bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hepatic vessel segmentation based on 3D swin-transformer with inductive biased multi-head self-attention
Authors: Wu Mian , Qian Yinling , Liao Xiangyun , Wang Qiong , Heng Pheng-Ann 
Published: July 2023

Abstract
Purpose
Segmentation of liver vessels from CT images is indispensable prior to surgical planning and aroused a broad range of interest in the medical image analysis community. Due to the complex structure and low-contrast background, automatic liver vessel segmentation remains particularly challenging. Most of the related researches adopt FCN, U-net, and V-net variants as a backbone. However, these methods mainly focus on capturing multi-scale local features which may produce misclassified voxels due to the convolutional operator’s limited locality reception field.

Methods
We propose a robust end-to-end vessel segmentation network called Inductive BIased Multi-Head Attention Vessel Net(IBIMHAV-Net) by expanding swin transformer to 3D and employing an effective combination of convolution and self-attention. In practice, we introduce voxel-wise embedding rather than patch-wise embedding to locate precise liver vessel voxels and adopt multi-scale convolutional operators to gain local spatial information.
On the other hand, we propose the inductive biased multi-head self-attention which learns inductively biased relative positional embedding from initialized absolute position embedding. Based on this, we can gain more reliable queries and key matrices.

Results
We conducted experiments on the 3DIRCADb dataset. The average dice and sensitivity of the four tested cases were 74.8$$\%$$
%
and 77.5$$\%$$
%
, which exceed the results of existing deep learning methods and improved graph cuts method. The Branches Detected(BD)/Tree-length Detected(TD) indexes also proved the global/local feature capture ability better than other methods.

Conclusion
The proposed model IBIMHAV-Net provides an automatic, accurate 3D liver vessel segmentation with an interleaved architecture that better utilizes both global and local spatial features in CT volumes. It can be further extended for other clinical data.
Association between periodontal disease status and risk of atrial fibrillation: a nationwide population-based cohort study
Authors: Park Jung-Hyun , Lee Hyungwoo , Kim Jin-Woo , Song Tae-Jin 
Published: July 2023

Abstract
Background
Periodontal disease can activate an immune process linked to systemic diseases, including atrial fibrillation. However, the relationship between periodontal disease and atrial fibrillation remains unclear.

Aim
This study aimed to investigate whether changes in periodontal disease status are associated with the risk of atrial fibrillation.

Methods
Using the National Health Insurance Database Korea, participants who underwent the first oral health examination in 2003 and a second examination in 2005–2006 without a history of atrial fibrillation were included. Participants were grouped according to changes in periodontal disease status during two oral examinations: periodontal disease-free, periodontal disease-recovered, periodontal disease-developed, and periodontal disease-chronic. The outcome was the incidence of atrial fibrillation.

Results
The study included 1,254,515 participants, with a median follow-up of 14.3 years and 25,402 (2.02%) cases of atrial fibrillation occurred. During follow-up, the risk of atrial fibrillation was highest in the periodontal disease-chronic group, followed by the periodontal disease-developed, periodontal disease-recovered, and periodontal disease-free groups (p for trend < 0.001). Moreover, recovery from periodontal disease was associated with a reduced risk of atrial fibrillation compared to a chronic periodontal disease status (Hazard ratio: 0.97, 95% Confidence interval: 0.94—0.99, p = 0.045). The development of periodontal disease was associated with an increased risk of atrial fibrillation compared to being periodontal disease-free (Hazard ratio: 1.04, 95% Confidence interval: 1.01—1.08, p = 0.035).

Conclusion
Our findings suggest that changes in periodontal disease status impact the risk of atrial fibrillation. Management of periodontal disease may help prevent atrial fibrillation.
Oral colonization by gram-negative bacilli in patients with hematologic malignancies and solid tumors compared with healthy controls
Authors: Santibañez-Bedolla Karla E. , Orozco-Uriarte Maria J. , Alvarez-Canales Jose A. , Macias Alejandro E. , Amador-Medina Lauro F. 
Published: July 2023

Abstract
Background
Colonization of the oropharynx with gram-negative bacilli (GNB) is considered a negative prognostic factor in immunocompromised individuals. Hemato-oncologic patients represent a high-risk group due to their immunodeficiencies and associated treatments. This study aimed to determine the rates of oral colonization by GNB, associated factors, and clinical outcomes in patients with hematologic malignancies and solid tumors compared with healthy subjects.

