adult T cell leukemia (ATL) caused by human T cell leukemia virus type 1 (HTLV-1). We demonstrate that NF-κB
CA
via the HTLV-1 trans-activator/oncoprotein Tax causes R-loop accumulation, DNA double-strand breaks, and senescence and that R-loop processing by the transcription-coupled nucleotide excision repair (TC-NER) pathway contributes to senescence induction. We show that TC-NER deficits occur in ATL. They enable senescence escape and outgrowth of HTLV-1–infected and ATL cells with NF-κB
CA
, but render ATL cells hypersensitive to ultraviolet light. With NF-κB
CA
, ATL cells continue to accumulate abundant R-loops. TC-NER deficiency and excess R-loop accumulation represent vulnerabilities of ATL that can be exploited therapeutically.
Evaluating the potential efficacy and limitations of a phage for joint antibiotic and phage therapy of
Staphylococcus aureus
infections
Authors: Berryhill Brandon A. , Huseby Douglas L. , McCall Ingrid C. , Hughes Diarmaid , Levin Bruce R.
Published: March 2021

Significance

This study explores the potential of a phage, PYO
Sa
, for treating 
Staphylococcus aureus
infections in combination with antibiotics. Population dynamic and genomic analysis identified a limitation and potential liability of using PYO
Sa
 for therapy. Due to the production of potentially pathogenic atypical small colony variants, PYO
Sa
 alone cannot eliminate 
S. aureus
populations. However, we demonstrate that by following the administration of PYO
Sa
with bactericidal antibiotics, this limitation and potential liability can be addressed. The methods used in this investigation to explore the efficacy of combinations of PYO
Sa
 and antibiotics for treating 
S. aureus 
infections can be employed to evaluate the clinical potential and facilitate the design of treatment protocols for any bacteria and phage that can be cultured in vitro.
Evolutionary relationships between drought-related traits and climate shape large hydraulic safety margins in western North American oaks
Authors: Skelton Robert P. , Anderegg Leander D. L. , Diaz Jessica , Kling Matthew M. , Papper Prahlad , Lamarque Laurent J. , Delzon Sylvain , Dawson Todd E. , Ackerly David D.
Published: March 2021

Significance

A fundamental association between sustained water transport and downstream tissue survival should select for xylem that avoids embolism in long-lived woody plants. Previous studies suggest that long-vessel species, such as oaks and vines, are more susceptible to drought-induced loss of function than other species. We show that western North American oaks—even those occurring in wet temperate forest—possess xylem capable of tolerating substantial water stress. Evolutionary relationships between drought tolerance traits combined with plant–climate interactions yield positive hydraulic safety margins in oaks from diverse habitats, demonstrating that these key species are not yet on the verge of hydraulically mediated loss of function. Quantifying physical tolerance limits to desiccation is imperative for predicting ecological consequences of future droughts.
The store-operated Ca
2+
entry complex comprises a small cluster of STIM1 associated with one Orai1 channel
Authors: Shen Yihan , Thillaiappan Nagendra Babu , Taylor Colin W.
Published: March 2021

Significance

Store-operated Ca
2+
entry (SOCE) links Ca
2+
release from endoplasmic reticulum (ER) to Ca
2+
entry across the plasma membrane (PM). SOCE is unusual in requiring interaction between proteins in different membranes. STIM1, when it senses loss of ER Ca
2+
, unfurls domains that interact with Orai1 PM Ca
2+
channels. The stoichiometry of the SOCE complex is contentious, but it determines the regulation and functional consequences of SOCE. We show that native complexes are likely to comprise a single Orai1 channel and a few STIM1 dimers, too few to cluster Orai1 channels. We suggest that SOCE may be digitally regulated by local ER depletion, and that local SOCE-evoked Ca
2+
fluxes are small enough to allow substantial intracellular redistribution of Ca
2+
through ER tunnels.
IDO1 scavenges reactive oxygen species in myeloid-derived suppressor cells to prevent graft-versus-host disease
Authors: Ju Ji-Min , Nam Giri , Lee Young-Kwan , Jung Minho , Chang Hanna , Kim Woojin , Shon Woo Jeong , Lim Ji Young , Kim Joo Young , Chang Jun , Min Chang Ki , Lee Dong-Sup , Choi Kyungho , Shin Dong-Mi , Choi Eun Young
Published: March 2021

