bluuebunny/crossref_metadata_2025 huggingface dataset:
Synthesis of ionizable lipopolymers using split-Ugi reaction for pulmonary delivery of various size RNAs and gene editing
Authors: Vlasova K. Yu. , Kerr A. , Pennock N.D. , Jozic A. , Sahel D.K. , Gautam M. , Murthy N.T.V. , Roberts A. , Ali M.W. , MacDonald K.D. , Walker J. , Luxenhofer R. , Sahay G.
Published: June 2024

We present an efficient approach for synthesizing cationic poly(ethylene imine) derivatives using the multicomponent split-Ugi reaction to rapidly create a library of complex functional ionizable lipopolymers. We synthesized a diverse library of 155 polymers, formulated them into polyplexes to establish structure-activity relationships crucial for endosomal escape and efficient transfection. After discovering a lead structure, lipopolymer-lipid hybrid nanoparticles are introduced to preferentially deliver to and elicit effective mRNA transfection in lung endothelium and immune cells, including T cells with lowin vivotoxicity. The lipopolymer-lipid hybrid nanoparticles showed 300-fold improvement in systemic mRNA delivery to the lung compared toin vivo-JetPEI®. Lipopolymer-lipid hybrid nanoparticles demonstrated efficient delivery of mRNA-based therapeutics for treatment of two different disease models. Lewis Lung cancer progression was significantly delayed after treatment with loaded IL-12 mRNA in U155@lipids after repeated i.v. administration. Systemic delivery of human CFTR (hCFTR) mRNA resulted in production of functional form of CFTR protein in the lungs. The functionality of hCFTR protein was confirmed by restoration of CFTR- mediated chloride secretion in conductive airway epithelia in CFTR knockout mice after nasal instillation of hCFTR mRNA loaded U155@lipids. We further showed that, U155@lipids nanoparticles can deliver complex CRISPR-Cas9 based RNA cargo to the lung, achieving 5.6 ± 2.4 % gene editing in lung tissue. Moreover, we demonstrated successful PD-1 gene knockout of T cellsin vivo. Our results highlight a versatile delivery platform for systemic delivering of mRNA of various sizes for gene therapy for a variety of therapeutics.
Bridging health registry data acquisition and real-time data analytics
Authors: Schmidt Johannes , Arjune Sita , Böhm Volker , Müller Roman-Ulrich , Antczak Philipp
Published: June 2024

The number of clinical studies and associated research has increased significantly in the last few years. Particularly in rare diseases, an increased effort has been made to integrate, analyse, and develop new knowledge to improve patient stratification and wellbeing. Clinical databases, including digital medical records, hold significant amount of information that can help understand the impact and progression of diseases. Combining and integrating this data however, has provided a challenge for data scientists due to the complex structures of digital medical records and the lack of site wide standardisation of data entry. To address these challenges we present a python backed tool, Meda, which aims to collect data from different sources and combines these in a unified database structure for near real-time monitoring of clinical data. Together with an R shiny interface we can provide a near complete platform for real-time analysis and visualization.
Pre-stimulus beta power mediates explicit and implicit perceptual biases in distinct cortical areas
Authors: Forster Carina , Stephani Tilman , Grund Martin , Panagoulas Eleni , Al Esra , Hofmann Simon M. , Nikulin Vadim V. , Villringer Arno
Published: June 2024

Perception is biased by expectations and previous actions. Pre-stimulus brain oscillations are a potential candidate for implementing biases in the brain. In two EEG studies on somatosensory near-threshold detection, we investigated the pre-stimulus neural correlates of an (implicit) previous choice bias and an explicit bias. The explicit bias was introduced by informing participants about stimulus probability on a single-trial level (volatile context) or block-wise (stable context). Behavioural analysis confirmed adjustments in the decision criterion and confidence ratings according to the cued probabilities and choice history biases. Pre-stimulus beta power with distinct sources in sensory and higher-order cortical areas predicted explicit and implicit biases, respectively, on a subject level and partially mediated the impact of previous choice and stimulus probability on the detection response. We suggest pre-stimulus beta oscillations in distinct brain areas as a neural correlate of explicit and implicit biases in somatosensory perception.
Phollow: Visualizing Gut Bacteriophage Transmission within Microbial Communities and Living Animals
Authors: Ortiz de Ora Lizett , Wiles Elizabeth T , Zünd Mirjam , Bañuelos Maria S , Haro-Ramirez Nancy , Suder Diana S , Ujagar Naveena , Angulo Julio Ayala , Trinh Calvin , Knitter Courtney , Gonen Shane , Nicholas Dequina A , Wiles Travis J
Published: June 2024

