bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of Amino Acid Metabolism-Related Prognostic Model and Immune Infiltration Analysis in Patients with Stomach Adenocarcinoma
Authors: Zhu Wenjun , Fu Min , Li Qianxia , Chen Xin , Li Xiaoyu , Luo Na , Tang Wenhua , Yang Feng , Chen Ziqi , Zhang Yiling , Zhang Yuanyuan , Peng Xiaohong , Hu Guangyuan 
Published: April 2023

Abstract
Stomach adenocarcinoma (STAD) is a major contributor to cancer mortality worldwide. Alterations in amino acid metabolism have been reported in various tumors. However, the prognostic value of amino acid metabolism-related genes in STAD deserves to be further elucidated. In this study, we constructed a prognostic risk model consisting of 3 amino acid metabolism-related genes (SERPINE1, NRP1, MATN3) in STAD. Based on the median risk score, STAD patients were divided into high- and low-risk groups. The patients with high-risk scores had a worse prognosis. A nomogram consisting of risk score and various clinical characteristics accurately predicted the 1-, 3-, and 5-year survival time of STAD patients. Notably, KEGG pathway enrichment analysis indicated immune-related pathways enriched in the high-risk group. High-risk scores were significantly related to C6 (TGF-β dominant type), while low-risk scores were significantly related to C4 (lymphocyte-depleted type). The higher risk score was associated with higher immune infiltration, immune-related function, lower tumor purity and worse response to immunotherapy. In addition, the model genes were correlated with antitumor drug sensitivity. Finally, functional assays confirmed that interference of model gene MATN3 inhibited the proliferation and migration of STAD cells. In conclusion, the amino acid metabolism-related prognostic model might be used as a biomarker to predict the prognosis and guide immunotherapy for STAD patients.
Long-read sequencing revealed alterations of microbial relationship between tongue coating and gastric mucosa in patients with gastric intestinal metaplasia
Authors: Wu Jianping , Wu Zhenfeng , Li Meifeng , Hua Zhaolai , Lu Bin , Shen Rui , Xiang Jiao , Cheng Chun , Zhang Junfeng 
Published: April 2023

Abstract
Abnormalities of microbiota in tongue coating (TC) are associated with gastric cancer, however, the correlation between microbiota colonizing in TC and in gastric mucosa (GM) and their roles in the development of gastric cancer remain poorly understood. In this study, using long-read sequencing, we profiled the microbiota in both TC and GM from 44 patients with the precancerous gastric intestinal metaplasia (GIM) and 28 matched controls who were rapid urease test (RUT)-negative and had with non-symptomatic chronic superficial gastritis. While no significant difference in diversity of microbiota in either TC or GM was observed between GIM patients and the controls, the distribution of bacteria (operational taxonomic units, OTUs) shared by TC and GM was significantly different between GIM patients and the controls as well as between RUT-positive and RUT-negative GIM patients. LEfSe (Linear discriminant analysis effect size) identified TC Prevotella melaninogenica and three GM Helicobacter species (i.e., H. pylori, H. pylori XZ274, and H. pylori 83) that were enriched in GIM patients, suggesting a potential role of Hp infection in the development of GIM. In RUT-negative GIM patients, gastric Veillonella, Pseudonocardia, and Mesorhizobium were enriched. The commensal network between TC and GM was more complex in patients with GIM than that in controls, and more closely correlated in RUT-positive than in RUT-negative GIM patients. Consistent with the known contribution of H. pylori to lower values of PG-I/PG-II, the serum ratio of PG-I to PG-II was found negatively correlated with the three gastric Helicobacter species (H. pylori, H. pylori XZ274, and H. pylori 83) in RUT-negative GIM patients and negatively correlated with two TC species (Fusobacterium nucleatum subsp. nucleatum and Campylobacter showae) in RUT-positive GIM patients. In summary, the oral and gastric commensal linkage as well as H. pylori infection were promoted in GIM.
Environmentally Friendly Catalyst- and Solvent-Free Synthesis of 2-Anilino Nicotinic Acids Derivatives as a Potential Lead COX Inhibitors
Authors: Yarhorhosseini Mahsa , Javanshir Shahrzad , Sadr Ahmad Shahir , Noori Milad , Dastyafteh Navid , Esmkhani Maryam , Iraji Aida , Mahdavi Mohammad 
Published: April 2023

