bluuebunny/crossref_metadata_2025 huggingface dataset:
A dynamic microRNA profile that tracks a chemotherapy resistance phenotype in osteosarcoma. Implications for novel therapeutics
Authors: Lietz Christopher E. , Newman Erik T. , Kelly Andrew D. , Xiang David H. , Zhang Ziying , Ramavenkat Nikhil , Bowers Joshua J. , Lozano-Calderon Santiago A. , Ebb David H. , Raskin Kevin A. , Cote Gregory M. , Choy Edwin , Nielsen G. Petur , Vlachos Ioannis S. , Haibe-Kains Benjamin , Spentzos Dimitrios
Published: June 2024

Osteosarcoma is a rare primary bone tumor for which no significant therapeutic advancement has been made since the late 1980s despite ongoing efforts. Overall, the five-year survival rate remains about 65%, and is much lower in patients with tumors unresponsive to methotrexate, doxorubicin, and cisplatin therapy. Genetic studies have not revealed actionable drug targets, but our group, and others, have reported that epigenomic biomarkers, including regulatory RNAs, may be useful prognostic tools for osteosarcoma. We tested if microRNA (miRNA) transcriptional patterns mark the transition from a chemotherapy sensitive to resistant tumor phenotype. Small RNA sequencing was performed using 14 patient matched pre-chemotherapy biopsy and post-chemotherapy resection high-grade osteosarcoma frozen tumor samples. Independently, small RNA sequencing was performed using 14 patient matched biopsy and resection samples from untreated tumors. Separately, miRNA specific Illumina DASL arrays were used to assay an independent cohort of 65 pre-chemotherapy biopsy and 26 patient matched post-chemotherapy resection formalin fixed paraffin embedded (FFPE) tumor samples. mRNA specific Illumina DASL arrays were used to profile 37 pre-chemotherapy biopsy and five post-chemotherapy resection FFPE samples, all of which were also used for Illumina DASL miRNA profiling. The National Cancer Institute Therapeutically Applicable Research to Generate Effective Treatments dataset, including PCR based miRNA profiling and RNA-seq data for 86 and 93 pre-chemotherapy tumor samples, respectively, was also used. Paired differential expression testing revealed a profile of 17 miRNAs with significantly different transcriptional levels following chemotherapy. Genes targeted by the miRNAs were differentially expressed following chemotherapy, suggesting the miRNAs may regulate transcriptional networks. Finally, anin vitropharmacogenomic screen using miRNAs and their target transcripts predicted response to a set of candidate small molecule therapeutics which potentially reverse the chemotherapy resistance phenotype and synergize with chemotherapy in otherwise treatment resistant tumors. Importantly, these novel therapeutic targets are distinct from targets identified by a similar pharmacogenomic analysis of previously published prognostic miRNA profiles from pre chemotherapy biopsy specimens.
Directed exploration is reduced by an aversive interoceptive state induction in healthy individuals but not in those with affective disorders
Authors: Li Ning , Lavalley Claire A. , Chou Ko-Ping , Chuning Anne E. , Taylor Samuel , Goldman Carter M. , Torres Taylor , Hodson Rowan , Wilson Robert C. , Stewart Jennifer L. , Khalsa Sahib S. , Paulus Martin P. , Smith Ryan
Published: June 2024

Elevated anxiety and uncertainty avoidance are known to exacerbate maladaptive choice in individuals with affective disorders. However, the differential roles of state vs. trait anxiety remain unclear, and underlying computational mechanisms have not been thoroughly characterized. In the present study, we investigated how a somatic (interoceptive) state anxiety induction influences learning and decision-making under uncertainty in individuals with clinically significant levels of trait anxiety. A sample of 58 healthy comparisons (HCs) and 61 individuals with affective disorders displaying elevated anxiety symptoms (iADs; i.e., anxiety and/or depression) completed a previously validated explore-exploit decision task, with and without an added breathing resistance manipulation designed to induce state anxiety. Computational modeling revealed a significant group-by-condition interaction, such that information-seeking (i.e., directed exploration) in HCs was reduced by the anxiety induction (Cohen’sd=.47,p=.013), while no change was observed in iADs. The iADs also showed slower learning rates than HCs across conditions (Cohen’sd=.52,p=.003), suggesting more persistent uncertainty. These findings highlight a complex interplay between trait anxiety and state anxiety. Specifically, state anxiety may attenuate reflection on uncertainty in healthy individuals, while familiarity with anxious states in those with high trait anxiety may create an insensitivity to this effect.
A comprehensive tandem repeat catalog of the human genome
Authors: Chiu Readman , Rajan Babu Indhu Shree , Friedman Jan M , Birol Inanc
Published: June 2024

With the increasing availability of long-read sequencing data, high-quality human genome assemblies, and software for fully characterizing tandem repeats, genome-wide genotyping of tandem repeat loci on a population scale becomes more feasible. Such efforts not only expand our knowledge of the tandem repeat landscape in the human genome but also enhance our ability to differentiate pathogenic tandem repeat mutations from benign polymorphisms. To this end, we analyzed 272 genomes assembled using datasets from three public initiatives that employed different long-read sequencing technologies. Here, we report a catalog of over 18 million tandem repeat loci, many of which were previously unannotated. Some of these loci are highly polymorphic, and many of them reside within coding sequences.
Unidirectional and Bidirectional Causation between Smoking and Blood DNA Methylation: Evidence from Twin-based Mendelian Randomisation
Authors: Singh Madhurbain , Dolan Conor V. , Lapato Dana M. , Hottenga Jouke-Jan , Pool René , Verhulst Brad , Boomsma Dorret I. , Breeze Charles E. , de Geus Eco J. C. , Hemani Gibran , Min Josine L. , Peterson Roseann E. , Maes Hermine H. M. , van Dongen Jenny , Neale Michael C.
Published: June 2024

