bluuebunny/crossref_metadata_2025_split huggingface dataset:
BPIFB4 and its longevity-associated haplotype protect from cardiac ischemia in humans and mice
Authors: Cattaneo Monica , Aleksova Aneta , Malovini Alberto , Avolio Elisa , Thomas Anita , Alvino Valeria Vincenza , Kilcooley Michael , Pieronne-Deperrois Marie , Ouvrard-Pascaud Antoine , Maciag Anna , Spinetti Gaia , Kussauer Sophie , Lemcke Heiko , Skorska Anna , Vasudevan Praveen , Castiglione Stefania , Raucci Angela , David Robert , Richard Vincent , Beltrami Antonio Paolo , Madeddu Paolo , Puca Annibale Alessandro 
Published: August 2023

AbstractLong-living individuals (LLIs) escape age-related cardiovascular complications until the very last stage of life. Previous studies have shown that a Longevity-Associated Variant (LAV) of the BPI Fold Containing Family B Member 4 (BPIFB4) gene correlates with an extraordinarily prolonged life span. Moreover, delivery of the LAV-BPIFB4 gene exerted therapeutic action in murine models of atherosclerosis, limb ischemia, diabetic cardiomyopathy, and aging. We hypothesize that downregulation of BPIFB4 expression marks the severity of coronary artery disease (CAD) in human subjects, and supplementation of the LAV-BPIFB4 protects the heart from ischemia. In an elderly cohort with acute myocardial infarction (MI), patients with three-vessel CAD were characterized by lower levels of the natural logarithm (Ln) of peripheral blood BPIFB4 (p = 0.0077). The inverse association between Ln BPIFB4 and three-vessel CAD was confirmed by logistic regression adjusting for confounders (Odds Ratio = 0.81, p = 0.0054). Moreover, in infarcted mice, a single administration of LAV-BPIFB4 rescued cardiac function and vascularization. In vitro studies showed that LAV-BPIFB4 protein supplementation exerted chronotropic and inotropic actions on induced pluripotent stem cell (iPSC)-derived cardiomyocytes. In addition, LAV-BPIFB4 inhibited the pro-fibrotic phenotype in human cardiac fibroblasts. These findings provide a strong rationale and proof of concept evidence for treating CAD with the longevity BPIFB4 gene/protein.
Diversity, distribution and intrinsic extinction vulnerability of exploited marine bivalves
Authors: Huang Shan , Edie Stewart M. , Collins Katie S. , Crouch Nicholas M. A. , Roy Kaustuv , Jablonski David 
Published: August 2023

AbstractMarine bivalves are important components of ecosystems and exploited by humans for food across the world, but the intrinsic vulnerability of exploited bivalve species to global changes is poorly known. Here, we expand the list of shallow-marine bivalves known to be exploited worldwide, with 720 exploited bivalve species added beyond the 81 in the United Nations FAO Production Database, and investigate their diversity, distribution and extinction vulnerability using a metric based on ecological traits and evolutionary history. The added species shift the richness hotspot of exploited species from the northeast Atlantic to the west Pacific, with 55% of bivalve families being exploited, concentrated mostly in two major clades but all major body plans. We find that exploited species tend to be larger in size, occur in shallower waters, and have larger geographic and thermal ranges—the last two traits are known to confer extinction-resistance in marine bivalves. However, exploited bivalve species in certain regions such as the tropical east Atlantic and the temperate northeast and southeast Pacific, are among those with high intrinsic vulnerability and are a large fraction of regional faunal diversity. Our results pinpoint regional faunas and specific taxa of likely concern for management and conservation.
Data-driven predictions of complex organic mixture permeation in polymer membranes
Authors: Lee Young Joo , Chen Lihua , Nistane Janhavi , Jang Hye Youn , Weber Dylan J. , Scott Joseph K. , Rangnekar Neel D. , Marshall Bennett D. , Li Wenjun , Johnson J. R. , Bruno Nicholas C. , Finn M. G. , Ramprasad Rampi , Lively Ryan P. 
Published: August 2023