Significance

This study reveals that the tryptophan-degrading reaction catalyzed by indoleamine 2,3-dioxygenase 1 (IDO1) is linked to reactive oxygen species (ROS) scavenging in Gr-1+CD11b+myeloid cells. The IDO1-mediated ROS scavenging promotes myeloid-derived suppressor cell characteristics in Gr-1+CD11b+cells, suppressing their differentiation into proinflammatory neutrophils. These results could explain the increased lethality in graft-versus-host disease as well as the enhanced proinflammatory and reduced regulatory T cell responses after transplantation of IDO1-deficient bone marrow cells. Our findings provide a mechanistic insight into the immune-modulatory roles of IDO1.
Structural insights into α-synuclein monomer–fibril interactions
Authors: Kumari Pratibha , Ghosh Dhiman , Vanas Agathe , Fleischmann Yanick , Wiegand Thomas , Jeschke Gunnar , Riek Roland , Eichmann Cédric
Published: March 2021

Significance

The characteristic feature of Parkinson’s disease is the deposition of α-synuclein into insoluble amyloid fibrils. The so-called secondary nucleation mechanism appears to be key for the aggregation kinetics, because binding of monomers on the fibril surface can autocatalytically induce new amyloid seeds. We show by nuclear magnetic and electron paramagnetic resonance spectroscopy that α-synuclein monomer–fibril binding is primarily mediated by transient electrostatic interactions. These intermolecular contacts result in an unfolding of the loosely packed α-synuclein structures and expose the otherwise protected aggregation-prone non-amyloid-β component of the protein. Our data demonstrate that intramolecular unfolding of α-synuclein is a prerequisite for protein aggregation that leads to rapid multiplication of α-synuclein amyloid fibrils via the secondary nucleation process.
Cysteinyl-specialized proresolving mediators link resolution of infectious inflammation and tissue regeneration via TRAF3 activation
Authors: Chiang Nan , de la Rosa Xavier , Libreros Stephania , Pan Hui , Dreyfuss Jonathan M. , Serhan Charles N.
Published: March 2021

Significance

Resolution of inflammation, infection, and injury are essential for host defense and homeostasis. Cysteinyl-specialized proresolving mediators (cys-SPMs) are potent chemical signals that accelerate resolution of inflammation, control infection, and display proregenerative properties. We sought evidence for cys-SPM–activated primordial pathways that might link resolution of inflammation and regeneration using planaria because of their robust regenerative ability. RNA sequencing was carried out with surgically resected planaria exposed to cys-SPMs, and we identified genes and pathways regulated by cys-SPMs during the regeneration, including TRAF3. In mammalian systems, TRAF3 contributes to cys-SPM–stimulated phagocyte functions and resolution of infection.
Unique molecular characteristics and microglial origin of Kv1.3 channel–positive brain myeloid cells in Alzheimer’s disease
Authors: Ramesha Supriya , Rayaprolu Sruti , Bowen Christine A. , Giver Cynthia R. , Bitarafan Sara , Nguyen Hai M. , Gao Tianwen , Chen Michael J. , Nwabueze Ngozi , Dammer Eric B. , Engstrom Amanda K. , Xiao Hailian , Pennati Andrea , Seyfried Nicholas T. , Katz David J. , Galipeau Jacques , Wulff Heike , Waller Edmund K. , Wood Levi B. , Levey Allan I. , Rangaraju Srikant
Published: March 2021

