bluuebunny/crossref_metadata_2025_split huggingface dataset:
Layered Green and Ampt Infiltration With Redistribution
Authors: La Follette Peter , Ogden Fred L. , Jan Ahmad 
Published: April 2023

AbstractNumerical solution of the one‐dimensional Richards equation (RE) accurately partitions precipitation into infiltration and runoff in capillary dominated soils. However, its application sometimes requires significant computational effort and presents reliability challenges. The Green and Ampt (G&A) approach represents a conservative and efficient method to calculate one‐dimensional infiltration but is limited to deep, well drained, uniform, non‐layered soils for a single rainfall event. The original G&A model and subsequent advancements represent wetting fronts as discrete objects, rather than discretizing the model domain in space, yielding a computationally simpler model than the RE. This paper describes an extension of the G&A method into layered soils on a continuous basis that we call Layered Green and Ampt with Redistribution (LGAR). Assumptions employed in the derivation include: uniform soil hydraulic properties within layers, single‐valued capillary head at the interface between soil layers, and no influence of groundwater table on soil moisture. Wetting fronts advance due to the combined effects of gravity and wetting front capillary drive in a layered soil profile. Results of multi‐month continuous LGAR simulations of infiltration using forcing and soil hydraulic data from USDA SCAN sites are compared against infiltration calculated using the HYDRUS‐1D RE solver using standard metrics. The assumptions employed in deriving the LGAR method limit its application to situations where cumulative potential evapotranspiration is greater than cumulative precipitation, typical of arid or semi‐arid conditions. LGAR is a mass‐conservative, computationally efficient, reliable and reasonably accurate method for simulating infiltration over extended time periods compared to the numerical solution of the RE in layered soils in arid and semi‐arid regions.
Neural‐Network Parameterization of Subgrid Momentum Transport in the Atmosphere
Authors: Yuval Janni , O’Gorman Paul A. 
Published: April 2023

AbstractAttempts to use machine learning to develop atmospheric parameterizations have mainly focused on subgrid effects on temperature and moisture, but subgrid momentum transport is also important in simulations of the atmospheric circulation. Here, we use neural networks to develop a subgrid momentum transport parameterization that learns from coarse‐grained output of a high‐resolution atmospheric simulation in an idealized aquaplanet domain. We show that substantial subgrid momentum transport occurs due to convection. The neural‐network parameterization has skill in predicting momentum fluxes associated with convection, although its skill for subgrid momentum fluxes is lower compared to subgrid energy and moisture fluxes. The parameterization conserves momentum, and when implemented in the same atmospheric model at coarse resolution it leads to stable simulations and tends to reduce wind biases, although it over‐corrects for one configuration tested. Overall, our results show that it is challenging to predict subgrid momentum fluxes and that machine‐learning momentum parameterization gives promising results.
From Planning to Implementation: Developing an ACE Screening Protocol in a Rural Integrated Primary Care Clinic Serving Latino Children
Authors: Rosado Javier I. , Reyes Elena , Montgomery Jordan , Wang Yuxia , Malloy Conor , Simpson-O’Reggio Anna M. 
Published: April 2023

Objective: The purpose of the study was to implement a comprehensive adverse childhood experiences (ACEs) screening protocol in a rural Integrated Primary Care Clinic serving Latino Children utilizing implementation science as a framework. Methods: The Exploration, Preparation, Implementation, Sustainment (EPIS) framework was utilized to guide and evaluate the implementation. There were 2,347 children who were screened with the developed protocol which included screening for ACEs, psychosocial problems, adolescent depression, and parental depression. Several implementation outcomes were collected and are reported, including a list of screening barriers and adaptations, a list of developed staff training, a clinician stakeholder survey and focus group, and a patient stakeholder survey. Results: Clinicians reported being satisfied with the protocol and indicated that screenings provided new clinical information, changed their clinical care and helped to inform the medical needs of patients. Barriers included inadequate time to complete screenings and over-screening for prevalent stressors in the community. Conclusions: Implementation science provides a reliable framework for the implementation of a comprehensive ACE screening process by identifying the necessary conditions for high-quality implementation. With the appropriate resources in place, screenings are possible and enhance patient care. More attention is needed to identify primary care interventions for ACEs. Implications for Impact Statement Implementation science provides models for implementation that can improve the uptake of ACE screenings in Pediatric Primary Care settings. Integrated Care presents a comprehensive interdisciplinary approach that aids in providing appropriate responses to positive screenings.
cmtj: Simulation package for analysis of multilayer spintronic devices
Authors: Mojsiejuk Jakub , Ziętek Sławomir , Grochot Krzysztof , Skowroński Witold , Stobiecki Tomasz 
Published: April 2023

