bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrated analysis of single-cell and bulk RNA sequencing predicts prognosis and therapeutic response using malignant epithelial cells marker genes in bladder cancer
Authors: Hu Caoyang , Zhang Wei , Ren Xiaolu , Li Zhenhua , Jiang Xin , Chang Lina , Ma Zhifang , Wang Xin 
Published: April 2024

Abstract
Bladder cancer remains a prevalent malignancy of the urinary system, closely tied to aberrations in bladder epithelial tissue. To better understand its complexities, this study delved into single-cell data to identify key marker genes of malignant cells. Subsequent analyses uncovered significant pathways facilitating intercellular communication, including COLLAGEN, PTN, and MK pathways. Additionally, pivotal transcription factors like SMARCA4 and CEBPD were identified, shedding light on regulatory mechanisms within malignant cells. Furthermore, leveraging these marker genes, patients with bladder cancer were stratified into distinct groups, with implications for prognosis and immunotherapeutic response. Group C1 exhibited a favorable prognosis, contrasting with Group C2, characterized by heightened immune microenvironment infiltration and expression of immune checkpoints, particularly responsive to PD-1 inhibitors. Building upon these findings, a robust four-gene prognostic model was developed and validated across diverse datasets, offering insights into personalized treatment strategies. Moreover, the study spotlighted CD109 as a noteworthy player in bladder cancer pathogenesis, evidenced by its heightened expression in tumor tissues and its role in promoting proliferation, migration, and invasion of bladder cancer cells, as demonstrated through immunohistochemistry experiments following CD109 knockout. In summary, this research uncovers vital pathways and regulatory elements driving bladder cancer progression.
Molecular characteristics, potential mechanisms and prognostic gene model of younger female patients with gastric cancer
Authors: Luan Xiaoyi , Zhao Lulu , Wang Wanqing , Niu Penghui , Han Xue , Wang Zerong , Zhang Xiaojie , Zhao Dongbing , Chen Yingtai 
Published: April 2024

Abstract

Background
Male patients were twice as likely to develop gastric cancer (GC) compared to females, partly due to the protective effect of estrogen. However, the proportion of females increased in the young GC patients. The study was designed to explore comprehensive molecular profiles of younger female GC patients, as well as develop a prognostic gene model for female GC patients.
Methods
Gene expression and clinical data of GC and non-tumor patients were downloaded from the Gene Expression Omnibus (GEO) database. Gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and gene set enrichment analysis (GSEA) were used to find molecular characteristics and potential mechanisms of younger female GC patients. The prognostic gene model containing 6 differential expressed genes (DEGs), which were between younger and older female patients, was established using Lasso-Cox regression. Its performance was validated by external validation. Then, receiver operating characteristic (ROC) curve was applied to determine the prognostic value of the prognostic gene model.
Results
Six GEO cohorts with 305 female GC patients (69 younger patients and 236 older patients) and 38 female non-tumor patients were included. A total of 4557 DEGs between female GC patients and non-tumor patients were identified, including 2212 up-regulated genes and 2345 down-regulated genes. Estrogen response early (p < 0.001) and estrogen response late (p < 0.001) were enriched in female GC patients. In KEGG analysis, aldosterone (p = 0.023) and relaxin pathways (p = 0.043) were concentrated in younger group. Moreover, we further used GSE84437 cohort to construct a prognostic gene model containing 6 genes, namely NREP, GAD1, SLCO4A1, KRT17, DEFB1, and P3H2, to predict the overall survival (OS) of female GC patients (AUC = 0.810). Younger female patients, who were related with high-risk at the genetic level, showed worse OS compared with older female patients who showed low-risk (HR = 5.7688, 95%CI: 3.0108–11.0530, P < 0.001).
Conclusions
In conclusion, we provided the comprehensive molecular profiles of younger female GC patients and found that there was a significant difference in enriched hormone-related pathways between younger group and older group. In addition, we found younger female patients showed worse OS compared with older female patients using the prognostic gene model we created.
LncRNA-004686 regulates muscle fibre type switching in chicken embryos by affecting the expression of MYH1B
Authors: Chen Ruonan , Zhang Ruotong , Yang Chaoyong , Sun Nanzhen , Sun Jie 
Published: April 2024

