syedzayyan/paper_mill_benchmark huggingface dataset:
NECScanNet: Novel Method for Cervical Neuroendocrine Cancer Screening from Whole Slide Images

As a rare malignant tumor, cervical neuroendocrine cancer (nec) is difficult in diagnosis even for experienced pathologists.A computer-assisted diagnosis may be helpful for the improvement of diagnostic accuracy.Nevertheless, the computer-aided pathological diagnosis has to face a great challenge that the hundred-million-pixels or even gig-pixels whole slide images (wsis) cannot be applied directly in the existing deep convolution network for training and analysis.Therefore, the construction of a neural network to realize the automatic screening of cervical nec is challenging; meanwhile, as far as we know, little attention has been paid to this field.In order to address this problem, here we present a multiple-instance learning method for automatic recognition of cervical nec on pathological wsi, which consists of the sliding detector module and lesion analyzer module.A pathological wsi dataset, which is composed of 84 nec cases and 216 nec-free cases from the pathological department of west china second university hospital, is applied to evaluate the performance of the method.The experimental results show that the recall rate, accuracy rate, and precision rate of our method for automatic recognition are 92.9%, 92.7%, and 83.0%, respectively, demonstrating the effectiveness and the potential in clinical practice.The application of this method in computer-assisted pathological diagnosis is expected to decrease the misdiagnosis as well as the false diagnosis of rare cervical nec, and, consequently, improve the therapeutic effect of cervical cancers.

Journal: Security and Communication Networks (2021)
Publication types: Research Article;
Natural Antioxidants Improve the Vulnerability of Cardiomyocytes and Vascular Endothelial Cells under Stress Conditions: A Focus on Mitochondrial Quality Control

Cardiovascular disease has become one of the main causes of human death.In addition, many cardiovascular diseases are accompanied by a series of irreversible damages that lead to organ and vascular complications.In recent years, the potential therapeutic strategy of natural antioxidants in the treatment of cardiovascular diseases through mitochondrial quality control has received extensive attention.Mitochondria are the main site of energy metabolism in eukaryotic cells, including myocardial and vascular endothelial cells.Mitochondrial quality control processes ensure normal activities of mitochondria and cells by maintaining stable mitochondrial quantity and quality, thus protecting myocardial and endothelial cells against stress.Various stresses can affect mitochondrial morphology and function.Natural antioxidants extracted from plants and natural medicines are becoming increasingly common in the clinical treatment of diseases, especially in the treatment of cardiovascular diseases.Natural antioxidants can effectively protect myocardial and endothelial cells from stress‐induced injury by regulating mitochondrial quality control, and their safety and effectiveness have been preliminarily verified.This review summarises the damage mechanisms of various stresses in cardiomyocytes and vascular endothelial cells and the mechanisms of natural antioxidants in improving the vulnerability of these cell types to stress by regulating mitochondrial quality control.This review is aimed at paving the way for novel treatments for cardiovascular diseases and the development of natural antioxidant drugs.

Journal: Oxidative Medicine and Cellular Longevity (2021)
Publication types: Review Article;
Multimodal MRI-Based Radiomic Nomogram for the Early Differentiation of Recurrence and Pseudoprogression of High-Grade Glioma

To evaluate the diagnostic value of multimodal mri radiomics based on t2‐weighted fluid attenuated inversion recovery imaging (t2wi‐flair) combined with t1‐weighted contrast enhanced imaging (t1wi‐ce) in the early differentiation of high‐grade glioma recurrence from pseudoprogression.Methods .A total of one hundred eighteen patients with brain gliomas who were diagnosed from march 2014 to april 2020 were retrospectively analyzed.According to the clinical characteristics, the patients were randomly split into a training group ( n = 83) and a test group ( n = 35) at a 7 : 3 ratio.The region of interest (roi) was delineated, and 2632 radiomic features were extracted.We used multiple logistic regression to establish a classification model, including the t 1 model, t 2 model, and t 1 + t 2 model, to differentiate recurrence from pseudoprogression.The diagnostic efficiency of the model was evaluated by calculating the area under the receiver operating characteristic curve (auc) and accuracy (acc) and by analyzing the calibration curve of the nomogram and decision curve.Results .There were 75 cases of recurrence and 43 cases of pseudoprogression.The diagnostic efficacies of the multimodal mri‐based radiomic model were relatively high.The auc values and acc of the training group were 0.831 and 77.11%, respectively, and the auc values and acc of the test group were 0.829 and 88.57%, respectively.The calibration curve of the nomogram showed that the discrimination probability was consistent with the actual occurrence in the training group, and the discrimination probability was roughly the same as the actual occurrence in the test group.In the decision curve analysis, the t 1 + t 2 model showed greater overall net efficiency.Conclusion .The multimodal mri radiomic model has relatively high efficiency in the early differentiation of recurrence from pseudoprogression, and it could be helpful for clinicians in devising correct treatment plans so that patients can be treated in a timely and accurate manner.

