bluuebunny/crossref_metadata_2025_split huggingface dataset:
The prognostic value of bioinformatics analysis of ECM receptor signaling pathways and LAMB1 identification as a promising prognostic biomarker of lung adenocarcinoma
Authors: Liu Tingjun , Hu Ankang , Chen Quangang , Wu lianlian , Zhang Lingzhi , Qiao Dandan , Huang Zhutao , Lu Tianyuan , Wang Jie 
Published: December 2023

Abstract
Background
Our study attempts to investigate the impact of genes related to the extracellular matrix (ECM) receptor interaction pathway on immune-targeted therapy and lung adenocarcinoma (LUAD) prognosis.
Methods
This study obtained LUAD chip data (GSE68465, GSE31210, GSE116959) from NCBI GEO. Moreover, we downloaded the gene data associated with the ECM receptor interaction pathway from the MsigDB database. Differentially expressed genes (DEGs) were identified using GEO2R, followed by analyzing their correlation with immune cell infiltration. Univariate Cox regression analysis screened out ECM-related genes significantly related to the survival prognosis of LUAD patients. Additionally, Lasso regression and multivariate Cox regression analysis helped construct a prognostic model. Patients were stratified by risk score and survival analyses. The prognostic models were evaluated using receiver operating characteristic curves, and risk scores and prognosis associations were analyzed using univariate and multivariate Cox regression analyses. We selected a core gene for GSEA and CIBERSORT analysis to determine its function and tumor-infiltrating immune cell proportion, respectively.
Results
The most abundant pathways among DEGs in LUAD primarily involved the cell cycle, ECM receptor interaction, protein digestion and absorption, p53 signaling pathway, complement and coagulation cascade, and tyrosine metabolism. Two ECM-associated subtypes were identified by consensus clustering. Besides, we validated an ECM-related prognostic model to predict LUAD survival, and it was associated with the tumor immune microenvironment (TME). Additional cross-analysis screened LAMB1 for further research. The results indicated that the survival time of LUAD patients with elevated LAMB1 expression was longer than those with low LAMB1 expression. GSEA and CIBERSORT analyses revealed that LAMB1 expression correlated with TME.
Conclusions
According to the GEO and TCGA databases, a prognostic model of LUAD patients depending on the ECM receptor interaction pathway was constructed. Screening out LAMB1 can become a prognostic risk factor for LUAD patients or a potential target during LUAD treatment.
Impact of a teat disinfectant based on Lactococcus cremoris on the cow milk proteome
Authors: Addis Maria Filippa , Maffioli Elisa Margherita , Gazzola Alessandra , Santandrea Federica , Tedeschi Gabriella , Piccinini Renata 
Published: December 2023

Abstract

Background.
Dairy cow milking practices require cleaning and disinfection of the teat skin before and after milking to ensure the safety and quality of milk and prevent intramammary infections. Antimicrobial proteins of natural origin can be valuable alternatives to traditional disinfectants. In a recent field trial, we demonstrated that a teat dip based on a nisin A-producing Lactococcus cremoris (L) had comparable efficacy to conventional iodophor dip (C) in preventing dairy cow mastitis. Here, we present the differential shotgun proteomics investigation of the milk collected during the trial.
Methods.
Four groups of matched quarter milk with low (LSCC) and high somatic cell count (HSCC) collected at the beginning (T0) and end (TF) of the trial were selected, for a total of 28 LSCC and 12 HSCC samples. Milk proteins were digested into peptides, separated by nanoHPLC, and analyzed by tandem mass spectrometry (LC-MS/MS) on an Orbitrap Fusion Tribrid mass spectrometer. The proteins were identified with MaxQuant and interaction networks of the differential proteins were investigated with STRING. The proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD045030.
Results.
In healthy mlk (LSCC), we detected 90 and 80 differential proteins at T0 and TF, respectively. At TF, the Lactococcus group showed higher levels of antimicrobial proteins. In mastitis milk (HSCC), we detected 88 and 106 differential proteins at T0 and TF, respectively. In the Lactococcus group, 14 proteins with antimicrobial and immune defense functions were enriched at TF vs. 4 proteins at T0. Cathelicidins were among the most relevant enriched proteins. Western immunoblotting validation confirmed the differential abundance.
Conclusions.
At T0, the proteomic differences observed in healthy milk of the two groups were most likely dependent on physiological variation. On the other hand, antimicrobial and immune defense functions were higher in the milk of cows with mammary gland inflammation of the Lactococcus-treated group. Among other factors, the additional immunostimulatory action of nisin A might play a role in the observed changes.
miR199a represses the proliferation of hepatocellular carcinoma cells by targeting SGK3 through Akt/mTOR pathway
Authors: Wu Ting , Qi Guilin , Liu Pan , Li Jing , Guo Min , Yu Hui , Yang Huidongfang , Jin Yuyin , Zhou Wen , Hu Wangheng , Yu Han , Duan Peng 
Published: December 2023

