Now showing items 1-20 of 60004

    • Millennia-old coral holobiont DNA provides insight into future adaptive trajectories

      Scott, Carly B.; Cárdenas, Anny; Mah, Matthew; Narasimhan, Vagheesh M.; Rohland, Nadin; Toth, Lauren T.; Voolstra, Christian R.; Reich, David; Matz, Mikhail V. (Molecular Ecology, Wiley, 2022-08-09) [Article]
      Ancient DNA (aDNA) has been applied to evolutionary questions across a wide variety of taxa. Here, for the first time, we leverage aDNA from millennia-old fossil coral fragments to gain new insights into a rapidly declining western Atlantic reef ecosystem. We sampled four Acropora palmata fragments (dated 4215 BCE - 1099 CE) obtained from two Florida Keys reef cores. From these samples, we established that it is possible both to sequence ancient DNA from reef cores and place the data in the context of modern-day genetic variation. We recovered varying amounts of nuclear DNA exhibiting the characteristic signatures of aDNA from the A. palmata fragments. To describe the holobiont sensu lato, which plays a crucial role in reef health, we utilized metagenome-assembled genomes as a reference to identify a large additional proportion of ancient microbial DNA from the samples. The samples shared many common microbes with modern-day coral holobionts from the same region, suggesting remarkable holobiont stability over time. Despite efforts, we were unable to recover ancient Symbiodiniaceae reads from the samples. Comparing the ancient A. palmata data to whole-genome sequencing data from living acroporids, we found that while slightly distinct, ancient samples were most closely related to individuals of their own species. Together, these results provide a proof-of-principle showing that it is possible to carry out direct analysis of coral holobiont change over time, which lays a foundation for studying the impacts of environmental stress and evolutionary constraints.
    • The SWI/SNF chromatin remodeling factor DPF3 regulates metastasis of ccRCC by modulating TGF-β signaling

      Cui, Huanhuan; Yi, Hongyang; Bao, Hongyu; Tan, Ying; Tian, Chi; Shi, Xinyao; Gan, Diwen; Zhang, Bin; Liang, Weizheng; Chen, Rui; Zhu, Qionghua; Fang, Liang; Gao, Xin; Huang, Hongda; Tian, Ruijun; Sperling, Silke R.; Hu, Yuhui; Chen, Wei (Nature Communications, Springer Science and Business Media LLC, 2022-08-09) [Article]
      DPF3, a component of the SWI/SNF chromatin remodeling complex, has been associated with clear cell renal cell carcinoma (ccRCC) in a genome-wide association study. However, the functional role of DPF3 in ccRCC development and progression remains unknown. In this study, we demonstrate that DPF3a, the short isoform of DPF3, promotes kidney cancer cell migration both in vitro and in vivo, consistent with the clinical observation that DPF3a is significantly upregulated in ccRCC patients with metastases. Mechanistically, DPF3a specifically interacts with SNIP1, via which it forms a complex with SMAD4 and p300 histone acetyltransferase (HAT), the major transcriptional regulators of TGF-β signaling pathway. Moreover, the binding of DPF3a releases the repressive effect of SNIP1 on p300 HAT activity, leading to the increase in local histone acetylation and the activation of cell movement related genes. Overall, our findings reveal a metastasis-promoting function of DPF3, and further establish the link between SWI/SNF components and ccRCC.
    • Nonseparable Space-Time Stationary Covariance Functions on Networks cross Time

      Porcu, Emilio; White, Philip A.; Genton, Marc G. (arXiv, 2022-08-09) [Preprint]
      The advent of data science has provided an increasing number of challenges with high data complexity. This paper addresses the challenge of space-time data where the spatial domain is not a planar surface, a sphere, or a linear network, but a generalized network (termed a graph with Euclidean edges). Additionally, data are repeatedly measured over different temporal instants. We provide new classes of nonseparable space-time stationary covariance functions where {\em space} can be a generalized network, a Euclidean tree, or a linear network, and where time can be linear or circular (seasonal). Because the construction principles are technical, we focus on illustrations that guide the reader through the construction of statistically interpretable examples. A simulation study demonstrates that we can recover the correct model when compared to misspecified models. In addition, our simulation studies show that we effectively recover simulation parameters. In our data analysis, we consider a traffic accident dataset that shows improved model performance based on covariance specifications and network-based metrics.
    • Laser-Powered UAVs for Wireless Communication Coverage: A Large-Scale Deployment Strategy

