bioRxiv Pub Date : 2024-08-09 DOI: 10.1101/2024.08.07.606907

Jorge Martinez Armas, Kenneth Knoblauch, H. Kennedy, Zoltan Toroczkai

引用次数: 0

Revealing unseen dynamical regimes of ecosystems from population time-series data 从种群时间序列数据揭示生态系统的未知动态机制

bioRxiv Pub Date : 2024-08-09 DOI: 10.1101/2024.08.07.607005

Lucas P. Medeiros, Darian K. Sorenson, Bethany J. Johnson, E. Palkovacs, Stephan B. Munch

{"title":"Revealing unseen dynamical regimes of ecosystems from population time-series data","authors":"Lucas P. Medeiros, Darian K. Sorenson, Bethany J. Johnson, E. Palkovacs, Stephan B. Munch","doi":"10.1101/2024.08.07.607005","DOIUrl":"https://doi.org/10.1101/2024.08.07.607005","url":null,"abstract":"Many ecosystems can exist in alternative dynamical regimes for which small changes in an environmental driver can cause sudden jumps between regimes. However, predicting the dynamics of regimes that occur under unobserved levels of the environmental driver has remained an unsolved challenge in ecology with important implications for conservation and management. Here we show that integrating population time-series data and information on the putative driver into an empirical dynamic model allows us to predict new dynamical regimes without the need to specify a population dynamics model. As a proof of concept, we demonstrate that we can accurately predict fixed-point, cyclic, or chaotic dynamics under unseen driver levels for a range of simulated models. For a model with an abrupt population collapse, we show that our approach can anticipate the regime that follows the tipping point. We then apply our approach to data from an experimental microbial ecosystem and from a lake planktonic ecosystem. We find that we can reconstruct transitions away from chaos in the experimental ecosystem and anticipate the dynamics of the oligotrophic regime in the lake ecosystem. These results lay the groundwork for making rational decisions about preventing, or preparing for, regime shifts in natural ecosystems.","PeriodicalId":505198,"journal":{"name":"bioRxiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141923391","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Research on the Mechanism of Lphn1 Knockout in Inhibiting Colorectal Cancer Lphn1 基因敲除抑制结直肠癌的机制研究

bioRxiv Pub Date : 2024-08-09 DOI: 10.1101/2024.08.07.606975

Yi Wang

引用次数: 0

Stability of cross-sensory input to primary somatosensory cortex across experience 初级体感皮层跨感觉输入在不同经历中的稳定性

bioRxiv Pub Date : 2024-08-09 DOI: 10.1101/2024.08.07.607026

Daniel D. Kato, Randy M. Bruno

{"title":"Stability of cross-sensory input to primary somatosensory cortex across experience","authors":"Daniel D. Kato, Randy M. Bruno","doi":"10.1101/2024.08.07.607026","DOIUrl":"https://doi.org/10.1101/2024.08.07.607026","url":null,"abstract":"Merging information from across sensory modalities is key to forming robust, disambiguated percepts of the world, yet how the brain achieves this feat remains unclear. Recent observations of cross-modal influences in primary sensory cortical areas have suggested that multisensory integration may occur in the earliest stages of cortical processing, but the role of these responses is still poorly understood. We address these questions by testing several hypotheses about the possible functions served by auditory influences on the barrel field of mouse primary somatosensory cortex (S1) using in vivo 2-photon calcium imaging. We observed sound-evoked spiking activity in a small fraction of cells overall, and moreover that this sparse activity was insufficient to encode auditory stimulus identity; few cells responded preferentially to one sound or another, and a linear classifier trained to decode auditory stimuli from population activity performed barely above chance. Moreover S1 did not encode information about specific audio-tactile feature conjunctions that we tested. Our ability to decode auditory audio-tactile stimuli from neural activity remained unchanged after both passive experience and reinforcement. Collectively, these results suggest that while a primary sensory cortex is highly plastic with regard to its own modality, the influence of other modalities are remarkably stable and play a largely stimulus-non-specific role.","PeriodicalId":505198,"journal":{"name":"bioRxiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141921206","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Temporal changes in surface tension guide the accurate asymmetric division of Arabidopsis zygotes 表面张力的时间变化引导拟南芥子实体准确的不对称分裂

bioRxiv Pub Date : 2024-08-09 DOI: 10.1101/2024.08.07.605794

Zichen Kang, Sakumi Nakagawa, Hikari Matsumoto, Yukitaka Ishimoto, T. Nonoyama, Yuga Hanaki, Satoru Tsugawa, Minako Ueda

