bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neural network kinetics for exploring diffusion multiplicity and chemical ordering in compositionally complex materials
Authors: Xing Bin , Rupert Timothy J. , Pan Xiaoqing , Cao Penghui 
Published: May 2024

AbstractDiffusion involving atom transport from one location to another governs many important processes and behaviors such as precipitation and phase nucleation. The inherent chemical complexity in compositionally complex materials poses challenges for modeling atomic diffusion and the resulting formation of chemically ordered structures. Here, we introduce a neural network kinetics (NNK) scheme that predicts and simulates diffusion-induced chemical and structural evolution in complex concentrated chemical environments. The framework is grounded on efficient on-lattice structure and chemistry representation combined with artificial neural networks, enabling precise prediction of all path-dependent migration barriers and individual atom jumps. To demonstrate the method, we study the temperature-dependent local chemical ordering in a refractory NbMoTa alloy and reveal a critical temperature at which the B2 order reaches a maximum. The atomic jump randomness map exhibits the highest diffusion heterogeneity (multiplicity) in the vicinity of this characteristic temperature, which is closely related to chemical ordering and B2 structure formation. The scalable NNK framework provides a promising new avenue to exploring diffusion-related properties in the vast compositional space within which extraordinary properties are hidden.
A common polymorphism in the Intelectin-1 gene influences mucus plugging in severe asthma
Authors: Everman Jamie L. , Sajuthi Satria P. , Liegeois Maude A. , Jackson Nathan D. , Collet Erik H. , Peters Michael C. , Chioccioli Maurizio , Moore Camille M. , Patel Bhavika B. , Dyjack Nathan , Powell Roger , Rios Cydney , Montgomery Michael T. , Eng Celeste , Elhawary Jennifer R. , Mak Angel C. Y. , Hu Donglei , Huntsman Scott , Salazar Sandra , Feriani Luigi , Fairbanks-Mahnke Ana , Zinnen Gianna L. , Michel Cole R. , Gomez Joe , Zhang Xing , Medina Vivian , Chu Hong Wei , Cicuta Pietro , Gordon Erin D. , Zeitlin Pamela , Ortega Victor E. , Reisdorph Nichole , Dunican Eleanor M. , Tang Monica , Elicker Brett M. , Henry Travis S. , Bleecker Eugene R. , Castro Mario , Erzurum Serpil C. , Israel Elliot , Levy Bruce D. , Mauger David T. , Meyers Deborah A. , Sumino Kaharu , Gierada David S. , Hastie Annette T. , Moore Wendy C. , Denlinger Loren C. , Jarjour Nizar N. , Schiebler Mark L. , Wenzel Sally E. , Woodruff Prescott G. , Rodriguez-Santana Jose , Pearson Chad G. , Burchard Esteban G. , Fahy John V. , Seibold Max A. 
Published: May 2024

AbstractBy incompletely understood mechanisms, type 2 (T2) inflammation present in the airways of severe asthmatics drives the formation of pathologic mucus which leads to airway mucus plugging. Here we investigate the molecular role and clinical significance of intelectin-1 (ITLN-1) in the development of pathologic airway mucus in asthma. Through analyses of human airway epithelial cells we find that ITLN1 gene expression is highly induced by interleukin-13 (IL-13) in a subset of metaplastic MUC5AC+ mucus secretory cells, and that ITLN-1 protein is a secreted component of IL-13-induced mucus. Additionally, we find ITLN-1 protein binds the C-terminus of the MUC5AC mucin and that its deletion in airway epithelial cells partially reverses IL-13-induced mucostasis. Through analysis of nasal airway epithelial brushings, we find that ITLN1 is highly expressed in T2-high asthmatics, when compared to T2-low children. Furthermore, we demonstrate that both ITLN-1 gene expression and protein levels are significantly reduced by a common genetic variant that is associated with protection from the formation of mucus plugs in T2-high asthma. This work identifies an important biomarker and targetable pathways for the treatment of mucus obstruction in asthma.
Hyphal Als proteins act as CR3 ligands to promote immune responses against Candida albicans
Authors: Zhou Tingting , Solis Norma V. , Marshall Michaela , Yao Qing , Garleb Rachel , Yang Mengli , Pearlman Eric , Filler Scott G. , Liu Haoping 
Published: May 2024

