bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of Intense Summer Arctic Cyclones Between the Marginal Ice Zone and Central Arctic
Authors: Kong Yang , Lu Chuhan , Guan Zhaoyong , Chen Xiaoxiao 
Published: February 2024

AbstractArctic cyclone activity is an important component of the local climate, and the frequent occurrence of extreme summer storms has raised widespread scientific interest. In this paper, we investigated the distinctive structural characteristics of intense summer Arctic cyclones by utilizing ERA‐Interim reanalysis data and employing a deep learning algorithm for cyclone detection. We found that the northern edge of Eurasia (i.e., the marginal ice zone (MIZ)) and the Alpha Ridge of Arctic Ocean (AR, i.e. central Arctic) are the two most active regions for intense Arctic cyclone activities in summer (from June to September). However, the surface conditions and coupling frequency between surface cyclone and tropopause polar vortices (TPVs) are distinct over these two regions. By further analysis of 100 intense cyclone activities in these two areas, respectively, we found that cyclones in MIZ are often smaller in size but higher in intensity at their maximum intensity, and their life cycles are generally shorter. MIZ cyclones are typically accompanied by a large Eady growth rate and frontal structure in the lower troposphere and their intensification primarily attributed to the thermal‐baroclinic process. In contrast, cyclones in AR are more frequently associated with higher potential vorticity (PV) values and pronounced PV downward intrusion from the stratosphere, as well as notable “upper warm‐lower cold” structures. The downward intrusion of TPVs and stratosphere vortices contribute to a decrease in the upper and column air mass deficit, leading to the intensification of surface Arctic cyclones in these regions.
A Mixed‐Integer Linear Programming Framework for Optimization of Water Network Operations Problems
Authors: Thomas Meghna , Sela Lina 
Published: February 2024

AbstractWater distribution systems (WDSs) are critical infrastructure used to convey water from sources to consumers. The mathematical framework governing the distribution of flows and heads in extended period simulations of WDSs lends itself to application in a wide range of optimization problems. Applying the classical mixed integer linear programming (MILP) approach to model WDSs hydraulics within an optimization framework can contribute to higher solution accuracy with lower computational effort. However, adapting WDSs models to conform to a MILP formulation has proven challenging because of the intrinsic non‐linearity of system hydraulics and the complexity associated with modeling hydraulic devices that influence the state of the WDS. This paper introduces MILPNet, an adjustable framework for WDSs that can be used to build and solve an extensive array of MILP optimization problems. MILPNet includes constraints that represent the mass balance and energy conservation equations, hydraulic devices, control rules, and status checks. To conform to MILP structure, MILPNet employs piece‐wise linear approximation and integer programming. MILPNet was implemented and tested using Gurobi Python API. Modeling accuracy was shown to be comparable to EPANET, a public domain software for hydraulic modeling, and sensitivity analyses were conducted to examine the impacts of the modeling assumptions on the performance of MILPNet. Additionally, application of the framework was demonstrated using pump scheduling optimization examples in single and rolling horizon scenarios. Our results show that MILPNet can facilitate the construction and solution of optimization problems for a range of applications in WDSs operations.
Large-scale groundwater flow and sedimentary diagenesis in continental shelves influence marine chemical budgets
Authors: Wilson Alicia M. , Osborne Andrew , White Scott M. 
Published: February 2024

AbstractThe major ion chemistry of the ocean has been assumed to be controlled by river input, hydrothermal circulation at mid-ocean ridges, carbonate production, and low-temperature alteration of seafloor basalt, but marine chemical budgets remain difficult to balance. Here we propose that large-scale groundwater flow and diagenetic reactions in continental shelf sediments have been overlooked as an important contributor to major ion budgets in the ocean. Based on data synthesized from 17 passive margin basins, continental shelves contribute fluid exchanges comparable to hydrothermal circulation at mid-ocean ridges. Chemical exchange is similarly significant, indicating removal of Mg2+ from the oceans at rates similar to mid-ocean ridge convection. Continental shelves likely contribute Ca2+ and K+ to the oceans at rates that, in combination with low-temperature basalt alteration, can close current budget deficits. Flow and reaction in continental shelf sediments should be included in a new generation of studies addressing marine isotope budgets.
Combinatorial optimization of gene expression through recombinase-mediated promoter and terminator shuffling in yeast
Authors: Cautereels Charlotte , Smets Jolien , Bircham Peter , De Ruysscher Dries , Zimmermann Anna , De Rijk Peter , Steensels Jan , Gorkovskiy Anton , Masschelein Joleen , Verstrepen Kevin J. 
Published: February 2024