Abstract

Muscle fibres constitute the majority of an animal's muscle, and the kind of muscle fibres has a substantial impact on the quality of muscle. Long non-coding RNAs (lncRNAs) are well-known to participate in various critical regulatory processes in muscle fibre type switching. Immunohistochemistry was employed in this study to determine the ratio of fast and slow muscle fibres in the leg muscles of two breeds during the embryonic stage. Finally, leg muscle samples at 8 days and 15 days of embryonic stage were selected for high-throughput sequencing. The highly differentially expressed lncRNA-004686 was identified between two breeds, and its putative target gene is MYH1B. To investigate its effect on the proliferation, differentiation, and muscle fibre switching of chicken myoblasts, interference and overexpression vectors of lncRNA-004686 were designed and transfected into chicken myoblasts. The findings suggested that lncRNA-004686 may influence the target gene MYH1B, hence increasing myoblast proliferation, restricting myoblast differentiation, and influencing muscle fibre type. This study offers fresh perspectives on how to investigate the molecular mechanism of muscle fibre type switching in chicken embryos and enhance meat quality.
Artificial Intelligence for Breast Cancer Screening in Mammography (AI-STREAM): Preliminary Interim Analysis of a Prospective Multicenter Cohort Study
Authors: Chang Yun-Woo , Ryu Jung Kyu , An Jin Kyung , Choi Nami , Park Young Mi , Ko Kyung Hee , Han Kyunghwa 
Published: April 2024

Abstract

While retrospective studies have shown that artificial intelligence (AI) improve mammography screening accuracy, prospective data, particularly in a single-read setting, is lacking. This study aimed to address this knowledge gap by assessing the diagnostic accuracy of radiologists, with and without an AI-based computer-aided detection algorithm (AI-CAD), for interpretating screening mammograms in a single-read setting. A prospective multicenter cohort study in six academic hospitals participant in Korea’s national breast screening program was done, where women aged ³40 years were eligible for enrolment between February 2021, and December 2022. Radiologists interpreting screening mammograms first without, followed by with AI-CAD, and compared cancer detection rates (CDRs) and recall rate (RRs) for breast radiologists, general radiologists, and standalone AI. Of 24,543 women aged ³40 years were included in the final cohort (mean age 61 years [IQR 51-68]), with 131 (0.53%) screen-detected cancers confirmed based on pathologic diagnosis within six months. The CDR was significantly higher by 13.7% for breast radiologists with AI-CAD (n=124 [5.05 ‰]) versus those without AI (n=109 [4.44 ‰]; p <0.001), with no significant difference in RRs (p =0.564). Similar trends were observed for general radiologist, with significant higher CDRs by 25.1% for those with AI-CAD (n=105 [4·28 ‰]) versus those without AI-CAD (n=84 [3·42 ‰]; p <0·001); the CDR of standalone AI (n=118 [4·81 ‰]) was also significantly higher than that of general radiologists without AI, with no significant differences in RRs (p =0·795). Findings from this prospective, multicenter cohort study demonstrated significant improvement in CDRs and unaffected RRs of breast radiologist when using AI-CAD, as compared to not using AI-CAD, when interpreting screening mammograms in a single-read setting, highlighting the positive effects of AI-CAD as an assistive diagnostic tool to help radiologists, regardless of experience, in a real-world, breast cancer screening population.
Safety of local thermal ablation in hepatocellular carcinoma patients with cirrhosis and severe thrombocytopenia
Authors: Zhao Feiyu , Yang Qinna , Yang Fan , Zhang Xiaoming , Qian Niansong , Zhang Tian Lan 
Published: April 2024

