bluuebunny/crossref_metadata_2025 huggingface dataset:
Impaired microglial phagocytosis promotes seizure development
Authors: Bosco Dale B. , Kremen Vaclav , Haruwaka Koichiro , Zhao Shunyi , Wang Lingxiao , Ebner Blake A. , Zheng Jiaying , Dheer Aastha , Perry Jadyn F. , Xie Manling , Nguyen Aivi T. , Worrell Gregory A. , Wu Long-Jun
Published: January 2024

In the central nervous system, triggering receptor expressed on myeloid cells 2 (TREM2) is exclusively expressed by microglia and is critical for microglial proliferation, migration, and phagocytosis. TREM2 plays an important role in neurodegenerative diseases, such as Alzheimer’s disease and amyotrophic lateral sclerosis. However, little is known about the role TREM2 plays in epileptogenesis. To investigate this, we utilized TREM2 knockout (KO) mice within the murine intra-amygdala kainic acid seizure model. Electroencephalographic analysis, immunocytochemistry, and RNA sequencing revealed that TREM2 deficiency significantly promoted seizure-induced pathology. We found that TREM2 KO increased both acutestatus epilepticusand spontaneous recurrent seizures characteristic of chronic focal epilepsy. Mechanistically, phagocytic clearance of damaged neurons by microglia was impaired in TREM2 KO mice and the reduced phagocytic capacity correlated with increased spontaneous seizures. Analysis of human tissue from patients who underwent surgical resection for drug resistant temporal lobe epilepsy also showed a negative correlation between microglial phagocytic activity and focal to bilateral tonic-clonic generalized seizure history. These results indicate that microglial TREM2 and phagocytic activity may be important to epileptogenesis and the progression of focal temporal lobe epilepsy.

One Sentence Summary

Phagocytic activity of microglia may impact generalized seizure development within both mice and humans.
Translating phenotypic prediction models from big to small anatomical MRI data using meta-matching
Authors: Wulan Naren , An Lijun , Zhang Chen , Kong Ru , Chen Pansheng , Bzdok Danilo , Eickhoff Simon B , Holmes Avram J , Yeo B. T. Thomas
Published: January 2024

Individualized phenotypic prediction based on structural MRI is an important goal in neuroscience. Prediction performance increases with larger samples, but small-scale datasets with fewer than 200 participants are often unavoidable. We have previously proposed a “meta-matching” framework to translate models trained from large datasets to improve the prediction of new unseen phenotypes in small collection efforts. Meta-matching exploits correlations between phenotypes, yielding large improvement over classical machine learning when applied to prediction models using resting-state functional connectivity as input features. Here, we adapt the two best performing meta-matching variants (“meta-matching finetune” and “meta-matching stacking”) from our previous study to work with T1-weighted MRI data by changing the base neural network architecture to a 3D convolution neural network. We compare the two meta-matching variants with elastic net and classical transfer learning using the UK Biobank (N = 36,461), Human Connectome Project Young Adults (HCP-YA) dataset (N = 1,017) and HCP-Aging dataset (N = 656). We find that meta-matching outperforms elastic net and classical transfer learning by a large margin, both when translating models within the same dataset, as well as translating models across datasets with different MRI scanners, acquisition protocols and demographics. For example, when translating a UK Biobank model to 100 HCP-YA participants, meta-matching finetune yielded a 136% improvement in variance explained over transfer learning, with an average absolute gain of 2.6% (minimum = -0.9%, maximum = 17.6%) across 35 phenotypes. Overall, our results highlight the versatility of the meta-matching framework.
A General-Purpose Non-invasive Neurotechnology Research Platform
Authors: Schalk Gerwin , Shao Shiyun , Xiao Kewei , Li Jintao , Xie Jiaxin , Guan Yinkui , Wu Zehan , Chen Liang , Zhong Xingyi , Xu Ce , Li Guangye , Yu Huan
Published: January 2024

This article describes our initial work toward a general-purpose platform for non-invasive neurotechnology research. This platform consists of a multi-modal wireless recording device, an associated software API, and full integration into BCI2000 software. The device is placed on the forehead and features two electroencephalographic (EEG) sensors, an inertial movement sensor (IMU), a photoplethysmogram (PPG) sensor, a microphone, and vibration-based feedback. Herein, we demonstrate different technical characteristics of our platform and its use in the context of sleep monitoring/modulation, simultaneous and synchronized recordings from different hardware, and evoked potentials. With further development and widespread dissemination, our platform could become an important tool for research into new non-invasive neurotechnology protocols in humans.
A geometric parameterization for beta turns
Authors: Newell Nicholas E.
Published: January 2024

