bluuebunny/crossref_metadata_2025 huggingface dataset:
De novo assembly and characterization of a highly degenerated ZW sex chromosome in the fish Megaleporinus macrocephalus
Authors: Borges Carolina Heloisa de Souza , Utsunomia Ricardo , Varani Alessandro , Uliano-Silva Marcela , Lira Lieschen Valeria G. , Butzge Arno J. , Agudelo John F. Gomez , Manso Shisley , Freitas Milena V. , Ariede Raquel B. , Mastrochirico-Filho Vito A. , Penaloza Carolina , Barria Agustín , Porto-Foresti Fábio , Foresti Fausto , Hattori Ricardo , Guiguen Yann , Houston Ross D. , Hashimoto Diogo Teruo
Published: March 2024

Background

Megaleporinus macrocephalus(piauçu) is a Neotropical fish within Characoidei that presents a well-established heteromorphic ZZ/ZW sex-determination system and thus, constitutes a good model for studying W and Z chromosomes in fishes. We used PacBio reads and Hi-C to assemble a chromosome-level reference genome forM. macrocephalus. We generated family segregation information to construct a genetic map, pool-seq of males and females to characterize its sex system, and RNA-seq to highlight candidate genes ofM. macrocephalussex determination.

Results

M. macrocephalusreference genome is 1,282,030,339 bp in length and has a contig and scaffold N50 of 5.0 Mb and 45.03 Mb, respectively. Based on patterns of recombination suppression, coverage, Fst,and sex-specific SNPs, three major regions were distinguished in the sex chromosome: W-specific (highly differentiated), Z-specific (in degeneration), and PAR. The sex chromosome gene repertoire was composed of genes from the TGF-β family(amhr2,bmp7) and Wnt/β-catenin pathway (wnt4,wnt7a), and some of them were differentially expressed.

Conclusions

The chromosome-level genome of piauçu exhibits high quality, establishing a valuable resource for advancing research within the group. Our discoveries offer insights into the evolutionary dynamics of Z and W sex chromosomes in fish, emphasizing ongoing degenerative processes and indicating complex interactions between Z and W sequences in specific genomic regions. Notably,amhr2andbmp7are potential candidate genes for sex determination inM. macrocephalus.
Inhibition of NFAT promotes loss of tissue resident uterine natural killer cells and attendant pregnancy complications in humans
Authors: Asiimwe Rebecca , Knott Brittney , Greene Morgan E. , Wright Emma , Bell Markayla , Epstein Daniel , Yates Stefani D. , Gonzalez Michael V. , Fry Samantha , Boydston Emily , Clevenger Stephanie , Locke Jayme E. , Brocato Brian E. , Burgan Constantine M. , Burney Richard , Arora Nitin , Duncan Virginia E. , Richter Holly E. , Gunn Deidre , Freud Aharon G. , Little Shawn C. , Porrett Paige M.
Published: March 2024

Uterine natural killer cells (uNKs) are a tissue resident lymphocyte population that are critical for pregnancy success. Although mouse models have demonstrated that NK deficiency results in abnormal placentation and poor pregnancy outcomes, the generalizability of this knowledge to humans remains unclear. Here we identify uterus transplant (UTx) recipients as a human population with reduced uNK cells and altered pregnancy phenotypes. We show that the NK reduction in UTx correlates with impaired transcriptional programming of NK tissue residency arising from the inhibition of NFAT-mediated signaling. Our observations suggest that NFAT-dependent genes modulate multiple molecular tissue residency programs in uNKs. These include early residency programs involving AP-1-family transcription factors and TGF-β-mediated upregulation of surface integrins. Collectively, our data identify a previously undescribed role for NFAT in uterine NK tissue residency and provide novel mechanistic insights into the biologic basis of pregnancy complications due to alteration of tissue resident NK subsets in humans.

One Sentence Summary

Role of NFAT in uterine NK cell tissue residency
Post-Translational Modifications Control Phase Transitions of Tau
Authors: Powell Wyatt C. , Nahum McKinley , Pankratz Karl , Herlory Morgane , Greenwood James , Poliyenko Darya , Holland Patrick , Jing Ruiheng , Biggerstaff Luke , Stowell Michael H. B. , Walczak Maciej A.
Published: March 2024

The self-assembly of Tau(297-391) into filaments, which mirror the structures observed in Alzheimer’s disease (AD) brains, raises questions about the role of AD-specific post-translational modifications (PTMs) in the formation of paired helical filaments (PHFs). To investigate this, we developed a synthetic approach to produce Tau(291-391) featuring N-acetyllysine, phosphoserine, phosphotyrosine, and N-glycosylation at positions commonly modified in post-mortem AD brains, thus facilitating the study of their roles in Tau pathology. Using transmission electron microscopy (TEM), cryo-electron microscopy (cryo-EM), and a range of optical microscopy techniques, we discovered that these modifications generally hinder thein vitroassembly of Tau into PHFs. Interestingly, while acetylation’s effect on Tau assembly displayed variability, either promoting or inhibiting phase transitions in the context of cofactor free aggregation, heparin-induced aggregation, and RNA-mediated liquid-liquid phase separation (LLPS), phosphorylation uniformly mitigated these processes. Our observations suggest that PTMs, particularly those situated outside the fibril’s rigid core are pivotal in the nucleation of PHFs. Moreover, in scenarios involving heparin-induced aggregation leading to the formation of heterogeneous aggregates, most AD-specific PTMs, except for K311, appeared to decelerate the aggregation process. The impact of acetylation on RNA-induced LLPS was notably site-dependent, exhibiting both facilitative and inhibitory effects, whereas phosphorylation consistently reduced LLPS across all proteoforms examined. These insights underscore the complex interplay between site-specific PTMs and environmental factors in modulating Tau aggregation kinetics, enhancing our understanding of the molecular underpinnings of Tau pathology in AD and highlighting the critical role of PTMs located outside the ordered filament core in driving the self-assembly of Tau into PHF structures.
High-resolution analysis of the treated coeliac disease microbiome reveals strain-level variation
Authors: Slager Jelle , Simpson Hanna L. , Gacesa Ranko , Chen Lianmin , Tan Ineke L. , Gelderloos Jody , Maatman Astrid , Wijmenga Cisca , Zhernakova Alexandra , Fu Jingyuan , Weersma Rinse K. , Gonera Gieneke , Jonkers Iris H. , Withoff Sebo
Published: March 2024