Methods
We conducted a comparative study of hemato-oncologic patients and healthy subjects from August to October 2022. Swabs were taken from the oral cavity; specimens with GNB were identified and tested for antimicrobial susceptibility.

Results
We included 206 participants (103 hemato-oncologic patients and 103 healthy subjects). Hemato-oncologic patients had higher rates of oral colonization by GNB (34% vs. 17%, P = 0.007) and GNB resistant to third-generation cephalosporins (11.6% vs. 0%, P < 0.001) compared to healthy subjects. Klebsiella spp. was the predominant genus in both groups. The factor associated with oral colonization by GNB was a Charlson index ≥ 3, while ≥ 3 dental visits per year were a protective factor. Regarding colonization by resistant GNB in oncology patients, antibiotic therapy and a Charlson index ≥ 5 were identified as associated factors, while better physical functionality (ECOG ≤ 2) was associated with less colonization. Hemato-oncologic patients colonized with GNB had more 30-day infectious complications (30.5% vs. 2.9%, P = 0.0001) than non-colonized patients.

Conclusion
Oral colonization by GNB and resistant GNB are prevalent in cancer patients, especially those with higher scores on the severity scales. Infectious complications occurred more frequently in colonized patients. There is a knowledge gap about dental hygiene practices in hemato-oncologic patients colonized by GNB. Our results suggest that patients’ hygienic-dietary habits, especially frequent dental visits, are a protective factor against colonization.
Brief literature review and comprehensive bioinformatics analytics unravel the potential mechanism of curcumin in the treatment of periodontitis
Authors: Huang Xufeng , Liu Ying , Wang Qi , Rehman Hafiz Muzzammel , Horváth Dorottya , Zhou Shujing , Fu Rao , Zhang Ling , Szöllősi Attila Gábor , Li Zhengrui 
Published: July 2023

Abstract
Objective
Periodontitis is a chronic oral disease prevalent worldwide, and natural products are recommended as adjunctive therapy due to their minor side effects. Curcumin, a widely used ancient compound, has been reported to possess therapeutic effects in periodontitis. However, the exact mechanism underlying its activity remains unclear. In this context, the present study aimed to conduct computational simulations to uncover the potential mechanism of action of Curcumin in the treatment of periodontitis.

Materials and methods
Single-cell analysis was conducted using a dataset (i.e., GSE164241) curated from the Gene Expression Omnibus (GEO) database through an R package "Seurat package." Bulk RNA sequencing data were curated from GSE10334 and GSE16134 and processed by R package "Limma." Then, the marker genes in the single-cell transcriptome and differentially expressed genes (DEGs) in the bulk transcriptome were integrated. Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analyses were also carried out to reveal their functionalities. Key targets were mined from their protein–protein interaction (PPI) network topologically. Afterward, molecular docking was performed. The top-ranked pose was subjected to molecular dynamics simulations to investigate the stability of the docking result.

Results
FOS, CXCL1, CXCL8, and IL1B, were filtered after a series of selected processes. The results of molecular modeling suggested that except for IL1B, the Vena Scores of the rest exceeded -5 kcal/mol. Furthermore, the molecular dynamic simulation indicated that the binding of the CXCL8-Curcumin complex was stable over the entire 100 ns simulation.

Conclusion
The present study unlocked the binding modes of CXCL1, FOS, and CXCL8 with the Curcumin molecule, which were relatively stable, especially for CXCL8, hindering its promising potential to serve as the critical targets of Curcumin in periodontitis treatment.
Artificial intelligence and medical research databases: ethical review by data access committees
Authors: McKay Francis , Williams Bethany J. , Prestwich Graham , Bansal Daljeet , Treanor Darren , Hallowell Nina 
Published: July 2023

Abstract
Background
It has been argued that ethics review committees—e.g., Research Ethics Committees, Institutional Review Boards, etc.— have weaknesses in reviewing big data and artificial intelligence research. For instance, they may, due to the novelty of the area, lack the relevant expertise for judging collective risks and benefits of such research, or they may exempt it from review in instances involving de-identified data.

