bluuebunny/crossref_metadata_2025 huggingface dataset:
Horizontal gene transfer-initiated reorganization of lipid metabolism drives lifestyle innovation in a eukaryote
Authors: Rao Bhagyashree Dasari , Gomez Gil Elisa , Peter Maria , Balogh Gabor , Nunes Vanessa , MacRae James I. , Chen Qu , Rosenthal Peter , Oliferenko Snezhana
Published: August 2024

Horizontal gene transfer is a source of metabolic innovation and adaptation to new environments. Yet, how horizontally transferred metabolic functionalities are integrated into host cell biology remains an open question. Here, we use the fission yeast Schizosaccharomyces japonicus to probe how eukaryotic lipid metabolism is rewired in response to the acquisition of a horizontally transferred squalene-hopene cyclase Shc1. We show that Shc1-dependent production of hopanoids, the structural mimics of eukaryotic sterols, allows S. japonicus to thrive in anoxia, where sterol biosynthesis is not possible. We further demonstrate that glycerophospholipid fatty acyl asymmetry, prevalent in S. japonicus, is crucial for accommodating both sterols and hopanoids in membranes, and explain how Shc1 functions alongside the native sterol biosynthetic pathway to support membrane properties. Through engineering experiments in the sister species S. pombe, which naturally lacks Shc1, we show that the acquisition of Shc1 may entail new physiological traits; however, to maximize Shc1 performance, sterol biosynthesis must be dampened. Our work sheds new light on the mechanisms underlying cellular integration of horizontally transferred genes in eukaryotes and provides broader insights into the evolution of membrane organization and function.
Testing and overcoming the limitations of Modular Response Analysis
Authors: Borg Jean-Pierre , Colinge Jacques , Ravel Patrice
Published: August 2024

Modular Response Analysis (MRA) is an effective method to infer biological networks from perturbation data. However, it has several limitations, such as strong sensitivity to noise, need of performing independent perturbations that hit a single node at a time, and linear approximation of dependencies within the network. Previously, we addressed MRA sensitivity to noise by revisiting MRA as a multilinear regression problem. Here, we provide new contributions to complement this theory. First, we overcame the need of perturbations to be independent, thereby augmenting MRA applicability. Second, using analysis of variance (ANOVA) and lack of fit tests, we assessed MRA compatibility with the data and identified the primary source of errors. If nonlinearity prevails, we propose a polynomial extension to the model. Third, we demonstrated how to effectively use the prior knowledge of the network studied. Finally, we added these innovations to our R software package MRARegress to provide a complete, extended theory around MRA and to facilitate its access by the community.
Therapeutically targeting the classical complement pathway with antisense oligonucleotides in Alzheimer’s disease
Authors: Wang Yuanyuan , Wu Tiffany , Gogineni Alvin , Tsai Ming-Chi , Kielpinski Lukasz , Mahajan Anubha , Pandey Shristi , Schachner Luis , Tran John C. , Wu Cong , Schauer Stephen , Biever Anne , Boesen Sidsel , Li Meiling , Munk Alexander , Meilandt William J , Elstrott Justin , Easton Amy , Gylling Helene M , Hanson Jesse E
Published: August 2024

The complement classical pathway (CP) is a key mediator of synapse loss and neurodegeneration in mouse models of Alzheimer’s (AD) and other neurodegenerative diseases. We analyzed human brain proteomics and found consistent elevations of all CP proteins, but not other complement pathways, in AD patient brains. We performed human genetics analysis that identified a rare variant in theC1Sgene within the Finnish population that is associated with AD and we found that a common AD-associatedC1Svariant correlates with increased C1S protein levels. A targeted assay detected elevated C1S activation in AD patient CSF. Given this specific implication of the CP in AD, we next evaluated the therapeutic approach of targeting the CP in the brain using antisense oligonucleotides (ASOs). To identify promising CP targets for knockdown using ASOs we first tested for rescue of synapse loss in an AD mouse model using heterozygous and homozygous complement knockout mice and examined the relative brain expression levels of different CP genes. Based on these experiments we prioritized C1r, C1s and C4 as promising targets for therapeutic knockdown using ASOs. We then screened for ASOs for each target, evaluatingin vitroandin vivoknockdown and toxicity, and identified optimal ASOs targeting C1r, C1s and C4. Experiments with AD model mice demonstrated significant rescue of synapse loss following treatment with C1r, C1s or C4 ASOs. Overall, our findings provide proof of concept for using nucleic acid-based medicine to target the CP in AD and demonstrate the translational potential of this approach.
Unlocking new avenues for non-invasive brain monitoring with combined electroencephalography and functional magnetic resonance imaging at ultra-high field
Authors: Sainz Martinez Cristina , Wirsich Jonathan , Jäger Cilia , Warbrick Tracy , Vulliémoz Serge , Lemay Mathieu , Bastiaansen Jessica , Wiest Roland , Jorge João
Published: August 2024

