bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pointwise density estimation on metric spaces and applications in seismology
Authors: Cleanthous G. , Georgiadis Athanasios G. , White P. A. 
Published: February 2024

Abstract
We are studying the problem of estimating density in a wide range of metric spaces, including the Euclidean space, the sphere, the ball, and various Riemannian manifolds. Our framework involves a metric space with a doubling measure and a self-adjoint operator, whose heat kernel exhibits Gaussian behaviour. We begin by reviewing the construction of kernel density estimators and the related background information. As a novel result, we present a pointwise kernel density estimation for probability density functions that belong to general Hölder spaces. The study is accompanied by an application in Seismology. Precisely, we analyze a globally-indexed dataset of earthquake occurrence and compare the out-of-sample performance of several approximated kernel density estimators indexed on the sphere.
Use of Aureobasidium in a sustainable economy
Authors: Rensink Stephanie , van Nieuwenhuijzen Elke J. , Sailer Michael F. , Struck Christian , Wösten Han A. B. 
Published: February 2024

Abstract
Aureobasidium is omnipresent and can be isolated from air, water bodies, soil, wood, and other plant materials, as well as inorganic materials such as rocks and marble. A total of 32 species of this fungal genus have been identified at the level of DNA, of which Aureobasidium pullulans is best known. Aureobasidium is of interest for a sustainable economy because it can be used to produce a wide variety of compounds, including enzymes, polysaccharides, and biosurfactants. Moreover, it can be used to promote plant growth and protect wood and crops. To this end, Aureobasidium cells adhere to wood or plants by producing extracellular polysaccharides, thereby forming a biofilm. This biofilm provides a sustainable alternative to petrol-based coatings and toxic chemicals. This and the fact that Aureobasidium biofilms have the potential of self-repair make them a potential engineered living material avant la lettre.

Key points
•Aureobasidium produces products of interest to the industry
•Aureobasidium can stimulate plant growth and protect crops
•Biofinish of A. pullulans is a sustainable alternative to petrol-based coatings
•Aureobasidium biofilms have the potential to function as engineered living materials
Targeting metabolic sensing switch GPR84 on macrophages for cancer immunotherapy
Authors: Li Jianying , Ma Anjun , Zhang Ruohan , Chen Yao , Bolyard Chelsea , Zhao Bao , Wang Cankun , Pich Thera , Li Wantong , Sun Nuo , Ma Qin , Wen Haitao , Clinton Steven K. , Carson William E. , Li Zihai , Xin Gang 
Published: February 2024

Abstract
Introduction
As one of the major components of the tumor microenvironment, tumor-associated macrophages (TAMs) possess profound inhibitory activity against T cells and facilitate tumor escape from immune checkpoint blockade therapy. Converting this pro-tumorigenic toward the anti-tumorigenic phenotype thus is an important strategy for enhancing adaptive immunity against cancer. However, a plethora of mechanisms have been described for pro-tumorigenic differentiation in cancer, metabolic switches to program the anti-tumorigenic property of TAMs are elusive.

Materials and methods
From an unbiased analysis of single-cell transcriptome data from multiple tumor models, we discovered that anti-tumorigenic TAMs uniquely express elevated levels of a specific fatty acid receptor, G-protein-coupled receptor 84 (GPR84). Genetic ablation of GPR84 in mice leads to impaired pro-inflammatory polarization of macrophages, while enhancing their anti-inflammatory phenotype. By contrast, GPR84 activation by its agonist, 6-n-octylaminouracil (6-OAU), potentiates pro-inflammatory phenotype via the enhanced STAT1 pathway. Moreover, 6-OAU treatment significantly retards tumor growth and increases the anti-tumor efficacy of anti-PD-1 therapy.