AbstractWe present cmtj—a simulation package for large-scale macrospin analysis of multilayer spintronics devices. Apart from conventional simulations, such as magnetoresistance and magnetisation hysteresis loops, cmtj implements a mathematical model of dynamic experimental techniques commonly used for spintronics devices characterisation, for instance: spin diode ferromagnetic resonance, pulse-induced microwave magnetometry, or harmonic Hall voltage measurements. We find that macrospin simulations offer a satisfactory level of agreement, demonstrated by a variety of examples. As a unified simulation package, cmtj aims to accelerate wide-range parameter search in the process of optimising spintronics devices.
Laboratory studies of ship hull’s material degradation scenarios to optimize a cathodic protection modelling software
Authors: Minola Marie , Roche Virginie , Rouve Laure-Line , Pinaud Olivier , Chadebec Olivier , Nale Michaël , Goëau Cédric , Lepretre Jean-Claude 
Published: April 2023

AbstractThis work presents the experimental research carried out to optimize a current computational software “CorOns”, to obtain a better ship hull electrical signature modelling. Middle-term ageing (597 days) of anticorrosion paints, highlights the appearance of additional corrosion processes, despite an absence of visual defects. A specific model is proposed for an aged surface in seawater based on Electrochemical Impedance Spectroscopy (“EIS”) data analysis. We also investigate the impact of the interruption of cathodic protection on the corrosion process, with the objective of modelling the electrical signature in real conditions that could be encountered. These studies’ interruption of the cathodic protection during 24 h, do not seem to have an impact on the current densities. However, EIS studies, highlight that the protection interruptions damage the calcareous deposit, well-known for it is protective effect once formed.
An engineered HIV-1 Gag-based VLP displaying high antigen density induces strong antibody-dependent functional immune responses
Authors: Tarrés-Freixas Ferran , Aguilar-Gurrieri Carmen , Rodríguez de la Concepción María Luisa , Urrea Victor , Trinité Benjamin , Ortiz Raquel , Pradenas Edwards , Blanco Pau , Marfil Sílvia , Molinos-Albert Luis Manuel , Barajas Ana , Pons-Grífols Anna , Ávila-Nieto Carlos , Varela Ismael , Cervera Laura , Gutiérrez-Granados Sònia , Segura María Mercedes , Gòdia Francesc , Clotet Bonaventura , Carrillo Jorge , Blanco Julià 
Published: April 2023

AbstractAntigen display on the surface of Virus-Like Particles (VLPs) improves immunogenicity compared to soluble proteins. We hypothesised that immune responses can be further improved by increasing the antigen density on the surface of VLPs. In this work, we report an HIV-1 Gag-based VLP platform engineered to maximise the presence of antigen on the VLP surface. An HIV-1 gp41-derived protein (Min), including the C-terminal part of gp41 and the transmembrane domain, was fused to HIV-1 Gag. This resulted in high-density MinGag-VLPs. These VLPs demonstrated to be highly immunogenic in animal models using either a homologous (VLP) or heterologous (DNA/VLP) vaccination regimen, with the latter yielding 10-fold higher anti-Gag and anti-Min antibody titres. Despite these strong humoral responses, immunisation with MinGag-VLPs did not induce neutralising antibodies. Nevertheless, antibodies were predominantly of an IgG2b/IgG2c profile and could efficiently bind CD16-2. Furthermore, we demonstrated that MinGag-VLP vaccination could mediate a functional effect and halt the progression of a Min-expressing tumour cell line in an in vivo mouse model.
Electrochemical synthesis of propylene from carbon dioxide on copper nanocrystals
Authors: Gao Jing , Bahmanpour Alimohammad , Kröcher Oliver , Zakeeruddin Shaik M. , Ren Dan , Grätzel Michael 
Published: April 2023

