bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of extraction and RT-PCR protocols on stool RNA detection: A study on CRC- associated immune-genes in various patient groups
Authors: Omran Thura Akrem , Madsø Inger Line , Saether Per Christian , Bemanian Vahid , Tunsjø Hege Smith 
Published: October 2024

Abstract

There is a growing interest in using fecal mRNA transcripts as biomarkers for non-invasive detection of colorectal cancer (CRC). The following study compares different RNA extraction and reverse transcription PCR (RT-PCR) methods for mRNA detection in stool and identifies a robust and sensitive protocol.
A combination of the Stool total RNA purification kit (Norgen) and the Superscript III one-step RT-PCR kit (Invitrogen) provided high RNA purity and sensitive and consistent mRNA detection, making them well-suited candidates for large-scale studies. We tested the protocol by detecting the mRNA of several immune genes (CXCL1, IL8, IL1B, IL6, PTGS2, and SPP1) in 22 CRCs, 24 adenomatous polyps, and 22 control stool samples. All these inflammatory markers, except for CXCL1, showed a strong association with CRC. Cancer stool samples showed increased levels of IL1B, IL8, and PTGS2 transcripts compared to polyp and control groups.Thus, this work supports the potential use of fecal mRNA for CRC biomarker detection.
Mendelian Randomization Reveals Causal Links Between Vertigo Types and structural characteristics of specific brain regions
Authors: Huang Junwei , Zhu Xiao , Yao Jingxin , Lu Wei , Zhu Zhenhua 
Published: October 2024

Abstract

Background
Vertigo is a common clinical symptom that involves multiple neurobiological processes; however, its exact mechanism remains elusive. In neuroimaging studies focusing on vertigo and its central correlation, potential reverse causality and unmeasured confounding factors frequently introduce biases. Furthermore, the causal relationship between vertigo and specific neuroimaging features is not yet established. Employing the Mendelian randomization (MR) method can provide a more precise understanding of the causal relationships between vertigo and changes in brain structure and function.
Methods
Based on the large-scale genome-wide association study data from UK Biobank, this study employed bidirectional MR analysis to explore the causal relationships between brain MRI features associated with vertigo and the condition itself. The research focuses on brain imaging-derived phenotypes (IDPs) such as whole brain volume, and the volumes of both gray matter and white matter.
Results
In this study, MR analysis revealed that for benign paroxysmal positional vertigo (BPV), an increase in specific brain regions such as BA-exvivo lh volume BA2, aparc-Desikan rh area rostralmiddlefrontal, IDP dMRI TBSS L2 Corticospinal tract R, and rfMRI connectivity (ICA100 edge 1323) was significantly correlated with a reduction in BPV risk. Conversely, an increase in IDP dMRI TBSS MD Cingulum hippocampus L and rfMRI connectivity (ICA100 edge 82 and 357) was associated with an increased risk of BPV. For peripheral vertigo (PERIPHVERTIGO), an increase in aparc-a2009s rh volume Pole-occipital significantly increased the risk. For general vertigo (VERTIGO), increases in IDP dMRI TBSS FA Superior fronto-occipital fasciculus R and rfMRI connectivity (ICA100 edge 236) were associated with increased risk, while a decrease in rfMRI connectivity (ICA100 edge 184) was associated with decreased risk. For central vertigo (VERTIGOCENT), an increase in rfMRI connectivity (ICA100 edge 1387) and BA-exvivo rh thickness BA4a significantly reduced the risk, whereas an increase in aparc-Desikan rh area annularcingulate significantly increased the risk.
Conclusion
The genetic susceptibility of the vertigo network, extending from the vestibular labyrinth in the cerebellum and brainstem to the cerebral cortex, is causally related to an increase in white matter volume and total brain volume. Volume changes in several cortical regions may suggest a higher risk of vertigo; thus, further studies of causal inference at the sub-brain regional level are strongly recommended. Our results offer genetic evidence that helps elucidate the underlying pathophysiological mechanisms of neuroanatomical abnormalities related to vertigo.
Postoperative recurrence of atypical odontoma: a case report
Authors: Qin Han , Gong Yong-qing 
Published: October 2024