AbstractMembrane-based organic solvent separations are rapidly emerging as a promising class of technologies for enhancing the energy efficiency of existing separation and purification systems. Polymeric membranes have shown promise in the fractionation or splitting of complex mixtures of organic molecules such as crude oil. Determining the separation performance of a polymer membrane when challenged with a complex mixture has thus far occurred in an ad hoc manner, and methods to predict the performance based on mixture composition and polymer chemistry are unavailable. Here, we combine physics-informed machine learning algorithms (ML) and mass transport simulations to create an integrated predictive model for the separation of complex mixtures containing up to 400 components via any arbitrary linear polymer membrane. We experimentally demonstrate the effectiveness of the model by predicting the separation of two crude oils within 6-7% of the measurements. Integration of ML predictors of diffusion and sorption properties of molecules with transport simulators enables for the rapid screening of polymer membranes prior to physical experimentation for the separation of complex liquid mixtures.
Deep transfer learning for inter-chain contact predictions of transmembrane protein complexes
Authors: Lin Peicong , Yan Yumeng , Tao Huanyu , Huang Sheng-You 
Published: August 2023

AbstractMembrane proteins are encoded by approximately a quarter of human genes. Inter-chain residue-residue contact information is important for structure prediction of membrane protein complexes and valuable for understanding their molecular mechanism. Although many deep learning methods have been proposed to predict the intra-protein contacts or helix-helix interactions in membrane proteins, it is still challenging to accurately predict their inter-chain contacts due to the limited number of transmembrane proteins. Addressing the challenge, here we develop a deep transfer learning method for predicting inter-chain contacts of transmembrane protein complexes, named DeepTMP, by taking advantage of the knowledge pre-trained from a large data set of non-transmembrane proteins. DeepTMP utilizes a geometric triangle-aware module to capture the correct inter-chain interaction from the coevolution information generated by protein language models. DeepTMP is extensively evaluated on a test set of 52 self-associated transmembrane protein complexes, and compared with state-of-the-art methods including DeepHomo2.0, CDPred, GLINTER, DeepHomo, and DNCON2_Inter. It is shown that DeepTMP considerably improves the precision of inter-chain contact prediction and outperforms the existing approaches in both accuracy and robustness.
Structural basis for negative regulation of the Escherichia coli maltose system
Authors: Wu Yuang , Sun Yue , Richet Evelyne , Han Zhifu , Chai Jijie 
Published: August 2023

AbstractProteins from the signal transduction ATPases with numerous domains (STAND) family are known to play an important role in innate immunity. However, it remains less well understood how they function in transcriptional regulation. MalT is a bacterial STAND that controls the Escherichia coli maltose system. Inactive MalT is sequestered by different inhibitory proteins such as MalY. Here, we show that MalY interacts with one oligomerization interface of MalT to form a 2:2 complex. MalY represses MalT activity by blocking its oligomerization and strengthening ADP-mediated MalT autoinhibition. A loop region N-terminal to the nucleotide-binding domain (NBD) of MalT has a dual role in mediating MalT autoinhibition and activation. Structural comparison shows that ligand-binding induced oligomerization is required for stabilizing the C-terminal domains and conferring DNA-binding activity. Together, our study reveals the mechanism whereby a prokaryotic STAND is inhibited by a repressor protein and offers insights into signaling by STAND transcription activators.
In situ observation of coalescence of nuclei in colloidal crystal-crystal transitions
Authors: Peng Yi , Li Wei , Still Tim , Yodh Arjun G. , Han Yilong 
Published: August 2023

AbstractCoalescence of nuclei in phase transitions significantly influences the transition rate and the properties of product materials, but these processes occur rapidly and are difficult to observe at the microscopic scale. Here, we directly image the coalescence of nuclei with single particle resolution during the crystal-crystal transition from a multilayer square to triangular lattices. The coalescence process exhibits three similar stages across a variety of scenarios: coupled growth of two nuclei, their attachment, and relaxation of the coalesced nucleus. The kinetics vary with nucleus size, interface, and lattice orientation; the kinetics include acceleration of nucleus growth, small nucleus liquefaction, and generation/annihilation of defects. Related mechanisms, such as strain induced by nucleus growth and the lower energy of liquid-crystal versus crystal-crystal interfaces, appear to be common to both atomic and colloidal crystals.
Non-destructive erosive wear monitoring of multi-layer coatings using AI-enabled differential split ring resonator based system
Authors: Balasubramanian Vishal , Niksan Omid , Jain Mandeep C. , Golovin Kevin , Zarifi Mohammad H. 
Published: August 2023