Beta turns, in which the protein backbone abruptly changes direction over four amino acid residues, are the most common type of protein secondary structure after alpha helices and beta sheets and play many key structural and functional roles. Previous work has produced classification systems for turn backbone geometry at multiple levels of precision, but these all operate in backbone dihedral-angle (Ramachandran) space, and the absence of a local Euclidean-space coordinate system and structural alignment for turns, or of any systematic Euclidean-space characterization of turn backbone shape, presents challenges for the visualization, comparison and analysis of the wide range of turn conformations and the design of turns and the structures that incorporate them. This work derives a local coordinate system that implicitly aligns turns, together with a simple geometric parameterization for turn backbone shape that describes modes of structural variation not explicitly captured by existing systems. These modes are shown to be meaningful by the demonstration of clear relationships between parameter values and the electrostatic energy of the beta-turn H-bond, the overrepresentation of key side-chain motifs, and the structural contexts of turns. Geometric turn parameters, which complement existing Ramachandran-space classifications, can be used to tune turn structures for compatibility with particular side-chain interactions or contexts, and they should prove valuable in applications, such as protein design, where an enhanced Euclidean-space description of turns may improve understanding or performance. The web-based tools ExploreTurns, MapTurns and ProfileTurn, available atwww.betaturn.com, incorporate turn-local coordinates and turn parameters and demonstrate their utility.
Control of ciliary transcriptional programs during spermatogenesis by antagonistic transcription factors
Authors: Wang Weihua , Xing Junqiao , Zhang Xiqi , Liu Hongni , Liu Xingyu , Jiang Haochen , Xu Cheng , Zhao Xue , Hu Zhangfeng
Published: January 2024

Existence of cilia in the last eukaryotic common ancestor (LECA) raises a fundamental question in biology: how the transcriptional regulation of ciliogenesis has evolved? One conceptual answer to this question is by an ancient transcription factor regulating ciliary gene expression in both unicellular and multicellular organisms, but examples of such transcription factors in eukaryotes are lacking. Previously, we showed that an ancient transcription factor XAP5 is required for flagellar assembly inChlamydomonas. Here, we show that XAP5 and XAP5L are two conserved pairs of antagonistic transcription regulators that control ciliary transcriptional programs during spermatogenesis. Male mice lacking either XAP5 or XAP5L display infertility, as a result of meiotic prophase arrest and sperm flagella malformation, respectively. Mechanistically, XAP5 positively regulates the ciliary gene expression by activating the key regulators including FOXJ1 and RFX families during the early stage of spermatogenesis. In contrast, XAP5L negatively regulates the expression of ciliary genes via repressing these ciliary transcription factors during the spermiogenesis stage. Our results provide new insights into the mechanisms by which temporal and spatial transcription regulators are coordinated to control ciliary transcriptional programs during spermatogenesis.
Predicting functionally important breast cancer SNPs using pleiotropy, conservation, and protein structure
Authors: Carpenter Meredith A. , Cheng Alan C.
Published: January 2024

Motivation

With over 24,000 SNPs associated with breast cancer in ClinVar, there is a need to prioritize the subset most likely to be causally linked to diagnostic, prognostic, and other clinical outcomes of disease. Building off currently known breast cancer oncogenes and SNPs, we identify the subset of SNPs with pleiotropic effects, with the goal of identifying mutations functionally relevant to disease progression. We further use sequence and structure analysis to prioritize missense mutations most likely to impact protein function.

Results

From the known breast cancer SNPs, we identified co-associated mutations located at evolutionarily conserved positions and contributing significant protein stability as potential focal points for disease biomarkers, protein function studies, and therapeutic intervention. To identify regions likely integral to protein function, we plotted genomic intervals where multiple disease density peaks overlap. Of the breast cancer SNPs, 1,714 were co-associated in-frame mutations, of which 930 occurred at conserved residue positions (Shannon Entropy <1.0) and 833 were also missense mutations. Building structure-based models of the 277 SNPs with available protein structure resulted in identification of 133 SNPs that are calculated to affect protein thermostability by >100-fold (>3 kcal/mol). The workflow we built can be applied to other diseases to help identify functional mutations.

Availability

Python code for the integrated analysis workflow available athttp://github.com/mcarpenter-brandeis/brc-pleiotropyand detailed data tables available in Supplemental Information.

Contact

acheng@brandeis.edu,meredith.a.carpenter@gmail.coms
ThermoFinder: A sequence-based thermophilic proteins prediction framework
Authors: Yu Han , Luo Xiaozhou
Published: January 2024

Motivation

Thermophilic proteins are important for academic research and industrial processes, and various computational methods have been developed to identify and screen them. However, their performance has been limited due to the lack of high-quality labeled data and efficient models for representing protein. Here, we proposed a novel sequence-based thermophilic proteins prediction framework, called ThermoFinder.

Results

In this study, we demonstrated that ThermoFinder outperforms previous state-of-the-art tools on two benchmark datasets, and feature ablation experiments confirmed the effectiveness of our approach. Additionally, ThermoFinder exhibited exceptional performance and consistency across two newly constructed datasets, one of these was specifically constructed for the regression-based prediction of temperature optimum values directly derived from protein sequences. The feature importance analysis, using shapley additive explanations, further validated the advantages of ThermoFinder. We believe that ThermoFinder will be a valuable and comprehensive framework for predicting thermophilic proteins.
The genome ofLolium multiflorumreveals the genetic architecture of paraquat resistance
Authors: Brunharo Caio A. , Short Aidan W. , Bobadilla Lucas K. , Streisfeld Matthew A.
Published: January 2024

- Herbicide resistance in agricultural weeds has become one of the greatest challenges for sustainable crop production. The repeated evolution of herbicide resistance provides an excellent opportunity to study the genetic and physiological basis of the resistance phenotype and the evolutionary responses to human-mediated selection pressures.Lolium multiflorumis a ubiquitous weed that has evolved herbicide resistance repeatedly around the world in various cropping systems.

