bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comprehensive clinicopathological significance and putative transcriptional mechanisms of Forkhead box M1 factor in hepatocellular carcinoma
Authors: Wu Hua-Yu , Luo Li-Feng , Wei Fang , Jiang Hong-Mian 
Published: November 2023

Abstract
Background
The Forkhead box M1 factor (FOXM1) is a crucial activator for cancer cell proliferation. While FOXM1 has been shown to promote hepatocellular carcinoma (HCC) progression, its transcriptional mechanisms remain incompletely understood.

Methods
We performed an in-house tissue microarray on 313 HCC and 37 non-HCC tissue samples, followed by immunohistochemical staining. Gene chips and high throughput sequencing data were used to assess FOXM1 expression and prognosis. To identify candidate targets of FOXM1, we comprehensively reanalyzed 41 chromatin immunoprecipitation followed by sequencing (ChIP-seq) data sets. We predicted FOXM1 transcriptional targets in HCC by intersecting candidate FOXM1 targets with HCC overexpressed genes and FOXM1 correlation genes. Enrichment analysis was employed to address the potential mechanisms of FOXM1 underlying HCC. Finally, single-cell RNA sequencing analysis was performed to confirm the transcriptional activity of FOXM1 on its predicted targets.

Results
This study, based on 4235 HCC tissue samples and 3461 non-HCC tissue samples, confirmed the upregulation of FOXM1 in HCC at mRNA and protein levels (standardized mean difference = 1.70 [1.42, 1.98]), making it the largest multi-centered study to do so. Among HCC patients, FOXM1 was increased in Asian and advanced subgroups, and high expression of FOXM1 had a strong ability to differentiate HCC tissue from non-HCC tissue (area under the curve = 0.94, sensitivity = 88.72%, specificity = 87.24%). FOXM1 was also shown to be an independent exposure risk factor for HCC, with a pooled hazard ratio of 2.00 [1.77, 2.26]. The predicted transcriptional targets of FOXM1 in HCC were predominantly enriched in nuclear division, chromosomal region, and catalytic activity acting on DNA. A gene cluster encoding nine transcriptional factors was predicted to be positively regulated by FOXM1, promoting the cell cycle signaling pathway in HCC. Finally, the transcriptional activity of FOXM1 and its targets was supported by single-cell analysis of HCC cells.

Conclusions
This study not only confirmed the upregulation of FOXM1 in HCC but also identified it as an independent risk factor. Moreover, our findings enriched our understanding of the complex transcriptional mechanisms underlying HCC pathogenesis, with FOXM1 potentially promoting HCC progression by activating other transcription factors within the cell cycle pathway.
Clinical application of calcium silicate-based bioceramics in endodontics
Authors: Wang Xinyuan , Xiao Yizhi , Song Wencheng , Ye Lanxiang , Yang Chen , Xing Yuzhen , Yuan Zhenglin 
Published: November 2023

AbstractPulp treatment is extremely common in endodontics, with the main purpose of eliminating clinical symptoms and preserving tooth physiological function. However, the effect of dental pulp treatment is closely related to the methods and materials used in the process of treatment. Plenty of studies about calcium silicate-based bioceramics which are widely applied in various endodontic operations have been reported because of their significant biocompatibility and bioactivity. Although most of these materials have superior physical and chemical properties, the differences between them can also have an impact on the success rate of different clinical practices. Therefore, this review is focused on the applications of several common calcium silicate-based bioceramics, including Mineral trioxide aggregate (MTA), Biodentine, Bioaggregate, iRoot BP Plus in usual endodontic treatment, such as dental pulp capping, root perforation repair, regenerative endodontic procedures (REPs), apexification, root-end filling and root canal treatment (RCT). Besides, the efficacy of these bioceramics mentioned above in human trials is also compared, which aims to provide clinical guidance for their clinical application in endodontics.
Automatic generation of alloreactivity-reduced donor lymphocytes and hematopoietic stem cells from the same mobilized apheresis product
Authors: Wiercinska E. , Quade-Lyssy P. , Hümmer C. , Beifuß J. , Akarkach K. , Poppe C. , Olevska V. , Dzionek J. , Lahnor H. , Bosio A. , Papanikolaou E. , Bonig Halvard 
Published: November 2023