Background

Coeliac disease (CeD) is an immune-mediated disorder primarily affecting the small intestine, characterised by an inflammatory immune reaction to dietary gluten. CeD onset results from a multifaceted interplay of genetic and environmental factors. While recent data show that alterations in gut microbiome composition could play an important role, many current studies are constrained by small sample sizes and limited resolution.

Methods

To address these limitations, we analysed faecal gut microbiota from two Dutch cohorts, CeDNN (128 treated CeD patients (tCeD), 106 controls) and the Lifelines Dutch Microbiome Project (24 self-reported tCeD, 654 controls), using shotgun metagenomic sequencing. Self-reported IBS (570 cases, 1710 controls) and IBD (93 cases, 465 controls) were used as comparative conditions of the gastrointestinal tract. Interindividual variation within the case and control groups was calculated at whole microbiome and strain level. Finally, species-specific gene repertoires were analysed in tCeD patients and controls.

Results

Within-individual microbiome diversity was decreased in patients with self-reported IBS and IBD but not in tCeD patients. Each condition displayed a unique microbial pattern and, in addition to confirming previously reported microbiome associations, we identify an increase in the levels ofClostridium sp. CAG:253,Roseburia hominis, andEggerthella lenta, amongst others. We further show that the observed changes can partially be explained by gluten-free diet adherence. We also observe increased interindividual variation of gut microbiome composition among tCeD patients and a higher bacterial mutation frequency in tCeD that contributes to higher interindividual variation at strain level. In addition, the immotile European subspecies ofEubacterium rectale, which has a distinct carbohydrate metabolism potential, was nearly absent in tCeD patients.

Conclusion

Our study sheds light on the complex interplay between the gut microbiome and CeD, revealing increased interindividual variation and strain-level variation in tCeD patients. These findings expand our understanding of the microbiome’s role in intestinal health and disease.

Highlights

This is the largest microbiome collection of coeliac disease (CeD) patients assembled to date, providing insights into gut microbiome composition down to strain level.

Compared to controls, treated CeD (tCeD) patients adhering to a gluten-free diet show novel gut microbiome associations.

tCeD patients also have a less uniform gut microbiome than controls.

Bacteria display higher mutation frequency in tCeD compared to controls.

Hallmarks of the European subspecies ofEubacterium rectaleare nearly absent in tCeD patients, implying selection at strain level.
Variant mutation in SARS-CoV-2 nucleocapsid enhances viral infection via altered genomic encapsidation
Authors: Kubinski Hannah C. , Despres Hannah W. , Johnson Bryan A. , Schmidt Madaline M. , Jaffrani Sara A. , Mills Margaret G. , Lokugamage Kumari , Dumas Caroline M. , Shirley David J. , Estes Leah K. , Pekosz Andrew , Crothers Jessica W. , Roychoudhury Pavitra , Greninger Alexander L. , Jerome Keith R. , Di Genova Bruno Martorelli , Walker David H. , Ballif Bryan A. , Ladinsky Mark S. , Bjorkman Pamela J. , Menachery Vineet D. , Bruce Emily A.
Published: March 2024

The evolution of SARS-CoV-2 variants and their respective phenotypes represents an important set of tools to understand basic coronavirus biology as well as the public health implications of individual mutations in variants of concern. While mutations outside of Spike are not well studied, the entire viral genome is undergoing evolutionary selection, particularly the central disordered linker region of the nucleocapsid (N) protein. Here, we identify a mutation (G215C), characteristic of the Delta variant, that introduces a novel cysteine into this linker domain, which results in the formation of a disulfide bond and a stable N-N dimer. Using reverse genetics, we determined that this cysteine residue is necessary and sufficient for stable dimer formation in a WA1 SARS-CoV-2 background, where it results in significantly increased viral growth bothin vitroandin vivo. Finally, we demonstrate that the N:G215C virus packages more nucleocapsid per virion and that individual virions are larger, with elongated morphologies.
Click-free imaging of carbohydrate trafficking in live cells using an azido photothermal probe
Authors: Xia Qing , Perera Harini A. , Bolarinho Rylie , Piskulich Zeke A. , Guo Zhongyue , Yin Jiaze , He Hongjian , Li Mingsheng , Ge Xiaowei , Cui Qiang , Ramström Olof , Yan Mingdi , Cheng Ji-Xin
Published: March 2024