Abstract
Purpose
Previous studies have suggested that some microRNAs (miRNAs) play a vital role in carcinogenesis and progression of hepatocellular carcinoma (HCC). As one of these newly found miRNAs, miR-199a-3p (miR199a), has been shown to be highly involved in the regulation of HCC growth. However, the mechanism underlying miR199a regulation in HCC remains unclear.
Methods
In this study, the evaluation of miR199a expression in HCC cells (HCCs) and tissues was evaluated by RT-qPCR. Bioinformatics analysis and luciferase reporter assay were performed to prove the regulation effect of miR199a on SGK3. CCK-8 assay was performed to assess the proliferation of HCCs (HepG2 and HuH7) after transfection. Subsequently, the biological function of miR199a/SGK3 axis in HCCs was investigated.
Results
Herein, we found that miR199a is usually underexpressed in the HCC tissue and cell lines (HepG2 and HuH7) compared with their corresponding control. The expression pattern of SGK3, as a direct target of miR199a, was opposite that of miR199a. shRNA-mediated silencing of SGK3 decreased the proliferation of HCC cells (HCCs) in vitro; however, these phenotypes were promoted by miR199a mimics. Mechanistically, miR199a inhibited the proliferation of HCCs through the downregulation Akt/mTOR signalling by targeting SGK3.
Conclusion
our findings demonstrated an important role for SGK3 as a miR199a target and a mediator of the Akt/mTOR signaling pathway. These findings highlight the miR199a/SGK3 axis as a potential therapeutic target for managing HCC.
Assessment of hippocampal-related behavioral changes in adolescent rats of both sexes following voluntary intermittent ethanol intake and noise exposure: a putative underlying mechanism and implementation of a non-pharmacological preventive strategy
Authors: Buján Gustavo Ezequiel , D’Alessio Luciana , Serra Héctor Alejandro , Guelman Laura Ruth , Molina Sonia Jazmín 
Published: December 2023

Abstract

Ethanol (EtOH) intake and noise exposure are particularly concerning among human adolescents because the potential to harm brain. Unfortunately, putative underlying mechanisms remain to be elucidated. Moreover, although neuroprotection tools could aid to prevent individuals from injury, limited data are available. Using an adolescent animal model, present study aims to explore a possible mechanism that could underlie the altered hippocampus-dependent behaviors induced by EtOH intake and/or noise exposure, as well as the neuroprotective impact of an environmental challenge. Adolescent Wistar rats of both sexes were subjected to an intermittent voluntary EtOH intake paradigm for one week. A subgroup of animals was exposed to white noise for two hours after the last session of EtOH intake. Some animals of both groups were housed in EE cages. Hippocampal-dependent behavioral assessment and hippocampal oxidative state evaluation were performed. Present results show that different behavioral alterations might be induced in animals of both sexes after EtOH intake, with or without sequential exposure to noise, that in some cases are sex-specific. Moreover, hippocampal oxidative imbalance seems to be one of the potential underlying mechanisms. Additionally, most behavioral and oxidative alterations were prevented by EE. These findings suggest that two recreational agents may impact behavior via oxidative pathways, in both sexes, in an animal model. In addition, improved housing resulted an effective neuroprotective strategy. Therefore, it could be suggested that a non-pharmacological approach might potentially provide neuroprotective advantages against other challenges. Finally, it might be worth considering its potential for translational human benefit.
Starch-cellulose-gelatin hydrogels obtained by reactive extrusion aiming an ecologically friendly perspective
Authors: MARIM BEATRIZ , Pereira Jessica , Andrello Avacir , Mali Suzana 
Published: December 2023