Abstract

Background: Generally, invasive treatment is contraindication for patients with severe thrombocytopenia, because it may increase risk of bleeding. However, many early hepatocellular carcinoma (HCC) patients with cirrhosis have platelet counts (PC) less than 50×109/L due to hypersplenism. These patients are often accompanied by hepatic insufficiency, which makes hepatectomy impossible, and local thermal ablation (LTA) has become a major treatment. The aim of our study is to investigate the correlation between severe thrombocytopenia and bleeding after LTA in HCC patients with cirrhosis, and evaluate risk factors of bleeding.
Methods: 473 patients with cirrhosis who underwent LTA for HCC from 2016 to 2020 were enrolled, and 709 ablations were performed in total. Based on preoperative PC, cases were divided into three groups, namely, group A (PC>50×109/L), group B (30×109/L<PC≤50×109/L) and group C (PC≤30×109/L). The incidence of bleeding after LTA was compared among the three groups. Logistic regression was used to explore the risk factors for bleeding after ablation.
Results: The overall incidence of bleeding complications was 4.4%, and no significant difference was observed between group A, B, and C (3.9% vs. 6.4% vs. 3.3%, P=0.410). In multivariate analysis, tumor diameter (OR=2.657 per 1cm, P<0.001), and multiple lesions (≥3) (OR=3.723, P=0.006) were found to be independent predictors of bleeding after LTA.
Conclusion: In small HCC patients with cirrhosis and hypersplenism, the PC range 30-50×109/L will not increase the risk of bleeding after LTA. Tumor diameter and number of lesions are independent predictors for bleeding after LTA in HCC patients.
Biomonitoring Serum Levels of Three Monoterpenes and Their Association with Liver Function Tests in US adults: NHANES 2013-2014
Authors: Fang Yu-Wei , Wang Chikang , Lin Chien-Yu 
Published: April 2024

Abstract

Purpose
Monoterpenes are organic compounds that have been extensively researched for their medicinal benefits. However, experimental evidence has raised concerns about their adverse effects on liver. Despite this, the impact of monoterpenes on liver function in the general population remains uncertain. Furthermore, the biomonitoring of monoterpenes exposure in the general population is an area that has been relatively underexplore.
Methods
We investigated the association between three monoterpenes (α-pinene, β-pinene, and limonene), the total quantity of three monoterpenes (Σmonoterpene), and liver function tests using data from the 2013–2014 National Health and Nutrition Examination Survey (NHANES) in adults aged 18 years and older.
Results
Among the 1670 subjects, the detection rate for α-pinene, β-pinene, and limonene was 74.1%, 74.3%, and 100%, respectively. Our results also revealed a positive correlation between the three ln-monoterpenes, ln-Σmonoterpene, and alanine aminotransferase (ALT), with ß coefficient of 3.571 (S.E. = 1.160, P = 0.008) for ln-Σmonoterpene. By considering a reference group of individuals with all three monoterpenes at or below the 50th percentile, we observed an upward trend in ALT levels when each of the monoterpene levels exceeded the 50th percentile (P for trend = 0.008).
Conclusions
We found a high prevalence of monoterpene exposure among American adults and observed a possible association between monoterpenes and liver function tests. Our findings also suggest a possible synergistic effect between these three monoterpenes with regards to liver function. Further research is necessary to fully comprehend the underlying mechanisms and clinical implications of this association.
A cross-sectional study measuring management of third stage of labour by midwives and maternity nurses in Oman
Authors: Al-Jabri Noora Saleh , Kelly Janet , Harvey Gillian , Lynch Elizabeth , Cusack Lynette 
Published: April 2024

Abstract

Background The World Health Organisation (WHO) recommends implementing evidence-based active management of the third stage of labour (AMTSL) guidelines for all women during the third stage of labour (TSL). Midwives and maternity nurses play a major role in the management of third stage of labour and prevention of postpartum haemorrhage.Aim To investigate midwives' and maternity nurses' knowledge, attitude and self-reported practices in Oman towards management of third stage of labour and factors that influence implementation of AMTSL guidelines.Methods A cross-sectional survey of 300 midwives and maternity nurses working in childbirth wards in six hospitals in Oman between July and September 2019. Descriptive statistics and binary logistic regressions were used to identify the factors associated with knowledge, attitude and self-reported practice.Results The survey achieved a response rate of 80% (n = 240; 231 midwives and 9 maternity nurses). Just over half of the respondents (n = 132, 55%) correctly identified the core characteristics of the recommended management of TSL of WHO guidelines. Fewer respondents correctly identified specific components of AMTSL, such as the administration of recommended dose of oxytocin following birth (n = 108, 45%), cord clamping and cutting (n = 130, 54.2%) and no continuous uterine massage (n = 23, 9.6%). Regarding self-reported practice, 149 respondents (62%) reported always adhering to the AMTSL guidelines. Staff age and years of experience in the birthing ward were both independently associated with knowledge that was consistent with the WHO guidelines (p = 0.05). Hospital type, job title and staff age were associated with self-reported adherence to WHO guidelines (p = 0.05). Participants in all hospital types consistently identified lack of time and staff shortages as barriers to guidelines implementation.Conclusions There is a gap between knowledge and self-reported practice in the management of the third stage of labour, and between international WHO guidelines and current maternity care in Oman. This study provides insights for nursing and midwifery leaders and policymakers and informs future workforce training and strategies.
Study on the Osteogenesis Effect of Bio-Oss Bone Powder Combined with Medical Collagen Sponge Following Jaw Cyst Surgery
Authors: WEN Hailong , ZHANG Tonghan 
Published: April 2024