Abstract
Introduction
In vitro or in vivo depletion of alloreactive T cells can facilitate haplo-identical hematopoietic stem cell transplantation (HSCT). Very satisfactory transplant outcomes were thus reported for TCRαβ/CD19-depleted hematopoietic stem/progenitor cell (HSPC) grafts. The current semi-automatic manufacturing process on the CliniMACS Plus, although robust, still requires a significant amount of manual labor to be completed. Towards advancing and further facilitating large scale cell processing, a new TCRαβ/CD19 depletion module combined with the previously described CD45RA depletion module (to serve as allo-reactivity attenuated donor lymphocyte infusion) was established on the CliniMACS Prodigy.

Methods
We evaluated six apheresis products from G-CSF-mobilized volunteer donors which were split automatically by the Prodigy, one portion each depleted of CD45RA+ or of TCRαβ+ and CD19+ cells. We investigated critical quality attributes for both products. Products were assessed for recovery of HSPCs and mature subsets, as well as depletion efficiency of targeted cells using flow cytometry. Effects of apheresis and product age post 48 h storage at 2–6 °C as well as freeze-thawing on product viability and recovery of WBC and HPSCs were assessed by flow cytometry.

Results
Ten sequential automatic processes were completed with minimal hands-on time beyond tubing set installation. Depletion efficiency of CD45RA+ resp. TCRαβ+ and CD19+ cells was equivalent to previous reports, achieving mean depletions of 4 log of targeted cells for both products. HSPC products retained TCRγδ+ and NK cells. 48 h storage of apheresis product was associated with the expected modest loss of HSPCs, but depletions remained efficient. Depleted products were stable until at least 72 h after apheresis with stem cell viabilities > 90%. Freeze-thawing resulted in loss of NK cells; post-thaw recovery of viable CD45+ and HSPCs was > 70% and in line with expectation.

Conclusion
The closed, GMP-compatible process generates two separate medicinal products from the same mobilized apheresis product. The CD45RA-depleted products contained functional memory T cells, whereas the TCRαβ/CD19-depleted products included HSPCs, TCRγδ+ and NK cells. Both products are predicted to be effectively depleted of GVH-reactivity while providing immunological surveillance, in support of haplo-identical HSCT.

Graphical Abstract
Paneth cell-derived iNOS is required to maintain homeostasis in the intestinal stem cell niche
Authors: Huang Lingxiao , Xu Zhenni , Lei Xudan , Huang Yujun , Tu Siyu , Xu Lu , Xia Jieying , Liu Dengqun 
Published: November 2023

Abstract
Background
Mammalian intestinal epithelium constantly undergoes rapid self-renewal and regeneration sustained by intestinal stem cells (ISCs) within crypts. Inducible nitric oxide synthase (iNOS) is an important regulator in tissue homeostasis and inflammation. However, the functions of iNOS on ISCs have not been clarified. Here, we aimed to investigate the expression pattern of inducible nitric oxide synthase (iNOS) within crypts and explore its function in the homeostatic maintenance of the ISC niche.

Methods
Expression of iNOS was determined by tissue staining and qPCR. iNOS−/− and Lgr5 transgenic mice were used to explore the influence of iNOS ablation on ISC proliferation and differentiation. Enteroids were cultured to study the effect of iNOS on ISCs in vitro. Ileum samples from wild-type and iNOS−/− mice were collected for RNA-Seq to explore the molecular mechanisms by which iNOS regulates ISCs.

Results
iNOS was physiologically expressed in Paneth cells. Knockout of iNOS led to apparent morphological changes in the intestine, including a decrease in the small intestine length and in the heights of both villi and crypts. Knockout of iNOS decreased the number of Ki67+ or BrdU+ proliferative cells in crypts. Loss of iNOS increased the number of Olfm4+ ISCs but inhibited the differentiation and migration of Lgr5+ ISCs in vivo. iNOS depletion also inhibited enteroid formation and the budding efficiency of crypts in vitro. Moreover, iNOS deficiency altered gluconeogenesis and the adaptive immune response in the ileum transcriptome.