Bacterial viruses (known as “phages”) shape the ecology and evolution of microbial communities, making them promising targets for microbiome engineering. However, knowledge of phage biology is constrained because it remains difficult to study phage transmission dynamics within multi-member communities and living animal hosts. We therefore created “Phollow”: a live imaging-based approach for tracking phage replication and spread in situ with single-virion resolution. Combining Phollow with optically transparent zebrafish enabled us to directly visualize phage outbreaks within the vertebrate gut. We observed that virions can be rapidly taken up by intestinal tissues, including by enteroendocrine cells, and quickly disseminate to extraintestinal sites, including the liver and brain. Moreover, antibiotics trigger waves of interbacterial transmission leading to sudden shifts in spatial organization and composition of defined gut communities. Phollow ultimately empowers multiscale investigations connecting phage transmission to transkingdom interactions that have the potential to open new avenues for viral-based microbiome therapies.
Spatio-temporal learning in a mass-recruiting leaf-cutting ant (Acromyrmex subterraneus)
Authors: Ferreira Fernanda Tiemi Nakashima , Constantino Pedro Brisola , de Toledo Marcelo Arruda Fiuza , Helene André Frazão
Published: June 2024

The ability to anticipate periodically available resources is observed in several animals and improves performance in obtaining resources and adaptability. Spatio-temporal learning occurs when they associate the correct time and location of future events. We evaluate whether leaf-cutting antsAcromyrmex subterraneuscan anticipate the presence of sucrose and examine potential anticipatory effects. Five colonies were used in an experimental setup where, from a central tray, two trails in opposite directions gave access to either the sucrose or to nothing. For 21 consecutive days sucrose was offered at the same place and the same time. Cameras recorded the flow of individuals at 4 different phases: before feeding (10h00-11h00), pre-feeding (11h30–12h00), feeding (12h00-13h00) and after feeding (14h00-15h00). On the 22ndday sugar was not supplied. On the 21stday the ants were marked and the next day, observed. Our results shows that: (1) the ants responded positively to the stimulus presented by forming the foraging trail to collect sucrose; (2) before feeding there was no significant difference in ant flow between the trails, but after feeding, the ant flow was consistently higher on trail that led to sucrose, which we called a keep going behavior; (3) there was a progressive spatio-temporal learning, given that ants began to appear earlier in pre-feeding throghout the weeks; (4) on the 22ndday, the ants presented themselves 10 minutes in advance and remained in the correct place; (5) the marked ants indicated that even without any resource the empty place continued to be explored. The colonies were able to learn where and when to look for food. Due to the adjustment of the ants to the stimuli of the environment it was possible to prepare for the collection of sucrose and the success in foraging for the colony.

Summary statement

Leaf-cutting ants are capable of spatio-temporal learning and this process has relevance on mass foraging recruitment and overall social organization of the colony.
External morphometric and microscopic analysis of the reproductive system inin- vitroreared stingless bee queens,Heterotrigona itama, and their mating frequency
Authors: Wongsa Kanyanat , Duangphakdee Orawan , Poolprasert Pisit , Rattanawannee Atsalek
Published: June 2024

Abstract

Stingless bees, prevalent in tropical and subtropical regions, are a tribe of eusocial bees that are crucial pollinators for economic crops and native plants, producing honey and pollen. However, colony expansion is limited by a shortage of queens for new colonies. Therefore, mass artificial rearing of virgin queens could address this in commercially managed meliponiculture. Furthermore, the in vitro rearing of queen stingless bees can improve meliponiculture management and conservation efforts. Herein, we explored the efficacy of in vitro queen rearing forHeterotrigona itamaassessing the queen’s body size, reproductive organ size (ovary and spermatheca), acceptance rate into new, small colonies, and mating frequency.H. itamalarvae developed into queens when fed with 120 µL–150 µL of larval food, resulting inin vitroqueens having body sizes similar to those of naturally produced queens. Microscopic analysis revealed well-developed ovaries and spermathecae inin vitro-reared queens, unlike the smaller ovaries and the absence of spermathecae in the naturally produced workers. Acceptance ofin vitro-reared queens was independent of worker age, and mating frequency was low but not significantly different from naturally produced queens. These findings could enhance stingless beekeeping practices and conservation efforts for the native stingless bee species.
Description of new micro-colonial fungi speciesNeophaeococcomyces mojavensis,Coniosporium tulheliwenetii, and Taxawa tesnikishiicultured from biological soil crusts
Authors: Kurbessoian Tania , Ahmed Sarah A. , Quan Yu , de Hoog Sybren , Stajich Jason E.
Published: June 2024

Black yeasts and relatives comprise Micro-Colonial Fungi (MCFs) which are slow-growing stress-tolerant micro-eukaryotes that specialize in extreme environments. MCFs are paraphyletic and found in the OrdersChaetothyriales(Eurotiomycetes) andDothideales(Dothidiomycetes). We have isolated and described three new MCFs species from desert biological soil crusts (BSCs) collected from two arid land regions: Joshua Tree National Park (Mojave Desert) and UC Natural Reserve at Boyd Deep Canyon (confluence of Mojave and Sonoran Deserts). BSCs are composite assemblages of cyanobacteria, eukaryotic algae, fungi, lichens, and bryophytes embedded into the surface of desert soils, providing a protective buffer against the harsh desert environment. Our work focused on one type of desert BSC, the cyanolichen crust dominated byCollema sp.Using culture-dependent protocols, three MCFs were axenically isolated from their respective samples along with the extracted DNA. Their genomes were sequenced using Illumina and Nanopore, and finally assembled and annotated using hybrid assembly approaches and established bioinformatics pipelines to conduct final taxonomic phylogenetic analysis and placement. The three species described here are unique specimen from desert BSCs, here we introduce,Neophaeococcomyces mojavensis(Chaetothyriales),Cladosporium tulheliwenetii(Dothideales), andTaxawa tesnikishii(Dothideales).
Small nuclear RNAs enhance protein-free RNA-programmable base conversion on mammalian coding transcripts
Authors: Smargon Aaron A. , Pant Deepak , Glynne Sofia , Gomberg Trent A. , Yeo Gene W.
Published: June 2024

