bluuebunny/crossref_metadata_2025 huggingface dataset:
Identifying life-history patterns along the fast-slow continuum of mammalian viral carriers
Authors: Tonelli Andrea , Caceres-Escobar Hernan , Blagrove Marcus S. C. , Wardeh Maya , Di Marco Moreno
Published: July 2024

Life-history traits have been identified as major indicators of mammals' susceptibility and exposure to viruses due to evolutionary constraints that link life-history speed with species’ ecology and immunity. Nonetheless, it is unclear where along the fast-slow continuum of mammalian life-history lies the greatest diversity of host species. Consequently, life-history patterns that govern host–virus associations remain largely unknown. Here we analyse the virome of 1350 wild mammals and detect the characteristics that drive species' compatibility with different groups of viruses. We highlight that mammals with larger body size and either very rapid or very slow life histories are more likely to carry different groups of viruses, particularly zoonotic ones. While some common life-history patterns emerge across carriers, eco-evolutionary characteristics of viral groups appear to determine association with certain carrier species. Our findings underline the importance of incorporating both mammals’ life-history information and viruses' ecological diversity into surveillance strategies to identify potential zoonotic carriers in wildlife.
Study on the interior equilibrium point of a special class of 2 × 2 × 2 asymmetric evolutionary games
Authors: Song Sha , Pan Qiuhui , He Mingfeng
Published: July 2024

Many behavioural interactions in real life involve three individuals. When each individual has two alternative strategies, they can be abstracted into mathematical models by means of

2
×
2
×
2

asymmetric games. In this paper, we explore a special class of

2
×
2
×
2

asymmetric games satisfying fixed conditions. Firstly, we analyse two solitary interior equilibrium points and provide the judgement condition for their instability based on the Jacobi matrix local stability analysis method. Secondly, we analyse the interior equilibrium points that are continuously distributed within a line and probe into their stability conditions based on generalized Hamiltonian systems theory. Under the circumstances, the stable interior equilibrium point is surrounded by closed orbits in phase space, which presents an observable stable state where two strategies coexist and fluctuate in each of the three game populations. This work enriches the study of

2
×
2
×
2

asymmetric games’ evolutionary dynamics.
On modelling airborne infection risk
Authors: Drossinos Yannis , Stilianakis Nikolaos I.
Published: July 2024

Airborne infection risk analysis is usually performed for enclosed spaces where susceptible individuals are exposed to infectious airborne respiratory droplets by inhalation. It is usually based on exponential, dose-response models of which a widely used variant is the Wells–Riley (WR) model. We revisit this infection-risk estimate and extend it to the population level. We use an epidemiological model where the mode of pathogen transmission, airborne or contact, is explicitly considered. We illustrate the link between epidemiological models and the WR and the Gammaitoni and Nucci models. We argue that airborne infection quanta are, up to an overall density, airborne infectious respiratory droplets modified by a parameter that depends on biological properties of the pathogen, physical properties of the droplet and behavioural properties of the individual. We calculate the time-dependent risk of being infected for two scenarios. We show how the epidemic infection risk depends on the viral latent period and the event time, the time infection occurs. Infection risk follows the dynamics of the infected population. As the latent period decreases, infection risk increases. The longer a susceptible is present in the epidemic, the higher its risk of infection for equal exposure time to the pathogen is.
Combined perceptual and chemical analyses show no compelling evidence for ovulatory cycle shifts in women’s axillary odour
Authors: Zetzsche Madita , Weiß Brigitte M. , Kücklich Marlen , Stern Julia , Birkemeyer Claudia , Widdig Anja , Penke Lars
Published: July 2024

Although men’s attraction to women’s body odour has been suggested to vary over the ovulatory cycle, peaking around the fertile window, we still lack methodologically robust evidence corroborating this effect. Further, the chemical underpinnings of male preference for the odour of ovulating women remain unknown. Here, we combined perceptual and chemical analyses to investigate the axillary odour of naturally cycling women over 10 days, covering the gradual change in fertility across the ovulatory cycle with a focus on fertile days. The fertile state was confirmed by urinary ovulation tests as well as salivary oestradiol and progesterone levels. Men rated the scent of unfamiliar women, resembling a first encounter. We used multivariate analyses to relate variation in both odour ratings and chemical composition to female conception probability, temporal distance to ovulation and ovarian hormone levels. Our results provide no evidence that males prefer the odour of fertile women. Furthermore, the volatile analysis indicated no link between axillary odour composition and current fertility status. Together, our results showed no convincing support for a chemical fertility cue in women’s axillary odour, questioning the presence of olfactory fertility information that is recognizable during first encounters in modern humans.
Deep antiquity of seagrasses supporting European eel fisheries in the western Baltic
Authors: Guiry Eric , Robson Harry K.
Published: July 2024

