Miracle-dz/UniFAR-FTUs huggingface dataset:
Crosstalk of tumor stromal cells orchestrates invasion and spreading of gastric cancer

Tumors contain various stromal cells that support cancer progression. Some types of cancer, such as scirrhous gastric cancer, are characterized by large areas of fibrosis accompanied by cancer‐associated fibroblasts (CAFs). Asporin (ASPN) is a small leucine‐rich proteoglycan highly expressed in CAFs of various tumors. ASPN accelerates CAF migration and invasion, resulting in CAF‐led cancer cell invasion. In addition, ASPN further upregulated the expression of genes specific to a characteristic subgroup of fibroblasts in tumors. These cells were preferentially located at the tumor periphery and could be generated by a unique mechanism involving the CAF‐mediated education of normal fibroblasts (CEFs). In this review, we at first describe recent findings regarding the function of ASPN in the tumor microenvironment, as well as the mechanism involved in the generation of CEFs. CAFs are derived from heterogeneous origins besides resident normal fibroblasts. Among them, CAFs derived from mesothelial cells (mesothelial cell‐derived CAF [MC‐CAFs]) play pivotal roles in peritoneal carcinomatosis. We observed that MC‐CAFs on the surfaces of organs also participate in tumor formation by infiltrating into the parenchyma, promoting local invasion by gastric cancers. This review also highlights the potential functions of macrophages in the formation of MC‐CAFs in gastric cancers, by transfer the contents of cancer cell‐derived extracellular vesicles.
Demographic features, clinical characteristics, and prognostic factors of non-epithelial ovarian tumors at Princess Noorah Oncology Center, National Guard Hospital, Jeddah, Saudi Arabia

Objectives: To reveal the demographic features, prognostic factors, and tumor characteristics of patients with non-epithelial ovarian tumors (NEOTs). Methods: This cross-sectional study was performed using data from all female patients diagnosed with NEOT (germ cell [GC], sex cord–stromal cells [SCSC], sarcoma, and small cell carcinoma) from 2002 to 2017 at Princess Noorah Oncology Center, National Guard Hospital Jeddah, Saudi Arabia. Results: Forty patients with NEOTs were identified. There were equal percentages of GC (45%) and SCSC (45%) origin tumors, and these were the most common histological types. The remaining tumors were sarcomas. Germ cell tumors were more common in younger patients, while SCSC tumors were more frequent in the older age group. Conclusion: The findings for protective and risk factors were inconclusive. Patients with GC tumors had better survival outcomes than those with the other subtypes.
Independent origins of a novel atympanic middle ear system within Chamaeleonidae

The evolution of the vertebrate ear is a complicated story of convergence, co‐option, loss of function, and occasional regaining of said function. An incredible variety of structures has been adopted as sound receptors, but only chameleons are known to have a bony airborne sound receiver. In some chameleons, the pterygoid bone captures sound vibrations and relays them to the inner ear via a connection to the extracolumella. The distribution of this unique hearing system has not been examined across Chamaeleonidae. Here, I report on dissections on 12 species across four genera and describe their middle ear anatomy for the first time. Half of these species were found to have a link between their extracolumella and pterygoid, and ancestral state reconstruction supports four independent acquisitions of this novel sound‐conduction pathway. Species with this pathway tend to have a gular pouch, which seems to produce biotremors and possibly airborne sound, suggesting that this hearing system plays some role in intraspecific communication. Three species were also μ‐CT scanned using enhanced contrast to investigate differences in the musculature surrounding the middle ear cavity. In species with a middle ear connected to the pterygoid, the muscles directly lateral to the pterygoid insert farther anterior onto the mandible, which may serve to minimize dampening of vibrations on the pterygoid. Together, these data suggest that the ear plays a more significant role in the lives of some chameleons than has been recognized, and that parallelism is common in the evolution of the ear.
SARS-CoV-2 Omicron Variant, Lineage BA.1, Is Associated with Lower Viral Load in Nasopharyngeal Samples Compared to Delta Variant