The combination of electroencephalography (EEG) and functional magnetic resonance imaging (fMRI) at ultra-high field (7 Tesla) offers unprecedented possibilities to probe human brain function non-invasively with high coverage, millisecond temporal precision and sub-millimeter spatial precision, unraveling cortical layers and small subcortical structures. Unfortunately, this technique has remained largely inaccessible at 7T, due to prohibitive cross-modal interference effects and physical constraints. Here, we developed a first-of-its-kind EEG-fMRI acquisition framework on a clinical 7T system combining key improvements from previous works: compact EEG transmission chain to reduce artifact incidence, reference sensors for artifact correction, and adapted leads for compatibility with a dense radiofrequency receive-array allowing state-of-the-art fMRI sensitivity and acceleration. Two implementations were tested: one using an EEG cap adapted in-house, and another using a recently-designed prototype from an industrial manufacturer, intended to be further developed into a commercial product accessible to the broader community. A comprehensive evaluation in humans showed that simultaneous acquisitions, including with sub-millimeter fMRI resolution, could be conducted without detectable safety issues or major practical constraints. The EEG exerted relatively mild perturbations on fMRI quality (6–11% loss in temporal SNR), without measurably affecting the detection of resting-state networks and visual responses. The artifacts induced on EEG could be corrected to a degree where the spatial, spectral and temporal characteristics were comparable to outside recordings, and hallmark features such as resting-state alpha and eyes-closing alpha modulation could be clearly detected. Altogether, these findings indicate excellent prospects for neuroimaging applications, that can leverage the unique possibilities achievable at 7T.
Reduction of SEM charging artefacts in native cryogenic biological samples
Authors: Velazco Abner , Glen Thomas , Klumpe Sven , Pennington Avery , Zhang Jianguo , Smith Jake LR , Glynn Calina , Bowles William , Kobylynska Maryna , Fleck Roland A. , Naismith James H. , Kim Judy S , Darrow Michele C. , Grange Michael , Kirkland Angus I , Dumoux Maud
Published: August 2024

Scanning electron microscopy (SEM) of frozen-hydrated biological samples allows imaging of subcellular structures at the mesoscale in their native state. Combined with focused ion beam milling (FIB), serial FIB/SEM can be used to build a 3-dimensional picture of cells and tissues. The correlation of specific regions of interest with cryo-electron microscopy (cryoEM) can additionally enable subsequent high-resolution analysis. However, the adoption of serial FIB/SEM imaging-based methods is limited due to artefacts arising from insulating areas of cryogenically preserved samples. Here, we demonstrate the use of interleaved scanning to reduce charging artefacts, allowing the observation of biological features that otherwise would be masked or perturbed. We apply our method to samples where inherent features are not visible. These examples include membrane contact sites within mammalian cells, visualisation of the degradation compartment in the algae E.gracilis and observation of a network of membranes within different types of axons in an adult mouse cortex. We further propose an alternative scanning method that could also be widely applicable to imaging any non-conductive.
Spatio-temporal segmentation of contraction waves in the extra-embryonic membranes of the red flour beetle
Authors: Pereyra Marc , Golden Mariia , Lange Zoë , Golden Artemiy , Strobl Frederic , Stelzer Ernst H.K. , Matthäus Franziska
Published: August 2024

In this paper, we introduce an image analysis approach for spatio-temporal segmentation, quantification and visualization of movement or contraction patterns in 2D+t or 3D+t microscopy recordings of biological tissues. The imaging pipeline is applied to time lapse images of the embryonic development of the red flour beetleTribolium castaneumrecorded with light-sheet fluorescence microscopy (LSFM). We are particularly interested in the dynamics of extra-embryonic membranes, and provide quantitative evidence of the existence of contraction waves during late stages of development. These contraction waves are a novel observation of which neither origin, nor function are yet known. The proposed pipeline relies on particle image velocimetry (PIV) for quantitative movement analysis, surface detection, tissue cartography, and an algorithmic approach to detect characteristic movement dynamics. This approach locates contraction waves in 2D+t and 3D+t reliably and efficiently and allows the automated quantitative analysis, such as the area involved in the contractile behavior, contraction wave duration and frequency, path of contractile area, or the relation to the spatio-temporal velocity distribution. The pipeline will be used in the future to conduct a large-scale characterization and quantification of contraction wave behavior inTribolium castaneumdevelopment and can be adapted easily to the identification and segmentation of characteristic tissue dynamics in other systems of interest.
Functional high capacity exosome-encapsulating bioinspired hydrogel promotes microvascular bed expansion in diabetic mice
Authors: Subhan Bibi S , Cortes Troncoso Juan F , Katyal Priya , Meleties Michael , Mestvirishvili Tamara , Arias Fernando , Wang Andrew , Ruggles Kelly , Dolgalev Igor , Mita Paolo , Montclare Jin Kim , Rabbani Piul S
Published: August 2024

Chronic wounds present a significant clinical challenge due to impaired skin microvasculature, particularly in diabetes. The tissue engineering study introduces therapeutic Exo-Q, a unique thermoresponsive polymer hydrogel created with Q protein nanofibers and cultured human bone marrow multipotent stromal cell exosomes with consistent gene signature. Limited, local and topical application of Exo-Q hydrogel is feasible for maximum neovascularization during murine diabetic wound closure in a xenotransplantation model, as well as compatibility and vascular delivery in human skin in a xenograft model. Exo-Q hydrogel treatment significantly reduces diabetic wound closure time within ranges of non-diabetic wounds. This innovative, non-invasive tissue engineered therapeutic option offers a promising approach to addressing the complex pathologies of non-healing wounds.
Increased Postprandial Metabolic Flexibility is Associated with Higher Body Fat Percentages in Healthy Young Adults
Authors: Foreman Nicholas A. , Rajwade Sahil , Bluth Jaiden , Skoglund Lauren C. , Letts Audrey M. , DiPietro Loretta , Ciarleglio Adam , Barberio Matthew D.
Published: August 2024

PURPOSE

High levels of adiposity are associated with an increased risk for chronic cardiometabolic disease. Adipose tissue is a critical metabolic tissue during the postprandial (feeding) period. We sought to assess the relationship between body composition (body fat percentage) and measures of postprandial metabolic flexibility in otherwise healthy young adults.