Protecting ocean habitats is critical for international efforts to mitigate climate impacts and ensure food security, but the ecological data upon which policy makers base conservation and restoration targets often reflect ecosystems that have already been deeply impacted by anthropogenic change. The archaeological record is a biomolecular archive offering a temporal scope that cannot be gathered from historical records or contemporary fieldwork. Insights from biogeochemical and osteometric analyses of fish bones, combined with context from contemporary field studies, show how prehistoric fisheries in the western Baltic relied on seagrass meadows. European eels (
Anguilla anguilla
) harvested by Mesolithic and Neolithic peoples over millennia showed a strong fidelity for eelgrass foraging habitats, an ecological relationship that remains largely overlooked today, demonstrating the value of protecting these habitats. These data open new windows onto ecosystem- and species-level behaviours, highlighting the need for wider incorporation of archaeological data in strategies for protecting our oceans.
Anthropogenic noise disrupts acoustic cues for recruitment
Authors: Williams Brittany R. , McAfee Dominic , Connell Sean D.
Published: July 2024

Anthropogenic noise is rising and may interfere with natural acoustic cues used by organisms to recruit. Newly developed acoustic technology provides enriched settlement cues to boost recruitment of target organisms navigating to restoration sites, but can it boost recruitment in noise-polluted sites? To address this dilemma, we coupled replicated aquarium experiments with field experiments. Under controlled and replicated laboratory conditions, acoustic enrichment boosted recruitment by 2.57 times in the absence of anthropogenic noise, but yielded comparable recruitment in its presence (i.e. no boosting effect). Using the same technique, we then tested the replicability of these responses in real-world settings where independently replicated ‘sites’ are unfeasible owing to the inherent differences in soundscapes. Again, acoustic enrichment increased recruitment where anthropogenic noise was low (by 3.33 times), but had no effect at a site of noise pollution. Together, these coupled laboratory-to-field outcomes indicate that anthropogenic noise can mask the signal of acoustic enrichment. While noise pollution may reduce the effectiveness of acoustic enrichment, some of our reported observations suggest that anthropogenic noise
per se
might also provide an attractive cue for oyster larvae to recruit. These findings underscore the complexity of larval behavioural responses to acoustic stimuli during recruitment processes.
Enhanced nutrient supply promotes mutualistic interactions between cyanobacteria and bacteria in oligotrophic ocean
Authors: Liu Weiyue , Zhao Feng , Li Xuegang , Zheng Shan , Li Longzhao , Zhao Rongjie , Xu Kuidong
Published: July 2024

Cyanobacteria can form complex interactions with heterotrophic microorganisms, but this relationship is susceptible to nutrient concentrations. Disentangling the cyanobacteria–bacteria interactions in relation to nutrient supply is essential to understanding their roles in geochemical cycles under global change. We hypothesize that enhanced nutrient supply in oligotrophic oceans can promote interactions among cyanobacteria and bacteria. Therefore, we investigated the planktonic bacteria and their interactions with cyanobacteria in relation to elevated nutrients caused by enhanced upwelling around a shallow and a deep seamount in the tropical western Pacific Ocean. We found obviously higher complexity of network occurred with significantly more cyanobacteria in the deep chlorophyll maximum layer of the shallow seamount when compared with that of the deep seamount. Cyanobacteria can shape bacterial interaction and community evenness in response to relatively high nutrient concentrations. The effects of the nutrients on cyanobacteria-related networks were further estimated based on the
Tara
Oceans data. Statistical analyses further showed a facilitative effect of nitrate concentrations on cyanobacteria–bacteria mutualistic interactions in the global oligotrophic ocean. By analysing the
Tara
Ocean macrogenomic data, we detected functional genes related to cyanobacteria–bacteria interactions in all samples, indicating the existence of a mutualistic relationship. Our results reveal cyanobacteria–bacteria interaction in response to nutrient elevation in oligotrophic ocean and highlight the potentially negative effects of global change on the bacterial community from the view of the bio-interaction.
Speeding up the recovery of coastal habitats through management interventions that address constraints on dispersal and recruitment
Authors: Brown Christopher J. , Campbell Max D. , Collier Catherine J. , Turschwell Mischa P. , Saunders Megan I. , Connolly Rod M.
Published: July 2024

Plans for habitat restoration will benefit from predictions of timescales for recovery. Theoretical models have been a powerful tool for informing practical guidelines in planning marine protected areas, suggesting restoration planning could also benefit from a theoretical framework. We developed a model that can predict recovery times following restoration action, under dispersal, recruitment and connectivity constraints. We apply the model to a case study of seagrass restoration and find recovery times following restoration action can vary greatly, from <1 to >20 years. The model also shows how recovery can be accelerated when restoration actions are matched to the constraints on recovery. For example, spreading of propagules can be used when connectivity is the critical restriction. The recovery constraints we articulated mathematically also apply to the restoration of coral reefs, mangroves, saltmarsh, shellfish reefs and macroalgal forests, so our model provides a general framework for choosing restoration actions that accelerate coastal habitat recovery.
Repetition in social contacts: implications in modelling the transmission of respiratory infectious diseases in pre-pandemic and pandemic settings
Authors: Loedy Neilshan , Wallinga Jacco , Hens Niel , Torneri Andrea
Published: July 2024

