bluuebunny/crossref_metadata_2025_split huggingface dataset:
Extracting Latent Variables From Forecast Ensembles and Advancements in Similarity Metric Utilizing Optimal Transport
Authors: Nishizawa S. 
Published: May 2024

AbstractThis study presents a novel methodology for extracting latent variables from high‐dimensional sparse data, particularly emphasizing spatial distributions such as precipitation distribution. This approach utilizes multidimensional scaling with a distance matrix derived from a new similarity metric, the Unbalanced Optimal Transport Score (UOTS). UOTS effectively captures discrepancies in spatial distributions while preserving physical units. This is similar to mean absolute error, however it considers location errors, providing a more robust measure crucial for understanding differences between observations, forecasts, and ensembles. Probability distribution estimation of these latent variables enhances the analytical utility, quantifying ensemble characteristics. The adaptability of the method to spatiotemporal data and its ability to handle errors suggest its potential as a promising tool for diverse research applications.
VOLTA: an enVironment-aware cOntrastive ceLl represenTation leArning for histopathology
Authors: Nakhli Ramin , Rich Katherine , Zhang Allen , Darbandsari Amirali , Shenasa Elahe , Hadjifaradji Amir , Thiessen Sidney , Milne Katy , Jones Steven J. M. , McAlpine Jessica N. , Nelson Brad H. , Gilks C. Blake , Farahani Hossein , Bashashati Ali 
Published: May 2024

AbstractIn clinical oncology, many diagnostic tasks rely on the identification of cells in histopathology images. While supervised machine learning techniques necessitate the need for labels, providing manual cell annotations is time-consuming. In this paper, we propose a self-supervised framework (enVironment-aware cOntrastive cell represenTation learning: VOLTA) for cell representation learning in histopathology images using a technique that accounts for the cell’s mutual relationship with its environment. We subject our model to extensive experiments on data collected from multiple institutions comprising over 800,000 cells and six cancer types. To showcase the potential of our proposed framework, we apply VOLTA to ovarian and endometrial cancers and demonstrate that our cell representations can be utilized to identify the known histotypes of ovarian cancer and provide insights that link histopathology and molecular subtypes of endometrial cancer. Unlike supervised models, we provide a framework that can empower discoveries without any annotation data, even in situations where sample sizes are limited.
Aptameric hirudins as selective and reversible EXosite-ACTive site (EXACT) inhibitors
Authors: Yu Haixiang , Kumar Shekhar , Frederiksen James W. , Kolyadko Vladimir N. , Pitoc George , Layzer Juliana , Yan Amy , Rempel Rachel , Francis Samuel , Krishnaswamy Sriram , Sullenger Bruce A. 
Published: May 2024

AbstractPotent and selective inhibition of the structurally homologous proteases of coagulation poses challenges for drug development. Hematophagous organisms frequently accomplish this by fashioning peptide inhibitors combining exosite and active site binding motifs. Inspired by this biological strategy, we create several EXACT inhibitors targeting thrombin and factor Xa de novo by linking EXosite-binding aptamers with small molecule ACTive site inhibitors. The aptamer component within the EXACT inhibitor (1) synergizes with and enhances the potency of small-molecule active site inhibitors by many hundred-fold (2) can redirect an active site inhibitor’s selectivity towards a different protease, and (3) enable efficient reversal of inhibition by an antidote that disrupts bivalent binding. One EXACT inhibitor, HD22-7A-DAB, demonstrates extraordinary anticoagulation activity, exhibiting great potential as a potent, rapid onset anticoagulant to support cardiovascular surgeries. Using this generalizable molecular engineering strategy, selective, potent, and rapidly reversible EXACT inhibitors can be created against many enzymes through simple oligonucleotide conjugation for numerous research and therapeutic applications.
Polar Bloch points in strained ferroelectric films
Authors: Wang Yu-Jia , Feng Yan-Peng , Tang Yun-Long , Zhu Yin-Lian , Cao Yi , Zou Min-Jie , Geng Wan-Rong , Ma Xiu-Liang 
Published: May 2024

