bluuebunny/crossref_metadata_2025 huggingface dataset:
Prospective evaluation of cystatin C in the assessment of kidney dysfunction and survival in liver transplant candidates
Authors: Gonzalez Stevan A. , Shankar Nagasri , Mehta Ashwini , Garcia-Saenz-de-Sicilia Mauricio , Klintmalm Goran B. , Trotter James F. , Asrani Sumeet K. , Fischbach Bernard V. , Duarte-Rojo Andres
Published: September 2024

Kidney dysfunction is associated with decreased survival in liver transplant (LT) candidates, yet serum creatinine (sCr) is a poor surrogate for glomerular filtration rate (GFR) in this population. Serum cystatin C (CysC) may provide a more accurate assessment of kidney function and predict outcomes. We performed a multicenter prospective cohort study of consecutive candidates for LT. CysC was obtained at LT evaluation (n = 244), and a subset underwent simultaneous I125-iothalamate clearance for measured GFR (mGFR) assessment (n = 137). Patients were followed to assess the need for pre-LT renal replacement therapy, simultaneous liver and kidney transplant, and survival. Estimated GFR (eGFR) based on MDRD-4, GRAIL, Royal Free Hospital Cirrhosis GFR, and the CKD-EPI equations was assessed for bias, precision, and accuracy in reference to mGFR. Receiver operator characteristic (AUROC) and competing risk survival analyses were performed. CysC more accurately discriminated mGFR than sCr at thresholds of ≤60 and ≤30 mL/min/1.73 m2 with AUROC 0.92 (p = 0.005) and 0.96 (p=0.01), respectively. All eGFR equations overestimated GFR, especially among females (p < 0.05). The GRAIL equation demonstrated the least bias, while CKD-EPI-cystatin C was associated with the greatest precision and lowest frequency of GFR overestimation. Among 165 recipients of LT, CysC discriminated pre-LT renal replacement therapy and the need for simultaneous liver and kidney transplant with AUROC of 0.70 and 0.85, respectively. Cumulative incidence of death, accounting for LT as a competing event, increased with CysC (p = 0.002) but was not observed with sCr overall or among subgroups (p = NS). CysC more accurately predicts thresholds of mGFR than sCr in candidates for LT. Elevated CysC discriminates pre-LT renal replacement therapy and simultaneous liver and kidney transplant and is strongly associated with survival in contrast with sCr. CysC is a promising tool to improve prognostication among candidates for LT.
Quintuplet pregnancy: a case report from Pakistan
Authors: Qayyum Sardar Noman , Alamgir Eman , Alamgir Iqra , Khan Gulmeena Aziz , Alamgir Unsa , Rehan Muhammad , Noori Samim
Published: September 2024

Introduction and importance:

Quintuplet pregnancies are exceptionally rare outcomes of fertility treatments, that is clomiphene citrate therapy. These high-order multiple pregnancies carry significant risks for both maternal and neonatal health, necessitating specialized care to manage complications effectively.

Case presentation:

A 26-year-old woman, gravida three para two, presented with preterm labor at 32 weeks gestation following clomiphene citrate self-medication. Diagnosed with quintuplets, she underwent an emergency cesarean section at Allied-1 Hospital, Faisalabad, delivering five neonates alive. Unfortunately, all five neonates succumbed to death due to perinatal asphyxia, three within 24 h and two on the third day.

Clinical discussion:

Higher-order multiple pregnancies, such as quintuplets, are associated with increased risks of obstetric complications, including pre-eclampsia, gestational diabetes, and fetal growth restriction. Preterm birth further exacerbates the risk of neonatal complications like respiratory distress syndrome, perinatal asphyxia, and death. The patient’s care highlights the challenges of managing such pregnancies in resource-limited settings, emphasizing the need for specialized antenatal and neonatal care facilities.

Conclusion:

This case highlights the critical need for advanced medical care in managing high-order multiple pregnancies. The outcomes reflect the significant challenges posed by preterm labor and neonatal complications in quintuplet pregnancies. There is the need for enhanced antenatal care, healthcare infrastructure, and multidisciplinary teams for the efficient management of high-order multiple pregnancies in Pakistan, where neonatal and maternal mortality rates are surprisingly high.
Examining Unusual Patterns of Cancer and Environmental Concerns: The Importance of Community Input and Engagement
Authors: Foster Stephanie L. , Condon Suzanne K. , Lavery Amy M. , Etheredge Alisha A. , Kennedy Brian S. , Svendsen Erik R. , Breysse Patrick N.
Published: September 2024

Context:

In fiscal year 2019, the Department of Health and Human Services (DHHS) received an appropriation from Congress specifically to update guidelines for investigating community cancer concerns. This resulted in the DHHS directing the Centers for Disease Control and Prevention (CDC) to fulfill this responsibility.

Program:

The CDC and the Agency for Toxic Substances and Disease Registry (ATSDR) provide guidance to state, tribal, local, and territorial (STLT) health departments and play important roles in supporting STLT programs in addressing community cancer concerns.

Implementation:

The updated guidelines offer enhancements addressing limitations and challenges regarding the process for investigating cancer clusters as expressed by STLT programs responsible for responding to inquiries and by communities impacted by unusual patterns of cancer. Additionally, the updated guidelines offer new tools and approaches associated with scientific advancements. Issues associated with improving communications and community engagement were a priority. Details in the updated guidelines provide suggestions for building and maintaining trust; provide resources via additional tools, templates, and methodology to facilitate sharing of information; provide suggestions for identifying agency and community points of contacts; and provide suggestions for establishing a community advisory committee.

