bluuebunny/crossref_metadata_2025 huggingface dataset:
Microbiome signatures of virulence in the oral-gut-brain axis influence Parkinson’s disease and cognitive decline pathophysiology
Authors: Clasen Frederick , Yildirim Suleyman , Arıkan Muzaffer , Garcia-Guevara Fernando , Hanoğlu Lütfü , Yılmaz Nesrin H. , Şen Aysu , Demir Tuğçe Kahraman , Yıldız Zeynep , Mardinoglu Adil , Uhlen Mathias , Shoaie Saeed
Published: October 2024

The human microbiome is increasingly recognized for its crucial role in the development and progression of neurodegenerative diseases. While the gut-brain axis has been extensively studied, the contribution of the oral microbiome and gut-oral tropism in neurodegeneration has been largely overlooked. Cognitive impairment (CI) is common in neurodegenerative diseases and develops on a spectrum. In Parkinson’s Disease (PD) patients, CI is one of the most common non-motor symptoms but its mechanistic development across the spectrum remains unclear, complicating early diagnosis of at-risk individuals. Here, we generated 228 shotgun metagenomics samples of the gut and oral microbiomes across PD patients with either mild cognitive impairment (PD-MCI) or dementia (PDD), and a healthy cohort, to study the role of the gut and oral microbiomes on CI in PD. In addition to revealing compositional and functional signatures, the role of pathobionts, and dysregulated metabolic pathways of the oral and gut microbiome in PD-MCI and PDD, we also revealed the importance of oral-gut translocation in increasing abundance of virulence factors in PD and CI. The oral-gut virulence was further integrated with saliva metaproteomics and demonstrated their potential role in dysfunction of host immunity and brain endothelial cells. Our findings highlight the significance of the oral-gut-brain axis and underscore its potential for discovering novel biomarkers for PD and CI.
Spatial organization of supercoil dynamics during DNA replication
Authors: Kusano Yoshiharu , Shinkai Soya , Nozawa Ryu-Suke , Sun Jiying , Onami Shuichi , Tashiro Satoshi , Hirota Toru
Published: October 2024

Progression of DNA replication inevitably generates helical tension and resulting super-helical structures, or supercoils, that originate from the double helix of DNA. As DNA polymerases progress, negative supercoils accumulate in the wake of the replication fork, thereby impeding fork progression unless the supercoils are resolved topologically. Using super-resolution microscopy combined with spatial distribution analysis, here we describe that SMC5/6-mediated confinement of negative supercoils lies at the basis of releasing them by topoisomerase Top2A. Along with DNA replication, SMC5/6 progressively associates with chromatin and locally increases the density of supercoil clusters behind the fork, allowing Top2A to efficiently target and release the accumulated supercoils. These processes are essential to complete DNA replication prior to mitosis and therefore to ensure genome stability. Remarkably, we found that HeLa cells over-accumulate poorly confined negative supercoils beyond the processing capacity of cellular SMC5/6, which may exemplify the condition associated with genome instability of cancer cells.
TRPM8 channels control Golgi morphology through an AR-dependent induction of the Scd1 gene and modulation of unsaturated lipid content
Authors: Wehbi Mariam , Gouriou Yves , Borowiec Anne-sophie , Geoffray Juliette , Badawi Sally , Chouabe Christophe , Slomianny Christian , Gordienko Dmitri , Gonnot Fabrice , Dewailly Etienne , Delcourt Philippe , Ferrera René , Pais-de-Barros Jean-Paul , Kurdi Mazen , Héliot Laurent , Van Coppenolle Fabien , Lemonnier Loic , Prevarskaya Natalia , Bidaux Gabriel
Published: October 2024

Transient receptor potential melastatin 8 (TRPM8), the cold and menthol receptor is essential to thermosensation, although its roles in organs within the body are still unclear. Besides TRPM8, we previously cloned several isoforms, like 4TM-TRPM8, which can be expressed with or without TRPM8.

In this study, we characterize the human TRPM8(85) in ER membranes in the vicinity of Golgi apparatus (GA) and mitochondria in prostate epithelial cells. Silencing of TRPM8(85) induces lipid droplet accumulation, GA expansion and fragmentation associated with a drop in the vesicular trafficking to plasmalemma. Furthermore, lipidomic analysis reveals a strong shift in unsaturated fatty acids (UFAs), induced by TRPM8(85) silencing and to a lesser extent silencing of TRPM8. UFAs increase is caused by the induction of Δ9 stearoyl desaturase (Scd1) gene. Silencing SCD1 or palmitate incubation prevent GA expansion in TRPM8(85)-silenced cells. Finally, we demonstrated that TRPM8 regulates SCD1 via the androgen receptor.
Membrane-bound Guanylyl Cyclase COP5/HKR1 changes ciliary beat pattern and biases cell steering during chemotaxis inChlamydomonas reinhardtii
Authors: Strain Alexis , Kratzberg Nathan , Vu Dan , Miller Emmaline , Wakabayashi Ken-ichi , Melvin Adam , Kato Naohiro
Published: October 2024

This study investigates the control of ciliary beat patterns during ammonium chemotaxis in the model ciliate microalgaeChlamydomonas reinhardtii. Screening the chemotaxis response of mutant strains with ciliary defects revealed that a strain lacking CAV2, the alpha subunit of the voltage-gated Ca2+channel, is deficient in ammonium chemotaxis. CAV2 regulates the switching of the ciliary beat pattern from the asymmetric to the symmetric waveform. Strains lacking COP5/HKR1 (chlamyopsin 5/histidine kinase rhodopsin 1), a membrane-bound guanylyl cyclase, are also deficient in ammonium chemotaxis. Conversely, strains defective in phototaxis perform ammonium chemotaxis normally.

