bluuebunny/crossref_metadata_2025 huggingface dataset:
Erysipelothrix rhusiopathiae-associated bloodstream infection in a patient with systemic lupus erythematosus: a case report and literature review
Authors: Lo Calvin Ka-Fung , Schonhofer Cole , Mina Neil , Masud Shazia , Wong Patrick Ho Pun , Chapman Michael G.
Published: July 2024

Introduction

Systemic human infections caused by Erysipelothrix rhusiopathiae have been increasingly reported especially within immunocompromised hosts and those with significant occupational exposure to livestock and aquatic animals. We report a case of Erysipelothrix rhusiopathiae bacteremia in a patient with systemic lupus erythematosus (SLE) and present a literature review on clinical outcomes and microbiologic diagnosis for this organism.

Case Presentation

A 43-year-old female patient was reporting a 1-month history of intermittent fevers. She recently increased her immunosuppression medication for her underlying SLE on advice of her rheumatologist. The patient sustained a finger laceration from butchering cattle meat two weeks after onset of her initial symptoms, with worsening index finger swelling and increased febrile episodes. Two weeks post-injury, multiple blood cultures were drawn and each isolated Gram-positive bacilli. Given her recurrent intermittent fevers, there was concern for ongoing infection and therefore intravenous vancomycin was started with prompt referral to outpatient parenteral antibiotic therapy clinic. The Gram-positive bacillus was confirmed as Erysipelothrix rhusiopathiae via MALDI-TOF analysis. Given intrinsic resistance to vancomycin, intravenous ceftriaxone was then initiated as targeted antimicrobial therapy for two weeks. Reassuringly, there was no echocardiographic evidence of infective endocarditis warranting prolonged treatment course. Post-treatment, she remained symptom-free with resolution of joint symptoms and fevers.

Conclusion

Our report illustrates a case of Erysipelothrix rhusiopathiae bacteremia from a relatively immunocompromised host, with prompt microbiologic diagnosis and intervention with appropriate antimicrobial coverage. Literature reflects the rarity of this infection, predilections to specific susceptible hosts and the importance for raising awareness of zoonotic infections.
Lysobacter stagni sp. nov. and Limnohabitans lacus sp. nov., isolated from a pond
Authors: Jung Yonghee , Chhetri Geeta , Kim Inhyup , So Yoonseop , Park Sunho , Woo Haejin , Seo Taegun
Published: July 2024

Two Gram-negative bacteria, designated as strains LF1T and HM2-2T, were isolated from an artificial pond in a honey farm at Hoengseong-gun, Gangwon-do, Republic of Korea. The 16S rRNA sequence analysis results revealed that strain LF1T belonged to the genus Lysobacter and had the highest sequence similarity to Lysobacter niastensis GH41-7T (99.0 %), Lysobacter panacisoli CJ29T (98.9 %), and Lysobacter prati SYSU H10001T (98.2 %). Its growth occurred at 20–37 °C, at pH 5.0–12.0, and in the presence of 0–2% NaCl. The major fatty acids were iso-C15 : 0, iso-C16 : 0, and summed feature 9 (iso-C17 : 1
 ω9c and/or C16 : 0 10-methyl). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol. The DNA G+C content was 67.5 mol%. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between strain LF1T and species of the genus Lysobacter were 79.1–84.4% and 22.0–27.5 %, respectively. The 16S rRNA sequence analysis results revealed that strain HM2-2T belonged to the genus Limnohabitans and was most closely related to Limnohabitans planktonicus II-D5T (98.9 %), Limnohabitans radicicola JUR4T (98.4%), and Limnohabitans parvus II-B4T (98.4 %). Its growth occurred at 10–35 °C, at pH 5.0–11.0, and in the presence of 0–2% NaCl. The major fatty acids were C16 : 0 and summed feature 3 (C16 : 1
 ω7c/C16 : 1
 ω6c). The major polar lipid was phosphatidylethanolamine. The DNA G+C content was 59.9 mol%. The ANI and dDDH values between strain HM2-2T and its closely related strains were 75.1–83.0% and 20.4–26.4 %, respectively. Phenotypic, genomic, and phylogenetic data revealed that strains LF1T and HM2-2T represent novel species in the genera Lysobacter and Limnohabitans, for which the names Lysobacter stagni sp. nov. and Limnohabitans lacus sp. nov. are proposed, respectively. The type strain of Lys. stagni is LF1T (=KACC 23251T=TBRC 17648T), and that of Lim. lacus is HM2-2T (=KACC 23250T=TBRC 17649T).
Loss of the lysosomal lipid flippase ATP10B leads to progressive dopaminergic neurodegeneration and Parkinsonian motor deficits
Authors: Sanchiz-Calvo María , Coccia Elena , Cawthorne Christopher , Parfitt Gustavo Morrone , Van Laere Koen , Torre-Muruzabal Teresa , Cabezudo Diego , Tsafaras George , Cascalho Ana , Van den Haute Chris , Vangheluwe Peter , Blanchard Joel , Bentea Eduard , Baekelandt Veerle
Published: July 2024

Background

ATP10B, a transmembrane lipid flippase located in late endosomes and lysosomes, facilitates the export of glucosylceramide and phosphatidylcholine by coupling this process to ATP hydrolysis. Recently, loss-of-function mutations in theATP10Bgene have been identified in Parkinson’s disease patients, pointing toATP10Bas a candidate genetic risk factor. Previous studies have shown compromised lysosomal functionality uponATP10Bknockdown in human cell lines and primary cortical neurons. However, its rolein vivoand specifically in the nigrostriatal dopaminergic system remains poorly understood.