Journal: BioMed Research International (2022)
Publication types: Research Article;
Modification in Silver Staining Procedure for Enhanced Protein Staining

Silver staining is an excellent technique for detecting proteins that are separated by sodium dodecyl sulfate‐polyacrylamide gel electrophoresis (sds‐page).Protein silver staining technology has higher sensitivity and is suitable for the detection of low‐concentration proteins compared to other staining techniques including the coomassie brilliant blue detection method.The present study was conducted to enhance the detection ability of the protein staining method.Herein, we modified the recipe of silver staining, a very reproducible method, by adding amp, pvp, tween‐80, and xylene to enhance the detection ability of protein staining.Furthermore, the particle size and potentiometer were used to detect the particle size and potential difference of the silver ions in the prepared dyeing materials, and then, the morphology, transparency, and size of the dyed silver particles in different dyeing solutions were studied using a transmission electron microscopy (tem).The obtained results revealed that the use of 0.5% of amp, pvp, tween‐80, and xylene improved the staining ability of protein silver staining, compared with the original method.Furthermore, 0.5% amp, 0.5% pvp, 0.5% tween‐80 reagents significantly influenced the morphology, size, potential, and dispersion of silver ions.These results suggested a new idea for further improving the detection ability of protein silver staining.

Journal: BioMed Research International (2022)
Publication types: Research Article;
Mitochondrial ROS Produced by Skeletal Muscle Mitochondria Promote the Decisive Signal for UPRmt Activation

The m itochondrial unfolded protein response (uprmt) can repair and remove misfolded or unfolded proteins in mitochondria and enhance mitochondrial protein homeostasis.Reactive oxygen species (ros) produced by regular exercise is a crucial signal for promoting health, and skeletal muscle mitochondria are the primary source of ros during exercise.To verify whether uprmt is related to ros produced by mitochondria in skeletal muscle during regular exercise, we adapted mito tempo, mitochondrially targeted antioxidants, and ros production by mitochondria.Our results showed that m itochondrial ros is the key factor for activating uprmt in different pathways.

Journal: BioMed Research International (2022)
Publication types: Research Article;
miR-92b-3p Exerts Neuroprotective Effects on Ischemia/Reperfusion-Induced Cerebral Injury via Targeting NOX4 in a Rat Model

The necessity to increase the efficiency of organ preservation has pushed researchers to consider the mechanisms to minimize cerebral ischemia/reperfusion (i/r) injury.Hence, we evaluated the role of the mi r-92b-3p/nox4 pathway in cerebral i/r injury.A cerebral i/r injury model was established by blocking the left middle cerebral artery for 2 h and reperfusion for 24 h, and a hypoxia/reoxygenation (h/r) model was established.Thereafter, cerebral i/r increased obvious neurobiological function and brain injury (such as cerebral infarction, apoptosis, and cell morphology changes).In addition, we noted a significant decrease in the expression of mi r-92b-3p, as well as increases in apoptosis and oxidative stress and an increase in nox4.Furthermore, overexpression of mi r-92b-3p blocked the inhibitory effect of mi r-92b-3p on the expression of nox4 and the accumulation of oxygen-free radicals.Bioinformatics analysis found that nox4 may be the target gene regulated by mi r-92b-3p.In conclusion, the involvement of the mi r-92b-3p/nox4 pathway ameliorated cerebral i/r injury through the prevention of apoptosis and oxidative stress.The mi r-92b-3p/nox4 pathway could be considered a potential therapeutic target to alleviate cerebral i/r injury.