Cell motility analysis revealed wild-type cells reduce the incidences of switching the ciliary beat pattern from the asymmetric to symmetric waveform when swimming up the ammonium gradient. In contrast, the COP5/HKR1 disrupted strain does not bias ciliary beat pattern switching in the gradient. This finding reveals that a membrane-bound guanylyl cyclase plays a critical role inChlamydomonaschemotaxis signaling transduction, similarly to animal chemotaxis. On the other hand, ciliary beat pattern switching induces randomized directional changes, analogous to run-and-tumble chemotaxis of bacteria and archaea. This study reveals thatChlamydomonassignaling transduction is similar to the eukaryotic mechanism, yet the cellular locomotion follows the bacteria and archaea mechanism.
Farm exposure is associated with human breast milk immune profile and microbiome
Authors: Swaney Mary Hannah , Steidl Olivia Rae , Tackett Anastasia , Fye Samantha , Lee Kristine E. , Ong Irene M. , Bendixsen Casper , Spicer Gretchen , DeLine James , Gern James E , Lucey John , Seroogy Christine M. , Kalan Lindsay , Singh Anne Marie
Published: October 2024

Prenatal and early life farm exposure, and breastfeeding, are associated with protection from allergic diseases. We hypothesize that farm exposure influences the human breast milk microbiome and immune proteins. The immune protein profiles and microbial communities of 152 human breast milk samples were compared among three maternal farm exposure groups (traditional agrarian, farm, and non-farm) in rural Wisconsin to identify signatures associated with farm status and atopic disease. We found significant differences between farm groups for 23 immune proteins (p-adj<0.05), microbiome diversity (p=2.2E-05), and microbiome richness (p=8.0e-06). Traditional agrarian human breast milk had the highest immune protein levels and microbiome diversity and richness, followed by farm and non-farm human breast milk. Furthermore, Gram-positive bacterial species correlated with IL-23 mediated signaling events (p-adj<1.0E-05). These data suggest that increased farm exposures promotes human breast milk that is more microbially-diverse and rich in immune-associated proteins, ultimately influencing immune development in the infant.
Genome-wide analysis ofEnterococcus faecalisgenes that facilitate interspecies competition withLactobacillus crispatus
Authors: Lam Ling Ning , Savage Kathryn E. , Shakir Camille N. , Lemos José A.
Published: October 2024

Enterococci are opportunistic pathogens notorious for causing a variety of infections. While bothEnterococcus faecalisandLactobacillus crispatusare commensal residents of the vaginal tract, the molecular mechanisms that enableE. faecalisto outcompeteL. crispatus,and consequently cause vaginal infections remains unknown. To begin to address this, we need to gain a better understanding of the competitive interactions betweenE. faecalisandL. crispatus. Here, we show thatL. crispatuseradicatesE. faecalisin a contact-independent manner. Using transposon sequencing to identifyE. faecalisOG1RF transposon (Tn) mutants that are either under-represented or over-represented when co-cultured withL. crispatus, we found that Tn mutants with disruption in thedltABCDoperon, that encodes the biosynthetic pathway for D-alanylation of teichoic acids, andOG1RF_11697encoding for an uncharacterized hypothetical protein are more susceptible to killing byL. crispatus. Inversely, Tn mutants with disruption inldh1,that encodes for L-lactate dehydrogenase, are more resistant toL. crispatus killing. Using theGalleria mellonellainfection model, we show that co-injection ofL. crispatuswithE. faecalisOG1RF enhances larvae survival while thisL. crispatus-mediated protection was lost in larvae co-infected with eitherL. crispatusandE. faecalisΔldh1or Δldh1Δldh2strains. Last, using RNA sequencing to identifyE. faecalisgenes that are differently expressed in the presence ofL. crispatus, we found major changes in expression of genes associated with glycerophospholipid metabolism, central metabolism and general stress responses. The findings in this study provide insights on howE. faecalismitigate assaults byL. crispatus.

IMPORTANCE

Enterococcus faecalisis an opportunistic pathogen notorious for causing a multitude of infections. WhileE. faecalismust compete withLactobacillus crispatusto cause vaginal infections, howE. faecalisovercomesL. crispatuskilling remains unknown. We show thatL. crispatuseradicatesE. faecalistemporally in a contact-independent manner. Using high throughput molecular approaches, we identified genetic determinants that enableE. faecalisto compete withL. crispatus. This study represents an important first step for the identification of adaptive genetic traits required for enterococci to compete with lactobacilli.
Efficient epistasis inference via higher-order covariance matrix factorization
Authors: Shimagaki Kai S. , Barton John P.
Published: October 2024