The spread of viral respiratory infections is intricately linked to human interactions, and this relationship can be characterized and modelled using social contact data. However, many analyses tend to overlook the recurrent nature of these contacts. To bridge this gap, we undertake the task of describing individuals’ contact patterns over time by characterizing the interactions made with distinct individuals during a week. Moreover, we gauge the implications of this temporal reconstruction on disease transmission by juxtaposing it with the assumption of random mixing over time. This involves the development of an age-structured individual-based model, using social contact data from a pre-pandemic scenario (the POLYMOD study) and a pandemic setting (the Belgian CoMix study), respectively. We found that accounting for the frequency of contacts impacts the number of new, distinct, contacts, revealing a lower total count than a naive approach, where contact repetition is neglected. As a consequence, failing to account for the repetition of contacts can result in an underestimation of the transmission probability given a contact, potentially leading to inaccurate conclusions when using mathematical models for disease control. We, therefore, underscore the necessity of acknowledging contact repetition when formulating effective public health strategies.
Planococcus shenhongbingii sp. nov., Planococcus shixiaomingii sp. nov. and Planococcus liqunii sp. nov., isolated from soil of the Qinghai-Tibet Plateau
Authors: Ning Shuo , Hou Qiang , Yang Jing , Ma Caiyun , Chen Yulu , Liu Yue , Zhou Huimin , Ma Jiajia , Huang Yuyuan , Cao Linglin , Liu Xiaorui , Pu Ji , Jin Dong , Lu Shan , Xu Jianguo
Published: July 2024

Six novel bacterial strains, designated N016T, N017, N022T, N028, N056T, and N064, were isolated from soil sampled on the Qinghai-Tibet Plateau. Cells were aerobic, orange or yellow, globular or rod-shaped, non-motile, non-spore-forming, Gram-stain-positive, catalase-positive and oxidase-negative. All the isolates were salt-tolerant and could grow in the range of 4–42 °C. Results of phylogenomic analyses based on 16S rRNA gene sequences and core genomic genes showed that the three pairs of strains (N016T/N017, N022T/N028, and N056T/N064) were closely related to the members of the genus Planococcus, and clustered with Planococcus ruber, Planococcus glaciei, and Planococcus chinensis. The digital DNA–DNA hybridization and average nucleotide identity values of the six novel strains with other members of the genus Planococcus were within the ranges of 18.7–53 % and 70.58–93.49 %, respectively, all below the respective recommended thresholds of 70.0 % and 95–96 %. The genomic DNA G+C content of the six strains ranged from 43.5 to 46.0 mol%. The major fatty acids of the six strains were anteiso-C15 : 0, iso-C14 : 0, and C16 : 1
 ω7c alcohol. The predominant polar lipids of strains N016T, N022T, and N056T were diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. Menaquinones 7 and 8 were the respiratory quinones. The results of the above analyses indicated that the six strains represent three novel species of the genus Planococcus, for which the names Planococcus shenhongbingii sp. nov. (type strain N016T=GDMCC 1.4062T=JCM 36224T), Planococcus shixiaomingii sp. nov. (type strain N022T=GDMCC 1.4063T=JCM 36225T), and Planococcus liqunii sp. nov. (type strain N056T=GDMCC 1.4064T=JCM 36226T) are proposed.
Deep Neural Networks to Register and Annotate the Cells of theC. elegansNervous System
Authors: Atanas Adam A. , Lu Alicia Kun-Yang , Kim Jungsoo , Baskoylu Saba , Kang Di , Kramer Talya S. , Bueno Eric , Wan Flossie K. , Flavell Steven W.
Published: July 2024

Aligning and annotating the heterogeneous cell types that make up complex cellular tissues remains a major challenge in the analysis of biomedical imaging data. Here, we present a series of deep neural networks that allow for automatic non-rigid registration and cell identification in the context of the nervous system of freely-movingC. elegans. A semi-supervised learning approach was used to train aC. elegansregistration network (BrainAlignNet) that aligns pairs of images of the bendingC. eleganshead with single pixel-level accuracy. When incorporated into an image analysis pipeline, this network can link neuronal identities over time with 99.6% accuracy. A separate network (AutoCellLabeler) was trained to annotate >100 neuronal cell types in theC. eleganshead based on multi-spectral fluorescence of genetic markers. This network labels >100 different cell types per animal with 98% accuracy, exceeding individual human labeler performance by aggregating knowledge across manually labeled datasets. Finally, we trained a third network (CellDiscoveryNet) to perform unsupervised discovery and labeling of >100 cell types in theC. elegansnervous system by analyzing unlabeled multi-spectral imaging data from many animals. The performance of CellDiscoveryNet matched that of trained human labelers. These tools will be useful for a wide range of applications inC. elegansresearch and should be straightforward to generalize to many other applications requiring alignment and annotation of dense heterogeneous cell types in complex tissues.
Validation of an MPS based intestinal cell culture model for the evaluation of drug-induced toxicity
Authors: Hoffmann Stefanie , Hewitt Philip , Koscielski Isabel , Kurek Dorota , Strijker Wouter , Kosim Kinga
Published: July 2024

