bluuebunny/crossref_metadata_2025 huggingface dataset:
Leveraging CRISPR-Cas13d in an inducible knockdown system to interrogateDrosophilagerm granule mRNAs
Authors: Gauhar Zoya A. , Myhrvold Cameron , Gavis Elizabeth R.
Published: September 2024

Ribonucleoprotein (RNP) germ granules are hallmarks of germ cells across the animal kingdom and are thought to be hubs for post-transcriptional regulation that promote formation of the germ cell precursors. While numerous RNAs are associated with germ granules inDrosophila, the functions of many in germline development are poorly understood. Current methods for RNA knockdown, such as RNAi, do not allow local depletion of transcripts such as those found in the germ granules. We leveraged CRISPR-Cas13 to create a subcellular RNA knockdown system and tested it on two mRNAs,nanos (nos)andsarah (sra), whose abundance in germ granules differs. Because Cas13 has bothcisandtranscleavage activities, we evaluated the effect of target abundance on off-target RNA depletion. We show on and off-target RNA depletion is coupled when targeting the more abundantnosgerm granule transcripts. Off-target RNA knockdown is less potent when the system is used for less abundantsratranscripts. Whensrais knocked down in germ granules, we observe defective primordial germ cell migration, and an increase in the calcium indicator GCaMP at the posterior, consistent withsraencoding a negative regulator of calcium signaling. In sum, we report anin vivoCas13-based system for subcellular knockdown, evaluate its feasibility, and uncover a novel function forsragerm granule transcripts in promoting germline development.
Comparing newly developed SNP barcode panels with microsatellites to explore population genetics of malaria parasites in the Peruvian Amazon
Authors: Cabrera-Sosa Luis , Safarpour Mahdi , Kattenberg Johanna H. , Ramirez Roberson , Vinetz Joseph , Rosanas-Urgell Anna , Gamboa Dionicia , Delgado-Ratto Christopher
Published: September 2024

Malaria molecular surveillance (MMS) can provide insights into transmission dynamics, guiding national control/elimination programs. Considering the genetic differences among parasites from different areas in the Peruvian Amazon, we previously designed SNP barcode panels forPlasmodium vivax(Pv) andP. falciparum(Pf), integrated into AmpliSeq assays, to provide population genetics estimates of malaria parasites. These AmpliSeq assays are ideal for MMS: multiplexing different traits of interest, applicable to many use cases, and high throughput for large numbers of samples. The present study compares the genetic resolution of the SNP barcode panels in the AmpliSeq assays with widely used microsatellite (MS) panels to investigate Amazonian malaria parasites.

Malaria samples collected in remote areas of the Peruvian Amazon (51 Pv & 80 Pf samples) were characterized using the Ampliseq assays and MS. Population genetics estimates (complexity of infection, genetic diversity and differentiation, and population structure) were compared using the SNP barcodes (Pv: 40 SNPs & Pf: 28 SNPs) and MS panels (Pv: 16 MS & Pf: 7 MS).

The genetic diversity of Pv (expected heterozygosity,He) was similar across the subpopulations for both makers:HeMS= 0.68 - 0.78 (p = 0.23) andHeSNP= 0.36 - 0.38 (p = 0.80). Pairwise genetic differentiation (fixation index, FST) was also comparable: FST-MS= 0.04 - 0.14 and FST-SNP= 0.03 - 0.12 (p = 0.34 – 0.85). No geographic clustering was observed with any panel. In addition, Pf genetic diversity trends (HeMS= 0 – 0.48 p = 0.03 – 1;HeSNP= 0 - 0.09, p = 0.03 – 1) and pairwise FSTcomparisons (FST-MS= 0.14 – 0.65, FST-SNP= 0.19 – 0.61, p = 0.24 – 0.83) were concordant between the panels. Similar population structure clustering was observed with both SNP and MS, highlighting one Pf subpopulation in an indigenous community.

The SNP barcodes in the Pv AmpliSeq v2 Peru and Pf AmpliSeq v1 Peru assays offer comparable results to MS panels when investigating population genetics in Pv and Pv populations. Therefore, the AmpliSeq assays can efficiently characterize malaria transmission dynamics and population structure and support malaria elimination efforts in Peru.
Climatic-environmental influences on hominin brain size over the last 5 million years
Authors: Nicholson Samuel L , Puschel Thomas , Baker Joanna , Venditti Chris
Published: September 2024

A large brain relative to body mass is considered a distinguishing hominin trait. It has frequently been related to a suite of social, behavioral, technological, and other cognitive adaptations that differentiate humans from other species. The processes underlying large brain size evolution have therefore been a subject of rigorous scientific debate. Many hypotheses have been proposed to explain how climate and environment drive the selection of larger brain sizes, but monotonic influences of climate-environmental selective pressures are often assumed and rarely have between- and within-species effects been considered. Here, we apply Bayesian phylogenetic comparative techniques to the hominin fossil record to test the effect of climatic and environmental pressures (C-E) on brain size evolution, whilst simultaneously accounting for body mass and chronological age. We find that colder and more variable temperatures have a positive within-species effect on brain size evolution, likely related to biological adaptations to mitigate against hypothermia. However, in Homo, the strength of this effect diminishes over time suggesting that in later species (Homo sapiens and Homo neanderthalensis) brain sizes were less affected by C-E conditions.
Osterix Facilitates Osteocytic Communication by Targeting Connexin43
Authors: Wu Zuping , Chen Qian , Gao Qian , Liang Muchun , Zhou Yumeng , Zhu Li , Wang Jiahe , Shen Yang , Jing Junjun , Xie Jing , Liu Xiaoheng , Zou Shujuan , Zhang Demao , Zhou Chenchen
Published: September 2024