Endogenous U small nuclear RNAs (U snRNAs) form RNA-protein complexes responsible for eukaryotic processing of pre-mRNA into mature mRNA. Previous studies have demonstrated the utility of guide-programmable U snRNAs in targeted exon inclusion and exclusion. We investigated whether snRNAs can also enhance conversion of RNA bases over state-of-the-art RNA targeting technologies in human cells. When compared to adenosine deaminase acting on RNA (ADAR)-recruiting circular RNAs, we find that guided A>I snRNAs consistently increase adenosine-to-inosine editing efficiency for genes with higher exon counts, perturb substantially fewer genes in the transcriptome, and localize more persistently to the nucleus where ADAR is expressed. A>I snRNAs can also edit pre-mRNA 3′ splice sites to promote splicing changes. Finally, snRNA fusions to H/ACA box snoRNAs (U>Ψ snRNAs) increase targeted RNA pseudouridylation efficiency. Altogether, our results advance the protein-free RNA base conversion toolbox and enhance minimally invasive RNA targeting technologies to treat genetic diseases.
Clinical validation of an RSV neutralization assay and testing of cross-sectional sera pre- and post- RSV outbreaks from 2021-2023
Authors: Piliper Eli A. , Reed Jonathan , Greninger Alexander L.
Published: June 2024

Background

Respiratory syncytial virus (RSV) is a leading cause of acute respiratory infections and hospitalization in infants and the elderly. Newly approved vaccines and the prophylactic antibody nirsevimab have heightened interest in RSV immunologic surveillance, necessitating development of high-throughput assays assessing anti-RSV neutralizing activity.

Objectives

We validated an RSV focus-reduction neutralization test (RSV FRNT), a high-throughput, automation-ready neutralization assay using RSV strain A2. The assay was then used to investigate the immunity debt hypothesis for resurgent RSV outbreaks in the 2022-2023 season.

Study design

We evaluated precision, sensitivity, specificity, linearity, and accuracy of RSV FRNT using reference sera, contrived specimens, and clinical remnant specimens. RSV neutralizing activity of remnant serum specimens, sampled for HSV-1/2 antibody testing during and after the COVID-19 pandemic (February and September 2022 & 2023), was measured and correlated with concurrent trends in RSV prevalence.

Results

RSV FRNT was shown to be accurate, generating reference serum neutralizing titers within 2-fold of established assays, with a linear analytical measurement range between 20 to 4,860 ND50 and ND80 units. Neutralizing activity measured with the assay was positively correlated with antibody titer determined via indirect ELISA (ρ = 1.0, p = 0.0014). Among individuals sampled within 3 months of RSV PCR test, RSV positives had a 9.14-fold higher geometric mean neutralizing titer (GMT) relative to RSV PCR negatives (p = 0.09). There was no difference in geometric mean anti-RSV neutralizing titers between sera sampled pre- and post-2023 RSV outbreak (p = 0.93).

Conclusions

We validated a high-throughput assay for assessing anti-RSV neutralizing activity and found no significant difference in neutralizing titers between pre- and post-pandemic outbreak specimens.

Highlights

We report the full clinical validation of an RSV neutralization assay

No evidence of immune debt found in Washington State RSV 2022-2023 outbreak

Our assay offers high throughput testing applicable to vaccine/drug studies
Acetylation of the yeast Hsp40 chaperone protein Ydj1 fine-tunes proteostasis and translational fidelity
Authors: Omkar Siddhi , Shrader Courtney , Hoskins Joel R. , Kline Jake T. , Mitchem Megan M. ,   Nitika, Fornelli Luca , Wickner Sue , Truman Andrew W.
Published: June 2024

Proteostasis, the maintenance of cellular protein balance, is essential for cell viability and is highly conserved across all organisms. Newly synthesized proteins, or “clients,” undergo sequential processing by Hsp40, Hsp70, and Hsp90 chaperones to achieve proper folding and functionality. Despite extensive characterization of post-translational modifications (PTMs) on Hsp70 and Hsp90, the modifications on Hsp40 remain less understood. This study aims to elucidate the role of lysine acetylation on the yeast Hsp40, Ydj1. By mutating acetylation sites on Ydj1’s J-domain to either abolish or mimic constitutive acetylation, we observed that preventing acetylation had no noticeable phenotypic impact, whereas acetyl-mimic mutants exhibited various defects indicative of impaired Ydj1 function. Proteomic analysis revealed several Ydj1 interactions affected by J-domain acetylation, notably with proteins involved in translation. Further investigation uncovered a novel role for Ydj1 acetylation in stabilizing ribosomal subunits and ensuring translational fidelity. Our data suggest that acetylation may facilitate the transfer of Ydj1 between Ssa1 and Hsp82. Collectively, this work highlights the critical role of Ydj1 acetylation in proteostasis and translational fidelity.