Conclusion:

Enhancements to the previous guidelines were included to address advancements in statistical approaches and methods for understanding exposure pathways and also to respond to limitations described in the previous guidelines. Furthermore, these enhancements ensure communities have a voice in the process and offer methods to enhance transparency throughout the investigative process. Ultimately, the 2022 Guidelines are designed to ensure that community engagement, community input, and communication remains paramount to the process of assessing unusual patterns of cancer and environmental concerns.
Discovery of Natural Products for Cancer Prevention
Authors: Blanco Carcache Peter J. , Clinton Steven K. , Kinghorn A. Douglas
Published: September 2024

“Cancer chemoprevention” is a term referring to the slowing or reversal of this disease, using nontoxic natural or synthetic compounds. For about 50 years, there has been a strong scientific interest in discovering plant-derived compounds to prevent cancer, and strategies for this purpose using a concerted series ofin vitro,ex vivo, andin vivolaboratory bioassays have been developed. Five examples of the more thoroughly investigated agents of this type are described herein, which are each supported by detailed literature reports, inclusive of ellagic acid, isoliquiritigenin, lycopene,trans-resveratrol, and sulforaphane. In addition, extracts of the plants avocado (Persea americana), noni (Morinda citrifolia), açai (Euterpe oleracea), and mangosteen (Garcinia mangostana) have all shown inhibitory activity in anin vivoorex vivobioassay using a carcinogen and germane to cancer chemoprevention, and selectedin vitro–active constituents are described for each of these 4 species.
Mapping the Landscape of Those Left Behind When a Person With Dementia Dies
Authors: Baker Zachary G. , Han SeungYong , Sefcik Justine S. , Petrovsky Darina V. , Ma Kris Pui Kwan , Smith Matthew Lee , Bacsu Juanita-Dawne R. , Rahemi Zahra , Saenz Joseph
Published: September 2024

Introduction:

People with dementia can have many family and friends who might be affected by their deaths. Pursuing the long-term aim of understanding how dementia deaths affect close family and friends, this project lays groundwork through estimates of who those close family and friends are, with special attention to race and ethnicity.

Method:

Regression models estimated associations between dementia, race/ethnicity, and close family and friend network size, controlling for age, sex, education, marital status, and household wealth for 1386 deceased people with dementia from the Health and Retirement Study (2004 to 2018).

Results:

Persons with dementia had an average of 9.4 close family and friends at death. But patterns of close family and friends were different among non-Latino Black (10.8), Latino (9.9), and non-Latino White (9.2) people with dementia at death. Notably, non-Latino White persons with dementia had the fewest close family (3.7), followed by non-Latino Black (5.1), and Latino (7.7) persons with dementia.

Discussion:

Knowing who might be affected by dementia deaths is the first step to explore how dementia-related deaths impact close family and friends. Future work can now sample bereaved family and friends of people with dementia to explore their experiences and develop culturally appropriate supports.
Virgibacillus tibetensis sp. nov., isolated from salt lake on the Tibetan plateau of China
Authors: Li Dongyang , Phurbu Dorji , Zhang Xuan , Liu Zi-Xuan , Wang Rui , Zheng Yan-Yan , Zhou Yu-Guang , Yu Ya-Jing , Xue Lu , Li Ai-Hua
Published: September 2024

One bacterial strain, designated as C22-A2T, was isolated from Lake LungmuCo in Tibet. Cells of strain C22-A2T were long rod-shaped, Gram-stain-negative, non-spore-forming, with positive catalase and oxidase activity. Optimal growth occurred at 20–25 °C, pH 8.0 and with 3.0–7.0% (w/v) NaCl. Phylogenetic analysis of 16S rRNA gene and whole genome sequences revealed that strain C22-A2T belonged to the genus Virgibacillus, showing the highest 16S rRNA gene similarity to Virgibacillus halodenitrificans DSM 10037T (97.6%). The average nucleotide identity values between strain C22-A2T and the type strains of related species in the genus Virgibacillus were less than 74.4% and the digital DNA–DNA hybridization values were less than 20.2%, both below the species delineation thresholds of 95 and 70% respectively. The genome analysis revealed that strain C22-A2T harboured genes responsible for osmotic and oxidative stress, enabling it to adapt to its surrounding environment. In terms of biochemical and physiological characteristics, strain C22-A2T shared similar characteristics with the genus Virgibacillus, including the predominant cellular fatty acid anteiso-C15 : 0, the major respiratory quinone MK-7, as well as the polar lipids phosphatidylglycerol and diphosphatidylglycerol. Based on the comprehensive analysis of phylogenetic, phylogenomic, morphological, physiological and biochemical characteristics, strain C22-A2T is proposed to represent a novel species of the genus Virgibacillus, named as Virgibacillus tibetensis sp. nov. (=CGMCC 1.19202T=KCTC 43426T).
FcγR- and CD9-dependent synapse engulfing microglia in the thalamus drives cognitive impairment following cortical brain injury
Authors: Matoba Ken , Kochi Takahiro , Mreyoud Yassin R , Badrani Jana H. , Patel Hency , Tsujioka Hiroshi , Yamashita Toshihide , Crossman David K. , Niwa Minae , Kano Shin-ichi
Published: September 2024