AbstractMicrobes are increasingly employed as cell factories to produce biomolecules. This often involves the expression of complex heterologous biosynthesis pathways in host strains. Achieving maximal product yields and avoiding build-up of (toxic) intermediates requires balanced expression of every pathway gene. However, despite progress in metabolic modeling, the optimization of gene expression still heavily relies on trial-and-error. Here, we report an approach for in vivo, multiplexed Gene Expression Modification by LoxPsym-Cre Recombination (GEMbLeR). GEMbLeR exploits orthogonal LoxPsym sites to independently shuffle promoter and terminator modules at distinct genomic loci. This approach facilitates creation of large strain libraries, in which expression of every pathway gene ranges over 120-fold and each strain harbors a unique expression profile. When applied to the biosynthetic pathway of astaxanthin, an industrially relevant antioxidant, a single round of GEMbLeR improved pathway flux and doubled production titers. Together, this shows that GEMbLeR allows rapid and efficient gene expression optimization in heterologous biosynthetic pathways, offering possibilities for enhancing the performance of microbial cell factories.
N2FXm, a method for joint nuclear and cytoplasmic volume measurements, unravels the osmo-mechanical regulation of nuclear volume in mammalian cells
Authors: Pennacchio Fabrizio A. , Poli Alessandro , Pramotton Francesca Michela , Lavore Stefania , Rancati Ilaria , Cinquanta Mario , Vorselen Daan , Prina Elisabetta , Romano Orso Maria , Ferrari Aldo , Piel Matthieu , Cosentino Lagomarsino Marco , Maiuri Paolo 
Published: February 2024

AbstractIn eukaryotes, cytoplasmic and nuclear volumes are tightly regulated to ensure proper cell homeostasis. However, current methods to measure cytoplasmic and nuclear volumes, including confocal 3D reconstruction, have limitations, such as relying on two-dimensional projections or poor vertical resolution. Here, to overcome these limitations, we describe a method, N2FXm, to jointly measure cytoplasmic and nuclear volumes in single cultured adhering human cells, in real time, and across cell cycles. We find that this method accurately provides joint size over dynamic measurements and at different time resolutions. Moreover, by combining several experimental perturbations and analyzing a mathematical model including osmotic effects and tension, we show that N2FXm can give relevant insights on how mechanical forces exerted by the cytoskeleton on the nuclear envelope can affect the growth of nucleus volume by biasing nuclear import. Our method, by allowing for accurate joint nuclear and cytoplasmic volume dynamic measurements at different time resolutions, highlights the non-constancy of the nucleus/cytoplasm ratio along the cell cycle.
Statistics of modal condensation in nonlinear multimode fibers
Authors: Zitelli Mario , Mangini Fabio , Wabnitz Stefan 
Published: February 2024

AbstractOptical pulses traveling through multimode optical fibers encounter the influence of both linear disturbances and nonlinearity, resulting in a complex and chaotic redistribution of power among different modes. In our research, we explore the phenomenon where multimode fibers reach stable states marked by the concentration of energy into both single and multiple sub-systems. We introduce a weighted Bose-Einstein law, demonstrating its suitability in describing thermalized modal power distributions in the nonlinear regime, as well as steady-state distributions in the linear regime. We apply the law to experimental results and numerical simulations. Our findings reveal that, at power levels situated between the linear and soliton regimes, energy concentration occurs locally within higher-order modal groups before transitioning to global concentration in the fundamental mode within the soliton regime. This research broadens the application of thermodynamic principles to multimode fibers, uncovering previously unexplored optical states that exhibit characteristics akin to optical glass.
Overlay databank unlocks data-driven analyses of biomolecules for all
Authors: Kiirikki Anne M. , Antila Hanne S. , Bort Lara S. , Buslaev Pavel , Favela-Rosales Fernando , Ferreira Tiago Mendes , Fuchs Patrick F. J. , Garcia-Fandino Rebeca , Gushchin Ivan , Kav Batuhan , Kučerka Norbert , Kula Patrik , Kurki Milla , Kuzmin Alexander , Lalitha Anusha , Lolicato Fabio , Madsen Jesper J. , Miettinen Markus S. , Mingham Cedric , Monticelli Luca , Nencini Ricky , Nesterenko Alexey M. , Piggot Thomas J. , Piñeiro Ángel , Reuter Nathalie , Samantray Suman , Suárez-Lestón Fabián , Talandashti Reza , Ollila O. H. Samuli 
Published: February 2024