Significance

The potassium channel Kv1.3 in brain myeloid cells represents a promising therapeutic target for Alzheimer’s disease (AD). The patterns of expression and functional roles of Kv1.3 channels in brain myeloid subpopulations and the microglial-versus-peripheral myeloid origin of Kv1.3-expressing cells in AD remain unclear. Here, we show that in mice, Kv1.3 is selectively up-regulated in an Aβ-dependent manner by a subset of microglia-derived cells, expresses higher levels of proinflammatory genes, and confirms the presence of Kv1.3-expressing microglial subpopulations in human AD. Furthermore, blocking Kv1.3 in an AD model reduces Aβ neuropathology, increases synaptic protein expression, and skews the microglial transcriptome toward pro-phagocytic and protective phenotypes. Our findings strengthen the preclinical rationale for targeting microglial Kv1.3 channels for therapeutic immunomodulation in AD.
A multitaxa assessment of the effectiveness of agri-environmental schemes for biodiversity management
Authors: Boetzl Fabian A. , Krauss Jochen , Heinze Jonathan , Hoffmann Hannes , Juffa Jan , König Sebastian , Krimmer Elena , Prante Maren , Martin Emily A. , Holzschuh Andrea , Steffan-Dewenter Ingolf
Published: March 2021

Significance

The loss of biodiversity challenges agriculture as crop yields depend on biodiversity-mediated ecosystem services. Targeted agri-environmental schemes (AES), like sown flowering fields, provide additional food resources and shelter for wild plants and animals. Such AES have been implemented to restore biodiversity in agricultural landscapes and ensure ecosystem services provision. However, little is known about the comparative benefits of different AES for functional biodiversity and whether temporal continuity, covered area, or perennial source habitats in the surrounding landscape limit the success of an AES. Here, we systematically evaluate within one study design how temporal continuity, size, and seminatural habitat cover in the surrounding landscape affect multitaxa diversity in different AES types and assess their potential for biodiversity conservation in agricultural landscapes.
Structural basis for a bacterial Pip system plant effector recognition protein
Authors: Luo Shukun , Coutinho Bruna G. , Dadhwal Prikshat , Oda Yasuhiro , Ren Jiahong , Schaefer Amy L. , Greenberg E. Peter , Harwood Caroline S. , Tong Liang
Published: March 2021

Significance

This work examines a fundamental question of how bacteria sense plant-released chemicals. We recently identified an effector of one member of a plant-responsive PipR family of transcription factors present in many plant-associated bacteria. This compound (abbreviated HEHEAA) requires a specific transporter for import into bacterial cells. We have solved crystal structures of one component of the transporter free and bound to HEHEAA. We discovered that a close homolog of the transporter protein cannot bind HEHEAA, implying there are other effector compound(s) for the widespread PipR signaling system family. Understanding the molecular details of these plant-responsive systems could identify a means of controlling plant colonization.
Source apportionment of methane escaping the subsea permafrost system in the outer Eurasian Arctic Shelf
Authors: Steinbach Julia , Holmstrand Henry , Shcherbakova Kseniia , Kosmach Denis , Brüchert Volker , Shakhova Natalia , Salyuk Anatoly , Sapart Célia J. , Chernykh Denis , Noormets Riko , Semiletov Igor , Gustafsson Örjan
Published: March 2021

Significance

Extensive release of methane from sediments of the world’s largest continental shelf, the East Siberian Arctic Ocean (ESAO), is one of the few Earth system processes that can cause a net transfer of carbon from land/ocean to the atmosphere and thus amplify global warming on the timescale of this century. An important gap in our current knowledge concerns the contributions of different subsea pools to the observed methane releases. This knowledge is a prerequisite to robust predictions on how these releases will develop in the future. Triple-isotope–based fingerprinting of the origin of the highly elevated ESAO methane levels points to a limited contribution from shallow microbial sources and instead a dominating contribution from a deep thermogenic pool.
Evolution of Ycf54-independent chlorophyll biosynthesis in cyanobacteria
Authors: Chen Guangyu E. , Hitchcock Andrew , Mareš Jan , Gong Yanhai , Tichý Martin , Pilný Jan , Kovářová Lucie , Zdvihalová Barbora , Xu Jian , Hunter C. Neil , Sobotka Roman
Published: March 2021

