bluuebunny/crossref_metadata_2025_split huggingface dataset:
The prognostic and predictive significance of perineural invasion in stage I to III colon cancer: a propensity score matching-based analysis
Authors: Chu Chun-Hui , Lai I-Li , Jong Bor-Kang , Chiang Sum-Fu , Tsai Wen-Sy , Hsieh Pao-Shiu , Yeh Chien-Yuh , You Jeng-Fu 
Published: May 2024

Abstract
Background
Colorectal cancer (CRC) presents with varying prognoses, and identifying factors for predicting metastasis and outcomes is crucial. Perineural invasion (PNI) is a debated prognostic factor for CRC, particularly in stage I-III patients, but its role in guiding adjuvant chemotherapy for node-positive colon cancer remains uncertain.

Methods
We conducted a single-center study using data from the Colorectal Section Tumor Registry Database at Chang Gung Memorial Hospital, Taiwan. This prospective study involved 3,327 CRC patients, 1,536 of whom were eligible after application of the exclusion criteria, to investigate the prognostic value of PNI in stage I-III patients and its predictive value for node-positive/negative cancer patients receiving adjuvant chemotherapy. Propensity score matching (PSM) was used to minimize selection bias, and follow-up was performed with standardized procedures.

Results
PNI-positive (PNI+) tumors were associated with higher preoperative CEA levels and more frequent adjuvant chemotherapy. After PSM, PNI + tumors were associated with marginally significantly lower 5-year disease-free survival (DFS) and significantly lower overall survival (OS) rates in stages III CRC. However, no significant differences were observed in stages I and II. Subgroup analysis showed that among PNI + tumors, only poorly differentiated tumors had higher odds of recurrence. PNI did not predict outcomes in node-negative colon cancer. Adjuvant chemotherapy benefited PNI + patients with node-positive but not those with node-negative disease.

Conclusions
Our study indicates that PNI is an independent poor prognostic factor in stage III colon cancer but does not predict outcomes in node-negative disease. Given the potential adverse effects of adjuvant chemotherapy, our findings discourage its use in node-negative colon cancer when PNI is present.
Surgical treatment and reproductive outcomes in caesarean scar pregnancy at a single center
Authors: Lei Yan , Du Xin , Liu Yu , Le Fangshu , Zhou Jianshan 
Published: May 2024

Abstract
Background
To investigate factors associated with different reproductive outcomes in patients with Caesarean scar pregnancies (CSPs).

Methods
Between May 2017 and July 2022, 549 patients underwent ultrasound-guided uterine aspiration and laparoscopic scar repair at the Gynaecology Department of Hubei Maternal and Child Health Hospital. Ultrasound-guided uterine aspiration was performed in patients with type I and II CSPs, and laparoscopic scar repair was performed in patients with type III CSP. The reproductive outcomes of 100 patients with fertility needs were followed up and compared between the groups.

Results
Of 100 patients, 43% had live births (43/100), 19% had abortions (19/100), 38% had secondary infertility (38/100), 15% had recurrent CSPs (RCSPs) (15/100). The reproductive outcomes of patients with CSPs after surgical treatment were not correlated with age, body mass index, time of gestation, yields, abortions, Caesarean sections, length of hospital stay, weeks of menopause during treatment, maximum diameter of the gestational sac, thickness of the remaining muscle layer of the uterine scar, type of CSP, surgical method, uterine artery embolisation during treatment, major bleeding, or presence of uterine adhesions after surgery. Abortion after treatment was the only risk factor affecting RCSPs (odds ratio 11.25, 95% confidence interval, 3.302–38.325; P < 0.01) and it had a certain predictive value for RCSP occurrence (area under the curve, 0.741).