Real-time tracking of intracellular carbohydrates remains challenging. While click chemistry allows bio-orthogonal tagging with fluorescent probes, the reaction permanently alters the target molecule and only allows a single snapshot. Here, we demonstrate click-free mid-infrared photothermal (MIP) imaging of azide-tagged carbohydrates in live cells. Leveraging the micromolar detection sensitivity for 6-azido-trehalose (TreAz) and the 300-nm spatial resolution of MIP imaging, the trehalose recycling pathway in single mycobacteria, from cytoplasmic uptake to membrane localization, is directly visualized. A peak shift of azide in MIP spectrum further uncovers interactions between TreAz and intracellular protein. MIP mapping of unreacted azide after click reaction reveals click chemistry heterogeneity within a bacterium. Broader applications of azido photothermal probes to visualize the initial steps of the Leloir pathway in yeasts and the newly synthesized glycans in mammalian cells are demonstrated.
WITHDRAWN: Dynamics of NeonatalMyoclonic Encephalopathy
Authors: Verma Vishal
Published: March 2024

Withdrawal Statement

The authors have withdrawn their manuscript owing to incomplete references, author’s list and affiliations. Therefore, the authors do not wish this work to be cited as a reference for the project.
A consensus motif inASH1and further transcripts unifies several RNA motifs required for interaction with the She2p/She3p transport machinery and mRNA localization in yeast
Authors: Seiler Markus , Niedner Annika , Heber Simone , Feldbrügge Michael , Jansen Ralf-Peter , Niessing Dierk , Zarnack Kathi
Published: March 2024

Asymmetric localization of theASH1transcript is a central step in the regulation of mating type switching inSaccharomyces cerevisaeand a paradigm for localized mRNAs specifically recognized by the She2p/3p transport machinery. Four RNA elements inASH1are known to mediate bud localization, but it remained unclear what a consensus motif of all four She2p/3p recognition sites (SRS) might look like. In this study, we derive the SRS consensus motif, which is characterized by an L-shaped, double-stranded RNA conformation with two cytosine-containing sequence motifs at conserved positions and a central asymmetric bulge. It is noteworthy that the spatial arrangement of these features can be retained, despite their altered order within the nucleotide sequence. We termed these variations “configurations” and confirmed in biochemical studies that SRS function inASH1elements is preserved when changing configurations. We tested other known and predicted SRS elements in target transcripts of She2p/3p by biochemical and biophysical studies and confirmed the conserved SRS function even in switched configuration. Consistently, we present theSRS instance collection, which includes further predictions of SRS instances of transcript targets of the She2p/3p translocation pathway.
Latent tuberculosis infection and incident cardiovascular and non-cardiovascular death
Authors: Magodoro Ita M , Wilkinson Katalina A , Claggett Brian L , Aluoch Aloice , Siedner Mark J , Ntsekhe Mpiko , Ntusi Ntobeko AB , Nyirenda John M , Wilkinson Robert J
Published: March 2024

Active tuberculosis may heighten the risk of incident cardiovascular morbidity and premature mortality, whereas whether latent TB infection (LTBI) recapitulates these adverse outcomes is unclear. We evaluated the effect of LTBI on all-cause and cardiovascular-specific death among US adults who underwent tuberculin skin testing in 1999-2000 and were followed up to December 31st, 2019. We also examined the impact of co-occuring traditional risk factors on these outcomes. Adjustments were made for socio-economic and demographic factors. LTBI was defined as tuberculin skin induration ≥10mm, and cause of death as cardiovascular if from heart or cerebrovascular diseases, and non-cardiovascular if otherwise. LTBI was associated with increased of overall and non-cardiovascular specific death but not cardiovascular-specific death. Risk of death was highest when LTBI was comorbid LTBI with diabetes. LTBI may increase risk of death by mechanisms other than progression to active TB disease.
Novel Ser74 of NF-κB/CgIκBα Phosphorylated by MAPK/ERK Regulates Temperature Adaptation in Oysters
Authors: Wang Chaogang , Jiang Zhuxiang , Du Mingyang , Cong Rihao , Wang Wei , Zhang Taiping , Chen Jincheng , Zhang Guofan , Li Li
Published: March 2024

Phosphorylation of IκBα at Ser32 and Ser36 by IKKs during biotic stress triggers its ubiquitin-proteasome degradation, causing to the nuclear translocation of REL, representing a key cascade mechanism in metazoans conserved and immune core signaling pathway, NF-κB. However, studies on its response to abiotic stress and signal transduction by phosphorylation in mollusks are lacking. Here, we firstly report a novel heat-induced phosphorylation site (Ser74) at the major NF-κB/CgIκBα of oysters, phosphorylated by MAPK/CgERK1/2, which independently mediated the subsequent ubiquitin-proteasome degradation without phosphorylation at Ser32 and Ser36 and decreased thermal stability. The degradation ofCgIκBα promotedCgREL nuclear translocation, which stimulated cell survival related gene expression to defend against thermal stress. The MAPK and NF-κB pathways exhibited stronger activation patterns in higher environmental temperature and in the warm-adaptedCrassostrea angulatathan those in the cold-adaptedC. gigas-two allopatric congeneric oyster species with differential habitat temperatures. These findings unveil the complex and unique phosphorylation-mediated signal transduction mechanisms in marine invertebrates, and further expand our understanding of the evolution and function of established classical pathway crosstalk mechanisms.
Pre-trained molecular representations enable antimicrobial discovery
Authors: Olayo-Alarcon Roberto , Amstalden Martin K. , Zannoni Annamaria , Bajramovic Medina , Sharma Cynthia M. , Brochado Ana Rita , Rezaei Mina , Müller Christian L.
Published: March 2024