Methods

To investigate the role ATP10B in PD neuropathology, we induced ATP10B knockdown specifically insubstantia nigra pars compactaneurons of rats using viral vector technology. Two different microRNA-based shRNA constructs targeting distinct regions of the ATP10B mRNA were used to cross-validate the findings. Behavioral evaluation, dopamine transporter18F-FE-PE2I positron emission tomography imaging and neuropathological examination of the nigrostriatal pathway at one year post-injection were conducted. Additionally, midbrain neuronal cultures derived from ATP10B knock-out human induced pluripotent stem cells clones were used to study the impact of ATP10B loss in dopaminergic neurons in a more translational model.

Results

ATP10Bknockdown in rat brain induced Parkinsonian motor deficits, and longitudinal striatal dopamine transporter18F-FE-PE2I PET imaging revealed a progressive decrease in binding potential. Immunohistochemical analysis conducted one year post-injection confirmed the loss of dopaminergic terminals in thestriatum, alongside a loss of dopaminergic neurons in thesubstantia nigra pars compacta. The expression of LAMP1, LAMP2a, cathepsin B and glucocerebrosidase was studied by immunofluorescence in the surviving dopaminergic neurons. A decrease in lysosomal numbers and an increase in lysosomal volume were observed more consistently in one of the knockdown constructs. The vulnerability of dopaminergic neurons to ATP10B loss-of-function was also observed in midbrain neuronal cultures derived from ATP10B knock-out human induced pluripotent stem cells clones, which showed a significant reduction in TH-positive neurons.

Conclusion

Taken together, our findings demonstrate that ATP10B depletion detrimentally impacts the viability of dopaminergic neurons bothin vivoandin vitro. Moreover, a broader impact on the functionality of the nigrostriatal pathway was evidenced as rats withATP10Bknockdown exhibited motor impairments similar to those observed in PD patients.
Longitudinal Multi-Tensor Analysis of Neocortical Microstructure in an Animal Model of Cortical Dysplasia
Authors: Villasenõr Paulina J. , Luna-Munguía Hiram , Ramirez-Manzanares Alonso , Coronado-Leija Ricardo , Concha Luis
Published: July 2024

The neocortex is a highly organized structure, with region-specific spatial patterns of cells and fibers constituting cyto- and myelo-architecture, respectively. These architectural features are modulated during neurodevelopment, aging, and disease. While invasive techniques have contributed significantly to our understanding of cortical patterning, the task remains challenging through non-invasive methods. Structural magnetic resonance imaging (MRI) has advanced to improve sensitivity in identifying cortical features, yet most methods focus on capturing macrostructural characteristics, often overlooking critical microscale components. Diffusion-weighted MRI (dMRI) offers an opportunity to extract quantitative information reflecting microstructural changes. Here we investigate whether advanced multi-tensor dMRI methods can detect microstructural characteristics related to the orientational organization of the myelo- and cyto-architecture in an animal model of cortical dysplasia, a malformation of cortical development. We scanned 32 animals (n=16 experimental; n=16 control) at four different time points (30, 60, 120, and 150 post-natal days) using both structural and multi-shell dMRI. Our dMRI metrics were sampled using a 2D curvilinear system of coordinates as a common anatomical descriptor across animals. Diffusion tensors were labeled according to their orientation with respect to the cortical surface, and derived metrics were analyzed separately. We identified abnormalities in the perpendicular and parallel diffusion components in deeper cortical areas, consistent with histological findings of neuronal and fiber disorganization in animals with dysplasia. Although our methodology is tailored for small species, our protocol shows promise for clinical applications.
Single-cell resolved differentiation of pre-Kranz anatomy in maize leaf primordia
Authors: Yi Juan , Su Hong , Tian Shilong , Sedelnikova Olga , Chen Yonghe , Zhao Caiyao , Yang Jianzhao , Zhang Yijing , Zhu Xin-Guang , Langdale Jane A. , Wang Jia-Wei , Wang Peng
Published: July 2024

Typical C4plants such as maize possess highly optimized Kranz-type leaf anatomy, whereby concentric wreaths of mesophyll and bundle sheath cells surround closely spaced veins. The veins and the cells that surround them are derived from the middle ground meristem (mGM) through processes that are as yet undefined. Here we distinguished the active zone of vascular development within early leaf primordia, and used comparative transcriptomics of sub-sectioned maize and rice primordia to identify cohorts of genes likely involved in early Kranz development. Leveraging single-nucleus RNA sequencing (snRNA-seq) we then explored the cell heterogeneity and developmental trajectories within single maize leaf primordia. Assisted byin situhybridization, cell clusters of mGM and procambium were identified, with candidate marker genes showing different yet inter-related expression patterns. Localization of the vascular markerZmSHR1was preceded by that ofZmEREB161andZmEREB114in terms of procambium initiation. Potential subclusters of bundle sheath cells and different layer of mesophyll cells were depicted from developing cells toward the tip of sub-sectioned maize primordia. Collectively our results identify potential mGM derived or procambium localized Kranz regulators and provide resources for investigating leaf vein development in maize and rice, at sub-primordium and single-cell resolution.
Taking a BREATH (Bayesian Reconstruction and Evolutionary Analysis of Transmission Histories) to simultaneously infer phylogenetic and transmission trees for partially sampled outbreaks
Authors: Colijn Caroline , Hall Matthew , Bouckaert Remco
Published: July 2024

