bluuebunny/crossref_metadata_2025_split huggingface dataset:
Activation of Ca2+ oscillations in rice (Oryza sativa) root hairs expressing the legume-specific Nod factor receptor kinases MtNFP and MtLYK3
Authors: Singh Anjulata , Altúzar-Molina Alma , Kaur Gurdeep , Sidhu Gurbir Kaur , MANDAL PRANAB KUMAR , Reddy Pallavolu Maheswara 
Published: June 2024

Abstract

Nitrogen is a critical nutrient for rice production. Chemical fertilizers have been the main source of nitrogen for crop production, but their indiscriminate use has adversely affected human and environmental health. Legumes form symbiosis with rhizobia as well as arbuscular mycorrhizal fungi (AMF) to fix atmospheric nitrogen and uptake of phosphorus, respectively. Formation of symbiotic associations in legumes with rhizobia and AMF utilize a shared genetic network known as a common symbiotic signalling pathway (CSSP). Similar to legumes rice forms a symbiotic association only with AMF and possesses a similar CSSP that promotes the formation of arbuscular mycorrhizal symbiosis (AMS). Some vital genes for Nod factor (NF) perception are not conserved in rice, while a part of the genetic network for rhizobial symbiosis in legumes is conserved in rice. Hence, to make a symbiotic association with Rhizobium, we developed transgenic rice lines expressing legume nodulation-specific receptor kinase genes (MtLYK3 and MtNFP) and evaluated their ability to perceive rhizobial NF. Besides, we crossed these transgenic plants with others expressing the Cameleon calcium (Ca2+) sensor and assessed the NF-induced Ca2+ fluxes and spiking around nuclei in root hairs. Confocal microscopy of the root hairs in the hybrid transgenic plants revealed that NF can promote Ca2+ fluxes at root hair tips as well as Ca2+ spiking around nuclei. These results showed that the rice plants expressing MtLYK3 and MtNFP gained the ability to perceive NF and transmit nod signals appropriately to trigger calcium fluxes and spiking akin to that in legume roots.
Analysis and identification of mitochondrial DNA associated with age-related hearing loss
Authors: ma Tianyu , Zeng Xiaoyun , Liu Mengting , Xu Shijia , Wang Yuyao , Wu Qilong , Zhang# Tianhong 
Published: June 2024

Abstract

Background
To explore the mitochondrial genes that play a key role in the occurrence and development of age-related hearing loss(ARHL), provide a basis for the study of the mechanism of ARHL.
Results
A total of 503 differentially expressed genes (DEGs) were detected in the GSE49543 dataset,233 genes were up-regulated and 270 genes were down-regulated. There are a total of 1140 genes in the mitochondrial gene bank and 28 DE-MFRGS related to ARHL. These genes are mainly involved in mitochondrial respiratory chain complex assembly, small molecule catabolism, NADH dehydrogenase complex assembly, organic acid catabolism, precursor metabolites and energy production, and mitochondrial span Membrane transport, metabolic processes of active oxygen species. Then, the three key genes were identified by Cytoscape software :Aco2,Bcs1l and Ndufs1. Immunofluorescence and Western blot experiments confirmed that the protein content of three key genes in aging cochlear hair cells decreased.
Conclusion
We employed bioinformatics analysis to screen 503 differentially expressed genes and identified three key genes associated with ARHL. Subsequently, we conducted in vitro experiments to validate their significance, thereby providing a valuable reference for further elucidating the role of mitochondrial function in the pathogenesis and progression of ARHL.
Low Concentration Cell Painting Images Enable the Identification of Highly Potent Compounds
Authors: Ha Son V. , Jaensch Steffen , Freitas Lorena G. A. , Herman Dorota , Czodrowski Paul , Ceulemans Hugo 
Published: June 2024