- We assembled and annotated a chromosome-scale genome forL. multiflorumand elucidated the genetic architecture of paraquat resistance by performing quantitative trait loci analysis, genome-wide association studies, genetic divergence analysis, and transcriptome analyses from paraquat-resistant and -susceptibleL. multiflorumpopulations.

- Results suggested that two regions of chromosome 5 were associated with paraquat resistance. The regions contain candidate genes that encode cellular transport functions, including a novel multidrug and toxin extrusion (MATE) protein, and a cation transporter previously shown to interact with polyamines.

- Our results reveal the genetic architecture of paraquat resistance and identified promising candidate genes for future functional studies. Given thatL. multiflorumis a weed and a cultivated crop species, the genomic resources generated will prove valuable to a wide spectrum of the plant science community.
Identification of a chromatin-bound ERRα interactome network in mouse liver
Authors: Scholtes Charlotte , Dufour Catherine Rosa , Pleynet Emma , Kamyabiazar Samaneh , Hutton Phillipe , Baby Reeba , Guluzian Christina , Giguère Vincent
Published: January 2024

Objective

Estrogen-related-receptor α (ERRα) plays a critical role in the transcriptional regulation of cellular bioenergetics and metabolism, and perturbations in its activity have been associated with metabolic diseases. While several coactivators and corepressors of ERRα have been identified to date, a knowledge gap remains in understanding the extent to which ERRα cooperates with coregulators in the control of gene expression. Herein, we mapped the primary chromatin-bound ERRα interactome in mouse liver.

Methods

RIME (Rapid Immuno-precipitation Mass spectrometry of Endogenous proteins) analysis using mouse liver samples from two circadian time points was used to catalog ERRα-interacting proteins on chromatin. The genomic crosstalk between ERRα and its identified cofactors in the transcriptional control of precise gene programs was explored through cross-examination of genome-wide binding profiles from chromatin immunoprecipitation-sequencing (ChIP-seq) studies. The dynamic interplay between ERRα and its newly uncovered cofactor Host cell factor C1 (HCFC1) was further investigated by loss-of-function studies in hepatocytes.

Results

Characterization of the hepatic ERRα chromatin interactome led to the identification of 48 transcriptional interactors of which 42 were previously unknown including HCFC1. Interrogation of available ChIP-seq binding profiles highlighted oxidative phosphorylation (OXPHOS) under the control of a complex regulatory network between ERRα and multiple cofactors. While ERRα and HCFC1 were found to bind to a large set of common genes, only a small fraction showed their co-localization, found predominately near the transcriptional start sites of genes particularly enriched for components of the mitochondrial respiratory chain. Knockdown studies demonstrated inverse regulatory actions of ERRα and HCFC1 on OXPHOS gene expression ultimately dictating the impact of their loss-of-function on mitochondrial respiration.

Conclusions

Our work unveils a repertoire of previously unknown transcriptional partners of ERRα comprised of chromatin modifiers and transcription factors thus advancing our knowledge of how ERRα regulates metabolic transcriptional programs.
The asymmetric transfers of visual perceptual learning determined by the stability of geometrical invariants
Authors: Yang Yan , Zhuo Yan , Zuo Zhentao , Zhuo Tiangang , Chen Lin
Published: January 2024

We quickly and accurately recognize the dynamic world by extracting invariances from highly variable scenes, a process can be continuously optimized through visual perceptual learning (VPL). While it is widely accepted that the visual system prioritizes the perception of more stable invariants, the influence of the structural stability of invariants on VPL remains largely unknown. In this study, we designed three geometrical invariants with varying levels of stability for VPL: projective (e.g., collinearity), affine (e.g., parallelism), and Euclidean (e.g., orientation) invariants, following the Klein’s Erlangen program. We found that learning to discriminate low-stability invariant transferred asymmetrically to those with higher stability, and that training on high-stability invariants enabled location transfer. To explore learning-associated plasticity in the visual hierarchy, we trained deep neural networks (DNNs) to model this learning procedure. We reproduced the asymmetric transfer between different invariants in DNN simulations and found that the distribution and time course of plasticity in DNNs suggested a neural mechanism similar to the reverse hierarchical theory (RHT), yet distinct in that invariant stability—not task difficulty or precision—emerged as the key determinant of learning and generalization. We propose that VPL for different invariants follows the Klein hierarchy of geometries, beginning with the extraction of high-stability invariants in higher-level visual areas, then recruiting lower-level areas for the further optimization needed to discriminate less stable invariants.
FveDAD2 negatively regulates branch crowns by affecting abscisic acid metabolism through FveHB7 in woodland strawberry
Authors: Sun Hongying , Zhang Junxiang , Li Weijia , Wang Yan , Zhang Zhihong
Published: January 2024

