bluuebunny/crossref_metadata_2025_split huggingface dataset:
Convolutional Neural Network‐Based Adaptive Localization for an Ensemble Kalman Filter
Authors: Wang Zhongrui , Lei Lili , Anderson Jeffrey L. , Tan Zhe‐Min , Zhang Yi 
Published: October 2023

AbstractFlow‐dependent background error covariances estimated from short‐term ensemble forecasts suffer from sampling errors due to limited ensemble sizes. Covariance localization is often used to mitigate the sampling errors, especially for high dimensional geophysical applications. Most applied localization methods, empirical or adaptive ones, multiply the Kalman gain or background error covariances by a distance‐dependent parameter, which is a simple linear filtering model. Here two localization methods based on convolutional neural networks (CNNs) learning from paired data sets are proposed. The CNN‐based localization function (CLF) aims to minimize the sampling error of the estimated Kalman gain, and the CNN‐based empirical localization function (CELF) aims to minimize the posterior error of state variables. These two CNN‐based localization methods can provide localization functions that are nonlinear, spatially and temporally adaptive, and non‐symmetric with respect to displacement, without requiring any prior assumptions for the localization functions. Results using the Lorenz05 model show that CLF and CELF can better capture the structures of the Kalman gain than the best Gaspari and Cohn (GC) localization function and the adaptive reference localization method. For both perfect‐ and imperfect‐model experiments, CLF produces smaller errors of the Kalman gain, prior and posterior than the best GC and reference localization, especially for spatially averaged observations. Without model error, CELF has smaller prior and posterior errors than the best GC and reference localization for spatially averaged observations, while with model error, CELF has smaller prior and posterior errors than the best GC and reference localization for single‐point observations.
Subgrid Parameterizations of Ocean Mesoscale Eddies Based on Germano Decomposition
Authors: Perezhogin Pavel , Glazunov Andrey 
Published: October 2023

AbstractOcean models at intermediate resolution (1/4°), which partially resolve mesoscale eddies, can be seen as Large eddy simulations of the primitive equations, in which the effect of unresolved eddies must be parameterized. In this work, we propose new subgrid models that are consistent with the physics of two‐dimensional flows. We analyze subgrid fluxes in barotropic decaying turbulence using Germano (1986, https://doi.org/10.1063/1.865568) decomposition. We show that Leonard and Cross stresses are responsible for the enstrophy dissipation, while the Reynolds stress is responsible for additional kinetic energy (KE) backscatter. We utilize these findings to propose a new model, consisting of three parts, that is compared to a baseline dynamic Smagorinsky model. The three‐component model accurately simulates the spectral transfer of energy and enstrophy and improves the representation of KE spectrum, resolved KE and enstrophy decay in a posteriori experiments. The backscattering component of the new model (Reynolds stress) is implemented both in quasi‐geostrophic and primitive equation ocean models and improves statistical characteristics, such as the vertical profile of eddy KE, meridional overturning circulation and cascades of kinetic and potential energy.
Identification of a serum-based microRNA signature that detects recurrent oral squamous cell carcinoma before it is clinically evident
Authors: Towle Rebecca , Dickman Christopher T. D. , MacLellan Sara A. , Chen Jiahua , Prisman Eitan , Guillaud Martial , Garnis Cathie 
Published: October 2023

Abstract
Background
Survival rates for oral squamous cell carcinoma (OSCC) have remained poor for decades, a fact largely attributable to late-stage diagnoses and high recurrence rates. We report analysis of serum miRNA expression in samples from patients with high-risk oral lesions (HRL, including OSCC/carcinoma in situ lesions) and healthy non-cancer controls, with the aim of non-invasively detecting primary or recurrent disease before it is clinically evident.

Methods
Discovery, test, and validation sets were defined from a total of 468 serum samples (305 HRL and 163 control samples). Samples were analysed using multiple qRT-PCR platforms.

Results
A two-miRNA classifier comprised of miR-125b-5p and miR-342-3p was defined following discovery and test analyses. Analysis in an independent validation cohort reported sensitivity and specificity of ~74% for this classifier. Significantly, when this classifier was applied to serial serum samples taken from patients both before treatment and during post-treatment surveillance, it identified recurrence an average of 15 months prior to clinical presentation.