Abstract
Biopolymeric hydrogels represent a versatile class of materials with a wide range of potential applications, including their use in agricultural materials, drug delivery systems, biosensors, and food packaging. This investigation primarily centered on the synthesis and characterization of biodegradable hydrogels based on starch, cellulose, and gelatin, acting as a polymeric matrix intended for water retention in agricultural contexts. Prior to their incorporation into the hydrogels formulations, cassava starch and cellulose extracted from oat hulls underwent modification via reactive extrusion involving reaction with citric acid (CA) and sodium trimetaphosfate (STMP) as crosslinking agents, respectively. The hydrogels were obtained through a reactive extrusion process to produce porous pellets. These pellets were characterized according to their porosity, thermal properties, degree of swelling at different times and pHs, and water adsorption capacities. The hydrogel sample formulated with both CA-modified starch and STMP-modified cellulose, and gelatin, presented the highest values of porosity (> 45%) and open pores (> 5%), and the higher degree of swelling (607%). These materials as promising candidates for application in agriculture to increase water and/or fertilizers retention capacity in soil, with important advantages, including their biodegradability and low toxicity. It is worth mentioning that the reactive extrusion process used is a continuous process, with low effluent generation and scalable for large-scale production.
Ki-67 index as a predictive marker of meningioma clinicopathologic course and recurrence following surgical resection: a retrospective study
Authors: Mizrachi Mark , Hartley Benjamin , Saleem Shahzaib , Hintz Eric , Ziemba Yonah , Li Jianyi , Schulder Michael 
Published: December 2023

Abstract
Purpose
Meningiomas are the most common primary intracranial tumors in adults. Although benign in a majority of cases, they have a variable clinical course and may recur even after a thorough surgical resection. Ki-67, a nuclear protein involved in cell cycle regulation, has been widely studied as a marker of cellular proliferation in various cancers. However, the prognostic significance of Ki-67 in meningiomas remains controversial. Here, we investigate the Ki-67 index, as a predictive marker of meningioma recurrence following surgical resection and compare it to established prognostic markers such as WHO grade and degree of resection.
Methods
The medical records of 451 consecutive patients with previously untreated cranial meningiomas who underwent resections from January 2011 to January 2021 at North Shore University Hospital (NSUH) were reviewed. Collected data included WHO grade, Ki-67 proliferative index, degree of resection — gross (GTR) vs subtotal (STR) — as judged by the surgeon, and meningioma recurrence. This study was approved by the NSUH Institutional Review Board IRB 21-1107
Results
There were 290 patients with grade I, 154 with grade II, and 7 with grade III meningiomas. The average post-resection follow-up period was 4 years, and 82 tumors (18%) recurred. Higher WHO grades were associated with higher rates of recurrence, with rates of 11.4%, 27.9%, and 71.4% for grades 1, 2, and 3, respectively, and subtotal resection corresponded to a higher rate of recurrence than gross resection (34.3% and 13.4%, respectively). Higher WHO grades also correlated with higher Ki-67 scores (2.59, 10.01, and 20.71) for grades 1, 2, and 3, respectively. A multivariate logistic regression model identified Ki-67 and degree of resection as independent predictive variables for meningioma recurrence.
Conclusion
Our 10-year retrospective study suggests that the Ki-67 index is an important predictive marker for recurrence of intracranial meningiomas following surgical resection, particularly among patients with WHO grade 2 tumors. Our findings add to a growing body of data which supports inclusion of Ki-67 index in the WHO grading criteria for patients with meningiomas.
Suppression of noise in SEM images using adaptive anisotropic partial differential equations
Authors: Pang Shuiquan , Wu Shihuang , Wang Zhizhe , Luo Jun , Li Hai , Zhang Xianmin 
Published: December 2023

Abstract

Image denoising is an effective way to enhance the quality of scanning electron microscope (SEM) images, and improve the accuracy of detection analysis and automatic operation. However, most existing denoising methods rely on global parameters and are not suitable for noise removal in all regions of the image. To address this issue, this paper proposes a denoising method based on the adaptive anisotropic partial differential equations (AAPDE), which can adaptively select denoising parameters for different regions according to the gradient amplitude of SEM images and effectively solve the problem of global parameters not being applicable to noise in all regions of the image. Both simulation and experimental results demonstrate that the proposed method outperforms global denoising methods in terms of denoising performance.
Comparative study on clinical and imaging characteristics between patients with ruptured and large, unruptured abdominal aortic aneurysms
Authors: Hoste Xavier , Coudyzer Walter , Laenen Annouschka , Fourneau Inge , Maleux Geert 
Published: December 2023