We introduce and apply Bayesian Reconstruction and Evolutionary Analysis of Transmission Histories (BREATH), a method to simultaneously construct phylogenetic trees and transmission trees using sequence data for a person-to-person outbreak. BREATH’s transmission process that accounts for a flexible natural history of infection (including a latent period if desired) and a separate process for sampling. It allows for unsampled individuals and for individuals to have diverse within-host infections. BREATH also accounts for the fact that an outbreak may still be ongoing at the time of analysis, using a recurrent events approach to account for right truncation. We perform a simulation study to verify our implementation, and apply BREATH to a previously-described 13-year outbreak of tuber-culosis. We find that using a transmission process to inform the phylogenetic reconstruction results in better resolution of the phylogeny (in topology, branch length and tree height) and a more precise estimate of the time of origin of the outbreak. Considerable uncertainty remains about transmission events in the outbreak, but our reconstructed transmission network resolves two major waves of transmission consistent with the previously-described epidemiology, estimates the numbers of unsampled individuals, and describes some highprobability transmission pairs. An open source implementation of BREATH is available fromhttps://github.com/rbouckaert/transmissionas theBREATHpackage to BEAST 2.
Assessing the Relationship Between Cannabis Use and DKA Outcomes: Insights from a National Inpatient Sample Study
Authors: Randhawa Aastha , Jana Kundan , Sattar Moin
Published: July 2024

DKA hospitalizations in the United States have risen across all age groups, with the highest rates observed in individuals under 45 years of age. While the ongoing decline in in-hospital DKA mortality is encouraging, further efforts are needed to identify at-risk populations. Cannabis is one of the most used recreational drugs in the world, and studies have shown that it may be related to an increased risk of DKA. While prior data assessed it impact on incidence on DKA, there exists a knowledge gap about its impact on in-patient outcomes of DKA. We designed a study aimed to investigate the impact of cannabis use on DKA outcomes using the National Inpatient Sample (NIS) dataset. Our study is a retrospective observational study, in which, we identified patient with DKA and divided them into two cohorts: those who use cannabis and those who don’t. After matching both the groups for age groups, medical conditions (e.g., AIDS, COPD, heart failure, hypertension, liver disease, malignancy), gender, obesity, smoking status, and race/ethnicity, the two groups were compared for the primary outcome of inpatient mortality and secondary outcomes including shock, acute kidney injury, acute coronary syndrome, ischemic stroke, acute respiratory failure, invasive mechanical ventilation, cardiac arrest. Contrary to prior studies showing increased overall mortality risk associated with cannabis use, out study does not show worse DKA outcomes in cannabis users. In fact, cannabis is associated with a statistically significant decrease in the odds of mortality in the matched cohort. While no conclusion regarding causative or protective effects could be drawn from this study, it helps explore unique demographic and clinical characteristics of populations, to identify at-risk populations for various outcomes of in-patient DKA admissions.
Real-time dynamic polygenic prediction for streaming data
Authors: Tubbs Justin D. , Chen Yu , Duan Rui , Huang Hailiang , Ge Tian
Published: July 2024

Polygenic risk scores (PRSs) are promising tools for advancing precision medicine. However, existing PRS construction methods rely on static summary statistics derived from genome-wide association studies (GWASs), which are often updated at lengthy intervals. As genetic data and health outcomes are continuously being generated at an ever-increasing pace, the current PRS training and deployment paradigm is suboptimal in maximizing the prediction accuracy of PRSs for incoming patients in healthcare settings. Here, we introduce real-time PRS-CS (rtPRS-CS), which enables online, dynamic refinement and calibration of PRS as each new sample is collected, without the need to perform intermediate GWASs. Through extensive simulation studies, we evaluate the performance of rtPRS-CS across various genetic architectures and training sample sizes. Leveraging quantitative traits from the Mass General Brigham Biobank and UK Biobank, we show that rtPRS-CS can integrate massive streaming data to enhance PRS prediction over time. We further apply rtPRS-CS to 22 schizophrenia cohorts in 7 Asian regions, demonstrating the clinical utility of rtPRS-CS in dynamically predicting and stratifying disease risk across diverse genetic ancestries.
The Abelson kinase and the Nedd4-family E3 ligases co-regulate Notch trafficking to limit signaling
Authors: Miranda-Alban Julio , Sanchez-Luege Nicelio , Valbuena Fernando M. , Rangel Chyan , Rebay Ilaria
Published: July 2024