      Lahmeri, Mohamed-Amine; Kishk, Mustafa A.; Alouini, Mohamed-Slim (IEEE Transactions on Wireless Communications, IEEE, 2022-08-09) [Article]
      The use of unmanned aerial vehicles (UAVs) is strongly advocated for sixth-generation (6G) networks, as the 6G standard will not be limited to improving broadband services, but will also target the extension of the geographical cellular coverage. In this context, the deployment of UAVs is considered a key solution for seamless connectivity and reliable coverage. That being said, it is important to underline that although UAVs are characterized by their high mobility and their ability to establish line-of-sight (LOS) links, their use is still impeded by several factors such as weather conditions, their limited computing power, and, most importantly, their limited energy. In this work, we are aiming for the novel technology that enables indefinite wireless power transfer for UAVs using laser beams. We propose a novel UAV deployment strategy, based on which we analyze the overall performance of the system in terms of wireless coverage. To this end, we use tractable tools from stochastic geometry to model the complex communication system. We analyze the user’s connectivity profile under different laser charging capabilities and in different type of environments. We show a decrease in the coverage probability by more than 12% in moderate-to-strong turbulence conditions compared to low turbulence conditions. We also show how the connection rate to the aerial network significantly decreases in favor of the terrestrial network for short laser charging ranges. We conclude that laser-powered drones are considered interesting alternatives when placed in LOS with users, in low-to-moderate optical turbulence, and at reasonable ranges from the charging stations.
    • PYK2 senses calcium through a disordered dimerization and calmodulin-binding element

      Momin, Afaque Ahmad Imtiyaz; Mendes, Tiago; Barthe, Philippe; Faure, Camille; Hong, Seungbeom; Yu, Piao; Kadaré, Gress; Jaremko, Mariusz; Girault, Jean Antoine; Jaremko, Lukasz; Arold, Stefan T. (Communications Biology, Springer Science and Business Media LLC, 2022-08-09) [Article]
      Multidomain kinases use many ways to integrate and process diverse stimuli. Here, we investigated the mechanism by which the protein tyrosine kinase 2-beta (PYK2) functions as a sensor and effector of cellular calcium influx. We show that the linker between the PYK2 kinase and FAT domains (KFL) encompasses an unusual calmodulin (CaM) binding element. PYK2 KFL is disordered and engages CaM through an ensemble of transient binding events. Calcium increases the association by promoting structural changes in CaM that expose auxiliary interaction opportunities. KFL also forms fuzzy dimers, and dimerization is enhanced by CaM binding. As a monomer, however, KFL associates with the PYK2 FERM-kinase fragment. Thus, we identify a mechanism whereby calcium influx can promote PYK2 self-association, and hence kinase-activating trans-autophosphorylation. Collectively, our findings describe a flexible protein module that expands the paradigms for CaM binding and self-association, and their use for controlling kinase activity.
    • Fast water transport and molecular sieving through ultrathin ordered conjugated-polymer-framework membranes