Abstract
Purpose
to determine potential clinical and computed tomography (CT) imaging predictors for abdominal aortic aneurysm (AAA) rupture based on a comparative analysis of patients presenting with large (> 6.5 cm diameter) unruptured AAA (uAAA) and patients presenting with ruptured AAA (rAAA) respectively.
Methods
consecutive patients presenting with large unruptured or rAAA and having undergone a contrast-enhanced CT at admission between January 2005 and June 2019 were included. Patients’ demographics and CT-imaging characteristics were collected from the institutional electronic medical records. Both patient groups were compared using Fisher’s exact test for categorical variables and the Mann-Whitney U test for continuous variables.
Results
we included 101 patients, of which 57 patients presenting with a rAAA and 44 patients with a large, uAAA. Patients in the large, uAAA group were younger, mean age of 76 years vs 83 years (P < 0.001), had less coronary artery disease (47.6% vs 72.5%; P = 0.026) and had a lower left common iliac artery to maximum aneurysm diameter ratio (0.15 vs 0.18; P = 0.034), a lower sum of right + left common iliac artery to maximum aneurysm diameter ratio (0.31 vs 0.39; P = 0.028) and a lower infrarenal neck to maximum aneurysm diameter ratio (0.29 vs 0.35; P = 0.039).
Conclusion
patients with large, uAAA’s were younger with less coronary artery disease and presented with lower ratio of right + left common iliac artery to maximum aneurysm diameter as well as a lower ratio of infrarenal neck to maximum aneurysm diameter on CT-imaging compared to patients with rAAA.
Intraoperative opioids and disease-free survival in glioblastoma multiforme
Authors: Naufal Rodrigo Ferrari Fernandes , Izadora Lorenna , Reyes Capovilla Martins Gonzalez , Junior Mario Wolak , Pokorny Gabriel , Carvalho Georgea Carneiro , Fukushima Fernanda Bono , Romero Flávio Ramalho 
Published: December 2023

Abstract
Introduction: Glioblastoma multiforme (GBM) is a primary tumor of the Central Nervous System (CNS). It is one of the most aggressive tumors that can affect humans, with no cure so far and an extremely inverse prognosis, with an average survival ranging from 7 to 15 months. Recently, the role of opioids, either in stopping or stimulating tumor progression, has been demonstrated for both sides. The main objective of this study was to investigate the influence of intraoperative opioid use on the overall and disease-free survival of these patients.
Methods: This observational and retrospective study analyzed the medical records of 133 patients who underwent 167 surgical procedures for resection of Glioblastoma Multiforme. Inclusion and exclusion criteria were as follows: patients older than 18 years of age, of both sexes, and who had confirmed GBM. Patients who died in the postoperative period from causes unrelated to the underlying disease were excluded, as were those who did not have specific data on the medications used in the perioperative period in their records. The following outcomes were analyzed: age, preoperative and postoperative Karnofsky scale (KPS), duration of the surgical procedure, opioid doses, overall survival, disease-free survival, sex, and race. To verify the existence of a correlation between quantitative variables, the Spearman Test was applied; for categorical (qualitative) variables, the Chi-square Test was used. The Kruskal–Wallis test was used to evaluate the variance in means between groups. In addition, the log-rank test was used to evaluate survival between the groups. The significance level adopted for all tests was 5% (p≤0.05).
Results: Analysis of the correlation between total opioid dosage and the investigated variables showed that surgical duration and age at surgery were significantly correlated with total opioid dosage. There was no correlation between total opioid dosage and the overall and disease-free survival times of patients.
Conclusion: This study suggests that there is no relationship between the intraoperative opioid dose and overall and disease-free survival in patients undergoing surgical treatment for Glioblastoma Multiforme.
Inverse spectral problems for Dirac-type operators with global delay on a star graph
Authors: Wang Feng , Yang Chuan-Fu , Buterin Sergey , Djuric Nebojsa 
Published: December 2023