AbstractThe conversion of carbon dioxide to value-added products using renewable electricity would potentially help to address current climate concerns. The electrochemical reduction of carbon dioxide to propylene, a critical feedstock, requires multiple C–C coupling steps with the transfer of 18 electrons per propylene molecule, and hence is kinetically sluggish. Here we present the electrosynthesis of propylene from carbon dioxide on copper nanocrystals with a peak geometric current density of −5.5 mA cm−2. The metallic copper nanocrystals formed from CuCl precursor present preponderant Cu(100) and Cu(111) facets, likely to favour the adsorption of key *C1 and *C2 intermediates. Strikingly, the production rate of propylene drops substantially when carbon monoxide is used as the reactant. From the electrochemical reduction of isotope-labelled carbon dioxide mixed with carbon monoxide, we infer that the key step for propylene formation is probably the coupling between adsorbed/molecular carbon dioxide or carboxyl with the *C2 intermediates that are involved in the ethylene pathway.
Experimental characterization of de novo proteins and their unevolved random-sequence counterparts
Authors: Heames Brennen , Buchel Filip , Aubel Margaux , Tretyachenko Vyacheslav , Loginov Dmitry , Novák Petr , Lange Andreas , Bornberg-Bauer Erich , Hlouchová Klára 
Published: April 2023

AbstractDe novo gene emergence provides a route for new proteins to be formed from previously non-coding DNA. Proteins born in this way are considered random sequences and typically assumed to lack defined structure. While it remains unclear how likely a de novo protein is to assume a soluble and stable tertiary structure, intersecting evidence from random sequence and de novo-designed proteins suggests that native-like biophysical properties are abundant in sequence space. Taking putative de novo proteins identified in human and fly, we experimentally characterize a library of these sequences to assess their solubility and structure propensity. We compare this library to a set of synthetic random proteins with no evolutionary history. Bioinformatic prediction suggests that de novo proteins may have remarkably similar distributions of biophysical properties to unevolved random sequences of a given length and amino acid composition. However, upon expression in vitro, de novo proteins exhibit moderately higher solubility which is further induced by the DnaK chaperone system. We suggest that while synthetic random sequences are a useful proxy for de novo proteins in terms of structure propensity, de novo proteins may be better integrated in the cellular system than random expectation, given their higher solubility.
Vaccine plus microbicide effective in preventing vaginal SIV transmission in macaques
Authors: Rahman Mohammad Arif , Bissa Massimiliano , Silva de Castro Isabela , Helmold Hait Sabrina , Stamos James D. , Bhuyan Farzana , Hunegnaw Ruth , Sarkis Sarkis , Gutowska Anna , Doster Melvin N. , Moles Ramona , Hoang Tanya , Miller Jenkins Lisa M. , Appella Ettore , Venzon David J. , Choo-Wosoba Hyoyoung , Cardozo Timothy , Baum Marc M. , Appella Daniel H. , Robert-Guroff Marjorie , Franchini Genoveffa 
Published: April 2023

AbstractThe human immunodeficiency virus epidemic continues in sub-Saharan Africa, and particularly affects adolescent girls and women who have limited access to antiretroviral therapy. Here we report that the risk of vaginal simian immunodeficiency virus (SIV)mac251 acquisition is reduced by more than 90% using a combination of a vaccine comprising V1-deleted (V2 enhanced) SIV envelope immunogens with topical treatment of the zinc-finger inhibitor SAMT-247. Following 14 weekly intravaginal exposures to the highly pathogenic SIVmac251, 80% of a cohort of 20 macaques vaccinated and treated with SAMT-247 remained uninfected. In an arm of 18 vaccinated-only animals without microbicide, 40% of macaques remained uninfected. The combined SAMT-247/vaccine regimen was significantly more effective than vaccination alone. By analysing immune correlates of protection, we show that, by increasing zinc availability, SAMT-247 increases natural killer cytotoxicity and monocyte efferocytosis, and decreases T-cell activation to augment vaccine-induced protection.
Acetylation of histone H2B marks active enhancers and predicts CBP/p300 target genes
Authors: Narita Takeo , Higashijima Yoshiki , Kilic Sinan , Liebner Tim , Walter Jonas , Choudhary Chunaram 
Published: April 2023