Journal: Oxidative Medicine and Cellular Longevity (2022)
Publication types: Research Article;
Mild Hypothermia Promotes Ischemic Tolerance and Survival of Neural Stem Cell Grafts by Enhancing Global SUMOylation

Cerebral infarct penumbra due to hypoxia and toxin accumulation is not conducive to the transplantation of neural stem cells (nscs), although mild hypothermia can improve the local microenvironment of the ischemic penumbra and exert neuroprotective effects.However, insufficient understanding of the molecular mechanism by which mild hypothermia protects the brain limits widespread clinical application.This study evaluated the molecular mechanism of mild hypothermia-induced brain protection from the perspective of global protein small ubiquitin-like modifier (sumo) modification, with the aim of improving nsc transplant survival rates in the penumbra to enhance neurological function.Nscs from neonatal rats were extracted to detect the effects of hypoxia and mild hypothermia on sumoylation modification levels, cell stemness, and hypoxia-induced injury.Overexpression and knockdown of ubc9 in nscs were used to evaluate their ability to maintain stemness and withstand hypoxic injury.Finally, a rat middle cerebral artery occlusion (mcao) model was used to verify the effect of mild hypothermia treatment and ubc9 overexpression on neural function of nscs following penumbra transplantation in rats.Results showed that hypoxia and mild hypothermia promoted both the sumoylation modification and maintenance of nsc stemness.Overexpression of ubc9 enhanced the abilities of nscs to maintain stemness and resist hypoxic injury, while ubc9 knockdown had the opposite effect.Following transplantation into the ischemic penumbra of mcao model rats, mild hypothermia and ubc9-overexpressing nscs significantly reduced cerebral infarct areas and improved neurological function.In conclusion, this study demonstrated that global protein sumoylation is an important molecular mechanism for nscs to tolerate hypoxia, and mild hypothermia can further increase the degree of global sumoylation to enhance the hypoxia tolerance of nscs, which increases their survival during transplantation in situ and ability to perform nerve repair in the penumbra of cerebral infarction.

Journal: Oxidative Medicine and Cellular Longevity (2022)
Publication types: Research Article;
Might Patients with Metastatic Gastrointestinal Stromal Tumors Benefit from Operative Management? A Population-Based Retrospective Study

With respect to effect of surgery on the therapy of patients with metastatic gastrointestinal stromal tumors (m gists), still no consensus has been reached.This research designed to investigate the effect of surgical treatment on prognosis in patients with m gists.Methods .The population‐based study consisted of 6282 gist patients diagnosed between 2001 and 2016, from the surveillance, epidemiology, and end results (seer) database registry.The kaplan‐meier method and cox model were employed for the exploration of the effect of surgery on overall survival (os) and gist‐specific survival (gss).Results .In total, 6282 patients were diagnosed with gists, including 1238 (19.7%) m gist patients and 5044 (80.3%) non‐m gist patients.Compared with the patients with non‐m gists, metastatic patients assumed relatively lower proportion of surgical management (756 [61.1%] vs.4666 [92.5%], p &lt; 0.001).Based on unadjusted analysis, m gist patients with operative management presented higher five years os together with gss in comparison with those without operative management (os: 58.3% vs.33.1%, p &lt; 0.001; gss: 61.6% vs.36.7%, p &lt; 0.001).Multivariable analysis found that no surgery was correlated to more than 2‐fold increased death risk (os, adjusted hr = 2.27, 95% ci: 1.90‐2.71; gss, adjusted hr = 2.42, 95% ci: 2.00‐2.93).Conclusion .Metastatic gist patients could potentially benefit from operative management with improved gss and os.