Abstract

Background: The purpose of this study was to analyze a case of recurrent atypical odontoma after surgical resection, in order to provide some references for the etiology analysis and treatment of this disease.
Methods：The detailed clinical data and history of related clinical symptoms of this patient were retrieved at first visit. Intraoral examination showed permanent dentition, no left maxillary first premolar (24). However, there were several anomalous tooth-like tissues in the affected area. Imaging studies showed several small, highly dense image aggregates above tooth 24. The erupting and un-erupting teeth-like tissues were removed in accordance with the surgical method of extraction of supernumerary teeth under local anesthesia. The patient was returned to our clinic one month later, and periapical radiography examination showed irregular and unorganized radiopaque mass surrounded by a clear thin radiographic halo above the crown of tooth 24. The imaging data indicated that this was a typical manifestation of odontoma. After full communication with the child's parents, the second surgical resection was performed to remove the cyst wall and the hard tissue inside the capsule.
Results: When the patient returned 3 months after the second operation, the intraoral examination showed tooth 24 had erupted normally, and periapical radiography examination showed no abnormal root development.
Conclusion: The case gives us three inspirations: atypical odontoma is easy to cause misdiagnosis and lead to incomplete resection and postoperative recurrence; Intraoperative stimulation can promote the rapid growth of odontoma. Young permanent teeth can erupt normally after removing mechanical blockages without special treatment.
Indocyanine Green Dyed Gauze-Guided Minimum Invasive Surgery for Anatomical Landmarks and Preventing Gauze Remnants: A Pilot Study
Authors: Tashiro Yoshihiko , Aoki Takeshi , Yasunaga Hidekazu , Ando Shinji 
Published: October 2024

Abstract

Purpose
We aimed to develop a novel fluorescent surgical gauze dyed with indocyanine green (ICG) to guide surgeons to the target anatomical destination during surgery for real-time navigation and to prevent gauze remnants after surgery.
Methods
Surgical gauze was dyed with an aqueous solution of ICG (5.0 × 10− 5 mol L− 1 for Steraze, 1.5 × 10− 4 mol L− 1 for BK-Opeze ) at 132°C (inside pressure: 2.82 atm, 286 kPa) for 15 min using an autoclave, followed by washing with distilled water, drying at room temperature, and sterilizing at 132°C for 8 min before surgery. Fluorescence (FL) intensity was examined preclinically in the resected specimens using the SPY PHI (Stryker) system. Fourteen patients who underwent laparoscopic- and robotic-assisted gastroenterological surgery at Showa University Hospital were included.
Results
Fluorescent emission of ICG-dyed gauze was clearly observed through resected specimens with a thickness of approximately 10 mm or more. In a clinical trial, the ICG-dyed gauze was detected earlier with near-infrared (near-IR) FL imaging than under white light during seven cases of laparoscopic and robotic surgery, which could become a precise marker for surgeons to locate the dissection site despite overlaying tissues and nearby disturbances. Additionally, no seepage of ICG from the gauze was observed in all surgical fields.
Conclusion
We successfully developed ICG-dyed gauze exhibiting bright near-IR FL which can guide surgeons to the target anatomical destination and prevent gauze remnants during surgery. This invention would be a powerful support for real-time navigation surgery.
Diagnostic Utility of Fluorescence and Diffuse Reflectance Imaging in Gastrointestinal Luminal Pathology
Authors: Padikala John Anto , Subhash N , George Phebe , Manogli Sandeep P , Suvarnadas Rinoy , Raveendranadh Ajay , Mathew Stanley 
Published: October 2024

Abstract

BACKGROUND:
Cancer is a fatal disease with significant global mortality. Because cancer is so diverse and lacks biomolecular indicators, it is difficult to diagnose at an early stage using current histopathological diagnostic techniques. However, recent cutting-edge fluorescence and diffuse reflectance (DR) imaging techniques, which use sub-cellular spectral features, have proven beneficial in cancer diagnostics. This study aimed to investigate the diagnostic potential of these methods for discriminating malignant from normal gastrointestinal tissue in an ex vivo setting.
MATERIALS AND METHODS:
An experimental trial was conducted on 42 patients attending the Department of General Surgery, Kasturba Medical College, Manipal. Fluorescence and DR at 399 sites were measured using a handheld multimodal device. The spectral readings were taken immediately after the surgical resection of the specimen. Light-emitting diodes (LED) emitting at 375 nm, 545 nm, 575 nm, and 610 nm wavelengths were used for tissue illumination, and the backscattered light was analyzed using proprietary software. The DR ratio (R610/R545) intensity values were determined for all the different sites examined, and a scatter plot diagram was made to correlate with tissue pathology.
RESULTS:
Spectral readings of histologically confirmed malignant tissues were compared with those of histologically verified normal tissues and were used as controls. In total, 399 sites yielded 766 spectral findings. In an ex vivo context, our study demonstrated a sensitivity of 78.8% and specificity of 98.3% for differentiating between malignant and normal tissues. Additionally, the study showed a 90% specificity and 92% sensitivity for differentiating between benign and malignant tissues.
CONCLUSION:
The diagnostic utility of fluorescence and DR imaging demonstrates its potential to discriminate between normal tissues and pathological lesions of the gastrointestinal tract in real-time.
Identification of a immune-related genes signature for survival prediction in stage I lung adenocarcinoma
Authors: Zhang Xin , Li ShiNing , Luo SiSheng , Liu XinYu , Ao Yong , Zhong LeQi , Luo KongJia , Hu Yi 
Published: October 2024