Conclusions
These results indicate this serum miRNA classifier is effective as a simple, non-invasive monitoring tool for earlier detection of recurrent disease when lesions are typically smaller and amenable to a wider array of treatment options to improve survival.
Macrophage-mediated trogocytosis contributes to destroying human schistosomes in a non-susceptible rodent host, Microtus fortis
Authors: Shen Jia , Zhao Siyu , Peng Mei , Li Yanguo , Zhang Lichao , Li Xiaoping , Hu Yunyi , Wu Mingrou , Xiang Suoyu , Wu Xiaoying , Liu Jiahua , Zhang Beibei , Chen Zebin , Lin Datao , Liu Huanyao , Tang Wenyan , Chen Jun , Sun Xi , Liao Qi , Hide Geoff , Zhou Zhijun , Lun Zhao-Rong , Wu Zhongdao 
Published: October 2023

AbstractSchistosoma parasites, causing schistosomiasis, exhibit typical host specificity in host preference. Many mammals, including humans, are susceptible to infection, while the widely distributed rodent, Microtus fortis, exhibits natural anti-schistosome characteristics. The mechanisms of host susceptibility remain poorly understood. Comparison of schistosome infection in M. fortis with the infection in laboratory mice (highly sensitive to infection) offers a good model system to investigate these mechanisms and to gain an insight into host specificity. In this study, we showed that large numbers of leukocytes attach to the surface of human schistosomes in M. fortis but not in mice. Single-cell RNA-sequencing analyses revealed that macrophages might be involved in the cell adhesion, and we further demonstrated that M. fortis macrophages could be mediated to attach and kill schistosomula with dependence on Complement component 3 (C3) and Complement receptor 3 (CR3). Importantly, we provided direct evidence that M. fortis macrophages could destroy schistosomula by trogocytosis, a previously undescribed mode for killing helminths. This process was regulated by Ca2+/NFAT signaling. These findings not only elucidate a novel anti-schistosome mechanism in M. fortis but also provide a better understanding of host parasite interactions, host specificity and the potential generation of novel strategies for schistosomiasis control.
Posterior vitreous detachment and retinal tear – a prospective study of community referrals
Authors: Nixon Thomas R. W. , Davie Rebecca L. , Snead Martin P. 
Published: October 2023

Abstract
Background
Retinal tears (RT) from posterior vitreous detachment (PVD) are an important and treatable cause of rhegmatogenous retinal detachment (RRD). Better understanding of the risk of RT from PVD will help plan urgent eye care.

Methods
Prospective observational case series over two years. Patients presenting to their optometrist, family doctor or emergency department with flashes and floaters were directed to a research clinic. History and examination, including slit-lamp biomicroscopy (SLB) and indentation indirect ophthalmoscopy (IIO), were performed by a single investigator, with two month follow-up for patients with confirmed PVD. Main outcome measures were incidence of PVD, RT, and RRD.

Results
1010 patients were recruited. 896 (89%) patients had PVD at first assessment, of which 89 (8.8% of total cohort, 9.9% of PVD eyes) had RT and 8 had RRD. 21 (3%) of the remaining PVD patients developed RT in the subsequent two months and a further 9 (11%) patients with RT at initial assessment developed further tears by two months. 7 (0.7%) had asymptomatic RT in the fellow eye. 15% of RT were only visible on IIO and not SLB. Weiss ring was absent in 32% of eyes with RT. Patients with RT or RRD were more likely than ‘PVD-only’ eyes to have blurred or missing vision (p < 0.001), have higher rate of blue-green cataracts (p < 0.001), and longer axial lengths (p < 0.05).

Conclusions and Relevance
This large, prospective study demonstrates a 9.9% rate of RT or RRD at the time of PVD, and emphasises the importance of IIO examination.
Modulation-doping a correlated electron insulator
Authors: Mondal Debasish , Mahapatra Smruti Rekha , Derrico Abigail M. , Rai Rajeev Kumar , Paudel Jay R. , Schlueter Christoph , Gloskovskii Andrei , Banerjee Rajdeep , Hariki Atsushi , DeGroot Frank M. F. , Sarma D. D. , Narayan Awadhesh , Nukala Pavan , Gray Alexander X. , Aetukuri Naga Phani B. 
Published: October 2023