Abstract

Image-based models that use features extracted from cell microscopy images can estimate the activity of small molecules in various biological assays. Typically, models are trained on images stained by an optimized protocol (e.g. Cell Painting) after exposure to a fairly high small molecule concentration (referred to as ’image concentration’) of 10μM or higher. Low concentration images (e.g. 0.16μM, 0.8μM, 4μM) tend to yield models with worse performance. In this work, we nevertheless report a practical use for low image concentration data. We propose the combination of well-performing models trained at higher image concentrations, with lower image concentration for inference to identify more potent compounds. We show that this approach improves on the traditional method (directly training a high-potency model) in 65% of assays investigated in terms of AUC-ROC, and 75% of assays in terms of RIPtoP-corrected AUC-PR.
Machine learning model based on clinical features to diagnose unexplained dizziness with patent foramen ovale
Authors: Li Yanping , Xiang Wenwen , Luo Haowen , Qiao Luyao , Xu Lijun , Tang Zhenyu 
Published: June 2024

Abstract

Objectives: Until recently, unexplained dizziness has received little attention. Clinicians have troubles to offer for the prevention and treatment of unexplained dizziness. This study aims to develop a machine learning model for diagnosing unexplained dizziness with patent foramen ovale and investigate key clinical features of this disorder.
Methods: A cross-sectional, observational study of adults referred for unexplained dizziness enrolled from January 2019 to June 2023 at our tertiary hospital was undertaken. Subjects were split into dizziness with PFO group and non-PFO group. Demographic and clinical characteristics were collected. We randomly sampled data into training and validation sets by 7:3. LASSO regression was used to select the saliently important features in the training sets. Seven machine learning algorithms were used to develop a machine learning model for diagnosing unexplained dizziness with PFO. The area under the receiver operating characteristic curve (AUROC), the area under the precision-recall curve (AUPRC), accuracy, sensitivity, specificity, and F1-score were measured to evaluate the performance of models. The SHapley Additive exPlanations (SHAP) value was used to visualize the importance of key factors.
Results:233 unexplained dizziness patients met the criteria for PFO,160 unexplained dizziness patients without PFO. Dizziness triggers and aggravating factors, recurrent episodes, chest tightness, amaurosis, palpitation, chronic persistent and age were selected according to LASSO regression in the training sets. Repeated cross-validation showed that the LGB model had the highest AUROC of 0.871(95%CI 0.86,0.882), AUPRC of 0.886(95%CI 0.878,0.894) among seven models. The model had high comprehensive performance and strong predictive power. SHAP analysis demonstrated the visual interpretation of the optimal model and revealed how the interaction of age and other features in the model affected the diagnosis of PFO.
Conclusions: The LGB diagnosing model could effectively and reliably diagnose unexplained dizziness with PFO. SHAP analysis could improve the visual interpretation of machine learning models and help physicians better understand how the features affect outcomes.
Polystyrene micro- and nanoplastics aggravates colitis in a mouse model – effects on biodistribution, macrophage polarization, and gut microbiome
Authors: Kopatz Verena , Draganic Kristina , Horvath Angela , Pfneissl Janette , Kabiljo Julijan , Mödl Bernadette , Timelthaler Gerald , Wallner Julia , Mirzaei Zeynab , Beratlyte Saule , Schlederer Michaela , Hollóczki Oldamur , Raigel Martin , Widder Joachim , Resch Ulrike , Kufferath Iris , Wadsak Wolfgang , Sarau George , Christiansen Silke , Kolev Nikola Zlatkov , Eferl Robert , Egger Gerda , Stadlbauer-Köllner Vanessa , Pichler Verena , Kenner Lukas 
Published: June 2024