AbstractTopological domain structures have drawn great attention as they have potential applications in future electronic devices. As an important concept linking the quantum and classical magnetism, a magnetic Bloch point, predicted in 1960s but not observed directly so far, is a singular point around which magnetization vectors orient to nearly all directions. Here we show polar Bloch points in tensile-strained ultrathin ferroelectric PbTiO3 films, which are alternatively visualized by phase-field simulations and aberration-corrected scanning transmission electron microscopic imaging. The phase-field simulations indicate local steady-state negative capacitance around the Bloch points. The observation of polar Bloch points and their emergent properties consequently implies novel applications in future integrated circuits and low power electronic devices.
Mechanically induced correlated errors on superconducting qubits with relaxation times exceeding 0.4 ms
Authors: Kono Shingo , Pan Jiahe , Chegnizadeh Mahdi , Wang Xuxin , Youssefi Amir , Scigliuzzo Marco , Kippenberg Tobias J. 
Published: May 2024

AbstractSuperconducting qubits are among the most advanced candidates for achieving fault-tolerant quantum computing. Despite recent significant advancements in the qubit lifetimes, the origin of the loss mechanism for state-of-the-art qubits is still subject to investigation. Furthermore, the successful implementation of quantum error correction requires negligible correlated errors between qubits. Here, we realize long-lived superconducting transmon qubits that exhibit fluctuating lifetimes, averaging 0.2 ms and exceeding 0.4 ms – corresponding to quality factors above 5 million and 10 million, respectively. We then investigate their dominant error mechanism. By introducing novel time-resolved error measurements that are synchronized with the operation of the pulse tube cooler in a dilution refrigerator, we find that mechanical vibrations from the pulse tube induce nonequilibrium dynamics in highly coherent qubits, leading to their correlated bit-flip errors. Our findings not only deepen our understanding of the qubit error mechanisms but also provide valuable insights into potential error-mitigation strategies for achieving fault tolerance by decoupling superconducting qubits from their mechanical environments.
Temperature alters the predator-prey size relationships and size-selectivity of Southern Ocean fish
Authors: Eskuche-Keith Patrick , Hill Simeon L. , López-López Lucía , Rosenbaum Benjamin , Saunders Ryan A. , Tarling Geraint A. , O’Gorman Eoin J. 
Published: May 2024

AbstractA primary response of many marine ectotherms to warming is a reduction in body size, to lower the metabolic costs associated with higher temperatures. The impact of such changes on ecosystem dynamics and stability will depend on the resulting changes to community size-structure, but few studies have investigated how temperature affects the relative size of predators and their prey in natural systems. We utilise >3700 prey size measurements from ten Southern Ocean lanternfish species sampled across >10° of latitude to investigate how temperature influences predator-prey size relationships and size-selective feeding. As temperature increased, we show that predators became closer in size to their prey, which was primarily associated with a decline in predator size and an increase in the relative abundance of intermediate-sized prey. The potential implications of these changes include reduced top-down control of prey populations and a reduction in the diversity of predator-prey interactions. Both of these factors could reduce the stability of community dynamics and ecosystem resistance to perturbations under ocean warming.
Herpes simplex encephalitis due to a mutation in an E3 ubiquitin ligase
Authors: Bibert Stéphanie , Quinodoz Mathieu , Perriot Sylvain , Krebs Fanny S. , Jan Maxime , Malta Rita C. , Collinet Emilie , Canales Mathieu , Mathias Amandine , Faignart Nicole , Roulet-Perez Eliane , Meylan Pascal , Brouillet René , Opota Onya , Lozano-Calderon Leyder , Fellmann Florence , Guex Nicolas , Zoete Vincent , Asner Sandra , Rivolta Carlo , Du Pasquier Renaud , Bochud Pierre-Yves 
Published: May 2024

AbstractEncephalitis is a rare and potentially fatal manifestation of herpes simplex type 1 infection. Following genome-wide genetic analyses, we identified a previously uncharacterized and very rare heterozygous variant in the E3 ubiquitin ligase WWP2, in a 14-month-old girl with herpes simplex encephalitis. The p.R841H variant (NM_007014.4:c.2522G > A) impaired TLR3 mediated signaling in inducible pluripotent stem cells-derived neural precursor cells and neurons; cells bearing this mutation were also more susceptible to HSV-1 infection compared to control cells. The p.R841H variant increased TRIF ubiquitination in vitro. Antiviral immunity was rescued following the correction of p.R841H by CRISPR-Cas9 technology. Moreover, the introduction of p.R841H in wild type cells reduced such immunity, suggesting that this mutation is linked to the observed phenotypes.
Fragment ion intensity prediction improves the identification rate of non-tryptic peptides in timsTOF
Authors: Adams Charlotte , Gabriel Wassim , Laukens Kris , Picciani Mario , Wilhelm Mathias , Bittremieux Wout , Boonen Kurt 
Published: May 2024