Main body
Focusing on the example of medical research databases we highlight here ethical issues around de-identified data sharing which motivate the need for review where oversight by ethics committees is weak. Though some argue for ethics committee reform to overcome these weaknesses, it is unclear whether or when that will happen. Hence, we argue that ethical review can be done by data access committees, since they have de facto purview of big data and artificial intelligence projects, relevant technical expertise and governance knowledge, and already take on some functions of ethical review. That said, like ethics committees, they may have functional weaknesses in their review capabilities. To strengthen that function, data access committees must think clearly about the kinds of ethical expertise, both professional and lay, that they draw upon to support their work.

Conclusion
Data access committees can undertake ethical review of medical research databases provided they enhance that review function through professional and lay ethical expertise.
Data envelopment analysis on the efficiency of vaccination services and its influencing factors in Beijing, China
Authors: Hu Mingzheng , Wang Yanshang , Wang Ming , Zhu Dawei , Li Wentao , Yu Rui , Wu Jiang , Lv Min , He Ping 
Published: July 2023

Abstract
Objectives
Vaccination is an important part of public health services. We aim to assess the efficiency of vaccination services in Beijing, the capital of China, and to further study the influencing factors of efficiency.

Methods
Using the immunization service data of Beijing, China in 2020, we firstly developed a data envelopment analysis (DEA) model to calculate the score of vaccination efficiency. Secondly, we used DEA model scenario simulations with different combinations of input–output factors to derive the magnitude of the effect of each input factor on the efficiency. Finally, combined with the data from the Beijing Regional Statistical Yearbook 2021, we developed the Tobit model to examine the effect of external social environmental factors on efficiency.

Results
The average scores of efficiency of POVs (Point of Vaccination) in different areas of Beijing vary greatly. Different input factors had different degrees of positive effects on the efficiency score. In addition, the number of populations served by POV was positively associated with efficiency, the GDP and financial allocation of the POVs’ district was also positively associated with efficiency score, while the total dependency ratio of the POVs’ district was negatively associated with efficiency score.

Conclusion
The efficiency of vaccination services varied considerably across POVs. Constrained by limited resources, efficiency scores can be increased by increasing input factors that have a larger impact on efficiency score and reducing those that have a smaller impact on efficiency. In addition, the social environment should be considered in allocating vaccination resources, and more resources should be invested in areas with low levels of economic development, low financial allocation, and high population.
The in vitro effects of probiotic bacteria on genital pathogens of female dogs
Authors: Edyta Golińska , Natalia Sowińska , Marlena Szydło , Natalia Witka , Joanna Lenarczyk , Arent Zbigniew , Magdalena Strus 
Published: July 2023

Abstract
Background
An important aspect in the microbiology of the reproductive system of small animals is the potential occurrence of probiotic bacteria, such as lactic acid bacteria (LAB) of the genus Lactobacillus. The presence of these microorganisms is significant due to their strong antibacterial and antifungal properties. This study aimed to select probiotic strains from the oral cavity and vagina that have outstanding antibacterial properties against typical genital pathogens of the female dog reproductive tract.

Results
The antagonistic activity of ten LAB strains was tested against seven etiological agents isolated from the genital tract of female dogs with signs of inflammation. LAB strains with the greatest ability to inhibit the growth of indicator bacteria were Lactobacillus plantarum and L. acidophilus, while L. fermentum and L. brevis strains inhibited growth the least. Almost all strains showed a complete lack of adherence to Caco-2 epithelial cells.