Osteocytes, terminal-differentiated cells in bone, are now considered as more pivotal regulators of mature bone homeostasis than other bone cells, since they constitute 90- 95% of the bone cell population. Given their non-migratory nature within the mineralized matrix, their unique dendrites are crucial for cell-to-cell communication in response to both intracellular and extracellular stimuli, such as bone fracture or mechanical load. Here, we showed that Osterix (Osx), usually recognized as a specific doorkeeper for osteoblast differentiation during new bone formation marked by collagen type I α 1 (Col1α1), was unexpectedly co-expressed with Col1α1 in osteocytes within the cortical bone of mice. Deleting Osx in Col1α1-positive osteocytes disrupted cortical bone structure and osteocytic dendrites in mice, thus impairing transcellular fluid flow and intercellular communication. Conversely, overexpression of Osx in osteocytes enhanced these processes. Furthermore, we identified Connexin43, a critical protein of gap junction channel, was a direct transcriptional target of Osx in regulating dendrites of osteocytes. Pharmacological restoration of Connexin43 levels rescued the dysfunction in Osx-deficient osteocytes both in vitro and in vivo. Taken together, this work demonstrated Osx’s distinct role in osteocyte function through maintaining intercellular signaling, which broadened the current understanding of its role in Col1α1-positive bone cells, extending beyond osteoblasts and bone mineralization, offering new insights into bone diseases such as fracture nonunion or disuse osteoporosis.
Long-term protein synthesis with PURE in a mesoscale dialysis system
Authors: Julià Laura Roset , Grasemann Laura , Stellacci Francesco , Maerkl Sebastian J.
Published: September 2024

Cell-free systems are powerful tools in synthetic biology with versatile and wide-ranging applications. However, a significant bottleneck for these systems, particularly the PURE cell-free system, is their limited reaction lifespan and yield. Dialysis offers a promising approach to prolong reaction lifetimes and increase yields, yet most custom dialysis systems require access to sophisticated equipment like 3D printers or microfabrication tools. In this study, we utilized an easy-to-assemble, medium-scale dialysis system for cell-free reactions using commercially available components. By employing dialysis with periodic exchange of the feeding solution, we achieved a protein yield of 1.16 mg/mL GFP in the PURE system and extended protein synthesis for at least 12.5 consecutive days, demonstrating the system’s excellent stability.
Comparative analysis of uncoupled succinate production by the FeII/2-oxoglutarate-dependent dioxygenases
Authors: Das Susmita , Ranjan Saumya , Keerthana Carmel , Seenivasan Gayathri , Tuti Nikhil , Shaji Unnikrishnan P , Meur Gargi , Anindya Roy
Published: September 2024

Non-heme iron (FeII) and 2-oxoglutarate(2OG)-dependent dioxygenases catalyse a diverse array of biological reactions. These enzymes couple the oxidative decarboxylation of 2OG to the hydroxylation of the substrates. However, in the absence of the substrate, oxidative decarboxylation of 2OG generates succinate. We have determined succinate level by using succinyl-CoA synthetase to monitor this uncoupled decarboxylation of FeII/2OG-dependent dioxygenases and measured the uncoupled 2OG turnover of different FeII/2OG-dependent dioxygenases. We also performed comparative analysis and verified the functionality of human dioxygenase ALKBH6.
The Structure of Cilium Inner Junctions Revealed by Electron Cryo-tomography
Authors: Li Sam , Fernandez Jose-Jesus , Ruehle Marisa D. , Howard-Till Rachel A. , Fabritius Amy , Pearson Chad G. , Agard David A. , Winey Mark E.
Published: September 2024

The cilium is a microtubule-based organelle critical for many cellular functions. Its assembly initiates at a basal body and continues as an axoneme that projects out of the cell to form a functional cilium. This assembly process is tightly regulated. However, our knowledge of the molecular architecture and the mechanism of assembly is limited. By applying electron cryo-tomography and subtomogram averaging, we obtained subnanometer resolution structures of the inner junction in three distinct regions of the cilium: the proximal region of the basal body, the central core of the basal body, and the flagellar axoneme. The structures allowed us to identify several basal body and axoneme components. While a few proteins are distributed throughout the entire length of the organelle, many are restricted to particular regions of the cilium, forming intricate local interaction networks and bolstering local structural stability. Finally, by knocking out a critical basal body inner junction component Poc1, we found the triplet MT was destabilized, resulting in a defective structure. Surprisingly, several axoneme-specific components were found to “infiltrate” into the mutant basal body. Our findings provide molecular insight into cilium assembly at its inner junctions, underscoring its precise spatial regulation.
Non-allometric expansion and enhanced compartmentalization of Purkinje cell dendrites in the human cerebellum
Authors: Busch Silas E. , Hansel Christian
Published: September 2024