Journal: BioMed Research International (2022)
Publication types: Research Article;
Meta-Analysis on the Effects of Electric Acupuncture on Neural Functional Recovery and Related Pathways of Rats after Spinal Cord Injury

Spinal cord injury (sci) is a type of damage to the central nervous system (cns) caused by various factors.The secondary injury of sci is more complicated.Studies have found that electroacupuncture can help the recovery of nerve function during spinal cord injury.Therefore, this study explored the efficacy of electroacupuncture on complications after spinal cord injury through meta‐analysis.Methods .Relevant literatures published from january 2010 to march 2022 were searched with “electric acupuncture, spinal cord injury, neural functional recovery, spinal cord injury in rats, neuronal signaling” as search words.The risk of bias of included references was analyzed and assessed using rev man 5.3 software and stata software.Heterogeneity between studies was assessed using the q ‐test and heterogeneity ( i 2 ).Results .There was no heterogeneity among the study groups.The comparison on the therapeutic effects of electroacupuncture and conventional therapy suggested that electroacupuncture was more effective for nerve recovery after spinal cord injury than conventional therapy.It can better improve the recovery of motor function after spinal cord injury in rats.On the other hand, sci+ea had a good inhibitory effect on the expression of rho a protein signal in rats and had a positive effect on the signal pathway.Discussion .The results of meta‐analysis confirmed that electroacupuncture was more effective than conventional therapy in inhibiting pathways.

Journal: BioMed Research International (2022)
Publication types: Meta-Analysis;
Medical Image Encryption Based on 2D Zigzag Confusion and Dynamic Diffusion

For the security of medical image, a new algorithm of medical image encryption is designed.The novel algorithm is based on a chaotic system composed of the two-dimensional sine logistic modulation map (2d-slmm) and the two-dimensional hénon-sine map (2d-hsm).The main encryption procedure includes zigzag scan scramble, pixel grey value transformation, and dynamic diffusion.On the pixel grey value transformation stage, a password feedback is added.This makes the relationship between password and key more complicated.The proposed scheme is lossless for medical image encryption and decryption.It avoids the problems of low-dimensional chaotic map such as narrow interval and few parameters, as well as the problem of the special texture and contour of medical images.The key space of the novel algorithm is big enough, and the encryption and decryption processing are sensitive to the key.Simulation and experiments validate the effectiveness and efficiency of the novel algorithm.Security analysis proves the algorithm is resistant to common attacks.

Journal: Security and Communication Networks (2021)
Publication types: Research Article;
Mechanism of Shishiwei Wendan Decoction in the Prevention and Treatment of Lung Adenocarcinoma Using Network Pharmacology and Molecular Docking

This study used network pharmacology and molecular docking technology to elucidate the mechanism of action of shishiwei wendan decoction against lung adenocarcinoma.Methods .By using the world’s largest tcm system pharmacology database and analysis technology platform (tcmsp) system to conduct in‐depth mining analysis and data collection of the main active components of the medicinal components in shishiwei wendan decoction and using the human gene card database (gene cards), human mendelian inheritance online system (omim), and human disease‐related gene and mutation information database (dis ge net) to collect the pathogenic targets of lung adenocarcinoma and build a ppi network; for the core drug targets, use go enrichment analysis and kegg pathway analysis; use cytoscape software to build relevant network maps; and use auto dock to achieve molecular docking.Results .Shishiwei wendan decoction screened 144 active ingredients and 384 drug targets; 7680 lung adenocarcinoma disease targets were obtained, including 380 targets for shishiwei wendan decoction in the treatment of lung adenocarcinoma.Go enrichment analysis demonstrated 2,299 downstream genes, and key target genes were closely related to nutrient levels, membrane rafts, and protein serine/threonine kinase activity; kegg functional enrichment analysis yielded 179 related pathways, including tumor necrosis factor signaling pathway which is related to the target gene.Molecular docking showed that the core active ingredients and key targets could be well combined.Conclusion .Through the network pharmacology analysis and molecular docking experiments of shishiwei wendan decoction against lung adenocarcinoma, it is found that shishiwei wendan decoction has multidimensional effects on the treatment of lung adenocarcinoma, and it is the first shiwei wendan decoction to treat lung adenocarcinoma.Decoction in the treatment of lung adenocarcinoma provides biointellectual support and the oretical support.