Various states of microglia appear in neuroinflammation, but their impact on brain function and behavior is not fully understood. Here we report that synapse engulfing microglia in the thalamus are crucial for cognitive impairment after cortical brain injury. Region-specific manipulations of reactive microglia in the chronic phase of injuries showed that microglial changes in the thalamus, but not in the hippocampus, impaired recognition memory. Single-cell RNA-sequencing analysis revealed the enrichment of synapse engulfing microglia in the thalamus, which developed in a CD9-dependent manner and caused synaptic loss and recognition memory deficits. In the thalamus, the blood-brain barrier was disrupted, and extravasated γ-immunoglobulins (IgG) co-localized with synapse engulfing microglia. Fcγ receptor III blockade in the thalamus reduced synapse engulfing microglia, synapse loss, and recognition memory deficits. These findings demonstrate that the induction of synapse engulfing microglia in the thalamus by extravasated IgG/FcγRIII and CD9 signals causes recognition memory deficits after cortical brain injury.
Adaptive immunity shapes innate and epithelial cell landscapes by silencing tonic IFN-γ in innate lymphoid cells during homeostasis
Authors: Mejri Ousséma , Ma Li , Aoudi Amneh , Labiad Ossama , Mondot Stanislas , Igalouzene Ramdane , Codan Clément , Hernandez-Vargas Hector , Rousseaux Noémi , Lapaque Nicolas , Paul Stéphane , Walzer Thierry , Marie Julien C. , Soudja Saïdi
Published: September 2024

During homeostasis, innate and epithelial cells undergo continuous maturation, shaped by microbial, molecular and cellular interactions. While these cells influence adaptive immunity during steady-state conditions, the reciprocal homeostatic role of adaptive immune cells in the maturation and function of innate and epithelial cells remains underexplored. Here, through computational approaches and murine models, we establish that adaptive immunity shapes innate immune and epithelial homeostatic landscapes. Mechanistically, adaptive immunity acts as a brake on type 1 polarization and diversification of innate lymphocytes (ILCs). Without adaptive immunity, the innate cellular interactions within the mesenteric lymph nodes are dominated by an interferon-gamma (IFNγ) signaling network. Moreover, the innate immune and epithelial cells follow distinct phenotypic and functional trajectories, including ILCs acquiring myeloid markers, monocytes adopting an inflammatory path, and colonic epithelial cells expressing altered antimicrobial peptides and losing Paneth-like features. Depleting ILCs, abolishing IFNγ signaling, or restoring adaptive immunity reduces these IFNγ-driven changes. Thus, our findings highlight a homeostatic function of adaptive immunity in modulating innate and epithelial cell communication, diversity, composition, function, and differentiation, notably by limiting ILC-derived IFNγ.
Using machine learning to forecast peak health care service demand in real-time during the 2022-23 winter season: a pilot in England, UK
Authors: Morbey Roger A , Todkill Dan , Moura Phil , Tollinton Liam , Charlett Andre , Watson Conall H. , Elliot Alex J
Published: September 2024

During winter months, there is increased pressure on health care systems in temperature climates due to seasonal increases in respiratory illnesses. Providing real-time short-term forecasts of the demand for health care services helps managers plan their services.

During the Winter of 2022-23 we piloted a new forecasting pipeline, using existing surveillance indicators which are sensitive to increases in respiratory syncytial virus (RSV). Indicators including telehealth cough calls and ED bronchiolitis attendances, both in children under 5 years. We utilised machine learning techniques to train and select models that would best forecast the timing and intensity of peaks up to 28 days ahead. Forecast uncertainty was modelled usings a novel gamlss approach which enabled prediction intervals to vary according to the level of the forecast activity.

The winter of 2022-23 was atypical because the demand for healthcare services in children was exceptionally high, due to RSV circulating in the community and increased concerns around invasive Group A streptococcal (GAS) infections. However, our short-term forecasts proved to be adaptive forecasting a new higher peak once the increasing demand due to GAS started. Thus, we have demonstrated the utility of our approach, adding forecasts to existing surveillance systems.
SARS-CoV-2, the human placenta, and adverse perinatal outcomes
Authors: Linn Rebecca L. , Forkpa Markolline , Leite Rita , Guerrero Jessenia C. , Reyes Maria C. , Schwartz Lauren E. , Simmons Rebecca A. , Parry Samuel , Golden Thea N.
Published: September 2024