Strigolactones (SLs) are a significant hormone in plant growth response, crucial for regulating branching. DECREASED APICAL DOMINANCE2 (DAD2) is a novel receptor of SL. Here, FveDAD2 in woodland strawberries (Fragaria vesca) as the receptor for SL was identified, and three FveDAD2-RNAi transgenic lines that exhibited the phenotype of multi-branched crowns and smaller fruits were obtained. Gene expression, phenotypic analysis, and yeast assays were used to investigate the function of FveDAD2 in regulating branch crowns in strawberries. Like the alpha/beta hydrolase D14, FveDAD2 interacts with FveSMXL7 and depends on SL. Furthermore, the yeast single-hybrid, GUS activity assay, and LUC assay results demonstrate that FveSMXL7 binds to the promoter ofFveHB7and repress its transcription. FveHB7, a homeobox transcription factor, negatively regulates the transcription ofFveABA8’OH1, which encodes the enzyme that catabolizes abscisic acid (ABA). ABA contents were reduced in the shoot tips of the FveDAD2-RNAi lines, while treating wide-type plants with 20 μM ABA significantly suppressed the number of branches. In conclusion, we discovered a novel pathway of SL signaling to regulate branching through ABA.

One-sentence summary

FveDAD2 negatively regulates branch crowns by affecting abscisic acid levels by interacting with FveSMXL7 to regulate the expression ofFveABA8’OH1via the transcription factor FveHB7.
Effects of long-term high dose aspartame on body mass, bone strength, femoral geometry, and microbiota composition in a young and aged cohort of male and female mice
Authors: Cyphert Erika L. , Liu Chongshan , Morales Angie L. , Nixon Jacob C. , Blackford Emily , Garcia Matthew , Cevallos Nicolas , Turnbaugh Peter J. , Brito Ilana L. , Booth Sarah L. , Hernandez Christopher J.
Published: January 2024

Background:

Recent reassessment of the safety of aspartame has prompted increased evaluation of its effect on the health of a range of tissues. The gut microbiome is altered by oral aspartame. One prior study suggested that changes in the microbiome caused by aspartame could influence the strength of bone in young skeletally developing mice. Here we ask how aspartame influences bone in mice of different age and sex.

Objective:

The objective of this study was to determine the effect of aspartame on the bone strength and gut microbiota of young and aged mice.

Methods:

Male and female C57Bl/6J mice were untreated or treated with a high dose of aspartame in their drinking water from 1 month of age until 4 (young cohort; n = 80) or 22 months (aged cohort; n = 52).

Results:

In aged males, mice treated with aspartame had greater body mass, whole bone strength, and femoral geometry relative to untreated. Specifically, in aged males, aspartame led to 9% increase in body mass (p < 0.001), 22% increase in whole bone strength (p = 0.006), and 17% increase in section modulus (p < 0.001) relative to untreated mice. Aged males and females receiving aspartame had a different microbiota than untreated mice and a decreased abundance ofOdoribacter. No differences in body mass, whole bone strength, or femoral geometry were associated with aspartame dosing in young males or young or aged females.

Conclusions:

Aspartame treated aged males had greater whole bone strength and the effect appeared to be explained by greater body mass. Aspartame treatment did not alter whole bone strength in young males or young or aged females despite the aspartame having a similar effect on the microbiota of both aged males and females.
Insights into Yeast Response to Chemotherapeutic Agent through Time Series Genome-Scale Metabolic Models
Authors: Karabekmez Muhammed Erkan
Published: January 2024

Background

Organism-specific genome-scale metabolic models (GSMMs) can unveil molecular mechanisms within cells and are commonly used in diverse applications, from synthetic biology, biotechnology, and systems biology to metabolic engineering. There are limited studies incorporating time-series transcriptomics in GSMM simulations. Yeast is an easy-to-manipulate model organism for tumor research;

Methods

Here, a novel approach (TS-GSMM) was proposed to integrate time-series transcriptomics with GSMMs to narrow down the feasible solution space of all possible flux distributions and attain time-series flux samples. The flux samples were clustered using machine learning techniques, and the clusters’ functional analysis was performed using reaction set enrichment analysis;

Results

A time series transcriptomics response of Yeast cells to a chemotherapeutic reagent – doxorubicin - was mapped onto a Yeast GSMM. Eleven flux clusters were obtained with our approach, and pathway dynamics were displayed. Induction of fluxes related to bicarbonate formation and transport, ergosterol and spermidine transport, and ATP production were captured;

Conclusions

Integrating time-series transcriptomics data with GSMMs is a promising approach to reveal pathway dynamics without any kinetic modeling and detects pathways that cannot be identified through transcriptomics-only analysis. The codes are available athttps://github.com/karabekmez/TS-GSMM.
Antigen density and applied force control enrichment of nanobody-expressing yeast cells in microfluidics
Authors: Sanicas Merlin , Torro Rémy , Limozin Laurent , Chames Patrick
Published: January 2024

In vitro display technologies such as yeast display have been instrumental in developing the selection of new antibodies, antibody fragments or nanobodies that bind to a specific target, with affinity towards the target being the main factor that influences selection outcome. However, the roles of mechanical forces are being increasingly recognized as a crucial factor in the regulation and activation of effector cell function. It would thus be of interest to isolate binders behaving optimally under the influence of mechanical forces. We developed a microfluidic assay allowing the selection of yeast displaying nanobodies through antigen-specific immobilization on a surface under controlled hydrodynamic flow. This approach enabled enrichment of model yeast mixtures using tunable antigen density and applied force. This new force-based selection method opens the possibility of selecting binders by relying on both their affinity and force resistance, with implications for the design of more efficient immunotherapeutics.
Contrast-enhanced photon-counting micro-CT of tumor xenograft models
Authors: Li Mengzhou , Guo Xiaodong , Verma Amit , Rudkouskaya Alena , McKenna Antigone M. , Intes Xavier , Wang Ge , Barroso Margarida
Published: January 2024