High viral load in upper respiratory tract specimens observed for Delta cases may contributed to its increased infectivity compared to the Alpha variant. Herein, we showed that the RT-PCR Ct values in Health Care Workers sampled within five days after symptom onset were significantly higher for Omicron cases than Delta cases (+2.84 Ct, p=0.008). This result comfort the studies showing that the increased transmissibility of Omicron is related to other mechanisms than higher virus excretion.
MACHINE LEARNING IMPACT ASSESSMENT OF CLIMATE FACTORS ON DAILY COVID-19 CASES

Coronavirus disease 2019 (also known as COVID-19) is a vastly infectious virus instigated by the coronavirus-2, which causes severe acute respiratory illness (SARS-Cov-2). Scientists and researchers are conducting a number of studies to better understand the COVID-19 pandemic's behavioral nature and spread, and machine learning provides useful tools. We used machine learning techniques to study the effect of climate conditions on daily instances of COVID-19 in this study. The study has three main objectives: first, to investigate the most climatic features that could affect the spread of novel COVID-19 cases; second, to assess the influence of government strategies on COVID-19 using our dataset; third, to do a comparative analysis of two different machine learning models, and develop a model to predict accurate response to the most features on COVID-19 spread. The goal of this research is to assist health-care facilities and governments with planning and decision-making. The study compared random forest and artificial neural network models for analysis. In addition, feature importance among the independent variables (climate variables) were identified with the random forest. The study used publicly available datasets of COVID-19 cases from the World Health Organization and climate variables from National Aeronautics and Space Administration websites respectively. Our results showed that relative humidity and solar had significant impact as a feature of weather variables on COVID-19 recorded cases; and that random forest predicted accurate response to the most climatic features on COVID-19 spread. Based on this, we propose the random forest model to predict COVID-19 cases using weather variables.
Albanian Fake News Detection

Recent years have witnessed the vast increase of the phenomenon known as the fake news. Among the main reasons for this increase are the continuous growth of internet and social media usage and the real-time information dissemination opportunity offered by them. Deceiving, misleading content, such as the fake news, especially the type made by and for social media users, is becoming eminently hazardous. Hence, the fake news detection problem has become an important research topic. Despite the recent advances in fake news detection, the lack of fake news corpora for the under-resourced languages is compromising the development and the evaluation of existing approaches in these languages. To fill this huge gap, in this article, we investigate the issue of fake news detection for the Albanian language. In it, we present a new public dataset of labeled true and fake news in Albanian and perform an extensive analysis of machine learning methods for fake news detection. We performed a comprehensive feature engineering and feature selection experiments. In doing so, we explored the Albanian language-related feature categories such as the lexical, syntactic, lying-detection, and psycho-linguistic features. Each article was also modeled in four different ways: with the traditional bag-of-words (BoW) and with three distributed text representations using the state-of-the-art Word2Vec, FastText, and BERT methods. Additionally, we investigated the best combination of features and various types of classification methods. The conducted experiments and obtained results from evaluations are finally used to draw some conclusions. They shed light on the potentiality of the methods and the challenges that the Albanian fake news detection presents.
Morphological and genetic variability of the cryptic Gyrodactylus sphinx and Gyrodactylus gerasevi n. sp. (Platyhelminthes: Monogenea) from the Mediterranean Sea and Black Sea: two new members of the cross-ocean distributed Gyrodactylus orecchiae species group