AbstractUnprotected surfaces where a coating has been removed due to erosive wear can catastrophically fail from corrosion, mechanical impingement, or chemical degradation, leading to major safety hazards, financial losses, and even fatalities. As a preventive measure, industries including aviation, marine and renewable energy are actively seeking solutions for the real-time and autonomous monitoring of coating health. This work presents a real-time, non-destructive inspection system for the erosive wear detection of coatings, by leveraging artificial intelligence enabled microwave differential split ring resonator sensors, integrated to a smart, embedded monitoring circuitry. The differential microwave system detects the erosion of coatings through the variations of resonant characteristics of the split ring resonators, located underneath the coating layer while compensating for the external noises. The system’s response and performance are validated through erosive wear tests on single- and multi-layer polymeric coatings up to a thickness of 2.5 mm. The system is capable of distinguishing which layer is being eroded (for multi-layer coatings) and estimating the wear depth and rate through its integration with a recurrent neural network-based predictive analytics model. The synergistic combination of artificial intelligence enabled microwave resonators and a smart monitoring system further demonstrates its practicality for real-world coating erosion applications.
Word and bit line operation of a 1 × 1 μm2 superconducting vortex-based memory
Authors: Golod Taras , Morlet-Decarnin Lise , Krasnov Vladimir M. 
Published: August 2023

AbstractThe lack of dense random access memory is one of the main bottlenecks for the creation of a digital superconducting computer. In this work we study experimentally vortex-based superconducting memory cells. Three main results are obtained. First, we test scalability and demonstrate that the cells can be straightforwardly miniaturized to submicron sizes. Second, we emphasize the importance of conscious geometrical engineering. In the studied devices we introduce an asymmetric easy track for vortex motion and show that it enables a controllable manipulation of vortex states. Finally, we perform a detailed analysis of word and bit line operation of a 1 × 1 μm2 cell. High-endurance, non-volatile operation at zero magnetic field is reported. Remarkably, we observe that the combined word and bit line threshold current is significantly reduced compared to the bare word-line operation. This could greatly improve the selectivity of individual cell addressing in a multi-cell RAM. The achieved one square micron area is an important milestone and a significant step forward towards creation of a dense cryogenic memory.
AAV-mediated base-editing therapy ameliorates the disease phenotypes in a mouse model of retinitis pigmentosa
Authors: Wu Yidong , Wan Xiaoling , Zhao Dongdong , Chen Xuxu , Wang Yujie , Tang Xinxin , Li Ju , Li Siwei , Sun Xiaodong , Bi Changhao , Zhang Xueli 
Published: August 2023

AbstractBase editing technology is an ideal solution for treating pathogenic single-nucleotide variations (SNVs). No gene editing therapy has yet been approved for eye diseases, such as retinitis pigmentosa (RP). Here, we show, in the rd10 mouse model, which carries an SNV identified as an RP-causing mutation in human patients, that subretinal delivery of an optimized dual adeno-associated virus system containing the adenine base editor corrects the pathogenic SNV in the neuroretina with up to 49% efficiency. Light microscopy showed that a thick and robust outer nuclear layer (photoreceptors) was preserved in the treated area compared with the thin, degenerated outer nuclear layer without treatment. Substantial electroretinogram signals were detected in treated rd10 eyes, whereas control treated eyes showed minimal signals. The water maze experiment showed that the treatment substantially improved vision-guided behavior. Together, we construct and validate a translational therapeutic solution for the treatment of RP in humans. Our findings might accelerate the development of base-editing based gene therapies.
Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish
Authors: García-López Juan P. , Grimaldi Alexandre , Chen Zelin , Meneses Claudio , Bravo-Tello Karina , Bresciani Erica , Banderas Alvaro , Burgess Shawn M. , Hernández Pedro P. , Feijoo Carmen G. 
Published: August 2023

