bluuebunny/crossref_metadata_2025_split huggingface dataset:
Radiology of fibrosis part II: abdominal organs
Authors: Tarchi Sofia Maria , Salvatore Mary , Lichtenstein Philip , Sekar Thillai , Capaccione Kathleen , Luk Lyndon , Shaish Hiram , Makkar Jasnit , Desperito Elise , Leb Jay , Navot Benjamin , Goldstein Jonathan , Laifer Sherelle , Beylergil Volkan , Ma Hong , Jambawalikar Sachin , Aberle Dwight , D’Souza Belinda , Bentley-Hibbert Stuart , Marin Monica Pernia 
Published: July 2024

AbstractFibrosis is the aberrant process of connective tissue deposition from abnormal tissue repair in response to sustained tissue injury caused by hypoxia, infection, or physical damage. It can affect almost all organs in the body causing dysfunction and ultimate organ failure. Tissue fibrosis also plays a vital role in carcinogenesis and cancer progression. The early and accurate diagnosis of organ fibrosis along with adequate surveillance are helpful to implement early disease-modifying interventions, important to reduce mortality and improve quality of life. While extensive research has already been carried out on the topic, a thorough understanding of how this relationship reveals itself using modern imaging techniques has yet to be established. This work outlines the ways in which fibrosis shows up in abdominal organs and has listed the most relevant imaging technologies employed for its detection. New imaging technologies and developments are discussed along with their promising applications in the early detection of organ fibrosis.
Tissue of origin detection for cancer tumor using low-depth cfDNA samples through combination of tumor-specific methylation atlas and genome-wide methylation density in graph convolutional neural networks
Authors: Nguyen Trong Hieu , Doan Nhu Nhat Tan , Tran Trung Hieu , Huynh Le Anh Khoa , Doan Phuoc Loc , Nguyen Thi Hue Hanh , Nguyen Van Thien Chi , Nguyen Giang Thi Huong , Nguyen Hoai-Nghia , Giang Hoa , Tran Le Son , Phan Minh Duy 
Published: July 2024

Abstract
Background
Cell free DNA (cfDNA)-based assays hold great potential in detecting early cancer signals yet determining the tissue-of-origin (TOO) for cancer signals remains a challenging task. Here, we investigated the contribution of a methylation atlas to TOO detection in low depth cfDNA samples.

Methods
We constructed a tumor-specific methylation atlas (TSMA) using whole-genome bisulfite sequencing (WGBS) data from five types of tumor tissues (breast, colorectal, gastric, liver and lung cancer) and paired white blood cells (WBC). TSMA was used with a non-negative least square matrix factorization (NNLS) deconvolution algorithm to identify the abundance of tumor tissue types in a WGBS sample. We showed that TSMA worked well with tumor tissue but struggled with cfDNA samples due to the overwhelming amount of WBC-derived DNA. To construct a model for TOO, we adopted the multi-modal strategy and used as inputs the combination of deconvolution scores from TSMA with other features of cfDNA.

Results
Our final model comprised of a graph convolutional neural network using deconvolution scores and genome-wide methylation density features, which achieved an accuracy of 69% in a held-out validation dataset of 239 low-depth cfDNA samples.

Conclusions
In conclusion, we have demonstrated that our TSMA in combination with other cfDNA features can improve TOO detection in low-depth cfDNA samples.
Targeted metabolomics identifies accurate CSF metabolite biomarkers for the differentiation between COVID-19 with neurological involvement and CNS infections with neurotropic viral pathogens
Authors: Neu Frieder , Nay Sandra , Schuchardt Sven , Klawonn Frank , Skripuletz Thomas , Suehs Kurt-Wolfram , Pessler Frank 
Published: July 2024

Abstract
Background
COVID-19 is primarily considered a respiratory tract infection, but it can also affect the central nervous system (CNS), which can result in long-term sequelae. In contrast to CNS infections by classic neurotropic viruses, SARS-CoV-2 is usually not detected in cerebrospinal fluid (CSF) from patients with COVID-19 with neurological involvement (neuro-COVID), suggesting fundamental differences in pathogenesis.