Abstract
In this study, an environmentally friendly, solvent- and catalyst-free synthesis of 2-anilino nicotinic acids derivatives is reported. This operationally simple and green procedure was applied to a selection of primary aromatic amines giving rise to 23 derivatives of 2-anilino nicotinic acids in a very short reaction time (15–120 min) with good to excellent yield. Next, similarity searches were executed on these derivatives to find the possible biological target. These products were screened for inhibition of COX-1 and COX-2 by molecular docking and dynamic studies. In silico studies revealed that among these derivatives, the structure 10 bearing meta-chlorine substitutions could act as COX-1 and COX-2 inhibitors. These results can be used in designing important lead compounds for further development as potential anti-inflammatory drugs.
Learning differential equations from mixed nonlinear dynamics models
Authors: Shen Yue , Zhang Qi , Chen Yu 
Published: April 2023

Abstract
For decades, researchers have attempted to use computational algorithms for finding analytical laws from the recorded data. However, previous studies mainly focused on proposing more efficient regression algorithms for learning equations from the given data. An equally important problem, namely how can we algorithmically ensure that the set of candidate variables in the search space are complete and spared from the unnecessary terms has not been given much attention. In this study, we propose a framework to realize the identification of inappropriate potential variables in the equation learning. Specifically, by introducing the causal inference method into the procedure of equation learning, we can effectively recognize terms that confound in the variable space. The pipeline of our method is given, while examples of ecological and physical systems are used to show that we can improve the accuracy of the learnt equations by eliminating the identified confusing terms in the library of potential variables.
Relative abundance of major insect pests and natural enemies in high yielding rice varieties of Assam
Authors: Baruah Mayuri , Dutta Bijon Chandra 
Published: April 2023

Abstract
The relative abundance of major insect pests and natural enemies were studied at three different growth stages in seven high yielding varieties, Ranjit, Ranjit Sub-1, Bahadur, Bahadur Sub-1, Gitesh, Swarna Sub-1 and Shraboni in kharif and rabi season at Titabar, Assam during 2020–2022. White stem borer (47.49%) was the most predominantly abundant species followed by yellow stem borer (41.97%) among seven major insect pest species e.g., leaf folder, gall midge, caseworm, whorl maggot and gundhi bug in kharif season. But, yellow stem borer (48.69%) was abundantly observed followed by white stem borer (40.63%) among all major insect pests during rabi season. Both the species of stem borer gradually increased and reached peak due to availability of enough food at reproductive stage and decreased in the ripening stage in both the season comparatively higher in rabi season Leaf folder was the most abundant leaf feeder and its population abundance was higher in Shraboni (9.89%) followed by Bahadur (9.67%), Bahadur Sub-1 (9.61%) and Swarna Sub-1 (8.47%) at vegetative stage which reached peak at reproductive stage during kharif season. The population of caseworm and whorl maggot was higher in vegetative stage and subsequently declined till the reproductive stage in kharif season. No caseworm population was observed during rabi season due to scanty rainfall. The gundhi bug population was higher in rabi season as compared to khairf season. Spider was the most prominent predator followed by coccinellid beetle in all the seven varieties during kharif and rabi season.
Correlation of LOXL2 expression in non-small cell lung cancer with immunotherapy and clinical prognosis
Authors: Chen Haoyan , Liu Lele , Zhu Bei , Zhang Lili , Zhang Yuxing , Ma Miao , Wu Jianqing 
Published: April 2023

Abstract
Background Lung cancer is the worst and deadliest disease globally, with about 80% of cases being non-small cell lung cancer (NSCLC). NSCLC mainly consists of lung squamous cell carcinoma (LUSC) and lung adenocarcinoma (LUAD). Although chemotherapy is currently the mainstay of treatment for NSCLC, chemotherapy resistance is still an urgent problem for patients. Studies in recent years have proposed immunotherapy as a new direction for treating NSCLC.Methods Based on the available datasets from TCGA, the association between the LOXL2 gene and NSCLC was explored by using multiple online tools (e.g., GEIPA, Oncomine, Dreimt) and bioinformatics analysis software (R or GSEA). The immune microenvironment of the tumor was explored by calculating ImmuneScore, StromalScore, and TumorPurity of LUAD and LUSC and analyzing the infiltration of 22 immune cells in lung cancer tissues. LOXL2-related loads were obtained from the Xena database for LUSC and LUAD patients, and relevant prognostic genes were identified by analyzing survival curves. Functional and pathway enrichment analyses of prognostic, predictive genes were performed using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG). The expression of LOXL2 in NSCLC was detected by RT-qPCR.Results LOXL2 may involve in the progression of the course of LUAD and LUSC and is closely related to the T-lymphocyte subpopulation, T-reg cells. SEMA7A and VEGFC were identified as the genes that interact with LOXL2 and could be used as prognostic signature genes in NSCLC patients.Conclusion LOXL2 may become a prognostic marker and a new target for immunotherapy.
Neural network analysis of pharyngeal sounds can detect obstructive upper respiratory disease in brachycephalic dogs
Authors: McDonald Andrew , Agarwal Anurag , Williams Ben , Liu Nai-Chieh , Ladlow Jane 
Published: April 2023