Abstract

Background
With the popularization of low-dose spiral computed tomography (CT), an increasing number of stage I lung cancers have been discovered. Although most of the patients with stage I lung adenocarcinoma have a favorable prognosis, some patients still have a poor prognosis of recurrence and metastasis after surgery. The immune system has been shown to play an important role in the development of cancer. Our aim is to identify a reliable prognostic signature of immune-related genes that can predict prognosis and help in the individualized management of patients with stage I lung adenocarcinoma.
Methods
In this study, the immune-related genes were first extracted by the ImmPort database. Subsequently, these genes were screened using univariate Cox regression and LASSO regression to identify prognostic signatures, followed by construction of a prognostic model using multivariate Cox regression. A nomogram was developed to predict the prognosis of stage I lung adenocarcinoma and to evaluate the nomogram differentiation and accuracy using the receiver operating characteristic curve, clinical decision analysis and calibration curve. The model was validated in two independent data sets: GSE31210 and GSE30219. Then, patients were stratified based on median risk scores, and differential expression genes between the two groups were analyzed. Finally, the enrichment analysis and the immune infiltration analysis were performed.
Results
In this study, we found 29 immune-related genes and developed a gene signature with poor prognosis in stage I lung adenocarcinoma. Our model was validated using two independent datasets and demonstrated robust performance with good AUC values and clinical utility. Enrichment analysis indicated that immune-related genes signature has multifaceted effects on stage I lung adenocarcinoma, especially related to tumor development, proliferation, and metastasis. Patients in the high-risk group had higher tumor purity, lower matrix, estimated and immune scores, suggesting a potentially immunosuppressive tumor microenvironment.
Conclusion
This study constructed a gene signature related to immunity in stage I lung adenocarcinoma and analyzed its impact on tumor development and its relationship with the tumor microenvironment. The findings can contribute to a more precise survival risk stratification and personalized clinical management for stage I lung adenocarcinoma patients. Furthermore, we provide related opinions for future immune-related research by elucidating potential underlying mechanisms.
Study protocol for a prospective, longitudinal cohort study investigating the Intestinal permeability in critically ill patients
Authors: Hejazi Samin , Norouzy© Abdol Reza , Safarian Mohammad , Moghaddam Ahmad Bagheri , Alinezhad-Namaghi Maryam , Rezaiyan Majid Khadem , Dehbalaei Moazzameh Ghorbani , Dorchin Mohsen , Hasani Atefeh Sepehri 
Published: October 2024

Abstract

Aim: The research is a prospective cohort study focusing on assessing intestinal permeability in critically ill individuals. The primary aim of the study is to investigate the impact of intestinal permeability on disease severity and the 28-day and 60-day mortality rates among critically ill patients.
Introduction: Preserving the integrity of the gastrointestinal (GI) tract is essential for maintaining intestinal barrier function, as its compromise can result in the translocation of detrimental substances, such as bacteria. Critically ill patients are particularly vulnerable to changes in intestinal permeability (IP), which can elevate the chances of developing severe conditions like sepsis, multiple organ dysfunction syndrome (MODS), and systemic inflammatory response syndrome (SIRS), ultimately leading to mortality.
Method: The research will involve 73 ICU patients needing enteral feeding for a minimum of one day, who will undergo screening based on specific criteria for inclusion and exclusion. Small-bowel permeability will be assessed using the dual-sugar absorption method (lactulose and mannitol), a prevalent noninvasive technique in critically ill individuals, to determine their small-bowel permeability accurately.
Conclusion: Consequently, addressing altered intestinal permeability becomes a critical focus for therapeutic interventions and a pivotal factor influencing the outcomes of patients in the intensive care unit (ICU). Its straightforwardness, consistency, and reliability of this measuring make it ideal for routine clinical applications, enabling the quantification of intestinal permeability with ease and accuracy.
Aneurysm and subacute type A aortic dissection, in a pediatric patient with aortopathy
Authors: Ceballos Andres Aranzazu , Zapata Margarita Maria , Suarez Sharoon , Mendieta Ivan , Aguilar Ubaldo Rivas 
Published: October 2024