Methods
To assess differences in CNS metabolism in neuro-COVID compared to CNS infections with classic neurotropic viruses, we applied a targeted metabolomic analysis of 630 metabolites to CSF from patients with (i) COVID-19 with neurological involvement [n = 16, comprising acute (n = 13) and post-COVID-19 (n = 3)], (ii) viral meningitis, encephalitis, or myelitis (n = 10) due to herpes simplex virus (n = 2), varicella zoster virus (n = 6), enterovirus (n = 1) and tick-borne encephalitis virus (n = 1), and (iii) aseptic neuroinflammation (meningitis, encephalitis, or myelitis) of unknown etiology (n = 21) as additional disease controls.

Results
Standard CSF parameters indicated absent or low neuroinflammation in neuro-COVID. Indeed, CSF cell count was low in neuro-COVID (median 1 cell/µL, range 0–12) and discriminated it accurately from viral CNS infections (AUC = 0.99) and aseptic neuroinflammation (AUC = 0.98). 32 CSF metabolites passed quality assessment and were included in the analysis. Concentrations of differentially abundant (fold change ≥|1.5|, FDR ≤ 0.05) metabolites were both higher (9 and 5 metabolites) and lower (2 metabolites) in neuro-COVID than in the other two groups. Concentrations of citrulline, ceramide (d18:1/18:0), and methionine were most significantly elevated in neuro-COVID. Remarkably, triglyceride TG(20:1_32:3) was much lower (mean fold change = 0.09 and 0.11) in neuro-COVID than in all viral CNS infections and most aseptic neuroinflammation samples, identifying it as highly accurate biomarker with AUC = 1 and 0.93, respectively. Across all samples, TG(20:1_32:3) concentration correlated only moderately with CSF cell count (ρ = 0.65), protein concentration (ρ = 0.64), and Q-albumin (ρ = 0.48), suggesting that its low levels in neuro-COVID CSF are only partially explained by less pronounced neuroinflammation.

Conclusions
The results suggest that CNS metabolite responses in neuro-COVID differ fundamentally from viral CNS infections and aseptic neuroinflammation and may be used to discover accurate diagnostic biomarkers in CSF and to gain insights into differences in pathophysiology between neuro-COVID, viral CNS infections and aseptic neuroinflammation.
Graphene-based hybrid composites for cancer diagnostic and therapy
Authors: Asadi Mahnaz , Ghorbani Seyed Hosein , Mahdavian Leila , Aghamohammadi Mohammad 
Published: July 2024

AbstractThe application of graphene-based nanocomposites for therapeutic and diagnostic reasons has advanced considerably in recent years due to advancements in the synthesis and design of graphene-based nanocomposites, giving rise to a new field of nano-cancer diagnosis and treatment. Nano-graphene is being utilized more often in the field of cancer therapy, where it is employed in conjunction with diagnostics and treatment to address the complex clinical obstacles and problems associated with this life-threatening illness. When compared to other nanomaterials, graphene derivatives stand out due to their remarkable structural, mechanical, electrical, optical, and thermal capabilities. The high specific surface area of these materials makes them useful as carriers in controlled release systems that respond to external stimuli; these compounds include drugs and biomolecules like nucleic acid sequences (DNA and RNA). Furthermore, the presence of distinctive sheet-like nanostructures and the capacity for photothermal conversion have rendered graphene-based nanocomposites highly favorable for optical therapeutic applications, including photothermal treatment (PTT), photodynamic therapy (PDT), and theranostics. This review highlights the current state and benefits of using graphene-based nanocomposites in cancer diagnosis and therapy and discusses the obstacles and prospects of their future development. Then we focus on graphene-based nanocomposites applications in cancer treatment, including smart drug delivery systems, PTT, and PDT. Lastly, the biocompatibility of graphene-based nanocomposites is also discussed to provide a unique overview of the topic.
Intermittent hypoxia exacerbates anxiety in high-fat diet-induced diabetic mice by inhibiting TREM2-regulated IFNAR1 signaling
Authors: Ni Wenyu , Niu Yun , Cao Sitong , Fan Chunsun , Fan Jian , Zhu Li , Wang Xueting 
Published: July 2024

Abstract
Background
Type 2 diabetes mellitus (T2DM) and obstructive sleep apnea (OSA) are mutual risk factors, with both conditions inducing cognitive impairment and anxiety. However, whether OSA exacerbates cognitive impairment and anxiety in patients with T2DM remains unclear. Moreover, TREM2 upregulation has been suggested to play a protective role in attenuating microglia activation and improving synaptic function in T2DM mice. The aim of this study was to explore the regulatory mechanisms of TREM2 and the cognitive and anxiety-like behavioral changes in mice with OSA combined with T2DM.