Cigarette smoking is associated with numerous differentially-methylated genomic loci in multiple human tissues. These associations are often assumed to reflect the causal effects of smoking on DNA methylation (DNAm), which may underpin some of the adverse health sequelae of smoking. However, prior causal analyses with Mendelian Randomisation (MR) have found limited support for such effects. Here, we apply an integrated approach combining MR with twin causal models to examine causality between smoking and blood DNAm in the Netherlands Twin Register (N=2577). Analyses revealed potential causal effects of current smoking on DNAm at >500 sites in/near genes enriched for functional pathways relevant to known biological effects of smoking (e.g., hemopoiesis, cell- and neuro-development, and immune regulation). Notably, we also found evidence of reverse and bidirectional causation at several DNAm sites, suggesting that variation in DNAm at these sites may influence smoking liability. Seventeen of the loci with putative effects of DNAm on smoking showed highly specific enrichment for gene-regulatory functional elements in the brain, while the top three sites annotated to genes involved in G protein-coupled receptor signalling and innate immune response. These novel findings are partly attributable to the analyses ofcurrentsmoking in twin models, rather thanlifetimesmoking typically examined in MR studies, as well as the increased statistical power achieved using multiallelic/polygenic scores as instrumental variables while controlling for potential horizontal pleiotropy. This study highlights the value of twin studies with genotypic and DNAm data for investigating causal relationships of DNAm with health and disease.
High mortality and complications in patients admitted with Takotsubo cardiomyopathy without improvement in outcomes over the years
Authors: Movahed Mohammad Reza , Javanmardi Elimira , Hashemzadeh Mehrtash
Published: June 2024

Introduction

Takotsubo cardiomyopathy continues to be a major cause of mortality and morbidity. The goal of this study was to evaluate the outcome data of patients with Takotsubo cardiomyopathy using a large inpatient database.

Methods

We used the Nationwide inpatient sample (NIS) database for our study. We evaluated trends, mortality, and complications of patients admitted with Takotsubo cardiomyopathy from available 2016-2020 years in adults over the age of 18.

Results

A total of 199,890 patients with Takotsubo were found in our database with 83% being female and higher prevalence with age, Caucasian race, and highest income. Mortality was high at 6.5 % with no significant improvement over the years studied. Furthermore, major complications were substantial. Cardiogenic shock occurred in 6.6%, atrial fibrillation in 20.7%, Cardiac arrest in 3.4%, congestive heart failure in 35.9% and stroke in 5.3%.

Conclusion

Takotsubo cardiomyopathy is associated with high mortality and complications with no improvement in outcome over the 5 years study. Further improvement in care is needed to improve outcomes.
Stress-induced hyperglycemia predicts poor outcomes in primary ICH patients
Authors: Gilotra Kevin , Basem Jade , Janssen Melissa , Swarna Sujith , Mani Racheed , Ren Benny , Dashti Reza
Published: June 2024

Introduction

The current literature suggests hyperglycemia can predict poor outcomes in patients with primary intracerebral hemorrhage (ICH). Chronic hyperglycemia is seen in patients with pre-existing diabetes (DM), however, acute hyperglycemia in non-diabetic patients is defined as stress-induced hyperglycemia (SIH). This study explored the influence of hyperglycemia on outcomes of primary ICH patients both in the presence and absence of pre-existing DM.

Methods

Data regarding admission glucose, pre-existing DM, inpatient mortality, and modified Rankin scale (mRS) scores at discharge were available for 636 patients admitted to Stony Brook Hospital from January 2011 to December 2022 with a primary diagnosis of ICH. Regression models were used to compare outcomes between patients with admission hyperglycemia and/or pre-existing DM to a control group of normoglycemic and non-diabetic ICH patients.

Results

Patients with SIH had higher inpatient mortality rates and worse mRS scores at discharge (p<0.001). An association with higher mortality and worse mRS scores at discharge was also seen in patients with hyperglycemia secondary to DM, although the strength of this association was weaker when compared to patients with SIH.

Conclusion

In conclusion, our study’s findings suggest that SIH may play a greater role in predicting poor outcomes at discharge rather than a history of poorly controlled DM with chronic hyperglycemia. To develop a more thorough understanding of this topic, prospective studies evaluating the effect of changes in serum glucose during hospital stay on short and long-term outcomes is needed.
Targeted metagenomics reveals pangenomic diversity of the nitroplast (UCYN-A) and its algal host plastid
Authors: Kantor Ella Joy H , Robicheau Brent M , Tolman Jennifer , Archibald John M , LaRoche Julie
Published: June 2024