Significance

Photosynthesis uses chlorophylls to utilize solar energy. In oxygenic phototrophs, formation of the isocyclic fifth ring of chlorophyll, responsible for its green color, is catalyzed by AcsF/CycI and the auxiliary protein Ycf54. Removal of Ycf54 causes severe chlorophyll deficiency and impaired photoautotrophic growth. We analyzed laboratory-evolved suppressor mutants of a Ycf54-less strain of the cyanobacteriumSynechocystiswhere chlorophyll biosynthesis and phototrophy were restored. A single point mutation in CycI significantly weakens its dependence on Ycf54, mimicking natural evolution of the enzyme in marine cyanobacteria that lack Ycf54. A second mutation resulting in overaccumulation of chlorophyll inactivates an enzyme with in vitro chlorophyll dephytylase activity. Our results provide insights into the important regulatory role of Ycf54 in chlorophyll biosynthesis.
Towards a discourse-semantic approach to visual narrative analysis
Authors: Salama Amir H.Y.
Published: March 2021

The present study propounds a novel discourse-semantic approach that problematizes the social semiotic analysis of
visual narrative in two respects: (i) the lack of a model that can explain the plurifunctional structure of visual acts of
communication in general and (ii) the failure to provide the deep structure underlying the characters and/or objects in visual
narrative in particular. Redressing these two shortcomings, the approach is methodologically geared towards analysing the visual
narrative grammar that encodes the 2017 BBC image-enabled news story of Islamic State (IS). The proposed approach rests on two
theoretical models: (i) Roman Jakobson’s (1960) communication model of language
functions; (ii) Algirdas Julien Greimas’s (1966, 1987) structural-semantic model of actant grammar. The study has reached two major findings. First, theoretically, the
visual narrative analysis of images demands the presence of both (1) a theory that can adequately explain the plurifunctional
structure associated with the semiotic complexity of visual communication and (2) a structural-semantic model that reveals the
deep structure of the actants that enable the dramatis personae to relate to the events featuring in the
mono-/multimodal discourse of narrative. Second, on a practical level of the BBC’s visual storyline, IS has been represented
within three actant-based enunciation-spectacles: (a) victimhood with Subject versus Object, (b) beneficiariness with Sender
versus Receiver, and (c) villainy (self-presented and other-presented) with Opponent/Victim versus Helper.
A15 Nb3Si: a ‘high’ T
c superconductor synthesized at a pressure of one megabar and metastable at ambient conditions
Authors: Lim Jinhyuk , Kim J S , Hire Ajinkya C , Quan Yundi , Hennig R G , Hirschfeld P J , Hamlin J J , Stewart G R , Olinger Bart
Published: March 2021

A15 Nb3Si is, until now, the only ‘high’ temperature superconductor produced at high pressure (∼110 GPa) that has been successfully brought back to room pressure conditions in a metastable condition. Based on the current great interest in trying to create metastable-at-room-pressure high temperature superconductors produced at high pressure, we have restudied explosively compressed A15 Nb3Si and its production from tetragonal Nb3Si. First, diamond anvil cell pressure measurements up to 88 GPa were performed on explosively compressed A15 Nb3Si material to trace T
c as a function of pressure. T
c is suppressed to ∼5.2 K at 88 GPa. Then, using these T
c (P) data for A15 Nb3Si, pressures up to 92 GPa were applied at room temperature (which increased to 120 GPa at 5 K) on tetragonal Nb3Si. Measurements of the resistivity gave no indication of any A15 structure production, i.e. no indications of the superconductivity characteristic of A15 Nb3Si. This is in contrast to the explosive compression (up to P ∼ 110 GPa) of tetragonal Nb3Si, which produced 50%–70% A15 material, T
c = 18 K at ambient pressure, in a 1981 Los Alamos National Laboratory experiment. This implies that the accompanying high temperature (1000 °C) caused by explosive compression is necessary to successfully drive the reaction kinetics of the tetragonal → A15 Nb3Si structural transformation. Our theoretical calculations show that A15 Nb3Si has an enthalpy vs the tetragonal structure that is 70 meV atom−1
smaller at 100 GPa, while at ambient pressure the tetragonal phase enthalpy is lower than that of the A15 phase by 90 meV atom−1. The fact that ‘annealing’ the A15 explosively compressed material at room temperature for 39 years has no effect shows that slow kinetics can stabilize high pressure metastable phases at ambient conditions over long times even for large driving forces of 90 meV atom−1.
Mo
x
Si1−