Methods
A T2DM with OSA model was developed by treating mice with a 60% kcal high-fat diet (HFD) combined with intermittent hypoxia (IH). Spatial learning memory capacity and anxiety in mice were investigated. Neuronal damage in the brain was determined by the quantity of synapses density, the number and morphology of brain microglia, and pro-inflammatory factors. For mechanism exploration, an in vitro model of T2DM combined with OSA was generated by co-treating microglia with high glucose (HG) and IH. Regulation of TREM2 on IFNAR1-STAT1 pathway was determined by RNA sequencing and qRT-PCR.

Results
Our results showed that HFD mice exhibited significant cognitive dysfunction and anxiety-like behavior, accompanied by significant synaptic loss. Furthermore, significant activation of brain microglia and enhanced microglial phagocytosis of synapses were observed. Moreover, IH was found to significantly aggravate anxiety in the HFD mice. The mechanism of HG treatment may potentially involve the promotion of TREM2 upregulation, which in turn attenuates the proinflammatory microglia by inhibiting the IFNAR1-STAT1 pathway. Conversely, a significant reduction in TREM2 in IH-co-treated HFD mice and HG-treated microglia resulted in the further activation of the IFNAR1-STAT1 pathway and consequently increased proinflammatory microglial activation.

Conclusions
HFD upregulated the IFNAR1-STAT1 pathway and induced proinflammatory microglia, leading to synaptic damage and causing anxiety and cognitive deficits. The upregulated TREM2 inT2DM mice brain exerted a negative regulation of the IFNAR1-STAT1 pathway. Mice with T2DM combined with OSA exacerbated anxiety via the downregulation of TREM2, causing heightened IFNAR1-STAT1 pathway activation and consequently increasing proinflammatory microglia.

Graphical Abstract
Correlates of fertility desires in women with urogenital fistula in the Democratic Republic of Congo: a cross-sectional study of 1,646 women
Authors: Mugisho-Munkwa Guerschom , Maroyi Raha , Mukwege Denis 
Published: July 2024

AbstractBackgroundStudies on fertility desires among fistula patients in the Democratic Republic of Congo (DRC) have been conducted on fewer patients. Furthermore, these studies have adopted a univariate descriptive approach. This study aims to examine the determinants of fertility desires among patients with fistula in the DRC.MethodsThis cross-sectional study included women aged 15–49 whose fistulas were repaired by the Panzi Hospital mobile team in seven DRC regions between 2013 and 2018. Univariate and bivariate descriptive analyses were performed using the frequency distribution table and the chi-square test. Adjusted odds ratios with their 95 confidence intervals from logistic regression were used to analyze factors associated with fertility desire after fistula repair. All analyses were stratified by parity level for all women aged 15–49 and 20–34 years.ResultsOf the 1,646 women aged 15–49 and 808 aged 20–34, 948 (57.6%) and 597 (73.8%), respectively, wanted to have children after fistula repair. Among women aged 15–49 and 20–34 years, the desire to have children was parity-specific. It was negatively associated with age at all parity levels. In women with low parity, the desire for children was significantly negatively associated with a high number of surgeries, abortions, and fistula duration. It tended to decrease with time, but was particularly high in 2014 and 2017. It was high among the Protestant women. Among medium-parity women, it was significantly lower in urban areas and among widows, but higher among women who had more than two abortions. Among high-parity women, it was negatively associated with education level.ConclusionTo help women with fistula achieve or approach their desired number of children, our findings suggest that (1) counseling is needed for women with a high desire for children; (2) the human, material, and financial resources needed to eliminate fistula in the DRC should be made available; and (3) medical and nursing staff should be sufficiently and effectively trained to minimize the number of unsuccessful surgeries performed on women with fistula.
U shape association between triglyceride glucose index and congestive heart failure in patients with diabetes and prediabetes
Authors: Shi Yumeng , Yu Chao 
Published: July 2024

Abstract
Background
While previous population studies have shown that higher triglyceride-glucose (TyG) index values are associated with an increased risk of congestive heart failure (CHF), the relationship between TyG and CHF in patients with abnormal glucose metabolism remains understudied. This study aimed to evaluate the association between TyG and CHF in individuals with diabetes and prediabetes.