UCYN-A (Cand. Atelocyanobacterium thalassa) has recently been recognized as a globally-distributed, early stage, nitrogen-fixing organelle (the 'nitroplast') of cyanobacterial origin present in select species of haptophyte algae (e.g., Braarudosphaera bigelowii). Although the nitroplast was recognized as the UCYN-A2 sublineage, it is yet to be confirmed in other sublineages of the algal/UCYN-A complex. We used water samples collected from Halifax Harbour (Bedford Basin, Nova Scotia, Canada) and the offshore Scotian Shelf to further our understanding of B. bigelowii and UCYN-A in the coastal Northwest Atlantic. Sequencing data revealed UCYN-A-associated haptophyte signatures and yielded near-complete metagenome-assembled genomes (MAGs) for UCYN-A1, UCYN-A4, and the plastid of the A4-associated haptophyte. Comparative genomics provided new insights into the pangenome of UCYN-A. The UCYN-A4 MAG is the first genome sequenced from this sublineage and shares ~85% identity with the UCYN-A2 nitroplast. Genes missing in the reduced genome of the nitroplast were also missing in the A4 MAG supporting its likely classification as a nitroplast as well. The UCYN-A1 MAG was found to be nearly 100% identical to the reference genome despite coming from different ocean basins. Time-series data paired with the recurrence of specific microbes in enrichment cultures gave insight into the microbes that frequently co-occur with the algal/UCYN-A complex (e.g., Pelagibacter ubique). Overall, our study expands knowledge of UCYN-A and its host across major ocean basins and investigates their co-occurring microbes in the coastal Northwest Atlantic (NWA), thereby facilitating future studies on the underpinnings of haptophyte-associated diazotrophy in the sea.
α-Synuclein acts as a cholesteryl-ester sensor on lipid droplets regulating organelle size and abundance
Authors: Jacob Reeba Susan , Dema Alessandro , Chérot Hélène , Dumesnil Calvin , Cohen Shira , Shalom Hadas Sar , Rimon Nitzan , Sibony-Nevo Odelia , Beck Gilad , Ainbinder Elena , Wolinski Heimo , Athenstaedt Karin , Theillet Francois-Xavier , Thiam Abdou Rachid , Selenko Philipp
Published: June 2024

While aggregated alpha-Synuclein (αSyn) is commonly associated with Parkinson’s disease, its physiological function as a membrane-binding protein is poorly understood. Here, we show that endogenous αSyn binds lipid droplets (LDs) in multiple human cell lines and in stem cell-derived dopaminergic neurons. LD-binding encompasses αSyn residues 1-100, which masks their detection by immunofluorescence microscopy, probably explaining the scarcity of similar observations in earlier studies. αSyn-LD interactions are highly temperature-sensitive and selective for cholesteryl-ester-rich LDs. They promote the formation of αSyn multimers that dissociate from LDs at non-permissive temperatures. αSyn remains LD-bound throughout starvation-induced lipolysis, whereas siRNA-knockdown diminishes LD abundance and compromises cell viability upon nutrient depletion, without affecting LD biosynthesis. Reciprocally, excess αSyn stimulates LD accumulation in dependence of lipid availability, restricts organelle size and ensures intracellular LD organization, which strictly depends on functional membrane-binding. Supporting a general role of αSyn in cellular lipid and cholesterol metabolism, our results point to additional loss-of-function similarities between Parkinson’s, Alzheimer’s and Gaucher’s disease.
A comparative study of the cryo-EM structures ofS. cerevisiaeand human anaphase-promoting complex/cyclosome (APC/C)
Authors: Vazquez-Fernandez Ester , Yang Jing , Zhang Ziguo , Andreeva Antonina E. , Emsley Paul , Barford David
Published: June 2024

The anaphase-promoting complex/cyclosome (APC/C) is a large multi-subunit E3 ubiquitin ligase that controls progression through the cell cycle by orchestrating the timely proteolysis of mitotic cyclins and other cell cycle regulatory proteins. Although structures of multiple human APC/C complexes have been extensively studied over the past decade, theS. cerevisiaeAPC/C has been less extensively investigated. Here, we describe medium resolution structures of threeS. cerevisiaeAPC/C complexes: unphosphorylated apo-APC/C and the ternary APC/CCDH1-substrate complex, and phosphorylated apo-APC/C. Whereas the overall architectures of human andS. cerevisiaeAPC/C are conserved, as well as the mechanism of CDH1 inhibition by CDK-phosphorylation, specific variations exist, including striking differences in the mechanism of coactivator-mediated stimulation of E2 binding, and the activation of APC/CCDC20by phosphorylation. In contrast to human APC/C in which coactivator induces a conformational change of the catalytic module APC2:APC11 to allow E2 binding, inS. cerevisiaeapo-APC/C the catalytic module is already positioned to bind E2. Furthermore, we find no evidence of a phospho-regulatable auto-inhibitory segment of APC1, that in the unphosphorylated human APC/C, sterically blocks the CDC20C-boxbinding site of APC8. Thus, although the functions of APC/C are conserved fromS. cerevisiaeto humans, molecular details relating to their regulatory mechanisms differ.
Identify Regulatory eQTLs by Multiome Sequencing in Prostate Single Cells
Authors: Tian Yijun , Wu Lang , Huang Chang-Ching , Wang Liang
Published: June 2024