Conclusion
Overall, we report a previously unappreciated fatty acid receptor, GPR84, that serves as an important metabolic sensing switch for orchestrating anti-tumorigenic macrophage polarization. Pharmacological agonists of GPR84 hold promise to reshape and reverse the immunosuppressive TME, and thereby restore responsiveness of cancer to overcome resistance to immune checkpoint blockade.
Stimulating T cell responses against patient-derived breast cancer cells with neoantigen peptide-loaded peripheral blood mononuclear cells
Authors: Sueangoen Natthaporn , Grove Harald , Chuangchot Nisa , Prasopsiri Jaturawitt , Rungrotmongkol Thanyada , Sanachai Kamonpan , Darai Nitchakan , Thongchot Suyanee , Suriyaphol Prapat , Sa-Nguanraksa Doonyapat , Thuwajit Peti , Yenchitsomanus Pa-thai , Thuwajit Chanitra 
Published: February 2024

AbstractBreast cancer stands as a formidable global health challenge for women. While neoantigens exhibit efficacy in activating T cells specific to cancer and instigating anti-tumor immune responses, the accuracy of neoantigen prediction remains suboptimal. In this study, we identified neoantigens from the patient-derived breast cancer cells, PC-B-142CA and PC-B-148CA cells, utilizing whole-genome and RNA sequencing. The pVAC-Seq pipeline was employed, with minor modification incorporating criteria (1) binding affinity of mutant (MT) peptide with HLA (IC50 MT) ≤ 500 nm in 3 of 5 algorithms and (2) IC50 wild type (WT)/MT > 1. Sequencing results unveiled 2513 and 3490 somatic mutations, and 646 and 652 non-synonymous mutations in PC-B-142CA and PC-B-148CA, respectively. We selected the top 3 neoantigens to perform molecular dynamic simulation and synthesized 9–12 amino acid neoantigen peptides, which were then pulsed onto healthy donor peripheral blood mononuclear cells (PBMCs). Results demonstrated that T cells activated by ADGRL1E274K, PARP1E619K, and SEC14L2R43Q peptides identified from PC-B-142CA exhibited significantly increased production of interferon-gamma (IFN-γ), while PARP1E619K and SEC14L2R43Q peptides induced the expression of CD107a on T cells. The % tumor cell lysis was notably enhanced by T cells activated with MT peptides across all three healthy donors. Moreover, ALKBH6V83M and GAAI823T peptides from PC-B-148CA remarkably stimulated IFN-γ- and CD107a-positive T cells, displaying high cell-killing activity against target cancer cells. In summary, our findings underscore the successful identification of neoantigens with anti-tumor T cell functions and highlight the potential of personalized neoantigens as a promising avenue for breast cancer treatment.
Synergistic combination therapy using cowpea mosaic virus intratumoral immunotherapy and Lag-3 checkpoint blockade
Authors: Karan Sweta , Jung Eunkyeong , Boone Christine , Steinmetz Nicole F. 
Published: February 2024

AbstractImmune checkpoint therapy (ICT) for cancer can yield dramatic clinical responses; however, these may only be observed in a minority of patients. These responses can be further limited by subsequent disease recurrence and resistance. Combination immunotherapy strategies are being developed to overcome these limitations. We have previously reported enhanced efficacy of combined intratumoral cowpea mosaic virus immunotherapy (CPMV IIT) and ICT approaches. Lymphocyte-activation gene-3 (LAG-3) is a next-generation inhibitory immune checkpoint with broad expression across multiple immune cell subsets. Its expression increases on activated T cells and contributes to T cell exhaustion. We observed heightened efficacy of a combined CPMV IIT and anti-LAG-3 treatment in a mouse model of melanoma. Further, LAG-3 expression was found to be increased within the TME following intratumoral CPMV administration. The integration of CPMV IIT with LAG-3 inhibition holds significant potential to improve treatment outcomes by concurrently inducing a comprehensive anti-tumor immune response, enhancing local immune activation, and mitigating T cell exhaustion.
Human identification: an investigation of 3D models of paranasal sinuses to establish a biological profile on a modern UK population
Authors: Robles Madeline , Nakhaeizadeh Sherry , Rando Carolyn , Morgan Ruth M. 
Published: February 2024