The relationship among timing and severity of COVID-19 during pregnancy, placental pathology, and adverse pregnancy outcomes is not well understood. We conducted a prospective cohort study of 497 pregnant patients with COVID-19 whose placentas underwent systematic pathologic examination. The main exposure was timing of COVID-19 during pregnancy (first or second versus third trimester). The primary outcome was composite placental pathology that included high grade maternal vascular malperfusion or greater than 25 percent perivillous fibrin deposition. There were 63 patients who had the composite placental pathology outcome. In adjusted analyses that controlled for maternal age, parity, active infection at delivery, interval from time of diagnosis to delivery and COVID-19 variant, timing of COVID-19 during pregnancy was not associated with risk of the composite placental pathology outcome. Among secondary COVID-19 related exposures we investigated, severity of disease and treatment for COVID-19 were associated with risk of the composite placental pathology outcome. In addition, patients with COVID-19 in the first nine months of the pandemic had the highest rate of the composite placental pathology outcome. In this large cohort, placental vascular pathology was common among COVID-19 cases but was unrelated to timing of COVID-19 during pregnancy or adverse pregnancy outcomes. These findings suggest that uncomplicated COVID-19 during pregnancy does not require intensive fetal surveillance or detailed pathologic examination of the placenta after delivery.
Pelvic Stability During Total Hip Arthroplasty: A Comparison of Traction and Standard Surgical Tables Using Augmented Reality Navigation
Authors: Ima Musashi , Kabata Tamon , Inoue Daisuke , Yanagi Yu , Iyobe Takahiro , Fujimaru Naoya , Demura Satoru
Published: September 2024

Background

Total hip arthroplasty enhances quality of life by improving joint function. However, the success of this procedure heavily relies on precise acetabular cup positioning, which is insufficient using traditional placement guidelines. This insufficiency is evidenced by the persistent occurrence of dislocations, highlighting the critical need for enhanced pelvic alignment accuracy. Standard surgical tables present challenges in maintaining consistent pelvic positioning during the procedure, making it difficult to achieve optimal alignment.

Purpose

This study aimed to evaluate the effectiveness of a traction surgical table in stabilizing pelvic movements during total hip arthroplasty and compare it with the use of a standard surgical table.

Methods

This retrospective study assessed 88 total hip arthroplasties performed using the AR-HIP (Zimmer Biomet Japan, Tokyo, Japan) system for real-time pelvic navigation. Procedures were performed using either a standard surgical table (n=48) or a traction surgical table (n=40). Pelvic alignment was monitored at multiple surgical stages, and stability was statistically analyzed to compare the efficacy of the two table types.

Results

The traction table significantly stabilized anteroposterior pelvic movements across all critical surgical stages (p<0.05), except during anterior capsular release. In contrast, procedures performed on the standard table exhibited less stability in anteroposterior pelvic movements, suggesting the superior performance of the traction table.

Conclusions

Compared with the standard table, the use of the traction table in total hip arthroplasty effectively controls anteroposterior pelvic movements and improves acetabular cup alignment. However, lateral pelvic stability remains uncontrolled using both table types, indicating a need for further technological advancements in surgical practice to improve the outcomes of total hip arthroplasty.
Resource Recovery from Wastewater By Directing Microbial Metabolism Toward Production of Value-added Biochemicals
Authors: Zhou Xueyang , Manna Bharat , Lyu Boyu , Lear Gavin , Kingsbury Joanne M. , Singhal Naresh
Published: September 2024

Transitioning wastewater treatment from mere pollutant removal to resource recovery necessitates exploiting the metabolic capabilities of microbial communities. Studies suggest that under low-oxygen conditions, microbes activate oxygen-responsive regulons that suppress the tricarboxylic acid (TCA) cycle, diverting carbon flux towards biosynthetic pathways and accumulating valuable organic metabolites. We hypothesized that dynamically altering dissolved oxygen levels in activated sludge would disrupt aerobic metabolic equilibrium, enhancing the production of valuable biochemicals like amino acids and fatty acids. To test this, batch experiments were conducted with activated sludge under constant aeration and rapid cycling between oxygen-rich and oxygen-poor states. Fluctuating oxygen concentrations between 0 and 2 mg/L significantly increased valuable biochemical production compared to constant aeration (P<0.05). Continuous oxygen perturbations increased free amino acids by 35.7±7.6% and free fatty acids by 76.4±13.0%, while intermittent perturbations with anoxic periods enhanced free amino acids by 42.4±8.1% and free fatty acids by 39.3±7.7%. Notably, 14 standard amino acids showed significant increases, and most fatty acids had carbon chain lengths between C12-C22. Mechanistically, compared to stable oxygen, oxygen perturbations activated the FNR and ArcA regulons, resulting in lower relative abundances of TCA cycle enzymes such as malate dehydrogenase, isocitrate dehydrogenase, and 2-oxoglutarate dehydrogenase, while higher relative abundances of amino acid (ilv cluster) and fatty acid (acc cluster) biosynthetic enzymes. Our findings demonstrate that introducing controlled oxygen fluctuations in wastewater treatment can enhance the biochemical value of activated sludge with minimal process modifications, facilitating resource recovery.

Abstract Figure
Identification of the orphan GPR25 as a receptor of the chemokine CXCL17
Authors: Hu Wen-Feng , Yu Jie , Wang Juan-Juan , Sun Ru-Jiao , Zheng Yong-Shan , Zhang Teng , Liu Ya-Li , Xu Zeng-Guang , Guo Zhan-Yun
Published: September 2024