Conclusion
Paneth cell-derived iNOS is required to maintain a healthy ISC niche, and Knockout of iNOS hinders ISC function in mice. Therefore, iNOS represents a potential target for the development of new drugs and other therapeutic interventions for intestinal disorders.
Radiogenomic analysis of cellular tumor-stroma heterogeneity as a prognostic predictor in breast cancer
Authors: Fan Ming , Wang Kailang , Zhang You , Ge Yuanyuan , Lü Zhong , Li Lihua 
Published: November 2023

Abstract
Background
The tumor microenvironment and intercellular communication between solid tumors and the surrounding stroma play crucial roles in cancer initiation, progression, and prognosis. Radiomics provides clinically relevant information from radiological images; however, its biological implications in uncovering tumor pathophysiology driven by cellular heterogeneity between the tumor and stroma are largely unknown. We aimed to identify radiogenomic signatures of cellular tumor-stroma heterogeneity (TSH) to improve breast cancer management and prognosis analysis.

Methods
This retrospective multicohort study included five datasets. Cell subpopulations were estimated using bulk gene expression data, and the relative difference in cell subpopulations between the tumor and stroma was used as a biomarker to categorize patients into good- and poor-survival groups. A radiogenomic signature-based model utilizing dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) was developed to target TSH, and its clinical significance in relation to survival outcomes was independently validated.

Results
The final cohorts of 1330 women were included for cellular TSH biomarker identification (n = 112, mean age, 57.3 years ± 14.6) and validation (n = 886, mean age, 58.9 years ± 13.1), radiogenomic signature of TSH identification (n = 91, mean age, 55.5 years ± 11.4), and prognostic (n = 241) assessments. The cytotoxic lymphocyte biomarker differentiated patients into good- and poor-survival groups (p < 0.0001) and was independently validated (p = 0.014). The good survival group exhibited denser cell interconnections. The radiogenomic signature of TSH was identified and showed a positive association with overall survival (p = 0.038) and recurrence-free survival (p = 3 × 10–4).

Conclusion
Radiogenomic signatures provide insights into prognostic factors that reflect the imbalanced tumor-stroma environment, thereby presenting breast cancer-specific biological implications and prognostic significance.
Acute phase protein concentration in pharyngeal swabs from clinically healthy commercial dairy calves
Authors: Petersen Mette Bisgaard , Capion Nynne 
Published: November 2023

Abstract
Background
Early diagnosis of disease in calves is crucial for fast recovery and prudent use of antibiotics. The serum concentration of acute phase proteins (APPs) is up- or downregulated in response to tissue injury and has been studied widely in human medicine. There is growing interest in using APPs as biomarkers for different diseases and as a tool to initiate and monitor treatment in veterinary medicine as well. The concentration of APPs in saliva in healthy calves has not been established and the use of pharyngeal swabs offers a non-invasive alternative to blood sampling. Pharyngeal swabs, tracheal aspirate (TA) and blood samples were collected from 84 clinically healthy commercial dairy calves and analyzed for the APPs serum amyloid A (SAA), haptoglobin (Hp) and lipopolysaccharide binding protein (LBP).

Results
We found detectable concentrations of SAA, Hp and LBP in pharyngeal swabs from calves, as well as in TA and serum. There were no biologically interesting correlations between the SAA concentrations in serum and TA or pharyngeal swabs. This also applied to Hp and LBP concentrations in serum and TA or pharyngeal swabs.

Conclusions
SAA, Hp and LBP can be measured in saliva and TA from calves, but there was no correlation between the specific APP concentration in serum and pharyngeal swab or TA. There was a considerable technical variation in the sampling method for both pharyngeal swab and TA, and further validation of the methods is needed.
Endoscopy-based IBD identification by a quantized deep learning pipeline
Authors: Datres Massimiliano , Paolazzi Elisa , Chierici Marco , Pozzi Matteo , Colangelo Antonio , Dorian Donzella Marcello , Jurman Giuseppe 
Published: November 2023

Abstract
Background
Discrimination between patients affected by inflammatory bowel diseases and healthy controls on the basis of endoscopic imaging is an challenging problem for machine learning models. Such task is used here as the testbed for a novel deep learning classification pipeline, powered by a set of solutions enhancing characterising elements such as reproducibility, interpretability, reduced computational workload, bias-free modeling and careful image preprocessing.

