Miracle-dz/UniFAR-FTUs huggingface dataset:
Two-Stage Liver and Tumor Segmentation Algorithm Based on Convolutional Neural Network

The liver is an essential metabolic organ of the human body, and malignant liver tumors seriously affect and threaten human life. The segmentation algorithm for liver and liver tumors is one of the essential branches of computer-aided diagnosis. This paper proposed a two-stage liver and tumor segmentation algorithm based on the convolutional neural network (CNN). In the present study, we used two stages to segment the liver and tumors: liver localization and tumor segmentation. In the liver localization stage, the network segments the liver region, adopts the encoding–decoding structure and long-distance feature fusion operation, and utilizes the shallow features’ spatial information to improve liver identification. In the tumor segmentation stage, based on the liver segmentation results of the first two steps, a CNN model was designed to accurately identify the liver tumors by using the 2D image features and 3D spatial features of the CT image slices. At the same time, we use the attention mechanism to improve the segmentation performance of small liver tumors. The proposed algorithm was tested on the public data set Liver Tumor Segmentation Challenge (LiTS). The Dice coefficient of liver segmentation was 0.967, and the Dice coefficient of tumor segmentation was 0.725. The proposed algorithm can accurately segment the liver and liver tumors in CT images. Compared with other state-of-the-art algorithms, the segmentation results of the proposed algorithm rank the highest in the Dice coefficient.
Metabolomics of Chlorophylls and Carotenoids: Analytical Methods and Metabolome-Based Studies

Chlorophylls and carotenoids are two families of antioxidants present in daily ingested foods, whose recognition as added-value ingredients runs in parallel with the increasing number of demonstrated functional properties. Both groups include a complex and vast number of compounds, and extraction and analysis methods evolved recently to a modern protocol. New methodologies are more potent, precise, and accurate, but their application requires a better understanding of the technical and biological context. Therefore, the present review compiles the basic knowledge and recent advances of the metabolomics of chlorophylls and carotenoids, including the interrelation with the primary metabolism. The study includes material preparation and extraction protocols, the instrumental techniques for the acquisition of spectroscopic and spectrometric properties, the workflows and software tools for data pre-processing and analysis, and the application of mass spectrometry to pigment metabolomics. In addition, the review encompasses a critical description of studies where metabolomics analyses of chlorophylls and carotenoids were developed as an approach to analyzing the effects of biotic and abiotic stressors on living organisms.
TRP Channels as Sensors of Aldehyde and Oxidative Stress

The transient receptor potential (TRP) cation channel superfamily comprises more than 50 channels that play crucial roles in physiological processes. TRP channels are responsive to several exogenous and endogenous biomolecules, with aldehydes emerging as a TRP channel trigger contributing to a cellular cascade that can lead to disease pathophysiology. The body is not only exposed to exogenous aldehydes via tobacco products or alcoholic beverages, but also to endogenous aldehydes triggered by lipid peroxidation. In response to lipid peroxidation from inflammation or organ injury, polyunsaturated fatty acids undergo lipid peroxidation to aldehydes, such as 4-hydroxynonenal. Reactive aldehydes activate TRP channels via aldehyde-induced protein adducts, leading to the release of pro-inflammatory mediators driving the pathophysiology caused by cellular injury, including inflammatory pain and organ reperfusion injury. Recent studies have outlined how aldehyde dehydrogenase 2 protects against aldehyde toxicity through the clearance of toxic aldehydes, indicating that targeting the endogenous aldehyde metabolism may represent a novel treatment strategy. An addition approach can involve targeting specific TRP channel regions to limit the triggering of a cellular cascade induced by aldehydes. In this review, we provide a comprehensive summary of aldehydes, TRP channels, and their interactions, as well as their role in pathological conditions and the different therapeutical treatment options.
The Bacterial Diversity of Spontaneously Fermented Dairy Products Collected in Northeast Asia

Spontaneously fermented dairy products have a long history, and present diverse microorganisms and unique flavors. To provide insight into the bacterial diversity, 80 different types of spontaneously fermented dairy product samples’ sequence data that were downloaded from MG-RAST and NCBI and 8 koumiss and 4 shubat were sequenced by the PacBio SMRT sequencing platform. All samples including butter, sour cream, cottage cheese, yogurt, koumiss, shubat, and cheese, were collected from various regions in Russia, Kazakhstan, Mongolia and Inner Mongolia (China). The results revealed that Firmicutes and Proteobacteria were the most dominant phyla (>99%), and 11 species were identified with a relative abundance exceeding 1%. Furthermore, Streptococcus salivarius, Lactobacillus helveticus, Lactobacillus delbrueckii, Enterobacter xiangfangensis, and Acinetobacter baumannii were the primary bacterial species in the fermented dairy product samples. Principal coordinates analysis showed that koumiss and shubat stood out from the other samples. Moreover, permutational ANOVA tests revealed that the types of fermented dairy products and geographical origin significantly affected microbial diversity. However, different processing techniques did not affect microbial diversity. In addition, results of hierarchical clustering and canonical analysis of the principal coordinates were consistent. In conclusion, geographical origin and types of fermented dairy products determined the bacterial diversity in spontaneously fermented dairy product samples.
Comparison of Epidermal Barrier Integrity in Adults with Classic Atopic Dermatitis, Atopic Prurigo and Non-Atopic Prurigo Nodularis