C-X-C motif chemokine ligand 17 (CXCL17) is a small secretory protein primarily expressed in mucosal tissues and likely functions as a chemoattractant, but its receptor is still controversial. In the present study, we identified the rarely studied orphan G protein-coupled receptor 25 (GPR25) as a receptor of CXCL17 via prediction by the newly developed AlphaFold 3 algorithm and validation by the NanoBiT-based β-arrestin recruitment assay. In the β-arrestin recruitment assay, recombinant human CXCL17 could activate human GPR25 in transfected human embryonic kidney (HEK) 293T cells with an EC50value around 100 nM, but it had no activation effect on 17 other tested G protein-coupled receptors (GPCRs). Deletion of three conserved C-terminal residues of human CXCL17 almost abolished its activity, and alanine replacement of W95 or R178 of human GPR25, two conserved residues in the predicted orthosteric ligand binding pocket, almost abolished its response towards CXCL17. These results are consistent with the AlphaFold 3-predicted binding model in which the highly conserved C-terminal fragment of CXCL17 inserts into the orthosteric ligand binding pocket of the receptor GPR25. According to the expression pattern of CXCL17 and GPR25 shown at the Human Protein Atlas, CXCL17 might be an endogenous agonist of GPR25 in human and other mammals, but this hypothesis needs to be tested in future studies via more assays. The present deorphanization paves the way for further functional characterization of the orphan receptor GPR25 and the orphan ligand CXCL17.
Leveraging Illumina iSeq100 for Whole Genome Sequencing ofSalmonella Typhi: a practical approach for resource-limited setting
Authors: Katuwal Nishan , Naga Shiva Ram , Shrestha Aastha , Shahi Sabin Bikram , Tamrakar Dipesh , Shrestha Rajeev
Published: September 2024

Bacterial whole genome sequencing helps to improve our understanding of epidemiology and pathogenesis of bacterial infections and allows comprehensive investigation on virulence, evolution and resistance mechanisms. Nepal, in recent times, has seen some increase in sequencing capabilities but faces numerous hurdles for optimum utilization. However, these hurdles can be alleviated with use of Illumina iSeq100. Therefore, this study aimed at performing whole genome sequencing of bacteria isolated utilizing the iSeq100 platform.

For this study, 6 bankedSalmonella entericaserovar Typhi bacterial isolates were selected. These isolates were extracted for DNA, confirmed by qPCR and then, their libraries were prepared. The libaries were checked and loaded in Illumina iSeq100 at loading concentration of 200pM. The consensus was generated from the raw genomic data by reference-based assembly, mapping onto S. Typhi CT18. These consensus genomes and coverage parameters were compared to data from using HiSeq and NextSeq. The raw reads were also evaluated using pathogenwatch (v22.3.8) to observe for genotype, mutations and resistance genes.

The coverage parameters (coverage width and depth) of the genomes from this study were compared to same genomes sequenced using Illumina HiSeq and NextSeq. The average coverage width (96.81%) and depth (63.75x) of genomes sequenced in iSeq100 were comparable to that of HiSeq (width: 98.72% and depth: 69.87x). When the genomes sequenced were compared, the genotypes detected, number of SNPs and genetic determinants of AMR genes were identical.

The data from bacterial whole genome sequencing using the Illumina iSeq100 is equally informative when compared to other high-end sequencers. Therefore, the primary goal of this study is to advocate for optimum utlisation of iSeq100 while still ensuring a high standard of quality. This optimum utilization would create capacity to fill critical surveillance gaps.
Neural geometry efficiently representing abstract form of value and modality in the primate basal ganglia
Authors: Hwang Seong-Hwan , Lee Ji-Woo , Kim Sung-Phil , Kim Hyoung F.
Published: September 2024

Basal ganglia process diverse values from various modalities using limited resources, necessitating efficient processing. This involves converging tactile and visual information within bimodal value-coding neurons, ensuring efficient processing with limited number of neurons. However, convergence at the single neuron level may compromise modality-specific information, raising the question: Does efficient processing inevitably degrade information quality? We investigated the representational geometry in the putamen of macaque monkeys trained to learn values from tactile and visual inputs. Here, we demonstrated that the population representation of bimodal value-coding neurons in the putamen preserved both value and modality information, and these representations were shared to efficiently maintain quality. Notably, these representations were generalized across identical modalities and values, resulting in an efficient low-dimensional representation. Furthermore, a faster transformation to a generalized value representation within neural geometry reflected greater confidence in value-guided choice behavior—this correlation not observed in conventional decoding. Our results suggest that bimodal value-coding neurons play a key role in balancing efficiency and information fidelity, facilitating cognitive states required for confident decision-making.
Bridging the gap between the connectome and whole-brain activity inC. elegans
Authors: Creamer Matthew S. , Leifer Andrew M. , Pillow Jonathan W.
Published: September 2024

A fundamental goal of neuroscience is to understand how anatomy determines the functional properties of the nervous system. However, previous work has failed to show how the functional connections between neurons are derived from the connectome in the nematodeC. elegans, raising questions about whether anatomy is informative of signaling1-3. Here, we address this problem using a connectome-constrained dynamical model of the brain, which we fit to whole-brain recordings of neural activity during optogenetic perturbation of single neurons2. This dynamical model, which contains non-zero weights only between anatomically connected neurons, captured causal interactions between all pairs of neurons 92% as well as the reproducibility of the perturbation data itself. This included interactions between anatomically unconnected neurons, which the model accounted for in terms of signal propagation over multiple neurons. Strikingly, alternative models fit using a shuffled connectome achieved much lower performance. Finally, we found that adding connections beyond those in the connectome did not improve the model’s ability to capture causal interactions. Our model thus provides the strongest link yet between the connectivity of theC. elegansnervous system and its causal interactions and provides a blueprint for exploring the link between structure and function in other organisms.
Inferring Effective Networks of Spiking Neurons Using a Continuous-Time Estimator of Transfer Entropy
Authors: Shorten David P. , Priesemann Viola , Wibral Michael , Lizier Joseph T.
Published: September 2024

