bluuebunny/crossref_metadata_2025 huggingface dataset:
Extracting the lifetime of a synthetic two-level system
Authors: Margiani Gabriel , Guerrero Sebastián , Heugel Toni L. , Marty Christian , Pachlatko Raphael , Gisler Thomas , Vukasin Gabrielle D. , Kwon Hyun-Keun , Miller James M. L. , Bousse Nicholas E. , Kenny Thomas W. , Zilberberg Oded , Sabonis Deividas , Eichler Alexander
Published: October 2022

The Kerr Parametric Oscillator (KPO) is a nonlinear resonator system that is often described as a synthetic two-level system. In the presence of noise, the system switches between two states via a fluctuating trajectory in phase space, instead of following a straight path. The presence of such fluctuating trajectories makes it hard to establish a precise count or even a useful definition, of the “lifetime” of the state. Addressing this issue, we compare several rate counting methods that allow to estimate a lifetime for the levels. In particular, we establish that a peak in the Allan variance of fluctuations can also be used to determine the levels' lifetime. Our work provides a basis for characterizing KPO networks for simulated annealing where an accurate determination of the state lifetime is of fundamental importance.
Photoelectron imaging of cryogenically cooled BiO− and BiO2− anions
Authors: Kocheril G. Stephen , Gao Han-Wen , Yuan Dao-Fu , Wang Lai-Sheng
Published: October 2022

The advent of ion traps as cooling devices has revolutionized ion spectroscopy as it is now possible to efficiently cool ions vibrationally and rotationally to levels where truly high-resolution experiments are now feasible. Here, we report the first results of a new experimental apparatus that couples a cryogenic 3D Paul trap with a laser vaporization cluster source for high-resolution photoelectron imaging of cold cluster anions. We have demonstrated the ability of the new apparatus to efficiently cool BiO− and BiO2− to minimize vibrational hot bands and allow high-resolution photoelectron images to be obtained. The electron affinities of BiO and BiO2 are measured accurately for the first time to be 1.492(1) and 3.281(1) eV, respectively. Vibrational frequencies for the ground states of BiO and BiO2, as well as those for the anions determined from temperature-dependent studies, are reported.
Socioeconomic inequalities in molecular risk for chronic diseases observed in young adulthood
Authors: Shanahan Michael J. , Cole Steven W. , Ravi Sudharshan , Chumbley Justin , Xu Wenjia , Potente Cecilia , Levitt Brandt , Bodelet Julien , Aiello Allison , Gaydosh Lauren , Harris Kathleen Mullan
Published: October 2022

Many common chronic diseases of aging are negatively associated with socioeconomic status (SES). This study examines whether inequalities can already be observed in the molecular underpinnings of such diseases in the 30s, before many of them become prevalent. Data come from the National Longitudinal Study of Adolescent to Adult Health (Add Health), a large, nationally representative sample of US subjects who were followed for over two decades beginning in adolescence. We now have transcriptomic data (mRNA-seq) from a random subset of 4,543 of these young adults. SES in the household-of-origin and in young adulthood were examined as covariates of
a priori
-defined mRNA-based disease signatures and of specific gene transcripts identified
de novo
. An SES composite from young adulthood predicted many disease signatures, as did income and subjective status. Analyses highlighted SES-based inequalities in immune, inflammatory, ribosomal, and metabolic pathways, several of which play central roles in senescence. Many genes are also involved in transcription, translation, and diverse signaling mechanisms. Average causal-mediated effect models suggest that body mass index plays a key role in accounting for these relationships. Overall, the results reveal inequalities in molecular risk factors for chronic diseases often decades before diagnoses and suggest future directions for social signal transduction models that trace how social circumstances regulate the human genome.
The impact of flooding on food security across Africa
Authors: Reed Connor , Anderson Weston , Kruczkiewicz Andrew , Nakamura Jennifer , Gallo Dominy , Seager Richard , McDermid Sonali Shukla
Published: October 2022

Recent record rainfall and flood events have prompted increased attention to flood impacts on human systems. Information regarding flood effects on food security is of particular importance for humanitarian organizations and is especially valuable across Africa's rural areas that contribute to regional food supplies. We quantitatively evaluate where and to what extent flooding impacts food security across Africa, using a Granger causality analysis and panel modeling approaches. Within our modeled areas, we find that ∼12% of the people that experienced food insecurity from 2009 to 2020 had their food security status affected by flooding. Furthermore, flooding and its associated meteorological conditions can simultaneously degrade food security locally while enhancing it at regional spatial scales, leading to large variations in overall food security outcomes. Dedicated data collection at the intersection of flood events and associated food security measures across different spatial and temporal scales are required to better characterize the extent of flood impact and inform preparedness, response, and recovery needs.
Structures and mechanisms of actin ATP hydrolysis
Authors: Kanematsu Yusuke , Narita Akihiro , Oda Toshiro , Koike Ryotaro , Ota Motonori , Takano Yu , Moritsugu Kei , Fujiwara Ikuko , Tanaka Kotaro , Komatsu Hideyuki , Nagae Takayuki , Watanabe Nobuhisa , Iwasa Mitsusada , Maéda Yuichiro , Takeda Shuichi
Published: October 2022