The potential for drug-induced gastrointestinal (GI) toxicity is significant, since the GI tract is one of the first barriers which come in to contact with oral drugs. In pharmaceutical research, the complex behavior of human intestinal cells is traditionally investigated using 2D cultures, in which one cell type grows under static conditions. With the development of advanced microphysiological systems (MPS) more in vivo like conditions can be generated which increase the physiological nature and also the predictive validity of these models. Caco-2 cells are known for their capability to build tight junctions. These connections are responsible for the maintenance of intestinal homeostasis and can be used as a specific safety endpoint, by measuring the Trans Epithelial Electrical Resistance (TEER), for the investigation of drug-induced GI toxicity. Compared to a widely used Caco-2 cell 2D Transwell model, the advanced MPS model (Mimetas OrganoPlate) allows for the recapitulation of the enterocyte cell layer of the intestinal barrier as the Caco-2 cells grow in a tubular structure through which the medium continuously flows. The OrganoPlate intestinal model was qualified to be implemented as a routine test system for the early prediction of drug-induced GI toxicity based on the measurement of the tightness of the cell layer by measuring changes in the TEER. For this qualification 23 well known compounds as well as a positive, negative and solvent control were selected. The compounds were selected based on their known effect on the GI system (chemotherapeutics, tight junction disruptor, liver toxins, controls, NSAIDs and a mixed group of drugs). The TEER values were measured 4h and 24h after treatment. In parallel the cell viability was determined after 24h to be able to distinguish between an unspecific cytotoxic effect or direct tight junction damage. Overall, from the 23 tested compounds, 15 showed the expected outcome, i.e.,the compound led to a decrease of the TEER for the positive control compounds, or the TEER value remained stable after treatment with non-GI-toxic compounds. In summary, this MPS model allowed the recapitulation of the human intestinal GI barrier and will enable a faster and more robust assessment of drug-induced damage in the GI tract.
Inhibition of nitric oxide synthase transforms carotid occlusion-mediated benign oligemia intode novolarge cerebral infarction
Authors: Kim Ha , Chung Jinyong , Kang Jeong Wook , Schellingerhout Dawid , Lee Soo Ji , Jang Hee Jeong , Park Inyeong , Kim Taesu , Gwak Dong-Seok , Lee Ji Sung , Hong Sung-Ha , Je Kang-Hoon , Bae Hee-Joon , Sung Joohon , Lo Eng H. , Faber James , Ayata Cenk , Kim Dong-Eog
Published: July 2024

It remains unclear why unilateral proximal carotid artery occlusion (UCAO) causes benign oligemia, without progressing to cerebral infarction, in mice, yet leads to a wide variety of outcomes (ranging from asymptomatic to death) in humans. We hypothesized that inhibition of NOS both transforms UCAO-mediated oligemia into full infarction and expands pre-existing infarction. In support, intraperitoneal administration of Nω-nitro-L-arginine methyl ester (L-NAME) followed by UCAO induced large-arterial infarction in mice, unlike UCAO alone. Six-hour laser-speckle-contrast imaging detected spreading ischemia in mice with infarction as assessed at 24h. In agreement with vasoconstriction/microthrombus formation shown by intravital microscopy, the NO-donor, molsidomine and the endothelial-NOS- activating antiplatelet, cilostazol, attenuated or prevented progression to infarction. Moreover, UCAO without L-NAME caused infarction in mice with hyperglycemia and hyperlipidemia, which, in turn, were associated with greater symmetric dimethylarginine (SDMA) levels. Further, increased levels of glucose and cholesterol associated with significantly larger infarct volumes in 438 consecutive patients with UCAO-mediated infarction. Lastly, Mendelian randomization identified a causative role of NOS inhibition, particularly in elevated SDMA concentration, in ischemic stroke risk. Therefore, NOS activity is a key factor determining the fate of hypoperfused brain following acute carotid occlusion, where SDMA could be a potential risk predictor.
A Comprehensive Framework for Spatio-Temporal Analysis of DNA Damage Foci in Tumor Spheroids
Authors: Cazalès Martine , Liu Théo , Bernard David , Jullien Denis , Lorenzo Corinne
Published: July 2024

The evaluation of DNA damage response, particularly DNA damage foci formation, is crucial for understanding tumor biology and assessing the impacts of various drugs. We have developed a sophisticated semi-automated image analysis pipeline which generates quantitative map of the spatiotemporal distribution of DNA damage foci within live tumor spheroids. Our framework seamlessly integrates live imaging of tumor spheroids via Light Sheet Fluorescence Microscopy with a DNA damage foci formation assay using a genetically encoded fluorescently labeled DNA damage sensor. By combining advanced imaging techniques with computational tools, our framework offers a powerful tool for studying DNA damage response mechanisms in complex 3D cellular environments.

MOTIVATION

The motivation of this work is to propose a comprehensive framework that facilitates the study of DNA repair mechanisms within 3D contexts, specifically using tumor spheroid models. By integrating advanced imaging technologies and genetically encoded fluorescent sensors, our goal is to offer researchers a robust methodology for observing and analyzing DNA damage dynamics in realistic tissue-like environments. This framework is designed to enhance accessibility and streamline data processing, thereby empowering the scientific community to investigate DNA repair processes in 3D with greater precision and efficiency.
Developmental small RNA transcriptomics reveals divergent evolution of the conserved microRNAmiR-100and thelet-7-complexin nematodes
Authors: Sharma Devansh Raj , Röseler Waltraud , Witte Hanh , Werner Michael S. , Sommer Ralf J.
Published: July 2024