      Shen, Jie; Cai, Yichen; Zhang, Chenhui; Wei, Wan; Chen, Cailing; Liu, Lingmei; Yang, Kuiwei; Ma, Yinchang; Wang, Yingge; Tseng, Chien-Chih; Fu, Jui-Han; Dong, Xinglong; Li, Jiaqiang; Zhang, Xixiang; Li, Lain-Jong; Jiang, Jianwen; Pinnau, Ingo; Tung, Vincent; Han, Yu (Nature Materials, Springer Science and Business Media LLC, 2022-08-08) [Article]
      The development of membranes that block solutes while allowing rapid water transport is of great importance. The microstructure of the membrane needs to be rationally designed at the molecular level to achieve precise molecular sieving and high water flux simultaneously. We report the design and fabrication of ultrathin, ordered conjugated-polymer-framework (CPF) films with thicknesses down to 1 nm via chemical vapour deposition and their performance as separation membranes. Our CPF membranes inherently have regular rhombic sub-nanometre (10.3 × 3.7 Å) channels, unlike membranes made of carbon nanotubes or graphene, whose separation performance depends on the alignment or stacking of materials. The optimized membrane exhibited a high water/NaCl selectivity of ∼6,900 and water permeance of ∼112 mol m−2 h−1 bar−1, and salt rejection >99.5% in high-salinity mixed-ion separations driven by osmotic pressure. Molecular dynamics simulations revealed that water molecules quickly and collectively pass through the membrane by forming a continuous three-dimensional network within the hydrophobic channels. The advent of ordered CPF provides a route towards developing carbon-based membranes for precise molecular separation.
    • Secrecy Outage Performance Analysis of Dual-Hop RF-UOWC Systems

      Lei, Hongjiang; Zhu, Chen; Ansari, Imran Shafique; Park, Kihong; Pan, Gaofeng (IEEE Systems Journal, IEEE, 2022-08-08) [Article]
      This article investigates the secrecy performance of a dual-hop radio frequency-underwater optical wireless communication (RF-UOWC) system. Using stochastic geometry theory, the eavesdroppers are modeled as a Poisson point process distribution, and RF and UOWC links are modeled as Nakagami-m and mixture exponential-generalized gamma distributions, respectively. Firstly, we derive the statistical laws of signal-to-noise ratio for illegitimate receivers in both colluding and noncolluding scenarios and legitimate receivers when amplify-and-forward and decode-and-forward relaying strategies are employed. Subsequently, closed-form expressions for the lower bound of secrecy outage probability (SOP) are derived. Finally, analytical results are verified via Monte Carlo simulation results, and the effects of channel and system parameters on secrecy outage performance of dual-hop systems are analyzed. Numerical results demonstrate that environmental parameters, such as temperature and bubble levels, exhibit an important impact on the SOP of RF-UOWC systems.
    • Granger Causality using Neural Networks

      Horvath, Samuel; Sultan, Malik Shahid; Ombao, Hernando (arXiv, 2022-08-07) [Preprint]
      The Granger Causality (GC) test is a famous statistical hypothesis test for investigating if the past of one time series affects the future of the other. It helps in answering the question whether one time series is helpful in forecasting. Standard traditional approaches to Granger causality detection commonly assume linear dynamics, but such simplification does not hold in many real-world applications, e.g., neuroscience or genomics that are inherently non-linear. In such cases, imposing linear models such as Vector Autoregressive (VAR) models can lead to inconsistent estimation of true Granger Causal interactions. Machine Learning (ML) can learn the hidden patterns in the datasets specifically Deep Learning (DL) has shown tremendous promise in learning the non-linear dynamics of complex systems. Recent work of Tank et al propose to overcome the issue of linear simplification in VAR models by using neural networks combined with sparsity-inducing penalties on the learn-able weights. In this work, we build upon ideas introduced by Tank et al. We propose several new classes of models that can handle underlying non-linearity. Firstly, we present the Learned Kernal VAR(LeKVAR) model-an extension of VAR models that also learns kernel parametrized by a neural net. Secondly, we show one can directly decouple lags and individual time series importance via decoupled penalties. This decoupling provides better scaling and allows us to embed lag selection into RNNs. Lastly, we propose a new training algorithm that supports mini-batching, and it is compatible with commonly used adaptive optimizers such as Adam.he proposed techniques are evaluated on several simulated datasets inspired by real-world applications.We also apply these methods to the Electro-Encephalogram (EEG) data for an epilepsy patient to study the evolution of GC before , during and after seizure across the 19 EEG channels.
    • Interaction of tetrameric and dimeric FBP2 with CAMK2α, HIF1α and ALDOA