AbstractTools based on artificial intelligence (AI) are currently revolutionising many fields, yet their applications are often limited by the lack of suitable training data in programmatically accessible format. Here we propose an effective solution to make data scattered in various locations and formats accessible for data-driven and machine learning applications using the overlay databank format. To demonstrate the practical relevance of such approach, we present the NMRlipids Databank—a community-driven, open-for-all database featuring programmatic access to quality-evaluated atom-resolution molecular dynamics simulations of cellular membranes. Cellular membrane lipid composition is implicated in diseases and controls major biological functions, but membranes are difficult to study experimentally due to their intrinsic disorder and complex phase behaviour. While MD simulations have been useful in understanding membrane systems, they require significant computational resources and often suffer from inaccuracies in model parameters. Here, we demonstrate how programmable interface for flexible implementation of data-driven and machine learning applications, and rapid access to simulation data through a graphical user interface, unlock possibilities beyond current MD simulation and experimental studies to understand cellular membranes. The proposed overlay databank concept can be further applied to other biomolecules, as well as in other fields where similar barriers hinder the AI revolution.
Regulating protein corona on nanovesicles by glycosylated polyhydroxy polymer modification for efficient drug delivery
Authors: Miao Yunqiu , Li Lijun , Wang Ying , Wang Jiangyue , Zhou Yihan , Guo Linmiao , Zhao Yanqi , Nie Di , Zhang Yang , Zhang Xinxin , Gan Yong 
Published: February 2024

AbstractThe dynamic protein corona formed on nanocarriers has been revealed to strongly affect their in vivo behaviors. Precisely manipulating the formation of protein corona on nanocarriers may provide an alternative impetus for specific drug delivery. Herein, we explore the role of glycosylated polyhydroxy polymer-modified nanovesicles (CP-LVs) with different amino/hydroxyl ratios in protein corona formation and evolution. CP-LVs with an amino/hydroxyl ratio of approximately 0.4 (CP1-LVs) are found to efficiently suppress immunoglobulin adsorption in blood and livers, resulting in prolonged circulation. Moreover, CP1-LVs adsorb abundant tumor distinctive proteins, such as CD44 and osteopontin in tumor interstitial fluids, mediating selective tumor cell internalization. The proteins corona transformation specific to the environment appears to be affected by the electrostatic interaction between CP-LVs and proteins with diverse isoelectric points. Benefiting from surface modification-mediated protein corona regulation, paclitaxel-loaded CP1-LVs demonstrate superior antitumor efficacy to PEGylated liposomes. Our work offers a perspective on rational surface-design of nanocarriers to modulate the protein corona formation for efficient drug delivery.
One-pot redox cascade paired electrosynthesis of gamma-butyrolactone from furoic acid
Authors: Liu Shengqin , Jin Yangxin , Huang Shuquan , Zhu Qi , Shao Shan , Lam Jason Chun-Ho 
Published: February 2024

AbstractThe catalytic valorisation of biomass to afford synthetically useful small molecules is essential for sustainable biorefinery processes. Herein, we present a mild cascaded electrochemical protocol for converting furoic acid, a common biomass-derived feedstock, into a versatile platform chemical, gamma-butyrolactone. In the platinum(+)|nickel(−) electrode paired undivided cell, furoic acid is electrochemically oxidised with 84.2% selectivity to 2(5H)-furanone, the olefin of which is then hydrogenated to yield gamma-butyrolactone with 98.5% selectivity. The final gamma-butyrolactone yield is 69.1% with 38.3% Faradaic efficiency and 80.1% carbon balance when the reaction is performed with 100 mM furoic acid at 80 °C at +2.0 VAg/AgCl. Mechanistic investigation revealed the critical temperature and electrolyte pH conditions that maximise the production and protection of the key intermediate, furan radical, promoting its transition to 2(5H)-furanone rather than self-polymerising. The reaction is scalable, as 2.1 g of 98.1% pure gamma-butyrolactone is isolated through a simple solvent extraction.
Light-induced MOF synthesis enabling composite photothermal materials
Authors: Shelonchik Ofir , Lemcoff Nir , Shimoni Ran , Biswas Aritra , Yehezkel Elad , Yesodi Doron , Hod Idan , Weizmann Yossi 
Published: February 2024