Abstract

Objective
The aim of this study is to evaluate the osteogenesis effect following jaw cyst surgery by comparing three scenarios: no use of filling materials, the use of a medical collagen sponge alone, and the combined application of Bio-Oss bone powder with a medical collagen sponge. This comparison aims to provide evidence for selecting appropriate filling materials for post-surgical treatment of jaw cysts.
Methods
This research involved 52 patients with jaw cysts at the Zhongshan City Stomatological Hospital from October 2022 to September 2023. Patients were randomly assigned to three groups: Group A (control group with no filling material), Group B (medical collagen sponge), and Group C (Bio-Oss bone powder combined with a medical collagen sponge). CBCT scans were taken before surgery and at 3 and 6 months post-operation. The Mimics 21.0 software was utilized to analyze changes in the volume of the cyst cavity and the bone density values.
Results
Significant statistical differences in changes to the volume of the cyst cavity and bone density were observed among the three groups (P < 0.01). Group C demonstrated the most effective osteogenesis, with a reduction in cyst cavity volume by 51.74% and an increase in bone density by 321.24% at 3 months post-operation. By 6 months, the cyst cavity volume had decreased by 80.54%, and the bone density had increased by 422.72%. Group B had the second-best outcomes, while Group A had the least effective bone regeneration.
Conclusion
The study concluded that the combination of Bio-Oss bone powder and medical collagen sponge leads to the most effective osteogenesis in patients undergoing surgery for jaw cysts. The use of a medical collagen sponge alone was the second most effective, while no filling material resulted in the least effective postoperative bone regeneration.
The Impact of PD-1 Inhibitor Combined with Bevacizumab on Tumor Immune Cells in MSS/pMMR Advanced Colorectal Cancer Patients with Failed First-Line Treatment
Authors: Chen Xiaoqian , Wang Liang , Li Wenkui , Lei Xiaogai , Li Zhanhong , Diao Yongzhi , Zhang Shenglin , Li Chengbiao , Wang Chengjun , Guo Qijing , Ma Xinfu , Luo Yushuang 
Published: April 2024

Abstract

Objective: To investigate the effects of PD-1 inhibitor combined with bevacizumab monoclonal antibody on tumor immune cells in patients with first-line treatment failure in MSS/pMMR advanced colorectal cancer.
Methods: A total of 40 patients with advanced colorectal cancer who failed first-line treatment were selected using a random number table method from Qinghai University Affiliated Hospital from October 2021 to June 2023. Ten patients in the control group were treated with FOLFIRI combined with bevacizumab. The experimental group of 30 patients was treated with sintilimab combined with bevacizumab, and the post-treatment effects of the two groups of patients were compared. The expression levels of CD8+ T cells, tumor-associated macrophages, and tumor-associated fibroblasts were evaluated comprehensively to assess the effects of sintilimab combined with bevacizumab on patients with first-line treatment failure in MSS/pMMR advanced colorectal cancer.
Results: There was no statistically significant difference in the positive expression rates of CD8+ T lymphocytes, TAMs, and CAFs before and after treatment in both groups (P>0.05). There was no statistically significant difference in the comparison of the therapeutic effects of two groups of tumors (P>0.05), but the experimental group had higher PFS, mPFS, ORR, and DCR than the control group. There was no statistically significant difference in the occurrence rate of drug-related adverse reactions after treatment between the two groups (P>0.05).
Conclusion: By using the combination of sintilimab and bevacizumab in the first-line treatment of MSS/pMMR advanced colorectal cancer patients who failed first-line treatment, not only can the tumor immune microenvironment of patients be improved, but it can also transform the cold tumor immune suppression state into a hot tumor immune supportive state. While ensuring the safety of drug adverse reactions, it enhances the patients' anti-tumor ability and clinical treatment effects, further increasing the clinical application value.
Minimally invasive surgery of no tumor containment for cervical cancer surgery
Authors: Hu Min , Ji Limei , Jin Lanying , Shao Mingjun , Fu Xiujuan , Shi Baomei 
Published: April 2024