引用次数: 0

An Augmented Reality Visor for Intraoperative Visualization, Guidance and Temperature Monitoring using Fluorescence 利用荧光进行术中可视化、引导和温度监测的增强现实眼镜

bioRxiv Pub Date : 2024-08-09 DOI: 10.1101/2024.08.08.607031

Oscar Cipolato, Matthias Fauconneau, Paige J. LeValley, Robert Nißler, Benjamin Suter, Inge K. Herrmann

{"title":"An Augmented Reality Visor for Intraoperative Visualization, Guidance and Temperature Monitoring using Fluorescence","authors":"Oscar Cipolato, Matthias Fauconneau, Paige J. LeValley, Robert Nißler, Benjamin Suter, Inge K. Herrmann","doi":"10.1101/2024.08.08.607031","DOIUrl":"https://doi.org/10.1101/2024.08.08.607031","url":null,"abstract":"Fluorescence-guided surgical techniques, including tumor resection and tissue soldering, are advancing the frontiers of surgical precision by offering enhanced control that minimizes tissue damage and improves recovery as well as outcomes. However, integrating the visualization of the fluorescent signal and temperature monitoring seamlessly into surgical workflows has not been fully realized and remains a challenge, thus limiting their effectiveness and wide-spread clinical adoption. To address this issue, we introduce an augmented reality (AR) visor designed to unite nanomaterial excitation along with fluorescence detection, and temperature monitoring during surgical procedures. The AR visor was evaluated using advanced fluorescent nanoparticles, such as indocyanine green-doped particles and singlewalled carbon nanotubes. By consolidating fluorescence visualization, excitation monitoring, and precise temperature control into a single AR platform, we equip surgeons with a comprehensive view of both the surgical field and sub-surface conditions invisible to the naked eye. This integration notably improves the safety and efficacy of fluorescence-guided surgeries, as well as emerging technologies including laser tissue soldering, by ensuring the soldering temperature stays within therapeutic thresholds and the laser is accurately guided by real-time fluorescence signals. The presented technology not only enhances existing surgical techniques but also supports the development of new strategies and sensing technologies in areas where traditional methods fall short, marking significant progress in precision surgery, which could ultimately improve patient care.","PeriodicalId":505198,"journal":{"name":"bioRxiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141924758","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Adherence to the conservation of momentum to elucidate membrane transporter mechanisms 坚持动量守恒，阐明膜转运机制

bioRxiv Pub Date : 2024-08-09 DOI: 10.1101/2024.08.07.607056

B. Yorke, Helen M. Ginn

{"title":"Adherence to the conservation of momentum to elucidate membrane transporter mechanisms","authors":"B. Yorke, Helen M. Ginn","doi":"10.1101/2024.08.07.607056","DOIUrl":"https://doi.org/10.1101/2024.08.07.607056","url":null,"abstract":"The conformational landscape of proteins and associated dynamics is an essential component of function. Diverse conformations of highly populated metastable states are well-studied, but transitions between these states are rare, fleeting events. Neither molecular dynamics simulations nor experimental methods provide information about these. To address this conundrum, we present a computationally inexpensive algorithm, “cold-inbetweening”, which generates trajectories in torsion angle space. This minimises the overall kinetic energy needed to complete a transition between experimentally determined end-states. We use this method to provide mechanistic insight into three transporter superfamilies. This method allows interrogation of structural transitions, provides unique insights into coupled motion and hypotheses of action. The alternate access model of operation [1] is ubiquitous among many superfamilies of membrane transporters [2]. The model proposes that outward and inward pore opening is mutually exclusive, allowing ligand translocation but preventing damage from free solvent flow. Here, we study DraNramp (MntH) from Deinococcus radiodurians [3], MalT (bcMalT) from Bacillus cereus [4], and MATE (PfMATE) from Pyrococcus furiosus [5]. In MalT, the trajectory demonstrates elevator transport through unwinding of a supporter arm helix, maintaining the necessary and sufficient space to transport maltose. In DraNramp, this trajectory exhibited outward-gate closure prior to inward-gate opening, suggesting that the timing of gate closure is an inherent property of the protein architecture. In the MATE transporter, switching conformation involves the rewinding of an extended N-terminal helix. We suggest that the necessary motions to avoid steric backbone clashes forces this helix to plug the cavernous ligand-binding site during the conformational change. We propose helix unwinding as a general structural mechanism in membrane transporter function due to ease of helix register slippage in the lipid bilayer.","PeriodicalId":505198,"journal":{"name":"bioRxiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141922766","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Neuropeptide oxytocin facilitates its own brain-to-periphery uptake by regulating blood flow dynamics and permeability 神经肽催产素通过调节血流动力学和渗透性促进自身从大脑到外周的吸收