Author Summary

Cells require a suite of chaperone and co-chaperone proteins to maintain a healthy balance of functional proteins. A large number of modifications on chaperone and co-chaperone proteins have been identified, but their functional importance has not been fully explored. In this study, we identify acetylation sites on the yeast co-chaperone Ydj1 that impact its interactions with major chaperones and client proteins including those involved in protein synthesis. This work sheds light on how modifications on co-chaperones can also play an important role in the health of the proteome.
Di-Gluebodies as covalently-rigidified, modular protein assemblies enable simultaneous determination of high-resolution, low-size, cryo-EM structures
Authors: Yi Gangshun , Mamalis Dimitrios , Ye Mingda , Carrique Loic , Fairhead Michael , Li Huanyu , Duerr Katharina L. , Zhang Peijun , Sauer David B. , von Delft Frank , Davis Benjamin G. , Gilbert Robert J. C.
Published: June 2024

Cryo-EM has become a routine structural biology method, yet elucidation of small proteins (<100 kDa) and increasing throughput remain challenging. Here, we describe covalently-dimerized engineered nanobodies, Di-Gluebodies, as novel and modular imaging scaffolds to address the challenges. They can simultaneously display two copies of the same protein or two distinct proteins, providing sufficient rigidity required by cryo-EM. We validate this method with multiple soluble and membrane targets, demonstrating that this provides a flexible and scalable platform for expanded protein structure determination.
Single-Cell Phenotyping of Extracellular Electron Transfer via Microdroplet Encapsulation
Authors: Partipilo Gina , Bowman Emily K. , Palmer Emma J. , Gao Yang , Ridley Rodney S. , Alper Hal S. , Keitz Benjamin K.
Published: June 2024

Electroactive organisms contribute to metal cycling, pollutant removal, and other redox-driven environmental processes. Studying this phenomenon in high-throughput is challenging since extracellular reduction cannot easily be traced back to its cell of origin within a mixed population. Here, we describe the development of a microdroplet emulsion system to enrich EET-capable organisms. We validated our system using the model electroactive organismS. oneidensisand describe the tooling of a benchtop microfluidic system for oxygen-limited processes. We demonstrated enrichment of EET-capable phenotypes from a mixed wild-type and EET-knockout population. As a proof-of-concept application, bacteria were collected from iron sedimentation from Town Lake (Austin, TX) and subjected to microdroplet enrichment. We observed an increase in EET-capable organisms in the sorted population that was distinct when compared to a population enriched in a bulk culture more closely akin to traditional techniques for discovering EET-capable bacteria. Finally, two bacterial species,C. sakazakiiandV. fessusnot previously shown to be electroactive, were further cultured and characterized for their ability to reduce channel conductance in an organic electrochemical transistor (OECT) and to reduce soluble Fe(III). We characterized two bacterial species not previously shown to exhibit electrogenic behavior. Our results demonstrate the utility of a microdroplet emulsions for identifying putative EET-capable bacteria and how this technology can be leveraged in tandem with existing methods.
The reduction of nuptial gifts in sclerosomatid Opiliones coincides with increased behavioural sexual conflict
Authors: Brown Tyler A. , Marinko Emily , Burns Mercedes
Published: June 2024

Nuptial gifts serve to increase donor fitness through a variety of pathways. Some nuptial gifts deliver benefits similar to those of antagonistic male behaviours: functioning to secure additional copulations, increase sperm transfer or storage, or increase paternity share. These commonalities may result in evolutionary transitions between solicitous and coercive strategies, wherein behavioural sexual conflict could function to secure mates in lieu of nuptial gifts. In temperate leiobunine harvesters (Arachnida: Opiliones), nuptial gifts have been repeatedly lost, resulting in two primary mating syndromes: an ancestral, sacculate state in which males endogenously produce high-investment nuptial gifts and females lack pregenital barriers, and a derived, nonsacculate state in which females have pregenital barriers and males produce significantly reduced, low-investment nuptial gifts. In this study, we investigated whether behavioural sexual conflict compensates for reduced nuptial gifts in nonsacculate harvesters by comparing the intensity of pre-, peri-, and postcopulatory mating behaviour between the nonsacculate speciesLeiobunum vittatumandL. euserratipalpeand the sacculate speciesL. aldrichiandL. bracchiolum. We additionally sought to establish an automated behavioural analysis pipeline by developing analogues for metrics traditionally scored manually. Our results revealed significantly different, potentially coercive, behaviour in nonsacculate species, indicating that the loss and reduction of pre- and pericopulatory nuptial gifts may contribute to increased behavioural antagonism. Mating behaviour also differed significantly betweenL. vittatumandL. euserratipalpe, indicating there are multiple suites of potentially antagonistic behaviours. Together, these results suggest that multiple behavioural strategies may be effective substitutes for nuptial gifts in leiobunine Opiliones, although the mechanisms through which male fitness is increased requires further research.