The major cytoskeleton protein actin undergoes cyclic transitions between the monomeric G-form and the filamentous F-form, which drive organelle transport and cell motility. This mechanical work is driven by the ATPase activity at the catalytic site in the F-form. For deeper understanding of the actin cellular functions, the reaction mechanism must be elucidated. Here, we show that a single actin molecule is trapped in the F-form by fragmin domain-1 binding and present their crystal structures in the ATP analog-, ADP-Pi-, and ADP-bound forms, at 1.15-Å resolutions. The G-to-F conformational transition shifts the side chains of Gln137 and His161, which relocate four water molecules including W1 (attacking water) and W2 (helping water) to facilitate the hydrolysis. By applying quantum mechanics/molecular mechanics calculations to the structures, we have revealed a consistent and comprehensive reaction path of ATP hydrolysis by the F-form actin. The reaction path consists of four steps: 1) W1 and W2 rotations; 2) P
G
–O
3B
bond cleavage; 3) four concomitant events: W1–PO
3
−
formation, OH
−
and proton cleavage, nucleophilic attack by the OH
−
against P
G
, and the abstracted proton transfer; and 4) proton relocation that stabilizes the ADP-Pi–bound F-form actin. The mechanism explains the slow rate of ATP hydrolysis by actin and the irreversibility of the hydrolysis reaction. While the catalytic strategy of actin ATP hydrolysis is essentially the same as those of motor proteins like myosin, the process after the hydrolysis is distinct and discussed in terms of Pi release, F-form destabilization, and global conformational changes.
Alternating regimes of shallow and deep-sea diversification explain a species-richness paradox in marine fishes
Authors: Miller Elizabeth Christina , Martinez Christopher M. , Friedman Sarah T. , Wainwright Peter C. , Price Samantha A. , Tornabene Luke
Published: October 2022

The deep sea contains a surprising diversity of life, including iconic fish groups such as anglerfishes and lanternfishes. Still, >65% of marine teleost fish species are restricted to the photic zone <200 m, which comprises less than 10% of the ocean’s total volume. From a macroevolutionary perspective, this paradox may be explained by three hypotheses: 1) shallow water lineages have had more time to diversify than deep-sea lineages, 2) shallow water lineages have faster rates of speciation than deep-sea lineages, or 3) shallow-to-deep sea transition rates limit deep-sea richness. Here we use phylogenetic comparative methods to test among these three non-mutually exclusive hypotheses. While we found support for all hypotheses, the disparity in species richness is better described as the uneven outcome of alternating phases that favored shallow or deep diversification over the past 200 million y. Shallow marine teleosts became incredibly diverse 100 million y ago during a period of warm temperatures and high sea level, suggesting the importance of reefs and epicontinental settings. Conversely, deep-sea colonization and speciation was favored during brief episodes when cooling temperatures increased the efficiency of the ocean’s carbon pump. Finally, time-variable ecological filters limited shallow-to-deep colonization for much of teleost history, which helped maintain higher shallow richness. A pelagic lifestyle and large jaws were associated with early deep-sea colonists, while a demersal lifestyle and a tapered body plan were typical of later colonists. Therefore, we also suggest that some hallmark characteristics of deep-sea fishes evolved prior to colonizing the deep sea.
UBR2 targets myosin heavy chain IIb and IIx for degradation: Molecular mechanism essential for cancer-induced muscle wasting
Authors: Gao Song , Zhang Guohua , Zhang Zicheng , Zhu James Z. , Li Li , Zhou Yong , Rodney George G. , Abo-Zahrah Reem S. , Anderson Lindsey , Garcia Jose M. , Kwon Yong Tae , Li Yi-Ping
Published: October 2022

Cancer cachexia is a lethal metabolic syndrome featuring muscle wasting with preferential loss of fast-twitching muscle mass through an undefined mechanism. Here, we show that cancer induces muscle wasting by selectively degrading myosin heavy chain (MHC) subtypes IIb and IIx through E3 ligase UBR2-mediated ubiquitylation. Induction of MHC loss and atrophy in C2C12 myotubes and mouse tibialis anterior (TA) by murine cancer cells required UBR2 up-regulation by cancer. Genetic gain or loss of UBR2 function inversely altered MHC level and muscle mass in TA of tumor-free mice. UBR2 selectively interacted with and ubiquitylated MHC-IIb and MHC-IIx through its substrate recognition and catalytic domain, respectively, in C2C12 myotubes. Elevation of UBR2 in muscle of tumor-bearing or free mice caused loss of MHC-IIb and MHC-IIx but not MHC-I and MHC-IIa or other myofibrillar proteins, including α-actin, troponin, tropomyosin, and tropomodulin. Muscle-specific knockout of UBR2 spared KPC tumor-bearing mice from losing MHC-IIb and MHC-IIx, fast-twitching muscle mass, cross-sectional area, and contractile force. The rectus abdominis (RA) muscle of patients with cachexia-prone cancers displayed a selective reduction of MHC-IIx in correlation with higher UBR2 levels. These data suggest that UBR2 is a regulator of MHC-IIb/IIx essential for cancer-induced muscle wasting, and that therapeutic interventions can be designed by blocking UBR2 up-regulation by cancer.
A data-driven and topological mapping approach for the a priori prediction of stable molecular crystalline hydrates
Authors: Hong Richard S. , Mattei Alessandra , Sheikh Ahmad Y. , Tuckerman Mark E.
Published: October 2022