Abstract

Background
The increasing prevalence of inflammatory bowel disease (IBD) and rising pollution from micro- and nanoplastic (MNP) particles has prompted investigations on their potential interconnection. To elucidate the complex relationship between IBD and exposure to MNPs, we induced colitis in mice using dextran sodium sulfate (DSS) and orally administered a solution of differently sized polystyrene (PS) MNPs (diameter 10, 1, and 0.29 µm). These particles facilitated a detailed examination of MNP biodistribution, macrophage response, and gut microbiome alterations under inflammatory conditions.
Results
Specifically nanosized PS particles accumulated in the bloodstream and excretory organs, with enhanced accumulation in the colitis model. Macrophages shifted towards a pro-inflammatory phenotype, with decreased anti-inflammatory markers highlighting the intricate effects of MNPs on inflammation and immune cell behavior. Moreover, MNPs significantly disrupted the gut microbiome, reducing microbial diversity and shifting bacterial populations towards pro-inflammatory and potentially pathogenic species.
Conclusions
These changes suggest that MNP exposure could exacerbate colitis through complex interactions involving MNPs, immune responses, and microbial dynamics. The fast growing exposure to MNPs underscores the urgent need for comprehensive public health strategies to address MNP pollution, its implications for disease and potential impacts on public health.
How does the morphology of proximal femur affect the total hip arthroplasty of hemophilic patients: A retrospective study
Authors: Gong Yichen , Huang Hua , Su Hai , Zhou Haojin , Tong Peijian 
Published: June 2024

Abstract

Introduction: Patients with hemophilia (PWH) constantly suffer hemarthrosis, which leads to deformity of the hip joint. There is a lack of understanding on the unusual morphology of proximal femur in PWH. To explore how does the morphology of proximal femur affect the total hip arthroplasty (THA) of PWH, we conducted a 5-year retrospective study on PWH who underwent THA.
Methods: The retrospective study comprised data of adult patients who received THA from 2018 to 2022 in the research center. Patients having a diagnosis of hemophilic arthritis and received THA were included and divided into three groups according to Dorr classification. The surgical time, surgical blood loss, laboratory examinations post-operation including hemoglobin (HB), total protein (TP), activated partial thromboplastin time (APTT), D-dimer (D2), C-reactive protein level (CRP), erythrocyte sedimentation rate (ESR), and functional evaluations 1 year after surgery including visual analogue scale (VAS), Harris hip score (HHS), range of motion (ROM) were collected. Kolmogorov-Smirnov test was used to test data normality, and t-test were performed by SPSS 20. P<0.05 was considered statistically significant.
Results: 33 PWH were included in the study and finished follow-up. All cases were male patients. Among the 33 hips, 19 (57.6%) were classified to Dorr A, and 12 (36.4%) were Dorr B, and only 2 (6%) were Dorr C. No significant difference was found in expanse, hospital stay, surgical time and total blood loss. PWH with Dorr A requires significant less coagulation factor than Dorr B and Dorr C. All Dorr types of hips presented good recovery from the surgery according to the perioperative examinations including hemoglobin (HB), total protein (TP), activated partial thromboplastin time (APTT), D-dimer (D2), C-reactive protein level (CRP), erythrocyte sedimentation rate (ESR) and thigh circumference (TC). The 2-year follow-up demonstrated favorable functional rehabilitation according to functional evaluations including visual analogue scale (VAS), Harris hip score (HHS)) and range of motion (ROM).
Conclusion: In this study, we found that PWH tend to have more Dorr A than the normal. PWH with Dorr A requires smaller dosage to maintain the coagulation factor activity than the Dorr B and Dorr C. Additionally, all types of hip presented good recovery after THA. Finally, THA is an effective treatment for PWH with all Dorr classifications by alleviating the pain and improve the motor function.
Engaging with art in-the-wild at the Barnes Foundation and Penn Museum
Authors: Darda Kohinoor M. , Gonzalez Vicente Estrada , Christensen Alexander P. , Bobrow Isabella , Krimm Amy , Nasim Zuha , Cardillo Eileen R. , Perthes William , Chatterjee Anjan 
Published: June 2024

Abstract

As cultural consumption increasingly moves to a digital space, it is crucial to understand the evolving landscape of art consumption both in and outside of a physical museum context. The current study delves into this contrast, seeking to understand how art is perceived and appreciated in museums and on a digital medium (like a computer screen). Across two experiments at the Barnes Foundation and Penn Museum in Philadelphia, Pennsylvania, we explored how the aesthetic engagement of paintings and artifacts is influenced by the physical context in which an artwork is encountered and by the characteristics of the viewer. Our findings suggest that the cognitive and emotional impacts of artworks on viewers, as well as the viewers’ overall aesthetic experiences are comparable across physical museum spaces and digital platforms. However, participants reported gaining more understanding from art viewed in museums, compared to participants who viewed art in the lab. Art experience and openness to experience influenced aesthetic impacts and ratings differently in the museum and in the lab. Overall, routes to broader valuations of liking were more similar than different between the museum and lab contexts, whereas patterns of impacts that might lead to new knowledge or understanding gained differed between museum and lab contexts. As digital technologies are increasingly integrated into diverse processes in museums such as collections management, curation, exhibitions, and education and learning, our research highlights how museums can leverage digital expansion to achieve their missions as centers of learning and education.
A morphoelastic theory of biological shells: Application to the Volvox globator invagination
Authors: Chen Xiaoyi , Yu Xiang , Ciarletta Pasquale 
Published: June 2024