bioRxiv Pub Date : 2024-08-09 DOI: 10.1101/2024.08.07.606980

Preethi Rajamannar, O. Raz, G. Levkowitz

{"title":"Neuropeptide oxytocin facilitates its own brain-to-periphery uptake by regulating blood flow dynamics and permeability","authors":"Preethi Rajamannar, O. Raz, G. Levkowitz","doi":"10.1101/2024.08.07.606980","DOIUrl":"https://doi.org/10.1101/2024.08.07.606980","url":null,"abstract":"The hypothalamo-neurohypophyseal system is an important neuroendocrine brain-to-blood conduit through which the neurohormones oxytocin and arginine-vasopressin are released from the brain into the general circulation to affect peripheral physiological functions such as salt balance, metabolism and reproduction. However, whether an active mechanism executes fast and efficient neurohormone release to the periphery remains unsolved. We show that a hyperosmotic physiological challenge elicits a local increase in neurohypophyseal blood flow velocities and a change in capillary diameter, which is dictated by the geometry of the hypophyseal vascular microcircuit. Genetic ablation of oxytocin neurons and inhibition of oxytocin receptor signaling attenuated capillary blood flow and diameter. Optogenetic stimulation of oxytocin neurons resulted in an oxytocin receptor-dependent increase in blood flow velocities. Lastly, both osmotic challenge and oxytocin neuronal activation elicited a local rise in neurohypophyseal capillary permeability in an oxytocin signaling-dependent manner. Our study demonstrates that physiologically elicited changes in neurohypophyseal blood flow and permeability are regulated by oxytocin. We propose that oxytocin-dependent neuro-vascular coupling facilitates its efficient uptake into the blood circulation, suggesting a self-perpetuating mechanism of peripheral hormone transfer.","PeriodicalId":505198,"journal":{"name":"bioRxiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141923421","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The neural correlates of social rejection in the cyberball paradigm: An arterial spin labelling study 网络球范例中社交排斥的神经相关性：动脉自旋标记研究

bioRxiv Pub Date : 2024-08-09 DOI: 10.1101/2024.08.08.607136

K. Labek, Roberto Viviani

引用次数: 0

Deep learning–based automated prediction of mouse seminiferous tubule stage by using bright-field microscopy 利用明视野显微镜，基于深度学习自动预测小鼠曲细精管阶段

bioRxiv Pub Date : 2024-08-09 DOI: 10.1101/2024.08.07.606973

Y. Tokuoka, Tsutomu Endo, Takashi Morikura, Yuki Hiradate, Masahito Ikawa, Akira Funahashi

{"title":"Deep learning–based automated prediction of mouse seminiferous tubule stage by using bright-field microscopy","authors":"Y. Tokuoka, Tsutomu Endo, Takashi Morikura, Yuki Hiradate, Masahito Ikawa, Akira Funahashi","doi":"10.1101/2024.08.07.606973","DOIUrl":"https://doi.org/10.1101/2024.08.07.606973","url":null,"abstract":"Infertility is a global issue, with approximately 50% of cases attributed to defective spermatogenesis. For studies into spermatogenesis and spermatogenic dysfunction, evaluating the seminiferous tubule stage is essential. However, the current method of evaluation involves labor-intensive and time-consuming manual tasks such as staining, observation, and image analysis. Lack of reproducibility is also a problem owing to the subjective nature of visual evaluation by experts. In this study, we propose a deep learning–based method for automatically and objectively evaluating the seminiferous tubule stage. Our approach automatically predicts which of 12 seminiferous tubule stages is represented in bright-field microscopic images of mouse seminiferous tubules stained by hematoxylin-PAS. For training and validation of our model, we created a dataset of 1229 tissue images, each labeled with one of 12 distinct seminiferous tubule stages. The maximum prediction accuracy was 79.58% which rose to 98.33% with allowance for a prediction error of ±1 stage. Remarkably, although the model was not explicitly trained on the patterns of transition between stages, it inferred characteristic structural patterns involved in the process of spermatogenesis. This method not only advances our understanding of spermatogenesis but also holds promise for improving the automated diagnosis of infertility.","PeriodicalId":505198,"journal":{"name":"bioRxiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141923795","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

bioRxiv最新文献