AbstractCorrelated electron materials (CEMs) host a rich variety of condensed matter phases. Vanadium dioxide (VO2) is a prototypical CEM with a temperature-dependent metal-to-insulator (MIT) transition with a concomitant crystal symmetry change. External control of MIT in VO2—especially without inducing structural changes—has been a long-standing challenge. In this work, we design and synthesize modulation-doped VO2-based thin film heterostructures that closely emulate a textbook example of filling control in a correlated electron insulator. Using a combination of charge transport, hard X-ray photoelectron spectroscopy, and structural characterization, we show that the insulating state can be doped to achieve carrier densities greater than 5 × 1021 cm−3 without inducing any measurable structural changes. We find that the MIT temperature (TMIT) continuously decreases with increasing carrier concentration. Remarkably, the insulating state is robust even at doping concentrations as high as ~0.2 e−/vanadium. Finally, our work reveals modulation-doping as a viable method for electronic control of phase transitions in correlated electron oxides with the potential for use in future devices based on electric-field controlled phase transitions.
Nutrient and arsenic biogeochemistry of Sargassum in the western Atlantic
Authors: McGillicuddy Dennis Joseph , Morton Peter Lynn , Brewton Rachel Aileen , Hu Chuanmin , Kelly Thomas Bryce , Solow Andrew Robert , Lapointe Brian Edward 
Published: October 2023

AbstractThe oceanographic ecology of pelagic Sargassum, and the means by which these floating macroalgae thrive in the nutrient-poor waters of the open ocean, have been studied for decades. Beginning in 2011, the Great Atlantic Sargassum Belt (GASB) emerged, with Sargassum proliferating in the tropical Atlantic and Caribbean where it had not previously been abundant. Here we show that the nutritional status of Sargassum in the GASB is distinct, with higher nitrogen and phosphorus content than populations residing in its Sargasso Sea habitat. Moreover, we find that variations in arsenic content of Sargassum reflect phosphorus limitation, following a hyperbolic relationship predicted from Michaelis-Menten nutrient uptake kinetics. Although the sources of nutrients fueling the GASB are not yet clear, our results suggest that nitrogen and phosphorus content of Sargassum, together with its isotopic composition, can be used to identify those sources, whether they be atmospheric, oceanic, or riverine in origin.
Drivers of Antarctic sea ice advance
Authors: Himmich Kenza , Vancoppenolle Martin , Madec Gurvan , Sallée Jean-Baptiste , Holland Paul R. , Lebrun Marion 
Published: October 2023

AbstractAntarctic sea ice is mostly seasonal. While changes in sea ice seasonality have been observed in recent decades, the lack of process understanding remains a key challenge to interpret these changes. To address this knowledge gap, we investigate the processes driving the ice season onset, known as sea ice advance, using remote sensing and in situ observations. Here, we find that seawater freezing predominantly drives advance in the inner seasonal ice zone. By contrast, in an outer band a few degrees wide, advance is due to the import of drifting ice into warmer waters. We show that advance dates are strongly related to the heat stored in the summer ocean mixed layer. This heat is controlled by the timing of sea ice retreat, explaining the tight link between retreat and advance dates. Such a thermodynamic linkage strongly constrains the climatology and interannual variations, albeit with less influence on the latter.
Structure determination of ζ-N2 from single-crystal X-ray diffraction and theoretical suggestion for the formation of amorphous nitrogen
Authors: Laniel Dominique , Trybel Florian , Aslandukov Andrey , Spender James , Ranieri Umbertoluca , Fedotenko Timofey , Glazyrin Konstantin , Bright Eleanor Lawrence , Chariton Stella , Prakapenka Vitali B. , Abrikosov Igor A. , Dubrovinsky Leonid , Dubrovinskaia Natalia 
Published: October 2023

AbstractThe allotropy of solid molecular nitrogen is the consequence of a complex interplay between fundamental intermolecular as well as intramolecular interactions. Understanding the underlying physical mechanisms hinges on knowledge of the crystal structures of these molecular phases. That is especially true for ζ-N2, key to shed light on nitrogen’s polymerization. Here, we perform single-crystal X-ray diffraction on laser-heated N2 samples at 54, 63, 70 and 86 GPa and solve and refine the hitherto unknown structure of ζ-N2. In its monoclinic unit cell (space group C2/c), 16 N2 molecules are arranged in a configuration similar to that of ε-N2. The structure model provides an explanation for the previously identified Raman and infrared lattice and vibrational modes of ζ-N2. Density functional theory calculations give an insight into the gradual delocalization of electronic density from intramolecular bonds to intermolecular space and suggest a possible pathway towards nitrogen’s polymerization.
Single-cell analysis reveals altered tumor microenvironments of relapse- and remission-associated pediatric acute myeloid leukemia
Authors: Mumme Hope , Thomas Beena E. , Bhasin Swati S. , Krishnan Upaasana , Dwivedi Bhakti , Perumalla Pruthvi , Sarkar Debasree , Ulukaya Gulay B. , Sabnis Himalee S. , Park Sunita I. , DeRyckere Deborah , Raikar Sunil S. , Pauly Melinda , Summers Ryan J. , Castellino Sharon M. , Wechsler Daniel S. , Porter Christopher C. , Graham Douglas K. , Bhasin Manoj 
Published: October 2023