While genome-wide association studies and expression quantitative trait loci (eQTL) analysis have made significant progress in identifying noncoding variants associated with prostate cancer risk and bulk tissue transcriptome changes, the regulatory effect of these genetic elements on gene expression remains largely unknown. Recent developments in single-cell sequencing have made it possible to perform ATAC-seq and RNA-seq profiling simultaneously to capture functional associations between chromatin accessibility and gene expression. In this study, we tested our hypothesis that this multiome single-cell approach allows for mapping regulatory elements and their target genes at prostate cancer risk loci. We applied a 10X Multiome ATAC + Gene Expression platform to encapsulate Tn5 transposase-tagged nuclei from multiple prostate cell lines for a total of 65,501 high quality single cells from RWPE1, RWPE2, PrEC, BPH1, DU145, PC3, 22Rv1 and LNCaP cell lines. To address data sparsity commonly seen in the single-cell sequencing, we performed targeted sequencing to enrich sequencing data at prostate cancer risk loci involving 2,730 candidate germline variants and 273 associated genes. Although not increasing the number of captured cells, the targeted multiome data did improve eQTL gene expression abundance by about 20% and chromatin accessibility abundance by about 5%. Based on this multiomic profiling, we further associated RNA expression alterations with chromatin accessibility of germline variants at single cell levels. Cross validation analysis showed high overlaps between the multiome associations and the bulk eQTL findings from GTEx prostate cohort. We found that about 20% of GTEx eQTLs were covered within the significant multiome associations (p-value ≤ 0.05, gene abundance percentage ≥ 5%), and roughly 10% of the multiome associations could be identified by significant GTEx eQTLs. We also analyzed accessible regions with available heterozygous SNP reads and observed more frequent association in genomic regions with allelically accessible variants (p= 0.0055). Among these findings were previously reported regulatory variants including rs60464856-RUVBL1 (multiomep-value = 0.0099 in BPH1)and rs7247241-SPINT2 (multiomep-value = 0.0002- 0.0004 in 22Rv1). We also functionally validated a new regulatory SNP and its target gene rs2474694-VPS53 (multiomep-value = 0.00956 in BPH1 and 0.00625 in DU145) by reporter assay and SILAC proteomics sequencing. Taken together, our data demonstrated the feasibility of the multiome single-cell approach for identifying regulatory SNPs and their regulated genes.
Similarities and differences between brain and skinGNAQp.R183Q driven capillary malformations
Authors: Nasim Sana , Bichsel Colette , Pinto Anna , Alexandrescu Sanda , Kozakewich Harry , Bischoff Joyce
Published: June 2024

Capillary malformations (CM) are congenital vascular irregularities of capillary and venous blood vessels that appear in the skin, leptomeninges of the brain, and the choroid of the eye in the disorder known as Sturge Weber Syndrome (SWS). More common are non-syndromic CM found only in the skin, without brain or ocular involvement. A somatic activating mutation inGNAQ(p.R183Q) is found in ∼90% of syndromic and non-syndromic CM specimens and is present in CD31posendothelial cells isolated from brain and skin CM specimens. Endothelial expression of theGNAQp.R183Q variant is sufficient to form CM-like vessels in mice. Given the distinct features and functions of blood vessels in the brain versus the skin, we examined the features of CM vessels in both tissues to gain insights into the pathogenesis of CM. Herein, we present morphologic characteristics of CM observed in specimen from brain and skin. TheGNAQp.R183Q variant allelic frequency in each specimen was determined by droplet digital PCR. Sections were stained for endothelial cells, tight junctions, mural cells, and macrophages to assess the endothelium as well as perivascular constituents. CM blood vessels in brain and skin were enlarged, exhibited fibrin leakage and reduced zona occludin-1, and were surrounded by MRC1pos/LYVE1posmacrophages. In contrast, the CMs from brain and skin differ in endothelial sprouting activity and localization of mural cells. These characteristics might be helpful in the development of targeted and/or tissue specific therapies to prevent or reverse non-syndromic and syndromic CM.

Statements and Declarations

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PathogenicBacteroides fragilisstrains can emerge from gut-resident commensals
Authors: Oles Renee E. , Terrazas Marvic Carrillo , Loomis Luke R. , Neal Maxwell J. , Paulchakrabarti Mousumi , Zuffa Simone , Hsu Chia-Yun , Vasquez Ayala Adriana , Lee Michael H. , Tribelhorn Caitlin , Belda-Ferre Pedro , Bryant MacKenzie , Zemlin Jasmine , Young Jocelyn , Dulai Parambir , Sandborn William J. , Sivagnanam Mamata , Raffatellu Manuela , Pride David , Dorrestein Pieter C. , Zengler Karsten , Choudhury Biswa , Knight Rob , Chu Hiutung
Published: June 2024

Bacteroides fragilisis a prominent member of the human gut microbiota, playing crucial roles in maintaining gut homeostasis and host health. Although it primarily functions as a beneficial commensal,B. fragiliscan become pathogenic. To determine the genetic basis of its duality, we conducted a comparative genomic analysis of 813B. fragilisstrains, representing both commensal and pathogenic origins. Our findings reveal that pathogenic strains emerge across diverse phylogenetic lineages, due in part to rapid gene exchange and the adaptability of the accessory genome. We identified 16 phylogenetic groups, differentiated by genes associated with capsule composition, interspecies competition, and host interactions. A microbial genome-wide association study identified 44 genes linked to extra-intestinal survival and pathogenicity. These findings reveal how genomic diversity within commensal species can lead to the emergence of pathogenic traits, broadening our understanding of microbial evolution in the gut.
ER-GUARD: an evolutionarily conserved antioxidant defense system at ER membranes
Authors: Ji Zhijian , Pandey Taruna , de Belly Henry , Wang Bingying , Weiner Orion D. , Tang Yao , Guang Shouhong , Goddard Thomas D. , Ma Dengke K.
Published: June 2024