Abstract

Background
aortic dissection in pediatrics is an extremely rare condition, which is generally related to predisposing factors such as connective tissue disorders, congenital heart disease and systemic arterial hypertension.
Materials and methods: We report this case following the guidelines of the CARE guidelines.
Results: A 3-year-old girl, with a history of bileaflet aortic valve (BAV), hypoplasia of the aortic arch and repaired aortic coarctation at one month of age. She was admitted 2 months of atypical chest pain, dysphonia, and low tone of voice. The echocardiogram and CT angiography showed an image corresponding to a Stanford A aortic dissection, with false lumen perfusion that generated a pseudoaneurysmal dilation with a saccular morphology of 53x40x70 mm dimensions. Exposure of the ascending aorta, aneurysmal dissection, and replacement with a 22 mm supracoronary tube were performed. The aortic arch branches were managed with the island technique after the proximal and distal anastomoses, with good postoperative evolution.
Conclusion: We present a case of a 3-year-old pediatric patient with Stanford A aortic dissection, subacute evolution, with successful repair.
Prognostic relevance of MDK and TIMP1 with immune infiltration in lung adenocarcinoma
Authors: Zhu Qinghua , Huang Qingqing , He Xiaohua , Jiang Miaomiao , Fu Junkai , Ding Chenyuan 
Published: October 2024

Abstract

Background
LUAD is a prevalent and deadly lung cancer type. MDK and TIMP1 expression shows variations in different cancers. The specific contributions of these proteins to LUAD progression and tumor immunity, however, are not well delineated.
Methods
We leveraged RNA-seq data from TCGA and applied ggpubr R package to discern the expression disparity of MDK and TIMP1 in normal versus LUAD tissues. MDK and TIMP1 levels were further validated by qRT-PCR and western blot. Subsequently, LUAD patients were stratified into high and low expression groups based on MDK and TIMP1 expression, and the impact of their expression on overall survival (OS), disease-free interval (DFI), progression-free interval (PFI), and disease-specific survival (DSS) was analyzed. Kaplan-Meier survival curves and receiver operation characteristic curves were plotted. We also explored KEGG and GO annotations for 50 genes exhibiting expression profiles akin to MDK and TIMP1, and constructed a gene-gene interaction network using GeneMANIA. The enrichment of DEGs in the KEGG and GO pathways was scrutinized in both high and low expression groups of MDK and TIMP1. Furthermore, we investigated the mutational landscape of MDK and TIMP1 within LUAD and assessed correlation between their expression and infiltration of immune cells.
Results
MDK and TIMP1 were found to be markedly overexpressed in LUAD. LUAD patients with diminished expression of MDK and TIMP1 have extended OS, DFI, DSS, and PFI. Area under the curve values for MDK and TIMP1 were 0.943 and 0.875, respectively. Regression analysis identified TIMP1 as a risk factor influencing the OS of LUAD patients. Genes with similar expression profiles to MDK were notably enriched in the Proteasome pathway and peptidase activator activity, while those exhibit similar expression patterns to TIMP1 were predominantly involved in endopeptidase activity and the Cytoskeleton in muscle cells pathway. Functional predictions for the genes MDK and TIMP1 showed a parallel, particularly in their regulation of peptidase activity. Mutations in MDK and TIMP1 are not determinants of survival in LUAD patients. There was a negative correlation between MDK and TIMP1 expression and tumor purity. The tumor immune dysfunction and exclusion score was elevated in the group with high TIMP1 expression. The IPS_ctla_pos and IPS_pd1_pos scores are statistically significant in the high TIMP1 expression group. Infiltration of immune cells and immune-related functions is more substantial in MDK low expression and TIMP1 high expression groups.
Conclusion
A strong correlation exists between MDK and TIMP1 with both the prognosis and progression of LUAD, and the extent of immune cell infiltration, indicating that targeting these genes and their related pathways in immunotherapy could be of clinical value.
Breast Cancer Prediction Using Machine Learning: A YOLOv8 Approach
Authors: ABDELLAH MOHAMED REFAAT , Fawzy Ahmed Medhat , Hosny Mohamed Omar 
Published: October 2024