Small RNAs have emerged as one of the key post-transcriptional regulators and can be broadly categorised into microRNAs (miRNAs), small-interfering RNAs (siRNAs), and PIWI-interacting RNAs (piRNAs). Since their discovery as regulators of developmental timing in the nematodeCaenorhabditis elegans, some miRNAs were found to be highly conserved throughout animal evolution. miR-100 is a highly conserved miRNA, possibly predating the origin of bilaterians. Furthermore,miR-100is a member of the conservedlet-7-complex, a locus containing three ancient miRNA-coding genes (miR-100,let-7,miR-125/lin-4) that has been secondarily lost inC. elegans. Here, we performed small RNA-sequencing across development in the satellite nematodePristionchus pacificus, identifying miR-100 as the most abundant miRNA in post-embryonic juvenile stages. Additionally,P. pacificusexhibited a novel constellation of thelet-7- complex, whereinmir-100is closely linked tolet-7, but withoutlin-4in the same locus. Knockouts ofmir-100,let-7, andmir-100 let-7double mutants inP. pacificusresulted in viable worms with developmental defects related to dysregulation of collagen. Surprisingly,lin-4mutants showed nearly normal development. This study provides the first developmental small RNA transcriptome inP. pacificus, and indicates that thelet-7-complexand small RNA pathways undergo rapid evolutionary divergence in nematodes.
Hair cells in the cochlea must tune resonant modes to the edge of instability without destabilizing collective modes
Authors: Momi Asheesh S. , Abbott Michael C. , Rubinfien Julian , Machta Benjamin B. , Graf Isabella R.
Published: July 2024

Sound produces surface waves along the cochlea’s basilar membrane. To achieve the ear’s astonishing frequency resolution and sensitivity to faint sounds, dissipation in the cochlea must be canceled via active processes in hair cells, effectively bringing the cochlea to the edge of instability. But how can the cochlea be globally tuned to the edge of instability with only local feedback? To address this question, we use a discretized version of a standard model of basilar membrane dynamics, but with an explicit contribution from active processes in hair cells. Surprisingly, we find the basilar membrane supports two qualitatively distinct sets of modes: a continuum oflocalizedmodes and a small number of collectiveextendedmodes. Localized modes sharply peak at their resonant position and are largely uncoupled. As a result, they can be amplified almost independently from each other by local hair cells via feedback reminiscent of self-organized criticality. However, this amplification can destabilize the collective extended modes; avoiding such instabilities places limits on possible molecular mechanisms for active feedback in hair cells. Our work illuminates how and under what conditions individual hair cells can collectively create a critical cochlea.
A high-performance genetically encoded sensor for cellular imaging of PKC activityin vivo
Authors: Yahiro Takaki , Bayless-Edwards Landon , Jones James A. , Ma Lei , Qin Maozhen , Mao Tianyi , Zhong Haining
Published: July 2024

We report a genetically encoded fluorescence lifetime sensor for protein kinase C (PKC) activity, named CKAR3, based on Förster resonance energy transfer. CKAR3 exhibits a 10-fold increased dynamic range compared to its parental sensors and enablesin vivoimaging of PKC activity during animal behavior. Our results reveal robust PKC activity in a sparse neuronal subset in the motor cortex during locomotion, in part mediated by muscarinic acetylcholine receptors.
Conscious and Unconscious Emotional Processing: Insights from Behavioral and Pupillary Responses
Authors: Taghavi Helia , Sharbaf Leila , Ismailzad Fatemeh , Vahabie Abdol-Hossein , Hatami Javad , Rezayat Ehsan
Published: July 2024

Emotions are crucial in social interactions, influencing communication and relationships. Distinguishing the perceived emotion in conscious and unconscious emotional processing is a key research area with cognitive and physiological implications. This study investigates conscious and unconscious emotional processing through behavioral and pupillary responses. Participants completed emotion recognition tasks under varying states, revealing higher accuracy in conscious emotion identification. Emotions like anger, happiness, fear, surprise, and neutral elicited distinct response patterns. Pupillometry data showed pupil size suppression in the conscious state and enhancement in the unconscious state, with differences in peak pupil size across emotions. Task-related components, amplitude, and latency parameters differed between conscious and unconscious states, highlighting the role of awareness in emotional regulation. These findings emphasize the complex interplay of cognitive and physiological processes in emotional responses, providing insights into emotional recognition mechanisms. This study contributes to understanding emotional processing dynamics and has implications for psychology and neuroscience research.
Transform the Information Landscape Applying Waddington Landscape to Information Theory of Aging and Epigenetic Rejuvenation
Authors: Wu Yue
Published: July 2024

The Information Theory of Aging (ITOA) provides a framework for understanding aging and rejuvenation via changes in epigenetic information. These changes are visualized using Waddington landscape — a 3D topology that represents cell trajectories during changes in cell identity — constructed from field decomposition of scRNA velocity data. Studies have demonstrated that the Waddington landscape can serve as a mechanistic model of epigenetic information. It explains how age-driven decline in cellular function and reprogramming-induced rejuvenation can be understood by studying the transformations in the Waddington landscape. This study provides insights into the representation of epigenetic information and discusses how it can be reprogrammed to restore a younger cellular state.
Long shared haplotypes identify the Southern Urals as a primary source for the 10th century Hungarians
Authors: Gyuris Balázs , Vyazov Leonid , Türk Attila , Flegontov Pavel , Szeifert Bea , Langó Péter , Mende Balázs Gusztáv , Csáky Veronika , Chizhevskiy Andrey A. , Gazimzyanov Ilgizar R. , Khokhlov Aleksandr A. , Kolonskikh Aleksandr G. , Matveeva Natalia P. , Ruslanova Rida R. , Rykun Marina P. , Sitdikov Ayrat , Volkova Elizaveta V. , Botalov Sergei G. , Bugrov Dmitriy G. , Grudochko Ivan V. , Komar Oleksii , Krasnoperov Alexander A. , Poshekhonova Olga E. , Chikunova Irina , Sungatov Flarit , Stashenkov Dmitrii A. , Zubov Sergei , Zelenkov Alexander S. , Ringbauer Harald , Cheronet Olivia , Pinhasi Ron , Akbari Ali , Rohland Nadin , Mallick Swapan , Reich David , Szécsényi-Nagy Anna
Published: July 2024