Precise output from the conserved Notch signaling pathway governs a plethora of cellular processes and developmental transitions. Unlike other pathways that use a cytoplasmic relay, the Notch cell surface receptor transduces signaling directly to the nucleus, with endocytic trafficking providing critical regulatory nodes. Here we report that the cytoplasmic tyrosine kinase Abelson (Abl) facilitates Notch internalization into late endosomes/multivesicular bodies (LEs), thereby limiting signaling output in both ligand-dependent and -independent contexts. Abl phosphorylates the PPxY motif within Notch, a molecular target for its degradation via Nedd4-family ubiquitin ligases. We show that Su(dx), a family member, mediates the Abl-directed LE regulation of Notch via the PPxY, while another family member, Nedd4Lo, contributes to Notch internalization into LEs through both PPxY-dependent and independent mechanisms. Our findings demonstrate how a network of post-translational modifiers converging at LEs cooperatively modulate Notch signaling to ensure the precision and robustness of its cellular and developmental functions.
Proteome-wide Mendelian randomization study implicates inflammaging biomarkers in retinal vasculature, cardiometabolic diseases and longevity
Authors: Villaplana-Velasco Ana , Perrot Nicolas , Hang Yu , Chong Michael , Trucco Emmanuelle , Nelson Walter , Petch Jeremy , Gerstein Hertzel C , Parminder Raina , Yusuf Salim , Bernabeu Miguel O. , Tenesa Albert , Rawlik Konrad , Pare Guillaume , Doney Alexander , Pairo-Castineira Erola , Pigeyre Marie
Published: July 2024

With the increasing proportion of elderly individuals, improving understanding of the biological mechanisms involved in healthy aging is of utmost importance. Retinal vascular complexity obtained from retinal fundus photographs, and evaluated as fractal dimension (ie, Df), a measure of the geometric pattern of the retinal vasculature, has recently emerged as a valuable indicator of diseases and aging processes. The purpose of our study was to elucidate possible mechanisms underlying those relationships. By integrating retinal Df with genomic and plasma proteome biomarkers, we uncovered novel pathways involved in determining Df and its links with cardiometabolic diseases and longevity. First, we performed a genome wide association study (GWAS) of retinal vascular Df by meta-analysing signals from 74,434 participants from three large epidemiological cohorts, the Canadian Longitudinal Study of Aging (CLSA), the Genetics of Diabetes Audit and Research in Tayside Scotland (GoDARTS), and the UK Biobank (UKBB). We replicated four known loci associated with Df, and identified one novel locus within or near DAAM1, as well as found seven suggestive associations within or near CSNK1A1L, MAST4, HIVEP1, LOC283038, FNDC3A, SP100, and SUGP1 genes. GWAS summary statistics confirmed a negative correlation between Df and cardiovascular disease, stroke, and inflammation, but a positive correlation with longevity. Next, employing Mendelian randomization which combined genetic determinants of Df, and cis-protein Quantitative Trait Loci from 1,159 circulating proteins from the Prospective Urban and Rural Epidemiological (PURE) cohort (n=12,066), we identified eight causal mediators for Df, namely IgG Fc receptorIIb, BST1, LILRB2, IL16, MMP12, PON2, ALPP, and PDL2. Notably, MMP12 and IgG Fc receptorIIb have been suggested to connect Df to cardiometabolic outcomes (i.e., coronary artery disease, stroke, peripheral artery disease, and type 2 diabetes) and longevity, respectively. Pathway enrichment analyses highlighted the role of IgG Fc receptorIIb in immune and inflammatory responses to aging processes, referred to as inflammaging. This multi-pronged approach unveils IgG Fc recIIb and MMP12 as key mediators in immune and inflammation pathways, linking lower Df to a higher risk of cardiometabolic diseases and a shorter lifespan. Therefore, retinal Df may be a convenient way to estimate inflammaging, such that lower retinal Df, may indicate a higher inflammaging status. Targeting MMP12 and IgG Fc ReceptorIIb may promote healthy aging and mitigating the occurrence of cardiometabolic diseases in the elderly population.
Identification and characterization of collagen XXIII alpha 1 as a novel risk factor for eczema herpeticum
Authors: Chopra Shruti , Roesner Lennart M. , Döhner Katinka , Zeitvogel Jana , Traidl Stephan , Rodriguez Elke , Harder Inken , Lieb Wolfgang , Weidinger Stephan , Schulz Thomas F. , Sodeik Beate , Werfel Thomas
Published: July 2024

Eczema herpeticum (EH) is a potentially life-threatening disseminated skin infection caused by herpes simplex virus (HSV) in a subset of patients with atopic dermatitis (AD). Genetic factors play a pivotal role in EH development. Herein, we identify a single nucleotide polymorphism (SNP) rs2973744 in the gene encoding collagen XXIII alpha 1 chain (Col23a1) as a novel genetic risk factor for EH using whole exome sequencing. EH-patient-derived primary keratinocytes carrying the SNP rs2973744 show elevatedCOL23A1mRNA and total protein levels as well as increased susceptibility to HSV-1. We discover that increasing Col23a1 levels enhances HSV-1 infection in human keratinocytes. The transcriptomic analysis unveils thatCOL23A1overexpression dampens keratinocyte immune responses, thereby elucidating the molecular mechanism underlying exacerbated HSV-1 susceptibility. Our findings report a novel potential screening marker and therapeutic target for EH and reveal Col23a1’s unexplored role in HSV-1 pathogenesis.
Mendelian randomization infers the effect of 14 parental illnesses on 44 congenital anomalies
Authors: Tian Tian , Tan Lei , Shao Wenjing
Published: July 2024