Abstract
Brachycephalic obstructive airway syndrome (BOAS) is a highly prevalent respiratory disease affecting popular short-faced dog breeds such as Pugs and French bulldogs. BOAS causes significant morbidity, leading to poor exercise tolerance, sleep disorders and a shortened lifespan. Despite its severity, the disease is commonly missed by owners or disregarded by veterinary practitioners. A key clinical sign of BOAS is stertor, a low-frequency snoring sound. In recent years, a functional grading scheme has been introduced to semi-objectively grade BOAS based on the presence of stertor and other abnormal signs. However, correctly grading stertor requires significant experience and adding an objective component would aid accuracy and repeatability. This study proposes a recurrent neural network model to automatically detect and grade stertor in laryngeal electronic stethoscope recordings. The model is developed using a novel dataset of 665 labelled recordings, taken from 341 dogs with diverse BOAS symptoms. Evaluated via nested cross validation, the neural network predicts the presence of clinically significant BOAS with an area under the receiving operating characteristic of 0.85, an operating sensitivity of 69% and a specificity of 87%. The algorithm could enable widespread screening for BOAS to be conducted by both owners and veterinarians, improving treatment and breeding decisions.
Survival and prognostic factors in patients with de novo metastatic breast cancer according to estrogen receptor status: A retrospective study
Authors: Sun Jianna , Kong Lingjun , Mu Kun , Jiang Xiuzhen , Luo Ruizhen , Wu Yafei , Ren Chongxi 
Published: April 2023

Abstract
Purpose: The clinical outcomes of de novo metastatic breast cancer (dnMBC) differ between estrogen receptor (ER)-positive and ER-negative patients, but the respective prognostic factors in these two subpopulations have not been established. This study aimed to investigate the survival and prognostic factors in patients with dnMBC according to ER status.
Methods: Patients with dnMBC between February 2010 and December 2017 were retrospectively reviewed. Demographics, tumor characteristics, treatment types and survival data were collected. Patients were divided into ER-negative and ER-positive groups, and the propensity score matching (PSM) was used to balance the bias. Overall survival (OS) was compared between groups. Univariable and multivariable Cox regression analyses were performed to identify prognostic factors in each group.
Results: A total of 518 patients were included in the study. After PSM, there were 157 ER-negative and 165 ER-positive patients. With a median follow-up of 8.5 years, the median OS was 36 months (95% confidence interval [CI], 32-41) in the ER-positive group and 24 months (95% CI, 19-27) in the ER-negative group (P=0.001). Ki-67 index, endocrine therapy and radiotherapy for primary tumor were independent prognostic factors of OS in the ER-positive group, while initial chemotherapy cycles and chemotherapy after disease progression were independent prognostic factors of OS in the ER-negative group. Clinical T stage and initial metastatic sites were independent prognostic factors of OS regardless of ER status.
Conclusion: For dnMBC, ER-negative patients are clinically different from ER-positive patients, with shorter OS. The identified prognostic factors could guide treatment selection in these two subpopulations.
Long QT syndrome diagnosis may be affected by positive tilt table test; a cross-sectional study
Authors: Nikoo Mohammad Hossein , Hassani Amir Hossein , Kamrava Daniyal , Fatemian Hossein , Mousavi Seyed Mojtaba , Keshavarz Mohammad 
Published: April 2023