METHODS

Young adults (n = 27, n = 15 females) of varying body compositions (BMI = 27.1 ± 4.5; Body Fat (BF)% = 30.4 ± 8.7) but without overt pathology completed a 100g oral glucose tolerance test (OGTT). Indirect calorimetry was conducted before (fasting) and following (30, 60, 90, 120 min) consumption of the glucose beverage. Serum and plasma were collected at corresponding time points and analyzed for blood glucose, insulin, non-esterified fatty acids, and inflammatory markers. Linear mixed models were used to test for the effect of body composition on postprandial metabolism over time while controlling for sex, age, fasting metabolism, measures of insulin sensitivity, visceral adipose tissue volume, and the repeated measures design.

RESULTS

As expected, there was a significant (p < 0.05) increase in blood glucose, serum insulin, RER, and CHO with concomitant decreases in plasma NEFAs and whole-body FOX during the OGTT. Using mixed effects models, BF% modified the relationship between postprandial RER and time (β= -0.133, p = 0.019), as well as postprandial CHO and time (β= -0.134, p = 0.023) such that individuals with higher BF% increase their RER and CHO at a greater rate and to a greater extent than those with lower BF%. There was no evidence that BF% modifies the relationship between FOX and time.

CONCLUSION

We demonstrate that a higher body fat percentage is associated with greater postprandial metabolic flexibility (RER and CHO) during an OGTT in young adults without overt metabolic pathology. Metabolic flexibility in this sample may be preserved and represents a compensatory adaptation to decreased glucose storage in the anabolic, postprandial period.
Universal features of Alternative splicing in response to diverse environmental stimuli in rice and the vital roles of TFs in AS regulation
Authors: Xiao Benze , Yang Shuai , Wang Chengqi , Zhang Fangyu , Liu Yi , Xiao Zhuowei , Xie Guosheng , Zhang Zhengfeng
Published: August 2024

Background

Pre-mRNA alternative splicing (AS) plays essential roles in response to environmental stimuli in plants. However, the universal and specific features of splicing in response to diverse environmental conditions remain not fully understood. Recent studies have shown the co-transcriptional characteristics of splicing, which lead to the reasonable speculation that the elements or factors regulating transcription can also affect splicing. Among of which, the effects of transcription factors on alternative splicing in plants under environmental stimuli are still confusing. A large amount 0f public available RNA sequencing data are valuable resources to be re-analyzed for answering questions beyond the aims of their original studies.

Results

We explored the universal features of AS using a standard RNA-seq dataset TENOR, which stems from rice samples under controlled diverse conditions to provide comprehensive and comparable AS analysis under various conditions. We found that AS widely occurs in rice under stimuli, with significant tissue specificity, temporal dynamics, commonality among different stresses or treatments as well as significant difference between differential alternative splicing and expressed genes (DASGs and DEGs) in rice under environmental stimuli. The majority of DASGs under various stresses are splicing factors and transcription factors. The correlation analysis shows that the expression level of transcription factors is significantly correlated with the PSI of AS events. The predominant transcription factors correlating with alternative splicing events come from bHLH, bzip and hsfa families. We validated the effects of transcription factors on AS by analyzing RNA-seq data from transcription factor mutants and found substantial differential AS events between mutants and wild type. Furthermore, the significant correlation was discovered between the transcription levels of transcription factors and splicing factors.

Conclusion

We found universal features of AS and the predominant AS events of SFs and TFs in plants under diverse environments. We propose that TFs might regulated AS of download genes partly by changing the patterns of their own transcription and splicing to further regulate the transcription of SFs. This work illuminate the studies on the possible mechanisms by which TFs modulate AS in plant, especially under environmental stimuli.
Longitudinally cultured precision cut lung slices as a predictiveex vivomodel for lung cancer
Authors: Sargsian Ara , Girmatsion Hermon , Lenders Vincent , Ghesquière Bart , Takeno Cologna Camila , Soenen Stefaan J. , Manshian Bella B.
Published: August 2024

Exploring alternatives toin vivomodels, this study validates Precision Cut Lung Slices (PCLS) as a viableex vivoplatform for lung cancer research. We established the prolonged viability and structural preservation of PCLS, essential for accurate drug response studies. Using Paclitaxel as a benchmark drug and a therapeutically promising silver nanoparticles in combination with immunotherapy, we conducted a pioneering comparative analysis of its therapeutic effects on PCLS against traditionalin vivomodels. Results revealed that PCLS closely mimicsin vivoresponses, demonstrating comparable drug efficacy in tumor growth inhibition. This direct comparison not only confirms the utility of PCLS in simulating real-world outcomes but also emphasizes its potential in reducing animal testing. By providing a reliable, ethical, and efficient alternative for lung cancer studies, PCLS could significantly enhance preclinical research and drug development, marking a critical step towards more humane and representative scientific investigations.
Pelvic floor health in athletics: a cross-sectional study at the Lima World Athletics U20 Championships
Authors: Silvia Giagio , Stephane Bermon , Frederic Garrandes , Tamara Rial Rebullido , Paolo Pillastrini , Marco Vecchiato , Emilio Adami Paolo
Published: August 2024

Objectives

This study aims to investigate various aspects of pelvic floor health among male and female athletes participating in the Lima World Athletics U20 Championships.