AbstractThe current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins, and which exert non-overlapping functions. However, there is less known about the function and phenotype of ontogenetically distinct neutrophil populations. In this work, using a photoconvertible transgenic zebrafish line; Tg(mpx:Dendra2), we selectively label rostral blood island-derived and caudal hematopoietic tissue-derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single-cell expression profiles of both neutrophil populations at steady state we show that rostral neutrophils show highercsf3bexpression and migration capacity than caudal neutrophils. Upon injury, both populations share a core transcriptional profile as well as subset-specific transcriptional signatures. Accordingly, both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly, caudal neutrophils respond heterogeneously. Collectively, our results reveal that co-existing neutrophils populations with ontogenically distinct origin display functional differences.
Spatial organization of the mouse retina at single cell resolution by MERFISH
Authors: Choi Jongsu , Li Jin , Ferdous Salma , Liang Qingnan , Moffitt Jeffrey R. , Chen Rui 
Published: August 2023

AbstractThe visual signal processing in the retina requires the precise organization of diverse neuronal types working in concert. While single-cell omics studies have identified more than 120 different neuronal subtypes in the mouse retina, little is known about their spatial organization. Here, we generated the single-cell spatial atlas of the mouse retina using multiplexed error-robust fluorescence in situ hybridization (MERFISH). We profiled over 390,000 cells and identified all major cell types and nearly all subtypes through the integration with reference single-cell RNA sequencing (scRNA-seq) data. Our spatial atlas allowed simultaneous examination of nearly all cell subtypes in the retina, revealing 8 previously unknown displaced amacrine cell subtypes and establishing the connection between the molecular classification of many cell subtypes and their spatial arrangement. Furthermore, we identified spatially dependent differential gene expression between subtypes, suggesting the possibility of functional tuning of neuronal types based on location.
Embedded nano spin sensor for in situ probing of gas adsorption inside porous organic frameworks
Authors: Zhang Jie , Liu Linshan , Zheng Chaofeng , Li Wang , Wang Chunru , Wang Taishan 
Published: August 2023

AbstractSpin-based sensors have attracted considerable attention owing to their high sensitivities. Herein, we developed a metallofullerene-based nano spin sensor to probe gas adsorption within porous organic frameworks. For this, spin-active metallofullerene, Sc3C2@C80, was selected and embedded into a nanopore of a pyrene-based covalent organic framework (Py-COF). Electron paramagnetic resonance (EPR) spectroscopy recorded the EPR signals of Sc3C2@C80 within Py-COF after adsorbing N2, CO, CH4, CO2, C3H6, and C3H8. Results indicated that the regularly changing EPR signals of embedded Sc3C2@C80 were associated with the gas adsorption performance of Py-COF. In contrast to traditional adsorption isotherm measurements, this implantable nano spin sensor could probe gas adsorption and desorption with in situ, real-time monitoring. The proposed nano spin sensor was also employed to probe the gas adsorption performance of a metal–organic framework (MOF-177), demonstrating its versatility. The nano spin sensor is thus applicable for quantum sensing and precision measurements.
Ultra-thin lithium aluminate spinel ferrite films with perpendicular magnetic anisotropy and low damping
Authors: Zheng Xin Yu , Channa Sanyum , Riddiford Lauren J. , Wisser Jacob J. , Mahalingam Krishnamurthy , Bowers Cynthia T. , McConney Michael E. , N’Diaye Alpha T. , Vailionis Arturas , Cogulu Egecan , Ren Haowen , Galazka Zbigniew , Kent Andrew D. , Suzuki Yuri 
Published: August 2023

AbstractUltra-thin films of low damping ferromagnetic insulators with perpendicular magnetic anisotropy have been identified as critical to advancing spin-based electronics by significantly reducing the threshold for current-induced magnetization switching while enabling new types of hybrid structures or devices. Here, we have developed a new class of ultra-thin spinel structure Li0.5Al1.0Fe1.5O4 (LAFO) films on MgGa2O4 (MGO) substrates with: 1) perpendicular magnetic anisotropy; 2) low magnetic damping and 3) the absence of degraded or magnetic dead layers. These films have been integrated with epitaxial Pt spin source layers to demonstrate record low magnetization switching currents and high spin-orbit torque efficiencies. These LAFO films on MGO thus combine all of the desirable properties of ferromagnetic insulators with perpendicular magnetic anisotropy, opening new possibilities for spin based electronics.
Two-dimensional MXene membranes with biomimetic sub-nanochannels for enhanced cation sieving
Authors: Xu Rongming , Kang Yuan , Zhang Weiming , Pan Bingcai , Zhang Xiwang 
Published: August 2023