AbstractImmunopeptidomics is crucial for immunotherapy and vaccine development. Because the generation of immunopeptides from their parent proteins does not adhere to clear-cut rules, rather than being able to use known digestion patterns, every possible protein subsequence within human leukocyte antigen (HLA) class-specific length restrictions needs to be considered during sequence database searching. This leads to an inflation of the search space and results in lower spectrum annotation rates. Peptide-spectrum match (PSM) rescoring is a powerful enhancement of standard searching that boosts the spectrum annotation performance. We analyze 302,105 unique synthesized non-tryptic peptides from the ProteomeTools project on a timsTOF-Pro to generate a ground-truth dataset containing 93,227 MS/MS spectra of 74,847 unique peptides, that is used to fine-tune the deep learning-based fragment ion intensity prediction model Prosit. We demonstrate up to 3-fold improvement in the identification of immunopeptides, as well as increased detection of immunopeptides from low input samples.
Halide Perovskite Inducing Anomalous Nonvolatile Polarization in Poly(vinylidene fluoride)-based Flexible Nanocomposites
Authors: Wang Yao , Huang Chen , Cheng Ziwei , Liu Zhenghao , Zhang Yuan , Zheng Yantao , Chen Shulin , Wang Jie , Gao Peng , Shen Yang , Duan Chungang , Deng Yuan , Nan Ce-Wen , Li Jiangyu 
Published: May 2024

AbstractFerroelectric materials have important applications in transduction, data storage, and nonlinear optics. Inorganic ferroelectrics such as lead zirconate titanate possess large polarization, though they are rigid and brittle. Ferroelectric polymers are light weight and flexible, yet their polarization is low, bottlenecked at 10 μC cm−2. Here we show poly(vinylidene fluoride) nanocomposite with only 0.94% of self-nucleated CH3NH3PbBr3 nanocrystals exhibits anomalously large polarization (~19.6 μC cm−2) while retaining superior stretchability and photoluminance, resulting in unprecedented electromechanical figures of merit among ferroelectrics. Comprehensive analysis suggests the enhancement is accomplished via delicate defect engineering, with field-induced Frenkel pairs in halide perovskite stabilized by the poled ferroelectric polymer through interfacial coupling. The strategy is general, working in poly(vinylidene fluoride-co-hexafluoropropylene) as well, and the nanocomposite is stable. The study thus presents a solution for overcoming the electromechanical dilemma of ferroelectrics while enabling additional optic-activity, ideal for multifunctional flexible electronics applications.
Integrating spin-dependent emission and dielectric switching in FeII catenated metal-organic frameworks
Authors: Wu Xue-Ru , Wu Shu-Qi , Liu Zhi-Kun , Chen Ming-Xing , Tao Jun , Sato Osamu , Kou Hui-Zhong 
Published: May 2024

AbstractMechanically interlocked molecules (MIMs) including famous catenanes show switchable physical properties and attract continuous research interest due to their potential application in molecular devices. The advantages of using spin crossover (SCO) materials here are enormous, allowing for control through diverse stimuli and highly specific functions, and enabling the transfer of the internal dynamics of MIMs from solution to solid state, leading to macroscopic applications. Herein, we report the efficient self-assembly of catenated metal-organic frameworks (termed catena-MOFs) induced by stacking interactions, through the combination of rationally selected flexible and conjugated naphthalene diimide-based bis-pyridyl ligand (BPND), [MI(CN)2]− (M = Ag or Au) and Fe2+ in a one-step strategy. The obtained bimetallic Hofmann-type SCO-MOFs [FeII(BPND){Ag(CN)2}2]·3CHCl3 (1Ag) and [FeII(BPND{Au(CN)2}2]·2CHCl3·2H2O (1Au) possess a unique three-dimensional (3D) catena-MOF constructed from the polycatenation of two-dimensional (2D) layers with hxl topology. Both complexes undergo thermal- and light-induced SCO. Significantly, abnormal increases in the maximum emission intensity and dielectric constant can be detected simultaneously with the switching of spin states. This research opens up SCO-actuated bistable MIMs that afford dual functionality of coupled fluorescence emission and dielectricity.
Role of umbilical cord mesenchymal stromal cells in skin rejuvenation
Authors: Chang Le , Fan Wei-Wen , Yuan He-Ling , Liu Xin , Wang Qiang , Ruan Guang-Ping , Pan Xing-Hua , Zhu Xiang-Qing 
Published: May 2024