x
a versatile material for nanowire to microwire single-photon detectors from UV to near IR
Authors: Lita Adriana E , Verma Varun B , Chiles Jeff , Mirin Richard P , Nam Sae Woo
Published: March 2021

We investigate material properties in Mo
x
Si1−x
thin films with the goal of optimization for single-photon detection from UV to mid-IR wavelengths. Saturated internal detection efficiency appears to be related to film structure for this material. We demonstrate nanometer-wide meander devices with saturated internal efficiency at 370 nm wavelength and 3.4 K operation temperature. By reducing the film thickness in the optimized material, we demonstrate saturated internal detection efficiency at 1550 nm wavelength and 1 K operation temperature for micron-wide meander shaped single-photon detectors with wire widths up to 2.0 μm and active areas up to 362 × 362 μm2.
Experimental realization of an all-(RE)BaCuO hybrid trapped field magnet lens generating a 9.8 T concentrated magnetic field from a 7 T external field
Authors: Takahashi Keita , Fujishiro Hiroyuki , Namba Sora , Ainslie Mark D
Published: March 2021

In this work, we have verified experimentally an all-(RE)BaCuO hybrid trapped field magnet lens (HTFML) using only one cryocooler and a special technique named the ‘loose contact method’. In the experimental setup, only the inner magnetic lens was tightly connected to the cold stage and cooled at all times, and the outer trapped field magnet (TFM) cylinder was loosely connected to the cold stage before the magnetizing process by introducing a gap between the outer TFM and cold stage of the cryocooler. As a result, the superconducting state for zero-field cooled magnetization of the inner magnetic lens and the non-superconducting (normal) state for field-cooled magnetization of the outer TFM cylinder can co-exist at the same time. A maximum concentrated field of B
c = 9.8 T was achieved for the magnetizing process with an applied field of B
app = 7 T in the present HTFML, consistent with the numerical estimation in our previous conceptual study. These results validate the HTFML concept as a compact and desktop-type magnet device that can provide 10 T-class magnetic field enhancement from the viewpoint of the magnetizing method. However, during magnetization with a higher B
app of 10 T, thermal instability of the outer stacked TFM cylinder caused flux jumps to occur, resulting in mechanical fracture of multiple bulks. These results suggest that the further development of a practical cooling method that can realize a stable and controllable cooling process for each part of the HTFML is necessary based on fundamental studies relating to the thermal stability of the large stacked TFM cylinder.
Effect of entanglement embedded in environment on quantum non-Markovianity based on collision model
Authors: Li Xiao-Ming , Chen Yong-Xu , Xia Yun-Jie , Man Zhong-Xiao
Published: March 2021

By means of collision models (CMs) where the environment is simulated by a collection of ancillas consisting of two entangled qubits, we investigate the effects of entanglement in the environment on the non-Markovianity of an open quantum system. Two CMs are considered in this study, in the first one the open quantum system S directly collides with the environment, while in the second one the system interacts with two intermediate qubits which, in turn, are coupled to the environment. We show that it is possible to enhance the non-Markovianity by environment entanglement in both models. In particular, in the second model, we show that the initial state of the auxiliary qubits can also affect the non-Markovianity of the system and there exists the optimal combination of the initial environmental state and the initial state of auxiliary qubits. In this case, the non-Markovianity can be greatly enhanced.
LCH: A local clustering H-index centrality measure for identifying and ranking influential nodes in complex networks*
Authors: Xu Gui-Qiong , Meng Lei , Tu Deng-Qin , Yang Ping-Le
Published: March 2021