Photon-counting micro computed tomography (micro-CT) offers new potential in preclinical imaging, particularly in distinguishing materials. It becomes especially helpful when combined with contrast agents, enabling the differentiation of tumors from surrounding tissues. There are mainly two types of contrast agents in the market for micro-CT: small molecule-based and nanoparticle-based. However, despite their widespread use in liver tumor studies, there is a notable gap in research on the application of these commercially available agents for photon-counting micro-CT in breast and ovarian tumors. Herein, we explored the effectiveness of these agents in differentiating tumor xenografts from various origins (AU565, MDA-MB-231, and SKOV-3) in nude mice, using photon-counting micro-CT. Specifically, ISOVUE-370 (a small molecule-based agent) and Exitrone Nano 12000 (a nanoparticle-based agent) were investigated in this context. To improve tumor visualization, we proposed a novel color visualization method for photon-counting micro-CT, which changes color tones to highlight contrast media distribution, offering a robust alternative to traditional material decomposition methods with less computational demand. Ourin vivoexperiments confirm its effectiveness, showing distinct enhancement characteristics for each contrast agent. Qualitative and quantitative analyses suggested that Exitrone Nano 12000 provides superior vasculature enhancement and better quantitative consistency across scans, while ISOVUE-370 gives more comprehensive tumor enhancement but with a significant variance between scans due to its short blood half-time. This variability leads to high sensitivity to timing and individual differences among mice. Further, a paired t-test on mean and standard deviation values within tumor volumes showed significant differences between the AU565 and SKOV-3 tumor models with the nanoparticle-based (p-values < 0.02), attributable to their distinct vascularity, as confirmed by immunohistochemistry. These findings underscore the utility of photon-counting micro-CT in non-invasively assessing the morphology and anatomy of different tumor xenografts, which is crucial for tumor characterization and longitudinal monitoring of tumor development and response to treatments.
Dietary methionine/choline deficiency affects behavioural and molecular circadian rhythms
Authors: Saer Benjamin , Taylor George , Hayes Andrew , Ananthasubramaniam Bharath , Fustin Jean-Michel
Published: January 2024

The feeding/fasting cycles controlled by our circadian clock impose great daily metabolic and physiological changes, and yet investigations into the consequences of metabolic deficiencies, either dietary or genetic, have often ignored the time of day or the circadian time of the animals or subjects. In addition, these deficiencies may themselves disrupt our circadian clock, causing secondary metabolic, physiological and behavioural disorders.

Dietary methionine/choline deficiency in rodents is a common model for human non-alcoholic steatohepatitis, but methionine and choline are nutrients essential for many other processes beyond fatty acid synthesis in the liver, including biological methylations and 1-carbon metabolism, regulation of translation notably via the mTOR pathway, phospholipid synthesis, polyamine pathway and glutathione synthesis.

We have previously shown that circadian rhythms in many organisms are highly sensitive to deficiency or excesses of 1-carbon metabolites. Using a methionine/choline deficient diet in mice, we illustrate the nutrigenomic crosstalk between circadian rhythms and 1-carbon metabolism. We show not only that circadian locomotor activity behaviour is profoundly, rapidly and reversibly affected by methionine/choline deficiency, but also that the effects of methionine/choline deficiency on gene expression and 1-carbon metabolites are dependent on circadian time, illustrating the importance of considering circadian rhythms in metabolic studies. This study also highlights the impact of what we eat, or don’t, on our behaviour and biological rhythms.
Selfish behavior requires top-down control of prosocial motivation
Authors: Numano Shotaro , Frith Chris , Haruno Masahiko
Published: January 2024

Individuals must regularly choose between prosocial and proself behaviors. While past neuroscience research has revealed the neural foundations for prosocial behaviors, many studies have oversimplified proself behaviors, viewing them merely as a reward-maximization process. However, recent behavioral evidence suggests that response times for proself behaviors are often slower than those for prosocial behaviors, suggesting a more complex interdependence between prosocial and proself neural computations. To address this issue, we conducted an fMRI experiment with the ultimatum game, where participants were requested to accept (money distributed as proposed) or reject (both sides receive none) offers of money distribution. In the decisions, the participants could maximize self-interest by accepting the offer (i.e., proself), while by rejecting it, they could punish unfair proposers and promote the “equity” social norm (i.e., prosocial). We constructed a drift diffusion model (DDM) that considers both behavioral choices and response times and used the DDM parameters in our fMRI analysis. We observed that participants who suppressed inequity-driven rejection behaviors displayed heightened dACC activity in response to disadvantageous inequity. Importantly, our functional connectivity analysis demonstrated that the dACC exhibited negative functional connectivity with the amygdala when unfair offers were presented. Furthermore, the PPI connectivity encoded the average reaction time for accepting unfair offers (i.e., proself behaviors). Considering that the amygdala also responded to disadvantageous inequity in these experiments and previous studies, these results show that the top-down control of prosocial motives (i.e., aversion to disadvantageous inequity) plays a key role in implementing proself behaviors.
Linking brain-heart interactions to emotional arousal in immersive virtual reality
Authors: Fourcade A. , Klotzsche F. , Hofmann S. M. , Mariola A. , Nikulin V. V. , Villringer A. , Gaebler M.
Published: January 2024