Epistasis can profoundly influence evolutionary dynamics. Temporal genetic data, consisting of sequences sampled repeatedly from a population over time, provides a unique resource to understand how epistasis shapes evolution. However, detecting epistatic interactions from sequence data is technically challenging. Existing methods for identifying epistasis are computationally demanding, limiting their applicability to real-world data. Here, we present a novel computational method for inferring epistasis that significantly reduces computational costs without sacrificing accuracy. We validated our approach in simulations and applied it to study HIV-1 evolution over multiple years in a data set of 16 individuals. There we observed a strong excess of negative epistatic interactions between beneficial mutations, especially mutations involved in immune escape. Our method is general and could be used to characterize epistasis in other large data sets.
Direct and indirect selection in a proofreading polymerase
Authors: Husain Kabir , Sachdeva Vedant , Ravasio Riccardo , Peruzzo Michele , Liu Wanqiang , Good Benjamin H. , Murugan Arvind
Published: October 2024

The traits that affect evolvability are subject to indirect selection, as these traits affect the course of evolution over many generations rather than the direct replicative fitness of an individual. However, the evolution of evolvability-determining traits is often difficult to study because putative evolvability alleles often have confounding direct fitness effects of unknown origin and size. Here, we study theoretically and experimentally the evolution of mutation rates in proofreading polymerases with orthogonal control of direct and indirect selection. Mutagenic DNA polymerases enjoy a long-time fitness advantage by enhancing the rate of acquiring beneficial mutations. However, this is offset by a short-time fitness penalty, which we trace to a counterintuitive trade-off between mutation rates and activity in proofreading polymerases. Since these fitness effects act on different timescales, no one number characterizes the fitness of a mutator allele. We find unusual dynamic features in the resulting evolutionary dynamics, such as kinetic exclusion, selection by dynamic environments, and Rock-Paper-Scissors dynamics in the absence of ecology. Our work has implications for the evolution of mutation rates and more broadly, evolution in the context of an anti-correlation between mutation rates and short term fitness.
DIO-SPOTlight Transgenic Mouse to Functionally Monitor Protein Synthesis Regulated by the Integrated Stress Response
Authors: Oliver Matthew L. , Caffall Zachary F. , Eatman Callie B. , Faw Timothy D. , Calakos Nicole
Published: October 2024

The integrated stress response (ISR) is a core pathway for maintaining cellular proteostasis and a key regulator of translation in processes beyond the cellular response to stress. For example, the ISR regulates developmental axonogenesis, learning and memory, and synaptic plasticity in the brain. One barrier to uncovering ISR roles in health and disease is the challenge of monitoring its activity. The transient nature of regulatory phosphorylation events and lack of transgenic ISR reporter mouse lines make visually capturing the molecular hallmarks of ISR activation in specific cell types especially difficult. We recently developed the SPOTlight (SelectivePhospho-eIF2αOpen reading frameTracking light) reporter, which uniquely provides a readout of the functional state of protein synthesis initiation dynamics that are regulated by the ISR. Here, we report the generation of a transgenic mouse line with Cre-dependent expression of SPOTlight. This resource enables selective visualization of ISR-regulated functional activity across genetically defined cell populations body-wide. Using a pan-neuronal Cre line (Nestin-Cre), we demonstrate the reporter’s performance and applications for cell-specific discovery, live tissue assessments and quantitative comparisons across broad physical space. We also specifically investigated the extent to which the property of steady-state basal ISR activation, recently described in dorsal striatal cholinergic interneurons, extends to other classes of cholinergic neurons and provide a CNS-wide atlas of SPOTlight activity in these cells. The DIO-SPOTlight mouse enables a wide range of studies in all organ systems and functional monitoring opportunities not previously accessible.
Improving the annotation of amino acid biosynthesis pathways: GapMind 2024
Authors: Price Morgan N. , Shiver Anthony L. , Day Leslie A. , Torres Marta , Lesea Hira P. , Owens Trenton K. , Deutschbauer Adam M. , Arkin Adam P.
Published: October 2024

GapMind is an automated web-based tool for annotating amino acid biosynthesis pathways in bacterial and archaeal genomes. We updated GapMind to include recently identified enzymes, including new enzymes that we identified by using high-throughput genetics and comparative genomics. Across 206 prokaryotes that have high-quality genomes and are reported to grow in minimal media, the average number of unexplained missing steps or gaps dropped from 1.4 per genome to 0.8 per genome. The majority of the remaining gaps involve the gain or loss of phosphate groups.
Role of ribosomal protein bS1 in orthogonal mRNA start codon selection
Authors: Boyko Kristina V. , Bernstein Rebecca A. , Kim Minji , Cate Jamie H. D.
Published: October 2024