Highlights

Temperate Opiliones have repeatedly evolved reduced nuptial gift investment

Reduced-gift (nonsacculate) species possess morphology indicative of antagonism

We tested if mating behaviour differed between nonsacculate and sacculate species

Nonsacculates displayed significantly higher behavioural antagonism than sacculates

Nonsacculate species differed in their suites of antagonistic behaviours
CRISPR adaptation inStreptococcus thermophiluscan be driven by phage environmental DNA
Authors: Croteau FR , Tran J , Hynes AP
Published: June 2024

The CRISPR-Cas system is a bacterial adaptative immune system which protects against infection by phages: viruses that infect bacteria. To develop immunity, bacteria integrate spacers — fragments of the invading nucleic acids — into their CRISPR array to serve as the basis for sequence-targeted DNA cleavage. However, upon infection, phages quickly take over the metabolism of the bacteria, leaving little time for the bacteria to acquire new spacers, transcribe them and use them to cut the invading DNA. To develop CRISPR immunity, bacteria must be safely exposed to phage DNA. Phage infection releases eDNA which could be involved in the development of CRISPR immunity. UsingS. thermophilusand phages 2972 and 858 as a model for CRISPR immunity, we show that eDNA is crucial to the development of optimal CRISPR immunity, as generation of phage-immune bacterial colonies decrease with eDNA digestion. Furthermore, it is phage eDNA specifically that impacts CRISPR immunity since its addition increases the generation of phage-immune colonies. We also show that the effect of eDNA is phage-specific, sequence specific and can even be traced to a region of the genome covering the early-expressed genes which differ between phages 2972 and 858. However, we also show that eDNA is not used as a source of genetic information for spacer acquisition. This suggests that the effect of eDNA involves a new mechanism of phage resistance. Moreover, the effect of eDNA is highly dependent on environmental conditions as variation in media suppliers are sufficient to interfere with this effect. These results link environmental conditions, specifically eDNA, to the CRISPR-Cas system, providing a better understanding of the context of the emergence of CRISPR immunity and could inform our understanding of the mechanisms through which bacteria detect the presence of phages before infection.
Human cytomegalovirus induces neuronal gene expression for viral maturation
Authors: Kelnhofer-Millevolte Laurel E , Smith Julian R , Nguyen Daniel H , Wilson Lea S , Lewis Hannah C , Arnold Edward A , Brinkley Mia R , Geballe Adam P , Ramachandran Srinivas , Avgousti Daphne C
Published: June 2024

Viral invasion of the host cell causes some of the most dramatic changes in biology. Human cytomegalovirus (HCMV) extensively remodels host cells, altering nuclear shape and generating a cytoplasmic viral-induced assembly compartment (vIAC). How these striking morphology changes take place in the context of host gene regulation is still emerging. Here, we discovered that histone variant macroH2A1 is essential for producing infectious progeny. Because virion maturation and cellular remodeling are closely linked processes, we investigated structural changes in the host cell upon HCMV infection. We discovered that macroH2A1 is necessary for HCMV-induced reorganization of the host nucleus, cytoskeleton, and endoplasmic reticulum. Furthermore, using RNA-seq we found that while all viral genes were highly expressed in the absence of macroH2A1, many HCMV-induced host genes were not. Remarkably, hundreds of these HCMV-induced macroH2A1-dependent host genes are associated with neuronal synapse formation and vesicle trafficking. Knock-down of these HCMV-induced neuronal genes during infection resulted in malformed vIACs and smaller plaques, establishing their importance to HCMV infection. Together, our findings demonstrate that HCMV manipulates host gene expression by hijacking a dormant neuronal secretory pathway for efficient virion maturation.
Modeling neurodegenerative and neurodevelopmental disorders in theDrosophilamushroom body
Authors: Stahl Aaron , Tomchik Seth M.
Published: June 2024

The common fruit flyDrosophila melanogasterprovides a powerful platform to investigate the genetic, molecular, cellular, and neural circuit mechanisms of behavior. Research in this model system has shed light on multiple aspects of brain physiology and behavior, from fundamental neuronal function to complex behaviors. A major anatomical region that modulates complex behaviors is the mushroom body (MB). The MB integrates multimodal sensory information and is involved in behaviors ranging from sensory processing/responses to learning and memory. Many genes that underlie brain disorders are conserved, from flies to humans, and studies inDrosophilahave contributed significantly to our understanding of the mechanisms of brain disorders. Genetic mutations that mimic human diseases—such as Fragile X syndrome, neurofibromatosis type 1, Parkinson's disease, and Alzheimer's disease—affect MB structure and function, altering behavior. Studies dissecting the effects of disease-causing mutations in the MB have identified key pathological mechanisms, and the development of a complete connectome promises to add a comprehensive anatomical framework for disease modeling. Here, we reviewDrosophilamodels of human neurodevelopmental and neurodegenerative disorders via the effects of their underlying mutations on MB structure, function, and the resulting behavioral alterations.
Liouville-space neural network representation of density matrices
Authors: Kothe Simon , Kirton Peter
Published: June 2024

Neural network quantum states such as ansatz wave functions have shown a great deal of promise for finding the ground state of spin models. Recently, work has focused on extending this idea to mixed states for simulating the dynamics of open systems. Most approaches so far have used a purification ansatz where a copy of the system Hilbert space is added, which when traced out gives the correct density matrix. Here we instead present an extension of the restricted Boltzmann machine which directly represents the density matrix in Liouville space. This allows the compact representation of states which appear in mean-field theory. We benchmark our approach on two different versions of the dissipative transverse-field Ising model, which show our ansatz is able to compete with other state-of-the-art approaches.