When analysing high-dimensional time-series datasets, the inference of effective networks has proven to be a valuable modelling technique. This technique produces networks where each target node is associated with a set of source nodes that are capable of providing explanatory power for its dynamics. Multivariate Transfer Entropy (TE) has proven to be a popular and effective tool for inferring these networks. Recently, a continuous-time estimator of TE for event-based data such as spike trains has been developed which, in more efficiently representing event data in terms of inter-event intervals, is significantly more capable of measuring multivariate interactions. The new estimator thus presents an opportunity to more effectively use TE for the inference of effective networks from spike trains, and we demonstrate in this paper for the first time its efficacy at this task. Using data generated from models of spiking neurons — for which the ground-truth connectivity is known — we demonstrate the accuracy of this approach in various dynamical regimes. We further show that it exhibits far superior inference performance to a pairwise TE-based approach as well as a recently-proposed convolutional neural network approach. Moreover, comparison with Generalised Linear Models (GLMs), which are commonly applied to spike-train data, showed clear benefits, particularly in cases of high synchrony. Finally, we demonstrate its utility in revealing the patterns by which effective connections develop from recordings of developing neural cell cultures.
Memory effects in a sequence of measurements of noncommuting observables
Authors: Walls Sophia M. , Ford Ian J.
Published: September 2024

We use continuous, stochastic quantum trajectories within a framework of quantum state diffusion (QSD) to describe alternating measurements of two noncommuting observables. Projective measurement of an observable completely destroys memory of the outcome of a previous measurement of the conjugate observable. In contrast, measurement under QSD is not projective and it is possible to vary the rate at which information about previous measurement outcomes is lost by changing the strength of measurement. We apply our methods to a spin 1/2 system and a spin 1 system undergoing alternating measurements of the Sz and Sx spin observables. Performing strong Sz measurements and weak Sx measurements on the spin 1 system, we demonstrate return to the same eigenstate of Sz to a degree beyond that expected from projective measurements and the Born rule. Such a memory effect appears to be greater for return to the ±1 eigenstates than the 0 eigenstate. Furthermore, the spin 1 system follows a measurement cascade process where an initial superposition of the three eigenstates of the observable evolves into a superposition of just two, before finally collapsing into a single eigenstate, giving rise to a distinctive pattern of evolution of the spin components.

Published by the American Physical Society
2024
Bell inequality is violated in charmonium decays
Authors: Fabbrichesi M. , Floreanini R. , Gabrielli E. , Marzola L.
Published: September 2024

The experimental data on the helicity amplitudes of charmonium decays allow us to measure entanglement in final state spin correlations and test possible violations of the Bell inequality. We find that the Bell inequality is violated with a significance of 5σ or more in the decays ηc,χc0,J/ψ→Λ+Λ¯, J/ψ→Ξ−+Ξ¯+,Ξ0+Ξ¯0,Σ−+Σ¯+,Σ0+Σ¯0, ψ(3686)→Ξ−+Ξ¯+,Σ−+Σ¯+,Σ0+Σ¯0, χc0,χc1→ϕ+ϕ. The decays ψ(3686)→Λ+Λ¯ and Ξ0+Ξ¯0 show the same violation but with less significance. The decay ψ(3686)→Ω−+Ω¯+ displays entanglement. These results firmly establish the presence of entanglement and quantum nonseparability at high energies, in a setting with particles of different spins and interacting through electroweak and strong interactions. In addition, the relatively long lifetime of some of the strange baryons produced in the decays provides a natural probe to test whether quantum spin correlations remain after the particles have interacted with the beam pipe and the first few layers of the detector.

Published by the American Physical Society
2024
Toponium hunter’s guide
Authors: Aguilar-Saavedra J. A.
Published: September 2024

We address the discovery and characterization of toponium production at the Large Hadron Collider. In the dilepton decay mode, multivariate analyses of spin and color observables could provide evidence that an excess of events present near the tt¯ threshold corresponds to a spin-zero color singlet. The semileptonic decay mode may also exhibit an excess near threshold, but is not expected to play any role in the toponium characterization.

Published by the American Physical Society
2024
Exploring doubly heavy tetraquarks in a constituent-quark-model based meson-meson coupled-channels approach
Authors: Ortega P. G. , Entem D. R. , Fernández F. , Segovia J.
Published: September 2024

The LHCb Collaboration announced in 2021 the discovery of a new tetraquarklike state, named Tcc+, with minimum quark content ccu¯d¯, close to the D0D*+ threshold. This has motivated countless theoretical works trying to identify the dynamics which is responsible of the formation of such state; in particular, the one performed by us in Ortega [; ], where a D0D*+ molecular candidate whose mass, width, scattering length, and effective ranges are in reasonable agreement with experimental measurements. We explore herein the possibility of having Tcc+ partners in all doubly heavy tetraquark sectors, considering doubly represented light antiquarks u, d, or s, and taking into account all possible spin-parity quantum numbers. The computation is done using a constituent-quark-model based meson-meson coupled-channels framework which has been tested many times in the last fifteen years describing conventional heavy mesons and baryons, their coupling with hadron-hadron thresholds but also in exploring its application to compact multiquark structures. The advantage of using an approach with such a relatively large history is that it allows us to make predictions because all the parameters have already been constrained from our previous works. Then, from this perspective, we present a parameter-free model-dependent prediction of doubly-heavy tetraquarks that may be partners of the discovered Tcc+ state.