AbstractPatients with decreased levels of CD18 (β2 integrins) suffer from life-threatening bacterial and fungal infections. CD11b, the α subunit of integrin CR3 (CD11b/CD18, αMβ2), is essential for mice to fight against systemic Candida albicans infections. Live elongating C. albicans activates CR3 in immune cells. However, the hyphal ligands that activate CR3 are not well defined. Here, we discovered that the C. albicans Als family proteins are recognized by the I domain of CD11b in macrophages. This recognition synergizes with the β-glucan-bound lectin-like domain to activate CR3, thereby promoting Syk signaling and inflammasome activation. Dectin-2 activation serves as the “outside-in signaling” for CR3 activation at the entry site of incompletely sealed phagosomes, where a thick cuff of F-actin forms to strengthen the local interaction. In vitro, CD18 partially contributes to IL-1β release from dendritic cells induced by purified hyphal Als3. In vivo, Als3 is vital for C. albicans clearance in mouse kidneys. These findings uncover a novel family of ligands for the CR3 I domain that promotes fungal clearance.
Contemporary HIV-1 consensus Env with AI-assisted redesigned hypervariable loops promote antibody binding
Authors: Bai Hongjun , Lewitus Eric , Li Yifan , Thomas Paul V. , Zemil Michelle , Merbah Mélanie , Peterson Caroline E. , Thuraisamy Thujitha , Rees Phyllis A. , Hajduczki Agnes , Dussupt Vincent , Slike Bonnie , Mendez-Rivera Letzibeth , Schmid Annika , Kavusak Erin , Rao Mekhala , Smith Gabriel , Frey Jessica , Sims Alicea , Wieczorek Lindsay , Polonis Victoria , Krebs Shelly J. , Ake Julie A. , Vasan Sandhya , Bolton Diane L. , Joyce M. Gordon , Townsley Samantha , Rolland Morgane 
Published: May 2024

AbstractAn effective HIV-1 vaccine must elicit broadly neutralizing antibodies (bnAbs) against highly diverse Envelope glycoproteins (Env). Since Env with the longest hypervariable (HV) loops is more resistant to the cognate bnAbs than Env with shorter HV loops, we redesigned hypervariable loops for updated Env consensus sequences of subtypes B and C and CRF01_AE. Using modeling with AlphaFold2, we reduced the length of V1, V2, and V5 HV loops while maintaining the integrity of the Env structure and glycan shield, and modified the V4 HV loop. Spacers are designed to limit strain-specific targeting. All updated Env are infectious as pseudoviruses. Preliminary structural characterization suggests that the modified HV loops have a limited impact on Env’s conformation. Binding assays show improved binding to modified subtype B and CRF01_AE Env but not to subtype C Env. Neutralization assays show increases in sensitivity to bnAbs, although not always consistently across clades. Strikingly, the HV loop modification renders the resistant CRF01_AE Env sensitive to 10-1074 despite the absence of a glycan at N332.
Exploiting in silico modelling to enhance translation of liver cell therapies from bench to bedside
Authors: Ashmore-Harris Candice , Antonopoulou Evangelia , Finney Simon M. , Vieira Melissa R. , Hennessy Matthew G. , Muench Andreas , Lu Wei-Yu , Gadd Victoria L. , El Haj Alicia J. , Forbes Stuart J. , Waters Sarah L. 
Published: May 2024