Abstract

The embryo of Volvox globator, a monolayer spheroidal cell sheet, undergoes an inversion to release its flagella during the late stage of its de- velopment. This inversion, known as the type-B inversion, initiates from the equator. Other types of inversions also exist, such as the inversion from the anterior pole of Volvox carteri and the bowl-shaped inversion of Pleodorina. These inversions can be regarded as axisymmetric processes, during which complex fold patterns are generated. The invagination of the cell sheet plays a crucial role in embryonic development, and our aim is to understand this process from an interdisciplinary point of view, with a particular focus on the mechanical aspects. In this work, we first develop a morphoelastic shell theory for general deformations of biological shells, incorporating both active and passive biomechanical effects, as well as membrane and bending effects. By means of asymptotic analysis, we establish an analytical framework to study axisymmetric deformations of morphoelastic shells focusing mainly on the membrane effects. For illustrative purposes, we apply this framework to investigate the invagination of Volvox globator embryo. The underlying active stretches driving this process are derived analytically by inverse analysis of experimental data through the morphoelastic shell model. We highlight a two- order remodeling strategy that generates the observed invagination pattern: the Gaussian morphing of the cell sheet creates the first fundamental form of the stress-free folded patterns, while a secondary remodeling generates the membrane tension necessary to balance the external pressure and the second fundamental form of the invaginated pattern. This remodeling strategy unveils the complex interplay between geometry, mechanics, and biological processes during Volvox globator embryogenesis.
Mathematics Subject Classification (2020) MSC code1 · MSC code2 more
An Innovative Comparative Performance Analysis on Document Store Non- Relational Databases
Authors: Miah Shah , Fahd Kiran , Venkatraman Sitalakshmi , Parvin Sazia 
Published: June 2024

Abstract

The crucial role of competent software architecture is essential in managing the challenging of big data processing for both relational and nonrelational databases. Relational databases are designed to structure data for facilitating vertical scalability, while non-relational databases excel in handling vast volumes of unstructured data for enhancing horizontal scalability. Choosing the right database paradigm is determined by the needs of the organization, yet selecting the best option may often be a challenging task. Large number of applications still use relational databases due to its benefits of reliability, flexibility, robustness, and scalability. However, with the rapid growth in web and mobile applications as well as huge amounts of complex unstructured data generated via online and offline platforms, nonrelational databases are compensating for the inefficiency of relational databases. Since selecting the right nonrelational database method for high performing applications from a plethora of possibilities is a challenging task, existing studies are still at emergent stage to compare the performance of different popular nonrelational databases. This paper introduces a novel benchmarking approach for tailoring the comparative study of nonrelational databases. To illustrate our approach, we compare two leading non-relational databases, Aerospike and MongoDB, focusing on their average transaction times to evaluate the database performance. Our comprehensive analysis reveals the strengths of each database in read and write operations for single record and bulk record batch transactions.
Bibliometric analysis and visualisation of research hotspots and frontiers on omics in osteosarcoma
Authors: Wang Xinyu , Cao Xin , Dai Zhongshang , Dai Zhehao 
Published: June 2024