Identifying influential nodes in complex networks is one of the most significant and challenging issues, which may contribute to optimizing the network structure, controlling the process of epidemic spreading and accelerating information diffusion. The node importance ranking measures based on global information are not suitable for large-scale networks due to their high computational complexity. Moreover, they do not take into account the impact of network topology evolution over time, resulting in limitations in some applications. Based on local information of networks, a local clustering H-index (LCH) centrality measure is proposed, which considers neighborhood topology, the quantity and quality of neighbor nodes simultaneously. The proposed measure only needs the information of first-order and second-order neighbor nodes of networks, thus it has nearly linear time complexity and can be applicable to large-scale networks. In order to test the proposed measure, we adopt the susceptible-infected-recovered (SIR) and susceptible-infected (SI) models to simulate the spreading process. A series of experimental results on eight real-world networks illustrate that the proposed LCH can identify and rank influential nodes more accurately than several classical and state-of-the-art measures.
Microstructure and magnetocaloric properties in melt-spun and high-pressure hydrogenated La0.5Pr0.5Fe11.4Si1.6 ribbons*
Authors: Liu Qian , Tong Min , Zhao Xin-Guo , Sun Nai-Kun , Xiao Xiao-Fei , Guo Jie , Liu Wei , Zhang Zhi-Dong
Published: March 2021

The effects of wheel speeds and high-pressure hydrogen treatment on phase evolution, microstructure, and magnetocaloric properties in La0.5Pr0.5Fe11.4Si1.6 melt-spun ribbons are studied in this work. The results reveal that the increase of wheel speed is beneficial to the formation of cubic NaZn13-type phase and the grain refinement. The optimized wheel speed for microstructural and magnetocaloric properties is 30 m/s. The largest entropy change of 18.1 J/kg⋅K at 190 K under a magnetic field change of 0 T–5 T is obtained in La0.5Pr0.5Fe11.4Si1.6 ribbons melt-spun at 30 m/s. After a high-pressure hydrogen treatment of 50 MPa, the Curie temperature of the ribbons prepared at 30 m/s is adjusted to about 314 K and the large –ΔS
M of 17.9 J/kg⋅K under a magnetic field change of 0 T–5 T is achieved at room temperature with almost none hysteresis loss. The small thermal and magnetic hysteresis and the large –ΔS
M make the La0.5Pr0.5Fe11.4Si1.6 hydride ribbons appropriate for magnetic refrigerant applications around room temperature.
Probing thermal properties of vanadium dioxide thin films by time-domain thermoreflectance without metal film*
Authors: Lu Qing-Jian , Gao Min , Lu Chang , Long Fei , Pan Tai-Song , Lin Yuan
Published: March 2021

Vanadium dioxide (VO2) is a strongly correlated material, and it has become known due to its sharp metal-insulator transition (MIT) near room temperature. Understanding the thermal properties and their change across MIT of VO2 thin film is important for the applications of this material in various devices. Here, the changes in thermal conductivity of epitaxial and polycrystalline VO2 thin film across MIT are probed by the time-domain thermoreflectance (TDTR) method. The measurements are performed in a direct way devoid of deposition of any metal thermoreflectance layer on the VO2 film to attenuate the impact from extra thermal interfaces. It is demonstrated that the method is feasible for the VO2 films with thickness values larger than 100 nm and beyond the phase transition region. The observed reasonable thermal conductivity change rates across MIT of VO2 thin films with different crystal qualities are found to be correlated with the electrical conductivity change rate, which is different from the reported behavior of single crystal VO2 nanowires. The recovery of the relationship between thermal conductivity and electrical conductivity in VO2 film may be attributed to the increasing elastic electron scattering weight, caused by the defects in the film. This work demonstrates the possibility and limitation of investigating the thermal properties of VO2 thin films by the TDTR method without depositing any metal thermoreflectance layer.
Continuous-wave Nd:KGd(WO4)2 single-longitudinal-mode laser*
Authors: Lan Rui-Jun , Liu Guang-Hua , Min Huan-Huan , Dai Tong-Yu , Shen Ying-Jie , Mu Peng-Hua , Ren Cheng , Cao De-Zhong , Mateos Xavier
Published: March 2021