Abstract

Breast cancer is among the major concerns in global health, and its management starts with early diagnosis. This article presents an advanced machine learning approach with a deep learning YOLO algorithm (You Only Look Once). YOLOv8 is the definitive version of the YOLO deep learning algorithm. The breast cancer detection YOLOv8 model is based on ultrasound images. In the given case, deep learning techniques are being ended with to give detection high precision, speed, and performance. This paper presents an application of a deep learning algorithm, YOLOv8, in real-time breast cancer detection using ultrasound imaging. In comparison, this model represented higher accuracy and recall than both ResNet50 and VGG16, thereby representing good potential for its integration into clinical settings. Our model showed results of 93% accuracy and 92% recall, which exceeds the results of ResNet50 and VGG16 by 6% and 10%, respectively. Finally, we have described how the integration of this system will be implemented on a clinical level in a real-time web-based interface, closing our work and showing future work at the clinical level how this research may be a source of such advancements in the early detection of breast cancer.
Traumatic alterations in the exoskeleton of glyptodonts (Cingulata, Xenarthra) and associated to behavior
Authors: Lima Fábio Cunha Guimarães , Porpino Kleberson Oliveira , Ribeiro Ana Maria 
Published: October 2024

Abstract

Alterations in the exoskeleton of glyptodonts have provided valuable information about the behavior of these animals. Studying the exoskeleton of the most known genera of glyptodonts, we found traumatic alterations suggestive of impact provoked by armored parts of their bodies such as the tail. We linked our findings based on the anatomy and biomechanical traits and we used X-rays and digital microscopy to identify the lesions as complementary examination to the macroscopic analysis. Here we present the first records of traumatic alterations in Hoplophorus euphractus and Propalaeohoplophorus australis and we identified more cases of alterations in Panochthus and Glyptodon. The observed alterations were fractures, deformations and perforations with some of them associated with infections. These marks on the carapaces can be associated with caudal tube impacts, and the observed damages in the tails were made by the same nature of impact. The anatomy of the striking tail and the fighting behavior was probably guided by sexual selection, where males in intraspecific combats fought for territory or mates.
Clinical outcomes after coarctation surgery in a pediatric population at Heart Center Leipzig – a 2-decade experience
Authors: Schumacher Katja , Cuesta Manuela de la , Marin-Cuartas Mateo , Aydin Muhammed Ikbal , Meier Sabine , Dähnert Ingo , Borger Michael A. , Kostelka Martin , Vollroth Marcel 
Published: October 2024

Abstract

Background
Aortic coarctation accounts for 5–8% of congenital heart defects and patients’ symptoms can present from neonatal shock to hypertension in adolescence or even adulthood. While surgical repair is the gold standard, catheter-based therapies are increasingly utilized. Despite advancements, complications and recurrence rates necessitating re-intervention remain concerns.
Methods
We analyzed the postoperative outcomes and long-term intervention rates for pediatric patients undergoing extended end-to-end aortic coarctation repair without cardiopulmonary bypass between October 2002 and January 2024 at the Leipzig Heart Center. Data were prospectively collected and retrospectively analyzed.
Results
Among 168 patients, median age at surgery was 11 days (IQR 6–26). There was no early mortality. Median intensive care unit stay was 4 days (IQR 3–5), and hospital stay was 9 days (IQR 7–12). Early re-intervention during the same hospital stay was required in 3% due to re-coarctation. Median follow-up was 33 months (IQR 7 months − 8 years). Long-term survival at 1, 5, 10, and 14 years was 100%, 98.9%, 98.9%, and 98.9%, respectively. Freedom from catheter-based intervention was 74.3%, 70.1%, 67.9%, and 64.8% at the same intervals.
Conclusion
Extended end-to-end anastomosis for aortic coarctation repair in pediatric patients yields excellent survival and acceptable long-term outcomes, though re-intervention remains a consideration.