AbstractMedical imaging is a valuable source for facilitating empirical research and provides an accessible gateway for developing novel forensic anthropological methods for analysis including 3D modelling. This is especially critical for the United Kingdom (UK), where methods developed from modern UK populations do not currently exist. This study introduces a new approach to assist in human identification using 3D models of the paranasal sinuses. The models were produced from a database of 500 modern CT scans provided by University College London Hospital. Linear measurements and elliptic Fourier coefficients taken from 1500 three-dimensional models across six ethnic groups assessed by one-way ANOVA and discriminant function analysis showed a range of classification rates with certain rates reaching 75–85.7% (p < 0.05) in correctly classifying age and sex according to size and shape. The findings offer insights into the potential for employing paranasal sinuses as an attribute for establishing the identification of unknown human remains in future crime reconstructions.
Long-term results after surgical basal cell carcinoma excision in the eyelid region: revisited
Authors: Told Reinhard , Reumueller Adrian , Kreminger Judith , Lackner Birgit , Kuchar Andreas , Schmidt-Erfurth Ursula , Dunavoelgyi Roman 
Published: February 2024

Summary
The aim of the study was to readdress basal cell carcinoma (BCC) in the periocular region to prove the efficacy of histologically controlled surgical treatment and to identify high-risk characteristics.
Retrospective analysis of 451 microscopically controlled BCC excisions in the periocular region. Tumor location, tumor size, AJCC 7 classification, and histological results were recorded. The same procedure was followed for recurrences.
A recurrence rate of 5.0% was observed after the first microscopically controlled excision. Recurrent BCCs show a shift from nodular to sclerosing BCC as the primary histological type as well as a change in primary location from lower eyelid to medial canthus. The frequency of BCC with deep extension increased from 7.3% to 24.7%, and 57.1% after the second and third operations, respectively. The recurrence rate increased to 9.5% and 42.9%, after the second and third operations, respectively.
In conclusion, we are facing the same challenges in surgical BCC treatment as 30 years ago. The distribution of periocular BCC location, histologic subtype and recurrence rates mirror the literature und the general consensus. The recurrence rate increases with every operation needed. Sclerosing BCCs with deep extension at the medial canthus bear the greatest risk for recurrence. In such cases, centers of expertise should be consulted and additional treatment options should be considered.
Approximation of Almost Diagonal Non-linear Maps by Lattice Lipschitz Operators
Authors: Arnau Roger , Calabuig Jose M. , Erdoğan Ezgi , Sánchez Pérez Enrique A. 
Published: February 2024

AbstractLattice Lipschitz operators define a new class of nonlinear Banach-lattice-valued maps that can be written as diagonal functions with respect to a certain basis. In the n-dimensional case, such a map can be represented as a vector of size n of real-valued functions of one variable. In this paper we develop a method to approximate almost diagonal maps by means of lattice Lipschitz operators. The proposed technique is based on the approximation properties and error bounds obtained for these operators, together with a pointwise version of the interpolation of McShane and Whitney extension maps that can be applied to almost diagonal functions. In order to get the desired approximation, it is necessary to previously obtain an approximation to the set of eigenvectors of the original function. We focus on the explicit computation of error formulas and on illustrative examples to present our construction.
Two years of neurosurgical intraoperative MRI in Sweden - evaluation of use and costs
Authors: Kaijser Magnus , Frisk Henrik , Persson Oscar , Burström Gustav , Suneson Annika , El-Hajj Victor Gabriel , Fagerlund Michael , Edström Erik , Elmi-Terander Adrian 
Published: February 2024

Abstract

Background
The current shortage of radiology staff in healthcare provides a challenge for departments all over the world. This leads to more evaluation of how the radiology resources are used and a demand to use them in the most efficient way. Intraoperative MRI is one of many recent advancements in radiological practice. If radiology staff is performing intraoperative MRI at the operation ward, they may be impeded from performing other examinations at the radiology department, creating costs in terms of exams not being performed. Since this is a kind of cost whose importance is likely to increase, we have studied the practice of intraoperative MRI in Sweden.

Methods
The study includes data from the first four hospitals in Sweden that installed MRI scanners adjacent to the operating theaters. In addition, we included data from Karolinska University Hospital in Solna where intraoperative MRI is carried out at the radiology department.