Results
First, an automatic preprocessing procedure is devised, aimed to remove artifacts from clinical data, feeding then the resulting images to an aggregated per-patient model to mimic the clinicians decision process. The predictions are based on multiple snapshots obtained through resampling, reducing the risk of misleading outcomes by removing the low confidence predictions. Each patient’s outcome is explained by returning the images the prediction is based upon, supporting clinicians in verifying diagnoses without the need for evaluating the full set of endoscopic images. As a major theoretical contribution, quantization is employed to reduce the complexity and the computational cost of the model, allowing its deployment on small power devices with an almost negligible 3% performance degradation. Such quantization procedure holds relevance not only in the context of per-patient models but also for assessing its feasibility in providing real-time support to clinicians even in low-resources environments. The pipeline is demonstrated on a private dataset of endoscopic images of 758 IBD patients and 601 healthy controls, achieving Matthews Correlation Coefficient 0.9 as top performance on test set.

Conclusion
We highlighted how a comprehensive pre-processing pipeline plays a crucial role in identifying and removing artifacts from data, solving one of the principal challenges encountered when working with clinical data. Furthermore, we constructively showed how it is possible to emulate clinicians decision process and how it offers significant advantages, particularly in terms of explainability and trust within the healthcare context. Last but not least, we proved that quantization can be a useful tool to reduce the time and resources consumption with an acceptable degradation of the model performs. The quantization study proposed in this work points up the potential development of real-time quantized algorithms as valuable tools to support clinicians during endoscopy procedures.
IFN-γ in ovarian tumor microenvironment upregulates HLA-E expression and predicts a poor prognosis
Authors: Zheng Hui , Guan Xiaolin , Meng Xin , Tong Ying , Wang Yanchun , Xie Suhong , Guo Lin , Lu Renquan 
Published: November 2023

Abstract
Background
Inflammation and immunity are two main characteristics of tumor microenvironment (TME). Interferon-gamma (IFN-γ) is generally considered as a pro-inflammatory cytokine which mediates anti-tumor immune response. Recently, IFN-γ was also reported to play a protumorigenic role. However, the mechanisms of tumor-promoting effect induced by IFN-γ remain unclear.

Methods
The expression of leukocyte antigen-E (HLA-E), IFN-γ, CD3 and CD56 in clinical samples of ovarian cancer was detected by mutiplexed immunohistochemistry. The mechanism to induce HLA-E overexpression by IFN-γ was explored using human ovarian cancer cell lines through western blot and flow cytometry. We further clarify the role of overexpressed-HLA-E on natural killer (NK)-mediated cell lysis.

Results
We found that IFN-γ could upregulate HLA-E protein expression through activating of JAK/STAT1 signaling pathway, and increase cell surface HLA-E level through enhancing proteasome activity. We also observed that only high levels of membrane HLA-E expression contributed to the inhibition of NK-mediated cytotoxicity. We showed that progression-free survival (PFS) of ovarian cancer patients was negatively correlated with IFN-γ expression in their tumor tissues, due to more tumor infiltrating NK cells compared with T lymphocytes.

Conclusions
Our study revealed the protumorigenic role of IFN-γ by upregulation of HLA-E expression and rendering tumors less susceptible to immune attack. We also provided a novel insight into the relationship between tumor microenvironment and immune evasion.
Progress of the application clinical prediction model in polycystic ovary syndrome
Authors: Guixue Guan , Yifu Pu , Yuan Gao , Xialei Liu , Fan Shi , Qian Sun , Jinjin Xu , Linna Zhang , Xiaozuo Zhang , Wen Feng , Wen Yang 
Published: November 2023

AbstractClinical prediction models play an important role in the field of medicine. These can help predict the probability of an individual suffering from disease, complications, and treatment outcomes by applying specific methodologies. Polycystic ovary syndrome (PCOS) is a common disease with a high incidence rate, huge heterogeneity, short- and long-term complications, and complex treatments. In this systematic review study, we reviewed the progress of clinical prediction models in PCOS patients, including diagnosis and prediction models for PCOS complications and treatment outcomes. We aimed to provide ideas for medical researchers and clues for the management of PCOS. In the future, models with poor accuracy can be greatly improved by adding well-known parameters and validations, which will further expand our understanding of PCOS in terms of precision medicine. By developing a series of predictive models, we can make the definition of PCOS more accurate, which can improve the diagnosis of PCOS and reduce the likelihood of false positives and false negatives. It will also help discover complications earlier and treatment outcomes being known earlier, which can result in better outcomes for women with PCOS.
Efficacy of conditioned autologous serum therapy (Orthokine®) on the dorsal root ganglion in patients with chronic radiculalgia: study protocol for a prospective randomized placebo-controlled double-blind clinical trial (RADISAC trial)
Authors: Homs Marta , Milà Raimon , Valdés Ricard , Blay David , Borràs Rosa Maria , Parés David 
Published: November 2023