      Budziak, Bartosz (2022-08-06) [Poster]
      Macromolecular interactions are common mechanisms of protein function regulation. Emerging role of muscle fructose 1,6-bisphospatase (FBP2) in memory formation and cancer cells survival was hypothesized to be regulated by such interactions. FBP2 exists as mixture of different oligomeric states which presumably may interact with their binding partners in a different mode. Results presented here show how alterations of FBP2 quaternary structure affects interactions with such proteins as CAMK2?, HIF1? or ALDOA. We show that a dimeric FBP2 is preferred form of the enzyme for interaction with CAMK2?. On the other hand, an inactive tetrameric T-state of FBP2 binds HIF1? and, to a lesser extent, ALDOA stronger than the dimeric and an active R-state tetrameric FBP2.
    • Untargeted Metabolomic Profiling and Antioxidant Capacities of Different Solvent Crude Extracts of Ephedra foeminea

      Al-Nemi, Ruba (2022-08-06) [Poster]
      This study aims to investigate the chemical profiles of different solvent (Ace, acetone; DCM/MeOH, dichloromethane/methanol; EtOH, ethanol; EA, ethyl acetate; MeOH, methanol) extracts of Ephedra foeminea collected from Jordan via an untargeted metabolomics approach using NMR, GC-MS, LCMS and analyzing the data through Venn diagrams, PCA plots, and Metabolite Set Enrichment Analysis (MESA), while determining their antioxidant capacities using ABTS assays. Results revealed the dominant chemical groups as amino acids, fatty acids, carboxylic acids, and carbohydrates, it was also found that the DCM/MeOH and MeOH extracts had the most distinct composition and most unique compounds. The methanolic extract was relatively the most potent in the ABTS assay (IC50 249.6 µg/mL). In conclusion, solvents influenced the recovery of metabolites in E. foeminea and the antioxidant activity of the E. foeminea methanolic extract could be correlated to the abundant presence of diverse bioactive compounds.
    • Low-voltage ultrafast nonvolatile memory via direct charge injection through a threshold resistive-switching layer

      Li, Yuan; Zhang, Zhi Cheng; Li, Jiaqiang; Chen, Xu-Dong; Kong, Ya; Wang, Fu-Dong; Zhang, Guo-Xin; Lu, Tong-Bu; Zhang, Jin (Nature communications, Springer Science and Business Media LLC, 2022-08-06) [Article]
      The explosion in demand for massive data processing and storage requires revolutionary memory technologies featuring ultrahigh speed, ultralong retention, ultrahigh capacity and ultralow energy consumption. Although a breakthrough in ultrafast floating-gate memory has been achieved very recently, it still suffers a high operation voltage (tens of volts) due to the Fowler-Nordheim tunnelling mechanism. It is still a great challenge to realize ultrafast nonvolatile storage with low operation voltage. Here we propose a floating-gate memory with a structure of MoS2/hBN/MoS2/graphdiyne oxide/WSe2, in which a threshold switching layer, graphdiyne oxide, instead of a dielectric blocking layer in conventional floating-gate memories, is used to connect the floating gate and control gate. The volatile threshold switching characteristic of graphdiyne oxide allows the direct charge injection from control gate to floating gate by applying a nanosecond voltage pulse (20 ns) with low magnitude (2 V), and restricts the injected charges in floating gate for a long-term retention (10 years) after the pulse. The high operation speed and low voltage endow the device with an ultralow energy consumption of 10 fJ. These results demonstrate a new strategy to develop next-generation high-speed low-energy nonvolatile memory.
    • Investigating calcification-related candidates in a non-symbiotic scleractinian coral, Tubastraea spp.