Predictions of the structures of stoichiometric, fractional, or nonstoichiometric hydrates of organic molecular crystals are immensely challenging due to the extensive search space of different water contents, host molecular placements throughout the crystal, and internal molecular conformations. However, the dry frameworks of these hydrates, especially for nonstoichiometric or isostructural dehydrates, can often be predicted from a standard anhydrous crystal structure prediction (CSP) protocol. Inspired by developments in the field of drug binding, we introduce an efficient data-driven and topologically aware approach for predicting organic molecular crystal hydrate structures through a mapping of water positions within the crystal structure. The method does not require
a priori
specification of water content and can, therefore, predict stoichiometric, fractional, and nonstoichiometric hydrate structures. This approach, which we term a
mapping approach for crystal hydrates
(MACH), establishes a set of rules for systematic determination of favorable positions for water insertion within predicted or experimental crystal structures based on considerations of the chemical features of local environments and void regions. The proposed approach is tested on hydrates of three pharmaceutically relevant compounds that exhibit diverse crystal packing motifs and void environments characteristic of hydrate structures. Overall, we show that our mapping approach introduces an advance in the efficient performance of hydrate CSP through generation of stable hydrate stoichiometries at low cost and should be considered an integral component for CSP workflows.
Arabidopsis
ORP2A mediates ER–autophagosomal membrane contact sites and regulates PI3P in plant autophagy
Authors: Ye Hao , Gao Jiayang , Liang Zizhen , Lin Youshun , Yu Qianyi , Huang Shuxian , Jiang Liwen
Published: October 2022

Autophagy is an intracellular degradation system for cytoplasmic constituents which is mediated by the formation of a double-membrane organelle termed the autophagosome and its subsequent fusion with the lysosome/vacuole. The formation of the autophagosome requires membrane from the endoplasmic reticulum (ER) and is tightly regulated by a series of autophagy-related (ATG) proteins and lipids. However, how the ER contacts autophagosomes and regulates autophagy remain elusive in plants. In this study, we identified and demonstrated the roles of
Arabidopsis
oxysterol-binding protein–related protein 2A (ORP2A) in mediating ER–autophagosomal membrane contacts and autophagosome biogenesis. We showed that ORP2A localizes to both ER–plasma membrane contact sites (EPCSs) and autophagosomes, and that ORP2A interacts with both the ER-localized VAMP-associated protein (VAP) 27-1 and ATG8e on the autophagosomes to mediate the membrane contact sites (MCSs). In ORP2A artificial microRNA knockdown (KD) plants, seedlings display retarded growth and impaired autophagy levels. Both ATG1a and ATG8e accumulated and associated with the ER membrane in ORP2A KD lines. Moreover, ORP2A binds multiple phospholipids and shows colocalization with phosphatidylinositol 3-phosphate (PI3P) in vivo. Taken together, ORP2A mediates ER–autophagosomal MCSs and regulates autophagy through PI3P redistribution.
Notable impact of wildfires in the western United States on weather hazards in the central United States
Authors: Zhang Yuwei , Fan Jiwen , Shrivastava Manish , Homeyer Cameron R. , Wang Yuan , Seinfeld John H.
Published: October 2022

Increased wildfire events constitute a significant threat to life and property in the United States. Wildfire impact on severe storms and weather hazards is another pathway that threatens society, and our understanding of which is very limited. Here, we use unique modeling developments to explore the effects of wildfires in the western US (mainly California and Oregon) on precipitation and hail in the central US. We find that the western US wildfires notably increase the occurrences of heavy precipitation rates by 38% and significant severe hail (≥2 in.) by 34% in the central United States. Both heat and aerosols from wildfires play an important role. By enhancing surface high pressure and increasing westerly and southwesterly winds, wildfires in the western United States produce (1) stronger moisture and aerosol transport to the central United States and (2) larger wind shear and storm-relative helicity in the central United States. Both the meteorological environment more conducive to severe convective storms and increased aerosols contribute to the enhancements of heavy precipitation rates and large hail. Moreover, the local wildfires in the central US also enhance the severity of storms, but their impact is notably smaller than the impact of remote wildfires in California and Oregon because of the lessened severity of the local wildfires. As wildfires are projected to be more frequent and severe in a warmer climate, the influence of wildfires on severe weather in downwind regions may become increasingly important.
Calibration-free, high-precision, and robust terahertz ultrafast metasurfaces for monitoring gastric cancers
Authors: Lou Jing , Jiao Yanan , Yang Ruisheng , Huang Yindong , Xu Xing , Zhang Lei , Ma Zhaofu , Yu Ying , Peng Wenyu , Yuan Yifang , Zhong Yuan , Li Songyan , Yan Yang , Zhang Fuli , Liang Jiangang , Du Xiaohui , Chang Chao , Qiu Cheng-Wei
Published: October 2022