The rise in antimicrobial resistance poses a worldwide threat, reducing the efficacy of common antibiotics. Determining the antimicrobial activity of new chemical compounds through experimental methods is still a time-consuming and costly endeavor. Compound-centric deep learning models hold the promise to speed up this search and prioritization process. Here, we introduce a lightweight computational strategy for antimicrobial discovery that builds onMolE(Molecular representation through redundancy reducedEmbedding), a deep learning framework that leverages unlabeled chemical structures to learn task-independent molecular representations. By combiningMolErepresentation learning with experimentally validated compound-bacteria activity data, we design a general predictive model that enables assessing compounds with respect to their antimicrobial potential. The model correctly identified recent growth-inhibitory compounds that are structurally distinct from current antibiotics and discoveredde novothree human-targeted drugs asStaphylococcus aureusgrowth inhibitors which we experimentally confirmed. Our framework offers a viable cost-effective strategy to accelerate antibiotics discovery.
Estradiol and Flutamide Effects on the Song System of Developing Male Zebra Finches
Authors: Grisham William , McCormick Mary Ellen
Published: March 2024

Estradiol (E2) masculinizes the developing song system of female zebra finches (Taeniopygia castanotis) if it is administered in early life, but the effects of E2on the developing song system in males have not been thoroughly explored. Also, reports of early antiandrogen administration in developing male zebra finches differ in their findings. Therefore. this study was conducted to further explore the effects of administering E2alone, flutamide (Flut) alone, or the two in combination during early development. Brains and testes were examined after day 100. The results showed definite demasculinizing effects of early E2on the song nucleus HVC (proper name)—its volume and neuron number were markedly reduced. Nonetheless, early E2hypermasculinized HVC neuronal size. Flut slightly hypermasculinized RA volume (Robust nucleus of the Arcopallium), which replicates a previous study, but the absence of any additional effects is at odds with other studies. Arguments are put forward suggesting that early E2action on HVC development could be a consequence of differential steroid action on the male versus female genotype and/or a disruption of the temporal sequence of gene regulation in developing males. Early E2resulted in markedly reducing testes size, which is likely to be a consequence of hijacking endogenous endocrine feedback mechanisms. The reduction in testes size suggests low steroid secretion, which also could contribute to the demasculinization of HVC.
Enhanced tameness byLimosilactobacillus reuterifrom gut microbiota of selectively bred mice
Authors: Biswa Bhim B. , Mori Hiroshi , Toyoda Atsushi , Kurokawa Ken , Koide Tsuyoshi
Published: March 2024

Domestication alters animal behaviour, primarily their tameness. In this study, we examine the effect of gut bacteria on mouse tameness. We previously conducted selective breeding for active tameness, defined as the motivation to approach a human hand, using genetically heterogeneous mice derived from eight wild inbred strains. We examined gut microbiota in the selectively bred mice by analysing faecal samples from 80 mice through shotgun metagenomic analysis. In the current study, we found that the selectively bred mice exhibit higher levels of active tameness as well as higher levels of blood oxytocin, which plays a key role in social behaviours. Selection for tameness did not substantially alter the taxonomic or functional diversity of the gut microbiota. However, we observed an increased abundance ofLimosilactobacillus reuteriin the selected groups and higher pyruvate levels in their plasma. We isolatedL. reuteristrains secreting extracellular pyruvate from mice faeces and administrated the cultured bacteria through drinking water. Mice treated withL. reuterishowed higher colonization of the bacteria in the gut, as well as higher levels of active tameness behaviour and blood oxytocin. Additionally, we generated 374 high-quality metagenome-assembled genomes (MAGs) of bacteria across 11 phyla. This collection includes 27 novel species level bacterial MAGs not previously known to exist in the mouse gut. This study elucidates the potential role ofL. reuteriin the animal domestication process and explores the underlying mechanisms that may influence this process.
Rem2 interacts with CaMKII at synapses and restricts long-term potentiation in hippocampus
Authors: Anjum Rabia , Clarke Vernon R J , Nagasawa Yutaro , Murakoshi Hideji , Paradis Suzanne
Published: March 2024

Synaptic plasticity, the process whereby neuronal connections are either strengthened or weakened in response to stereotyped forms of stimulation, is widely believed to represent the molecular mechanism that underlies learning and memory. The holoenzyme CaMKII plays a well-established and critical role in the induction of a variety of forms of synaptic plasticity such as long-term potentiation (LTP), long-term depression (LTD) and depotentiation. Previously, we identified the GTPase Rem2 as a potent, endogenous inhibitor of CaMKII. Here, we report that knock out ofRem2enhances LTP at the Schaffer collateral to CA1 synapse in hippocampus, consistent with an inhibitory action of Rem2 on CaMKII in vivo. Further, re-expression of WT Rem2 rescues the enhanced LTP observed in slices obtained fromRem2conditional knock out (cKO) mice, while expression of a mutant Rem2 construct that is unable to inhibit CaMKII in vitro fails to rescue increased LTP. In addition, we demonstrate that CaMKII and Rem2 interact in dendritic spines using a 2pFLIM-FRET approach. Taken together, our data lead us to propose that Rem2 serves as a brake on runaway synaptic potentiation via inhibition of CaMKII activity. Further, the enhanced LTP phenotype we observe inRem2cKO slices reveals a previously unknown role for Rem2 in the negative regulation of CaMKII function.
Inhibition ofStreptococcus pyogenesbiofilm byLactiplantibacillus plantarumandLacticaseibacillus rhamnosus
Authors: Gómez-Mejia Alejandro , Orlietti Mariano , Tarnutzer Andrea , Shambat Srikanth Mairpady , Zinkernagel Annelies S.
Published: March 2024