Abstract Gyrodactylus sphinx Dmitrieva & Gerasev, 2000 is the only species of Gyrodactylus originally described from Aidablennius sphynx (Valenciennes) in the Black Sea. In the present study, monogeneans similar to G. sphinx are reported from the same host and from two other species of Blenniidae from the Black Sea, as well as from the Mediterranean Sea. This study aims to verify the taxonomic status of the specimens found in different hosts and localities, other than the type ones of G. sphinx. Twenty-two measurements of the haptoral structures of 169 gyrodactylids were used for the morphological study. Morphometric variability between different samples was analysed using analysis of variance, multivariate analysis of variance (MANOVA) and principal component analysis (PCA). Molecular studies were carried out using the nuclear internal transcribed spacer 2 and 5.8S ribosomal DNA regions. Network, Bayesian phylogenetic and species delimitation analyses were performed to infer the number of taxonomic units and the phylogeographic relationships occurring within and among them. MANOVA revealed a significant dependence of the morphometry of hamuli and marginal hooks on host species and regions, but a clear differentiation between samples was not confirmed by PCA. Moreover, the ranges of all dimensions overlapped between samples. However, molecular analyses suggested the occurrence of at least two taxonomic entities. The most common entity was present in individuals of the Black and Mediterranean seas, and is described here as Gyrodactylus gerasevi n. sp. , whereas a second entity recognized as a G. sphinx was found only in individuals from two localities off Crimea. The monophyletic cluster grouping of these two species was placed within a large clade that also included a separate sister cluster with seven other species of the Gyrodactylus orecchiae cross-ocean species group.
Lipid-related protein NECTIN2 is an important marker in the progression of carotid atherosclerosis: An intersection of clinical and basic studies

ABSTRACT Background: The nectin cell adhesion molecule 2 (NECTIN2) protein is a cell adhesion molecule involved in lipid metabolism. We aimed to explore the potential role of NECTIN2 in carotid atherosclerosis (CA). Materials and Methods: Patients who underwent carotid endarterectomy (CEA) at the First Affiliated Hospital of Zhengzhou University were enrolled in this study. APOE-/- rats fed western or normal diet were used to model early pathological changes in CA. The relationship between patients’ lipid indices and plaque severity was assessed using ordinal regression analysis. Mendelian randomisation (MR) analysis was used to determine the causal links between low-density lipoprotein cholesterol (LDL-C) and atherosclerosis. After matching analysis of the single-cell transcriptome and microarray data of carotid plaques, NECTIN2 was identified as a key factor affecting CA. The importance of NECTIN2 was further verified by immunofluorescence staining of CEA and APOE-/- rat specimens. Results: A total of 108 patients were included. The traditional lipid indices did not correlate significantly with the plaque severity (P > 0.05). NECTIN2 provided a strong causal link between LDL-C level and CA (MR effect size >0). Deep-sequencing data illustrated that NECTIN2 expression was cell specific. In early-stage CA, NECTIN2 expression was increased in endothelial cells; however, in advanced-stage CA, NECTIN2 was overexpressed in macrophages located in fibrous caps. APOE-/- rat carotid artery and human carotid plaques modelled the entire atherosclerotic process, showing an upregulation of NECTIN2 expression in CA. Conclusions: Lipid-related protein NECTIN2 is a potential marker in CA progression and can potentially be a new therapeutic target for clinical prevention.
Effect of local anti-vascular endothelial growth factor therapy to prevent the formation of stenosis in outflow vein in arteriovenous fistula