Optical sensors, with great potential to convert invisible bioanalytical response into readable information, have been envisioned as a powerful platform for biological analysis and early diagnosis of diseases. However, the current extraction of sensing data is basically processed via a series of complicated and time-consuming calibrations between samples and reference, which inevitably introduce extra measurement errors and potentially annihilate small intrinsic responses. Here, we have proposed and experimentally demonstrated a calibration-free sensor for achieving high-precision biosensing detection, based on an optically controlled terahertz (THz) ultrafast metasurface. Photoexcitation of the silicon bridge enables the resonant frequency shifting from 1.385 to 0.825 THz and reaches the maximal phase variation up to 50° at 1.11 THz. The typical environmental measurement errors are completely eliminated in theory by normalizing the Fourier-transformed transmission spectra between ultrashort time delays of 37 ps, resulting in an extremely robust sensing device for monitoring the cancerous process of gastric cells. We believe that our calibration-free sensors with high precision and robust advantages can extend their implementation to study ultrafast biological dynamics and may inspire considerable innovations in the field of medical devices with nondestructive detection.
FeMV is a cathepsin-dependent unique morbillivirus infecting the kidneys of domestic cats
Authors: Nambulli Sham , Rennick Linda J. , Acciardo Andrew S. , Tilston-Lunel Natasha L. , Ho Gregory , Crossland Nicholas A. , Hardcastle Kathy , Nieto Betsy , Bainbridge Graeme , Williams Tracey , Sharp Claire R. , Duprex W. Paul
Published: October 2022

Feline morbillivirus (FeMV) is a recently discovered pathogen of domestic cats and has been classified as a morbillivirus in the
Paramyxovirus
family. We determined the complete sequence of FeMV
US5
directly from an FeMV-positive urine sample without virus isolation or cell passage. Sequence analysis of the viral genome revealed potential divergence from characteristics of archetypal morbilliviruses. First, the virus lacks the canonical polybasic furin cleavage signal in the fusion (F) glycoprotein. Second, conserved amino acids in the hemagglutinin (H) glycoprotein used by all other morbilliviruses for binding and/or fusion activation with the cellular receptor CD150 (signaling lymphocyte activation molecule [SLAM]/F1) are absent. We show that, despite this sequence divergence, FeMV H glycoprotein uses feline CD150 as a receptor and cannot use human CD150. We demonstrate that the protease responsible for cleaving the FeMV F glycoprotein is a cathepsin, making FeMV a unique morbillivirus and more similar to the closely related zoonotic Nipah and Hendra viruses. We developed a reverse genetics system for FeMV
US5
and generated recombinant viruses expressing Venus fluorescent protein from an additional transcription unit located either between the phospho-protein (
P
) and matrix (
M
) genes or the
H
and large (
L
) genes of the genome. We used these recombinant FeMVs to establish a natural infection and demonstrate that FeMV causes an acute morbillivirus-like disease in the cat. Virus was shed in the urine and detectable in the kidneys at later time points. This opens the door for long-term studies to address the postulated role of this morbillivirus in the development of chronic kidney disease.
Regulated Restructuring of Mucins During Secretory Granule Maturation In Vivo
Authors: Syed Zulfeqhar A. , Zhang Liping , Tran Duy T. , Bleck Christopher K. E. , Ten Hagen Kelly G.
Published: October 2022

Mucins are large, highly glycosylated transmembrane and secreted proteins that line and protect epithelial surfaces. However, the details of mucin biosynthesis and packaging in vivo are largely unknown. Here, we demonstrate that multiple distinct mucins undergo intragranular restructuring during secretory granule maturation in vivo, forming unique structures that are spatially segregated within the same granule. We further identify temporally-regulated genes that influence mucin restructuring, including those controlling pH (Vha16-1), Ca2+ions (fwe) and Cl−ions (ClicandClC-c). Finally, we show that altered mucin glycosylation influences the dimensions of these structures, thereby affecting secretory granule morphology. This study elucidates key steps and factors involved in intragranular, rather than intergranular segregation of mucins through regulated restructuring events during secretory granule maturation. Understanding how multiple distinct mucins are efficiently packaged into and secreted from secretory granules may provide insight into diseases resulting from defects in mucin secretion.
Cryo-EM structures of light-harvesting 2 complexes from
Rhodopseudomonas palustris
reveal the molecular origin of absorption tuning
Authors: Qian Pu , Nguyen-Phan Cam T. , Gardiner Alastair T. , Croll Tristan I. , Roszak Aleksander W. , Southall June , Jackson Philip J. , Vasilev Cvetelin , Castro-Hartmann Pablo , Sader Kasim , Hunter C. Neil , Cogdell Richard J.
Published: October 2022

The genomes of some purple photosynthetic bacteria contain a multigene
puc
family encoding a series of α- and β-polypeptides that together form a heterogeneous antenna of light-harvesting 2 (LH2) complexes. To unravel this complexity, we generated four sets of
puc
deletion mutants in
Rhodopseudomonas palustris
, each encoding a single type of
pucBA
gene pair and enabling the purification of complexes designated as PucA-LH2, PucB-LH2, PucD-LH2, and PucE-LH2. The structures of all four purified LH2 complexes were determined by cryogenic electron microscopy (cryo-EM) at resolutions ranging from 2.7 to 3.6 Å. Uniquely, each of these complexes contains a hitherto unknown polypeptide, γ, that forms an extended undulating ribbon that lies in the plane of the membrane and that encloses six of the nine LH2 αβ-subunits. The γ-subunit, which is located near to the cytoplasmic side of the complex, breaks the C9 symmetry of the LH2 complex and binds six extra bacteriochlorophylls (BChls) that enhance the 800-nm absorption of each complex. The structures show that all four complexes have two complete rings of BChls, conferring absorption bands centered at 800 and 850 nm on the PucA-LH2, PucB-LH2, and PucE-LH2 complexes, but, unusually, the PucD-LH2 antenna has only a single strong near-infared (NIR) absorption peak at 803 nm. Comparison of the cryo-EM structures of these LH2 complexes reveals altered patterns of hydrogen bonds between LH2 αβ-side chains and the bacteriochlorin rings, further emphasizing the major role that H bonds play in spectral tuning of bacterial antenna complexes.
Ring-fused 2-pyridones effective against multidrug-resistant Gram-positive pathogens and synergistic with standard-of-care antibiotics
Authors: Nye Taylor M. , Tükenmez Hasan , Singh Pardeep , Flores-Mireles Ana L. , Obernuefemann Chloe L. P. , Pinkner Jerome S. , Sarkar Souvik , Bonde Mari , Lindgren Anders E. G. , Dodson Karen W. , Johansson Jörgen , Almqvist Fredrik , Caparon Michael G. , Hultgren Scott J.
Published: October 2022