The human pathobiontStreptococcus pyogenesforms biofilms and causes invasive infections, such as pharyngotonsillitis and necrotizing fasciitis. Bacterial biofilms are more resilient to antibiotic treatment and new therapeutic strategies are needed to control biofilm-associated infections, such as recurrent pharyngotonsillitis.Lactiplantibacillus plantarumandLacticaseibacillus rhamnosusare two bacterial commensals used for their probiotic properties. This study aimed to elucidate the anti-biofilm properties ofL. plantarumandL. rhamnosuscell-free supernatants (LPSN and LRSN, respectively) onS. pyogenesbiofilms grownin vitroin supplemented minimal medium. When planktonic or biofilmS. pyogeneswere exposed to LPSN or LRSN,S. pyogenessurvival was reduced significantly in a concentration-dependent manner and the effect was more pronounced on preformed biofilms. Enzymatic digestion of LPSN and LRSN suggested that glycolipid compounds might cause the antimicrobial effect. In conclusion, this study indicates thatL. plantarumandL. rhamnosusproduce glycolipid bioactive compounds that reduceS. pyogenesviability in planktonic and biofilm cultures.
Exploring RNA modifications in infectious non-coding circular RNAs
Authors: Vopalensky Pavel , Škríba Anton , Chiumenti Michela , Ďuričeková Lucia , Šimonová Anna , Lukšan Ondřej , di Serio Francesco , Navarro Beatriz , Cahova Hana
Published: March 2024

Viroids, small circular non-coding RNAs, act as infectious pathogens in higher plants, demonstrating high stability despite consisting solely of naked RNA. Their dependence of replication on host machinery poses the question of whether RNA modifications play a role in viroid biology. Here, we explore RNA modifications in the avocado sunblotch viroid (ASBVd) and the citrus exocortis viroid (CEVd), representative members of viroids replicating in chloroplasts and the nucleus, respectively, using LC–MS and Oxford Nanopore Technology (ONT) direct RNA sequencing. Although no modification was detected in ASBVd, CEVd contained approximately one m6A per RNA molecule. ONT sequencing predicted three m6A positions. Employing orthogonal SELECT method, we confirmed m6A in two positions A353 and A360, which are highly conserved among CEVd variants. These postitions are located in the left terminal region of the CEVd rod-like structure where likely RNA Pol II and and TFIIIA-7ZF bind, thus suggesting potential biological role of methylation in viroid replication.
Composite higher derivative operators in
d=2+ε
dimensions and the spectrum of asymptotically safe gravity
Authors: Martini Riccardo , Sauro Dario , Zanusso Omar
Published: March 2024

We discuss the renormalization of Einstein-Hilbert gravity in d=2+ε dimensions. We show that the application of the path-integral approach leads naturally to scheme- and gauge-independent results on shell, but also gives a natural notion of quantum metric off shell, which is the natural argument of the effective action, even at the leading order in perturbation theory. The renormalization group of Newton’s constant is consistent with the asymptotic safety scenario for quantum gravity in that it has a UV-relevant fixed point. We extend the approach to the analysis of curvature square operators, understood as composites operators, which allows for the determination of the spectrum of scaling operators at the scale-invariant fixed point. The analysis suggests that there is one operator that becomes relevant close to d=4 dimensions, while other operators previously found in the literature are either marginal or trivial on shell.

Published by the American Physical Society
2024
Direct versus indirect excitation of ultrafast magnetization dynamics in FeNi alloys
Authors: von Korff Schmising Clemens , Jana Somnath , Zülich Ole , Sommer Denny , Eisebitt Stefan
Published: March 2024

Ultrafast demagnetization can be induced either coherently by direct interaction with the optical light field or indirectly via excitation of the electron system, which subsequently couples to the magnetization. An intriguing direct process is optical intersite spin transfer (OISTR), which changes the local magnetic moments during the optical absorption process itself and leads to a potentially coherent net spin transport between two magnetic subsystems. In this paper, we find that both direct and indirect excitation of an FeNi alloy result in identical experimental signatures in transverse magneto-optical measurements in the extreme ultraviolet spectral range, which has been previously interpreted as evidence for the OISTR effect: a delayed onset of the ultrafast response of Ni with respect to Fe as well as an increasing signal for photons probing energies below the Ni resonance. Our findings align with recent theoretical and experimental investigations, which propose alternative explanations of these experimental observations and do not rely on a direct and coherent interaction between light and spin. Instead, the distinctly different magnetization dynamics of Fe and Ni may be governed by intersite spin transfer driven by electron scattering or be the result of element-specific microscopic properties such as inhomogeneous spin-orbit coupling or electron magnon scattering.

Published by the American Physical Society
2024
Dissipation, quantum coherence, and asymmetry of finite-time cross-correlations
Authors: Van Vu Tan , Vo Van Tuan , Saito Keiji
Published: March 2024

Recent studies have revealed a deep connection between the asymmetry of cross-correlations and thermodynamic quantities in the short-time limit. In this study, we address the finite-time domain of the asymmetry for both open classical and quantum systems. Focusing on Markovian dynamics, we show that the asymmetry observed in finite-time cross-correlations is upper bounded by dissipation. We prove that, for classical systems in a steady state with arbitrary operational durations, the asymmetry exhibits, at most, linear growth over time, with the growth speed determined by the rates of entropy production and dynamical activity. In the long-time regime, the asymmetry exhibits exponential decay, with the decay rate determined by the spectral gap of the transition matrix. Remarkably, for quantum cases, quantum coherence is equally important as dissipation in constraining the asymmetry of correlations. We demonstrate an example where only quantum coherence bounds the asymmetry while the entropy production rate vanishes. Furthermore, we generalize the short-time bounds on correlation asymmetry, as reported by Shiraishi [] and Ohga [], to encompass finite-time scenarios. These findings offer insights into the thermodynamic aspects of correlation asymmetry.