ABSTRACT Background and Objectives: Vascular stenosis and angiogenesis are the major causes of short expectancy of arteriovenous fistula (AVF). Increased expression of vascular endothelial growth factor-A (VEGF-A) has been suggested to play an important role in the pathophysiologic process. Anti-VEGF has been proved to be effective on anti-angiogenesis and applied in clinical practice, but its effect on anti-stenosis remains to be verified before it could be applied to prevent stenosis of AVF. This study was aimed to evaluate the effect of local anti-VEGF therapy to prevent the formation of stenosis in the outflow vein in AVF and its mechanism. Methods: Bioinformatics of VEGF-A and its downstream-regulated molecules from the STRING PPI database were analyzed in this study. The biopsy samples from outflow veins of AVF in patients and C57BL/6 mouse models were analyzed to examine the mechanisms of pathologic vascular stenosis associated with VEGF pathways and their potential therapeutic targets. Results: We found that the reduction of VEGF-A could downregulate downstream molecules and subsequently reduce the intimal hyperplasia and abnormal vascular remodeling by analyzing the STRING PPI database. Venous wall thickening, intimal neointima formation, and apoptosis of vascular endothelial cells in the proliferative outflow vein of the AVF were significantly more obvious, and upregulation of expression of VEGF was observed in dysfunctional AVF in patients. In mouse models, the expression of VEGF, Ephrin receptor B4 (EphB4), matrix metalloproteinase (MMP)2, MMP9, tissue inhibitor of metalloproteinase (TIMP)1, TIMP2, and caspase 3 in the control-shRNA surgical group was significantly higher than in the sham group (P < 0.05), and all of these indicators were significantly lower in lentiviral transfection group and Avastin group than in control-shRNA surgical group (P < 0.05) on the 14th day after AVF operation. Conclusion: VEGF expression is significantly increased in vascular endothelial cells in stenosed or occluded outflow veins of dysfunctional AVF. Local injection of Avastin into the adventitia of the proximal outflow vein in autologous AVF procedure has an excellent potential to prevent the subsequent local stenosis of the proximal outflow vein.
Analysis of stability of long-span concrete filled steel tube arched bridge in construction

The two methods for stability analysis,i.e.,the linear and nonlinear buckling analysis,were introduced.Then according to Jiangxi Ji'an Ganjiang concrete-filled steel tubular arch bridge,some aspects about stability were discussed.The results show that the coefficients of stability are smaller when the concrete is filled but not frozen and coefficients of stability increase when the concrete in the tube is frozen;the nonlinear must be considered in the analysis of stability of CFST arch bridge in construction;the material nonlinear has a greater influence than the geometrical nonlinear on the stability of the bridge.
Assessing functional connectivity differences and work-related fatigue in surviving COVID-negative patients

The Coronavirus Disease 2019 (COVID-19) has affected all aspects of life around the world. Neuroimaging evidence suggests the novel coronavirus can attack the central nervous system (CNS), causing cerebro-vascular abnormalities in the brain. This can lead to focal changes in cerebral blood flow and metabolic oxygen consumption rate in the brain. However, the extent and spatial locations of brain alterations in COVID-19 survivors are largely unknown. In this study, we have assessed brain functional connectivity (FC) using resting-state functional MRI (RS-fMRI) in 38 (25 males) COVID patients two weeks after hospital discharge, when PCR negative and 31 (24 males) healthy subjects. FC was estimated using independent component analysis (ICA) and dual regression. When compared to the healthy group, the COVID group demonstrated significantly enhanced FC in the basal ganglia and precuneus networks (family wise error (fwe) corrected, pfwe < 0.05), while, on the other hand, reduced FC in the language network (pfwe < 0.05). The COVID group also experienced higher fatigue levels during work, compared to the healthy group (p < 0.001). Moreover, within the precuneus network, we noticed a significant negative correlation between FC and fatigue scores across groups (Spearman’s ρ = - 0.47, p = 0.001, r2 = 0.22). Interestingly, this relationship was found to be significantly stronger among COVID survivors within the left parietal lobe, which is known to be structurally and functionally associated with fatigue in other neurological disorders. Significance Statement Early neuroimaging studies have mostly focused on structural MRI imaging to report brain abnormalities in acutely ill COVID-19 patients. It is not clear whether functional abnormalities co-exist with structural alterations in patients who have survived the infection and have been discharged from the hospital. A few recent studies have emerged which attempted to address the structural/functional alterations. However, further investigations across different sites are necessary for more conclusive inference. More importantly, fatigue is a highly prevalent symptom among COVID survivors, therefore, the relations of brain imaging abnormalities to fatigue should be investigated. In this study, we try to address these gaps, by collecting imaging data from COVID survivors, now PCR negative, and healthy subjects from a single site – the Indian Institute of Technology (IIT), Delhi, India. Furthermore, this is a continuation of an ongoing study. We have recently shown structural abnormalities and stronger gray matter volume (GMV) correlates of self-reported fatigue in this group of COVID survivors compared to healthy subjects (Hafiz et al., 2022).
Single-cell RNA profiling of Plasmodium vivax-infected hepatocytes reveals parasite- and host- specific transcriptomic signatures and therapeutic targets