The alarming rise of multidrug-resistant Gram-positive bacteria has precipitated a healthcare crisis, necessitating the development of new antimicrobial therapies. Here we describe a new class of antibiotics based on a ring-fused 2-pyridone backbone, which are active against vancomycin-resistant enterococci (VRE), a serious threat as classified by the Centers for Disease Control and Prevention, and other multidrug-resistant Gram-positive bacteria. Ring-fused 2-pyridone antibiotics have bacteriostatic activity against actively dividing exponential phase enterococcal cells and bactericidal activity against nondividing stationary phase enterococcal cells. The molecular mechanism of drug-induced killing of stationary phase cells mimics aspects of fratricide observed in enterococcal biofilms, where both are mediated by the Atn autolysin and the GelE protease. In addition, combinations of sublethal concentrations of ring-fused 2-pyridones and standard-of-care antibiotics, such as vancomycin, were found to synergize to kill clinical strains of VRE. Furthermore, a broad range of antibiotic resistant Gram-positive pathogens, including those responsible for the increasing incidence of antibiotic resistant healthcare-associated infections, are susceptible to this new class of 2-pyridone antibiotics. Given the broad antibacterial activities of ring-fused 2-pyridone compounds against Gram-positive (GmP) bacteria we term these compounds GmPcides, which hold promise in combating the rising tide of antibiotic resistant Gram-positive pathogens.
Targeted delivery of an anti-inflammatory corticosteroid to Ly6C/G-positive cells abates severity of influenza A symptoms
Authors: Pishesha Novalia , Harmand Thibault , Carpenet Claire , Liu Xin , Bhan Atul , Islam Ashraful , van den Doel Renate , Pinney William , Ploegh Hidde L.
Published: October 2022

The distribution of Ly6C/G-positive cells in response to an infection of the mouse respiratory tract with influenza A virus was followed noninvasively over time by immuno-positron emission tomography. We converted nanobodies that recognize Ly6C and Ly6G, markers of neutrophils and other myeloid cells, as well as an influenza hemagglutinin–specific nanobody, into
89
Zr-labeled PEGylated positron emission tomography (PET) imaging agents. The PET images showed strong accumulation of these imaging agents in the lungs of infected mice. Immunohistochemistry of influenza virus–infected mice and control mice, injected with a biotinylated and PEGylated version of the Ly6C/G-specific nanobody, showed the presence of abundant Ly6C/G-positive myeloid cells and positivity for Ly6C/G on bronchial epithelium in influenza virus–infected mice. This is consistent with focal inflammation in the lungs, a finding that correlated well with the immuno-PET results. No such signals were detected in control mice. Having shown by PET the accumulation of the Ly6C/G-specific nanobody in infected lungs, we synthesized conjugates of Ly6C/G-specific nanobodies with dexamethasone to enable targeted delivery of this immunosuppressive corticosteroid to sites of inflammation. Such conjugates reduced the weight loss that accompanies infection, while the equivalent amount of free dexamethasone was without effect. Nanobody-drug conjugates thus enable delivery of drugs to particular cell types at the appropriate anatomic site(s). By avoiding systemic exposure to free dexamethasone, this strategy minimizes its undesirable side effects because of the much lower effective dose of the nanobody-dexamethasone conjugate. The ability to selectively target inflammatory cells may find application in the treatment of other infections or other immune-mediated diseases.
Loss of grazing by large mammalian herbivores can destabilize the soil carbon pool
Authors: Naidu Dilip G. T. , Roy Shamik , Bagchi Sumanta
Published: October 2022

Grazing by mammalian herbivores can be a climate mitigation strategy as it influences the size and stability of a large soil carbon (soil-C) pool (more than 500 Pg C in the world’s grasslands, steppes, and savannas). With continuing declines in the numbers of large mammalian herbivores, the resultant loss in grazer functions can be consequential for this soil-C pool and ultimately for the global carbon cycle. While herbivore effects on the size of the soil-C pool and the conditions under which they lead to gain or loss in soil-C are becoming increasingly clear, their effect on the equally important aspect of stability of soil-C remains unknown. We used a replicated long-term field experiment in the Trans-Himalayan grazing ecosystem to evaluate the consequences of herbivore exclusion on interannual fluctuations in soil-C (2006 to 2021). Interannual fluctuations in soil-C and soil-N were 30 to 40% higher after herbivore exclusion than under grazing. Structural equation modeling suggested that grazing appears to mediate the stabilizing versus destabilizing influences of nitrogen (N) on soil-C. This may explain why N addition stimulates soil-C loss in the absence of herbivores around the world. Herbivore loss, and the consequent decline in grazer functions, can therefore undermine the stability of soil-C. Soil-C is not inert but a very dynamic pool. It can provide nature-based climate solutions by conserving and restoring a functional role of large mammalian herbivores that extends to the stoichiometric coupling between soil-C and soil-N.
Interference of nuclear wavepackets in a pair of proton transfer reactions
Authors: Zhang Xinzi , Schwarz Kyra N. , Zhang Luhao , Fassioli Francesca , Fu Bo , Nguyen Lucas Q. , Knowles Robert R. , Scholes Gregory D.
Published: October 2022