      Capasso, Laura; Aranda, Manuel; Cui, Guoxin; Pousse, Melanie; Tambutté, Sylvie; Zoccola, Didier (Scientific Reports, Springer Science and Business Media LLC, 2022-08-06) [Article]
      In hermatypic scleractinian corals, photosynthetic fixation of CO2 and the production of CaCO3 are intimately linked due to their symbiotic relationship with dinoflagellates of the Symbiodiniaceae family. This makes it difficult to study ion transport mechanisms involved in the different pathways. In contrast, most ahermatypic scleractinian corals do not share this symbiotic relationship and thus offer an advantage when studying the ion transport mechanisms involved in the calcification process. Despite this advantage, non-symbiotic scleractinian corals have been systematically neglected in calcification studies, resulting in a lack of data especially at the molecular level. Here, we combined a tissue micro-dissection technique and RNA-sequencing to identify calcification-related ion transporters, and other candidates, in the ahermatypic non-symbiotic scleractinian coral Tubastraea spp. Our results show that Tubastraea spp. possesses several calcification-related candidates previously identified in symbiotic scleractinian corals (such as SLC4-γ, AMT-1like, CARP, etc.). Furthermore, we identify and describe a role in scleractinian calcification for several ion transporter candidates (such as SLC13, -16, -23, etc.) identified for the first time in this study. Taken together, our results provide not only insights about the molecular mechanisms underlying non-symbiotic scleractinian calcification, but also valuable tools for the development of biotechnological solutions to better control the extreme invasiveness of corals belonging to this particular genus.
    • Multilevel Importance Sampling for McKean-Vlasov Stochastic Differential Equation

      Rached, Nadhir Ben; Haji-Ali, Abdul-Lateef; Mohan, Shyam; Tempone, Raul (arXiv, 2022-08-05) [Preprint]
      This work combines multilevel Monte Carlo methods with importance sampling (IS) to estimate rare event quantities that can be expressed as the expectation of a Lipschitz observable of the solution to the McKean-Vlasov stochastic differential equation. We first extend the double loop Monte Carlo (DLMC) estimator, introduced in this context in our previous work [Ben Rached et al. 2022], to the multilevel setting. We formulate a novel multilevel DLMC (MLDLMC) estimator, and perform a comprehensive work-error analysis yielding new and improved complexity results. Crucially, we also devise an antithetic sampler to estimate level differences that guarantees reduced work complexity for the MLDLMC estimator compared with the single level DLMC estimator. To tackle rare events, we apply the same single level IS scheme, obtained via stochastic optimal control in [Ben Rached et al. 2022], over all levels of the MLDLMC estimator. Combining IS and MLDLMC not only reduces computational complexity by one order, but also drastically reduces the associated constant, ensuring feasible estimates for rare event quantities. We illustrate effectiveness of proposed MLDLMC estimator on the Kuramoto model from statistical physics with Lipschitz observables, confirming reduced complexity from O(TOL−4r) for the single level DLMC estimator to O(TOL−3r) while providing feasible estimation for rare event quantities up to the prescribed relative error tolerance TOLr.
    • A Fractional Image Inpainting Model Using a Variant of Mumford-Shah Model

      Halim, Abdul; Rohim, Abdur; Kumar, B. V. Rathish; Saha, Ripan (arXiv, 2022-08-05) [Preprint]
      In this paper, we propose a fourth order PDE model for image inpainting based on a variant of the famous Mumford-Shah (MS) image segmentation model. Convexity splitting is used to discrtised the time and we replace the Laplacian by its fractional counterpart in the time discretised scheme. Fourier spectral method is used for space discretization. Consistency, stability and convergence of the time discretised model has been carried out. The model is tested on some standard test images and compared them with the result of some models existed in the literature.
    • Various Wavefront Sensing and Control Developments on the Santa Cruz Extreme AO Laboratory (SEAL) Testbed