AbstractChromatin features are widely used for genome-scale mapping of enhancers. However, discriminating active enhancers from other cis-regulatory elements, predicting enhancer strength and identifying their target genes is challenging. Here we establish histone H2B N-terminus multisite lysine acetylation (H2BNTac) as a signature of active enhancers. H2BNTac prominently marks candidate active enhancers and a subset of promoters and discriminates them from ubiquitously active promoters. Two mechanisms underlie the distinct H2BNTac specificity: (1) unlike H3K27ac, H2BNTac is specifically catalyzed by CBP/p300; (2) H2A–H2B, but not H3–H4, are rapidly exchanged through transcription-induced nucleosome remodeling. H2BNTac-positive candidate enhancers show a high validation rate in orthogonal enhancer activity assays and a vast majority of endogenously active enhancers are marked by H2BNTac and H3K27ac. Notably, H2BNTac intensity predicts enhancer strength and outperforms current state-of-the-art models in predicting CBP/p300 target genes. These findings have broad implications for generating fine-grained enhancer maps and modeling CBP/p300-dependent gene regulation.
Transport of Designed Ankyrin Repeat Proteins through reconstituted human bronchial epithelia and protection against SARS-CoV-2
Authors: Künzi Lisa , Ryter Sarah , Cornelius Andreas , Leni Zaira , Baumlin Nathalie , Salathe Matthias , Walser Marcel , Engler Olivier , Geiser Marianne 
Published: April 2023

AbstractClinical studies have proven antiviral effectiveness of treatment with a Designed Ankyrin Repeat Protein (DARPin) specific against the spike protein of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2). More information on transport mechanisms and efficiency to the site of action is desirable. Transepithelial migration through air–liquid interface (ALI) cultures of reconstituted human bronchial epithelia (HBE) was assessed by Enzyme-Linked Immunosorbent Assays and Confocal Laser Scanning Microscopy for different DARPin designs in comparison to a monoclonal antibody. Antiviral efficacy against authentic SARS-CoV-2, applied apically on HBE, was investigated based on viral titers and genome equivalents, after administration of therapeutic candidates on the basal side. Transepithelial translocation of all DARPin candidates and the monoclonal antibody was efficient and dose dependent. Small DARPins and the antibody migrated more efficiently than larger molecules, indicating different transport mechanisms involved.
Microscopic analyses support this, demonstrating passive paracellular transport of smaller DARPins and transcellular migration of the larger molecules. All therapeutic candidates applied to the basal side of HBE conferred effective protection against SARS-CoV-2 infection. In summary, we have shown that DARPins specific against SARS-CoV-2 translocate across intact airway epithelia and confer effective protection against infection and viral replication.
Usefulness of PIVKA-II for monitoring after liver transplantation in patients with hepatocellular carcinoma
Authors: Villalba-López Francisco , Sáenz-Mateos Luis Francisco , Sánchez-Lorencio Maria Isabel , De La Orden-García Virginia , Alconchel-Gago Felipe , Cascales-Campos Pedro Antonio , García-Bernardo Carmen , Noguera-Velasco José Antonio , Baroja-Mazo Alberto , Ramírez-Romero Pablo 
Published: April 2023

AbstractThe high morbidity and mortality of hepatocellular carcinoma (HCC) has encouraged the search for new biomarkers to be used alongside alpha-foetoprotein (AFP) and imaging tests. The aim of this study was to evaluate the clinical contribution of protein induced by vitamin K absence or antagonist-II (PIVKA-II) for HCC monitoring after liver transplantation (LT) and compare it with AFP, a routinely used tumour marker. A total of 46 HCC patients (Milan criteria) were enrolled in this study. Serum levels of PIVKA-II and AFP were measured before and after transplantation. Clinical features were determined for all the patients that were included. Significant correlations were found between PIVKA-II expression levels and some clinicopathological features, such as tumour size and number of pre-transplant transarterial chemoembolizations (TACEs). Serum levels of PIVKA-II and AFP decreased significantly after LT and increased in patients with tumour recurrence. Serum PIVKA-II levels may play an important role in predicting disease severity. Furthermore, monitoring PIVKA-II levels in HCC transplant recipients reflects the tumor early recurrence after transplantation and could be used, complementing AFP and imaging tests, as a novel biomarker of this pathology.
Chemical and genomic characterization of a potential probiotic treatment for stony coral tissue loss disease
Authors: Ushijima Blake , Gunasekera Sarath P. , Meyer Julie L. , Tittl Jessica , Pitts Kelly A. , Thompson Sharon , Sneed Jennifer M. , Ding Yousong , Chen Manyun , Jay Houk L. , Aeby Greta S. , Häse Claudia C. , Paul Valerie J. 
Published: April 2023