Published by the American Physical Society
2024
Quantum error thresholds for gauge-redundant digitizations of lattice field theories
Authors: Carena Marcela , Lamm Henry , Li Ying-Ying , Liu Wanqiang
Published: September 2024

In the quantum simulation of lattice gauge theories, gauge symmetry can be either fixed or encoded as a redundancy of the Hilbert space. While gauge-fixing reduces the number of qubits, keeping the gauge redundancy can provide code space to mitigate and correct quantum errors by checking and restoring Gauss’s law. In this work, we consider the correctable errors for generic finite gauge groups and design the quantum circuits to detect and correct them. We calculate the error thresholds below which the gauge-redundant digitization with Gauss’s law error correction has better fidelity than the gauge-fixed digitization involving only gauge-invariant states. Our results provide guidance for fault-tolerant quantum simulations of lattice gauge theories.

Published by the American Physical Society
2024
New
μ
forces from
νμ
sources
Authors: Cesarotti Cari , Kahn Yonatan , Krnjaic Gordan , Rocha Duncan , Spitz Joshua
Published: September 2024

Accelerator-based experiments reliant on charged pion and kaon decays to produce muon-neutrino beams also deliver an associated powerful flux of muons. Therefore, these experiments can additionally be sensitive to light new particles that preferentially couple to muons and decay to visible final states on macroscopic length scales. Such particles are produced through rare 3-body meson decays in the decay pipe or via muon scattering in the beam dump, and decay in a downstream detector. To demonstrate the potential of this search strategy, we recast existing MiniBooNE and MicroBooNE studies of neutral pion production in neutrino-induced neutral-current scattering (νμN→νμNπ0,π0→γγ) to place limits on light (<2mμ) muon-philic scalar particles that decay to diphotons through loops of virtual muons. While much of this parameter space has already been excluded by E137, we also project that SBND can be sensitive to unexplored parameter space for these models, and provide a road map for future neutrino experiments to perform dedicated searches for muon-philic forces.

Published by the American Physical Society
2024
Metastability of quantum fields in a thermal bath
Authors: Fan Zhiyi , Moroi Takeo
Published: September 2024

We investigate the metastability of scalar fields in quantum field theories at finite temperature, focusing on a detailed understanding of the bounce solution. At finite temperature, the bounce solution depends on two variables: the Euclidean time τ and the spatial radial distance r, and it is periodic in the τ direction. We propose a novel method to determine the bounce that describes transitions in a thermal bath, suitable for numerical calculations. Two types of bounces exist for transitions in a thermal bath: τ-dependent and τ-independent bounces. We apply our method to compute these bounces in several models, including both thin-wall and thick-wall scenarios, to examine their properties. Specifically, we evaluate the critical temperature below which the τ-independent bounce becomes destabilized due to fluctuations, rendering it irrelevant. We demonstrate that in the thick-wall case, the τ-dependent bounce smoothly transitions into the τ-independent one as temperature increases, whereas in the thin-wall case, the transition between the two types of bounces is discontinuous.

Published by the American Physical Society
2024
Enlarged super-
bms3
algebra and its flat limit
Authors: Matulich Javier , Rodríguez Evelyn
Published: September 2024

In this paper we analyze the asymptotic symmetries of the three-dimensional Chern-Simons supergravity for a supersymmetric extension of the semisimple enlargement of the Poincaré algebra, also known as AdS-Lorentz superalgebra, which is characterized by two fermionic generators. We propose a consistent set of asymptotic boundary conditions for the aforementioned supergravity theory, and we show that the corresponding charge algebra defines a supersymmetric extension of the semisimple enlargement of the bms3 algebra, with three independent central charges. This asymptotic symmetry algebra can alternatively be written as the direct sum of three copies of the Virasoro algebra, two of which are augmented by supersymmetry. Interestingly, we show that the flat limit of the obtained asymptotic algebra corresponds to a deformed super-bms3 algebra, being the charge algebra of the minimal Maxwell supergravity theory in three dimensions.

Published by the American Physical Society
2024
Equivalence of Noether charge and Hilbert action boundary term formulas for the black hole entropy in
F(Rabcd)
gravity theory
Authors: Guo Wei , Guo Xiyao , Li Mingfeng , Mou Zili , Zhang Hongbao
Published: September 2024

By working with the covariant phase space formalism, we have shown that not only can the Hamiltonian conjugate to a Killing vector field ξ be expressed as the sum of the associated Noether charge and ξ contracted with the Hilbert action boundary term for F(Rabcd) gravity, but it can also be written as its contraction with another ξ independent tensor field. With this, we have proven the equivalence of Noether charge and Hilbert action boundary term formulas for the stationary black hole entropy in F(Rabcd) gravity, which is further substantiated by our explicit computation using both formulas.