Background: Congenital anomalies (CA), including congenital malformations (CM) and congenital deformities (CD), are significant health concerns influenced by genetic and environmental factors. Parental illnesses, especially those with genetic components, may affect the risk of congenital anomalies in offspring. Although clinical studies have suggested associations between certain parental illnesses and increased CM and CD risk, causal relationships remain unclear. This study employs a Mendelian randomization (MR) approach to investigate these potential causal links. Methods: Fourteen parental illnesses were selected for this study: breast cancer, chronic bronchitis/emphysema, diabetes, heart disease, hypertension, and Alzheimer's disease in mothers; and Alzheimer's disease, bowel cancer, chronic bronchitis/emphysema, diabetes, heart disease, hypertension, lung cancer, and prostate cancer in fathers. Genetic variants associated with these illnesses were identified from genome-wide association studies (GWAS) in the UK Biobank. Genetic data for 44 congenital anomalies were sourced from the FinnGen database. Two-sample MR was conducted to estimate causal effects, with sensitivity analyses and multivariable MR (MVMR) to control for potential confounders. Results: MR analysis revealed causal relationships between 13 parental illnesses and 13 specific congenital anomalies. Notably, mother's hypertension significantly increased the risk of congenital hypothyroidism (IVW: OR = 7.969, 95% CI = 3.0826-20.6011, p = 4.20E-04), and father's diabetes increased the risk of congenital heart defects in offspring (IVW: OR = 3.8E+09, 95% CI = 2.2E+04-6.6E+14, p = 3E-04). The associations' strength varied with the type of parental illness and the specific congenital disease. Conclusion: This study underscores the utility of MR in elucidating genetic influences of parental health conditions on congenital anomalies. The findings highlight the importance of managing parental health to reduce congenital anomalies risk in offspring. Further research is needed to explore underlying biological mechanisms and validate these findings in diverse populations.
Site-specific DNA methylation in KCNJ11 promoter contributes to type 2 diabetes
Authors: Zhu Mengmeng , Huang Qiaoliang , Li Heng , Zhao Yujie , Guo Heming , Wang Tao , Liu Xiaodan , Huang Yun , Hu Ji , Fang Chen , Huang Jian
Published: July 2024

Aims

This study explores the correlation between site-specific methylation levels of the KCNJ11 promoter and type 2 diabetes mellitus (T2DM), analyzing potential molecular mechanisms.

Methods

Thirty patients newly diagnosed with T2DM and 30 healthy controls were selected to determine the CpG methylation levels in the promoter region of the KCNJ11 gene using the bisulfite assay. The online software JASPAR was used to predict transcription factors binding to differentially methylated sites. Key transcription factors were further validated through quantitative PCR (q-PCR) and chromatin immunoprecipitation followed by PCR (ChIP-PCR).

Results

Methylation at multiple CpG sites within the KCNJ11 gene promoter was significantly reduced in newly diagnosed T2DM patients compared to healthy individuals. The methylation status of CpG-471, a site crucial for the binding of the transcription factor TCF12, emerged as potentially influential in T2DM pathogenesis. This reduction in methylation at CpG-471 may enhance TCF12 binding, thereby altering KCNJ11 expression.

Conclusion

Hypomethylation of specific CpG sites in the promoter region of the KCNJ11 gene in patients with incipient T2DM potentially contributes to the disease’s pathogenesis. This hypomethylation enhances the transcriptional activity of TCF12, which binds to these sites, possibly influencing regulatory pathways involved in pancreatic beta-cell function.
Morph-linked variation in female pheromone signaling and male response in a polymorphic moth
Authors: De Pasqual Chiara , Selenius Eetu , Burdfield-Steel Emily , Mappes Johanna
Published: July 2024

Understanding the maintenance of genetic variation in reproductive strategies and polymorphisms in the wild requires a comprehensive examination of the complex interactions between genetic basis, behavior, and environmental factors.

We tested the association between three color genotypes and variation in female pheromone signaling and male antennal morphology in the wood tiger moth (Arctia plantaginis). These moths have genetically determined white (WW, Wy) and yellow (yy) hindwings that are linked to mating success and fitness, with heterozygotes (Wy) having an advantage. We hypothesized that attractiveness and reproductive success are correlated, with Wy females being more attractive than the other two genotypes which could contribute to maintaining the polymorphism.

Female attractiveness was tested by baiting traps with females of the three color genotypes both in low-(i.e., field setup) and in high-population density (i.e., large enclosure setup). Male’s ability to reach females was correlated to their own color genotype and antennal morphology (length, area, and lamellae count).

Contrary to our prediction, morph-related reproductive success and attractiveness were not correlated. Heavier Wy females attracted a lower proportion of males compared to WW and yy females. Specifically, an increase in weight corresponded to a decreased Wy but increased yy female attractiveness. yy females were generally more attractive than others likely due to earlier pheromone release. In males, lamellae count and genetic color morph were linked to the male’s ability to locate females. Furthermore, male traits affected their ability to reach females in a context-specific way. Males with denser antennae (i.e., higher lamellae count) and white males reached the females faster than yellows in the enclosure, while yellow males located females faster than whites in the field.