Oxidative protein folding in the endoplasmic reticulum (ER) is essential for all eukaryotic cells yet generates hydrogen peroxide (H2O2), a reactive oxygen species (ROS). The ER-transmembrane protein that provides reducing equivalents to ER and guards the cytosol for antioxidant defense remains unidentified. Here we combine AlphaFold2- based and functional reporter screens inC. elegansto identify a previously uncharacterized and evolutionarily conserved protein ERGU-1 that fulfills these roles.

DeletingC. elegansERGU-1 causes excessive H2O2 and transcriptional gene up- regulation through SKN-1, homolog of mammalian antioxidant master regulator NRF2. ERGU-1 deficiency also impairs organismal reproduction and behaviors. BothC. elegansand human ERGU-1 proteins localize to ER membranes and form network reticulum structures. We name this system ER-GUARD,EndoplasmicReticulumGuardianAegis ofRedoxDefense. Human andDrosophilahomologs of ERGU-1 can rescueC. elegansmutant phenotypes, demonstrating evolutionarily ancient and conserved functions. Together, our results reveal an ER-membrane-specific protein machinery and defense-net system ER-GUARD for peroxide detoxification and suggest a previously unknown but conserved pathway for antioxidant defense in animal cells.
Advancing Personalized Cancer Therapy: Onko_DrugCombScreen - A Novel Shiny App for Precision Drug Combination Screening
Authors: Yang Jingyu , Wang Meng , Dönitz Jürgen , Chapuy Björn , Beißbarth Tim
Published: June 2024

The employment of drug combinations in cancer therapy plays an important role, enhancing efficacy and reducing toxicity. However, the ability to identify and validate effective drug combinations is constrained by the exponential increase in combinatorial possibilities. In this context, we have developed Onko_DrugCombScreen, an innovative tool aimed at advancing precision medicine based on identifying significant drug combination candidates in a target cancer cohort compare to a control cohort. Onko_DrugCombScreen, inspired by Molecular Tumor Board (MTB) process, synergizes drug knowledge-base analysis with various statistical methodologies and data visualization techniques to pinpoint drug combination candidates. Validated through a TCGA-BRCA case study, Onko_DrugCombScreen has demonstrated its proficiency in discerning established drug combinations in a specific cancer type as well as in revealing potential novel drug combinations. By enhancing the capability of drug combination discovery through drug knowledge bases, this novel tool represents a significant advancement in personalized cancer treatment. It offers a novel solution to the challenge of identifying promising drug combinations, setting the stage for the development of more precise and potent combination treatments in cancer care for the future.
An Open-Source Deep Learning-Based GUI Toolbox For Automated Auditory Brainstem Response Analyses (ABRA)
Authors: Erra Abhijeeth , Chen Jeffrey , Chrysostomou Elena , Barret Shannon , Miller Cayla , Kassim Yasmin M. , Friedman Rick A. , Ceriani Federico , Marcotti Walter , Carroll Cody , Manor Uri
Published: June 2024

In this paper, we introduce a new, open-source software developed in Python for analyzing Auditory Brainstem Response (ABR) waveforms. ABRs are a far-field recording of synchronous neural activity generated by the auditory fibers in the ear in response to sound, and used to study acoustic neural information traveling along the ascending auditory pathway. Common ABR data analysis practices are subject to human interpretation and are labor-intensive, requiring manual annotations and visual estimation of hearing thresholds. The proposed new Auditory Brainstem Response Analyzer (ABRA) software is designed to facilitate the analysis of ABRs by supporting batch data import/export, waveform visualization, and statistical analysis. Techniques implemented in this software include algorithmic peak finding, threshold estimation, latency estimation, time warping for curve alignment, and 3D plotting of ABR waveforms over stimulus frequencies and decibels. The excellent performance on a large dataset of ABR collected from three labs in the field of hearing research that use different experimental recording settings illustrates the efficacy, flexibility, and wide utility of ABRA.
Quench dynamics in lattices above one dimension: The free fermionic case
Authors: Gibbins Molly , Jafarizadeh Arash , Gammon-Smith Adam , Bertini Bruno
Published: June 2024

We begin a systematic investigation of quench dynamics in higher-dimensional lattice systems considering the case of noninteracting fermions with conserved particle number. We prepare the system in a translational-invariant nonequilibrium initial state, the simplest example being a classical configuration with fermions at fixed positions on the lattice, and let it evolve in time. We characterize the system's dynamics by measuring the entanglement between a finite connected region and its complement. We observe the transmutation of entanglement entropy into thermodynamic entropy and investigate how this process depends on the shape and orientation of the region with respect to the underlying lattice. Interestingly, we find that irregular regions display a distinctive multislope entanglement growth, while the dependence on the orientation angle is generically fairly weak. This is particularly true for regions with a large (discrete) rotational symmetry group. The main tool of our analysis is the celebrated quasiparticle picture of Calabrese and Cardy, which we generalize to describe the case at hand. Specifically, we show that for generic initial configurations (even when restricting to classical ones) one has to allow for the production of multiplets involving n>2 quasiparticles and carrying nondiagonal correlations. We obtain quantitatively accurate predictions, tested against exact numerics, and propose an efficient Monte Carlo based scheme to evaluate them for arbitrary connected regions of generic higher-dimensional lattices.