AbstractCell therapies are emerging as promising treatments for a range of liver diseases but translational bottlenecks still remain including: securing and assessing the safe and effective delivery of cells to the disease site; ensuring successful cell engraftment and function; and preventing immunogenic responses. Here we highlight three therapies, each utilising a different cell type, at different stages in their clinical translation journey: transplantation of multipotent mesenchymal stromal/signalling cells, hepatocytes and macrophages. To overcome bottlenecks impeding clinical progression, we advocate for wider use of mechanistic in silico modelling approaches. We discuss how in silico approaches, alongside complementary experimental approaches, can enhance our understanding of the mechanisms underlying successful cell delivery and engraftment. Furthermore, such combined theoretical-experimental approaches can be exploited to develop novel therapies, address safety and efficacy challenges, bridge the gap between in vitro and in vivo model systems, and compensate for the inherent differences between animal model systems and humans. We also highlight how in silico model development can result in fewer and more targeted in vivo experiments, thereby reducing preclinical costs and experimental animal numbers and potentially accelerating translation to the clinic. The development of biologically-accurate in silico models that capture the mechanisms underpinning the behaviour of these complex systems must be reinforced by quantitative methods to assess cell survival post-transplant, and we argue that non-invasive in vivo imaging strategies should be routinely integrated into transplant studies.
Multiplex profiling of developmental cis-regulatory elements with quantitative single-cell expression reporters
Authors: Lalanne Jean-Benoît , Regalado Samuel G. , Domcke Silvia , Calderon Diego , Martin Beth K. , Li Xiaoyi , Li Tony , Suiter Chase C. , Lee Choli , Trapnell Cole , Shendure Jay 
Published: May 2024

AbstractThe inability to scalably and precisely measure the activity of developmentalcis-regulatory elements (CREs) in multicellular systems is a bottleneck in genomics. Here we develop a dual RNA cassette that decouples the detection and quantification tasks inherent to multiplex single-cell reporter assays. The resulting measurement of reporter expression is accurate over multiple orders of magnitude, with a precision approaching the limit set by Poisson counting noise. Together with RNA barcode stabilization via circularization, these scalable single-cell quantitative expression reporters provide high-contrast readouts, analogous to classic in situ assays but entirely from sequencing. Screening >200 regions of accessible chromatin in a multicellular in vitro model of early mammalian development, we identify 13 (8 previously uncharacterized) autonomous and cell-type-specific developmental CREs. We further demonstrate that chimeric CRE pairs generate cognate two-cell-type activity profiles and assess gain- and loss-of-function multicellular expression phenotypes from CRE variants with perturbed transcription factor binding sites. Single-cell quantitative expression reporters can be applied in developmental and multicellular systems to quantitatively characterize native, perturbed and synthetic CREs at scale, with high sensitivity and at single-cell resolution.
InsectSound1000 An insect sound dataset for deep learning based acoustic insect recognition
Authors: Branding Jelto , von Hörsten Dieter , Böckmann Elias , Wegener Jens Karl , Hartung Eberhard 
Published: May 2024

AbstractInsectSound1000 is a dataset comprising more than 169000 labelled sound samples of 12 insects. The insect sound level spans from very loud (Bombus terrestris) to inaudible to human ears (Aphidoletes aphidimyza). The samples were extracted from more than 1000 h of recordings made in an anechoic box with a four-channel low-noise measurement microphone array. Each sample is a four-channel wave-file of 2500 kHz length, at 16 kHz sample rate and 32 bit resolution. Acoustic insect recognition holds great potential to form the basis of a digital insect sensor. Such sensors are desperately needed to automate pest monitoring and ecological monitoring. With its significant size and high-quality recordings, InsectSound1000 can be used to train data-hungry deep learning models. Used to pretrain models, it can also be leveraged to enable the development of acoustic insect recognition systems on different hardware or for different insects. Further, the methodology employed to create the dataset is presented in detail to allow for the extension of the published dataset.
Co-located ecological data for exploring top- and subsoil carbon dynamics across grassland-woodland contrasts
Authors: Reinsch Sabine , Lebron Inma , Brentegani Michele , Brooks Milo , Busi Susheel Bhanu , Cagnarini Claudia , Cooper David , Day John , Emmett Bridget A. , Fitos Eleonora , Goodall Tim , Griffiths Robert , Jones Briony , Keenan Patrick , Keith Aidan , Lopes-Mazzetto Josiane M. , Mason Kelly E. , Pallett Denise , Pereira M. Glória , Pinder Adam , Robinson David A. , Smart Simon M. , Thomas Amy , Benham Sue , Vanguelova Elena , Cosby Bernhard J. 
Published: May 2024