Methods

This observational, cross-sectional study will be conducted through a web-based survey via SurveyMonkey. The survey will collect demographic and anthropometric data, as well as medical history, including any injuries to the lower abdomen or pelvic area and history of urinary tract infections. It will also gather information on athletics-related characteristics, such as event specialization, training intensity, and competition volume. Additionally, the survey will explore pelvic floor health by assessing athletes’ knowledge of pelvic floor function and dysfunctions, as well as related behaviors. The prevalence rates of pelvic floor dysfunction (PFD) —including urinary and anal incontinence, pelvic pain, overactive bladder, and pelvic organ prolapse—will be assessed, along with their impact on sports participation and potential risk factors. Urinary incontinence will be further evaluated using the International Consultation on Incontinence Questionnaire-UI Short-Form (ICIQ-UI-SF), with a focus on identifying specific triggers related to athletic activities. Participants will also provide information about their experiences with pelvic floor screening, discussions about these issues, symptom management strategies, and any medical assessments or treatments they have received. Data will be analyzed using descriptive statistics and subgroup analyses. Correlation between collected variables and the presence of PFD will be investigated using correlation analyses.

Conclusion

The findings from this study will provide valuable insights into the unique challenges faced by young elite athletes concerning pelvic floor health. This research represents an initial step toward an international initiative, promoted by World Athletics, to enhance pelvic floor health surveillance and promote overall well-being in athletics.
Population-based estimates of hepatitis E virus associated mortality in Bangladesh
Authors: Paul Repon , Gidding Heather F , Nazneen Arifa , Banik Kajal C , Sumon Shariful Amin , Paul Kishor K , Akram Arifa , Uzzaman M Salim , Tejada-Strop Alexandra , Kamili Saleem , Luby Stephen P , Hayen Andrew , Gurley Emily S
Published: August 2024

Background Hepatitis E virus (HEV) is endemic in many resource-poor countries. Despite an available vaccine, data on HEV-associated mortality are scarce, hindering informed decisions. This study aims to estimate the population-based rate of HEV-specific mortality in Bangladesh. Methods During December 2014-September 2017, we conducted surveillance in six tertiary hospitals in Bangladesh. Patients aged ≥14 years with acute jaundice were recruited, tested for IgM anti-HEV, and followed up post-discharge. A mortality survey in the hospital catchment areas identified deaths associated with acute jaundice, including maternal, stillbirths and neonatal deaths delivered by a mother with acute jaundice during pregnancy, confirmed by two independent physicians reviewing verbal autopsy data. Findings Out of 1,925 patients with acute jaundice identified and enrolled in the surveillance hospitals, 302 died, with 28 (9%) testing positive for IgM anti-HEV. In the hospital catchment areas, the team identified 587 jaundice-associated deaths, including 25 maternal deaths. Combining hospital-based surveillance and mortality survey data, the study estimated 986 (95% CI: 599-1338) HEV-associated deaths annually among individuals aged ≥14 years in Bangladesh, including 163 (95% CI: 57-395) maternal deaths. Additionally, 279 (95% CI: 101-664) stillbirths and 780 (95% CI: 365-1,297) neonatal deaths were attributed to HEV infection annually. Interpretation Prior Global Burden of Disease studies presented wildly varying modeling estimates of HEV-associated annual deaths, ranging from 50,000 in 2013 to 1,932 in 2019. This study is the first to directly measure population-based estimates of mortality in Bangladesh, which can be used to determine the cost-effectiveness of hepatitis E vaccination and other interventions.
A tactile discrimination task to study neuronal dynamics in freely-moving mice
Authors: Heimburg Filippo , Saluti Nadin Mari , Timm Josephine , Adlakha Avi , Castelanelli Melina , Klumpp Matthias , Embray Lee , Both Martin , Draguhn Andreas , Kuner Thomas , Groh Alexander
Published: August 2024