Published by the American Physical Society
2024
Energy loss of a heavy fermion in a collisional QED plasma
Authors: Guo Yun , Qiu Luhua , Zhao Ruizhe , Strickland Michael
Published: June 2024

We compute the energy loss of heavy fermions moving in a plasma, taking into account the modification of the photon collective modes induced by collisions using a Bhatnagar-Gross–Krook collisional kernel. We include contributions from both hard and soft scatterings of the heavy fermion using a collisionally modified hard-thermal-loop resummed propagator. Using this method, one does not need to introduce a separation scale between hard- and soft-momentum exchanges. To place our calculation in context, we review other theoretical approaches to computing the collisional energy loss of fermions and discuss the systematics and results obtained in each approach compared to using a resummed propagator for both hard and soft momentum exchanges. Our final results indicate that self-consistently including the effect of collisions in the self-energies of the resummed propagator results in an increased energy loss compared to using collisionless hard-thermal-loop propagators. The effect becomes larger as the magnitude of the coupling constant and the velocity of the fermion increase.

Published by the American Physical Society
2024
Flavor-violating ALPs, electron
g−2
, and the Electron-Ion Collider
Authors: Davoudiasl Hooman , Marcarelli Roman , Neil Ethan T.
Published: June 2024

We revisit the possibility that light axionlike particles (ALPs) with lepton-flavor-violating couplings could give significant contributions to the electron’s anomalous magnetic moment ge−2. Unlike flavor diagonal lepton-ALP couplings, which are exclusively axial, lepton-flavor-violating couplings can have arbitrary chirality. Focusing on the e−τ ALP coupling, we find that the size of the contribution to ge−2 depends strongly on the chirality of the coupling. A significant part of the parameter space for which such a coupling can explain experimental anomalies in ge−2 can be probed at the Electron-Ion Collider, which is uniquely sensitive to the chirality of the coupling using the polarization of the electron beam.

Published by the American Physical Society
2024
Binned top quark spin correlation and polarization observables for the LHC at 13.6 TeV
Authors: Bernreuther Werner , Chen Long , Si Zong-Guo
Published: June 2024

We consider top-antitop quark (tt¯) production at the Large Hadron Collider (LHC) with subsequent decays into dileptonic final states. We use and investigate a set of leptonic angular correlations and distributions with which all the independent coefficient functions of the top-spin-dependent parts of the tt¯ production spin density matrices can be experimentally probed. We compute these observables for the LHC center-of-mass energy 13.6 TeV within the Standard Model at next-to-leading order in the QCD coupling including the mixed QCD weak corrections. We determine also the tt¯ charge asymmetry where we take in addition also the mixed QCD-QED corrections into account. In addition we analyze and compute possible new physics (NP) effects on these observables within effective field theory in terms of a gauge-invariant effective Lagrangian that contains the operators up to mass dimension six that are relevant for hadronic tt¯ production. First, we compute our observables inclusive in phase space. Then, in order to investigate which region in phase space has, for a specific observable, a high NP sensitivity, we determine our observables also in two-dimensional (Mtt¯,cosθt*) bins, where Mtt¯ denotes the tt¯-invariant mass and θt* is the top quark scattering angle in the tt¯ zero-momentum frame.

Published by the American Physical Society
2024
Closer scrutiny of cosmic ray proton energy losses
Authors: Esmaeili AmirFarzan , Esmaili Arman , Serpico Pasquale Dario
Published: June 2024

The percent-level precision attained by modern cosmic ray (CR) observations motivates reaching a comparable or better control of theoretical uncertainties. Here we focus on energy-loss processes affecting low-energy CR protons (∼0.1–5  GeV), where the experimental errors are small and collisional effects play a comparatively larger role with respect to collisionless transport ones. We study three aspects of the problem: (i) We quantitatively assess the role of the nuclear elastic cross section, for the first time, providing analytical formulas for the stopping power and inelasticity; (ii) We discuss the error arising from treating both elastic and pion production inelastic interactions as continuous energy loss processes, as opposed to catastrophic ones. The former is the approximation used in virtually all modern numerical calculations; (iii) We consider subleading effects such as relativistic corrections, radiative and medium processes in ionization energy losses. Our analysis reveals that neglecting (i) leads to errors close to 1%, notably around and below 1 GeV, neglecting (ii) leads to errors reaching about 3% within the considered energy range, (iii) contributes to a minor effect, gauged at the level of 0.1%. Consequently, while (iii) can currently be neglected, (ii) warrants consideration, and we also recommend incorporating (i) into computations. We conclude with some perspectives on further steps to be taken towards a high-precision goal of theoretical CR predictions regarding the treatment of energy losses.