      Gerard, Benjamin L.; Perez-Soto, Javier; Chambouleyron, Vincent; Kooten, Maaike A. M. van; Dillon, Daren; Cetre, Sylvain; Jensen-Clem, Rebecca; Fu, Qiang; Amata, Hadi; Heidrich, Wolfgang (arXiv, 2022-08-05) [Preprint]
      Ground-based high contrast imaging (HCI) and extreme adaptive optics (AO) technologies have advanced to the point of enabling direct detections of gas-giant exoplanets orbiting beyond the snow lines around nearby young star systems. However, leftover wavefront errors using current HCI and AO technologies, realized as "speckles" in the coronagraphic science image, still limit HCI instrument sensitivities to detecting and characterizing lower-mass, closer-in, and/or older/colder exoplanetary systems. Improving the performance of AO wavefront sensors (WFSs) and control techniques is critical to improving such HCI instrument sensitivity. Here we present three different ongoing wavefront sensing and control project developments on the Santa cruz Extreme AO Laboratory (SEAL) testbed: (1) "multi-WFS single congugate AO (SCAO)" using the Fast Atmospheric Self-coherent camera (SCC) Technique (FAST) and a Shack Hartmann WFS, (2) pupil chopping for focal plane wavefront sensing, first with an external amplitude modulator and then with the DM as a phase-only modulator, and (3) a laboratory demonstration of enhanced linearity with the non-modulated bright Pyramid WFS (PWFS) compared to the regular PWFS. All three topics share a common theme of multi-WFS SCAO and/or second stage AO, presenting opportunities and applications to further investigate these techniques in the future.
    • Cellular automata imbedded memristor-based recirculated logic in-memory computing

      Liu, Yanming; Tian, He; Wu, Fan; Liu, Anhan; Li, Yihao; Sun, Hao; Lanza, Mario; Ren, Tian-Ling (Research Square Platform LLC, 2022-08-05) [Preprint]
      Cellular automata is an important tool to study the emergent properties of complex systems based on its well-known parallel, bio-inspired, computational characteristics. However, running cellular automata on conventional chips suffer from low parallelism, and high hardware cost. Establish dedicated hardware for cellular automata remains elusive. Here, we propose a recirculate logic operations scheme (RLOS) based on memristive hardware combined with 2D transistors to realize cellular automata evolution. The scheme utilizes the storage and calculation characteristics of memristive devices, which greatly reduces hardware complexity. The versatility of the RLOS scheme allows implementing multiple different cellular automata algorithms on the same circuitry. The entire rule (rule 1-254) of elementary cellular automata and more complicated 1D CA model majority classification algorithm have been verified to be applicable to this circuitry. Further, the edge detection algorithm based on 2D cellular automata has been authenticated through RLOS. The experimental and evaluation results reveal that the scheme reduces the hardware cost up to 79 times comparing to the Field Programmable Gate Array (FPGA) approach. To our best knowledge, RLOS has the lowest hardware cost (6 components/per cell) among state-of-art hardware implementations. This work can pave the road towards high-efficiency and low-cost cellular automata hardware realization, and also facilitates the exploration of memristive applications.
    • Topochemical Synthesis of Ca3CrN3H Involving a Rotational Structural Transformation for Catalytic Ammonia Synthesis

      Cao, Yu; Kirsanova, Maria; Ochi, Masayuki; Almaksoud, Walid; Zhu, Tong; Rai, Rohit Kumar; Gao, Shenghan; Tsumori, Tatsuya; Kobayashi, Shintaro; Kawaguchi, Shogo; Abou-Hamad, Edy; Kuroki, Kazuhiko; Tassel, Cédric; Abakumov, Artem; Kobayashi, Yoji; Kageyama, Hiroshi (Angewandte Chemie (International ed. in English), Wiley, 2022-08-05) [Article]
      Topochemical reactions have led to great progress in the discovery of new metastable compounds with novel chemical and physical properties. With these reactions, the overall crystal structure of the host material is generally maintained. Here we report a topochemical synthesis of a hexagonal nitride hydride, h-Ca3CrN3H, by heating an orthorhombic nitride, o-Ca3CrN3, under hydrogen at 673 K, accompanied by a rotational structural transformation. The hydrogen intercalation modifies the Ca-N rock-salt-like atomic packing in o-Ca3CrN3 to a face-sharing octahedral chain in h-Ca3CrN3H, mimicking a 'hinged tessellation' movement. In addition, the h-Ca3CrN3H exhibited stable ammonia synthesis activity when used as a catalyst.