In many bacteria, the location of the mRNA start codon is determined by a short ribosome binding site sequence that base pairs with the 3′-end of 16S ribosomal RNA (rRNA) in the 30S subunit. Many groups have changed these short sequences, termed the Shine-Dalgarno (SD) sequence in the mRNA and the anti-Shine-Dalgarno (ASD) sequence in 16S rRNA, to create “orthogonal” ribosomes to enable the synthesis of orthogonal polymers in the presence of the endogenous translation machinery. However, orthogonal ribosomes are prone to SD-independent translation. Ribosomal protein bS1, which binds to the 30S ribosomal subunit, is thought to promote translation initiation by shuttling mRNA to the ribosome. Thus, a better understanding of how the SD and bS1 contribute to start codon selection could help efforts to improve the orthogonality of ribosomes. Here we engineered theEscherichia coliribosome to prevent binding of bS1 to the 30S subunit, to separate the activity of bS1 binding to the ribosome from the role of the mRNA SD sequence in start codon selection. We find that ribosomes lacking bS1 are slightly less active than wild-type ribosomesin vitro. Furthermore, orthogonal 30S subunits lacking bS1 do not have improved orthogonality. Our findings suggest that mRNA features outside the SD sequence and independent of bS1 binding to the ribosome likely contribute to start codon selection and the lack of orthogonality of present orthogonal ribosomes.
Features and signals in precocious citation impact: a meta-research study
Authors: Ioannidis John P.A.
Published: October 2024

Some scientists reach top citation impact in a very short time once they start publishing. The current analysis defined precocious citation impact as rising to become a top-cited scientist within t≤8 years after the first publication year. Ultra-precocious citation impact was defined similarly for t ≤5 years. Top-cited authors included those in the top-2% of a previously validated composite citation indicator across 174 subfields of science or in the top-100,000 authors of that composite citation indicator across all science based on Scopus. Annual data between 2017 and 2023 show a strong increase over time, with 469 precocious and 66 ultra-precocious citation impact Scopus author IDs in 2023. In-depth assessment of validated ultra-precocious scientists in 2023, showed significantly higher frequency of less developed country affiliation (71%), clustering in 4 high-risk subfields (Environmental Sciences, Energy, Artificial Intelligence & Image Processing, Mechanical Engineering & Transports) (64%), self-citations for their field above the 95thpercentile (31%), being top-cited only when self-citations were included (20%), citations to citing papers ratio for their field above the 95thpercentile (15%), extreme publishing behavior (7%), and extreme citation orchestration metric c/h2<2.45 (15%) compared with all top-cited authors (p<0.005 for all signals). The 17 ultra-precocious citation impact authors in the 2017-2020 top-cited lists who had retractions by October 2024 showed on average 4 of these 7 signal indicators at the time they entered the top-cited list. While some authors with precocious citation impact may be stellar scientists, others probably herald massive manipulative or fraudulent behaviors infiltrating the scientific literature.

Significance statement

Extreme performance may herald either extreme excellence or extreme inappropriate and outright fraudulent practices. Some authors reach the very top ranks in cumulative citation impact within only a few years, while even accomplished scientists take decades to reach these levels, if ever. A science-wide analysis of the authors with the most impressively precocious citation performance reveals that most of them come from less developed countries with limited resources, they heavily cluster in some scientific subfields, and they often have multiple signal indicators that may suggest problematic behavior. Some of these scientists are unquestionably excellent, while others may be manipulative or fraudulent. Evaluation of extreme cases allows science-wide views of the penetration of massive manipulative practices in scientific publication and citation.
EMC regulates cell membrane fluidity to facilitate biogenesis of membrane proteins
Authors: Berraquero Modesto , Tallada Víctor A. , Jimenez Juan
Published: October 2024

The EMC complex is a highly conserved transmembrane chaperone located in the endoplasmic reticulum (ER). This complex has been associated in humans with sterol homeostasis and a myriad of different cellular activities, making the mechanism of EMC functionality enigmatic. Using fission yeast, we demonstrate that EMC assists biogenesis of the sterol transfer protein Lam6/Ltc1 at the ER-Plasma membrane and ER-Mitochondria contact sites. Cells losing EMC function sequester unfolded Lam6/Ltc1 and other proteins at the mitochondrial matrix, driving to surplus ergosterol, cold-sensitive growth and mitochondrial disfunctions. Remarkably, inhibition of the ergosterol biosynthesis, but also fluidization of cell membranes to counteract its rigidizing effects, reduce the ER-unfolded protein response and rescue growth and mitochondrial defects in EMC-deficient cells. These results indicate that EMC-assisted biogenesis of Lam6/Ltc1 provides, through ergosterol homeostasis, optimal membrane fluidity to facilitate biogenesis of other ER-membrane proteins.

HIGHLIGHTS

- Lam6/Ltc1 requires EMC for localization at ER-Plasma membrane and ER-Mitochondria contact sites.

- EMC-driven biogenesis of Lam6/Ltc1 is involved in membrane fluidity homeostasis.

- EMC-deficient cells accumulate misfolded proteins in the mitochondrial matrix.

- Cell membrane fluidization alleviates the ER-misfolded proteins response and rescues growth and mitochondrial defects of EMC-deficient cells.