Published by the American Physical Society
2024
Reentrant phase transitions of quantum black holes
Authors: Frassino Antonia M. , Pedraza Juan F. , Svesko Andrew , Visser Manus R.
Published: June 2024

We show that backreaction of quantum fields on black hole geometries can trigger new thermal phase transitions. Specifically, we study the phase behavior of the three-dimensional quantum-corrected static Bañados-Teitelboim-Zanelli black hole, an exact solution to specific semiclassical gravitational equations due to quantum conformal matter, discovered through braneworld holography. Focusing on the canonical ensemble, for large backreaction, we find novel reentrant phase transitions as the temperature monotonically increases, namely, from thermal anti–de Sitter space to the black hole and back to thermal anti–de Sitter. The former phase transition is first-order, a quantum analog of the classical Hawking-Page phase transition, while the latter is zeroth order and has no classical counterpart.

Published by the American Physical Society
2024
Combinatorics and topological weights of chromatin loop networks
Authors: Bonato Andrea , Chiang Michael , Corbett Dom , Kitaev Sergey , Marenduzzo Davide , Morozov Alexander , Orlandini Enzo
Published: June 2024

Polymer physics models suggest that chromatin spontaneously folds into loop networks with transcription units (TUs), such as enhancers and promoters, as anchors. Here we use combinatoric arguments to enumerate the emergent chromatin loop networks, both in the case where TUs are labeled and where they are unlabeled. We then combine these mathematical results with those of computer simulations aimed at finding the inter-TU energy required to form a target loop network. We show that different topologies are vastly different in terms of both their combinatorial weight and energy of formation. We explain the latter result qualitatively by computing the topological weight of a given network—i.e., its partition function in statistical mechanics language—in the approximation where excluded volume interactions are neglected. Our results show that networks featuring local loops are statistically more likely with respect to networks including more nonlocal contacts. We suggest our classification of loop networks, together with our estimate of the combinatorial and topological weight of each network, will be relevant to catalog three-dimensional structures of chromatin fibers around eukaryotic genes, and to estimate their relative frequency in both simulations and experiments.

Published by the American Physical Society
2024
Phase-space entropy cascade and irreversibility of stochastic heating in nearly collisionless plasma turbulence
Authors: Nastac Michael L. , Ewart Robert J. , Sengupta Wrick , Schekochihin Alexander A. , Barnes Michael , Dorland William D.
Published: June 2024

We consider a nearly collisionless plasma consisting of a species of “test particles” in one spatial and one velocity dimension, stirred by an externally imposed stochastic electric field—a kinetic analog of the Kraichnan model of passive advection. The mean effect on the particle distribution function is turbulent diffusion in velocity space—known as stochastic heating. Accompanying this heating is the generation of fine-scale structure in the distribution function, which we characterize with the collisionless (Casimir) invariant C2∝∫∫dxdv〈f2〉—a quantity that here plays the role of (negative) entropy of the distribution function. We find that C2 is transferred from large scales to small scales in both position and velocity space via a phase-space cascade enabled by both particle streaming and nonlinear interactions between particles and the stochastic electric field. We compute the steady-state fluxes and spectrum of C2 in Fourier space, with k and s denoting spatial and velocity wave numbers, respectively. In our model, the nonlinearity in the evolution equation for the spectrum turns into a fractional Laplacian operator in k space, leading to anomalous diffusion. Whereas even the linear phase mixing alone would lead to a constant flux of C2 to high s (towards the collisional dissipation range) at every k, the nonlinearity accelerates this cascade by intertwining velocity and position space so that the flux of C2 is to both high

k

and high s simultaneously. Integrating over velocity (spatial) wave numbers, the k-space (s-space) flux of C2 is constant down to a dissipation length (velocity) scale that tends to zero as the collision frequency does, even though the rate of collisional dissipation remains finite. The resulting spectrum in the inertial range is a self-similar function in the (k,s) plane, with power-law asymptotics at large k and s. Our model is fully analytically solvable, but the asymptotic scalings of the spectrum can also be found via a simple phenomenological theory whose key assumption is that the cascade is governed by a “critical balance” in phase space between the linear and nonlinear timescales. We argue that stochastic heating is made irreversible by this entropy cascade and that, while collisional dissipation accessed via phase mixing occurs only at small spatial scales rather than at every scale as it would in a linear system, the cascade makes phase mixing even more effective overall in the nonlinear regime than in the linear one.

Published by the American Physical Society
2024
Topological Spectra and Entropy of Chromatin Loop Networks
Authors: Bonato Andrea , Chiang Michael , Corbett Dom , Kitaev Sergey , Marenduzzo Davide , Morozov Alexander , Orlandini Enzo
Published: June 2024

The 3D folding of a mammalian gene can be studied by a polymer model, where the chromatin fiber is represented by a semiflexible polymer which interacts with multivalent proteins, representing complexes of DNA-binding transcription factors and RNA polymerases. This physical model leads to the natural emergence of clusters of proteins and binding sites, accompanied by the folding of chromatin into a set of topologies, each associated with a different network of loops. Here, we combine numerics and analytics to first classify these networks and then find their relative importance or statistical weight, when the properties of the underlying polymer are those relevant to chromatin. Unlike polymer networks previously studied, our chromatin networks have finite average distances between successive binding sites, and this leads to giant differences between the weights of topologies with the same number of edges and nodes but different wiring. These weights strongly favor rosettelike structures with a local cloud of loops with respect to more complicated nonlocal topologies. Our results suggest that genes should overwhelmingly fold into a small fraction of all possible 3D topologies, which can be robustly characterized by the framework we propose here.