AbstractMetal-organic frameworks (MOFs) are a class of porous materials known for their large surface areas. Thus, over the past few decades the development of MOFs and their applications has been a major topic of interest throughout the scientific community. However, many current conventional syntheses of MOFs are lengthy solvothermal processes carried out at elevated temperatures. Herein, we developed a rapid light-induced synthesis of MOFs by harnessing the plasmonic photothermal abilities of bipyramidal gold nanoparticles (AuBPs). The generality of the photo-induced method was demonstrated by synthesizing four different MOFs utilizing three different wavelengths (520 nm, 660 nm and 850 nm). Furthermore, by regulating light exposure, AuBPs could be embedded in the MOF or maintained in the supernatant. Notably, the AuBPs-embedded MOF (AuBP@UIO-66) retained its plasmonic properties along with the extraordinary surface area typical to MOFs. The photothermal AuBP@UIO-66 demonstrated a significant light-induced heating response that was utilized for ultrafast desorption and MOF activation.
Dual heterogeneous interfaces enhance X-ray excited persistent luminescence for low-dose 3D imaging
Authors: Lei Lei , Yi Minghao , Wang Yubin , Hua Youjie , Zhang Junjie , Prasad Paras N. , Xu Shiqing 
Published: February 2024

AbstractLanthanide-doped fluoride nanoparticles (NPs) showcase adjustable X-ray-excited persistent luminescence (XEPL), holding significant promise for applications in three-dimensional (3D) imaging through the creation of flexible X-ray detectors. However, a dangerous high X-ray irradiation dose rate and complicated heating procedure are required to generate efficient XEPL for high-resolution 3D imaging, which is attributed to a lack of strategies to significantly enhance the XEPL intensity. Here we report that the XEPL intensity of a series of lanthanide activators (Dy, Pr, Er, Tm, Gd, Tb) is greatly improved by constructing dual heterogeneous interfaces in a double-shell nanostructure. Mechanistic studies indicate that the employed core@shell@shell structure could not only passivate the surface quenchers to lower the non-radiative relaxation possibility, but also reduce the interfacial Frenkel defect formation energy leading to increase the trap concentration. By employing a NPs containing flexible film as the scintillation screen, the inside 3D electrical structure of a watch was clearly achieved based on the delayed XEPL imaging and 3D reconstruction procedure. We foresee that these findings will promote the development of advanced X-ray activated persistent fluoride NPs and offer opportunities for safer and more efficient X-ray imaging techniques in a number of scientific and practical areas.
Photolipid excitation triggers depolarizing optocapacitive currents and action potentials
Authors: Bassetto Carlos A. Z. , Pfeffermann Juergen , Yadav Rohit , Strassgschwandtner Simon , Glasnov Toma , Bezanilla Francisco , Pohl Peter 
Published: February 2024

AbstractOptically-induced changes in membrane capacitance may regulate neuronal activity without requiring genetic modifications. Previously, they mainly relied on sudden temperature jumps due to light absorption by membrane-associated nanomaterials or water. Yet, nanomaterial targeting or the required high infrared light intensities obstruct broad applicability. Now, we propose a very versatile approach: photolipids (azobenzene-containing diacylglycerols) mediate light-triggered cellular de- or hyperpolarization. As planar bilayer experiments show, the respective currents emerge from millisecond-timescale changes in bilayer capacitance. UV light changes photolipid conformation, which awards embedding plasma membranes with increased capacitance and evokes depolarizing currents. They open voltage-gated sodium channels in cells, generating action potentials. Blue light reduces the area per photolipid, decreasing membrane capacitance and eliciting hyperpolarization. If present, mechanosensitive channels respond to the increased mechanical membrane tension, generating large depolarizing currents that elicit action potentials. Membrane self-insertion of administered photolipids and focused illumination allows cell excitation with high spatiotemporal control.
Effects of open circuit immersion and vertex potential on potentiodynamic polarization scans of metallic biomaterials
Authors: Gattu V. K. , Obregon J. , Ebert W. L. , Indacochea J. E. 
Published: February 2024