Conclusions
All tested LAB isolates inhibited the in vitro growth of either Gram-positive or Gram-negative pathogens, suggesting that potential probiotic strains could contribute to the balance of the normal vaginal microbiota. Furthermore, they could be considered for use as prophylactic agents or as an alternative to antibiotic therapy for infections in dogs.
Explore the impact of hypoxia-related genes (HRGs) in Cutaneous melanoma
Authors: Ke Guolin , Cheng Nan , Sun Huiya , Meng Xiumei , Xu Lei 
Published: July 2023

Abstract
Background
Cutaneous melanoma (CM) has an overall poor prognosis due to a high rate of metastasis. This study aimed to explore the role of hypoxia-related genes (HRGs) in CM.

Methods
We first used on-negative matrix factorization consensus clustering (NMF) to cluster CM samples and preliminarily analyzed the relationship of HRGs to CM prognosis and immune cell infiltration. Subsequently, we identified prognostic-related hub genes by univariate COX regression analysis and the least absolute shrinkage and selection operator (LASSO) and constructed a prognostic model. Finally, we calculated a risk score for patients with CM and investigated the relationship between the risk score and potential surrogate markers of response to immune checkpoint inhibitors (ICIs), such as TMB, IPS values, and TIDE scores.

Results
Through NMF clustering, we identified high expression of HRGs as a risk factor for the prognosis of CM patients, and at the same time, increased expression of HRGs also indicated a poorer immune microenvironment. Subsequently, we identified eight gene signatures (FBP1, NDRG1, GPI, IER3, B4GALNT2, BGN, PKP1, and EDN2) by LASSO regression analysis and constructed a prognostic model.

Conclusion
Our study identifies the prognostic significance of hypoxia-related genes in melanoma and shows a novel eight-gene signature to predict the potential efficacy of ICIs.
Calcium-assisted sortase A cleavage of SUMOylated metallothionein constructs leads to high-yield production of human MT3
Authors: Singh Avinash Kumar , Krężel Artur 
Published: July 2023

AbstractBackgroundMammalian metallothioneins (MTs) are small (6–7 kDa), intracellular, cysteine-rich, metal-binding proteins involved, inter alia, in the homeostasis of zinc and copper, detoxification of heavy metals, antioxidation against reactive oxygen species, and protection against DNA damage. The high cysteine content (~ 30%) in MTs makes them toxic to bacterial cells during protein production, resulting in low yield. To address this issue, we present for the first time a combinatorial approach using the small ubiquitin-like modifier (SUMO) and/or sortase as fusion tags for high-level expression of human MT3 inE. coliand its purification by three different strategies.ResultsThree different plasmids were generated using SUMO, sortase A pentamutant (eSrtA), and sortase recognition motif (LPETG) as removable fusion tags for high-level expression and purification of human MT3 from the bacterial system. In the first strategy, SUMOylated MT3 was expressed and purified using Ulp1-mediated cleavage. In the second strategy, SUMOylated MT3 with a sortase recognition motif at the N-terminus of MT3 was expressed and purified using sortase-mediated cleavage. In the final strategy, the fusion protein His6-SUMO-eSrtA-LPETG-MT3 was expressed and purified by one-step sortase-mediated inducible on-bead autocleavage. Using these three strategies the apo-MT3 was purified in a yield of 11.5, 11, and 10.8 mg/L, respectively, which is the highest yield achieved for MT expression and purification to date. No effect of MT3 on Ni2+-containing resin was observed.ConclusionThe SUMO/sortase-based strategy used as the production system for MT3 resulted in a very high expression level and protein production yield. The apo-MT3 purified by this strategy contained an additional glycine residue and had similar metal binding properties as WT-MT3. This SUMO-sortase fusion system is a simple, robust, and inexpensive one-step purification approach for various MTs as well as other toxic proteins with very high yield via immobilized metal affinity chromatography (IMAC).
Prognostic factors in patients with thymoma who underwent surgery
Authors: Jiang Yu-Gang , Ma Mu-Yuan , Wu Jia-Jun , Ma Rong , Bai Xue-Hong , Zhao Ren , He Jin-Xi , Wang Yan-Yang 
Published: July 2023

Abstract
Purpose
Thymoma is the most common primary tumor in the anterior mediastinum. The prognostic factors of patients with thymoma still need to be clarified. In this study, we aimed to investigate the prognostic factors of patients with thymoma who received radical resection and establish the nomogram to predict the prognosis of these patients.