Graphical Abstract

Schematic representation of EMC-membrane fluidity homeostasis connecting protein folding and mitochondrial activity.
Structural organization of p62 filaments and the cellular ultrastructure of calcium-rich p62-enwrapped lipid droplet cargo
Authors: Berkamp Sabrina , jungbluth Lisa , Katranidis Alexandros , Mostafavi Siavash , Korculanin Olivera , Lu Peng-Han , Sharma Lokesh , Thukral Lipi , Fitter Jörg , Dunin-Borkowski Rafal E. , Sachse Carsten
Published: October 2024

The selective autophagy receptor p62/SQSTM1 (from hereon p62) is known to form higher-order filaments in vitro and to undergo liquid-liquid phase separation when mixed with poly-ubiquitin. We determined the full-length cryo-EM structure of p62 and elucidated a structured double helical filament scaffold composed of the PB1-domain associated with the flexible C-terminal part residing in the lumen and the solvent-accessible major groove. At different pH values and upon binding to soluble LC3, LC3-conjugated membranes and poly-ubiquitin, we observed p62 filament re-arrangements in the form of structural unwinding, disassembly, lateral association and bundling, respectively. In the cellular environment, under conditions of ATG5 knockdown leading to stalled autophagy, we imaged high-contrast layers consisting of p62 oligomers enwrapping lipid droplets by cryogenic electron tomography in cellulo, which we identified as calcium phosphate by compositional spectroscopy analysis. Together, we visualized the cellular ultrastructure of p62 oligomers with high calcium content as a potential intermediate step of autophagy initiation.
Seamless, rapid, and accurate analyses of outbreak genomic data using splitk-mer analysis
Authors: Derelle Romain , von Wachsmann Johanna , Mäklin Tommi , Hellewell Joel , Russell Timothy , Lalvani Ajit , Chindelevitch Leonid , Croucher Nicholas J. , Harris Simon R. , Lees John A.
Published: October 2024

Sequence variation observed in populations of pathogens can be used for important public health and evolutionary genomic analyses, especially outbreak analysis and transmission reconstruction. Identifying this variation is typically achieved by aligning sequence reads to a reference genome, but this approach is susceptible to reference biases and requires careful filtering of called genotypes. There is a need for tools that can process this growing volume of bacterial genome data, providing rapid results, but that remain simple so they can be used without highly trained bioinformaticians, expensive data analysis, and long-term storage and processing of large files. Here we describe splitk-mer analysis (SKA2), a method that supports both reference-free and reference-based mapping to quickly and accurately genotype populations of bacteria using sequencing reads or genome assemblies. SKA2 is highly accurate for closely related samples, and in outbreak simulations, we show superior variant recall compared with reference-based methods, with no false positives. SKA2 can also accurately map variants to a reference and be used with recombination detection methods to rapidly reconstruct vertical evolutionary history. SKA2 is many times faster than comparable methods and can be used to add new genomes to an existing call set, allowing sequential use without the need to reanalyze entire collections. With an inherent absence of reference bias, high accuracy, and a robust implementation, SKA2 has the potential to become the tool of choice for genotyping bacteria. SKA2 is implemented in Rust and is freely available as open-source software.
Phage Display Selection of Antibody Libraries: Panning Procedures
Authors: Peng Haiyong , Rader Christoph
Published: October 2024

The mining of naive, immune, and synthetic antibody repertoires by phage display has been widely applied to the de novo generation and in vitro evolution of monoclonal antibodies from multiple species. Once built, phage display antibody libraries can be selected by a variety of different strategies tailored toward the desired antigen binding properties. Here, we describe the selection of antibody libraries generated in a phage display vector of the pComb3 phagemid family. The approach includes panning procedures for immobilized antigens, biotinylated antigens in solution, and cell surface antigens. Although the typical format of these antibody libraries is human Fab or chimeric nonhuman/human Fab, the basic selection strategies provided in this protocol are compatible with a variety of formats.
Efficient, high-fidelity single-photon switch based on waveguide-coupled cavities
Authors: Duda Mateusz , Brunswick Luke , Wilson Luke R. , Kok Pieter
Published: October 2024

We demonstrate theoretically that waveguide-coupled cavities with embedded two-level emitters can act as a highly efficient, high-fidelity single-photon switch. The photon switch is an optical router triggered by a classical signal—the propagation direction of single input photons in the waveguide is controlled by changing the emitter-cavity coupling parameters , for example, using applied fields. The switch reflects photons in the weak emitter-cavity coupling regime and transmits photons in the strong coupling regime. By calculating transmission and reflection spectra using the input-output formalism of quantum optics and the transfer matrix approach, we obtain the fidelity and efficiency of the switch with a single-photon input in both regimes. We find that a single waveguide-coupled cavity can route input photon wave packets with near-unity efficiency and fidelity if the wave packet width is smaller than the cavity mode linewidth. We also find that using multiple waveguide-coupled cavities increases the switching bandwidth, allowing wider wave packets to be routed with high efficiency and fidelity. For example, an array of three waveguide-coupled cavities can reflect an input Gaussian wave packet with a full width at half-maximum of 1 nm (corresponding to a few-picosecond pulse) with an efficiency Er=96.4% and a fidelity Fr=97.7%, or transmit the wave packet with an efficiency Et=99.7% and a fidelity Ft=99.8%. Such efficient, high-fidelity single-photon routing is essential for scalable photonic quantum technologies.

Published by the American Physical Society
2024
Monte Carlo simulation code for polarized inverse Compton scattering sources
Authors: Zhang Hongze , Chi Zhijun , Du Yingchao , Huang Wenhui , Tang Chuanxiang
Published: October 2024

Polarized x rays or gamma rays generated from inverse Compton scattering (ICS) sources are high-brightness, quasimonochromatic, and polarization-tunable and are widely applied in medical imaging, material science, and nuclear physics research. In this paper, to simulate ICS between electron beams and polarized laser beams, a Monte Carlo simulation code has been developed and implemented based on the 4 toolkit. This code considers the polarization as well as the bandwidth of incident laser beams. The code is benchmarked by comparing its simulation results with those from the well-known Monte Carlo tool called and experimental results. The comparisons show that this code accurately reproduces the scattered photons, demonstrating its potential for various ICS-based applications.