The subjective experience of emotions is linked to the contextualized perception and appraisal of changes in bodily (e.g., heart) activity. Increased emotional arousal has been related to attenuated high-frequency heart rate variability (HF-HRV), lower EEG parieto-occipital alpha power, and higher heartbeat-evoked potential (HEP) amplitudes. We studied emotional arousal-related brain- heart interactions using immersive virtual reality (VR) for naturalistic yet controlled emotion induction. 29 healthy adults (13 women, age: 26±3) completed a VR experience that included rollercoasters while EEG and ECG were recorded. Continuous emotional arousal ratings were collected during a video replay immediately after. We analyzed emotional arousal-related changes in HF-HRV as well as in BHIs using HEPs. Additionally, we used the oscillatory information in the ECG and the EEG to model the directional information flows between the brain and heart activity.

We found that higher emotional arousal was associated with lower HEP amplitudes in a left fronto- central electrode cluster. While parasympathetic modulation of the heart (HF-HRV) and parieto- occipital EEG alpha power were reduced during higher emotional arousal, there was no evidence for the hypothesized emotional arousal-related changes in bidirectional information flow between them. Whole-brain exploratory analyses in additional EEG (delta, theta, alpha, beta and gamma) and HRV (low-frequency, LF, and HF) frequency bands revealed a temporo-occipital cluster, in which higher emotional arousal was linked to decreased brain-to-heart (i.e., gamma→HF-HRV) and increased heart-to-brain (i.e., LF-HRV→gamma) information flow. Our results confirm previous findings from less naturalistic experiments and suggest a link between emotional arousal and brain-heart interactions in temporo-occipital gamma power.
Developmental Reprogramming of Hypothalamic-Pituitary Axis in Mice by Common Environmental Pollutants
Authors: Mogus Joshua P. , Marin Marjorie , Arowolo Olatunbosun , Salemme Victoria , Suvorov Alexander
Published: January 2024

Humans are exposed to a large number of endocrine disrupting chemicals (EDCs). Many studies demonstrated that exposures to EDCs during critical windows of development can permanently affect endocrine health outcomes. Most of experimental studies address changes in secretion of hormones produced by gonads, thyroid gland and adrenals, and little is known about the ability of EDCs to produce long-term changes in the hypothalamic-pituitary (HP) control axes. Here, we examined the long-term effects of three common EDCs on male mouse HP gene expression, following developmental exposures. Pregnant mice were exposed to 0.2 mg/ml solutions of bisphenol S (BPS), 2,2’,4,4’-tetrabromodiphenyl ether (BDE-47), or 3,3’,5,5’-tetrabromobisphenol A (TBBPA) from pregnancy day 8 through lactation day 21 (weaning day). Male offspring were left untreated until postnatal day 140, where pituitaries and hypothalami were collected. Pituitaries were assed for gene expression via RNA sequencing, while specific genes were assessed for expression in hypothalami via RT-qPCR. Differential expression, as well as gene enrichment and pathway analysis, indicated that all three chemicals induced long-term changes, (mostly suppression) in pituitary genes involved in its endocrine function. BPS and BDE-47 produced effects overlapping significantly at the level of effected genes and pathways. All three chemicals altered genes and pathways of gonad and liver HP axes, while BPS altered HP-adrenal and BDE-47 altered HP-thyroid pathways specifically. All three chemicals also reduced expression of immune genes in the pituitaries. Targeted gene expression in the hypothalamus indicates a down regulation of hypothalamic endocrine control genes by BPS and BDE-47 groups, concordant with changes in the pituitary and suggests that these chemicals suppress the overall HP endocrine function. Interestingly, all three chemicals altered pituitary genes of GPCR-mediated intracellular signaling molecules, many of which are key signalers common to many pituitary responses to hormones. The results of this study show that developmental exposures to common and ubiquitous EDCs have long-term impacts on hormonal feedback control at the hypothalamic-pituitary level.
Stark control of solid-state quantum memory with spin-wave storage
Authors: Alqedra Mohammed K. , Horvath Sebastian P. , Kinos Adam , Walther Andreas , Kröll Stefan , Rippe Lars
Published: January 2024

Quantum memories for quantum communication need to be able to store photons for an extended time and then to release them on demand. This can be achieved in atomic frequency comb ensemble-based quantum memories by control pulses that transfer the excitation to and from long-lived spin states. However, such pulses can give rise to coherent and incoherent noise due to their interaction with the memory ensemble. In this paper, we experimentally demonstrate the ability to switch off the coherent noise from such control pulses during the echo emission in a spin-wave quantum memory, using the linear Stark effect in rare-earth-ion doped crystals. By applying an electric-field pulse, the echo emission was coherently switched off prior to the first spin transfer pulse, and the stored data pulse was restored only when both an optical recall pulse and a rephasing electrical pulse were applied, giving a high degree of control of both desired and undesired emissions. We estimate the effectiveness of this technique by turning off the free-induction decay of a narrow ensemble of ions. This technique can thus improve the noise performance of spin-wave storage at the single-photon level by quenching coherent optical radiation created by strong control pulses. The method demonstrated here represents a proof of principle that the spin-wave storage scheme can be combined with Stark control. The combined scheme serves as an addition to the toolbox of techniques that can be used to realize a full version of a quantum repeater.