AbstractSoil organic carbon (SOC) is a soil health indicator and understanding dynamics changing SOC stocks will help achieving net zero goals. Here we present four datasets featuring 11,750 data points covering co-located aboveground and below-ground metrics for exploring ecosystem SOC dynamics. Five sites across England with an established land use contrast, grassland and woodland next to each other, were rigorously sampled for aboveground (n = 109), surface (n = 33 soil water release curves), topsoil, and subsoil metrics. Commonly measured soil metrics were analysed in five soil increments for 0–1 metre (n = 4550). Less commonly measured soil metrics which were assumed to change across the soil profile were measured on a subset of samples only (n = 3762). Additionally, we developed a simple method for soil organic matter fractionation using density fractionation which is part of the less common metrics. Finally, soil metrics which may impact SOC dynamics, but with less confidence as to their importance across the soil profile were only measured on topsoil (~5–15 cm = mineral soil) and subsoil (below 50 cm) samples (n = 2567).
CH4 emissions from runoff water of Alaskan mountain glaciers
Authors: Konya Keiko , Sueyoshi Tetsuo , Iwahana Go , Morishita Tomoaki , Uetake Jun , Wakita Masahide 
Published: May 2024

AbstractRecent studies have observed high methane concentrations in runoff water and the ambient air at various glacier sites, including the Greenland Ice Sheet, the glacier forefield in Svalbard, and the ice cap in Iceland. This study extends these findings to smaller mountain glaciers in Alaska. Methane and carbon dioxide concentrations in the ambient air near the meltwater outlet, fluxes of these gases at the surface of runoff water and riverbank sediments, and dissolved methane content in the runoff water were measured at four glaciers. Three of the four glaciers showed conspicuous signals of methane emissions from runoff water, with the Castner Glacier terminus exhibiting a methane concentration three times higher than background levels, along with elevated dissolved methane levels in the runoff water. This study marks the detection of significant methane emissions from small mountain glacier runoff, contributing to the understanding that mountain glaciers also release methane into the atmosphere.
A novel type-II–II heterojunction for photocatalytic degradation of LEV based on the built-in electric field: carrier transfer mechanism and DFT calculation
Authors: Li Jiaquan , Tu Peng , Yang Qian , Cui Yanjun , Gao Chenyang , Zhou Hui , Lu Jun , Bian Hongxia 
Published: May 2024

AbstractHeterojunctions play a crucial role in improving the absorption of visible light and performance of photocatalysts for organic contaminants degradation in water. In this work, a novel type-II–II Ag2CO3/Bi2WO6 (AB) heterojunction was synthesized by hydrothermal reaction and in situ-precipitation methods. The mechanisms of charge transfer and carrier separation at the interface of heterojunctions and the influence on the photocatalytic activity were investigated. The degradation of levofloxacin (LEV) under visible light irradiation was employed to evaluate the photocatalytic performance of AB. The results showed that 85.4% LEV was degraded by AB, which was 1.38 and 1.39 times higher than that of Bi2WO6 and Ag2CO3, respectively. The work functions of the different crystal planes in the AB heterojunction, which was calculated by density functional theory, are a significant difference. The Fermi energy (Ef) of Ag2CO3 (− 6.005 eV) is lower than Bi2WO6 (− 3.659 eV), but the conduction band (CB) is higher. Therefore, using AB heterojunctions as an example, the research explored the mechanism of type-II–II which CB and Ef of one semiconductor cannot simultaneously surpass those of another material, based on the built-in electric field theory. Through this analysis, a deeper understanding of type-II heterojunctions was achieved, and providing valuable insights into the behavior of this specific heterojunction system.
An ensemble learning model for forecasting water-pipe leakage
Authors: Warad Ahmed Ali Mohamed , Wassif Khaled , Darwish Nagy Ramadan 
Published: May 2024