Our results indicate that higher yy female attractiveness was likely affected by the combined effect of early pheromone release, female weight and higher population density. Males’ searching success was affected by morph-specific behavioral strategies and local population density. Ultimately, the combined effect of genotype-related pheromone signaling strategies of females together with environment-dependent male behavior affect male response and potentially contribute to maintaining variation in fitness-related traits.
Varying importance of postzygotic isolation in polyploid speciation? A survey of the triploid block strength, its causal mechanisms, and evolutionary consequences
Authors: Salony Susnata , Clo Josselin , Kolář Filip , Lafon Placette Clément
Published: July 2024

The triploid block, primarily caused by endosperm developmental issues, is known as a significant barrier to interploidy hybridization among flowering plants and thereby, polyploid speciation. However, its strength varies across taxa, with some instances of leakiness, questioning its universal role as a barrier. We conducted a literature survey to explore the causes of the variation in the strength of triploid block across angiosperms. We particularly assessed the impact of interploidy cross direction, types of endosperm development, endosperm persistence at seed maturity, and ploidy divergence. None of these factors had a significant impact on triploid seed viability, likely due to limited data and inconsistencies in estimation methods across the literature. In addition, triploid seed viability in experimental crosses was sometimes correlated to the occurrence of triploid hybrids in nature, sometimes not, suggesting a mixed role of the triploid block in shaping interspecies gene flow. Altogether, our study highlights the need for unified approaches in future studies on the triploid block to advance our understanding of its variation and evolutionary implications.
The tubule-sheet continuum model links the pattern of nuclear envelope assembly to nuclear envelope integrity
Authors: Arun Sanjana , Zhao Gengjing
Published: July 2024

Nuclear envelope (NE) fragility is associated with a variety of human diseases. However, major questions about the causes of NE fragility are unresolved. In particular, the relationship between NE fragility and NE assembly is unclear. Here, using a panel of 13 mammalian cell lines, we show that normal cells and some cancer cells assemble the NE using distinct patterns from opposite ends of the "tubule-sheet continuum", and that the NE assembly pattern more utilised in cancer cells is a source of NE fragility. In normal cells, the mitotic endoplasmic reticulum (ER) morphology is dominated by ER tubules or small sheets and the NE assembles by "membrane infiltration". By contrast, in some cancer cells, the mitotic ER morphology is dominated by large ER sheets and the NE assembles by "lateral sheet expansion". Experimental manipulations that promote mitotic ER sheet formation and NE assembly by lateral sheet expansion in normal cells result in NE fragility. Thus, we propose that NE assembly by lateral sheet expansion is a source of NE fragility in cancer cells.
Physics-informed tracking of qubit fluctuations
Authors: Berritta Fabrizio , Krzywda Jan A. , Benestad Jacob , van der Heijden Joost , Fedele Federico , Fallahi Saeed , Gardner Geoffrey C. , Manfra Michael J. , van Nieuwenburg Evert , Danon Jeroen , Chatterjee Anasua , Kuemmeth Ferdinand
Published: July 2024

Environmental fluctuations degrade the performance of solid-state qubits but can in principle be mitigated by real-time Hamiltonian estimation down to timescales set by the estimation efficiency. We implement a physics-informed and an adaptive Bayesian estimation strategy and apply them in real time to a semiconductor spin qubit. The physics-informed strategy propagates a probability distribution inside the quantum controller according to the Fokker-Planck equation, appropriate for describing the effects of nuclear spin diffusion in gallium arsenide. Evaluating and narrowing the anticipated distribution by a predetermined qubit probe sequence enables improved dynamical tracking of the uncontrolled magnetic field gradient within the singlet-triplet qubit. The adaptive strategy replaces the probe sequence by a small number of qubit probe cycles, with each probe time conditioned on the previous measurement outcomes, thereby further increasing the estimation efficiency. The combined real-time estimation strategy efficiently tracks low-frequency nuclear spin fluctuations in solid-state qubits, and can be applied to other qubit platforms by tailoring the appropriate update equation to capture their distinct noise sources.

Published by the American Physical Society
2024
Interplay between charge and spin noise in the near-surface theory of decoherence and relaxation of
C3v
symmetry qutrit spin-1 centers
Authors: Candido Denis R. , Flatté Michael E.
Published: July 2024

Decoherence and relaxation of solid-state defect qutrits near a crystal surface, where they are commonly used as quantum sensors, originate from charge and magnetic field noise. A complete theory requires a formalism for decoherence and relaxation that includes all Hamiltonian terms allowed by the defect's point-group symmetry. This formalism, presented here for the C3v symmetry of a spin-1 defect in a diamond, silicon carbide, or similar host, relies on a Lindblad dynamical equation and clarifies the relative contributions of charge and spin noise to relaxation and decoherence, along with their dependence on the defect spin's depth and resonant frequencies. The calculations agree with the experimental measurements of Sangtawesin [], and corroborate the importance of charge noise.

Published by the American Physical Society
2024
Scalar curvature for metric spaces: Defining curvature for quantum gravity without coordinates
Authors: van der Duin Jesse , Silva Agustín
Published: July 2024

Geometrical properties of spacetime are difficult to study in nonperturbative approaches to quantum gravity like causal dynamical triangulations (CDT), where one uses simplicial manifolds to define the gravitational path integral, instead of Riemannian manifolds. In particular, in CDT one only relies on two mathematical tools, a distance measure and a volume measure. In this paper, we define a notion of scalar curvature, for metric spaces endowed with a volume measure or a random walk, without assuming nor using notions of tensor calculus. Furthermore, we directly define the Ricci scalar, without the need of defining and computing the Riemann or the Ricci tensor . For this, we make use of quantities, like the surface of a geodesic sphere, or the return probability of scalar diffusion processes, that can be computed in these metric spaces, as in a Riemannian manifold, where they receive scalar curvature contributions. Our definitions recover the classical results of scalar curvature when the sets are Riemannian manifolds. We propose two methods to compute the scalar curvature in these spaces, and we compare their features in natural implementations in discrete spaces. The defined generalized scalar curvatures are easily implemented on discrete spaces, like graphs. We present the results of our definitions on random triangulations of a 2D sphere and plane. Additionally, we show the results of our generalized scalar curvatures on the quantum geometries of 2D CDT, where we find that all our definitions indicate a flat ground state of the gravitational path integral.