Journal: BioMed Research International (2022)
Publication types: Research Article;
Machine Learning Approach for Cardiovascular Risk and Coronary Artery Calcification Score

Coronary artery calcification (cac) could assist in the discovery of new risk elements for coronary artery disorder.Cac evaluation, on the other hand, is difficult due to the wide range of cac in the populations.As a reason, evaluating and analysing data among research have become complicated.In the research of inherited risk factors for coronary atherosclerosis, we used cac information to test the effects of different analytical methodologies on the correlation with recognized cardiovascular risk elements in asymptomatic patients.Cardiac computed tomography (ct) is also seeing an increase in examinations, and machine learning (ml) could assist with the growing amount of extracted data.Furthermore, there are other sectors in cardiac ct where machine learning could be crucial, including coronary calcium scoring, perfusion, and ct angiography.The establishment of risk evaluation algorithms based on information from cac utilizing machine learning could assist in the categorization of patients undergoing cardiovascular into distinct risk groups and effectively adapt their treatments to their unique situations.Our findings imply that for forecasting cvd occurrences in asymptomatic people, age‐sex segmentation by cac percentile rank is as effective as absolute cac scoring.Longitudinal population‐based investigations are currently underway and would offer further definitive findings.While machine learning is a strong technology with a lot of possibilities, its implementations in the domain of cardiac cac are generally in the early stages of development and are not currently commonly accessible in medical practise because of the requirement for substantial verification.Enhanced machine learning will, however, have a significant effect on cardiovascular and coronary artery calcification in the upcoming years.

Journal: BioMed Research International (2022)
Publication types: Research Article;
LRSAM1 E3 Ubiquitin Ligase Promotes Choriocarcinoma Progression and Metastasis via p53/p21 Signaling Impediment

The e3 ubiquitin ligase lrsam1 (lrsam1) was involved in many cancers, but whether it exerts anti‐ or protumor efficacies on choriocarcinoma cellular structures remains unknown.We wanted to explore the efficacies of aberrant lrsam1 expression on human choriocarcinoma cellular structures and the underlying mechanisms.Methods .Lrsam1 m rna expressions in choriocarcinoma lines of cells jeg‐3 and jar cellular structures, as well as htr8/sev8 human trophoblastic cell line cellular structures, were assessed using assay analysis of quantitative real‐time polymerase chain reactions.We compared cell proliferation, migratory flow, invasive force, adhesion, and apoptotic process between cellular structures infected with si‐lrsam1 plasmids versus negative controls using cck‐8, clone formation, transwell, adhesion, and flow cytometry assays.Protein expressions of lrsam1, e‐cadherin, and n‐cadherin (indicators of epithelial‐mesenchymal transformation) and p53/p21 pathway components were quantitated using a western blot assay.The morphology of tumor lesions was observed in xenografted nude mice using immunohistochemistry (ihc) analyses.Results .Lrsam1 was markedly overexpressed within jeg‐3 and jar choriocarcinoma cellular structures compared to htr8/sev8 trophoblast cellular structures.Compared to si‐nc, lrsam1 knockdown robustly restricted cell proliferating, migratory flow, invasive force, and adhesion and fueled apoptotic cell process in jeg‐3 as well as jar cellular structures and suppressed tumor growth, as evidenced by the reduction in tumor volume and weight in naked mice inoculated with transfected cellular structures.Compared to si‐negative control (si‐nc), si‐lrsam1 significantly decreased ki67 (a proliferating indicator) and n‐cadherin expressions but reduced e‐cadherin expression in jeg‐3 and jar cellular structures.Blocking the p53/p21 pathway by pifithrin‐a (a p53 restrictor) successfully reversed the anti‐inhibitory effect of lrsam1 depletion, resulting in enhanced proliferating and metastasis in jeg‐3 and jar cellular structures.Conclusion .Lrsam1 exerts tumorigenic roles in choriocarcinoma.Via the activating of the p53/p21 pathway of signaling and impediment of choriocarcinoma cell proliferating, migratory flow, and invasive force, lrsam1 knockdown slows the course of the disease.For choriocarcinoma diagnosis and treatment, it serves as a new therapeutic target.

Journal: BioMed Research International (2022)
Publication types: Research Article;