AbstractAging is the main cause of many degenerative diseases. The skin is the largest and the most intuitive organ that reflects the aging of the body. Under the interaction of endogenous and exogenous factors, there are cumulative changes in the structure, function, and appearance of the skin, which are characterized by decreased synthesis of collagen and elastin, increased wrinkles, relaxation, pigmentation, and other aging characteristics. skin aging is inevitable, but it can be delayed. The successful isolation of mesenchymal stromal cells (MSC) in 1991 has greatly promoted the progress of cell therapy in human diseases. The International Society for Cellular Therapy (ISCT) points out that the MSC is a kind of pluripotent progenitor cells that have self-renewal ability (limited) in vitro and the potential for mesenchymal cell differentiation. This review mainly introduces the role of perinatal umbilical cord-derived MSC(UC-MSC) in the field of skin rejuvenation. An in-depth and systematic understanding of the mechanism of UC-MSCs against skin aging is of great significance for the early realization of the clinical transformation of UC-MSCs. This paper summarized the characteristics of skin aging and summarized the mechanism of UC-MSCs in skin rejuvenation reported in recent years. In order to provide a reference for further research of UC-MSCs to delay skin aging.
The risk of open angle glaucoma in young adults with allergic diseases: a Nationwide cohort study
Authors: Han Kyungdo , Jung Jin-Hyung , Jung Younhea , Ohn Kyoung , Moon Jung Il 
Published: May 2024

AbstractThis study investigated the potential associations between allergic diseases (asthma, allergic rhinitis, and atopic dermatitis) and the development of primary open-angle glaucoma. We utilized authorized data from the Korean National Health Information Database (KNHID), which provides comprehensive medical claims data and information from the National Health Screening Program. We compared the baseline characteristics of subjects with and without allergic diseases and calculated the incidence and risk of glaucoma development. Cox proportional hazard regression analysis was used to determine the risk of glaucoma development in subjects with allergic diseases. A total of 171,129 subjects aged 20–39 with or without allergic diseases who underwent a general health examination between 2009 and 2015 were included. Subjects with allergic diseases exhibited a higher incidence of glaucoma compared to the control group. The hazard ratio (HR) of glaucoma onset was 1.49 and 1.39 in subjects with at least one allergic disease before and after adjusting for potential confounding factors, respectively. Among allergic diseases, atopic dermatitis showed the highest risk for glaucoma development (aHR 1.73) after adjusting for confounders. Allergic rhinitis showed an increased risk for incident glaucoma after adjustment (aHR 1.38). Asthma showed the lowest but still increased risk for glaucoma (aHR 1.22). The associations were consistent in all subgroup analyses stratified by sex, smoking, drinking, exercise, diabetes, hypertension, dyslipidemia, or history of steroid. In conclusion, allergic diseases are associated with increased risk of glaucoma development. Among allergic diseases, atopic dermatitis showed the highest risk for glaucoma development followed by allergic rhinitis and asthma.
Fine tuning deep learning models for breast tumor classification
Authors: Heikal Abeer , El-Ghamry Amir , Elmougy Samir , Rashad M. Z. 
Published: May 2024

AbstractThis paper proposes an approach to enhance the differentiation task between benign and malignant Breast Tumors (BT) using histopathology images from the BreakHis dataset. The main stages involve preprocessing, which encompasses image resizing, data partitioning (training and testing sets), followed by data augmentation techniques. Both feature extraction and classification tasks are employed by a Custom CNN. The experimental results show that the proposed approach using the Custom CNN model exhibits better performance with an accuracy of 84% than applying the same approach using other pretrained models, including MobileNetV3, EfficientNetB0, Vgg16, and ResNet50V2, that present relatively lower accuracies, ranging from 74 to 82%; these four models are used as both feature extractors and classifiers. To increase the accuracy and other performance metrics, Grey Wolf Optimization (GWO), and Modified Gorilla Troops Optimization (MGTO) metaheuristic optimizers are applied to each model separately for hyperparameter tuning. In this case, the experimental results show that the Custom CNN model, refined with MGTO optimization, reaches an exceptional accuracy of 93.13% in just 10 iterations, outperforming the other state-of-the-art methods, and the other four used pretrained models based on the BreakHis dataset.
Parents' knowledge and attitudes towards extracorporeal membrane oxygenation and their post-traumatic stress symptoms
Authors: Sun Yuyan , Wang Huanhuan , Wu Yingying , Luo Leng , Shi Caixiao 
Published: May 2024