Purkinje cell (PC) dendrites are optimized to integrate the vast cerebellar input array and drive the sole cortical output. PCs are classically seen as stereotypical computational units, yet mouse PCs are morphologically diverse and those with multi-branched structure can receive non-canonical climbing fiber (CF) multi-innervation that confers independent compartment-specific signaling. While otherwise uncharacterized, human PCs are universally multi-branched. Do they exceed allometry to achieve enhanced integrative capacities relative to mouse PCs? To answer this, we used several comparative histology techniques in adult human and mouse to analyze cellular morphology, parallel fiber (PF) and CF input arrangement, and regional PC demographics. Human PCs are substantially larger than previously described; they exceed allometric constraint by cortical thickness and are the largest neuron in the brain with 6-7cm total dendritic length. Unlike mouse, human PC dendrites ramify horizontally to form a multi-compartment motif that we show can receive multiple CFs. Human spines are denser (6.9 vs 4.9 spines/μm), larger (∼0.36 vs 0.29μm), and include an unreported ‘spine cluster’ structure—features that may be congruent with enhanced PF association and amplification as human-specific adaptations. By extrapolation, human PCs may receive 500,000 to 1 million synaptic inputs compared with 30-40,000 in mouse. Collectively, human PC morphology and input arrangement is quantitatively and qualitatively distinct from rodent. Multi-branched PCs are more prevalent in posterior and lateral cerebellum, co-varying with functional boundaries, supporting the hypothesis that this morphological motif permits expanded input multiplexing and may subserve task-dependent needs for input association.
Early events in midzone formation stabilize nascent bipolar spindles
Authors: Sim Shannon , Moore Sean , Al-Naemi Khalid , El-Hajj Ziad , Vogel Jackie
Published: September 2024

The formation of a stable mitotic spindle is critical to the accurate partitioning of the chromosomes during mitosis. Interpolar microtubules of the spindle midzone consist of antiparallel microtubules crosslinked by kinesin-5 and stabilize the spindle by opposing forces produced when sister chromatids are attached to microtubules and under tension. Despite the importance of the interpolar microtubules, how and when they form and what determines their number remain unknown. In this study, we report that a γ-tubulin mutation (γtub-Y445D) disrupts the localization of kinesin-5 and the formation of the interpolar microtubules, resulting in spindle instability. We find that kinesin-5 crosslinking is intact in this mutant, but that it is incapable of the subsequent kinesin-5 microtubule sliding needed to stabilize the nascent spindle. Early activation of the PRC1 homolog Ase1 restores nascent spindle stability to the γtub-Y445D mutant but cannot stabilize spindles during centromere attachment. Our work shows that midzone assembly begins with the formation of interpolar microtubule precursors in monopolar spindles that persist until early metaphase and limit the formation of kinetochore attachments in new spindles.
Characterization and Antiatherogenic Potential of P3R99 Monoclonal Antibody Against Sulfated Glycosaminoglycans: Physicochemical and Functional Insights
Authors: Valencia Leidy M. , Martínez-Montano Yoandra , Gómez José A. , Sarduy Roger , Hernández Arletty , Proctor Spencer , Fernández-Calienes Aymé , Brito Víctor , Soto Yosdel
Published: September 2024

Atherosclerosis is initiated by the retention of ApoB-containing lipoproteins in the arterial wall, mediated by glycosaminoglycan chains of proteoglycans. At the Center for Molecular Immunology, we are developing the P3R99 monoclonal antibody (mAb) to target this process. This study characterizes new P3R99 mAb variants expressed in CHO-K1 and HEK-293 cell lines. We compared these variants with the parental mAb from NS0 cells using SDS-PAGE, size exclusion and cation exchange chromatography, dynamic light scattering, peptide mapping, far-UV circular dichroism, and PNGase F deglycosylation. All variants exhibited a molecular size of ∼150 kDa, ∼99% purity, and similar average particle sizes (12.5-13.7 nm). They displayed a high β-sheet content (>40%) and basic amino acids on the surface, with minor differences in peptide maps compared to the parental mAb. Notable differences were found in the content of acidic and basic species and glycosylation profiles. NS0-derived P3R99 had lower G0F content (10.39%), higher G1F (38.29%) and G2F (30.44%) levels, with more terminal galactose (83.07%) and sialylation (15.33%). In contrast, CHO-K1 and HEK-293 variants showed similar glycosylation patterns. Despite these differences, the antigen and atherosclerotic lesion recognition properties of the mAb were unaffectedin vitro. Biodistribution studies in Sprague Dawley rats (1 mg, IV, n=3) revealed preferential accumulation of the new P3R99 variants in aortas and reduced LDL arterial retention (1 mg, IP). Passive administration of the mAbs (2 mg every three days, three IV doses, n=6-7) in a Lipofundin 20%-induced atherosclerosis NZW rabbit model also demonstrated preferential accumulation in aortas and reduced atherosclerosis, with 60% of treated rabbits not developing lesions. These results suggest that the P3R99 mAb derived from CHO-K1 and HEK-293 cells retains its antiatherogenic properties despite structural differences from the NS0-derived mAb associated with the different expression systems.
Effect of Polygenic Scores on the Relationship Between Psychosis and Cognitive Performance
Authors: Varney Lauren , Jedlovszky Krisztina , Wang Baihan , Murtough Stephen , Cotic Marius , Richards-Belle Alvin , Khani Noushin Saadullah , Lau Robin , Abidoph Rosemary , McQuillin Andrew , Thygesen Johan , Alizadeh Behrooz Z. , Bender Stephan , Crespo-Facorro Benedicto , Hall Jeremy , Iyegbe Conrad , Kravariti Eugenia , Lawrie Stephen M , Mata Ignacio , McDonald Colm , Murray Robin M , Prata Diana P , Toulopoulou Timothea , van Haren Neeltje , Bramon Elvira
Published: September 2024

Background

Up to 80% of psychosis patients experience cognitive impairment. High heritability of both psychosis and cognition means cognitive performance could be an endophenotype for psychosis.