Published by the American Physical Society
2024
Complex-valued scatter compensation in nonlinear microscopy
Authors: Sohmen Maximilian , Borozdova Maria , Ritsch-Marte Monika , Jesacher Alexander
Published: October 2024

Nonlinear, i.e., multiphoton microscopy is a powerful technique for imaging deep into biological tissues. Its penetration depth can be increased further using adaptive optics. In this work, we present a fast, feedback-based adaptive-optics algorithm, termed C-DASH, for multiphoton imaging through multiple-scattering media. C-DASH utilizes complex-valued light shaping (i.e., joint shaping of amplitude and phase), which offers several advantages over phase-only techniques: it converges faster, it delivers higher image quality enhancement, it shows a robust performance largely insensitive to the axial position of the correction plane, and it has a higher ability to cope with, on the one hand, scattering media that vary over time and, on the other hand, scattering media that are partially absorbing. Furthermore, our method is practically self-aligning. We also present a simple way to implement C-DASH using a single reflection off a phase-only spatial light modulator. We provide a thorough characterization of our method, presenting results of numerical simulations as well as two-photon excited fluorescence imaging experiments.

Published by the American Physical Society
2024
First radial excitations of baryons in a contact interaction: Mass spectrum
Authors: Gutiérrez-Guerrero L. X. , Raya Alfredo , Albino L. , Hernández-Pinto R. J.
Published: October 2024

We compute masses of twenty positive parity first radial excitations of spin-1/2 and spin-3/2 baryons composed of u, d, s, c, and b quarks in a quark-diquark picture within a contact interaction model. These excitations comprise of two elements; one characterized by a zero in the Faddeev amplitude, representing a radial excitation of the quark-diquark system and the other marked by a zero in the diquark’s Bethe-Salpeter amplitude, corresponding to an intrinsic excitation of the diquark correlation. Wherever possible, we compare our results with other models and/or experiment. We verify that the masses obtained through our model conform to the spacing rules for all the baryons studied, whether light or heavy and whether of spin-1/2 or spin-3/2. The computed masses do not just offer a guide to the future experimental searches but also compare well with the existing candidates for the possible radial excitations of some heavy baryons.

Published by the American Physical Society
2024
Dynamical tidal Love numbers of Kerr-like compact objects
Authors: Chakraborty Sumanta , Maggio Elisa , Silvestrini Michela , Pani Paolo
Published: October 2024

We develop a framework to compute the tidal response of a Kerr-like compact object in terms of its reflectivity, compactness, and spin, both in the static and the frequency-dependent case. Here we focus on the low-frequency regime, which can be solved fully analytically. We highlight some remarkable novel features, in particular, the following: (i) Even in the zero-frequency limit, the tidal Love numbers (TLNs) depend on the linear-in-frequency dependence of the object’s reflectivity in a nontrivial way. (ii) Intriguingly, although the static limit of the (phenomenologically more interesting) frequency-dependent TLNs is continuous, it differs from the strictly static TLNs for compact objects other than black holes. This shows that earlier findings regarding the static TLNs of ultracompact objects correspond to a measure-zero region in the parameter space, though the logarithmic behavior of the TLNs in the black hole limit is retained. (iii) In the nonrotating case, the TLNs in the zero-frequency limit (just like for a black hole), except when the reflectivity is R=1+O(Mω), in which case they vanish with a model-dependent scaling, which is generically logarithmic, in the black-hole limit. The TLNs initially grow with frequency, for any nonzero reflectivity, and then display oscillations and resonances tied up with the quasinormal modes of the object. (iv) For rotating compact objects, the TLNs decrease when the reflectivity decreases or the rotation parameter increases. Our results lay the theoretical groundwork to develop model-independent tests of the nature of compact objects using tidal effects in gravitational-wave signals.

Published by the American Physical Society
2024
Atomic structure of different surface terminations of polycrystalline ZnPd
Authors: Lowe M. , Al-Mahboob A. , Ivarsson D. , Armbrüster M. , Ardini J. , Held G. , Maccherozzi F. , Bayer A. , Fournée V. , Ledieu J. , Sadowski J. T. , McGrath R. , Sharma H. R.
Published: October 2024

The intermetallic compound ZnPd has been found to have desirable characteristics as a catalyst for the steam reforming of methanol. The understanding of the surface structure of ZnPd is important to optimize its catalytic behavior. However, due to the lack of bulk single-crystal samples and the complexity of characterizing surface properties in the available polycrystalline samples using common experimental techniques, all previous surface science studies of this compound have been performed on surface alloy samples formed through thin-film deposition. In this study, we present findings on the chemical and atomic structure of the surfaces of bulk polycrystalline ZnPd studied by a variety of complementary experimental techniques, including scanning tunneling microscopy (STM), x-ray photoelectron spectroscopy (XPS), low energy electron microscopy (LEEM), photoemission electron microscopy (PEEM), and microspot low-energy electron diffraction (μ-LEED). These experimental techniques, combined with density functional theory (DFT)-based thermodynamic calculations of surface free energy and detachment kinetics at the step edges, confirm that surfaces terminated by atomic layers composed of both Zn and Pd atoms are more stable than those terminated by only Zn or Pd layers. DFT calculations also demonstrate that the primary contribution to the tunneling current arises from Pd atoms, in agreement with the STM results. The formation of intermetallics at surfaces may contribute to the superior catalyst properties of ZnPd over Zn or Pd elemental counterparts.