Methods
The study population was derived from the National Health and Nutrition Examination Survey (NHANES) spanning from 1999 to 2018. The exposure variable, TyG, was calculated based on triglyceride and fasting blood glucose levels, while the outcome of interest was CHF. A multivariate logistic regression analysis was employed to assess the association between TyG and CHF.

Results
A total of 13,644 patients with diabetes and prediabetes were included in this study. The results from the fitting curve analysis demonstrated a non-linear U-shaped correlation between TyG and CHF. Additionally, linear logistic regression analysis showed that each additional unit of TyG was associated with a non-significant odds ratio (OR) of 1.03 (95%CI: 0.88–1.22, P = 0.697) for the prevalence of CHF. A two-piecewise logistic regression model was used to calculate the threshold effect of the TyG. The log likelihood ratio test (p < 0.05) indicated that the two-piecewise logistic regression model was superior to the single-line logistic regression model. The TyG tangent point was observed at 8.60, and on the left side of this point, there existed a negative correlation between TyG and CHF (OR: 0.54, 95%CI: 0.36–0.81). Conversely, on the right side of the inflection point, a significant 28% increase in the prevalence of CHF was observed per unit increment in TyG (OR: 1.28, 95%CI: 1.04–1.56).

Conclusions
The findings from this study suggest a U-shaped correlation between TyG and CHF, indicating that both elevated and reduced levels of TyG are associated with an increased prevalence of CHF.
Localized fine-tuning and clinical evaluation of deep-learning based auto-segmentation (DLAS) model for clinical target volume (CTV) and organs-at-risk (OAR) in rectal cancer radiotherapy
Authors: Geng Jianhao , Sui Xin , Du Rongxu , Feng Jialin , Wang Ruoxi , Wang Meijiao , Yao Kaining , Chen Qi , Bai Lu , Wang Shaobin , Li Yongheng , Wu Hao , Hu Xiangmin , Du Yi 
Published: July 2024

Abstract
Background and purpose
Various deep learning auto-segmentation (DLAS) models have been proposed, some of which have been commercialized. However, the issue of performance degradation is notable when pretrained models are deployed in the clinic. This study aims to enhance precision of a popular commercial DLAS product in rectal cancer radiotherapy by localized fine-tuning, addressing challenges in practicality and generalizability in real-world clinical settings.

Materials and methods
A total of 120 Stage II/III mid-low rectal cancer patients were retrospectively enrolled and divided into three datasets: training (n = 60), external validation (ExVal, n = 30), and generalizability evaluation (GenEva, n = 30) datasets respectively. The patients in the training and ExVal dataset were acquired on the same CT simulator, while those in GenEva were on a different CT simulator. The commercial DLAS software was first localized fine-tuned (LFT) for clinical target volume (CTV) and organs-at-risk (OAR) using the training data, and then validated on ExVal and GenEva respectively. Performance evaluation involved comparing the LFT model with the vendor-provided pretrained model (VPM) against ground truth contours, using metrics like Dice similarity coefficient (DSC), 95th Hausdorff distance (95HD), sensitivity and specificity.

Results
LFT significantly improved CTV delineation accuracy (p < 0.05) with LFT outperforming VPM in target volume, DSC, 95HD and specificity. Both models exhibited adequate accuracy for bladder and femoral heads, and LFT demonstrated significant enhancement in segmenting the more complex small intestine. We did not identify performance degradation when LFT and VPM models were applied in the GenEva dataset.

Conclusions
The necessity and potential benefits of LFT DLAS towards institution-specific model adaption is underscored. The commercial DLAS software exhibits superior accuracy once localized fine-tuned, and is highly robust to imaging equipment changes.
Balloon atrial septostomy: a weapon to challenge right heart failure after cardiac surgery
Authors: Yang Weijun , Shen Zhean , Zhu Manxuan , Wang Xiaofang , Kong Minjian 
Published: July 2024