Quantum mechanics revolutionized chemists’ understanding of molecular structure. In contrast, the kinetics of molecular reactions in solution are well described by classical, statistical theories. To reveal how the dynamics of chemical systems transition from quantum to classical, we study femtosecond proton transfer in a symmetric molecule with two identical reactant sites that are spatially apart. With the reaction launched from a superposition of two local basis states, we hypothesize that the ensuing motions of the electrons and nuclei will proceed, conceptually, in lockstep as a superposition of probability amplitudes until decoherence collapses the system to a product. Using ultrafast spectroscopy, we observe that the initial superposition state affects the reaction kinetics by an interference mechanism. With the aid of a quantum dynamics model, we propose how the evolution of nuclear wavepackets manifests the unusual intersite quantum correlations during the reaction.
Flashbulb memories
Authors: Erll Astrid , Hirst William
Published: October 2022

The two authors – one from literary and cultural studies, the other a cognitive psychologist – explore how the
interdisciplinary perspective of Memory Studies can broaden and enrich current research efforts on flashbulb memories (FBMs). FBMs
are memories of the circumstances in which one learned of a public emotionally charged event, such as 9/11. Psychological research
on FBMs have focused on their cognitive properties, their putative accuracy and confidence. But we claim that when seen in the
broader interdisciplinary perspective of collective memory research, FBMs emerge as inextricably linked up with social, cultural,
and narrative dynamics. This article therefore locates FBMs at the intersection of individual and collective memory narratives.
Connecting research in cognitive psychology with cultural Memory Studies, we explore how flashbulb narratives bear on social
identity and how they might travel across national boundaries or across generations. We further discuss how FBMs are tied to
culture, aesthetics, and media history.
“Oh yeah, one more thing: It’s gonna be huge.”
Authors: Bourgeois Samuel
Published: October 2022

This paper investigates the use of oh yeah in written prose found in American journalistic articles using corpus data. It demonstrates that such uses are a recent phenomenon that have risen in frequency starting at end of the 20th century. These new written functions are adapted to the written medium, but still resemble how oh yeah is used in speech. These developments contribute further insights to the changes occurring in journalistic writing. Furthermore, this paper concentrates on how oh yeah is adapted into journalistic writing to inject an interpersonal flair into the articles in which it is used. The timing of these developments also indicates a later wave of change to journalism that has been until now under-discussed.
Retrieving Twitter argumentation with corpus queries and discourse analysis
Authors: Dykes Nathan , Heinrich Philipp , Evert Stephanie
Published: October 2022

We propose a corpus linguistic approach for retrieving argumentation from tweets about Brexit. We analyse two corpora, one from before the referendum in 2016 and one from early 2019. Our approach is based on the manual development of morphosyntactic corpus queries (in CQP syntax) that target specific argumentation patterns. For the present corpora we have developed 130 queries targeting 34 logical formulae. The paper showcases the query development and presents quantitative and qualitative results on how Brexit-related arguments have changed on Twitter from 2016 to 2019.
A data-driven approach to finding significant changes in language use through time series analysis
Authors: Kehoe Andrew , Gee Matt , Renouf Antoinette
Published: October 2022

This paper conducts a diachronic study of language change in a corpus covering almost 30 years of mainstream UK news text. In our previous studies, several databases were compiled from the corpus, including diachronic records of word frequency, collocation and morphological analysis. Upon user enquiry, our WebCorp Linguist’s Search Engine produced tailored output from these resources. The system was therefore passive, requiring a word or phrase to be specified before querying the databases. The aim now is to extend the data-driven functionality to track the frequency of words in the corpus across time automatically and alert users to statistically significant change patterns. Three tests are employed to find upward and downward trends, sudden jumps in frequency, and seasonal variation.
Influence of sintering time on diffusion bonding of WC-10Co and AISI4340 by spark plasma sintering
Authors: Hasan Mahadi , Islam Md. Ashraful , Huang Zhenyi , Zhao Jingwei , Jiang Zhengyi
Published: October 2022

It is challenging to obtain successful bonding between cemented tungsten carbide and steel due to the large differences in their physical and mechanical properties. We used spark plasma sintering (SPS) technique and successfully bonded WC-10Co and AISI4340 high-strength steel at a low temperature. The effects of sintering time (5–20 min with a gap of 5 min) on their diffusion bonding were examined. The microstructure of the bonded composite materials was evaluated, and formed phases were identified. The mechanical properties were investigated, and the importance of processing parameters of SPS was discussed. The results show a crack-free continuous metallurgical bonding achieved at 1000°C, and the bonding strength increased with increasing holding times of 5, 10, 15, and 20 min. The sintered WC-10Co powders obtained nearly full density (99.07%) with an average maximum hardness of 1763 HV5. A special arrangement was used to determine the tensile bonding-strength with maximum average of 152 MPa at 20 min.
Can microplastics mediate soil properties, plant growth and carbon/nitrogen turnover in the terrestrial ecosystem?
Authors: Yao Yao , Lili Wang , Shufen Pan , Gang Li , Hongmei Liu , Weiming Xiu , Lingxuan Gong , Jianning Zhao , Guilong Zhang , Dianlin Yang
Published: October 2022