AbstractAcute myeloid leukemia (AML) microenvironment exhibits cellular and molecular differences among various subtypes. Here, we utilize single-cell RNA sequencing (scRNA-seq) to analyze pediatric AML bone marrow (BM) samples from diagnosis (Dx), end of induction (EOI), and relapse timepoints. Analysis of Dx, EOI scRNA-seq, and TARGET AML RNA-seq datasets reveals an AML blasts-associated 7-gene signature (CLEC11A, PRAME, AZU1, NREP, ARMH1, C1QBP, TRH), which we validate on independent datasets. The analysis reveals distinct clusters of Dx relapse- and continuous complete remission (CCR)-associated AML-blasts with differential expression of genes associated with survival. At Dx, relapse-associated samples have more exhausted T cells while CCR-associated samples have more inflammatory M1 macrophages. Post-therapy EOI residual blasts overexpress fatty acid oxidation, tumor growth, and stemness genes. Also, a post-therapy T-cell cluster associated with relapse samples exhibits downregulation of MHC Class I and T-cell regulatory genes. Altogether, this study deeply characterizes pediatric AML relapse- and CCR-associated samples to provide insights into the BM microenvironment landscape.
Claudin-23 reshapes epithelial tight junction architecture to regulate barrier function
Authors: Raya-Sandino Arturo , Lozada-Soto Kristen M. , Rajagopal Nandhini , Garcia-Hernandez Vicky , Luissint Anny-Claude , Brazil Jennifer C. , Cui Guiying , Koval Michael , Parkos Charles A. , Nangia Shikha , Nusrat Asma 
Published: October 2023

AbstractClaudin family tight junction proteins form charge- and size-selective paracellular channels that regulate epithelial barrier function. In the gastrointestinal tract, barrier heterogeneity is attributed to differential claudin expression. Here, we show that claudin-23 (CLDN23) is enriched in luminal intestinal epithelial cells where it strengthens the epithelial barrier. Complementary approaches reveal that CLDN23 regulates paracellular ion and macromolecule permeability by associating with CLDN3 and CLDN4 and regulating their distribution in tight junctions. Computational modeling suggests that CLDN23 forms heteromeric and heterotypic complexes with CLDN3 and CLDN4 that have unique pore architecture and overall net charge. These computational simulation analyses further suggest that pore properties are interaction-dependent, since differently organized complexes with the same claudin stoichiometry form pores with unique architecture. Our findings provide insight into tight junction organization and propose a model whereby different claudins combine to form multiple distinct complexes that modify epithelial barrier function by altering tight junction structure.
Coherent propagation of spin-orbit excitons in a correlated metal
Authors: Zimmermann Valentin , Yogi Arvind Kumar , Wong Deniz , Schulz Christian , Bartkowiak Maciej , Habicht Klaus , Wang Lichen , Isobe Masahiko , Minola Matteo , Khaliullin Giniyat , Keimer Bernhard , Hepting Matthias 
Published: October 2023

AbstractCollective excitations such as plasmons and paramagnons are fingerprints of atomic-scale Coulomb and exchange interactions between conduction electrons in metals. The strength and range of these interactions, which are encoded in the excitations’ dispersion relations, are of primary interest in research on the origin of collective instabilities such as superconductivity and magnetism in quantum materials. Here we report resonant inelastic x-ray scattering experiments on the correlated 4d-electron metal Sr2RhO4, which reveal a spin-orbit entangled collective excitation. The dispersion relation of this mode is opposite to those of antiferromagnetic insulators such as Sr2IrO4, where the spin-orbit excitons are dressed by magnons. The presence of propagating spin-orbit excitons implies that the spin-orbit coupling in Sr2RhO4 is unquenched, and that collective instabilities in 4d-electron metals and superconductors must be described in terms of spin-orbit entangled electronic states.
COVID-19 mRNA vaccine-mediated antibodies in human breast milk and their association with breast milk microbiota composition
Authors: Zhao Shilin , Lok Kris Y. W. , Sin Zhen Y. , Peng Ye , Fan Heidi S. L. , Nagesh Nitya , Choi Martha S. L. , Kwok Jojo Y. Y. , Choi Edmond P. H. , Zhang Xi , Wai Hogan Kok-Fung , Tsang Leo C. H. , Cheng Samuel S. M. , Wong Matthew K. L. , Zhu Jie , Mok Chris K. P. , Ng Siew C. , Chan Francis K. L. , Peiris Malik , Poon Leo L. M. , Tun Hein M. 
Published: October 2023