Methods

Using samples of adults (N=4,506) and children (N=10,981), we investigated the effect of polygenic scores (PGSs) for schizophrenia and bipolar disorder on cognitive performance, and PGSs for intelligence and educational attainment on psychosis symptoms.

Results

Schizophrenia PGS was negatively associated with visuospatial processing/problem-solving in the adult sample (beta: −0.0569; 95% confidence interval [CI]: −0.0926, −0.0212) and working memory (beta: −0.0432; 95% CI: −0.0697, −0.0168), processing speed (b: −0.0491; 95% CI: −0.0760, −0.0223), episodic memory (betas: −0.0581 to −0.0430; 95% CIs: −0.0847 to −0.0162), executive functioning (beta: −0.0423; 95% CI: −0.0692, −0.0155), fluid intelligence (beta: −0.0583; 95% CI: −0.0847, −0.0320), and total intelligence (beta: −0.0458; 95% CI: −0.0709, −0.0206) in the child sample. Bipolar disorder PGS was not associated with any cognitive endophenotypes studied. Lower values on the PGS for intelligence were associated with higher odds of psychosis in adults (odds ratio [OR]: 0.886; 95% CI: 0.811– 0.968) and psychotic-like experiences in children (OR: 0.829; 95% CI: 0.777–0.884). In children, a lower polygenic score for educational attainment was associated with greater odds of psychotic-like experiences (OR: 0.771; 95% CI: 0.724–0.821).

Conclusions

The relationship between psychosis and cognitive impairment can be demonstrated bidirectionally at the neurobiological level. The effect of schizophrenia PGS on cognitive performance differs across the lifespan and cognitive domains. Specific cognitive domains may therefore be better endophenotypes than overall cognition.
Reactivation of Human Herpesvirus 6 and Epstein-Barr Virus in relapsing remitting multiple sclerosis: association with disabilities, disease progression, and inflammatory processes
Authors: Almulla Abbas F. , Vojdani Aristo , Zhang Yingqian , Vojdani Elroy , Maes Michael
Published: September 2024

Background

Multiple sclerosis (MS) is a chronic autoimmune disorder affecting the central nervous system (CNS). Reactivation of Human herpesvirus 6 (HHV-6) and Epstein-Barr virus (EBV) is observed in MS.

Objectives

This study investigates immunoglobulins (Ig)G, IgM, and IgA directed against EBV nuclear antigen EBNA-366-406, HHV-6 and EBV deoxyuridine-triphosphatase (dUTPase), and different immune profiles in 58 patients with relapsing remitting MS (RRMS) compared to 60 healthy controls.

Methods

We employed enzyme-linked immunosorbent assays (ELISA) to measure the immunoglobulins to viral antigens. Multiplex immunoassays were used to measure cytokines, chemokines and growth factor levels that were used to compute immune profiles, including M1 macrophage, T helper (Th)-1, Th-17, and overall immune activation. We assessed disabilities using the Expanded Disability Status Scale (EDSS) and disease progression using the Multiple Sclerosis Severity Score (MSSS).

Results

IgG/IgA/IgM directed to the three viral antigens were significantly higher in RRMS than in controls. RRMS was significantly discriminated from controls by using IgG and IgM against HHV-6 dUTPase, yielding an accuracy of 91.5% (sensitivity=87.3% and specificity=95.2%). Neural network analysis showed that using IgG to EBV-dUTPase, IgM to EBV-dUTPase, and immune profiles yielded an area under the ROC curve of 1 and a predictive accuracy of 97.1%. There were strong associations between IgG/IgM responses to HHV-6 and EBV-dUTPases and the EDSS/MSSS scores and aberrations in M1, Th-17, profiles, and overall immune activation.

Conclusions

HHV-6 and EBV reactivation play a key role in RRMS and these effects are mediated by activation of cytokine profiles.
Characterisation of cell cycle checkpoint kinases inToxoplasma gondii
Authors: Johnson Monique K. , Chelaghma Sara , Koreny Ludek , Waller Ross F. , Merrick Catherine J.
Published: September 2024

Toxoplasma gondiiis a protozoan parasite in the apicomplexan phylum. Apicomplexan parasites replicate using a variety of non-canonical cell division modes, distinct from binary fission, whose molecular regulation is incompletely understood.T. gondiireplicates by endodyogeny in its intermediate hosts, and by schizogony in its definitive host. To improve our understanding of how these unusual, flexible cell division modes are regulated, we characterised theT. gondiihomologues of the cell-cycle checkpoint kinases ATM and ATR. These phosphoinositol-3-kinase-like kinases are entirely absent in some related parasites includingPlasmodium; inT. gondiithey are present but their putative checkpoint roles were uncharacterised. BothTgATM andTgATR were found to be dispersed throughout the parasite and they did not detectably relocate to the nucleus after DNA damage. Nevertheless, they were both required for checkpoint responses to DNA damage, including acute replication slowing and phosphorylation of the DNA damage marker histone H2AX. Unusually, the two kinases seemed to cooperate in the checkpoint response, with the loss of either one largely ablating the response, regardless of the type of DNA damage. Thus,T. gondiiclearly retains a DNA-damage-responsive checkpoint, but some of its key features differ from the well-studied checkpoint in human cells.
Intracellular dry mass density increases under growth-induced pressure
Authors: Kim Hyojun , Alric Baptiste , Chan Nolan , Roul Julien , Delarue Morgan
Published: September 2024