During the Hungarian Conquest in the 10th century CE, the early medieval Magyars, a group of mounted warriors from Eastern Europe, settled in the Carpathian Basin. They likely introduced the Hungarian language to this new settlement area, during an event documented by both written sources and archaeological evidence. Previous archaeogenetic research identified the newcomers as migrants from the Eurasian steppe. However, genome-wide ancient DNA from putative source populations has not been available to test alternative theories of their precise source. We generated genome-wide ancient DNA data for 131 individuals from candidate archaeological contexts in the Circum-Uralic region in present-day Russia. Our results tightly link the Magyars to people of the Early Medieval Karayakupovo archaeological horizon on both the European and Asian sides of the southern Urals. Our analyes show that ancestors of the people of the Karayakupovo archaeological horizon were established in the Southern Urals by the Iron Age and that their descendants persisted locally in the Volga-Kama region until at least the 14th century.
Context-driven interaction retrieval and classification for modeling, curation, and reuse
Authors: Luo Haomiao , Hansen Casey , Telmer Cheryl A. , Tang Difei , Arazkhani Niloofar , Zhou Gaoxiang , Spirtes Peter , Miskov-Zivanov Natasa
Published: July 2024

Computational modeling seeks to construct and simulate intracellular signaling networks to understand health and disease. The scientific literature contains descriptions of experimental results that can be interpreted by machines using NLP or LLMs to itemize molecular interactions. This machine readable output can then be used to assess, update or improve existing biological models if there is a tool for comparing the existing model with the information extracted from the papers. Here we describe VIOLIN a tool for classifying machine outputs of molecular interactions with respect to a biological model. VIOLIN classifies interactions as corroborations, contradictions, flagged or extensions with subcategories of each class. This paper analyzes 2 different models, 9 reading sets, 2 NLP and 2 LLM tools to test VIOLIN’s capabilities. The results show that VIOLIN successfully classifies interaction types and can be combined with automated filtering to provide a versatile tool for use by the systems biology community.
Trait anxiety impairs reciprocity behavior: A multi-modal and computational modeling study
Authors: Fang Huihua , Wang Rong , Wang Zhihao , Liu Qian , Luo Yuejia , Xu Pengfei , Krueger Frank
Published: July 2024

Anxiety significantly impacts reciprocal behavior, crucial for positive social interactions. The neurocomputational mechanisms of anxiety’s effects on the core (individual propensity) and peripheral (decision context) factors shaping reciprocity remain unclear. Here, we investigated reciprocity in individuals with low and high trait anxiety using a binary trust game with gain/loss framing, combining computational modeling, eye-tracking, and event-related potentials (ERPs). Our computational model, validated by eye-tracking data, identified four psychological components driving reciprocal behavior: reward, guilt aversion, superiority aversion, and superiority attraction. Regarding the core of reciprocity, trait anxiety diminished both overall reciprocity and specific psychological components like guilt aversion and superiority attraction, irrespective of context. The reduction in guilt aversion was supported by ERP findings showing decreased P2 (selective attention) and increased LPP (emotion regulation) amplitudes in anxious individuals. Regarding the periphery of reciprocity, trait anxiety altered the contextual perception of both superiority aversion and reward. Further, trait anxiety reversed the perception of superiority aversion from gain to loss contexts, a pattern that was linked to the N2 amplitudes (cognitive control). Our findings revealed distinct effects of trait anxiety on core and peripheral factors in reciprocity, offering potential targets for interventions aimed at improving reciprocity in individuals with anxiety disorders.
Osteoprotegerin (OPG) and its ligands RANKL and TRAIL in falciparum, vivax and knowlesi malaria: correlations with disease severity, and B cell production of OPG
Authors: Nair Arya Sheela , Woodford John , Loughland Jessica , Andrew Dean , Piera Kim , Amante Fiona , William Timothy , Grigg Matthew J , McCarthy James S , Anstey Nicholas M , Boyle Michelle J , Barber Bridget E
Published: July 2024

Osteoprotegerin (OPG) is a soluble decoy receptor for receptor activator of NF-ƙB ligand (RANKL) and TNF-related apoptosis-inducing ligand (TRAIL), and is increasingly recognised as a marker of poor prognosis in a number of diseases. Here we demonstrate that in Malaysian adults with falciparum and vivax malaria, OPG is increased, and its ligands TRAIL and RANKL decreased, in proportion to disease severity. In volunteers experimentally infected withP. falciparumandP. vivax, RANKL was suppressed, while TRAIL was unexpectedly increased, suggesting binding of OPG to RANKL prior to TRAIL. We also demonstrate thatP. falciparumstimulates B cells to produce OPGin vitro, and that B cell OPG production is increasedex vivoin patients with falciparum, vivax and knowlesi malaria. Our findings provide further evidence of the importance of the OPG/RANKL/TRAIL pathway in pathogenesis of diseases involving systemic inflammation, and may have implications for adjunctive therapies. Further evaluation of the role of B cell production of OPG in host responses to malaria and other inflammatory diseases is warranted.
Order of the
SU(Nf)×SU(Nf)
chiral transition via the functional renormalization group
Authors: Fejős G. , Hatsuda T.
Published: July 2024