Sensory discrimination tasks are valuable tools to study neuronal mechanisms of perception and learning. Most of the previously developed discrimination tasks for electrophysiological and imaging studies in rodents require the animals to be head-fixed. However, implementing neurophysiological recordings into more ethologically realistic settings with unrestrained animals has been challenging, especially for somatosensory studies. This study introduces a tactile discrimination task for freely moving mice, integrating electrophysiology and calcium imaging with cellular resolution. In this go/no-go paradigm, mice learn to discriminate between different aperture widths within days in order to forage for food rewards on a linear platform. We demonstrate that the task is whisker-dependent and that mice reliably discriminate aperture differences as small as 6 mm. The setup’s versatility enables exploration into diverse behavioral aspects, including tactile discrimination thresholds, valence-dependent behavior, and cognitive flexibility following repeated task rule reversals. Rule learning was highly stereotypical, fast and reproducible across individual mice, with approximately 500 trials to attain expert level performance and approximately 1000 trials to relearn the first rule reversal. We further demonstrate that electrophysiological recordings and calcium imaging can be conducted in the same paradigm such that multiple behavioral read-outs (learning progression, whisker motion, whisker touch, reward licking) can be synchronized with respective electrophysiological and imaging data, providing a new versatile tool to elucidate neural mechanisms of cognition and sensory processing.
Exploring Youth-Perceived Barriers and Attitudes Towards the Clinical Use of Pharmacogenetic Testing to Optimise Antidepressant Pharmacotherapy
Authors: Roberts Bradley , Cooper Zahra , Landery Georgia , Stanley Susanne , Majda Bernadette T. , Khan  , Collins R. L. , Akkari P. Anthony , Hood Sean D. , Rodger Jennifer
Published: August 2024

The field of pharmacogenetics (PGx) is experiencing significant growth, with increasing evidence to support its application in psychiatric care, suggesting its potential to personalise treatment plans, optimise medication efficacy, and reduce adverse drug reactions. However, the perceived utility and practicability of PGx for psychiatric treatment in youth remains underexplored. This study investigated youth-perceived barriers and attitudes towards the implementation of PGx testing to guide antidepressant treatment in primary care. Semi-structured focus groups and interviews were conducted with 17 participants aged between 18 to 24 years. These sessions were recorded and transcribed before thematic analysis was used to identify collective themes. Three key themes were identified, including attitudes towards the medication prescription process, concerns and attitudes towards PGx testing, and perceived barriers to its clinical implementation. Although PGx testing was positively perceived by most participants, all participants shared concerns about PGx testing. Participants voiced concerns about the financial impact of PGx testing, the potential for treatment delays, and the accuracy of PGx testing in guiding antidepressant treatment. Additionally, participants noted that the low awareness and willingness of general practitioners to incorporate PGx testing into routine practice could hinder successful clinical implementation. Prior to the implementation of PGx testing into Australian primary practices, it is essential to acknowledge patient perspectives and ensure that clinical practices remain patient-focused. This study highlights important considerations for integrating PGx testing into antidepressant pharmacotherapy and emphasizes the need for future research to address and mitigate youth-perceived barriers.
Evaluating the clinical effectiveness and patient experience of an AI-based digital tool for home-based blood pressure management
Authors: Jelić Alan , Sesto Igor , Rotkvić Luka , Pavlović Luka , Erceg Nikola , Sesto Nina , Kraljevic Zeljko , Yeung Joshua Au , Folarin Amos , Dobson Richard , Laiou Petroula
Published: August 2024

Hypertension, a prevalent cardiovascular condition, requires effective management of multimodal health risk factors. This study examines the effectiveness of a digital health tool designed for hypertension management and explores user perspectives on its utility. We analyse a cohort of 5,136 participants who used the digital tool, which provides continuous blood pressure monitoring, real-time feedback, and personalized health recommendations. Our results show that users achieve significant reduction in their blood pressure values and this reduction is positively correlated with the duration for which users report their blood pressure values. Additionally, we obtain high retention rates even after one year of using the digital tool. User feedback was collected through an online survey revealing high satisfaction rates. Participants highlighted the tool’s ease of use, and felt less anxious. Overall, our study demonstrates the potential of digital health tools in enhancing hypertension management and highlights the importance of user-centred design in developing effective health interventions.
Diurnal rhythms in durum wheat triggered byRhopalosiphum padi(bird cherry-oat aphid)
Authors: Goldstein Yoshiahu , Han Jinlong , Kunk Daniel , Batushansky Albert , Nalam Vamsi , Tzin Vered
Published: August 2024

Wheat is a staple crop and one of the most widely consumed grains globally. Wheat yields can experience significant losses due to the damaging effects of herbivore infestation. However, little is known about the effect aphids have on the natural diurnal rhythms in plants. Our time-series transcriptomics and metabolomics study reveal intriguing molecular changes occurring in plant diurnal rhythmicity upon aphid infestation. Under control conditions, 15,366 out of the 66,559 genes in the tetraploid wheat cultivar Svevo, representing approximately 25% of the transcriptome, exhibited diurnal rhythmicity. Upon aphid infestation, 5,682 genes lost their rhythmicity, while additional 5,203 genes began to exhibit diurnal rhythmicity. The aphid-induced rhythmic genes were enriched in GO terms associated with plant defense, such as protein phosphorylation and cellular response to ABA and were enriched with motifs of the WRKY transcription factor families. Conversely, the genes that lost rhythmicity due to aphid infestation were enriched with motifs of the TCP and ERF transcription factor families. While the core circadian clock genes maintain their rhythmicity during infestation, we observed that approximately 60% of rhythmic genes experience disruptions in their rhythms during aphid infestation. These changes can influence both the plant’s growth and development processes as well as defense responses. Furthermore, analysis of rhythmic metabolite composition revealed that several monoterpenoids gained rhythmic activity under infestation, while saccharides retained their rhythmic patterns. Our findings highlight the ability of insect infestation to disrupt the natural diurnal cycles in plants, expanding our knowledge of the complex interactions between plants and insects.
Fibril Paint: a class of amyloid-targeting peptides
Authors: Pedrola Júlia Aragonès , Dekker Françoise A. , Guttmann Katrin , van Leeuwen Litske M. , Singh Shalini , Mayer Guy , Garfagnini Tommaso , Friedler Assaf , Rüdiger Stefan G. D.
Published: August 2024