AbstractBased on the benefits of different ensemble methods, such as bagging and boosting, which have been studied and adopted extensively in research and practice, where bagging and boosting focus more on reducing variance and bias, this paper presented an optimization ensemble learning-based model for a large pipe failure dataset of water pipe leakage forecasting, something that was not previously considered by others. It is known that tuning the hyperparameters of each base learned inside the ensemble weight optimization process can produce better-performing ensembles, so it effectively improves the accuracy of water pipe leakage forecasting based on the pipeline failure rate. To evaluate the proposed model, the results are compared with the results of the bagging ensemble and boosting ensemble models using the root-mean-square error (RMSE), the mean square error (MSE), the mean absolute error (MAE), and the coefficient of determination (R2) of the bagging ensemble technique, the boosting ensemble technique and optimizable ensemble technique are higher than other models. The experimental result shows that the optimizable ensemble model has better prediction accuracy. The optimizable ensemble model has achieved the best prediction of water pipe failure rate at the 14th iteration, with the least RMSE = 0.00231 and MAE = 0.00071513 when building the model that predicts water pipe leakage forecasting via pipeline failure rate.
Exploring toilet plume bioaerosol exposure dynamics in public toilets using a Design of Experiments approach
Authors: Paddy Elizabeth N. , Afolabi Oluwasola O. D. , Sohail M. 
Published: May 2024

AbstractBioaerosols generated during toilet flushing can contribute to the spread of airborne pathogens and cross-contamination in indoor environments. This presents an increased risk of fomite-mediated or aerosol disease transmission. This study systematically investigated the factors contributing to increased bioaerosol exposure following toilet flushing and developed an empirical model for predicting the exposure-relevant bioaerosol concentration. Air in a toilet cubicle was sampled by impaction after seeding with Clostridium difficile spores. Design of Experiments (DoE) main effects screening and full factorial design approaches were then employed to investigate the significant factors that heighten the risk of exposure to bioaerosols post-flush. Our findings reveal that the inoculated bacterial concentration (C), time elapsed after flushing (t), lateral distance (d), and mechanical ventilation (v) are significant predictors of bioaerosol concentration, with p-values < 0.05. The interaction term, C × d showed a marked increase in bioaerosol concentration up to 232 CFU/m3 at the closest proximity and highest pathogen load. The interplay of C and t (C × t) demonstrated a time-dependent attenuation of bioaerosol viability, with concentrations peaking at 241 CFU/m3 immediately post-flush and notably diminishing over time. The lateral distance and time post-flush (d × t) interaction also revealed a gradual decrease in bioaerosol concentration, highlighting the effectiveness of spatial and temporal dilution in mitigating bioaerosol exposure risks. Furthermore, there is an immediate rise in relative humidity levels post-flush, impacting the air quality in the toilet environment. This study not only advances our understanding of exposure pathways in determining bioaerosol exposure, but also offers pivotal insights for designing targeted interventions to reduce bioaerosol exposure. Recommendations include designing public toilets with antimicrobial surfaces, optimizing ventilation, and initiating timely disinfection protocols to prioritise surfaces closest to the toilet bowl during peak exposure periods, thereby promoting healthier indoor environments and safeguarding public health in high-traffic toilet settings.
Mechanically-flexible wafer-scale integrated-photonics fabrication platform
Authors: Notaros Milica , Dyer Thomas , Garcia Coleto Andres , Hattori Ashton , Fealey Kevin , Kruger Seth , Notaros Jelena 
Published: May 2024

AbstractThe field of integrated photonics has advanced rapidly due to wafer-scale fabrication, with integrated-photonics platforms and fabrication processes being demonstrated at both infrared and visible wavelengths. However, these demonstrations have primarily focused on fabrication processes on silicon substrates that result in rigid photonic wafers and chips, which limit the potential application spaces. There are many application areas that would benefit from mechanically-flexible integrated-photonics wafers, such as wearable healthcare monitors and pliable displays. Although there have been demonstrations of mechanically-flexible photonics fabrication, they have been limited to fabrication processes on the individual device or chip scale, which limits scalability. In this paper, we propose, develop, and experimentally characterize the first 300-mm wafer-scale platform and fabrication process that results in mechanically-flexible photonic wafers and chips. First, we develop and describe the 300-mm wafer-scale CMOS-compatible flexible platform and fabrication process. Next, we experimentally demonstrate key optical functionality at visible wavelengths, including chip coupling, waveguide routing, and passive devices. Then, we perform a bend-durability study to characterize the mechanical flexibility of the photonic chips, demonstrating bending a single chip 2000 times down to a bend diameter of 0.5 inch with no degradation in the optical performance. Finally, we experimentally characterize polarization-rotation effects induced by bending the flexible photonic chips. This work will enable the field of integrated photonics to advance into new application areas that require flexible photonic chips.