Microplastic (MP) pollution, a global environmental problem, has been recently studied in marine and freshwater environments. However, our understanding of MP effect on terrestrial ecosystems, especially carbon (C) and nitrogen (N) turnover remains poor. This review summarizes the sources and distribution characteristics of MPs in terrestrial ecosystems and explores their effects on soil properties, plant growth, C and N turnover. Once entering the terrestrial ecosystem, MPs could involve in sequestrating carbon and nitrogen by changing soil properties (e.g., pH, soil aggregate stability, and soil porosity). MPs could exert direct influences on plants or on soil physical environment and microbial metabolic environment to indirectly affect plant growth, thus altering the quantity and quality of soil C and N inputs by shifts in plant litter and roots. The changes of the dominant bacteria phyla, related functional genes, and enzymes caused by MP pollution could affect C and N cycles. Additionally, the MP effect varies with its properties (e.g., types, shapes, elemental composition, functional groups, released additives). Future researches should unify the standard system of MP separation, detection, and reveal the ecological effects of MPs, especially their impacts on terrestrial carbon and nitrogen cycles in the context of climate changes.
Force tuning through regulation of clathrin-dependent integrin endocytosis
Authors: Kyumurkov Alexander , Bouin Anne-Pascale , Boissan Mathieu , Manet Sandra , Baschieri Francesco , Proponnet-Guerault Mathilde , Balland Martial , Destaing Olivier , Régent-Kloeckner Myriam , Calmel Claire , Nicolas Alice , Waharte François , Chavrier Philippe , Montagnac Guillaume , Planus Emmanuelle , Albiges-Rizo Corinne
Published: October 2022

Integrin endocytosis is essential for many fundamental cellular processes. Whether and how the internalization impacts cellular mechanics remains elusive. Whereas previous studies reported the contribution of the integrin activator, talin, in force development, the involvement of inhibitors is less documented. We identified ICAP-1 as an integrin inhibitor involved in mechanotransduction by co-working with NME2 to control clathrin-mediated endocytosis of integrins at the edge of focal adhesions (FA). Loss of ICAP-1 enables β3-integrin-mediated force generation independently of β1 integrin. β3-integrin-mediated forces were associated with a decrease in β3 integrin dynamics stemming from their reduced diffusion within adhesion sites and slow turnover of FA. The decrease in β3 integrin dynamics correlated with a defect in integrin endocytosis. ICAP-1 acts as an adaptor for clathrin-dependent endocytosis of integrins. ICAP-1 controls integrin endocytosis by interacting with NME2, a key regulator of dynamin-dependent clathrin-coated pits fission. Control of clathrin-mediated integrin endocytosis by an inhibitor is an unprecedented mechanism to tune forces at FA.
Hybridization and localized flat band in the WSe2/MoSe2 heterobilayer
Authors: Khalil Lama , Pierucci Debora , Velez-Fort Emilio , Avila José , Vergnaud Céline , Dudin Pavel , Oehler Fabrice , Chaste Julien , Jamet Matthieu , Lhuillier Emmanuel , Pala Marco , Ouerghi Abdelkarim
Published: October 2022

Nearly localized moiré flat bands in momentum space, arising at particular twist angles, are the key to achieve correlated effects in transition-metal dichalcogenides. Here, we use angle-resolved photoemission spectroscopy (ARPES) to visualize the presence of a flat band near the Fermi level of van der Waals WSe2/MoSe2 heterobilayer grown by molecular beam epitaxy. This flat band is localized near the Fermi level and has a width of several hundred meVs. By combining ARPES measurements with density functional theory calculations, we confirm the coexistence of different domains, namely the reference 2H stacking without layer misorientation and regions with arbitrary twist angles. For the 2H-stacked heterobilayer, our ARPES results show strong interlayer hybridization effects, further confirmed by complementary micro- Raman spectroscopy measurements. The spin-splitting of the valence band at K is determined to be 470 meV. The valence band maximum (VBM) position of the heterobilayer is located at the Γ point. The energy difference between the VBM at Γ and the K point is of −60 meV, which is a stark difference compared to individual single monolayer WSe2 and monolayer WSe2, showing both a VBM at K.
A Variable Parameter Linear Tracking Differentiator and Its Application in Large Ground-based Telescopes
Authors: Yang Xiao-Xia , Deng Yong-Ting , Wang Jian-Li , Zhang Bin
Published: October 2022

This paper is concerned with the characteristics of a tracking differentiator (TD) in arranging transition process for the physical system. In order to overcome disadvantages of linear TD (LTD) in practice, a novel variable parameter linear tracking differentiator (VLTD) is proposed. By designing the speediness factor as a function of the tracking error, the VLTD can track a large range of set values with reasonable speed and acceleration. Analysis shows that VLTD can converge to its set value under certain conditions. Meanwhile, the speed and acceleration bounds are added to the VLTD, which guarantees that the proposed transition signal really plays a transitional role. The numerical simulation results emphasize necessity for adding speed and acceleration bounds to the VLTD. By comparing VLTD with the nonlinear TD (NLTD) in the simulations and experiments, VLTD can achieve almost the same performance as the NLTD while it is easier to be implemented.
Impact of the topology of urban streets on mobility optimization
Authors: Tokuda Eric K , Comin Cesar H , Costa Luciano da F
Published: October 2022