Published by the American Physical Society
2024
Femtosecond-laser direct-write photoconductive patterns on tellurite glass
Authors: Torun Gözden , Romashkina Anastasia , Kishi Tetsuo , Bellouard Yves
Published: January 2024

We report the formation of arbitrary photoconductive patterns made of tellurium (Te) nanocrystals by exposing a tellurite (TeO2-based) glass to femtosecond laser pulses. During this process, Te/TeO2-glass nanocomposite interfaces with photoconductive properties form on the tellurite glass substrate. We show that these laser-written patterns exhibit a photoresponse, from the near ultraviolet (263 nm) to the visible spectrum, stable over a few months. Specifically, high responsivity (16.55 A/W) and detectivity (5.25 × 1011 Jones) of a single laser-written line pattern are measured for an illumination dose of 0.07 mW/cm2 at 400 nm. This work illustrates a pathway for locally turning a tellurite glass into a functional photoconductor of arbitrary shape, without adding materials and using a single laser process step.

Published by the American Physical Society
2024
Probing vortical structures in heavy-ion collisions at RHIC-BES energies through helicity polarization
Authors: Yi Cong , Wu Xiang-Yu , Yang Di-Lun , Gao Jian-Hua , Pu Shi , Qin Guang-You
Published: January 2024

We investigate the azimuthal angle dependent local hydrodynamic helicity polarization of Λ hyperons, defined as the projection of the spin polarization vector along the directions of particle momenta, at BNL Relativistic Heavy Ion Collider beam energy scan energies by utilizing the relativistic (3+1)D CLVisc hydrodynamics framework with SMASH initial conditions. As opposed to local spin polarization at high energy collisions, our hydrodynamic simulations demonstrate that the azimuthal angle dependent helicity polarization induced by the kinetic vorticity dominates over other contributions at intermediate and low collision energies. Our findings provide an opportunity to probe the fine structure of local kinetic vorticity as a function of azimuthal angle at intermediate and low collision energies by mapping our predictions to the future measurements in experiments.

Published by the American Physical Society
2024
Decays of fully beauty scalar tetraquarks to
BqB¯q
and
Bq*B¯q*
mesons
Authors: Agaev S. S. , Azizi K. , Barsbay B. , Sundu H.
Published: January 2024

Decays of the fully beauty four-quark structures X4b and T4b to B meson pairs are investigated in the framework of the QCD three-point sum rule method. We model the scalar exotic mesons X4b and T4b as diquark-antidiquark systems composed of the axial-vector and pseudoscalar diquarks, respectively. The masses m=(18540±50)  MeV and m˜=(18858±50)  MeV of these compounds calculated in our previous articles fix possible decay channels of these particles. In the present work, we consider their decays to BqB¯q and Bq*B¯q* (q=u, d, s, c) mesons. In the case of X4b, the mass of which is below the 2ηb threshold, these channels determine essential part of its full width Γ4b. The tetraquark T4b can decay to the pair ηbηb; therefore, partial widths of processes with B(B*) mesons in the final state permit us to refine our estimate for the full width of this particle. The predictions Γ4b=(9.6±1.1)  MeV and Γ˜4bFull=(144±29)  MeV obtained in this article can be used in future experimental investigations of four b-quark mesons.

Published by the American Physical Society
2024
Nucleon isovector axial form factors
Authors: Jang Yong-Chull , Gupta Rajan , Bhattacharya Tanmoy , Yoon Boram , Lin Huey-Wen ,   Precision Neutron Decay Matrix Elements (PNDME) Collaboration
Published: January 2024

We present results for the isovector axial vector form factors obtained using thirteen 2+1+1-flavor highly improved staggered quark (HISQ) ensembles generated by the MILC collaboration. The calculation of nucleon two- and three-point correlation functions has been done using Wilson-clover fermions. In the analysis of these data, we quantify the sensitivity of the results to strategies used for removing excited state contamination and invoke the partially conserved axial current relation between the form factors to choose between them. Our data driven analysis includes removing contributions from multihadron Nπ states that make significant contributions. Our final results are gA=1.292(53)stat(24)sys for the axial charge; gS=1.085(50)stat(103)sys and gT=0.991(21)stat(10)sys for the scalar and tensor charges; ⟨rA2⟩=0.439(56)stat(34)sys  fm2 for the mean squared axial charge radius, gP*=9.03(47)stat(42)sys for the induced pseudoscalar charge; and gπNN=14.14(81)stat(85)sys for the pion-nucleon coupling. We also provide a parametrization of the axial form factor GA(Q2) over the range 0≤Q2≤1  GeV2 for use in phenomenology and a comparison with other lattice determinations. We find that the various lattice data agree within 10% but are significantly different from the extraction of GA(Q2) from the ν-deuterium scattering data.