Published by the American Physical Society
2024
Proximate Tomonaga-Luttinger liquid in an anisotropic Kitaev-Gamma model
Authors: Gohlke Matthias , Pelayo Jose Carlos , Suzuki Takafumi
Published: June 2024

The characterization of quantum spin liquid phases in Kitaev materials has been a subject of intensive studies over the recent years, both theoretically and experimentally. Most theoretical studies have focused on an isotropically interacting model with its coupling strength being equivalent on each bond in an attempt to simplify the problem. In this Letter, we study an extended spin-1/2 Kitaev-Γ model on a honeycomb lattice with an additional tuning parameter that controls the coupling strength on one of the bonds: We connect the limit of isolated Kitaev-Γ chains, which is known to exhibit an emergent SU(2)1 Tomonaga-Luttinger liquid phase [Yang , ], to the two-dimensional model. We report on an instance, in which properties of the Tomonaga-Luttinger liquid persist for finite interchain coupling forming a phase we call the proximate Tomonaga-Luttinger liquid (pTLL). This pTLL is strongly anisotropic in character analogous to , and features spinon-like excitations similar to those of the antiferromagnetic Heisenberg chain. We use numerical exact diagonalization and density matrix renormalization group on various cluster geometries in a complementary way to overcome finite-size limitations.

Published by the American Physical Society
2024
Induced moduli oscillation by radiation and space expansion in a higher-dimensional model
Authors: Otsuka Hajime , Sakamura Yutaka
Published: June 2024

We investigate the cosmological expansion of the 3D space in a 6D model compactified on a sphere, beyond the 4D effective theory analysis. We focus on a case where the initial temperature is higher than the compactification scale. In such a case, the pressure for the compact space affects the moduli dynamics and induces the moduli oscillation even if they are stabilized at the initial time. Under some plausible assumptions, we derive the explicit expressions for the 3D scale factor and the moduli background in terms of analytic functions. Using them, we evaluate the transition times between different cosmological eras as functions of the model parameters and the initial temperature.

Published by the American Physical Society
2024
Vector dark matter with Higgs portal in type II seesaw framework
Authors: Das Nandini , Jha Tapoja , Nanda Dibyendu
Published: June 2024

We study the phenomenology of a vector dark matter (VDM) in a U(1)X gauged extension of the Standard Model (SM), which is set in a type II seesaw framework. When this U(1)X symmetry is spontaneously broken by the vacuum expectation value (VEV) of a newly introduced complex scalar singlet, the gauge boson Z′ becomes massive. The stability of the dark matter (DM) is ensured by the presence of an exact charge conjugation symmetry resulting from the structure of the Lagrangian. On the other hand, the SU(2)L triplet scalar facilitates light neutrino masses via the type II seesaw mechanism. We have studied the phenomenology of the usual WIMP DM, considering all possible theoretical and experimental constraints that are applicable. Due to the presence of a triplet scalar, the present framework can also accommodate the observed 2σ deviation in h→Zγ decay rate, recently measured at the LHC. The possibility of nonthermal production of DM from the decay of the singlet scalar has also been briefly discussed.

Published by the American Physical Society
2024
Chiral phase transition and spin alignment of vector mesons in the polarized-Polyakov-loop Nambu–Jona-Lasinio model under rotation
Authors: Sun Fei , Shao Jingdong , Wen Rui , Xu Kun , Huang Mei
Published: June 2024

By using the analytic continuation method, a polarized Polykov-loop potential at finite real angular velocity is constructed from the lattice results at finite imaginary angular velocity. The chiral and deconfinement phase transitions under rotation have been simultaneously investigated in the polarized-Polyakov-loop Nambu–Jona-Lasinio (PPNJL) model. It is observed that both critical temperatures of deconfinement and chiral phase transition increase with the angular velocity, which is in consistent with lattice results. The spin alignment of vector meson has the negative deviation of ρ00−1/3 under rotation, and the deviation in the PPNJL model is much more significant than that in the NJL model and the quark coalescence model, which revealing the important role of rotating gluons on the quark polarization.

Published by the American Physical Society
2024
Alternative to perturbative renormalization in (
3+1
)-dimensional field theories
Authors: Romatschke Paul
Published: June 2024

Perturbative renormalization provides the bedrock of understanding quantum field theories. In this work, I point out an alternative way of renormalizing quantum field theories, which is naturally encountered and well-known for the case of large N scalar field theories. In terms of bare parameters, this nonperturbative alternative renormalization differs qualitatively from its perturbative cousin: in the continuum limit, the bare coupling constant goes to zero instead of infinity, and there is no wave-function counterterm. Despite these differences, the resulting n-point functions of the theory are finite. I provide explicit results for alternative renormalization for the O(N) model and QCD with Nf=12 flavors in 3+1 dimensions.