Renormalization group flows of the SU(Nf)×SU(Nf) symmetric Ginzburg-Landau potential are calculated for a general number of flavors, Nf. Our approach does not rely on the ε expansion, but uses the functional renormalization group, formulated directly in d=3 spatial dimensions, with the inclusion of all possible (perturbatively) relevant and marginal operators, whose number is considerably larger than those in d=4. We find new, potentially infrared stable fixed points spanned throughout the entire Nf range. By conjecturing that the thermal chiral transition is governed by these “flavor continuous” fixed points, stability analyses show that for Nf≥5 the chiral transition is of second order, while for Nf=2, 3, 4, it is of first order. We argue that the UA(1) anomaly controls the strength of the first-order chiral transition for Nf=2, 3, 4, and makes it almost indistinguishable from a second-order one, if it is sufficiently weak at the critical point. This could open up a new strategy to investigate the strength of the UA(1) symmetry breaking around the critical temperature.

Published by the American Physical Society
2024
Reduction for one-loop tensor Feynman integrals in the relativistic quantum field theories at finite temperature and/or finite density
Authors: Chang Hao-Ran
Published: July 2024

The Passarino-Veltman reduction is a systematic procedure based on the Lorentz covariance, which can efficiently reduce the one-loop tensor Feynman integrals in the relativistic quantum field theories (QFTs) at zero temperature and zero density. However, the Lorentz covariance is explicitly broken when either of the temperature and density is finite, due to a rest reference frame of the many-body system in which the temperature and density are measured, rendering the Passarino-Veltman reduction not applicable anymore to reduce the one-loop tensor Feynman integrals therein. In this paper, we report a Passarino-Veltman reduction which can efficiently simplify the one-loop tensor Feynman integrals in the relativistic QFTs at finite temperature and/or finite density. The Passarino-Veltman reduction can analyze the one-loop tensor Feynman integrals in a wide range of physical systems described by the relativistic QFTs at finite temperature and/or finite density, such as quark-gluon plasma in nuclear physics.

Published by the American Physical Society
2024
Spherically symmetric configurations in the quadratic
f(R)
gravity
Authors: Zhdanov V. I. , Stashko O. S. , Shtanov Yu. V.
Published: July 2024

We study spherically symmetric configurations of the quadratic f(R) gravity [f(R)=R−R2/6μ2]. In the case of a purely gravitational system, we have fully investigated the global qualitative behavior of all static solutions satisfying the conditions of asymptotic flatness. These solutions are proved to be regular everywhere except for a naked singularity at the center; they are uniquely determined by the total mass M and the “scalar charge” Q characterizing the strength of the scalaron field at spatial infinity. The case Q=0 yields the Schwarzschild solution, but an arbitrarily small

Q

≠

0

leads to the appearance of a central naked singularity having a significant effect on the neighboring region, even when the space-time metric in the outer region is practically insensitive to the scalaron field. Approximation procedures are developed to derive asymptotic relations near the naked singularity and at spatial infinity, and the leading terms of the solutions are presented. We have investigated the linear stability of the static solutions with respect to radial perturbations satisfying the null Dirichlet boundary condition at the center and numerically estimate the range of parameters corresponding to stable/unstable configurations. In particular, the configurations with sufficiently small Q turn out to be linearly unstable.

Published by the American Physical Society
2024
Functional renormalization group approach to dipolar fixed point which is scale invariant but nonconformal
Authors: Nakayama Yu
Published: July 2024

A dipolar fixed point introduced by Aharony and Fisher is a physical example of interacting scale-invariant but nonconformal field theories. We find that the perturbative critical exponents computed in ε expansions violate the conformal bootstrap bound. We formulate the functional renormalization group equations Wetterich and Polchinski to study the fixed point. We present some results in three dimensions within (uncontrolled) local potential approximations (with or without perturbative anomalous dimensions).

Published by the American Physical Society
2024
Machine learning that predicts well may not learn the correct physical descriptions of glassy systems
Authors: Swain Arabind , Ridout Sean Alexander , Nemenman Ilya
Published: July 2024

The complexity of glasses makes it challenging to explain their dynamics. Machine learning (ML) has emerged as a promising pathway for understanding glassy dynamics by linking their structural features to rearrangement dynamics. Support vector machine (SVM) was one of the first methods used to detect such correlations. Specifically, a certain output of SVMs trained to predict dynamics from structure, the distance from the separating hyperplane, was interpreted as being linearly related to the activation energy for the rearrangement. By numerical analysis of toy models, we explore under which conditions it is possible to infer the energy barrier to rearrangements from the distance to the separating hyperplane. We observe that such successful inference is possible only under very restricted conditions. Typical tests, such as the apparent Arrhenius dependence of the probability of rearrangement on the inferred energy and the temperature, or high cross-validation accuracy do not guarantee success. Since even in such relatively simple toy models, prediction success of ML models does not necessarily translate into success of learning the underlying physics, we suggest that more careful investigations are needed when such claims are made. For this, we propose practical approaches for measuring the quality of the energy inference and for modifying the inferred model to improve the inference, which should be usable in the context of realistic datasets.