Abstract

Background/objective
Omics technology has become a widely applied biological science that can be used to study the etiology, pathogenesis, and treatment of osteosarcoma(OS). Bibliometric analysis is still blank in this field.This study aimed to access the trends and hotspots of omics in OS research through the bibliometric analysis method.
Methods
Relevant articles and reviews from 1999 to 2023 were retrieved from the Web of Science Core Collection. The data were processed with CiteSpace, and some graphs were generated with Graphpad, VOSviewer, Scimago Graphica, Bibliometrix and R Studio.
Results
A total of 1581 papers were included. China (569, 36.0%) and the United States (523, 33.1%) took the dominant position in the number of published papers, and the links between countries most frequently occurred between North America and East Asia, and between Australia and Europe. Top institutions with the highest number of publications were almost located in the United States, with The University of Texas MD Anderson Cancer Center contributing the most (44, 2.78%). Among the researchers in this field, Cleton-Jansen AM was the author with the highest number of articles in the field (20, 1.27%). According to the keyword cluster analysis, most studies focused on the “comparative genomic hybridization” before 2012. The latest surge words "tumor microenvironment" and "immune infiltration" in the keyword heatmap indicate future research directions.
Conclusion
Our study provided the current status of the omics research in OS on a global level and the hottest directions. The field of omics in OS was developing rapidly, and the main focuses of research were revealing the characteristics of tumor microenvironment of OS and how to activate the immune system to fight cancer cells. Research on the immune microenvironment and its molecular mechanisms will be a priority in the future.
Sequence Tagging Approach in Grammar Error Detection: Identifying Areas of Improvement for the State-of-the-Art
Authors: Wang Qiao , Yuan Zheng 
Published: June 2024

Abstract

This study provides a qualitative evaluation of Seqtagger, a state-of-the-art machine learning-based sequence-tagging model developed for grammatical error detection (GED) and correction (GEC). The model's performance is evaluated on error detection against human benchmarks, with academic texts written by Japanese university students. Through human annotation and subsequent thematic analysis on failures in error detection, this study reveals that Seqtagger performs well in detecting errors related to simpler grammatical rules such as adverb position and prepositions in fixed collocations, with poorer performance in errors possibly influenced by the Japanese language, macro-structure errors and errors where human judgment is required. The underlying reasons for failures in detection are identified to be a narrow context window that fails to capture broader textual information, insufficient training data, particularly data that fully represents the linguistic characteristics of the Japanese students, and overgeneralization of patterns from the training data. These findings highlight the need for sequence-tagging GED and GEC tools to enhance their context window, be more adaptable to the diverse linguistic features of global learners and to enhance the ability to understand the linguistic complexities of the English language.
Wind tunnel tests on aerodynamic loads and structural responses of crescent-shaped wingsails
Authors: Zhu Heng , Chernoray Valery , Ringsberg Jonas W. , Ramne Bengt , Yao Hua-Dong 
Published: June 2024

Abstract

Wingsails as a classical means for wind-assisted ship propulsion is booming today. Crescent-shaped wingsails have shown great potential considering their aerodynamics in thrust generation. However, there have been few studies on its structural responses exposed to unsteady aerodynamic loads. In this study, a crescent-shaped wingsail at a \(1:100\) scale is investigated by using wind tunnel tests. The wingsail with aspect ratios of \(0.19\) and \(0.33\), which are derived from practical wingsail design, are measured at the angle of attack (\(\alpha\)) from \(0^\circ\) to \(90^\circ\), and at the wind speed from \(20 m/s\) to \(40 m/s\). The wind loads, pressure distribution, and wingsail tip displacements are measured and discussed. A study of the Reynolds number sensitivity indicates that the trends of the force coefficients and critical \(\alpha\) are changed when the Reynolds number (\(Re\)) is above \(3.1\times {10}^{5}\). Besides, at \(Re=3.1\times {10}^{5}\) a lift crisis is found for \(\alpha\) below \(10^\circ\), and a drag crisis happens for \(\alpha =0^\circ\) at \(Re=3.6\times {10}^{5}\). Structural response analysis is conducted based on the wingsail tip displacement in the direction perpendicular to the chord line. The fundamental eigenfrequency of the structure, instead of the flow-induced frequencies, is found to dominate the fluid-structure interaction measured in the tests. Furthermore, the aerodynamic performance of a three-wingsail system is analyzed based on experiments. Notable interactions are found among the three wingsails.