Published by the American Physical Society
2024
Ultrafast spectroscopy of coherent phonons across the pressure driven insulator to metal phase transition in
V2O3
Authors: Gauthier Thomas , Godin Nicolas , Privault Gaël , Bertoni Roman , Janod Etienne , Babich Danylo , Corraze Benoit , Tranchant Julien , Cario Laurent
Published: October 2024

Nowadays, materials science is moving towards the understanding and control of materials in nonequilibrium states by making use of perturbative techniques to investigate their dynamical responses. From this perspective, the use of ultrashort light pulses seems to be a relevant approach as it can selectively address different degrees of freedom in solid-state systems and more particularly electrons. Such a method can help to decipher the physical phenomena arising from electronic correlations and complements a more conventional methodology where the phase diagrams of materials are investigated at thermodynamical equilibrium. Here, we combine femtosecond optical spectroscopy and a high-pressure setup to monitor the ultrafast out-of-equilibrium photo response of a V2O3 thin film across the pressure driven insulator-to-metal transition. The experimental results demonstrate the possibility to use the spectroscopy of coherent phonons as a thermodynamical phase marker in V2O3 thin films. In addition, the frequency behavior of the ultrafast coherent phonon mode (A1g character) seems to reflect the manifestation of a strong coupling between the lattice and electronic degrees of freedom near first-order transition lines with a pronounced drop in frequency around the critical pressure.

Published by the American Physical Society
2024
Observing Quantum Measurement Collapse as a Learnability Phase Transition
Authors: Agrawal Utkarsh , Lopez-Piqueres Javier , Vasseur Romain , Gopalakrishnan Sarang , Potter Andrew C.
Published: October 2024

During a quantum measurement, superpositions of states with different observable properties probabilistically collapse into one with a sharp value of the measured observable. In macroscopic quantum systems, this collapse arises via a continuous measurement-induced phase transition (MIPT) at a critical value of the strength of interaction with the measurement apparatus. MIPTs lie outside established paradigms for equilibrium or nonequilibrium critical phenomena and delineate distinct, stable dynamical and computational phases of matter. Quantum computers enable programmable simulation of the interaction of a measurement apparatus with a dynamical quantum system, to explore MIPT phenomena over a range of system sizes while retaining quantum coherence. Yet, existing experimental protocols rely on fundamentally nonscalable postselection techniques or direct classical simulation of quantum circuits. Here, we report the scalable observation of finite-size scaling evidence for an observable-sharpening MIPT in monitored quantum circuits in a chain of Yb+171 ions in Quantinuum’s H1-1 trapped-ion quantum processor. By leveraging an equivalent description as a statistical physics problem, we implement scalable classical algorithms to infer the value of the measured observable from a single experimental shot. This technique enables a truly scalable protocol to observe observable-sharpening MIPTs in generic classes of circuits that cannot be directly classically simulated and also provides enhanced means to detect and suppress errors in the quantum simulation.

Published by the American Physical Society
2024
In situ/operando method for energy stability measurement of synchrotron radiation
Authors: Si Shangyu , Li Zhongliang , Xue Lian , Li Ke
Published: October 2024

A novel in situ/operando method is introduced to measure the photon beam stability of synchrotron radiation based on orthogonal diffraction imaging of a Laue crystal/analyzer, which can decouple the energy/wavelength and Bragg angle of the photon beam using the dispersion effect in the diffraction process. The method was used to measure the energy jitter and drift of the photon beam on BL09B and BL16U at the Shanghai Synchrotron Radiation Facility. The experimental results show that this method can provide a fast way to measure the beam stability of different light sources including bending magnet and undulator with meV-level energy resolution and ms-level time response.
Roodmus: a toolkit for benchmarking heterogeneous electron cryo-microscopy reconstructions
Authors: Joosten Maarten , Greer Joel , Parkhurst James , Burnley Tom , Jakobi Arjen J.
Published: October 2024

Conformational heterogeneity of biological macromolecules is a challenge in single-particle averaging (SPA). Current standard practice is to employ classification and filtering methods that may allow a discrete number of conformational states to be reconstructed. However, the conformation space accessible to these molecules is continuous and, therefore, explored incompletely by a small number of discrete classes. Recently developed heterogeneous reconstruction algorithms (HRAs) to analyse continuous heterogeneity rely on machine-learning methods that employ low-dimensional latent space representations. The non-linear nature of many of these methods poses a challenge to their validation and interpretation and to identifying functionally relevant conformational trajectories. These methods would benefit from in-depth benchmarking using high-quality synthetic data and concomitant ground truth information. We present a framework for the simulation and subsequent analysis with respect to the ground truth of cryo-EM micrographs containing particles whose conformational heterogeneity is sourced from molecular dynamics simulations. These synthetic data can be processed as if they were experimental data, allowing aspects of standard SPA workflows as well as heterogeneous reconstruction methods to be compared with known ground truth using available utilities. The simulation and analysis of several such datasets are demonstrated and an initial investigation into HRAs is presented.
Synthesis and structural study of the partially disordered complex hexagonal phase δ1-MnZn9.7
Authors: Mondal Amit , Pan Rahul , Kuila Sandip Kumar , Dey Riju , Jana Partha Pratim
Published: October 2024