A continuous-wave Nd:KGd(WO4)2 single-longitudinal-mode laser is demonstrated with Fabry–Perot etalons in a simple linear cavity. The thermal lens effect is dramatically lowered by propagating the laser beam along the ‘athermal’ direction inside the laser crystal, which is very beneficial to removing the heat generated in the mode selection process. The maximum single-longitudinal-mode output power obtained is 64.8 mW at incident pump power of 4.7 W, corresponding to an optical conversion efficiency of 1.3% and a slope efficiency of 1.7%.
Burning embers: synthesis of the health risks of climate change
Authors: Ebi Kristie L , Boyer Christopher , Ogden Nicholas , Paz Shlomit , Berry Peter , Campbell-Lendrum Diarmid , Hess Jeremy J , Woodward Alistair
Published: March 2021

Since 2001, a synthesizing element in Intergovernmental Panel on Climate Change assessment reports has been a summary of how risks in a particular system could change with additional warming above pre-industrial levels, generally accompanied by a figure called the burning embers. We present a first effort to develop burning embers for climate change risks for heat-related morbidity and mortality, ozone-related mortality, malaria, diseases carried by Aedes sp., Lyme disease, and West Nile fever. We used an evidence-based approach to construct the embers based on a comprehensive global literature review. Projected risks for these health outcomes under 1.5 °C, 2 °C, and >2 °C of warming were used to estimate at what temperatures risk levels increased from undetectable to medium, high, and very high, from the pre-industrial baseline, under three adaptation scenarios. Recent climate change has likely increased risks from undetectable to moderate for heat-related morbidity and mortality, ozone-related mortality, dengue, and Lyme disease. Recent climate change also was assessed as likely beginning to affect the burden of West Nile fever. A detectable impact of climate change on malaria is not yet apparent but is expected to occur with additional warming. The risk for each climate-sensitive health outcome is projected to increase as global mean surface temperature increases above pre-industrial levels, with the extent and pace of adaptation expected to affect the timing and magnitude of risks. The embers may be an effective tool for informing efforts to build climate-resilient health systems including through vulnerability, capacity, and adaptation assessments and the development of national adaptation plans. The embers also can be used to raise awareness of future threats from climate change and advocate for mitigation actions to reduce the overall magnitude of health risks later this century and to expand current adaptation efforts to protect populations now.
Modelling technique and analysis of porous anti-reflective coatings for reducing wide angle reflectance of thin-film solar cells
Authors: Pickering Timothy , Shanks Katie , Sundaram Senthil
Published: March 2021

Bio-inspired anti-reflective (AR) coatings with porous graded refractive index structures are known to considerably reduce the reflectance of light at optical interfaces, however, research is lacking for thin-film cell application. Ray Tracing software coupled with the Effective Medium Theory were used to simulate the reflectance of nanostructured coatings placed above a thin-film system. The most optimal coating was paraboloid-shaped, with 300 nm nipple heights and spacings of 15%. The non-zero refractive index ‘step’ aids light trapping and energy absorption. This coating reduced reflectance in the λ = 300–800 nm range by an average of 2.665% and 11.36% at 0∘ and 80∘ incident light, respectively, whilst increasing annual energy output by 4.39% and 5.39% for standard UK roof and vertical window tilts, respectively. Significant wide angle reflectance capabilities are demonstrated at specifically λ = 300 nm and 80∘ incident light, with a reflectance reduction of 19.192%. There are now many promising manufacturing techniques for these porous nanostructures, such as AR or wavelength filtering coatings for photovoltaics. Further understanding of the exact parameters needed to replicate these nanostructures must be explored to proceed.