AbstractNewborns can acquire immunological protection to SARS-CoV-2 through vaccine-conferred antibodies in human breast milk. However, there are some concerns around lactating mothers with regards to potential short- and long-term adverse events and vaccine-induced changes to their breast milk microbiome composition, which helps shape the early-life microbiome. Thus, we sought to explore if SARS-CoV-2 mRNA vaccine could change breast milk microbiota and how the changes impact the levels of antibodies in breast milk. We recruited 49 lactating mothers from Hong Kong who received two doses of BNT162b2 vaccine between June 2021 and August 2021. Breast milk samples were self-collected by participants pre-vaccination, one week post-first dose, one week post-second dose, and one month post-second dose. The levels of SARS-CoV-2 spike-specific IgA and IgG in breast milk peaked at one week post-second dose. Subsequently, the levels of both antibodies rapidly waned in breast milk, with IgA levels returning to baseline levels one month post-second dose. The richness and composition of human breast milk microbiota changed dynamically throughout the vaccination regimen, but the abundances of beneficial microbes such as Bifidobacterium species did not significantly change after vaccination. Additionally, we found that baseline breast milk bacterial composition can predict spike-specific IgA levels at one week post-second dose (Area Under Curve: 0.72, 95% confidence interval: 0.58–0.85). Taken together, our results identified specific breast milk microbiota markers associated with high levels of IgA in the breast milk following BNT162b2 vaccine. Furthermore, in lactating mothers, BNT162b2 vaccines did not significantly reduce probiotic species in breast milk.
Continuous wideband microwave-to-optical converter based on room-temperature Rydberg atoms
Authors: Borówka Sebastian , Pylypenko Uliana , Mazelanik Mateusz , Parniak Michał 
Published: October 2023

AbstractThe coupling of microwave and optical systems presents an immense challenge due to the natural incompatibility of energies, but potential applications range from optical interconnects for quantum computers to next-generation quantum microwave sensors, detectors and coherent imagers. Several of the engineered platforms that have emerged are constrained by specific conditions, such as cryogenic environments, impulse protocols or narrowband fields. Here we employ Rydberg atoms that allow the wideband coupling of optical and microwave photons at room temperature with the use of a modest set-up. We present continuous-wave conversion of a 13.9 GHz field to a near-infrared optical signal using an ensemble of Rydberg atoms via a free-space six-wave mixing process designed to minimize noise interference from any nearby frequencies. The Rydberg photonic converter exhibits a conversion dynamic range of 57 dB and a wide conversion bandwidth of 16 MHz. Using photon counting, we demonstrate the readout of photons of free-space 300 K thermal background radiation at 1.59 nV cm−1 rad−1/2 s−1/2 (3.98 nV cm−1 Hz−1/2) with a sensitivity down to 3.8 K of noise-equivalent temperature, allowing us to observe Hanbury Brown and Twiss interference of microwave photons.
Depletion of slow-cycling PDGFRα+ADAM12+ mesenchymal cells promotes antitumor immunity by restricting macrophage efferocytosis
Authors: Di Carlo Selene E. , Raffenne Jerome , Varet Hugo , Ode Anais , Granados David Cabrerizo , Stein Merle , Legendre Rachel , Tuckermann Jan , Bousquet Corinne , Peduto Lucie 
Published: October 2023

AbstractThe capacity to survive and thrive in conditions of limited resources and high inflammation is a major driver of tumor malignancy. Here we identified slow-cycling ADAM12+PDGFRα+ mesenchymal stromal cells (MSCs) induced at the tumor margins in mouse models of melanoma, pancreatic cancer and prostate cancer. Using inducible lineage tracing and transcriptomics, we demonstrated that metabolically altered ADAM12+ MSCs induced pathological angiogenesis and immunosuppression by promoting macrophage efferocytosis and polarization through overexpression of genes such as Gas6, Lgals3 and Csf1. Genetic depletion of ADAM12+ cells restored a functional tumor vasculature, reduced hypoxia and acidosis and normalized CAFs, inducing infiltration of effector T cells and growth inhibition of melanomas and pancreatic neuroendocrine cancer, in a process dependent on TGF-β. In human cancer, ADAM12 stratifies patients with high levels of hypoxia and innate resistance mechanisms, as well as factors associated with a poor prognosis and drug resistance such as AXL. Altogether, our data show that depletion of tumor-induced slow-cycling PDGFRα+ MSCs through ADAM12 restores antitumor immunity.