Abstract
Background Tilt Table Test (TTT) is usually used for assessment of syncope with undefined etiology. Positive test occurs in those with parasympathetic overstimulation. This overactivation of parasympathetic system may affect QTc measurement; not only through rate modulation, but also from through potassium ionic channels as muscarinic activated inward rectifying K + current.Methods and Materials: in this cross-sectional study, 478 patients with syncopal attacks of unknown origin underwent evaluation with TTT as well as 24-hour Holter electrocardiogram monitoring. Schwartz score (for diagnosis of Long QT syndrome) was calculated for all of them. Those with secondary causes of long QT excluded from survey. Then the association of positive TTT and Schwartz score was assessed.Results 478 patients entered the study 208 (43.4%) of whom were male and 270 (56.4%) were female. The mean age of the patients was 42.43 ± 17.979 years old. TTT was positive in 289 (60.46%) patients and was negative in 189 (39.54%) patients. the mean Schwartz score was significantly higher in patients with positive TTT (2.77 ± 0.08 vs. 1.99 ± 0.12) (P < 0.001).Conclusion Diagnosis of long QT syndrome as a cause of syncope should not be made hesitantly by the use of Schwartz score as this scoring system might need to be modified based on the results of tilt table test.
Identification of differentially expressed genes and signaling pathways in Esophageal squamous cell carcinoma using bioinformatics analysis
Authors: Zou Zhiyan , Lu Zhou , Hu Yan , Liang Yuanyuan , Li Xiaoan 
Published: April 2023

Abstract
Background: Esophageal squamous cell carcinoma (ESCC) is one of the histological types of esophageal cancers, with more than 80% of esophageal cancers being ESCC. Meanwhile, in Asia, ESCC has higher morbidity and mortality compared with western countries. Due to lack of effective molecular targets and treatments options, the prognosis and 5-year survival rate of ESCC are extremely poor. Therefore, there is an urgent need to identify key pathogenic genes involved in ESCC and reveal potential molecular mechanisms.
Methods: To explore potential therapeutic targets for ESCC, we analyzed three microarray datasets (GSE20347, GSE161533, and GSE38129) derived from the Gene Expression Omnibus (GEO) database of the National Center for Biotechnology Information (NCBI). We used the GEO2R tool to screen out differentially expressed genes (DEGs) between tumourtissues and normal tissues. Gene Ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of DEGs were performed via the Database for Annotation, Visualization and Integrated Discovery (DAVID, https://david.ncifcrf.gov/). The Search Tool for the Retrieval of Interacting Genes (STRING) database and Cytoscape software were used to construct a protein-protein interaction (PPI) network of these DEGs. Furthermore, we used the online GEPIA database to carry out survival analysis to evaluate the prognostic value of hub genes expression in ESCC patients.
Results: A total of 32 upregulated DEGs and 42 downregulated DEGs were identified in ESCC. Among them, we picked out ten hub genes with a high degree of connectivity. Overexpression of these some hub genes was associated with unfavorable prognosis of ESCC. Particularly, the overexpression of COL10A1 and SERPINE1 was observed using the qRT-PCR and indicated poor outcome of ESCC. Simultaneously, low expression of some hub genes was associated with shorter overall survival, such as ACPP and LDHA genes.
Conclusion The results in this study might provide some directive significance for further exploring the potential biomarkers for diagnosis and prognosis prediction of ESCC patients. Meanwhile, further study is needed to explore the value of hub genes in the treatment of ESCC.
Process optimization to high gymnemic acid content from Gymnema inodorum (Lour.) Decne. leaves
Authors: Nunta Rojarej , Khemacheewakul Julaluk , Sommanee Sumeth , Mahakuntha Chatchadaporn , Chompoo Mayuree , Phimolsiripol Yuthana , Jantanasakulwong Kittisak , Kumar Anbarasu , Leksawasdi Noppol 
Published: April 2023

Abstract

Gymnema inodorumor Phak Chiang Da (PCD) vegetable is an indigenous medicinal plant used in Northern Thailand for diabetic treatment since ancient times. However, the low concentration of an active molecule, gymnemic acid (GA) in the leaves limit its applications among the large population. Therefore, the present study aimed to maximize the extraction of GA from PCD leaves using the solvent extraction method. The effect of concentration of ethanol and extraction temperature were investigated for the determination of optimum extraction conditions. A process was developed for the production of GA-enriched PCD extract powder and characterized. Results showed that a concentration of 50% (v/v) ethanol at 70°C for 2 h was appropriate to extract a higher GA concentration of 8,307 mg/kg from dried PCD leaves. During the drying process, maltodextrin with a concentration of 0.5% (w/v) was appropriate to produce PCD extract powder with maximum GA concentration. The color analysis (L*, a* and b*) revealed that the overall appearance of the PCD extract powder was a dark greenish tint mixed with yellow. The antioxidant activity assay showed that PCD extract powder at 0.1 g was able to neutralize 75.8% of DPPH free radicals. The results suggested that PCD extract powder rich in GA could be used as a possible source of nutraceuticals or as a functional food ingredient.
Synthesis, molecular docking and evaluation of 1,5-diarylpyrazole/oxime hybrids targeting EGFR and JNK-2 as antiproliferative agents
Authors: Abdelrahman Kamal S. , Hassan Heba A. , Abdel-Aziz Salah A. , Marzouk Adel A. , shams Raef , Oswa Keima , Abdel-Aziz Mohamed , Konno Hiroyuki 
Published: April 2023