Results
Scanners that were moved into the operation theater and doing no or few other scans were used 11–12% of the days. Stationary scanners adjacent to the operation room were used 35–41% of the days. For scanners situated at the radiology department doing intraoperative scans interspersed among all other scans, the proportion was 92%.

Conclusion
Our study suggests that performing exams at the radiology department rather than at several locations throughout the hospital may be an efficient approach to tackle the simultaneous trends of increasing demands for imaging and increasing staff shortages at radiology departments.
Effect of meniscus modelling assumptions in a static tibiofemoral finite element model: importance of geometry over material
Authors: Yao Jiacheng , Crockett John , D’Souza Mathias , A. Day Gavin , K. Wilcox Ruth , C. Jones Alison , Mengoni Marlène 
Published: February 2024

AbstractFinite element studies of the tibiofemoral joint have increased use in research, with attention often placed on the material models. Few studies assess the effect of meniscus modelling assumptions in image-based models on contact mechanics outcomes. This work aimed to assess the effect of modelling assumptions of the meniscus on knee contact mechanics and meniscus kinematics. A sensitivity analysis was performed using three specimen-specific tibiofemoral models and one generic knee model. The assumptions in representing the meniscus attachment on the tibia (shape of the roots and position of the attachment), the material properties of the meniscus, the shape of the meniscus and the alignment of the joint were evaluated, creating 40 model instances. The values of material parameters for the meniscus and the position of the root attachment had a small influence on the total contact area but not on the meniscus displacement or the force balance between condyles. Using 3D shapes to represent the roots instead of springs had a large influence in meniscus displacement but not in knee contact area. Changes in meniscus shape and in knee alignment had a significantly larger influence on all outcomes of interest, with differences two to six times larger than those due to material properties. The sensitivity study demonstrated the importance of meniscus shape and knee alignment on meniscus kinematics and knee contact mechanics, both being more important than the material properties or the position of the roots. It also showed that differences between knees were large, suggesting that clinical interpretations of modelling studies using single geometries should be avoided.
TET2 mutations contribute to adverse prognosis in acute myeloid leukemia (AML): results from a comprehensive analysis of 502 AML cases and the Beat AML public database
Authors: Pan Xin’an , Chang Yingjun , Ruan Guorui , Zhou Songhai , Jiang Hao , Jiang Qian , Huang Xiaojun , Zhao Xiao-Su 
Published: February 2024

AbstractDespite the high incidence of tet methylcytosine dioxygenase 2 (TET2) mutations in acute myeloid leukemia (AML), the prognostic implications of these mutations in three AML risk groups based on the 2022 ELN AML risk classification are still unclear. A total of 502 consecutive de novo AML patients who had next-generation sequencing data available between March 2011 and July 2021 at the Peking University Institute of Hematology were enrolled in this study. Univariate and multivariate Cox regression analyses were performed to explore the prognostic impact of TET2 mutations in the above cohort and the Beat AML cohort. Of the 502 total AML patients, 76 (15.1%) carried TET2 mutations. Multivariate analysis revealed TET2 mutations as independent risk factor for overall survival (OS) in both the total AML cohort (OR = 1.649, p = 0.009) and in the 2022 ELN intermediate-risk cohort (HR = 1.967, p = 0.05). Analysis of RNA-seq data from the Beat AML study revealed 1042 differentially expressed genes (DEGs) between the TET2-mutant and TET2 wild-type groups. The results of enrichment analysis indicated the DEGs to be notably enriched in categories related to the PI3K-Akt signaling pathway. Collectively, our findings indicate that mutations in TET2 are prognostically disadvantageous in AML patients. Assessment of TET2 mutational status contributes to the stratification of intermediate-risk AML patients. Multiple genes and pathways of potential therapeutic relevance may be differentially modulated by TET2 mutations in AML.
Interpretable Radiomic Signature for Breast Microcalcification Detection and Classification
Authors: Prinzi Francesco , Orlando Alessia , Gaglio Salvatore , Vitabile Salvatore 
Published: February 2024