AbstractRight heart failure is a common complication after cardiac surgery, and its mortality remains high. The medical management and veno-arterial extracorporeal membrane oxygenation has shown significant improvement in the majority of cases. However, a minority of patients may still require long-term mechanical circulatory support or heart transplantation. Balloon atrial septostomy is a new method for the prevention and treatment of right heart failure, which may avoid the patient’s dependence on mechanical circulatory support. We used this method to try to treat patients with right heart failure after cardiac surgery, and all received good benefits. Therefore, we selected several representative cases to report, in order to guide other qualified cardiac surgeons to carry out relevant clinical practice.
Sinus rhythm restoration reverses tricuspid regurgitation in patients with atrial fibrillation: a systematic review and meta-analysis
Authors: Zhan Yufeng , Li Ning 
Published: July 2024

Abstract
Background
Tricuspid regurgitation (TR) is a common valvular heart disease worldwide, and current guidelines for TR treatment are relatively conservative, as well as with detrimental outcomes. Restoration of sinus rhythm was reported to improve the TR severity in those TR patients with atrial fibrillation (AF). However, relevant research was limited. The aim of this meta-analysis was to evaluate the clinical outcomes of restoration of sinus rhythm in TR patients with AF.

Methods
In this study, PubMed, Web of Science, and Scopus databases were searched for study enrollment until July 2023. This study was designed under the guidance of Preferred Reporting Items for Systematic Reviews and Meta-Analyses. These studies containing the patient’s baseline characteristics, surgical procedure, and at least one of the clinical outcomes were included. The primary endpoint was TR grade during follow-up after restoration of sinus rhythm.

Results
Out of 1074 records, 6 were enrolled. Restoration of sinus rhythm is associated with a reduction of TR severity (TR grade, odds ratio 0.11, 95% confidence interval (CI): 0.01 to 1.28, P = 0.08, I2 = 83%; TR area, mean difference (MD) -2.19 cm2, 95% CI: -4.17 to -0.21 cm2, P = 0.03, I2 = 96%). Additionally, remolding of right heart with a significant reduction of tricuspid valve annulus diameter (MD -0.36 cm, 95%CI: -0.47 to -0.26 cm, P < 0.00001, I2 = 29%) and right atrium volume index (MD -11.10 mL/m2, 95%CI: -16.81 to -5.39 mL/m2, P = 0.0001, I2 = 79%) was observed during follow-up.

Conclusions
In conclusion, rhythm-control therapy could reduce TR severity in AF patients with TR and is associated with right heart remodeling.
Impact of minimal invasive extracorporeal circulation on systemic inflammatory response – a randomized trial
Authors: Halle Deborah Richards , Benhassen Leila Louise , Søberg Karsten Lund , Nielsen Peter Fast , Kimose Hans-Henrik , Bauer Adrian , Hasenkam John Michael , Modrau Ivy Susanne 
Published: July 2024

Abstract
Background
Extracorporeal circulation causes a systemic inflammatory response, that may cause postoperative haemodynamic instability and end-organ dysfunction. This study aimed to investigate the impact of minimal invasive extracorporeal circulation (MiECC) on the systemic inflammatory response compared with conventional extracorporeal circulation (CECC).

Methods
Patients undergoing coronary artery bypass grafting were randomized to MiECC (n = 30) and CECC (n = 30). Primary endpoint was tumor necrosis factor-α. Secondary endpoints were other biochemical markers of inflammation (IL1β, IL6 and IL8, C-reactive protein, leukocytes), and markers of inadequate tissue perfusion and tissue damage (lactate dehydrogenase, lactate and creatine kinase-MB). In addition, we registered signs of systemic inflammatory response syndrome, haemodynamic instability, atrial fibrillation, respiratory dysfunction, and infection.

Results
Patients treated with MiECC showed significantly lower levels of tumor necrosis factor-α than CECC during and early after extracorporeal circulation (median: MiECC 3.4 pg/mL; CI 2.2–4.5 vs. CECC 4.6 pg/mL; CI 3.4–5.6; p = 0.01). Lower levels of creatine kinase-MB and lactate dehydrogenase suggested less tissue damage. However, we detected no other significant differences in any other markers of inflammation, tissue damage or in any of the clinical outcomes.

Conclusions
Lower levels of TNF-α after MiECC compared with CECC may reflect reduced inflammatory response, although other biochemical markers of inflammation were comparable. Our results suggest better end-organ protection with MiECC compared with CECC. Clinical parameters related to systemic inflammatory response were comparable in this study.

Clinical registration number
NCT03216720.