Neurodegenerative diseases, such as Alzheimer’s Disease, Parkinson’s Disease and Huntington’s Disease, are characterised by accumulation of amyloid fibrils, which remain incurable. It is of great importance to develop early-diagnosis approaches as well as disease-modifying therapies. Recently, we discovered the FibrilPaint1 peptide, a specific amyloid binder that can serve for fibril diagnosis. Here we introduce a class of FibrilPaint1 derivatives that bind to protein fibrils. The modifications include variation of the charge, termini and order of residues. As a result, we generated a class of peptides with general fibril-binding properties and with the potential for further adaptation, such as linkage to multiple dyes, optimisation for specific protein and aggregate strains, or adaptation for targeted protein degradation strategies. Thus, Fibril Paint peptides are a class of promising leads for targeting amyloid fibrils for diagnostic and therapeutic purposes.
Gynaecological health patterns and motherhood experiences of female professional football players
Authors: Ramagole Dimakatso , Rensburg Dina C Janse van , Cowie Charlotte , Mehta Ritan , Ramkilawon Gopika , Pluim Babette M. , Kerkhoffs Gino , Gouttebarge Vincent
Published: August 2024

Aims

To explore health patterns in female professional football players in the domains of gynaecological health patterns, contraceptive use, body perception and motherhood experiences, including return to play after childbirth.

Methods

An online questionnaire was emailed to active female professional football players via email. Participants were asked about their menstrual cycle,contraception use and motherhood. Validated questionnaires were used to assess body dissatisfaction (BD) and drive for thinness (DT).

Results

A total of 74 female professional football players were enrolled. The mean age at menarche was 13.5 years, average cycle length of 26 days and a bleeding period of 5 days. Cycle irregularities were experienced by 30% of participants, and menstrual symptoms by 74%. Half of the participants used contraceptives, with 60% using hormonal contraceptives, primarily oral contraceptive pills (38%), followed by implants (20%). Participants had a normal BD score, but a higher-than-expected DT score. The motherhood rate was low (1%), with normal conception, vaginal delivery, return to training after 6 weeks, and return to competition after 12 weeks.

Conclusion

Cycle irregularities are common in female professional football players, with a significant number of cycle-related symptoms. The majority on contraceptives preferred hormonal contraceptives, especially oral contraceptive pills (OCP) followed by implants, reflecting trends seen in elite athletes gynaecological health. While body satisfaction scores were normal, there was an unexpectedly high drive-for-thinness score, similar to that observed in lean or weight-category sports. The rate of motherhood was low, consistent with previous findings in professional football players.

What is already known on this topic

Elite female athletes have unique challenges related to their menstrual cycle and symptoms.

Elite athletes use mostly hormonal contraceptives, predominantly the OCP.

They often have to choose between professional sports and motherhood.

What this study adds

Our findings show some similarities to other to other elite female athletes:

30% have menstrual irregularities.

74% have negative menstrual symptoms.

Motherhood is low.

Our participants have a high drive for thinness.

How this study might affect research, practice or policy

This descriptive study is a basis for more prospective and epidemiological research in this cohort that has been established.

More research will be stimulated in the domains of menstrual symptoms and coping strategies, choice of contraception and motherhood.

This study should also stimulate communications regarding player contracts and maternity benefits, and include after career support for female professional football players.
Analytically controlling the laser-induced electron phase in sub-cycle motion
Authors: Trieu Doan-An , Nguyen Trong-Thanh D. , Nguyen Thanh-Duy D. , Tran Thanh , Le Van-Hoang , Phan Ngoc-Loan
Published: August 2024

We develop an approach to directly control the phase of an electron's sub-cycle motion in an intense laser field. The method is established by tuning a low-frequency electric field applied on a centrosymmetric gaseous target during its interaction with a few-cycle infrared laser pulse. We find a universal analytical relation between the low-frequency electric field and its induced harmonic frequency shift, derived by the strong-field approximation. This simple relation and its universality are confirmed numerically by directly solving the time-dependent Schrödinger equation. Moreover, we demonstrate the benefits of the discovered relation in applications, including continuously and precisely tuning XUV waves and developing a method of comprehensively sampling the THz pulse.

Published by the American Physical Society
2024
Thermal vibrations in the inversion of dynamical electron scattering
Authors: Herdegen Ziria , Diederichs Benedikt , Müller-Caspary Knut
Published: August 2024

Relativistic forward scattering of electrons at finite temperature involves the incoherent superposition of diffraction patterns formed by different snapshots of thermal atomic displacements. In experiments, thermal vibrations lead to thermal diffuse scattering (TDS), partly dominating diffraction patterns of thick specimens. This study sheds light on the effects of TDS on solutions to the inverse scattering problem using combined real- and diffraction-space information acquired in a scanning transmission electron microscope (STEM) to retrieve the object's phase. Using frozen phonon multislice within the Einstein approximation, realistic ground truth data of 20-nm-thick SrTiO3 is generated and subjected to contemporary inverse multislice schemes to retrieve the projected Coulomb potential slicewise. We first classify phase retrieval algorithms as to their assumptions on periodicity along the incident beam direction, as well as pixelwise and parametrized reconstruction methods. It is found that pixelwise object reconstructions are capable of retrieving structural details qualitatively while being prone to contain TDS-related artifacts which can result in unphysical potentials. For pixelwise reconstructions of multiple independent specimen slices, we observe that the origin of TDS, i.e., thermal atomic displacements, starts to emerge naturally. However, the quantitative assessment tends to too small mean squared thermal displacements, also when reconstructing multiple object modes. Using an atomistically parametrized inversion strategy which exploits the explicit separation of thermal vibrations and potentials, temperature and chemistry of the specimen can be retrieved quantitatively with high accuracy.