Cells that proliferate in confined environments develop mechanical compressive stress, referred to as growth-induced pressure, which inhibits growth and division across various organisms. Recent studies have shown that in these confined spaces, the diffusivity of intracellular nanoparticles decreases. However, the physical mechanisms behind this reduction remain unclear. In this study, we use quantitative phase imaging to measure the refractive index and dry mass density ofSaccharomyces cerevisiaecells proliferating under confinement in a microfluidic bioreactor. Our results indicate that the observed decrease in diffusivity can be at least attributed to the intracellular accumulation of macromolecules. Furthermore, the linear scaling between cell content and growth-induced pressure suggests that the concentrations of macromolecules and osmolytes are maintained proportionally under such pressure inS. cerevisiae.
Evidence for compensatory evolution within pleiotropic regulatory elements
Authors: Kliesmete Zane , Orchard Peter , Lee Victor Yan Kin , Geuder Johanna , Krauß Simon M. , Ohnuki Mari , Jocher Jessica , Vieth Beate , Enard Wolfgang , Hellmann Ines
Published: September 2024

Pleiotropy, measured as expression breadth across tissues, is one of the best predictors for protein sequence and expression conservation. In this study, we investigated its effect on the evolution ofcis-regulatory elements (CREs). To this end, we carefully reanalyzed the Epigenomics Roadmap data for nine fetal tissues, assigning a measure of pleiotropic degree to nearly half a million CREs. To assess the functional conservation of CREs, we generated ATAC-seq and RNA-seq data from humans and macaques. We found that more pleiotropic CREs exhibit greater conservation in accessibility, and the mRNA expression levels of the associated genes are more conserved. This trend of higher conservation for higher degrees of pleiotropy persists when analyzing the transcription factor binding repertoire. In contrast, simple DNA sequence conservation of orthologous sites between species tends to be even lower for pleiotropic CREs than for species-specific CREs. Combining various lines of evidence, we propose that the lack of sequence conservation in functionally conserved pleiotropic CREs is owing to within-element compensatory evolution. In summary, our findings suggest that pleiotropy is also a good predictor for the functional conservation of CREs, even though this is not reflected in the sequence conservation of pleiotropic CREs.
Theoretical analysis of the reactions induced by interaction of
Li6
with
H3
and
He3
nuclei
Authors: Lashko Yu. A. , Vasilevsky V. S. , Zhaba V. I.
Published: September 2024

We determine cross sections and astrophysical S factors of the reactions generated in collisions between Li6 and H3 and between Li6 and He3. A microscopic three-cluster model is employed to study the dynamics of reactions occurring in the mirror nuclei Be9 and B9. In a previous study [], this model was successfully applied to investigate the resonance structure of Be9 and B9, as well as reactions induced by the interaction of deuterons with Li7 and Be7. A fairly good agreement between theoretical results and available experimental data was achieved. To the best of our knowledge, appropriate experimental data for the astrophysical S factors of the reactions generated by the interaction of

Li

6

with H3 and with He3 are currently unavailable. Thus, our results can serve as a guideline for future experimental efforts.

Published by the American Physical Society
2024
Classical Casimir pressure in the presence of axion dark matter
Authors: Brax Philippe , Brun Pierre
Published: September 2024

We study the effects of an oscillating axion field on the pressure between two metallic plates. We consider the situation where a magnetic field parallel to the plates is present and show that the electric field induced by the coupling of the axion to photons leads to resonances. When the boundary plates are perfect conductors, the resonances are infinitely thin whilst they are broadened when the conductivity of the boundary plates is taken into account. The resonances take place at the tower of distances close to dn=(2n+1)πm, where m is the axion mass and have a finite width and height depending on the conductivity. The resulting resonant pressure on the plate depends on the induced polarization at the surface of the plates. We investigate the reach of future Casimir experiments in terms of the axion mass and the conductivity of the boundary plates. We find that for large enough conductivities, the axion-induced pressure could be larger than the quantum Casimir effect between the plates.

Published by the American Physical Society
2024
Black hole-neutron star mergers with massive neutron stars in numerical relativity
Authors: Chen Shichuan , Wang Luohan , Hayashi Kota , Kawaguchi Kyohei , Kiuchi Kenta , Shibata Masaru
Published: September 2024

We study the merger of black hole-neutron star (BH-NS) binaries in numerical relativity, focusing on the properties of the remnant disk and the ejecta, varying the mass of compactness of the NS and the mass and spin of the BH. We find that within the precision of our numerical simulations, the remnant disk mass and ejecta mass normalized by the NS baryon mass (M^rem and M^eje, respectively), and the cutoff frequency fcut normalized by the initial total gravitational mass of the system at infinite separation approximately agree among the models with the same NS compactness CNS=MNS/RNS, mass ratio Q=MBH/MNS, and dimensionless BH spin χBH irrespective of the NS mass MNS in the range of 1.092−1.691M⊙. This result shows that the merger outcome depends sensitively on Q, χBH, and CNS but only weakly on MNS. This justifies the approach of studying the dependence of NS tidal disruptions on the NS compactness by fixing the NS mass but changing the EOS. We further perform simulations with massive NSs of MNS=1.8M⊙, and compare our results of M^rem and M^eje with those given by existing fitting formulas to test their robustness for more compact NSs. We find that the fitting formulas obtained in the previous studies are accurate within the numerical errors assumed, while our results also suggest that further improvement is possible by systematically performing more precise numerical simulations.