Conclusions
The recurrence probability of CSPs was low, and women with childbearing intentions after CSPs should be encouraged to become pregnant again. Abortion after CSP is a risk factor for RCSP. No significant difference in reproductive outcomes was observed between the patients who underwent ultrasound-guided uterine aspiration and those who underwent laparoscopic scar repair for CSP.
Transcript and protein signatures derived from shared molecular interactions across cancers are associated with mortality
Authors: Zhao Yelin , Li Xinxiu , Loscalzo Joseph , Smelik Martin , Sysoev Oleg , Wang Yunzhang , Mahmud A. K. M. Firoj , Mansour Aly Dina , Benson Mikael 
Published: May 2024

Abstract
Background
Characterization of shared cancer mechanisms have been proposed to improve therapy strategies and prognosis. Here, we aimed to identify shared cell–cell interactions (CCIs) within the tumor microenvironment across multiple solid cancers and assess their association with cancer mortality.

Methods
CCIs of each cancer were identified by NicheNet analysis of single-cell RNA sequencing data from breast, colon, liver, lung, and ovarian cancers. These CCIs were used to construct a shared multi-cellular tumor model (shared-MCTM) representing common CCIs across cancers. A gene signature was identified from the shared-MCTM and tested on the mRNA and protein level in two large independent cohorts: The Cancer Genome Atlas (TCGA, 9185 tumor samples and 727 controls across 22 cancers) and UK biobank (UKBB, 10,384 cancer patients and 5063 controls with proteomics data across 17 cancers). Cox proportional hazards models were used to evaluate the association of the signature with 10-year all-cause mortality, including sex-specific analysis.

Results
A shared-MCTM was derived from five individual cancers. A shared gene signature was extracted from this shared-MCTM and the most prominent regulatory cell type, matrix cancer-associated fibroblast (mCAF). The signature exhibited significant expression changes in multiple cancers compared to controls at both mRNA and protein levels in two independent cohorts. Importantly, it was significantly associated with mortality in cancer patients in both cohorts. The highest hazard ratios were observed for brain cancer in TCGA (HR [95%CI] = 6.90[4.64–10.25]) and ovarian cancer in UKBB (5.53[2.08–8.80]). Sex-specific analysis revealed distinct risks, with a higher mortality risk associated with the protein signature score in males (2.41[1.97–2.96]) compared to females (1.84[1.44–2.37]).

Conclusion
We identified a gene signature from a comprehensive shared-MCTM representing common CCIs across different cancers and revealed the regulatory role of mCAF in the tumor microenvironment. The pathogenic relevance of the gene signature was supported by differential expression and association with mortality on both mRNA and protein levels in two independent cohorts.
Thymic gene expression analysis reveals a potential link between HIF-1A and Th17/Treg imbalance in thymoma associated myasthenia gravis
Authors: Altınönder İlayda , Kaya Mustafa , Yentür Sibel P. , Çakar Arman , Durmuş Hacer , Yegen Gülçin , Özkan Berker , Parman Yeşim , Sawalha Amr H. , Saruhan-Direskeneli Guher 
Published: May 2024

AbstractMyasthenia gravis (MG) is an immune-mediated disease frequently associated with thymic changes. Increased T helper 17 (Th17) cell activity and dysfunctional regulatory T (Treg) cells have been demonstrated in subgroups of MG. On the other hand, hypoxia-inducible factor 1 (HIF-1) has been shown to regulate the Th17/Treg balance by inducing Th17 differentiation while attenuating Treg development. To identify the underlying mechanisms of different thymic pathologies in MG development, we evaluated thymic samples from thymoma-associated myasthenia gravis (TAMG), MG with hyperplasia (TFH-MG) and thymoma without MG (TOMA) patients. Differential gene expression analysis revealed that TAMG and TFH-MG cells are associated with different functional pathways. A higher RORC/FOXP3 ratio provided evidence for Th17/Treg imbalance in TAMG potentially related to increased HIF1A. The hypoxic microenvironment in thymoma may be a driver of TAMG by increasing HIF1A. These findings may lead to new therapeutic approaches targeting HIF1A in the development of TAMG.
Surgical choice for the treatment of partial intestinal ischemic necrosis caused by acute type a aortic dissection combined with malperfusion of superior mesenteric artery
Authors: Yu Wenbo , Liang Yuan , Gao Jianfeng , Xie Dilin , Xiong Jianxian 
Published: May 2024