AbstractMembranes with high ion permeability and selectivity are of considerable interest for sustainable water treatment, resource extraction and energy storage. Herein, inspired by K+ channel of streptomyces A (KcsA K+), we have constructed cation sieving membranes using MXene nanosheets and Ethylenediaminetetraacetic acid (EDTA) molecules as building blocks. Numerous negatively charged oxygen atoms of EDTA molecules and 6.0 Å two-dimensional (2D) sub-nanochannel of MXene nanosheets enable biomimetic channel size, chemical groups and tunable charge density for the resulting membranes. The membranes show the capability to recognize monovalent/divalent cations, achieving excellent K+/Mg2+ selectivity of 121.2 using mixed salt solution as the feed, which outperforms other reported membranes under similar testing conditions and transcends the current upper limit. Characterization and simulations indicate that the cation recognition effect of EDTA and partial dehydration effects play critical roles in cations selective sieving and increasing the local charge density within the sub-nanochannel significantly improves cation selectivity. Our findings provide a theoretical basis for ions transport in sub-nanochannels and an alternative strategy for design ions separation membranes.
Facile synthesis of PEG-glycerol coated bimetallic FePt nanoparticle as highly efficient electrocatalyst for methanol oxidation
Authors: Baruah Sarmistha , Rani Barkha , Sahu Niroj Kumar 
Published: August 2023

AbstractDirect methanol fuel cell (DMFC) has shown excellent growth as an alternative candidate for energy sources to substitute fossil fuels. However, developing cost-effective and highly durable catalysts with a facile synthesis method is still challenging. In this prospect, a facile strategy is used for the preparation of hydrophilic Fe-Pt nanoparticle catalyst via a polyethylene glycol-glycerol route to utilize the advantages of nanostructured surfaces. The synthesized electrocatalysts are characterized by XRD, XPS, TEM, EDS and FTIR to confirm their structure, morphology, composition, and surface functionalization. The performance of the catalysts towards methanol oxidation reaction (MOR) was investigated by cyclic voltammetry and chronoamperometry in both acidic and alkaline media. The Fe-Pt bimetallic catalyst exhibits better current density of 36.36 mA cm−2 in acidic medium than in alkali medium (12.52 mA cm−2). However, the high If/Ib ratio of 1.9 in alkali medium signifies better surface cleaning/regenerating capability of catalyst. Moreover, the catalyst possessed superior cyclic stability of ~ 80% in the alkaline electrolyte which is 1.6 times higher than in the acidic one. The better stability and poison tolerance capacity of catalyst in alkaline media is attributed to the OH− ions provided by the electrolyte which interact with the metal species to form M-(OH)x and reversibly release OH− and regenerate metal surface for further oxidation reactions. But synergism provided by Fe and Pt gives better activity in acidic electrolyte as Pt is favourable catalyst for dehydrogenation of methanol in acidic medium. This study will be useful for designing anodic electrocatalysts for MOR.
Infrared optical signature reveals the source–dependency and along–transport evolution of dust mineralogy as shown by laboratory study
Authors: Di Biagio Claudia , Doussin Jean-François , Cazaunau Mathieu , Pangui Edouard , Cuesta Juan , Sellitto Pasquale , Ródenas Milagros , Formenti Paola 
Published: August 2023

AbstractAdvancing knowledge of the mineralogical composition of dust is key for understanding and predicting its climate and environmental impacts. The variability of dust mineralogy from one source to another and its evolution during atmospheric transport is not measured at large scale. In this study we use laboratory measurements to demonstrate that the extinction signature of suspended dust aerosols in the 740 − 1250 cm−1 atmospheric window can be used to derive dust mineralogy in terms of the main infrared − active minerals, namely quartz, clays, feldspars and calcite. Various spectral signatures in dust extinction enable to distinguish between multiple global sources with changing composition, whereas modifications of the dust extinction spectra with time inform on size − dependent particles mineralogy changes during transport. The present study confirms that spectral and hyperspectral infrared remote sensing observations offer great potential for elucidating the size − segregated mineralogy of airborne dust at regional and global scales.