Published by the American Physical Society
2024
Dynamic exchange correlation effects in the strongly coupled electron liquid
Authors: Dornheim Tobias , Tolias Panagiotis , Kalkavouras Fotios , Moldabekov Zhandos A. , Vorberger Jan
Published: August 2024

The first quasiexact path integral Monte Carlo (PIMC) investigation of the dynamic local field correction G̃(q,zl;rs,Θ) in the imaginary Matsubara frequency domain is reported, focusing on the unpolarized uniform electron gas in the warm dense matter and strongly coupled regimes. The impact of dynamic exchange–correlation effects on the static structure factor is investigated. A straightforward explanation is provided for previously reported spurious effects in the so-called [Dornheim , ], where the frequency dependence of the local field correction is neglected. The comprehensive analysis of the asymptotic Matsubara order behavior, the density dependence, and the temperature dependence hints at the intriguing possibility of constructing an analytical four-parameter representation of G̃(q,zl;rs,Θ) valid for a substantial part of the uniform electron gas phase diagram, which would constitute key input for thermal density functional theory simulations.

Published by the American Physical Society
2024
Integer quantum Hall transition: An
S
-matrix approach to random networks
Authors: Topchyan H. , Gruzberg I. A. , Nuding W. , Klümper A. , Sedrakyan A.
Published: August 2024

In this paper we propose an S-matrix approach to numerical simulations of network models and apply it to random networks that we proposed in a previous work [I. A. Gruzberg, A. Klümper, W. Nuding, and A. Sedrakyan, ]. Random networks are modifications of the Chalker-Coddington (CC) model for the integer quantum Hall transition that more faithfully captures the physics of electrons moving in a strong magnetic field and a smooth disorder potential. This method has considerable advantages compared to the transfer matrix approach and gives the value ν≈2.4 for the critical exponent of the localization length in a random network. This finding confirms our previous result and is surprisingly close to the experimental value νexpt≈2.38 observed at the integer quantum Hall transition but substantially different from the CC value νCC≈2.6.

Published by the American Physical Society
2024
Role of the short-distance interaction in
e+e−→γX(3872)
Authors: Duan Ming-Xiao
Published: August 2024

In this study, we analyze the cross-section data from the e+e−→γJ/ψω process to explore both short-distance and long-distance interactions for the radiative transition Y(4200)→γX(3872). We investigate the short-distance effects through the E1 transition among the cc¯ components, and the long-distance effects via hadronic loop diagrams. Our numerical analysis reveals that short-distance interactions play a significantly larger role in the radiative transition than that of the long-distance interactions. This finding underscores the importance of the compact cc¯ components in both the initial and the final states for accurately understanding the cross-section σ[e+e−→γJ/ψω]. Furthermore, with the help of relative branch ratio R we estimate the Γ[Y(4200)→γX(3872)] implied in the experimental study. Finally, we also discuss the possible existence of the ψ(4040) signal within the cross-section data.

Published by the American Physical Society
2024
TeV-scale lepton number violation: Connecting leptogenesis, neutrinoless double beta decay, and colliders
Authors: Harz Julia , Ramsey-Musolf Michael J. , Shen Tianyang , Urrutia-Quiroga Sebastián
Published: August 2024

In the context of TeV-scale lepton number violating (LNV) interactions, we illustrate the interplay between leptogenesis, neutrinoless double beta (0νββ) decay, and LNV searches at proton-proton colliders. Using a concrete model for illustration, we overcome the limitations of previous effective field theory analyses and are able to identify the parameter space where standard thermal leptogenesis is rendered unviable due to washout processes. Moreover, we show how 0νββ decay and pp collisions provide complementary probes. We find that the new particle spectrum can have a decisive impact on the relative sensitivity of these two probes.

Published by the American Physical Society
2024
Accreting black holes in dark matter halos
Authors: Kazempour Sobhan , Sun Sichun , Yu Chengye
Published: August 2024

We examine the thin accretion disk behaviors surrounding black holes embedded in cold dark matter halos and scalar field dark matter halos. We first calculate the event horizons and derive the equations of motion and effective potential in black hole geometries with different dark matter halos. We then compute the specific energy, specific angular momentum, and angular velocity of particles moving along circular orbits. We also derive the effective potentials to find the locations of the innermost stable circular orbit (ISCO) and compare them to the Schwarzschild and Kerr black holes without the dark matter halos. We also use the observed ISCO of the supermassive black hole at the Galactic Center of the Milky Way, Sagittarius A*, to constrain the dark matter halos.