AbstractAcute type A aortic dissection is a severe cardiovascular disease characterized by rapid onset and high mortality. Traditionally, urgent open aortic repair is performed after admission to prevent aortic rupture and death. However, when combined with malperfusion syndrome, the low perfusion of the superior mesenteric artery can further lead to intestinal necrosis, significantly impacting the surgery’s prognosis and potentially resulting in adverse consequences, bringing. This presents great significant challenges in treatment. Based on recent domestic and international research literature, this paper reviews the mechanism, current treatment approaches, and selection of surgical methods for poor organ perfusion caused by acute type A aortic dissection. The literature review findings suggest that central aortic repair can be employed for the treatment of acute type A aortic dissection with inadequate perfusion of the superior mesenteric artery. The superior mesenteric artery can be windowed and (/or) stented, followed by delayed aortic repair. Priority should be given to revascularization of the superior mesenteric artery, followed by central aortic repair. During central aortic repair, direct blood perfusion should be performed on the distal true lumen of the superior mesenteric artery, leading to resulting in favorable therapeutic outcomes. The research results indicate that even after surgical aortic repair, intestinal ischemic necrosis may still occur. In such cases, prompt laparotomy and necessary necrotic bowel resection are crucial for saving the patient’s life.
Chemotherapy-induced PTEN-L secretion promotes the selection of PTEN-deficient tumor cells
Authors: Wang Ming , Pan Zhenzhen , Chu Xu , Yao Xiaohan , Duan Xixi , Wan Jiajia , Lou Xiaohan , Li Wenqing , Yan Yan , Chen Lin , An Junfeng , Qin Zhihai 
Published: May 2024

Abstract
Background
PTEN loss has been identified in various tumor types and is linked to unfavorable clinical outcomes. In addition to PTEN mutation, multiple mechanisms contribute to PTEN loss during tumor development. However, the natural selection process of PTEN-deficient tumor cells remains unclear. Here, we aimed at further elucidating the role of PTEN-L in tumor progression.

Methods
PTEN knockout cell lines were generated using CRISPR/Cas9 technology. Ni-NTA affinity column chromatography was employed for PTEN-L purification. Tumor cell metastasis was evaluated in murine models and observed using the IVIS Spectrum Imaging System. RNA-sequencing, western blotting, PCR, flow cytometry, and cell proliferation assays were employed to investigate tumor cell dormancy and related mechanisms.

Results
The chemotherapeutic drugs, cisplatin, paclitaxel, and doxorubicin, induced tumor cells to secrete PTEN-long (PTEN-L), which shields PTEN-deficient tumor cells from chemotherapy-induced apoptosis better than it shields PTEN-intact cells. Further investigation revealed that PTEN-L treatment induced dormancy in PTEN-null tumor cells, characterized by an increase in p16 and p27 levels, cell-cycle arrest, reduced cell proliferation, and enhanced DNA repair. Furthermore, PTEN-L treatment selectively promoted the accumulation and growth of PTEN-null tumor cells in the lungs of C57BL/6J mice, while evading immune surveillance. Mechanistically, PTEN-L induced dormancy in PTEN-null tumor cells by activating the p38 signaling pathway. Addition of a p38 inhibitor effectively reversed dormancy and growth of PTEN-deficient tumor cells in the lungs. We also demonstrated that PTEN expression played a pivotal role in determining the outcome of PTEN-L-mediated antitumor therapy.

Conclusions
In summary, PTEN-L was identified as a potent inducer of dormancy in PTEN-deficient tumor cells, which increased their efficient selection within the tumor microenvironment.
Acetylation- and ubiquitination-regulated SFMBT2 acts as a tumor suppressor in clear cell renal cell carcinoma
Authors: Xie Qingpeng , Hu Bin , Li Haosong 
Published: May 2024

Abstract
Background
Clear cell renal cell carcinoma (RCC) is the most common kidney tumor. The analysis from medical database showed that Scm-like with four MBT domains protein 2 (SFMBT2) was decreased in advanced clear cell RCC cases, and its downregulation was associated with the poor prognosis. This study aims to investigate the role of SFMBT2 in clear cell RCC.