Published by the American Physical Society
2024
Dimer piling problems and interacting field theory
Authors: Ramirez Camasca Rolando , McGreevy John
Published: September 2024

The dimer tiling problem asks in how many ways can the edges of a graph be covered by dimers so that each site is covered once. In the special case of a planar graph, this problem has a solution in terms of a free fermionic field theory. We rediscover and explore an expression for the number of coverings of an arbitrary graph by arbitrary objects in terms of an interacting fermionic field theory first proposed by Samuel. Generalizations of the dimer tiling problem, which we call “dimer piling problems,” demand that each site be covered N times by indistinguishable dimers. Our field theory provides a solution of these problems in the large-N limit. We give a similar path integral representation for certain lattice coloring problems.

Published by the American Physical Society
2024
New physics at a neutron beam dump
Authors: Dev P. S. Bhupal , Dutta Bhaskar , Han Tao , Karthikeyan Aparajitha , Kim Doojin , Kim Hyunyong
Published: September 2024

We find a new utility of neutrons, usually treated as an experimental nuisance causing unwanted background, in probing new physics signals. The new physics signals can either be radiated from neutrons (neutron bremsstrahlung) or appear through secondary particles from neutron-on-target interactions, dubbed “neutron beam dump.” As a concrete example, we take the FASER/FASER2 experiment as a “factory” of high-energy neutrons that interact with the iron dump. We find that if new physics particles had the same interaction strength to protons and neutrons, their production rate via neutron-initiated bremsstrahlung would be comparable to that via proton-initiated ones, in terms of the resulting flux and the range of couplings that can be probed. The neutron bremsstrahlung can be used, for instance, to probe dark gauge bosons with nonzero neutron coupling. In particular, we investigate protophobic gauge bosons and find that FASER/FASER2 can probe new parameter space. We also illustrate the possibility of neutron-induced secondary particles by considering axionlike particles with electron couplings. We conclude that the physics potential of FASER/FASER2 in terms of new physics searches can be greatly extended and improved with the inclusion of neutron interactions.

Published by the American Physical Society
2024
Kardar-Parisi-Zhang fluctuations in the synchronization dynamics of limit-cycle oscillators
Authors: Gutiérrez Ricardo , Cuerno Rodolfo
Published: September 2024

The time-dependent process whereby one-dimensional systems of self-sustained oscillators synchronize is shown to display scale invariance in space and time, akin to that found in the dynamics of equilibrium critical phenomena. Remarkably, the process is largely independent of system details, sharing with a class of nonequilibrium surface kinetic roughening the universal scaling behavior of the Kardar-Parisi-Zhang equation with columnar noise, and featuring phase fluctuations that follow a Tracy-Widom probability distribution. This is revealed by a numerical exploration of rings of Stuart-Landau oscillators (the universal representation of an oscillating system close to a Hopf bifurcation) and rings of van der Pol oscillators, both paradigmatically supporting self-sustained oscillations. The critical behavior is very well-defined for limit-cycle oscillations near bifurcation, and still dominates comparatively far from it. In particular, the Tracy-Widom fluctuation distribution seems to be an extremely robust feature of the synchronization process. The nonequilibrium criticality here described appears to transcend the details of the coupled dynamical systems that synchronize, making plausible its experimental observation.

Published by the American Physical Society
2024
Simulating the quantum Fourier transform, Grover's algorithm, and the quantum counting algorithm with limited entanglement using tensor networks
Authors: Niedermeier Marcel , Lado Jose L. , Flindt Christian
Published: September 2024

Quantum algorithms reformulate computational problems as quantum evolutions in a large Hilbert space. Most quantum algorithms assume that the time evolution is perfectly unitary and that the full Hilbert space is available. However, in practice, the available entanglement may be limited, leading to a reduced fidelity of the quantum algorithms. To simulate the execution of quantum algorithms with limited entanglement, tensor-network methods provide a useful framework, since they allow us to restrict the entanglement in a quantum circuit. Thus, we here use tensor networks to analyze the fidelity of the quantum Fourier transform, Grover's algorithm, and the quantum counting algorithm as the entanglement is reduced, and we map out the entanglement that is generated during the execution of each algorithm. In all three cases, we find that the algorithms can be executed with high fidelity even if the entanglement is somewhat reduced. For example, the quantum counting algorithm can be executed with a high fidelity beyond a certain threshold level of entanglement. Our results provide an understanding of the entanglement that is required to execute the three algorithms, and our simulations based on tensor networks can easily be applied to other algorithms.

Published by the American Physical Society
2024
Tacking: Shear fragility and geometry reduces the dissipation for dense suspensions
Authors: Acharya Pappu , Trulsson Martin
Published: September 2024

Dense suspensions tend to shear jam at large packing fractions. However, it has recently been shown that various oscillation protocols can unjam as well as reduce viscosity and dissipation per strain. In this numerical work, we show that alternating shear rotations protocols also reduce the dissipation per strain similar to shear protocols with a steady primary shear and superimposed cross oscillations, even though the latter's viscosity reduction is more considerable. Furthermore, we find that alternating between primary and perpendicular oscillations yields a much higher dissipation than the two protocols mentioned above, yet has similar viscosity as the cross-oscillatory one. While self-organization has been shown to minimize viscosity, our findings challenge the idea that random organization is the underlying mechanism for reducing the dissipation per strain. Instead, we attribute it to shear “fragility” combined with geometry, which explains the counterintuitive decoupling of the minima of viscosity and dissipation for the alternating shear rotation protocol. This work paves the way for a new class of highly energy-efficient flow protocols.

Published by the American Physical Society
2024