Published by the American Physical Society
2024
Theory of angular momentum transfer from light to molecules
Authors: Maslov Mikhail , Koutentakis Georgios M. , Hrast Mateja , Heckl Oliver H. , Lemeshko Mikhail
Published: September 2024

We present a theory describing the interaction of structured light, such as light carrying orbital angular momentum, with molecules. The light-matter interaction Hamiltonian we derive is expressed through couplings between spherical gradients of the electric field and the (transition) electric multipole moments of a particle of any nontrivial rotation point group. Our model can therefore accommodate an arbitrary complexity of the molecular and electric field structure, and it can be straightforwardly extended to atoms or nanostructures. Applying this framework to rovibrational spectroscopy of molecules, we uncover the general mechanism of angular momentum exchange between the spin and orbital angular momenta of light, molecular rotation, and its center-of-mass motion. We show that the nonzero vorticity of Laguerre-Gaussian beams can strongly enhance certain rovibrational transitions that are considered forbidden in the case of nonhelical light. We discuss the experimental requirements for the observation of these forbidden transitions in state-of-the-art spatially resolved spectroscopy measurements.

Published by the American Physical Society
2024
Collective gradient sensing by dilute swimming bacteria without clustering
Authors: Kai Tatsuro , Abe Takahiro , Yoshinaga Natsuhiko , Nakamura Shuichi , Kudo Seishi , Toyabe Shoichi
Published: September 2024

We characterize the taxis enhancement of swimming bacteria by collective migration without apparent clustering. We confine a dilute suspension in a shallow channel and evaluate the thermotaxis response to local heating and diffusion. By combining cell tracking analysis and numerical simulation based on simple modeling, we show that the alignment interaction suppresses orientation fluctuation, strengthens migration bias, and also prevents the dispersion of accumulated population. The results show a prominent example of how a collective motion of active matter implements a biological function.

Published by the American Physical Society
2024
Mixed-State Quantum Phases: Renormalization and Quantum Error Correction
Authors: Sang Shengqi , Zou Yijian , Hsieh Timothy H.
Published: September 2024

Open system quantum dynamics can generate a variety of long-range entangled mixed states, yet it has been unclear in what sense they constitute phases of matter. To establish that two mixed states are in the same phase, as defined by their two-way connectivity via local quantum channels, we use the renormalization group (RG) and decoders of quantum error correcting codes. We introduce a real-space RG scheme for mixed states based on local channels which ideally preserve correlations with the complementary system, and we prove this is equivalent to the reversibility of the channel’s action. As an application, we demonstrate an exact RG flow of finite temperature toric code in two dimensions to infinite temperature, thus proving it is in the trivial phase. In contrast, for toric code subject to local dephasing, we establish a mixed-state toric code phase using local channels obtained by truncating an RG-type decoder and the minimum weight perfect matching decoder. We also discover a precise relation between mixed-state phase and decodability, by proving that local noise acting on toric code cannot destroy logical information without bringing the state out of the toric code phase.

Published by the American Physical Society
2024
An online error compensation strategy for hybrid robot based on grating feedback
Authors: Cheng Pengkun , Xiao Juliang , Zhao Wei , Zhang Yangyang , Liu Haitao , Shan Xianlei
Published: September 2024

Purpose

This paper aims to enhance the machining accuracy of hybrid robots by treating the moving platform as the first joint of a serial robot for direct position measurement and integrating external grating sensors with motor encoders for real-time error compensation.

Design/methodology/approach

Initially, a spherical coordinate system is established using one linear and two circular grating sensors. This system enables direct acquisition of the moving platform’s position in the hybrid robot. Subsequently, during the coarse interpolation stage, the motor command for the next interpolation point is dynamically updated using error data from external grating sensors and motor encoders. Finally, fuzzy proportional integral derivative (PID) control is applied to maintain robot stability post-compensation.

Findings

Experiments were conducted on the TriMule-600 hybrid robot. The results indicate that the following errors of the five grating sensors are reduced by 94%, 93%, 80%, 75% and 88% respectively, after compensation. Using the fourth drive joint as an example, it was verified that fuzzy adaptive PID control performs better than traditional PID control.

Practical implications

The proposed online error compensation strategy significantly enhances the positional accuracy of the robot end, thereby improving the actual processing quality of the workpiece.

Social implications

This method presents a technique for achieving online error compensation in hybrid robots, which promotes the advancement of the manufacturing industry.

Originality/value

This paper proposes a cost-effective and practical method for online error compensation in hybrid robots using grating sensors, which contributes to the advancement of hybrid robot technology.
Multimodal presentation of E-commerce product reviews and ratings: empirical investigation using multimodality
Authors: Ghandour Rajab
Published: September 2024

Purpose

The aim of the research is to evaluate different modality for product reviews presentation and its impact on users’ performance, purchase intention and enjoyment.

Design/methodology/approach

The study utilized an experimental approach with 48 opportunistic participants in three groups (16 users per group). Participants were randomly assigned to experimental conditions to ensure unbiased treatment. Data were collected through controlled interventions or manipulations, with pre-defined measures to assess specific outcomes. Statistical techniques such as ANOVA were employed to analyse the data, allowing for comparisons between experimental variables.