Published by the American Physical Society
2024
Prolonging a discrete time crystal by quantum-classical feedback
Authors: Camacho Gonzalo , Fauseweh Benedikt
Published: July 2024

Nonequilibrium phases of quantum matter featuring time crystalline eigenstate order have been realized recently on noisy intermediate-scale quantum (NISQ) devices. While ideal quantum time crystals exhibit collective subharmonic oscillations and spatiotemporal long-range order persisting for infinite times, the decoherence time of current NISQ devices sets a natural limit to the survival of these phases, restricting their observation to a shallow quantum circuit. Here we propose a time-periodic scheme that leverages quantum-classical feedback protocols in subregions of the system to enhance a time crystal signal significantly exceeding the decoherence time of the device. As a case of study, we demonstrate the survival of the many-body localized discrete time crystal phase in the one-dimensional periodically kicked Ising model, accounting for decoherence of the system with an environment. Based on classical simulation of quantum circuit realizations we find that this approach is suitable for implementation on existing quantum hardware and presents a prospective path to simulate complex quantum many-body dynamics that transcend the low depth limit of current digital quantum computers.

Published by the American Physical Society
2024
Study on the UV FEL single-shot damage threshold of an Au thin film
Authors: Wu Meiyi , Li Qinming , Wang Mingchang , Zhu Qinghao , Cai Jiandong , Xu Zhongmin , Zhou Hao , Huang Long , Zhang Bingbing , Qi Runze , Zhang Zhe , Li Wenbin , Zhong Yinpeng , Zhang Weiqing
Published: July 2024

The damage threshold of an Au-coated flat mirror, one of the reflective optics installed on the FEL-2 beamline of the Dalian Coherent Light Source, China, upon far-UV free-electron laser irradiation is evaluated. The surface of the coating is characterized by profilometer and optical microscope. A theoretical approach of the phenomenon is also presented, by application of conventional single-pulse damage threshold calculations, a one-dimensional thermal diffusion model, as well as finite-element analysis with ANSYS.
Chinese students in the global south: a case study of mobility to Chile
Authors: Bórquez Basáez Andrés , Morales Valdés José Manuel , Guzmán Núñez Osvaldo
Published: July 2024

Purpose

The following article Chinese students' migration projects to the global south. Little work has sought to deepen the understanding of Chinese students' mobility to developing countries. This is key to determining a more complete profile of Chinese students and whether they fit into the categories of foreign students described by mainstream literature.

Design/methodology/approach

In order to understand the respective experiences and points of view of foreign students in on the process of choosing the country of study, we proceeded to identify different students of Chinese origin who have made their trip to Chile during the last decade. In addition, documents on China's international student mobility policy were reviewed, mainly focusing on documents dealing with Chinese students going abroad.

Findings

Chinese students are increasingly looking to travel to countries in the Global South as an opportunity to differentiate themselves. Chile emerges as an attractive destination as it is seen as a stable country in Latin America. It is a place where China has several strategic interests that may allow future professional development.

Originality/value

This article focuses on this aspect, mainly on how Chinese students perceive Chile as a place to pursue higher education. There is strong evidence of Chinese student flows to developed countries, but there are still insufficient studies on South-South mobility.
3D bioprinted meat: the values-beliefs-norms evaluation of perceived future food source among younger generations
Authors: Ong Ardvin Kester S. , Arriola Raphael Sebastian L. , Eneria Zhyra Michaella R. , Lopez Lerryzel G. , Matias Erela Agatha L. , Diaz John Francis T. , German Josephine D. , Gumasing Ma. Janice J.
Published: July 2024

Purpose

The acceptance and perception of people regarding 3D bioprinted meat are considered as primary concerns but have not been widely evaluated. This study aimed to determine how biospheric, altruistic, egoistic, ecological worldviews, awareness of consequences, social norms and personal norms affect the consumption intention of 3D bioprinted meat as a future food source.

Design/methodology/approach

The values-beliefs-norms theory grounded this study. An online survey was conducted with 600 valid respondents for analysis utilizing the structural equation modeling method.

Findings

It was found that the ecological worldview had the highest significance, and biospheric and egoistic values positively impacted individuals’ ecological worldview. The awareness of consequences and social norms was also seen to directly influence personal norms, leading to consumption intention. However, it was determined that altruistic values toward an ecological worldview had no significant effect, as an individual's moral values are not affected by other people's well-being.

Practical implications

This study was able to assess and discover the positive consumption intention among Filipinos, highlighting societal norms and pro-environmental behavior. The findings may help manufacturers market 3D bioprinted meat effectively and aid studies on environmentalism, social movements and consumer behavior, leading to acceptance of the development and proliferation of cultured meats.

Originality/value

There have been no studies on cultured meats such as 3D bioprinted meat in the Philippines. The current study was able to fully assess the pro-environmental behavior among Filipinos and intention for 3D bioprinted meat against the generic behavioral assessment among related studies. Comparison was presented based on the findings.