Abstract
A series of new 1,5-diarylpyrazole oxime hybrid derivatives (scaffold A and B) were designed, synthesized, and their structures were examined for purity with different spectroscopic techniques. All the synthesized compounds (7a-j), (8a-j), (9a-c) and (10a-c) were biologically evaluated for their in vitro cytotoxicity against a panel of five cancer cell lines known to express EGFR and JNK-2, namely human colorectal adenocarcinoma cell line DLD-1, human cervical cancer cell line Hela, human leukemia cell line K562, human pancreatic cell line SUIT-2 and human hepatocellular carcinoma cell line HepG2. The oxime containing compounds (8a-j) and (10a-c) were more active as antiproliferative agents than their non-oxime congeners (7a-j) and (9a-c). Compounds 8d, 8g, 8i, and 10c inhibited EGFR with IC50 values ranging from 8 to 21 µM when compared to sorafenib. Compound 8i inhibited JNK-2 as effectively as sorafenib, with an IC50 of 1.00 µM. Furthermore, compound 8g showed cell cycle arrest at the G2/M phase in the Hela cell line cell cycle analysis, whereas compound 8i showed combined S phase and G2 phase arrest. Docking studies revealed that oxime derivatives fit well at the EGFR binding site, with binding free energies ranging from -12.98 to 32.30 kcl/mol for compounds 8d, 8g, 8i, and 10c, while compounds 8d and 8i had binding free energies ranging from -9.16 to -12.00 kcl/mol at the JNK-2 binding site.
Identification of conserved gene expression changes across common glomerular diseases by spatial transcriptomics
Authors: Kim Dong Ki , Cho Jeong Min , Kang Minji , Park Sehoon , Shin Ha Yeon , Koh Jung Hun , Cho Semin , Kim Yaerim , Lee Soojin , Kim Yong Chul , Han Seung Seok , Joo Kwon Wook , Kim Yon Su , Lee Hajeong , Kim Hyun Je 
Published: April 2023

Abstract

Background: Glomerular diseases encompass a group of kidney diseases that may share common gene expression pathways. We aimed to analyze glomerular-specific gene expression profiles across various glomerular diseases.
Methods: We performed spatial transcriptomic profiling using formalin-fixed paraffin-embedded kidney biopsy specimens of controls and patients with five types of glomerular diseases using the GeoMx Digital Spatial Profiler. We identified common differentially expressed genes (DEGs) across glomerular diseases and performed Gene Ontology (GO) annotation by using the ToppGene suite.
Results: A total of 35 DEGs were consistently downregulated in glomeruli across the disease compared to the control, while none of the DEGs were consistently upregulated. Twelve of 35 downregulated DEGs, including the two hub genes FOS and JUN, were annotated with molecular function GO terms related to DNA-binding transcription factor activity. Other notable DEGs consistently downregulated and annotated in the pathway analysis included NR4A3, KLF9, EGR1, and ATF3. The annotated biological process GO terms included response to lipid-related (17/35 DEGs), response to steroid hormone (12/35 DEGs), or cell cycle regulation (10/35 DEGs).
Conclusions: Identifying common DEGs by spatial transcriptomic analysis provides insights into the underlying molecular mechanisms of glomerular diseases and may lead to novel assessment or therapeutic strategies.
Identification to Fake Messages with Two PKCs
Authors: Dissanayake W.D.M.G.M. 
Published: April 2023

Abstract

In this paper, two public key cryptosystems are presented and analyzed. The first cryptosystem is an improvement of RSA public key cryptosystem. The second cryptosystem is a novel public key cryptosystem. The encryption/decryption moduli of the introduced new public key scheme is quite different from widely used encryption/decryption moduli by other public key cryptosystems. The introduced new public key cryptosystem based on the exponentiation congruence and use an interesting, computer-friendly modulus:2n. These primitives can be used in protocols for authentication, key exchanges and digital signatures. The introduced two public key cryptosystems are more suitable for highly confidential digital transactions. Both of the cryptosystems are strongly IND secure. The most important thing is, that the both of the public key cryptosystems can identify whether a message is fake or not. The introduced new public key cryptosystem is very collaborative with hash functions such as Whirlpool and SHA-512, because of the modulus 2n.