Methods
The expression of SFMBT2 in clear cell RCC specimens were determined by immunohistochemistry staining and western blot. The overexpression and knockdown of SFMBT2 was realized by infection of lentivirus loaded with SFMBT2 coding sequence or silencing fragment in 786-O and 769-P cells, and its effects on proliferation and metastasis were assessed by MTT, colony formation, flow cytometry, wound healing, transwell assay, xenograft and metastasis experiments in nude mice. The interaction of SFMBT2 with histone deacetylase 3 (HDAC3) and seven in absentia homolog 1 (SIAH1) was confirmed by co-immunoprecipitation.

Results
In our study, SFMBT2 exhibited lower expression in clear cell RCC specimens with advanced stages than those with early stages. Overexpression of SFMBT2 inhibited the growth and metastasis of clear cell RCC cells, 786-O and 769-P, in vitro and in vivo, and its silencing displayed opposites effects. HDAC3 led to deacetylation of SFMBT2, and the HDAC3 inhibitor-induced acetylation prevented SFMBT2 from SIAH1-mediated ubiquitination modification and proteasome degradation. K687 in SFMBT2 protein molecule may be the key site for acetylation and ubiquitination.

Conclusions
SFMBT2 exerted an anti-tumor role in clear cell RCC cells, and HDAC3-mediated deacetylation promoted SIAH1-controlled ubiquitination of SFMBT2. SFMBT2 may be considered as a novel clinical diagnostic marker and/or therapeutic target of clear cell RCC, and crosstalk between its post-translational modifications may provide novel insights for agent development.
The species and abundance of gut bacteria both positively impact Phortica okadai behavior
Authors: Li Di , Wang Lingjun , Wang Liang , Gou Yanting , Luo Bo , Yan Rong , Liu Hui 
Published: May 2024

Abstract
Background
Gut bacteria, which serve as essential modulators, exert a significant impact on insect physiology and behavior and have substantial application potential in pest management. The dynamics of gut bacteria and their impact on Phortica okadai behavior remain unclear.

Methods
In this study, the dynamics of gut bacteria at different developmental stages in P. okadai were analyzed using 16S ribosomal RNA (rRNA) gene sequencing, and the species and abundance of gut bacteria that affect host behavior were examined via behavioral experiments.

Results
A total of 19 phyla, 29 classes, 74 orders, 101 species, and 169 genera were identified. The results of the behavioral experiments indicated that the species Lactiplantibacillus argentoratensis, Acetobacter tropicalis, Leuconostoc citreum, and Levilactobacillus brevis effectively influenced the feeding preference of P. okadai, and the single-bacterium-seeded P. okadai exhibited feeding preferences distinct from those of the germ-free (GF) and wild-type P. okadai.

Conclusions
The species and relative abundance of gut bacteria together positively impact P. okadai behavior. Lactiplantibacillus argentoratensis, as the most attractive bacteria to P. okadai, presents opportunities for novel pest control strategies targeting this vector and agricultural pest.

Graphical Abstract
Research progress on the polysaccharide extraction and antibacterial activity
Authors: Liang Lihui , Su Qihang , Ma Yu , Zhao Shuzhen , Zhang Huanjie , Gao Xiaofeng 
Published: May 2024

Abstract
Background
Over time, the amount of germs resistant to antibacterial medications has been steadily rising because of their prolonged and indiscriminate use. The increase in drug resistance significantly threatens to human health and has become a globally recognized issue of concern. Therefore, identifying new antibacterial drugs is urgently needed.

Forward
Polysaccharides are natural macromolecular substances that exist in plants, microorganisms, and animals, They have an immense amount of use in the food and medical industries. Polysaccharides can be categorized as plant, animal, or microbial based on the sources of the polysaccharides.

Conclusion
Polysaccharides are natural compounds with antibacterial properties that exerts antibacterial activity by disrupting bacterial cell walls and cell membranes. They show potential as candidates for the creation and application of novel antibiotics. This article reviews the classification of polysaccharides, their isolation and purification, mechanisms of action, and antibacterial activity. The primary objective of this study is to lay down an empirical groundwork for examining the antibacterial properties of polysaccharides.
Management of complete intra-articular distal femur and patellar fractures in an achondroplastic young adult; small is challenging’ revisited: a case-report
Authors: Elrukby Hussein Samir , Mohamed Khalid Mohamed Abd Elhafiz , Hamed Elamin Mohamed Elamin 
Published: May 2024

Abstract
Background
People with achondroplasia exhibit distinct physical characteristics, but their cognitive abilities remain within the normal range. The challenges encountered during surgical procedures and perioperative care for achondroplastic individuals, are underrepresented in the existing literature.