Published by the American Physical Society
2024
Definition of fragmentation functions and the violation of sum rules
Authors: Collins John , Rogers Ted C.
Published: January 2024

We point out a problem with the formulation and derivations of sum rules for quark fragmentation functions that impacts their validity in QCD, but which potentially points toward an improved understanding of final states in inclusive hard processes. Fragmentation functions give the distribution of final-state hadrons arising from a parton exiting a hard scattering, and the sum rules for momentum, electric charge, etc. express conservation of these quantities. The problem arises from a mismatch between the quark quantum numbers of the initial quark and the fact that all observed final-state hadrons are confined bound states with color zero. We point that, in a confining theory like QCD, the Wilson line in the operator definition of a fragmentation function entails that the final state in a fragmentation function includes a bound state in the external field generated by the Wilson line. We justify this with the aid of general features of string hadronization. The anomalous bound states are restricted to fractional momentum z=0. They tend to invalidate sum rules like the one for charge conservation when applied to the fragmentation functions inferred from experimental data but not the momentum sum rule. We propose to exploit our ideas in future studies as a way to relate the fragmentation functions extracted from inclusive cross sections to more detailed nonperturbative descriptions of final state hadronization. We also describe scenarios wherein the traditional sum rules might remain approximately valid with a reasonably high degree of accuracy.

Published by the American Physical Society
2024
Nonequilibrium Schwinger-Keldysh formalism for density matrix states: Analytic properties and implications in cosmology
Authors: Barvinsky Andrei O. , Kolganov Nikita
Published: January 2024

Motivated by cosmological Hartle-Hawking and microcanonical density matrix prescriptions for the quantum state of the Universe we develop a Schwinger-Keldysh in-in formalism for generic nonequilibrium dynamical systems with the initial density matrix. We build the generating functional of in-in Green’s functions and expectation values for a generic density matrix of the Gaussian type and show that the requirement of particle interpretation selects a distinguished set of positive/negative frequency basis functions of the wave operator of the theory, which is determined by the density matrix parameters. Then we consider a special case of the density matrix determined by the Euclidean path integral of the theory, which in the cosmological context can be considered as a generalization of the no-boundary pure state to the case of the microcanonical ensemble, and show that in view of a special reflection symmetry its Wightman Green’s functions satisfy Kubo-Martin-Schwinger periodicity conditions which hold despite the nonequilibrium and nonstationary nature of the physical setup. Rich analyticity structure in the complex plane of the time variable reveals the combined Euclidean-Lorentzian evolution of the theory, which depending on the properties of the initial density matrix can be interpreted as a decay of a classically forbidden quantum state.

Published by the American Physical Society
2024
Preliminary study of plasma modes and electron-ion collisions in partially magnetized strongly coupled plasmas
Authors: Pak Chanhyun , Billings Virginia , Schlitters Matthew , Bergeson Scott D. , Murillo Michael S.
Published: January 2024

Magnetic fields influence ion transport in plasmas. Straightforward comparisons of experimental measurements with plasma theories are complicated when the plasma is inhomogeneous, far from equilibrium, or characterized by strong gradients. To better understand ion transport in a partially magnetized system, we study the hydrodynamic velocity and temperature evolution in an ultracold neutral plasma at intermediate values of the magnetic field. We observe a transverse, radial breathing mode that does not couple to the longitudinal velocity. The inhomogeneous density distribution gives rise to a shear velocity gradient that appears to be only weakly damped. This mode is excited by ion oscillations originating in the wings of the distribution where the plasma becomes non-neutral. The ion temperature shows evidence of an enhanced electron-ion collision rate in the presence of the magnetic field. Ultracold neutral plasmas provide a rich system for studying mode excitation and decay.

Published by the American Physical Society
2024
First-principles study of topological invariants of Weyl points in continuous media
Authors: Fonseca Guilherme R. , Prudêncio Filipa R. , Silveirinha Mário G. , Huidobro Paloma A.
Published: January 2024

In recent years there has been a great interest in topological photonics and protected edge states. Here, we present a first-principles method to compute topological invariants of three-dimensional gapless phases. The approach enables the calculation of the topological charges of Weyl points through the use of the photonic Green's function of the system. We take two different approaches, and show that they are consistent. In the first one, we rely on the computation of Chern numbers in two-dimensional cross-sectional planes away from the Weyl point. The second approach is based on direct calculation of the Berry curvature around the Weyl point. We particularize the framework to the Weyl points that emerge in a magnetized plasma due to the breaking of time-reversal symmetry. We discuss the relevance of modeling nonlocality when considering the topological properties of continuous media such as the magnetized plasma. Our theory may be extended to other three-dimensional topological phases or to Floquet systems.

Published by the American Physical Society
2024
When a dream comes true: birth of the African Crystallographic Association (AfCA)
Authors: Roodt Andreas
Published: January 2024

This paper summarizes brief perspectives on the historic process of establishing an African Crystallographic Association (AfCA) and includes representative references. It covers activities within four arbitrarily selected, approximate time slots, i.e., 1890s–1999, 2000–2013, 2014–2019 and 2020–2023. A genuine attempt is made to include appropriate role players, organizations and accompanying events within these periods. It concludes with the official admission of AfCA as the fifth Regional Associate of the IUCr at the 26th Congress and General Assembly of the IUCr in Melbourne, Australia in 2023.