The resilience of Plasmodium vivax, the most widely distributed malaria-causing parasite in humans, is attributed to its ability to produce dormant liver forms known as hypnozoites, which can activate weeks, months, or even years after an initial mosquito bite. The factors underlying hypnozoite formation and activation are poorly understood, as is the parasite’s influence on the host hepatocyte. Here, we shed light on transcriptome-wide signatures of both the parasite and the infected host cell by sequencing over 1,000 P. vivax-infected hepatocytes at single-cell resolution. We distinguish between replicating schizonts and hypnozoites at the transcriptional level, identifying key differences in transcripts encoding for RNA-binding proteins associated with cell fate. In infected hepatocytes, we show that genes associated with energy metabolism and antioxidant stress response were upregulated, and those involved in the host immune response downregulated, suggesting both schizonts and hypnozoites alter the host intracellular environment. The transcriptional markers in schizonts, hypnozoites, and infected hepatocytes revealed here pinpoint potential factors underlying dormancy and can inform therapeutic targets against P. vivax liver-stage infection.
Spatiotemporal dissociation of brain network connectivity in salience processing: A simultaneous pupillometry-EEG-fMRI study

The processing of salient stimuli involves a wide range of both bottom-up and top-down processes. Previous neuroimaging studies have identified multiple brain areas and networks for salience processing, including the salience network (SN), dorsal attention network (DAN), and the locus coeruleus-norepinephrine (LC-NE) neuromodulatory system. However, interactions among these networks and the cortico-subcortical systems in salience processing remain unclear. Here, we simultaneously recorded pupillometry, electroencephalogram (EEG), and functional magnetic resonance imaging (fMRI) during an auditory oddball paradigm. Using EEG-informed fMRI analysis, we temporally dissociated the target stimulus evoked activation, allowing us to identify the cascades of cortical areas associated with salience processing. Furthermore, functional connectivity analysis uncovered spatiotemporal functional network organizations of these salience processing neural correlates. Using pupillometry as a psychophysiological marker of LC-NE activity, we also assessed brain-pupil relationships. With state-space modeling of target modulated effective connectivity, we found that the target evoked pupillary response is associated with the network causal couplings from late to early subsystems, as well as the network switching initiated by the SN. These findings indicate that the SN might cooperate with pupil-indexed brainstem neuromodulatory systems, such as the LC-NE system, in the reorganization and dynamic switching of cortical networks, and shed light on the implications of their integrative framework in various cognitive processes and neurological diseases.
Clonal dynamics of SARS-CoV-2-specific T cells in children and adults with COVID-19

Children infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) develop less severe coronavirus disease 2019 (COVID-19) than adults. The mechanisms for the age-specific differences and the implications for infection-induced immunity are beginning to be uncovered. We show by longitudinal multimodal analysis that SARS-CoV-2 leaves a small footprint in the circulating T cell compartment in children with mild/asymptomatic COVID-19 compared to adult household contacts with the same disease severity who had more evidence of systemic T cell interferon activation, cytotoxicity and exhaustion. Children harbored diverse polyclonal SARS-CoV- 2-specific naïve T cells whereas adults harbored clonally expanded SARS-CoV-2-specific memory T cells. More naïve interferon-activated CD4+ T cells were recruited into the memory compartment and recovery was associated with the development of robust CD4+ memory T cell responses in adults but not children. These data suggest that rapid clearance of SARS-CoV-2 in children may compromise their cellular immunity and ability to resist reinfection. HIGHLIGHTS Children have diverse polyclonal SARS-CoV-2-specific naïve T cells Adults have clonally expanded exhausted SARS-CoV-2-specific memory T cells Interferon-activated naïve T cells differentiate into memory T cells in adults but not children Adults but not children develop robust memory T cell responses to SARS-CoV-2