Abstract
We introduce Dirac-type operators with a global constant delay on a star graph consisting of $m$ equal edges. For our introduced operators, we formulate an inverse spectral problem that is recovering the potentials from the spectra of two boundary value problems on the graph with a common set of boundary conditions at all boundary vertices except for a specific boundary vertex $v_{0}$ (called the root). For simplicity, we restrict ourselves to the constant delay not less than the edge length of the graph. Under the assumption that the common boundary conditions are of the Robin type and they are known and pairwise linearly independent, the uniqueness theorem is proven and a constructive procedure for solving the proposed inverse problem is obtained.
2000 Mathematics Subject Classification. 34A55; 34K29; 34B45.
Graphlet and Orbit Computation on Heterogeneous Graphs
Authors: Cleveland Colin , Lee Chin-Yen , Tsai Shen-Fu , Yu Wei-Hsuan , Lee Hsuan-Wei 
Published: December 2023

Abstract

Many applications, ranging from natural to social sciences, rely on graphlet analysis for the intuitive and meaningful characterization of networks employing micro-level structures as building blocks. However, it has not been thoroughly explored in heterogeneous graphs, which comprise various types of nodes and edges. Finding graphlets and orbits for heterogeneous graphs is difficult because of the heterogeneity and abundance of semantic information. We consider heterogeneous graphs, which can be treated as colored graphs. By applying the canonical label technique, we determine the graph isomorphism problem with multiple states on nodes and edges. With minimal parameters, we build all non-isomorphic graphs and associated orbits. We provide a Python package that can be used to generate orbits for colored directed graphs and determine the frequency of orbit occurrence. Finally, we provide four examples to illustrate the use of the Python package.
Graph neural network with classification accelerating
the discovery of Heusler catalysts for nitrogen
reduction reaction
Authors: Yuan Ding-Wang , Zhou Jing , Chen Xiayong , Jiang Xiao , Tian Zean , Hu Wangyu , Huang Bowen 
Published: December 2023

Abstract
Developing efficient catalysts for nitrogen reduction reaction is a meaningful yet challenging endeavor. Here, we employ machine learning to screen for efficient Heusler alloy catalysts (X2YZ). We incorporate classification tasks into the graph neural network to differentiate between adsorbates and adsorption sites, thereby improving the network's ability to recognize adsorption configurations and enhance its predictive accuracy of adsorption energy simultaneously. Following training on an adsorption dataset of 6000 density-functional theory calculations, our model can predict the adsorption energies of critical adsorbates (N2, NNH, NH, NH2, H) with a mean absolute error of 0.1 eV. Through a multi-criteria screening, we identified a series of Ru-based Heusler catalysts with low limiting potentials and the ability to suppress hydrogen evolution reactions. For example, Ru2HfTl exhibits a low limiting potential of -0.32 V. Statistical analysis reveals that the average d-electron of X and Y elements, along with the group number of Z element, can assess the catalyst activity of Heusler alloys. Furthermore, we discover that the unique geometric structure of four-fold hollow sites on the (110) surface of Heusler alloy can facilitate N2 activation and alter the potential determining step of NRR.
Subjectivity Analysis for Aspect-based Sentiment and Opinion Detection of YouTube Product Reviews
Authors: Tetteh Maxwell , Thushara MG 
Published: December 2023

Abstract
The advent of the internet has presented a novel paradigm for conducting consumer research and focus group investigations. Social media platforms enable organizations and entities to efficiently obtain and analyze public opinions regarding their products and services. This eliminates the need for extensive resource allocation towards traditional survey methods and information-gathering strategies. The present study investigates the potential of utilizing the YouTube platform as a valuable data source for product review analysis—our research centers on Apple Inc. and its most profitable product, the Apple iPhone. Using user feedback from review videos, we employ a lexicon-based subjectivity analysis methodology to identify statements articulating subjective viewpoints about the iPhone product. Traditional sentiment analysis methods categorize opinionated views into two broad categories: positive or negative. To assess the general market perception of the product, we employ SpaCy’s aspect extraction functionality to identify significant parts of the product that are subject to viewer critique. A BERTopic model processes the user’s text by using topic modeling techniques to extract latent themes that provide insights into the various detected characteristics. The BERTopic model has high efficiency and yields a coherence score of 69%.