Several natural and artificial structures and systems are somehow optimized for performing specific functionalities. The structure and topology of cities are no exception, as it is critically important to ensure effective access to the several resources as well as overall mobility. The present work addresses the important subject of improving the plan of a given city through the incorporation of avenues and other expressways such as bridges and tunnels. More specifically, we start with the topology of a real city and consider the incorporation of an expressway between any two locations in the city, keeping one location fixed and varying the angle of the other. The whole city area is covered in this manner, which allows us to derive a respective energy surface indicating the gain obtained regarding the average shortest path length for each of the possible situations. These surfaces therefore provide a complete picture of how much each city can be improved regarding minimal distances. Quite distinct surfaces have been obtained for 18 considered European cities. These surfaces are then characterized in terms of the number of local extrema and respective spatial complexity, expressed in terms of a raggedness measurement. Measurements are also obtained respectively to the geometry and topology of the considered cities. It is shown that the shortest path gain depends strongly on some of the considered measurements, especially lacunarity and transitivity. Interestingly, the intricacy of the energy surfaces resulted in relatively little correlation with the topological and geometrical measurements.
A geometric approach to contact Hamiltonians and contact Hamilton–Jacobi theory
Authors: Grabowska Katarzyna , Grabowski Janusz
Published: October 2022

We propose a novel approach to contact Hamiltonian mechanics which, in contrast to the one dominating in the literature, serves also for non-trivial contact structures. In this approach Hamiltonians are no longer functions on the contact manifold M itself but sections of a line bundle over M or, equivalently, 1-homogeneous functions on a certain

G
L

(
1
,

R

)

-principal bundle

τ
:
P
→
M

, which is equipped with a homogeneous symplectic form ω. In other words, our understanding of contact geometry is that it is not an ‘odd-dimensional cousin’ of symplectic geometry but rather a part of the latter, namely ‘homogeneous symplectic geometry’. This understanding of contact structures is much simpler than the traditional one and very effective in applications, reducing the contact Hamiltonian formalism to the standard symplectic picture. We develop in this language contact Hamiltonian mechanics in the autonomous, as well as the time-dependent case, and the corresponding Hamilton–Jacobi theory. Fundamental examples are based on canonical contact structures on the first jet bundles

J

1

L

of sections of line bundles L, which play in contact geometry a fundamental rôle, similar to that played by cotangent bundles in symplectic geometry.
Phasor-based multi-harmonic unmixing for in-vivo hyperspectral imaging
Authors: Vallmitjana Alexander , Lepanto Paola , Irigoin Florencia , Malacrida Leonel
Published: October 2022

Hyperspectral imaging (HSI) is a paramount technique in biomedical science, however, unmixing and quantification of each spectral component is a challenging task. Traditional unmixing relies on algorithms that need spectroscopic parameters from the fluorescent species in the sample. The phasor-based multi-harmonic unmixing method requires only the empirical measurement of the pure species to compute the pixel-wise photon fraction of every spectral component. Using simulations, we demonstrate the feasibility of the approach for up to 5 components and explore the use of adding a 6th unknown component representing autofluorescence. The simulations show that the method can be successfully used in typical confocal imaging experiments (with pixel photon counts between 101 and 103). As a proof of concept, we tested the method in living cells, using 5 common commercial dyes for organelle labeling and we easily and accurately separate them. Finally, we challenged the method by introducing a solvatochromic probe, 6-Dodecanoyl-N,N-dimethyl-2-naphthylamine (LAURDAN), intended to measure membrane dynamics on specific subcellular membrane-bound organelles by taking advantage of the linear combination between the organelle probes and LAURDAN. We succeeded in monitoring the membrane order in the Golgi apparatus, Mitochondria, and plasma membrane in the same in-vivo cell and quantitatively comparing them. The phasor-based multi-harmonic unmixing method can help expand the outreach of HSI and democratize its use by the community for it does not require specialized knowledge.
Influence of the mass conservation cavitation boundary on the tribo-dynamic responses of the micro-groove water-lubricated bearing
Authors: Cai Jianlin , Han Yanfeng , Xiang Guo , Wang Cheng , Wang Liwu , Chen Shouan
Published: October 2022

This study aims to reveal the role of the mass conversation cavitation boundary on the tribo-dynamic responses of five kinds of micro-groove water-lubricated bearing under mixed lubrication. By introducing the mass conservation boundary, the tribo-dynamic model of the water-lubricated micro-groove bearing is established and numerically solved by the control volume method. The accuracy of the developed model is verified by comparing the calculated results with the existing experimental and simulation results. The effects of cavitation under Reynolds and mass conservation boundary conditions on different micro-groove bearings were analyzed using the model, and the rotational speed and microgroove depth parameters were analyzed. The simulation results show that , regardless of the shape of the bottom of the microgroove, cavitation can stabilize the journal movement and enhance the dynamic pressure effect of the micro-grooves. The parameter analysis of rotational speed and micro-groove depth proves that rotational speed significantly influences the micro-groove cavitation zone and the dynamic pressure effect. Moreover, the greater the micro-groove depth, the smaller the enhancement effect of cavitation to dynamic pressure. The water-lubricated micro-groove bearing with the bottom shape of the left-triangle has the best lubricating performance during the whole analysis process.