Findings

The findings revealed that integrating facial expression avatars and emojis into an e-commerce platform effectively communicates product reviews and ratings. Moreover, the use of animation significantly enhanced user enjoyment. This suggests that visual representations not only convey information effectively but also contribute to a more engaging and enjoyable user experience.

Research limitations/implications

While this experiment offers valuable insights into the impact of different e-commerce presentation layouts on user behaviour, further research could delve deeper into specific aspects such as the influence of individual user characteristics and the long-term effects of layout preferences.

Originality/value

This study contributes original insights by demonstrating the efficacy of facial expressive avatars and emojis in conveying product reviews and ratings within e-commerce platforms. Moreover, it adds value by highlighting the positive impact of animation on user enjoyment. By combining these elements, the research offers a novel approach to enhancing user engagement and understanding of customer feedback in online shopping environments. The findings provide valuable guidance for e-commerce platforms seeking innovative ways to communicate product information effectively and enhance the overall user experience, ultimately benefiting both businesses and consumers.
Changing plant phosphorus acquisition strategies in relation to altered soil phosphorus fractions after wetland drainage
Authors: Jiang Zhenhui , Luo Wanqing , Zhu Erxiong , Zhao Yunpeng , Liu Chengzhu , Zhou Lei , Feng Xiaojuan
Published: September 2024

Plant phosphorus (P) acquisition strategy is considered to be an intrinsic driver behind plant succession. However, variations in plant P acquisition strategies in connection to soil P fraction changes after wetland drainage remain unclear.

To address this issue, here we conducted a study in six distinct wetlands that experienced long‐term (>20 years) artificial drainage, with the adjacent waterlogged wetlands as a control. We analysed plant community composition, biomass and soil P fractions, and identified three plant P acquisition strategies based on soil acid phosphatase activity, plant P resorption efficiency, and soil arbuscular mycorrhizal fungi (AMF) content.

We found that soil calcium‐bound P (PCa) and enzyme‐extractable P (Penzyme) were key factors influencing plant P acquisition. Soil PCa correlated negatively with acid phosphatase activity but positively with AMF content. Soil Penzyme negatively impacted P resorption efficiency. The wetlands were categorised into three types based on the change in plant richness and composition, with each exhibiting distinct plant P acquisition strategies. These changes in strategies after drainage corresponded with shifts in soil P fractions.

Overall, our study highlights the role of soil P fractions in explaining plant P acquisition strategies after wetland drainage, suggesting P regulations on plant succession and ecosystem services.

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Poisoning with table salt while treating drug poisoning
Authors: Smędra Anna , Wochna Katarzyna , Gruchała Jacek , Berent Jarosław
Published: September 2024

Hypernatremia is an increase in serum sodium concentration above 145 mmol/L. There are many causes of elevated sodium levels in the blood serum. One is incorrect actions performed by medical staff. The symptoms of excessively high serum sodium levels depend on the severity of hypernatremia, the rate of its increase and the accompanying volume disorders. Severe symptoms include altered consciousness, increased muscle tone and reflexes, convulsions, psychomotor hyperactivity or drowsiness (up to coma), respiratory failure, and even death. We present the case of a 45‐year‐old man who took seven tablets of a blood pressure‐lowering drug, and paramedics subsequently administered a concentrated solution of table salt to induce vomiting. However, vomiting did not occur, leading to hypernatremia. Ultimately, the man survived but developed persistent cognitive dysfunction, including disordered short‐term memory and encoding and retrieval of information from long‐term memory, weakening of attention function and fatigue, and disorders in abstract thinking. The patient's family went to the prosecutor's office to investigate the possibility of medical malpractice. Experts found that the paramedics' actions were incorrect. Although it has been known for many years that table salt solutions should not be used to induce vomiting, unfortunately, both laypeople and medical professionals are still using this technique. Iatrogenic salt poisoning may end not only in serious health complications but also in legal consequences.
Comparative single‐cell transcriptomic analysis across tissues of aging primates reveals specific autologous activation of ZNF281 to mitigate oxidative stress in cornea
Authors: Xiao Yuhua , Chen Xu , Chen Zheyao , Dai Wangxuan , Hu Xing , Zhang Shuyao , Zhong Jiawei , Chen Jia , Liu Xu , Liang Lingyi , Hu Youjin
Published: September 2024

Reactive oxygen species (ROS) and oxidative stress accelerate cellular aging, but their impact on different tissues varies. The cornea, known for its robust antioxidant defense systems, is relatively resistant to age‐related diseases like cancer. However, the precise mechanisms by which the cornea maintains ROS homeostasis during aging remain unclear. Through comparative single‐cell transcriptomic analysis of the cornea and other tissues in young and old nonhuman primates, we identified that a ZNF281 coding transcriptomic program is specifically activated in cornea during aging. Further investigation revealed that ZNF281 forms a positive feedback loop with FOXO3 to sense elevated levels of ROS and mitigate their effects potentially by regulating the mitochondrial respiratory chain and superoxide dismutase (SOD) expression. Importantly, we observed that overexpression of ZNF281 in MSCs prevented cellular senescence. In summary, these findings open up possibilities for understanding tissue‐specific aging and developing new therapies targeting ROS damage.
Plasma proteomics for risk prediction of Alzheimer's disease in the general population
Authors: Yang Sisi , Ye Ziliang , He Panpan , Zhang Yuanyuan , Liu Mengyi , Zhou Chun , Zhang Yanjun , Gan Xiaoqin , Huang Yu , Xiang Hao , Qin Xianhui
Published: September 2024