A detailed structural analysis of the Zn-rich δ1-MnZn9.7 phase using single-crystal X-ray diffraction is presented. The δ1 phase has been synthesized by the high-temperature synthetic route. The structure crystallizes in space group P63/mmc (Pearson symbol hP556) with unit-cell parameters: a = b = 12.9051 (2) Å and c = 57.640 (1) Å. The 556 atoms are distributed over 52 Wyckoff positions in the hexagonal unit cell: seven ordered Mn sites, 37 ordered Zn sites and eight positionally disordered Zn sites. The structure predominantly consists of Frank–Kasper polyhedra (endohedral icosahedra Zn12 and icosioctahedron Zn16) and four distinct types of glue Zn atoms. The structure comprises a 127-atom supercluster (Mn13Zn114), a 38-atom extended Pearce cluster (Mn3Zn35), a 46-atom L-tetrahedron (Mn4Zn42), a Friauf polyhedron (Zn17), a disordered icosahedral cluster (MnZn12) and four glue Zn atoms. Positionally disordered Zn sites around an Mn site can be visualized as the superimposition of three differently oriented Zn12 icosahedra.
From `crystallographic accuracy' to `thermodynamic accuracy': a redetermination of the crystal structure of calcium atorvastatin trihydrate (Lipitor®)
Authors: van de Streek Jacco , Firaha Dzmitry , Kaduk James A. , Blanton Thomas N.
Published: October 2024

With ever-improving quantum-mechanical computational methods, the accuracy requirements for experimental crystal structures increase. The crystal structure of calcium atorvastatin trihydrate, which has 56 degrees of freedom when determined with a real-space algorithm, was determined from powder diffraction data by Hodge et al. [Powder Diffr. (2020), 35, 136–143]. The crystal structure was a good fit to the experimental data, indicating that the electron density had been captured essentially correctly, but two independent quantum-mechanical calculations disagreed with the experimental structure and with each other. Using the same experimental data, the crystal structure was redetermined from scratch and it was shown that it can be reproduced within a root-mean-square Cartesian displacement of 0.1 Å by two independent quantum-mechanical calculations. The consequences for the calculated energies and solubilities are described.
Innovation capabilities and international competitiveness of agro-processing firms in Uganda
Authors: Ahimbisibwe Godwin Mwesigye , Ecel Aaron , Nuwagaba Dennis , Nakigudde Racheal , Mpiriirwe Rinah Faith , Kiplangat Leonard
Published: October 2024

Purpose

This paper aims to contribute to the understanding of the relationship between the different innovation capabilities and the international competitiveness of agro-processing firms in Uganda.

Design/methodology/approach

This study adopted a cross-sectional research design. Data were collected through a questionnaire survey of 125 firms exporting agro-processed products that are members of the Uganda Export Promotions Board (UEPB). Data was analyzed using the Statistical Package for Social Scientists (SPSS).

Findings

The study established that product innovation capabilities and organizational innovation capabilities are positively related to the international competitiveness of agro-processing firms in Uganda while process innovation capabilities and marketing innovation capabilities are not.

Research limitations/implications

A structured questionnaire was used to solicit responses and no follow-up interviews were conducted to inform the reasons behind the respondents’ responses. Nevertheless, the study reveals that agro-processing firms in Uganda should concentrate on building product and organizational innovation capabilities if they are to compete effectively in international markets.

Originality/value

To the authors’ knowledge, this is the first study to investigate the relationship between the four forms of innovation capabilities (product, process, marketing and organizational) and international competitiveness particularly among agro-processing firms from an African country.
Estimation on compressive strength of recycled aggregate self-compacting concrete using interpretable machine learning-based models
Authors: Yang Suhang , Chen Tangrui , Xu Zhifeng
Published: October 2024

Purpose

Recycled aggregate self-compacting concrete (RASCC) has the potential for sustainable resource utilization and has been widely applied. Predicting the compressive strength (CS) of RASCC is challenging due to its complex composite nature and nonlinear behavior.

Design/methodology/approach

This study comprehensively evaluated commonly used machine learning (ML) techniques, including artificial neural networks (ANN), random trees (RT), bagging and random forests (RF) for predicting the CS of RASCC. The results indicate that RF and ANN models typically have advantages with higher R2 values, lower root mean square error (RMSE), mean square error (MSE) and mean absolute error (MAE) values.

Findings

The combination of ML and Shapley additive explanation (SHAP) interpretable algorithms provides physical rationality, allowing engineers to adjust the proportion based on parameter analysis to predict and design RASCC. The sensitivity analysis of the ML model indicates that ANN’s interpretation ability is weaker than tree-based algorithms (RT, BG and RF). ML regression technology has high accuracy, good interpretability and great potential for predicting the CS of RASCC.

Originality/value

ML regression technology has high accuracy, good interpretability and great potential for predicting the CS of RASCC.