Published by the American Physical Society
2024
Impact of random nanoscale roughness on gas-scattering dynamics
Authors: Chen Yichong , Gibelli Livio , Borg Matthew K.
Published: June 2024

The impact of nanoscale wall roughness on rarefied gas transport is widely acknowledged, yet the associated scattering dynamics largely remain elusive. In this paper, we develop a scattering kernel for surfaces having nanoscale roughness that distinctly characterizes the two major types of interactions between gas molecules and rough surfaces. Namely these are (a) the weak perturbations arising from the thermal motion of wall atoms, essentially gas-phonon collisions, which are captured by the well-established Cercignani-Lampis model, and (b) the hard collisions owing to the irregularities of the rough, static potential energy surface, which are generally described by the fully diffuse model. Drawing an analogy between wave-surface and gas-surface scattering, a pseudo Debye-Waller factor is incorporated into the modeling as a weighting coefficient to allow the transition between smooth and rough surface conditions. The proposed scattering kernel is validated through high-fidelity molecular dynamics simulations that are performed for systems with varying roughness, temperature, and gas-surface combinations. The results indicate that the model well captures the scattering dynamics of gas molecular beams impinging on surfaces at different velocities, specifically for the accommodation coefficients and reflection patterns. Additionally, in flow and heat transport cases, it accurately predicts macroscopic quantities such as velocity slip and temperature jumps across the range of tested conditions.

Published by the American Physical Society
2024
Schwarzschild Black Hole from Perturbation Theory to All Orders
Authors: Damgaard Poul H. , Lee Kanghoon
Published: June 2024

Applying the quantum field theoretic perturbiner approach to Einstein gravity, we compute the metric of a Schwarzschild black hole order by order in perturbation theory. Using recursion, this calculation can be carried out in de Donder gauge to all orders in Newton’s constant. The result is a geometric series which is convergent outside a disk of finite radius, and it agrees within its region of convergence with the known de Donder gauge metric of a Schwarzschild black hole. It thus provides a first all-order perturbative computation in Einstein gravity with a matter source, and this series converges to the known nonperturbative expression in the expected range of convergence.

Published by the American Physical Society
2024
Long-Lived Coherence on a
μHz
Scale Optical Magnetic Quadrupole Transition
Authors: Klüsener V. , Pucher S. , Yankelev D. , Trautmann J. , Spriestersbach F. , Filin D. , Porsev S. G. , Safronova M. S. , Bloch I. , Blatt S.
Published: June 2024

We report on the coherent excitation of the ultranarrow S01–P23 magnetic quadrupole transition in Sr88. By confining atoms in a state insensitive optical lattice, we achieve excitation fractions of 97(1)% and observe linewidths as narrow as 58(1) Hz. With Ramsey spectroscopy, we find coherence times of 14(1) ms, which can be extended to 266(36) ms using a spin-echo sequence. We determine the lifetime of the P23 level for spontaneous emission of magnetic quadrupole radiation to be 110(31) min, confirming long-standing theoretical predictions. These results establish an additional clock transition in strontium and pave the way for applications of the metastable P23 state in quantum computing and quantum simulations.

Published by the American Physical Society
2024
Unveiling the odor representation in the inner brain of
Drosophila
through compressed sensing
Authors: Choi Kiri , Kim Won Kyu , Hyeon Changbong
Published: June 2024

The olfaction begins when odorant molecules stimulate a finite number of receptor types in the olfactory neurons. According to the recent connectomics data of the olfactory system, the olfactory neural circuit is multilayered and there is an overall dimensionality reduction from the input to output layer. Compressed sensing (CS) is an algorithm that enables the recovery of high-dimensional signals from the data compressed in a lower dimension when the representation of such signals is sufficiently sparse. By analyzing the recent connectomics data, we find that the organization of the olfactory system effectively satisfies the necessary conditions for CS to work. The neural activity profile of projection neurons (PNs) can be faithfully recovered from a low-dimensional response profile of mushroom body output neurons (MBONs), which can be reconstructed using the electrophysiological recordings of a wide range of odorants. By leveraging the residuals calculated between the measured and the predicted MBON responses, we visualize the perceptual odor space using the residual spectrum and discuss the differentiability of an odor from others. Our study highlights the sparse coding of odor to the receptor space as an essential component for odor identifiability, clarifying the principles underlying the concentration-dependent odor percept. Further, simultaneous exposure of the olfactory system to many different odorants saturates the neural activity profile of PNs, significantly degrading the capacity of signal recovery and resulting in a perceptual state analogous to “olfactory white.” Our study applying CS to the real connectomics data encompassing the neural circuitry from PNs to MBONs via Kenyon cells provides quantitative insights into the neural signal processing and odor representation in the inner brain of .