Published by the American Physical Society
2024
Optimization of nonequilibrium free energy harvesting illustrated on bacteriorhodopsin
Authors: Piñero Jordi , Solé Ricard , Kolchinsky Artemy
Published: March 2024

Harvesting free energy from the environment is essential for the operation of many biological and artificial systems. We use techniques from stochastic thermodynamics to investigate the maximum rate of harvesting achievable by optimizing a set of reactions in a Markovian system, possibly under various kinds of topological, kinetic, and thermodynamic constraints. This question is relevant for the optimal design of new harvesting devices as well as for quantifying the efficiency of existing systems. We first demonstrate that the maximum harvesting rate can be expressed as a constrained convex optimization problem. We illustrate it on bacteriorhodopsin, a light-driven proton pump from Archaea, which we find is close to optimal under realistic conditions. In our second result, we solve the optimization problem in closed-form in three physically meaningful limiting regimes. These closed-form solutions are illustrated on two idealized models of unicyclic harvesting systems.

Published by the American Physical Society
2024
RNA-induced Allosteric Coupling Drives Viral Capsid Assembly
Authors: Hamilton Sean , Modi Tushar , Šulc Petr , Ozkan S. Banu
Published: March 2024

Understanding the mechanisms by which single-stranded RNA viruses regulate capsid assembly around their RNA genomes has become increasingly important for the development of both antiviral treatments and drug delivery systems. In this study, we investigate the effects of RNA-induced allostery in a single-stranded RNA virus—Levivirus bacteriophage MS2 assembly—using the computational methods of the Dynamic Flexibility Index and the Dynamic Coupling Index. We demonstrate that not only does asymmetric binding of RNA to a symmetric MS2 coat protein dimer increase the flexibility of the distant FG-loop, inducing a conformational change to an asymmetric dimer, but also RNA binding reorganizes long-distance communications, making all the other positions extremely sensitive to the fluctuation of the ordered FG-loop. Additionally, we find that a point mutation in the FG-loop, W82R, leads to the loss of this asymmetry in communications, likely being a leading cause for assembly-deficient dimers. Lastly, this dominant communication that enhances its dynamic coupling with all the distal positions is not only a property of the dimer but is also exhibited by all the observed capsid intermediates. This strong dynamic coupling allows for unidirectional signal transduction that drives the formation of the experimentally observed capsid intermediates and fully assembled capsid.

Published by the American Physical Society
2024
Improved Precision Scaling for Simulating Coupled Quantum-Classical Dynamics
Authors: Simon Sophia , Santagati Raffaele , Degroote Matthias , Moll Nikolaj , Streif Michael , Wiebe Nathan
Published: March 2024

In this paper, we present a superpolynomial improvement in the precision scaling of quantum simulations for coupled quantum-classical systems. Such systems are found in, e.g., molecular-dynamics simulations within the Born-Oppenheimer approximation. By employing a framework based on the Koopman–von Neumann formulation of classical mechanics, we express the Liouville equation of motion as unitary dynamics and utilize phase kickback from a dynamical quantum simulation to calculate the quantum forces acting on classical particles. This approach allows us to simulate the dynamics of these classical particles without the overheads associated with measuring gradients and solving the equations of motion on a classical computer, resulting in a superpolynomial advantage at the price of increased space complexity. We demonstrate that these simulations can be performed in both microcanonical and canonical ensembles, enabling the estimation of thermodynamic properties from the prepared probability density.

Published by the American Physical Society
2024
A twofold interpenetrated two-dimensional zinc(II) coordination polymer for the highly sensitive detection of nitrofurantoin in aqueous medium
Authors: Wang Yan , Cheng Wei Wei , Mou Yi , Wen Shuai , Wang Dongkai , Xue Yun Shan
Published: March 2024

A novel ZnII coordination polymer, namely, poly[{μ2-bis[4-(2-methyl-1H-imidazol-1-yl)phenyl]methanone-κ2
N
3:N
3′}(μ2-5-bromobenzene-1,3-dicarboxylato-κ2
O
1:O
3)zinc(II)], [Zn(C8H3BrO4)(C21H18N4O)]
n
or [Zn(Br-BDC)(MIPMO)]
n
, (I), has been synthesized by the solvothermal method using 5-bromoisophthalic acid (Br-H2BDC), bis[4-(2-methyl-1H-imidazol-1-yl)phenyl]methanone (MIPMO) and Zn(NO3)2·6H2O. Structure analysis showed that compound (I) displays twofold parallel interwoven sql nets. Fluorescence experiments confirmed that the compound can sensitively and selectively detect nitrofurantoin (NFT) in aqueous medium. In addition, the possible fluorescence quenching mechanisms of compound (I) toward NFT are investigated.
Crystal structures of ten phosphane chalcogenide complexes of gold(III) chloride and bromide
Authors: Upmann Daniel , Bockfeld Dirk , Jones Peter G. , Târcoveanu Eliza
Published: March 2024

The structures of ten phosphane chalcogenide complexes of gold(III) halides, with general formula R
1
3–n