AbstractElectrodes made of commercially pure titanium (CP-Ti) and a CoCrMo alloy are immersed at an open circuit in a phosphate buffer saline electrolyte at room temperature for different durations prior to electrochemical analyses. Open circuit potential measurements, electrochemical impedance spectroscopy measurements, and cyclic potentiodynamic polarization (CPP) scans are used to assess the impact of the immersion time on derived property values. Stable passivation layers formed on both materials during immersion. The corrosion potentials determined from the anodic legs of CPP scans become more cathodic, and the corrosion currents decrease to lower values after longer immersion times. Measured currents indicate the layers formed on CP-Ti stabilize during forward anodic scans and persist to the vertex potential, whereas passivation breakdown occurs during anodic scans with CoCrMo with active corrosion at voltages up to the vertex potential. The characteristics of the return cathodic legs of CPP scans represent the surface conditions at the vertex potential: characteristic corrosion property values derived from the test responses represent passive surfaces on CP-Ti and leached surfaces on CoCrMo rather than intrinsic properties of those materials.
Potent induction of humoral and cellular immunity after bivalent BA.4/5 mRNA vaccination in dialysis patients
Authors: Bronder Saskia , Mihm Janine , Urschel Rebecca , Klemis Verena , Schmidt Tina , Marx Stefanie , Abu-Omar Amina , Hielscher Franziska , Guckelmus Candida , Widera Marek , Sester Urban , Sester Martina 
Published: February 2024

AbstractKnowledge on immunogenicity of the bivalent Omicron BA.4/5 vaccine in dialysis patients and the effect of a previous infection is limited. Therefore, vaccine-induced humoral and cellular immunity was analyzed in dialysis patients and immunocompetent controls with and without prior infection. In an observational study, 33 dialysis patients and 58 controls matched for age, sex and prior infection status were recruited. Specific IgG, neutralizing antibody activity and cellular immunity towards the spike-antigen from parental SARS-CoV-2 and Omicron-subvariants BA.1, BA.2 and BA.4/5 were analyzed before and 13-18 days after vaccination. The bivalent vaccine led to a significant induction of IgG, neutralizing titers, and specific CD4+ and CD8+ T-cell levels. Neutralizing activity towards the parental strain was higher than towards the Omicron-subvariants, whereas specific T-cell levels towards parental spike and Omicron-subvariants did not differ indicating substantial cross-reactivity. Dialysis patients with prior infection had significantly higher spike-specific CD4+ T-cell levels with lower CTLA-4 expression compared to infection-naive patients. When compared to controls, no differences were observed between infection-naive individuals. Among convalescent individuals, CD4+ T-cell levels were higher in patients and neutralizing antibodies were higher in controls. Vaccination was overall well tolerated in both dialysis patients and controls with significantly less adverse events among patients. In conclusion, our study did not provide any evidence for impaired immunogenicity of the bivalent Omicron BA.4/5 vaccine in dialysis patients. Unlike in controls, previous infection of patients was even associated with higher levels of spike-specific CD4+ T cells, which may reflect prolonged encounter with antigen during infection.
A molecular toolkit of cross-feeding strains for engineering synthetic yeast communities
Authors: Peng Huadong , Darlington Alexander P. S. , South Eric J. , Chen Hao-Hong , Jiang Wei , Ledesma-Amaro Rodrigo 
Published: February 2024

AbstractEngineered microbial consortia often have enhanced system performance and robustness compared with single-strain biomanufacturing production platforms. However, few tools are available for generating co-cultures of the model and key industrial host Saccharomyces cerevisiae. Here we engineer auxotrophic and overexpression yeast strains that can be used to create co-cultures through exchange of essential metabolites. Using these strains as modules, we engineered two- and three-member consortia using different cross-feeding architectures. Through a combination of ensemble modelling and experimentation, we explored how cellular (for example, metabolite production strength) and environmental (for example, initial population ratio, population density and extracellular supplementation) factors govern population dynamics in these systems. We tested the use of the toolkit in a division of labour biomanufacturing case study and show that it enables enhanced and tuneable antioxidant resveratrol production. We expect this toolkit to become a useful resource for a variety of applications in synthetic ecology and biomanufacturing.