AbstractThis cross-sectional study, conducted between January 2020 and July 2023, aimed to assess the knowledge, attitude, and post-traumatic stress symptoms (PTSS) among parents with children undergoing extracorporeal membrane oxygenation (ECMO) treatment. Out of 201 valid questionnaires collected, the median knowledge score was 3.00, the mean attitude score was 27.00 ± 3.20, and the mean PTSS score was 3.50 ± 1.54. Logistic regression identified associations between PTSS and parents with lower education levels, particularly junior high school and high school/technical secondary school education, as well as those occupied as housewives. Structural equation modeling highlighted direct effects, such as the impact of residence on education, education on employment status, and associations between knowledge, attitude, PTSS, employment status, monthly income, and parental demographics. The findings indicated inadequate knowledge and suboptimal attitudes among parents, especially those with lower education levels, emphasizing the need for educational resources. Furthermore, addressing parental PTSS through psychosocial support and screening was deemed essential, providing valuable insights for tailored interventions in this context.
Spatial differentiation and influencing factors of red tourism resources transformation efficiency in China based on RMP-IO analysis
Authors: Liao Zhenjie , Wang Lang 
Published: May 2024

AbstractThis study employs modified data envelopment analysis (DEA) models and spatial autocorrelation methods to analyze the characteristics of red tourism transformation efficiency and categorize them into efficiency zones. By utilizing geographic detector models, the interactive driving mechanisms behind spatial differentiation are revealed, providing valuable insights for the high-quality transformation and development of China's red tourism economy. The application of modified DEA models facilitates the evaluation of red tourism resource transformation efficiency by decomposing comprehensive efficiency into single-factor efficiency for individual input and output variables. The results indicate that: (1) Expansion of tourism factors is crucial for achieving red tourism resource transformation in China, with low efficiency in resource endowment investment acting as the primary constraint. (2) Local spatial correlation between production efficiency and resource transformation efficiency demonstrates a decreasing trend from east to west, leading to the classification of China’s red tourism resources into five types of efficiency zones. (3) Endogenous ability factors predominantly affect red tourism resource transformation efficiency, with interaction between internal and external factors driving spatial differentiation.
A chain mediation model reveals the association between family sense of coherence and quality of life in caregivers of advanced cancer patients
Authors: Cui Panpan , Cheng Chunyan , An Huiying , Chen Xinyi , Chen Changying , Hu Hengyu 
Published: May 2024

AbstractCaregivers of advanced cancer patients face challenges impacting their quality of life (QoL). While evidence suggests that family sense of coherence (FSOC) can enhance individual psychological well-being and reduce distress symptoms, the precise mechanism through which FSOC improves caregivers' QoL remains unclear. This study aimed to explore the relationships among FSOC, psychological resilience, psychological distress, and QoL in primary caregivers of advanced cancer patients. A cross-sectional observational study was undertaken from June 2020 to March 2021 across five tertiary hospitals in China. Instruments included a general characteristic questionnaire, the Family Sense of Coherence Scale, the Patient Health Questionnaire-4, the 10-item Connor–Davidson Resilience Scale, and the 8-item SF-8 health survey. Pearson’s correlation and chain mediation analyses were performed using IBM SPSS (version 21) and PROCESS macro (version 3.4). Out of 290 valid questionnaires, results demonstrated that FSOC directly and positively influences caregivers' QoL. Psychological distress partially mediated the FSOC-QoL association, with paths "FSOC-psychological distress-QoL" and "FSOC-psychological resilience-psychological distress-QoL" contributing 43.08% and 6.72% of the total effect, respectively. Furthermore, this study distinguished physical and mental aspects of QoL, confirming both conform to the chain mediation model. FSOC impacts caregivers' QoL directly and indirectly through the mediation of psychological distress and the chain mediation effect of "psychological resilience-psychological distress". These insights enhance our understanding of the complex interplay between FSOC and QoL, underscoring the potential benefits of bolstering FSOC to strengthen caregiver resilience, alleviate distress, and ultimately elevate their QoL.