AbstractConsidered one of the most devastating coral disease outbreaks in history, stony coral tissue loss disease (SCTLD) is currently spreading throughout Florida’s coral reefs and the greater Caribbean. SCTLD affects at least two dozen different coral species and has been implicated in extensive losses of coral cover. Here we show Pseudoalteromonas sp. strain McH1-7 has broad-spectrum antibacterial activity against SCTLD-associated bacterial isolates. Chemical analyses indicated McH1-7 produces at least two potential antibacterials, korormicin and tetrabromopyrrole, while genomic analysis identified the genes potentially encoding an L-amino acid oxidase and multiple antibacterial metalloproteases (pseudoalterins). During laboratory trials, McH1-7 arrested or slowed disease progression on 68.2% of diseased Montastraea cavernosa fragments treated (n = 22), and it prevented disease transmission by 100% (n = 12). McH1-7 is the most chemically characterized coral probiotic that is an effective prophylactic and direct treatment for the destructive SCTLD as well as a potential alternative to antibiotic use.
Experimental strategies to improve drug-target identification in mass spectrometry-based thermal stability assays
Authors: Phaneuf Clifford G. , Aizikov Konstantin , Grinfeld Dmitry , Kreutzmann Arne , Mourad Daniel , Lange Oliver , Dai Daniel , Zhang Bailin , Belenky Alexei , Makarov Alexander A. , Ivanov Alexander R. 
Published: April 2023

AbstractMass spectrometry (MS)-based thermal stability assays have recently emerged as one of the most promising solutions for the identification of protein-ligand interactions. Here, we have investigated eight combinations of several recently introduced MS-based advancements, including the Phase-Constrained Spectral Deconvolution Method, Field Asymmetric Ion Mobility Spectrometry, and the implementation of a carrier sample as improved MS-based acquisition approaches for thermal stability assays (iMAATSA). We used intact Jurkat cells treated with a commercially available MEK inhibitor, followed by heat treatment, to prepare a set of unfractionated isobarically-labeled proof-of-concept samples to compare the performance of eight different iMAATSAs. Finally, the best-performing iMAATSA was compared to a conventional approach and evaluated in a fractionation experiment. Improvements of up to 82% and 86% were demonstrated in protein identifications and high-quality melting curves, respectively, over the conventional approach in the proof-of-concept study, while an approximately 12% improvement in melting curve comparisons was achieved in the fractionation experiment.
The selection of a hydrophobic 7-phenylbutyl-7-deazaadenine-modified DNA aptamer with high binding affinity for the Heat Shock Protein 70
Authors: Mulholland Catherine , Jestřábová Ivana , Sett Arghya , Ondruš Marek , Sýkorová Veronika , Manzanares C. Lorena , Šimončík Oliver , Muller Petr , Hocek Michal 
Published: April 2023

AbstractNucleic acids aptamers often fail to efficiently target some proteins because of the hydrophilic character of the natural nucleotides. Here we present hydrophobic 7-phenylbutyl-7-deaadenine-modified DNA aptamers against the Heat Shock Protein 70 that were selected via PEX and magnetic bead-based SELEX. After 9 rounds of selection, the pool was sequenced and a number of candidates were identified. Following initial screening, two modified aptamers were chemically synthesised in-house and their binding affinity analysed by two methods, bio-layer interferometry and fluorescent-plate-based binding assay. The binding affinities of the modified aptamers were compared with that of their natural counterparts. The resulting modified aptamers bound with higher affinity (low nanomolar range) to the Hsp70 than their natural sequence (>5 µM) and hence have potential for applications and further development towards Hsp70 diagnostics or even therapeutics.
Modulation of antichiral edge states in zigzag honeycomb nanoribbons by side potentials
Authors: Yang Jia-En , Lü Xiao-Long , Xie Hang 
Published: April 2023

AbstractThe antichiral edge states induced by the modified Haldane model have been predicted in the previous studies. In this study, other types of antichiral edge states are proposed by applying the side potentials composed of a potential field, staggered electric field, and exchange field along the boundaries of zigzag honeycomb nanoribbons (zHNRs). Their corresponding transport properties are investigated. The results show that the side potentials can lift the spin degeneracy of the edge modes, inducing five types of antichiral edge states. By calculating the spin-dependent energies in K’ and K valleys of the edge modes, an interpretation for generating antichiral edge states is proposed. In addition, the spin/charge switcher in the three-terminal device consisting of zHNRs is developed based on the induced edge states. We believe that these results can be used in the design of future spintronic devices.