Case presentation
In this report, the management of a 26-year-old North-African achondroplastic male is highlighted. The patient suffered a complete intra-articular distal femur fracture (AO/OTA 33-C1) and an ipsilateral patella fracture (AO/OTA 34-C1). The patient’s unusual anatomical variations and the lack of suitable orthopedic implants posed significant surgical challenges, particularly in the context of a resource-limited developing country. Facial and spinal deformities, which are common in patients with achondroplasia, further complicated the anesthetic approach.

Conclusions
The limited information on operative management of fractures in achondroplastic patients necessitated independent decision-making and diverging from the convenient approach where clear guidance is available in the literature.
Large-scale transcriptomic and genomic analyses reveal a novel functional gene SERPINB6 for chicken carcass traits
Authors: Zhao Di , Liu Ranran , Tan Xiaodong , Kang Huimin , Wang Jie , Ma Zheng , Zhao Haiquan , Xiang Hai , Zhang Zhengfen , Li Hua , Zhao Guiping 
Published: May 2024

Abstract
Background
Carcass traits are crucial indicators of meat production efficiency. However, the molecular regulatory mechanisms associated with these traits remain unclear.

Results
In this study, we conducted comprehensive transcriptomic and genomic analyses on 399 Tiannong partridge chickens to identify key genes and variants associated with carcass traits and to elucidate the underlying regulatory mechanisms. Based on association analyses with the elastic net (EN) model, we identified 12 candidate genes (AMY1A, AP3B2, CEBPG, EEF2, EIF4EBP1, FGFR1, FOXD3, GOLM1, LOC107052698, PABPC1, SERPINB6 and TBC1D16) for 4 carcass-related traits, namely live weight, dressed weight, eviscerated weight, and breast muscle weight. SERPINB6 was identified as the only overlapping gene by 3 analyses, EN model analysis, weighted gene co-expression network analysis and differential expression analysis. Cell-level experiments confirmed that SERPINB6 promotes the proliferation of chicken DF1 cells and primary myoblasts. Further expression genome-wide association study and association analysis indicated that rs317934171 is the critical site that enhances SERPINB6 expression. Furthermore, a dual-luciferase reporter assay proved that gga-miR-1615 targets the 3′UTR of SERPINB6.

Conclusions
Collectively, our findings reveal that SERPINB6 serves as a novel gene for chicken carcass traits by promoting fibroblast and myoblast proliferation. Additionally, the downstream variant rs317934171 regulates SERPINB6 expression. These results identify a new target gene and molecular marker for the molecular mechanisms of chicken carcass traits.
Prerequisites-based course recommendation: recommending learning objects using concept prerequisites and metadata matching
Authors: Chanaa Abdessamad , El Faddouli Nour-eddine 
Published: May 2024

AbstractThe recommendation is an active area of scientific research; it is also a challenging and fundamental problem in online education. However, classical recommender systems usually suffer from item cold-start issues. Besides, unlike other fields like e-commerce or entertainment, e-learning recommendations must ensure that learners have the adequate background knowledge to cognitively receive the recommended learning objects. For that reason, when designing an efficient e-learning recommendation method, these challenges should be considered. To address those issues, in this paper, we first propose extracting pairs concept prerequisites using Linked Open Data (LOD). Then, we evaluate the proposed list of prerequisite relationships using machine learning predictive models. Then, we present the recommendation approach based on matching concept’s prerequisites relation and courses metadata through a similarity score. The experimental result of prerequisite identification was evaluated using four well-known machine learning algorithms while achieving an accuracy of 90%. Moreover, using three known evaluation metrics, the final prerequisite-based recommendation demonstrates very good results (NDCG@10 = 86%). This solution will enhance recommendations on online learning platforms. Additionally, it will overcome the cold-start issue and accomplish the needed prerequisites and background knowledge for learners to attain their learning objectives.