Published by the American Physical Society
2024
K
-inflation: The legitimacy of the classical treatment
Authors: Ageeva Y. , Petrov P.
Published: August 2024

In this paper we consider a general theory of k-inflation and find out that it may be in a strong coupling regime. We derive accurate conditions of classical description validity using unitarity bounds for this model. Next, we choose a simple toy model of k-inflation and obtain the explicit condition, which guarantees that the generation of perturbations is performed in a controllable way, i.e., the exit from the effective horizon occurs in the weak coupling regime. However, for the same toy model the corresponding experimental bounds on a nonlinear parameter fNLequil associated with non-Gaussianities of the curvature perturbation provide much stronger constraint than strong coupling absence condition. Nevertheless, for other known models of inflation this may not be the case. Generally, one should always check if classical description is legitimate for chosen models of inflation.

Published by the American Physical Society
2024
Centerless BMS charge algebra
Authors: Rignon-Bret Antoine , Speziale Simone
Published: August 2024

We show that when the Wald-Zoupas prescription is implemented, the resulting charges realize the Bondi-Van der Burg–Metzner-Sachs (BMS) symmetry algebra without any 2-cocycle nor central extension, at any cut of future null infinity. We refine the covariance prescription for application to the charge aspects, and introduce a new aspect for Geroch’s supermomentum with better covariance properties. For the extended BMS symmetry with singular conformal Killing vectors we find that a Wald-Zoupas symplectic potential exists, if one is willing to modify the symplectic structure by a corner term. The resulting algebra of Noether currents between two arbitrary cuts is centerless. The charge algebra at a given cut has a residual field-dependent 2-cocycle, but time-independent and nonradiative. More precisely, superrotation fluxes act covariantly, but superrotation charges act covariantly only on global translations. The take home message is that in any situation where 2-cocycles appears in the literature, covariance has likely been lost in the charge prescription, and that the criterium of covariance is a powerful one to reduce ambiguities in the charges, and can be used also for ambiguities in the charge aspects.

Published by the American Physical Society
2024
Fixed lines in four fermion models in two dimensions
Authors: A Sidan , Banks Tom
Published: August 2024

Motivated by conjectures about near-horizon dynamics in quantum gravity, we search for lines of perturbatively accessible fixed points emanating from models of N free fermions. Through two loops we find a new class of models, apart from the well-known Abelian Thirring models. Further study is needed to see whether these can lead to true conformal manifolds, or perhaps a new class of large-N fixed points.

Published by the American Physical Society
2024
Generalized entanglement capacity of de Sitter space
Authors: Banks Tom , Draper Patrick
Published: August 2024

Near horizons, quantum fields of low spin exhibit densities of states that behave asymptotically like 1+1 dimensional conformal field theories. In effective field theory, imposing some short-distance cutoff, one can compute thermodynamic quantities associated with the horizon, and the leading cutoff sensitivity of the heat capacity is found to equal to the leading cutoff sensitivity of the entropy. One can also compute contributions to the thermodynamic quantities from the gravitational path integral. For the cosmological horizon of the static patch of de Sitter space, a natural conjecture for the relevant heat capacity is shown to equal the Bekenstein-Hawking entropy. These observations allow us to extend the well-known notion of the generalized entropy to a generalized heat capacity for the static patch of de Sitter (dS). The finiteness of the entropy and the nonvanishing of the generalized heat capacity suggest it is useful to think about dS as a state in a finite dimensional quantum gravity model that is not maximally uncertain.

Published by the American Physical Society
2024
Excitation transmission through a non-Hermitian traversable wormhole
Authors: Cao Sizheng , Ge Xian-Hui
Published: August 2024

This study explores the intricate real-time dynamics of a non-Hermitian system composed of two interconnected Sachdev-Ye-Kitaev (SYK) models. A central finding reveals that an excitation initially localized in the right SYK subsystem can be efficiently transmitted to the left subsystem subsequent to the characteristic scrambling time, a phenomenon facilitated by the intrinsic non-Hermitian nature of the system. The defining hallmark of non-Hermiticity is manifest in the asymmetric conveyance of quantum states, with the non-Hermitian parameter functioning as a tunable knob that selectively amplifies or dampens propagation modes on either side. Despite this inherent directional bias in state transfer, the system sustains two distinct phases, analogously likened to black holes and wormholes.

Published by the American Physical Society
2024
Shapiro Steps in Driven Atomic Josephson Junctions
Authors: Singh Vijay Pal , Polo Juan , Mathey Ludwig , Amico Luigi
Published: August 2024

We study driven atomic Josephson junctions realized by coupling two two-dimensional atomic clouds with a tunneling barrier. By moving the barrier at a constant velocity, dc and ac Josephson regimes are characterized by a zero and nonzero atomic density difference across the junction, respectively. Here, we monitor the dynamics resulting in the system when, in addition to the above constant velocity protocol, the position of the barrier is periodically driven. We demonstrate that the time-averaged particle imbalance features a plateau behavior that is the analog of Shapiro steps observed in driven superconducting Josephson junctions. The underlying dynamics reveals an intriguing interplay of the vortex and phonon excitations, where Shapiro steps are induced via suppression of vortex growth. We study the system with a classical-field dynamics method, and benchmark our findings with a driven circuit dynamics.

Published by the American Physical Society
2024