Abstract

The aim of this study is to evaluate the oncologic outcomes of minimally invasive radical hysterectomy with no tumor containment. Between January 2017 and June 2020, we recruited 350 women with early stage of cervical cancer, all eligible patients were informed of the potential complications and benefits of abdominal radical hysterectomy and laparoscopic radical hysterectomy. All patients in our study were refrain from using uterine manipulator, myoma drill or uterus suture combined with protective vaginal closure of the colpotomy such as clamp, vaginal cuff or vaginal suture instead, put the specimen in a collection bag, and extraction of the collection bag via the vagina. This research was approved by the Ethics Committee of Jinhua Municipal Central Hospital (2020 − 268). Over a median follow-up of 51 (range 30–72) months period, there were 5 patients lost to follow-up, and 3 patients refused to treatment after surgery. A total of 342 women with cervical cancer were ultimately analyzed in our study. Initial International Federation of Gynecology and Obstetrics (FIGO) 2018 stage was IA1 lymphovascular space invasion (LVSI+) 22 (6.29%), IA2 36 (10.29%), IB1 137 (39.14%), IB2 126 (36%), IIA1 14 (4%) and IIIC1p 15 (4.29%) respectively, and histology was squamous cell in 269 (76.86%), adenocarcinoma in 75 (21.43%), and adenosquamous in 6 (1.71%) patients. Lymphovascular invasion was confirmed in 80 (22.86%) patients. Lymph nodes were tumor-free in 325 (92.86%) patients. After radical hysterectomy, 83 (23.71%) patients underwent adjuvant chemoradiation or/and radiation. After a median follow-up of 51 (range 30–72) months, we noted the disease-free survival and overall survival rate were 95.71% (335/350) and 98.86% (346/350) respectively. The technique of minimally invasive surgery using maneuvers to avoid peritoneal contamination during surgery provides excellent oncologic outcome for patients with early cervical cancer. Our retrospective data suggest that laparoscopical surgery may be oncologically safe and may be validated in further randomized trials.
Engineering controllable alteration of malonyl-CoA levels to enhance polyketide production and versatility in E. coli
Authors: Keasling Jay , Klass Sarah , Wesselkamper Mia , Cowan Aidan , Lee Namil , Cheong Seokjung , Wang Zilong , Chen Yan , Gin Jennifer , Petzold Christopher 
Published: April 2024

Abstract
Engineering the heterologous expression of polyketide synthases (PKSs) in Escherichia coli has led to the production of various valuable natural and unnatural products. However, the limited availability of malonyl-CoA (M-CoA) in E. coli remains a significant impediment to efficient polyketide overproduction. In this study, engineered E. coli strains were developed to augment M-CoA levels for enhanced polyketide production by introducing a malonate transport and CoA ligation pathway. Additionally, control over the M-CoA pool was achieved by disrupting the endogenous M-CoA pathway and reconstituting it through malonate supplementation. The engineered strains exhibited increased M-CoA, fatty acid and polyketide titers, improved substrate selectivity of PKSs, and successful production of > 99% uniformly labeled 13C polyketides. Adaptive laboratory evolution of these strains provided valuable insights into pathways governing the M-CoA pools and the accumulation of mutations that resulted in significantly increased M-CoA and polyketide levels. This approach not only enhances the utility of E. coli as a heterologous host for polyketides but also illuminates the intricate dynamics of M-CoA modulation in these systems.