Abstract
Background
Pulsed radiofrequency (PRF) treatment on the dorsal root ganglion (DRG) has been proposed as a good option for the treatment of persistent radicular pain based on its effect of neuromodulation on neuropathic pain. Autologous conditioned serum (ACS) therapy is a conservative treatment based on the patient’s own blood. The aim of this manuscript is to develop a study protocol using ACS on the DRG as a target for its molecular modulation.

Methods
We plan to conduct a randomized controlled study to compare the efficacy of PRF therapy plus ACS versus PRF therapy plus physiological saline 0.9% (PhS) on the DRG to reduce neuropathic pain in patients with persistent lower limb radiculalgia (LLR) and to contribute to the functional improvement and quality of life of these patients.
Study participants will include patients who meet study the inclusion/exclusion criteria. Eligible patients will be randomized in a 1:1 ratio to one of treatment with PRF plus ACS (experimental group) or PRF plus PhS (placebo group). The study group will consist of 70 patients (35 per group) who have experienced radicular pain symptoms for ≥ 6 months’ duration who have failed to respond to any therapy. Both groups will receive PRF on the DRG treatment before the injection of the sample (control or placebo). Patient assessments will occur at baseline, 1 month, 3 months, 6 months, and 12 months after therapy.
The primary efficacy outcome measure is Numeric Pain Rating Scale (NPRS) responders from baseline to 12 months of follow-up using validated minimal important change (MIC) thresholds. A reduction of ≥ 2 points in NPRS is considered a clinically significant pain relief.
The secondary efficacy outcome measure is the proportion of Oswestry Low Back Pain Disability Scale (ODS) responders from baseline to 12 months of follow-up in the experimental group (PRF plus ACS) versus the placebo group (PRF plus PhS). ODS responders are defined as those patients achieving the validated MIC of ≥ 10-point improvement in ODS from baseline to 12 months of follow-up as a clinically significant efficacy threshold.

Discussion
This prospective, double-blind, randomized placebo-controlled study will provide level I evidence of the safety and effectiveness of ACS on neuropathic symptoms in LLR patients.

Trial registration {2a}{2b}
EUDRACT number: 2021–005124-38. Validation date: 13 November 2021. Protocol version {3}: This manuscript presents the 2nd protocol version.
Pathogenetic detection, retrospective and pathogenicity analysis of a fatal case of Vibrio vulnificus in Shenzhen, China
Authors: Xu Shiqin , Wu Jinsong , Jin Ying , Ji Liyin , Zou Xuan , Hu Qinghua , Feng Tiejian , Wu Shuang , Jiang Yixiang , Chen Qiongcheng , Lu Huiqun , Qiu Shuxiang , Chen Huaisheng , Jiang Min , Cai Rui , Qiu Yaqun , Shi Xiaolu 
Published: November 2023

AbstractWe report a 36-year-old male patient died of V. vulnificus-induced septicaemia and multiple organ failure syndrome after oyster consumption at a restaurant. We isolated and identified V. vulnificus vv16015 from the patient’s blood sample and antibiotic susceptibility tests indicated sensitivity to all 21 antibiotics. Oyster samples were subsequently collected from the restaurant’s supplier and three strains of V. vulnificus were isolated. Whole genome sequencing and analysis revealed vv16015 to be distantly related to these strains and confirmed that V. vulnificus contamination was present in the seafood of the restaurant and supplier. Using a Galleria mellonella larvae infection model, the virulence of vv16015 was determined to be higher than that of comparison strains isolated from a surviving patient (vv15018) and an oyster (vv220015). The human and environment distribution of V. vulnificus in Shenzhen is sporadic and heterogeneous, and vv16015 is highly virulent compared to other strains.