Materials and methods
Patients who underwent radical resection for thymoma with complete follow-up data between 2005 and 2021 were enrolled. Their clinicopathological characteristics and treatment methods were retrospectively analyzed. Progression-free survival (PFS) and overall survival (OS) were estimated using the Kaplan–Meier method and compared by the log-rank test. Univariate and multivariate Cox proportional hazards regression analyses were performed to identify the independent prognostic factors. According to the results of the univariate analysis in the Cox regression model, the predictive nomograms were created.

Results
A total of 137 patients with thymoma were enrolled. With a median follow-up of 52 months, the 5-year and 10-year PFS rates were 79.5% and 68.1%, respectively. The 5-year and 10-year OS rates were 88.4% and 73.1%, respectively. Smoking status (P = 0.022) and tumor size (P = 0.039) were identified as independent prognostic factors for PFS. Multivariate analysis showed that a high level of neutrophils (P = 0.040) was independently associated with OS. The nomogram showed that the World Health Organization (WHO) histological classification contributed more to the risk of recurrence than other factors. Neutrophil count was the most important predictor of OS in patients with thymoma.

Conclusion
Smoking status and tumor size are risk factors for PFS in patients with thymoma. A high level of neutrophils is an independent prognostic factor for OS. The nomograms developed in this study accurately predict PFS and OS rates at 5 and 10 years in patients with thymoma based on individual characteristics.
Identification of mitochondrial related signature associated with immune microenvironment in Alzheimer’s disease
Authors: Zhang Yaodan , Miao Yuyang , Tan Jin , Chen Fanglian , Lei Ping , Zhang Qiang 
Published: July 2023

Abstract
Background
Alzheimer's disease (AD) is the most common neurodegenerative disease. Mitochondrial dysfunction and immune responses are important factors in the pathogenesis of AD, but their crosstalk in AD has not been studied. In this study, the independent role and interaction of mitochondria-related genes and immune cell infiltration in AD were investigated using bioinformatics methods.

Methods
The datasets of AD were obtained from NCBI Gene Expression Omnibus (GEO), and the data of mitochondrial genes was from MitoCarta3.0 database. Subsequently, differential expression genes (DEGs) screening and GSEA functional enrichment analysis were performed. The intersection of DEGs and mitochondrial related genes was used to obtain MitoDEGs. The MitoDEGs most relevant to AD were determined by Least absolute shrinkage and selection operator and multiple support vector machine recursive feature elimination, as well as protein–protein interactions (PPI) network and random forest. The infiltration of 28 kinds of immune cells in AD was analyzed by ssGSEA, and the relationship between hub MitoDEGs and the proportion of immune infiltration was studied. The expression levels of hub MitoDEGs were verified in cell models and AD mice, and the role of OPA1 in mitochondrial damage and neuronal apoptosis was investigated.

Results
The functions and pathways of DEGs were significantly enriched in AD, including immune response activation, IL1R pathway, mitochondrial metabolism, oxidative damage response and electron transport chain-oxphos system in mitochondria. Hub MitoDEGs closely related to AD were obtained based on PPI network, random forest and two machine learning algorithms. Five hub MitoDEGs associated with neurological disorders were identified by biological function examination. The hub MitoDEGs were found to be correlated with memory B cell, effector memory CD8 T cell, activated dendritic cell, natural killer T cell, type 17 T helper cell, Neutrophil, MDSC, plasmacytoid dendritic cell. These genes can also be used to predict the risk of AD and have good diagnostic efficacy. In addition, the mRNA expression levels of BDH1, TRAP1, OPA1, DLD in cell models and AD mice were consistent with the results of bioinformatics analysis, and expression levels of SPG7 showed a downward trend. Meanwhile, OPA1 overexpression alleviated mitochondrial damage and neuronal apoptosis induced by Aβ1-42.

Conclusions
Five potential hub MitoDEGs most associated with AD were identified. Their interaction with immune microenvironment may play a crucial role in the occurrence and prognosis of AD, which provides a new insight for studying the potential pathogenesis of AD and exploring new targets.