AbstractBreast microcalcifications are observed in 80% of mammograms, and a notable proportion can lead to invasive tumors. However, diagnosing microcalcifications is a highly complicated and error-prone process due to their diverse sizes, shapes, and subtle variations. In this study, we propose a radiomic signature that effectively differentiates between healthy tissue, benign microcalcifications, and malignant microcalcifications. Radiomic features were extracted from a proprietary dataset, composed of 380 healthy tissue, 136 benign, and 242 malignant microcalcifications ROIs. Subsequently, two distinct signatures were selected to differentiate between healthy tissue and microcalcifications (detection task) and between benign and malignant microcalcifications (classification task). Machine learning models, namely Support Vector Machine, Random Forest, and XGBoost, were employed as classifiers. The shared signature selected for both tasks was then used to train a multi-class model capable of simultaneously classifying healthy, benign, and malignant ROIs. A significant overlap was discovered between the detection and classification signatures. The performance of the models was highly promising, with XGBoost exhibiting an AUC-ROC of 0.830, 0.856, and 0.876 for healthy, benign, and malignant microcalcifications classification, respectively. The intrinsic interpretability of radiomic features, and the use of the Mean Score Decrease method for model introspection, enabled models’ clinical validation. In fact, the most important features, namely GLCM Contrast, FO Minimum and FO Entropy, were compared and found important in other studies on breast cancer.
Optimizing biodiesel production from waste with computational chemistry, machine learning and policy insights: a review
Authors: Osman Ahmed I. , Nasr Mahmoud , Farghali Mohamed , Rashwan Ahmed K. , Abdelkader Adel , Al-Muhtaseb Ala’a H. , Ihara Ikko , Rooney David W. 
Published: February 2024

AbstractThe excessive reliance on fossil fuels has resulted in an energy crisis, environmental pollution, and health problems, calling for alternative fuels such as biodiesel. Here, we review computational chemistry and machine learning for optimizing biodiesel production from waste. This article presents computational and machine learning techniques, biodiesel characteristics, transesterification, waste materials, and policies encouraging biodiesel production from waste. Computational techniques are applied to catalyst design and deactivation, reaction and reactor optimization, stability assessment, waste feedstock analysis, process scale-up, reaction mechanims, and molecular dynamics simulation. Waste feedstock comprise cooking oil, animal fat, vegetable oil, algae, fish waste, municipal solid waste and sewage sludge. Waste cooking oil represents about 10% of global biodiesel production, and restaurants alone produce over 1,000,000 m3 of waste vegetable oil annual. Microalgae produces 250 times more oil per acre than soybeans and 7–31 times more oil than palm oil. Transesterification of food waste lipids can produce biodiesel with a 100% yield. Sewage sludge represents a significant biomass waste that can contribute to renewable energy production.
Integration of satellite SAR and optical acquisitions for the characterization of the Lake Sarez landslides in Tajikistan
Authors: Nardini Olga , Confuorto Pierluigi , Intrieri Emanuele , Montalti Roberto , Montanaro Thomas , Robles Javier Garcia , Poggi Francesco , Raspini Federico 
Published: February 2024

AbstractTajikistan is an area characterized by several lakes created after rockfalls and moraine deposits collapsed due to its geographic position on the collisional area of the Euro-Asian and Indian tectonic plates. In 1911, a violent earthquake generated the Usoi dam, which led to the creation of Lake Sarez. The purpose of the article is to provide an overview of the ground deformation of the two landslides that affect and threaten the area of Lake Sarez exploiting the combination of two different techniques, the interferometric synthetic aperture radar (InSAR) method with the SqueeSAR approach and optical image analysis through the use of COSI-Corr software. The combination of these two techniques turned out to be useful and provide more information because InSAR method balances lack the optical analysis and vice versa giving the possibility to obtain a complete overview of the displacement of the area. Moreover, InSAR data have been used to reconstruct the geometry and depth of the sliding surface of a potential landslide that could affect the lake, generating a wave that could overtop the dam and affect the villages downstream.