We aimed to develop and validate a protein risk score for predicting Alzheimer's disease (AD) and compare its performance with a validated clinical risk model (Cognitive Health and Dementia Risk Index for AD [CogDrisk‐AD]) and apolipoprotein E (APOE) genotypes. The development cohort, consisting of 35,547 participants from England in the UK Biobank, was randomly divided into a 7:3 training–testing ratio. The validation cohort included 4667 participants from Scotland and Wales in the UK Biobank. In the training set, an AD protein risk score was constructed using 31 proteins out of 2911 proteins. In the testing set, the AD protein risk score had a C‐index of 0.867 (95% CI, 0.828, 0.906) for AD prediction, followed by CogDrisk‐AD risk factors (C‐index, 0.856; 95% CI, 0.823, 0.889), and APOE genotypes (C‐index, 0.705; 95% CI, 0.660, 0.750). Adding the AD protein risk score to CogDrisk‐AD risk factors (C‐index increase, 0.050; 95% CI, 0.008, 0.093) significantly improved the predictive performance for AD. However, adding CogDrisk‐AD risk factors (C‐index increase, 0.040; 95% CI, −0.007, 0.086) or APOE genotypes (C‐index increase, 0.000; 95% CI, −0.054, 0.055) to the AD protein risk score did not significantly improve the predictive performance for AD. The top 10 proteins with the highest coefficients in the AD protein risk score contributed most of the predictive power for AD risk. These results were verified in the external validation cohort. EGFR, GFAP, and CHGA were identified as key proteins within the protein network. Our result suggests that the AD protein risk score demonstrated a good predictive performance for AD risk.
Implications of the shift to DSM‐5 for alcohol use disorder prevalence estimates in the National Survey on Drug Use and Health
Authors: Bailey Allen J. , Quinn Patrick D. , McHugh R. Kathryn
Published: September 2024

Background and aims

The Substance Abuse and Mental Health Services Administration's annual National Survey on Drug Use and Health (NSDUH) is a commonly used source for estimating trends in alcohol use disorders (AUD) in the United States. From 2015 to 2019 the annual prevalence of people diagnosed with either Diagnostic and Statistical Manual 4th edition (DSM‐IV) alcohol abuse or dependence ranged from 5.3 to 5.9%. More recent estimates, using the DSM 5th edition (DSM‐5) AUD diagnostic formulation, have been higher, with AUD base rates ranging from 10.1 to 10.7% from 2020 to 2022. This study aimed to compare the past 12‐month base rates of AUD in the United States general population when using the DSM‐5 versus DSM‐IV AUD (i.e. abuse or dependence) and assess the AUD severity of individuals captured with each diagnostic formulation using DSM‐5 AUD symptom counts.

Methods

We examined descriptive trends in the rate of past‐year NSDUH AUD diagnoses from 2015 to 2022. We contrasted them with trends in drinking behavior: the percentage of individuals who had ever reported drinking and the number of drinking days and binge drinking days for those who drink. We also analyzed the concordance between DSM‐IV and DSM‐5 AUD diagnoses in the 2020 NSDUH, which concurrently assessed AUD with both diagnostic formulations.

Results

The transition to DSM‐5 AUD formulation coincided with a drastic increase in AUD prevalence rates that occurred without increases in drinking behavior. In 2020 NSDUH data, the estimated past‐year DSM‐5 AUD prevalence rate was 10.1% compared with a 5.4% rate of past‐year DSM‐IV abuse or dependence. The DSM‐5 AUD formulation captured more mild‐severity individuals than the DSM‐IV formulation.

Conclusions

Higher recent base rates of alcohol use disorders (AUD) in the National Survey on Drug Use and Health are likely, at least partially, explained by measurement changes in AUD; specifically, the shift from DSM‐IV abuse or dependence to DSM‐5 AUD. The DSM‐5 formulation appears substantially more inclusive than the DSM‐IV formulation, leading to a larger number of mild severity individuals being captured.
Micro‐computed tomography evaluation of minimally invasive root canal preparation in 3D‐printed C‐shaped canal
Authors: Supavititpattana Nutcha , Suebnukarn Siriwan , Phumpatrakom Panupat , Budsaba Kamon
Published: September 2024

This study aimed to evaluate and compare the shaping abilities and minimum dentin thickness of minimally invasive rotary instruments via micro‐computed tomography. Twelve 3D‐printed C‐shaped canal models from a mandibular molar were divided into two groups, and root canals were prepared with either XP‐endo Rise (XR) or TruNatomy (TN) systems. Pre‐ and post‐preparation evaluations included canal volume, prepared area and minimum dentin thickness. No significant differences were found in canal volume change (XR: 22.66 ± 4.28%, TN: 23.02 ± 5.10%), prepared canal area (XR: 31.86 ± 10.72%, TN: 30.26 ± 11.59%) and minimum dentin thickness (XR: 0.30 ± 0.05 mm, TN: 0.28 ± 0.05 mm) between groups (p > 0.05). The canal volume change in the middle third was significantly higher than that in the coronal and apical thirds (p < 0.05) in both groups. In conclusion, XR demonstrated comparable shaping abilities and minimum dentin thickness to TN in preparing 3D‐printed C‐shaped canals.