Published by the American Physical Society
2024
Tracy-Widom Distribution in Four-Dimensional Supersymmetric Yang-Mills Theories
Authors: Bajnok Zoltan , Boldis Bercel , Korchemsky Gregory P.
Published: July 2024

Various observables in different four-dimensional superconformal Yang-Mills theories can be computed exactly as Fredholm determinants of truncated Bessel operators. We exploit this relation to determine their dependence on the ’t Hooft coupling constant. Unlike the weak coupling expansion, which has a finite radius of convergence, the strong coupling expansion is factorially divergent, necessitating the inclusion of nonperturbative, exponentially small corrections. We develop a method to systematically compute these corrections and discuss the resurgent properties of the resulting transseries.

Published by the American Physical Society
2024
General Shiba mapping for on-site four-point correlation functions
Authors: Eßl Herbert , Reitner Matthias , Sangiovanni Giorgio , Toschi Alessandro
Published: July 2024

By applying the Shiba mapping on the two-particle level, we derive the relation between the local four-point correlation functions of bipartite lattice models with on-site electronic repulsion and those of the corresponding models with attractive interaction in the most general setting. In particular, we extend the results of [], which were limited to the rather specific situation of the static limit in strictly particle-hole symmetric models, (i) by explicitly including magnetic field and different values of the chemical potentials, and (ii) by considering the full dependence of the generalized susceptibilities on the transfer (bosonic) Matsubara frequency. The derived formalism is then applied, as a relevant benchmark, to the Hubbard atom by investigating the general properties of the divergences of its irreducible vertex functions as a function of chemical potential and applied magnetic field. The resulting phase diagrams provide an insightful compass for future studies of the breakdown of the self-consistent perturbation expansion beyond high-symmetric regimes.

Published by the American Physical Society
2024
Nanoscale terahertz conductivity and ultrafast dynamics of terahertz plasmons in periodic arrays of epitaxial graphene nanoribbons
Authors: Singh Arvind , Němec Hynek , Kunc Jan , Kužel Petr
Published: July 2024

The dynamics of plasmons in nanoribbons of (hydrogen intercalated) quasi-freestanding single-layer graphene is studied by terahertz spectroscopy both in the steady state and upon photoexcitation by an ultrashort near infrared laser pulse. The use of two-dimensional frequency-domain analysis of the optical pump–terahertz (THz) probe signals allows us to determine the evolution of carrier temperature and plasmon characteristics with ∼100 fs time resolution. Namely, we find that the carrier temperature decreases from more than 5000 K to the lattice temperature within about 7 ps and that during this evolution the carrier mobility remains practically constant. The time-resolved THz conductivity spectra suggest that graphene nanoribbons contain defects which act as low potential barriers causing a weak localization of charges; the potential barriers are overcome upon photoexcitation. Furthermore, the edges of graphene nanoribbons are found to slightly enhance the scattering of carriers. The results are supported by complementary measurements using THz scanning near-field microscopy, which confirm a high uniformity of the THz conductivity across the sample and demonstrate high enough sensitivity to resolve even the impact of nanometric terrace steps on SiC substrate under the graphene monolayer.

Published by the American Physical Society
2024
Rise and fall of patterns in driven-dissipative Rydberg polaritons
Authors: Alaeian Hadiseh , Walther Valentin
Published: July 2024

In this study, we present an exploration of spontaneous symmetry breaking and pattern formation in the driven-dissipative system of Rydberg exciton polaritons with long-range interactions. Our investigation unravels the pattern formations through modulational instability, characterized by scales in the micron range. We observe the dynamics of the polariton ensemble, studying the emergence of metastable patterns and their eventual collapse in the long-time limit. This phenomenon is attributed to the destructive interference between the polariton state and the external drive within the ensemble. Further, we delineate conditions conducive to the stable formation of patterns under incoherent pumping. These findings open up various avenues for delving into the burgeoning realm of driven-dissipative and long-range interacting gases through the unique characteristics of Rydberg excitons.

Published by the American Physical Society
2024
Finding synchronization state of higher-order motif networks by dynamic learning
Authors: Ye Zhiqiu , Wu Yong , Ding Qianming , Xie Ying , Jia Ya
Published: July 2024

Synchronization of action potentials is one of the important phenomena for neural networks to achieve biological functions. How to find the optimal parameter space of neural networks in a synchronized state is of great significance for studying their synchronization. This study explores the parameter space of triplet motif-based higher-order networks in a synchronized state through the dynamic learning of synchronization (DLS) technique, which dynamically modulates the connection weights between motifs to alter their firing patterns. Our study delves into regular, Erdós-Rënyi random graphs, small-world, and scale-free networks, emphasizing the high-order motif interactions that characterize these networks. Our key findings indicate that the DLS technique successfully promotes synchronization within high-order motif networks with various connection patterns, although the degree of synchronization in networks where motifs are interconnected by chemical synapses is slightly weaker than those interconnected by electrical synapses. Additionally, we demonstrate the pattern of weight changes during the regulation of network firing states by DLS, finding that the evolution of weight distributions correlates with the network's topological structure. This work might provide new insights into complex network synchronization and lays the foundation for further exploration of using DLS technology to synchronize higher-order networks through external factors.