R
2

n
PEAuX
3 (R
1 = t-butyl; R
2 = i-propyl; n = 0 to 3; E = S or Se; X = Cl or Br) are presented. The eight possible chlorido derivatives are: 9a, n = 3, E = S; 10a, n = 2, E = S; 11a, n = 1, E = S; 12a, n = 0, E = S; 13a, n = 3, E = Se; 14a, n = 2, E = Se; 15a, n = 1, E = Se; and 16a, n = 0, E = Se, and the corresponding bromido derivatives are 9b–16b in the same order. Structures were obtained for 9a, 10a (and a second polymorph 10aa), 11a (and its deuterochloroform monosolvate 11aa), 12a (as its dichloromethane monosolvate), 14a, 15a (as its deuterochloroform monosolvate 15aa, in which the solvent molecule is disordered over two positions), 9b, 11b, 13b and 15b. The structures of 11a, 15a, 11b and 15b form an isotypic set, and those of compounds 10aa and 14a form an isotypic pair. All structures have Z′ = 1. The gold(III) centres show square-planar coordination geometry and the chalcogenide atoms show approximately tetrahedral angles (except for the very wide angle in 12a, probably associated with the bulky t-butyl groups). The bond lengths at the gold atoms are lengthened with respect to the known gold(I) derivatives, and demonstrate a considerable trans influence of S and Se donor atoms on a trans Au—Cl bond. Each compound with an isopropyl group shows a short intramolecular contact of the type C—Hmethine...Xcis
; these may be regarded as intramolecular ‘weak’ hydrogen bonds, and they determine the orientation of the AuX
3 groups. The molecular packing is analysed in terms of various short contacts such as weak hydrogen bonds C—H...X and contacts between the heavier atoms, such as X...X (9a, 10aa, 11aa, 15aa and 9b), S...S (10aa, 11a and 12a) and S...Cl (10a). The packing of the polymorphs 10a and 10aa is thus quite different. The solvent molecules take part in C—H...Cl hydrogen bonds; for 15aa, a disordered solvent region at z ≃ 0 is observed. Structure 13b involves unusual inversion-symmetric dimers with Se...Au and Se...Br contacts, further connected by Br...Br contacts.
We can be heroes at work: the relationship between psychological capital, motivation and well-being during the great resignation
Authors: Plessis Cédric , Altintas Emin
Published: March 2024

Purpose

The Great Resignation has led to a significant increase in the number of people quitting their jobs due to reasons such as stagnant wages, rising cost of living, job dissatisfaction and safety concerns. Therefore, the aim of this study is that it is important to help people develop better cognitive resources to face adversity.

Design/methodology/approach

The Great Resignation has led to a significant increase in the number of people quitting their jobs due to reasons such as stagnant wages, rising cost of living, job dissatisfaction and safety concerns. Therefore, it is important to help people develop better cognitive resources to face adversity. In this study, we administered a questionnaire to 250 employees to determine the variables that could help them build cognitive resources. These variables included the satisfaction of basic psychological needs (autonomy, competence and affiliation), psychological capital, motivation regulation (within the self-determination theory) and well-being (assessed by self-esteem, positive emotions, positive automatic thoughts and vitality). The results revealed that satisfaction of basic needs is associated with better psychological capital and more self-autonomous behavior, which leads to higher psychological well-being. These findings are discussed in the paper, emphasizing the importance of management and work context that satisfy the basic needs and help to build resources with psychological capital.

Findings

The results revealed that satisfaction of basic needs is associated with better psychological capital and more self-autonomous behavior, which leads to higher psychological well-being. These findings are discussed in the paper, emphasizing the importance of management and work context that satisfy the basic needs and help to build resources with psychological capital.

Originality/value

Highlight the importance of consequences of the Great Resignation and the need to internationalize this concept.
The role of lived experience eye care champions in improving awareness and access to eye care services for people with learning disabilities and/or autism
Authors: Karas Marek , O'Brien Donna , Campbell Lance , Lunness Rebecca , Kennedy Joanne , McGill Grace , Kill Stephen , Donaldson Lisa
Published: March 2024

Background

Documented inequalities in access to eye care for people with learning disabilities and/or autism are caused by poor uptake of primary eye care services, poor identification of eye problems, lack of signposting and reasonable adjustments of existing services, concerns about costs of care and the low priority historically given to these issues in eye care policy at a regional and national level. In 2019, the charity SeeAbility employed four eye care champions (ECCs) with lived experience of learning disability and/or autism to work in local communities in London and the Northwest of England. They provided peer‐to‐peer support on understanding the need for good eye health and engaged with policy makers, and learning disability, autism and eye care professionals at the local, regional and national levels to influence both the clinical practice of individual practitioners (within existing service/pathway models) and more widely to influence the commissioning of the Easy Eye Care pathway. This study explores the experiences of these ECCs.

Methods

The study was conducted in April and May 2023. A case study approach was used to describe the experiences of the ECCs from March 2019 to March 2023. Data from structured interviews with the four ECCs and workload analysis were triangulated to provide a multifaceted understanding of this novel health promotion project.

Findings

The ECCs found the role useful and reported that confidence in their practice and impact grew with time but they required ongoing support in the role. A good understanding of the promotional messages was reported. Developing a good network of contacts at an early stage, both people with learning disabilities and healthcare professionals, was key. Relationships with professionals were supportive and positive and a positive emotive response to their lived experience was reported in these interactions.