Published by the American Physical Society
2024
Towards Adiabatic Quantum Computing Using Compressed Quantum Circuits
Authors: Mc Keever Conor , Lubasch Michael
Published: June 2024

We describe tensor network algorithms to optimize quantum circuits for adiabatic quantum computing. To suppress diabatic transitions, we include counterdiabatic driving in the optimization and utilize variational matrix product operators to represent adiabatic gauge potentials. Traditionally, Trotter product formulas are used to turn adiabatic time evolution into quantum circuits and the addition of counterdiabatic driving increases the circuit depth per time step. Instead, we classically optimize a parameterized quantum circuit of fixed depth to simultaneously capture adiabatic evolution together with counterdiabatic driving over many time steps. The methods are applied to the ground-state preparation of quantum Ising chains with transverse and longitudinal fields. We show that the classically optimized circuits can significantly outperform Trotter product formulas. Additionally, we discuss how the approach can be used for combinatorial optimization.

Published by the American Physical Society
2024
Trauma or autism? – understanding how the effects of trauma and disrupted attachment can be mistaken for autism
Authors: Al-Attar Zainab , Worthington Rachel
Published: June 2024

Purpose

Early bio-psycho-social experiences can dramatically impact all aspects of development. Both autism and traumagenic histories can lead to trans-diagnostic behavioural features that can be confused with one another during diagnostic assessment, unless an in-depth differential diagnostic evaluation is conducted that considers the developmental aetiology and underpinning experiences and triggers to trans-diagnostic behaviours.

Design/methodology/approach

This paper will explore the ways in which biological, cognitive, emotional and social sequelae of early trauma and attachment challenges, can look very similar to a range of neurodevelopmental disorders, including autism. Relevant literature and theory will be considered and synthesised with clinical knowledge of trauma and autism.

Findings

Recommendations are made for how the overlap between features of autism and trauma can be considered during assessments alongside consideration for interventions to enable people to access the most appropriate support for their needs.

Originality/value

Many features of the behaviours of individuals who have experienced early childhood trauma and disrupted or maladaptive attachments, may look similar to the behaviours associated with autism and hence diagnostic assessments of autism need to carefully differentiate traumagenic causes, to either dual diagnose (if both are present) or exclude autism, if it is not present. This has for long been recognised in child and adolescent autism specialist services but is less well developed in adult autism specialist services.
The effectiveness of family-based treatment and pharmacotherapy in an adolescent with anorexia nervosa and intellectual disability: a case report
Authors: Moradi Mehri , Salehian Razieh , Bozorg Bonnie , Bozorg Mina
Published: June 2024

Purpose

This study aims to report the effectiveness of family based treatment and pharmacotherapy on an adolescent boy with anorexia nervosa and intellectual disability.

Design/methodology/approach

The authors reported the case of a 16-year-old boy with AN and ID and referred him to a family therapist and psychiatrist in Tehran.

Findings

The patient experienced fatigue, weakness, dissatisfaction, suicidal thoughts and self-harm signs over the past one year. He also had behaviors such as abstinence from eating and voluntary vomiting. He was diagnosed with AN and MDD.

Originality/value

The results suggest that these interventions can be effective but should be used with special consideration. Combining family therapy and pharmacotherapy might offer a chance to alleviate anorexia symptoms in people with ID.
Artificial intelligence: a catalyst to organizational learning and development in 21st century
Authors: Olusegun Suleiman , Hinson Robert Ebo , Zekeri Ochidi
Published: June 2024

Purpose

The purpose of this study is to investigate how artificial intelligence is changing and promoting organizational learning and development in 21st century.

Design/methodology/approach

The paper adopted an exploratory study using the open-ended approach of quantum theory, including 55 depth interviews and one focus group discussion with employees representing top-level management, mid-level management and first-line management having mainly an artificial intelligence and organizational learning/strategies background.

Findings

The finding showed that when AI is strategically placed within an organization, there is opportunity for humans and AI to learn from one another to develop these new capabilities and core competencies that give an organizations added competitive advantage.

Research limitations/implications

Exploring artificial intelligence in a context at one sector (telecommunication sector), the research results may lack general acceptance because of disparities of AI adoption in other sectors. Therefore, researchers are encouraged to test the proposed propositions further in other sectors.

Practical implications

The paper includes implications for artificial intelligence sustainability as a tool for organizational learning and strategy. It is observed that AI has increased the demand for managerial skills such as creativity, innovation, troubleshooting, data mining, emotional intelligence, adaptability and problem-solving. The study showed that organizations will need to have an appropriate level of knowledge and skill in AI to be effective in leveraging it as an integral facet of their organizational strategy.

Originality/value

This study is novel on account of its applicability in AI’s ability to work harmoniously with human employees which can stimulate mutual learning between the two, resulting in a relationship similar to that of a relationship with a teammate or colleague in the workplace which will invariably results into competitive advantage.