Published by the American Physical Society
2024
High-angular-sensitivity X-ray phase-contrast microtomography of soft tissue through a two-directional beam-tracking synchrotron set-up
Authors: Navarrete-León Carlos , Patrick P. Stephen , Doherty Adam , Allan Harry , Cipiccia Silvia , Marathe Shashidhara , Wanelik Kaz , Esposito Michela , Hagen Charlotte K. , Olivo Alessandro , Endrizzi Marco
Published: July 2024

Two-directional beam-tracking (2DBT) is a method for phase-contrast imaging and tomography that uses an intensity modulator to structure the X-ray beam into an array of independent circular beamlets that are resolved by a high-resolution detector. It features isotropic spatial resolution, provides two-dimensional phase sensitivity, and enables the three-dimensional reconstructions of the refractive index decrement, δ, and the attenuation coefficient, μ. In this work, the angular sensitivity and the spatial resolution of 2DBT images in a synchrotron-based implementation is reported. In its best configuration, angular sensitivities of ∼20 nrad and spatial resolution of at least 6.25 µm in phase-contrast images were obtained. Exemplar application to the three-dimensional imaging of soft tissue samples, including a mouse liver and a decellularized porcine dermis, is also demonstrated.
Hard X-ray imaging and tomography at the Biomedical Imaging and Therapy beamlines of Canadian Light Source
Authors: Gasilov Sergey , Webb M. Adam , Panahifar Arash , Zhu Ning , Marinos Omar , Bond Toby , Cooper David M. L. , Chapman Dean
Published: July 2024

The Biomedical Imaging and Therapy facility of the Canadian Light Source comprises two beamlines, which together cover a wide X-ray energy range from 13 keV up to 140 keV. The beamlines were designed with a focus on synchrotron applications in preclinical imaging and veterinary science as well as microbeam radiation therapy. While these remain a major part of the activities of both beamlines, a number of recent upgrades have enhanced the versatility and performance of the beamlines, particularly for high-resolution microtomography experiments. As a result, the user community has been quickly expanding to include researchers in advanced materials, batteries, fuel cells, agriculture, and environmental studies. This article summarizes the beam properties, describes the endstations together with the detector pool, and presents several application cases of the various X-ray imaging techniques available to users.
Synthesis, molecular and crystal structures of 4-amino-3,5-difluorobenzonitrile, ethyl 4-amino-3,5-difluorobenzoate, and diethyl 4,4′-(diazene-1,2-diyl)bis(3,5-difluorobenzoate)
Authors: Novikov Egor M. , Guillen Campos Jesus , Read de Alaniz Javier , Fonari Marina S. , Timofeeva Tatiana V.
Published: July 2024

The crystal structures of two intermediates, 4-amino-3,5-difluorobenzonitrile, C7H4F2N2 (I), and ethyl 4-amino-3,5-difluorobenzoate, C9H9F2NO2 (II), along with a visible-light-responsive azobenzene derivative, diethyl 4,4′-(diazene-1,2-diyl)bis(3,5-difluorobenzoate), C18H14F4N2O4 (III), obtained by four-step synthetic procedure, were studied using single-crystal X-ray diffraction. The molecules of I and II demonstrate the quinoid character of phenyl rings accompanied by the distortion of bond angles related to the presence of fluorine substituents in the 3 and 5 (ortho) positions. In the crystals of I and II, the molecules are connected by N—H...N, N—H...F and N—H...O hydrogen bonds, C—H...F short contacts, and π-stacking interactions. In crystal of III, only stacking interactions between the molecules are found.
Digital competence of students in higher education: an assessment framework in Vietnam
Authors: Pham Tra Lam , Dau Thi Kim Thoa
Published: July 2024

Purpose

This study investigates the digital competence (DC) of undergraduate students, considering three key dimensions: use of Information and Communication Technologies (ICT) resources, knowledge about ICT resources, and attitude towards ICT. We also examined the relationship between these aspects in order to build a DC assessment framework.

Design/methodology/approach

A structured questionnaire was administered to students from several universities in Vietnam in order to assess their DC. A PLS analysis was conducted based on data from 551 valid responses.

Findings

Statistical analyses showed that the DC of students was quite low. The findings certify that knowledge of ICT resources is a total intermediate variable in the impact of attitude towards ICT on the use of ICT resources by students.

Practical implications

Our findings provide important implications for policymakers and teachers' insights for authorities, universities, and scholars to develop strategies for DC of students in higher education.

Originality/value

This study is the first to explore the DC assessment framework for students in higher education in an emerging market, Vietnam.
Using predictive methods to assess observation and measure importance
Authors: Briggs William M.
Published: July 2024

Purpose

This study aims to find suitable replacements for hypothesis testing and variable-importance measures.

Design/methodology/approach

This study explores under-used predictive methods.

Findings

The study's hypothesis testing can and should be replaced by predictive methods. It is the only way to know if models have any value.

Originality/value

This is the first time predictive methods have been used to demonstrate measure and variable importance. Hypothesis testing can never prove the goodness of models. Only predictive methods can.