Conclusions

From the perspective of the ECCs, the role is useful and beneficial. The work suggests some key recommendations for future development which include planning to build networks, support in presentation and communications skills and defining key messages and knowledge. Confidence of the ECCs builds with time in the role but also needs support the emotive impact of their lived experiences on audiences is highlighted. There is a need to evaluate how the programme is perceived by those who interact with it and how it changes behaviours which leads to better health outcomes.
RB1 loss induces quiescent state through downregulation of RAS signaling in mammary epithelial cells
Authors: Gong Linxiang , Voon Dominic Chih‐Cheng , Nakayama Joji , Takahashi Chiaki , Kohno Susumu
Published: March 2024

While loss of function (LOF) of retinoblastoma 1 (RB1) tumor suppressor is known to drive initiation of small‐cell lung cancer and retinoblastoma, RB1 mutation is rarely observed in breast cancers at their initiation. In this study, we investigated the impact on untransformed mammary epithelial cells given by RB1 LOF. Depletion of RB1 in anon‐tumorigenic MCF10A cells induced reversible growth arrest (quiescence) featured by downregulation of multiple cyclins and MYC, upregulation of p27KIP1, and lack of expression of markers which indicate cellular senescence or epithelial–mesenchymal transition (EMT). We observed a similar phenomenon in human mammary epithelial cells (HMEC) as well. Additionally, we found that RB1 depletion attenuated the activity of RAS and the downstream MAPK pathway in an RBL2/p130‐dependent manner. The expression of farnesyltransferase β, which is essential for RAS maturation, was found to be downregulated following RB1 depletion also in an RBL2/p130‐dependent manner. These findings unveiled an unexpected mechanism whereby normal mammary epithelial cells resist to tumor initiation upon RB1 LOF.
Machine‐learning model for the prediction of acute orthostatic hypotension after levodopa administration
Authors: Liu Zhu , Lin Shinuan , Zhou Junhong , Wang Xuemei , Wang Zhan , Yang Yaqin , Ma Huizi , Chen Zhonglue , Ren Kang , Wu Lingyu , Zhuang Haimei , Ling Yun , Feng Tao
Published: March 2024

Background

Levodopa could induce orthostatic hypotension (OH) in Parkinson's disease (PD) patients. Accurate prediction of acute OH post levodopa (AOHPL) is important for rational drug use in PD patients. Here, we develop and validate a prediction model of AOHPL to facilitate physicians in identifying patients at higher probability of developing AOHPL.

Methods

The study involved 497 PD inpatients who underwent a levodopa challenge test (LCT) and the supine‐to‐standing test (STS) four times during LCT. Patients were divided into two groups based on whether OH occurred during levodopa effectiveness (AOHPL) or not (non‐AOHPL). The dataset was randomly split into training (80%) and independent test data (20%). Several models were trained and compared for discrimination between AOHPL and non‐AOHPL. Final model was evaluated on independent test data. Shapley additive explanations (SHAP) values were employed to reveal how variables explain specific predictions for given observations in the independent test data.

Results

We included 180 PD patients without AOHPL and 194 PD patients with AOHPL to develop and validate predictive models. Random Forest was selected as our final model as its leave‐one‐out cross validation performance [AUC_ROC 0.776, accuracy 73.6%, sensitivity 71.6%, specificity 75.7%] outperformed other models. The most crucial features in this predictive model were the maximal SBP drop and DBP drop of STS before medication (ΔSBP/ΔDBP). We achieved a prediction accuracy of 72% on independent test data. ΔSBP, ΔDBP, and standing mean artery pressure were the top three variables that contributed most to the predictions across all individual observations in the independent test data.

Conclusions

The validated classifier could serve as a valuable tool for clinicians, offering the probability of a patient developing AOHPL at an early stage. This supports clinical decision‐making, potentially enhancing the quality of life for PD patients.
Neonatal magnesium sulphate for neuroprotection: A systematic review and meta‐analysis
Authors: Shepherd Emily , Karim Tasneem , McIntyre Sarah , Goldsmith Shona , Keir Amy , Badawi Nadia , Hunt Rod W. , Galinsky Robert
Published: March 2024

Aim

To review the evidence of the effects of neonatal magnesium sulphate for neuroprotection in perinatal asphyxia and hypoxic‐ischaemic encephalopathy (HIE).

Method

This was a systematic review of randomized controlled trials (RCTs) (with meta‐analysis) and non‐RCTs assessing magnesium sulphate for treating perinatal asphyxia and HIE at 35 weeks or more gestation (primary outcomes: neonatal death and death or long‐term major neurodevelopmental disability).

Results

Twenty‐five RCTs (2099 infants) and four non‐RCTs (871 infants) were included, 23 in low‐ and middle‐income countries (LMICs). In RCTs, reductions in neonatal death with magnesium sulphate versus placebo or no treatment (risk ratio [RR] = 0.68; 95% confidence interval [CI] = 0.53–0.86; 13 RCTs), and magnesium sulphate with melatonin versus melatonin alone (RR = 0.74; 95% CI = 0.58–0.95; one RCT) were observed. No difference in neonatal death was seen for magnesium sulphate with therapeutic hypothermia versus therapeutic hypothermia alone (RR = 0.66, 95% CI = 0.34–1.26; three RCTs), or magnesium sulphate versus phenobarbital (RR = 3.00; 95% CI = 0.86–10.46; one RCT). No reduction in death or long‐term neurodevelopmental disability (RR = 0.52; 95% CI = 0.14–1.89; one RCT) but reductions in several short‐term adverse outcomes were observed with magnesium sulphate. Evidence was low‐ to very‐low certainty because of risk of bias and imprecision.

Interpretation

Given the uncertainty of the current evidence, further robust neonatal magnesium sulphate research is justified. This may include high‐quality studies to determine stand‐alone effects in LMICs and effects with and after therapeutic hypothermia in high‐income countries.