Published by the American Physical Society
2024
Mitigation of channel tampering attacks in continuous-variable quantum key distribution
Authors: Kish S. P. , Thapa C. , Sayat M. , Suzuki H. , Pieprzyk J. , Camtepe S.
Published: June 2024

Despite significant advancements in continuous-variable quantum key distribution (CV-QKD), practical CV-QKD systems can be compromised by various attacks. Consequently, identifying new attack vectors and countermeasures for CV-QKD implementations is important for the continued robustness of CV-QKD. In particular, as CV-QKD relies on a public quantum channel, vulnerability to communication disruption persists from potential adversaries employing denial-of-service (DoS) attacks. Inspired by DoS attacks, this paper introduces a threat in CV-QKD called the channel amplification (CA) attack, wherein Eve manipulates the communication channel through amplification. We specifically model this attack in a CV-QKD optical fiber setup. To counter this threat, we propose a detection and mitigation strategy. Detection involves a machine learning (ML) model based on a decision tree classifier, classifying various channel tampering attacks, including CA and DoS attacks. For mitigation, Bob, postselects quadrature data by classifying the attack type and frequency. Our ML model exhibits high accuracy in distinguishing and categorizing these attacks. The CA attack's impact on the secret key rate (SKR) is explored concerning Eve's location and the relative intensity noise of the local oscillator (LO). The proposed mitigation strategy improves the attacked SKR for CA attacks and, in some cases, for hybrid CA-DoS attacks. Our study marks an application of both ML classification and postselection in this context. These findings are important for enhancing the robustness of CV-QKD systems against emerging threats on the channel.

Published by the American Physical Society
2024
High-Rate and High-Fidelity Modular Interconnects between Neutral Atom Quantum Processors
Authors: Li Yiyi , Thompson Jeff D.
Published: June 2024

Quantum links between physically separated modules are important for scaling many quantum computing technologies. The key metrics are the generation rate and fidelity of remote Bell pairs. In this work, we propose an experimental protocol for generating remote entanglement between neutral ytterbium atom qubits using an optical cavity. By loading a large number of atoms into a single cavity, and controlling their coupling using only local light shifts, we amortize the cost of transporting and initializing atoms over many entanglement attempts, maximizing the entanglement generation rate. A twisted ring cavity geometry suppresses many sources of error, allowing high-fidelity entanglement generation. We estimate a spin-photon entanglement rate of 5×105s−1, and a Bell pair rate approaching 105s−1, with an average fidelity near 0.999. Furthermore, we show that the photon detection times provide a significant amount of soft information about the location of errors, which may be used to improve the logical qubit performance. This approach provides a practical path to scalable modular quantum computing using neutral ytterbium atoms.

Published by the American Physical Society
2024
High-throughput and high-resolution powder X-ray diffractometer consisting of six sets of 2D CdTe detectors with variable sample-to-detector distance and innovative automation system
Authors: Kawaguchi Shogo , Kobayashi Shintaro , Yamada Hiroki , Ashitani Hirotaka , Takemoto Michitaka , Imai Yasuhiko , Hatsui Takaki , Sugimoto Kunihisa , Sakata Osami
Published: June 2024

The demand for powder X-ray diffraction analysis continues to increase in a variety of scientific fields, as the excellent beam quality of high-brightness synchrotron light sources enables the acquisition of high-quality measurement data with high intensity and angular resolution. Synchrotron powder diffraction has enabled the rapid measurement of many samples and various in situ/operando experiments in nonambient sample environments. To meet the demands for even higher throughput measurements using high-energy X-rays at SPring-8, a high-throughput and high-resolution powder diffraction system has been developed. This system is combined with six sets of two-dimensional (2D) CdTe detectors for high-energy X-rays, and various automation systems, including a system for automatic switching among large sample environmental equipment, have been developed in the third experimental hutch of the insertion device beamline BL13XU at SPring-8. In this diffractometer system, high-brilliance and high-energy X-rays ranging from 16 to 72 keV are available. The powder diffraction data measured under ambient and various nonambient conditions can be analysed using Rietveld refinement and the pair distribution function. Using the 2D CdTe detectors with variable sample-to-detector distance, three types of scan modes have been established: standard, single-step and high-resolution. A major feature is the ability to measure a whole powder pattern with millisecond resolution. Equally important, this system can measure powder diffraction data with high Q exceeding 30 Å−1 within several tens of seconds. This capability is expected to contribute significantly to new research avenues using machine learning and artificial intelligence by utilizing the large amount of data obtained from high-throughput measurements.
Bayesian inference for inflation volatility modeling in Ghana
Authors: Korkpoe Carl Hope , Ahiakpor Ferdinand , Amarteifio Edward Nii Amar
Published: June 2024

Purpose

The purpose of this paper is to emphasize the risks involved in modeling inflation volatility in the context of macroeconomic policy. For countries like Ghana that are always battling economic problems, accurate models are necessary in any modeling endeavor. We estimate volatility taking into account the heteroscedasticity of the model parameters.

Design/methodology/approach

The estimations considered the quasi-maximum likelihood-based GARCH, stochastic and Bayesian inference models in estimating the parameters of the inflation volatility.

Findings

A comparison of the stochastic volatility and Bayesian inference models reveals that the latter is better at tracking the evolution of month-on-month inflation volatility, thus following closely the data during the period under review.

Research limitations/implications

The paper looks at the effect of parameter uncertainty of inflation volatility alone while considering the effects of other key variables like interest and exchange rates that affect inflation.

Practical implications

Economists have battled with accurate modeling and tracking of inflation volatility in Ghana. Where the data is not well-behaved, for example, in developing economies, the stochastic nature of the parameter estimates should be incorporated in the model estimation.

Social implications

Estimating the parameters of inflation volatility models is not enough in a perpetually gyrating economy. The risks of these parameters are needed to completely describe the evolution of volatility especially in developing economies like Ghana.

Originality/value

This work is one of the first to draw the attention of policymakers in Ghana towards the nature of inflation data generated in the economy and the appropriate model for capturing the uncertainty of the model parameters.