Simple Summary Atopic dermatitis, also called neurodermatitis, is one of the best-known chronic inflammatory skin diseases with eczema, strong itch and dry skin. It is based on an impaired skin barrier with changes in the fats and proteins of the horny layer, which leads to a disturbed water balance. Prurigo nodularis is a less common and intractable chronic skin disease with very itchy nodules. It can be associated with atopic dermatitis (so called atopic prurigo) or with many other diseases. The aim of this study was to compare these three skin diseases classic atopic dermatitis, atopic prurigo and non-atopic prurigo nodularis with healthy control subjects with regard to their skin barrier. In all three disease groups, we then found marked disease severity, reduced water content and increased water loss through the skin, thickening and inflammation of the skin, altered levels of certain proteins and reduced fat layers, all of which demonstrate a severe disturbance of the skin barrier. The main therapeutic consequence is that basic barrier repair, as established for patients with atopic dermatitis in the form of consistent skincare, could also be crucial for patients with non-atopic prurigo nodularis due to this verified skin barrier damage. Abstract A deficient epidermal barrier is a key feature of atopic dermatitis (AD) and comprises altered lipid and protein content and composition of the stratum corneum resulting in disturbed water balance. Clinically, eczematous lesions on dry skin and pruritus develop. Pruritic nodules occur in prurigo nodularis (PN), another chronic skin disease, which can be associated with atopy. We aimed at comparing the three clinical pictures, classic AD, atopic prurigo (AP), and non-atopic PN, to healthy controls regarding the epidermal barrier. We determined clinical parameters and performed biophysical measurements, histology/immunohistochemistry, electron microscopy, and molecular biological analysis. We found distinctively elevated clinical scores, reduced hydration and increased transepidermal water loss, epidermal hyperplasia and inflammation reduced filaggrin and increased loricrin and involucrin expression, as well as reduced intercellular lipid lamellae in all three disease groups. These findings show a severe disruption in epidermal barrier structure and function in all three disorders so that epidermal barrier impairment is now proven not only for AD but also for PN.
Nuclear Dynamics and Chromatin Structure: Implications for Pancreatic Cancer

Changes in nuclear shape have been extensively associated with the dynamics and functionality of cancer cells. In most normal cells, nuclei have a regular ellipsoid shape and minimal variation in nuclear size; however, an irregular nuclear contour and abnormal nuclear size is often observed in cancer, including pancreatic cancer. Furthermore, alterations in nuclear morphology have become the ‘gold standard’ for tumor staging and grading. Beyond the utility of altered nuclear morphology as a diagnostic tool in cancer, the implications of altered nuclear structure for the biology and behavior of cancer cells are profound as changes in nuclear morphology could impact cellular responses to physical strain, adaptation during migration, chromatin organization, and gene expression. Here, we aim to highlight and discuss the factors that regulate nuclear dynamics and their implications for pancreatic cancer biology.
DJ-1 Acts as a Scavenger of α-Synuclein Oligomers and Restores Monomeric Glycated α-Synuclein

Glycation of α-synuclein (αSyn), as occurs with aging, has been linked to the progression of Parkinson’s disease (PD) through the promotion of advanced glycation end-products and the formation of toxic oligomers that cannot be properly cleared from neurons. DJ-1, an antioxidative protein that plays a critical role in PD pathology, has been proposed to repair glycation in proteins, yet a mechanism has not been elucidated. In this study, we integrate solution nuclear magnetic resonance (NMR) spectroscopy and liquid atomic force microscopy (AFM) techniques to characterize glycated N-terminally acetylated-αSyn (glyc-ac-αSyn) and its interaction with DJ-1. Glycation of ac-αSyn by methylglyoxal increases oligomer formation, as visualized by AFM in solution, resulting in decreased dynamics of the monomer amide backbone around the Lys residues, as measured using NMR. Upon addition of DJ-1, this NMR signature of glyc-ac-αSyn monomers reverts to a native ac-αSyn-like character. This phenomenon is reversible upon removal of DJ-1 from the solution. Using relaxation-based NMR, we have identified the binding site on DJ-1 for glycated and native ac-αSyn as the catalytic pocket and established that the oxidation state of the catalytic cysteine is imperative for binding. Based on our results, we propose a novel mechanism by which DJ-1 scavenges glyc-ac-αSyn oligomers without chemical deglycation, suppresses glyc-ac-αSyn monomer–oligomer interactions, and releases free glyc-ac-αSyn monomers in solution. The interference of DJ-1 with ac-αSyn oligomers may promote free ac-αSyn monomer in solution and suppress the propagation of toxic oligomer and fibril species. These results expand the understanding of the role of DJ-1 in PD pathology by acting as a scavenger for aggregated αSyn.
Antibiotics- and Heavy Metals-Based Titanium Alloy Surface Modifications for Local Prosthetic Joint Infections

Prosthetic joint infection (PJI) is the second most common cause of arthroplasty failure. Though infrequent, it is one of the most devastating complications since it is associated with great personal cost for the patient and a high economic burden for health systems. Due to the high number of patients that will eventually receive a prosthesis, PJI incidence is increasing exponentially. As these infections are provoked by microorganisms, mainly bacteria, and as such can develop a biofilm, which is in turn resistant to both antibiotics and the immune system, prevention is the ideal approach. However, conventional preventative strategies seem to have reached their limit. Novel prevention strategies fall within two broad categories: (1) antibiotic- and (2) heavy metal-based surface modifications of titanium alloy prostheses. This review examines research on the most relevant titanium alloy surface modifications that use antibiotics to locally prevent primary PJI.
QTL Mapping and GWAS Reveal the Genetic Mechanism Controlling Soluble Solids Content in Brassica napus Shoots

Oilseed-vegetable-dual-purpose (OVDP) rapeseed can effectively alleviate the land contradiction between crops and it supplements vegetable supplies in winter or spring. The soluble solids content (SSC) is an important index that is used to evaluate the quality and sugar content of fruits and vegetables. However, the genetic architecture underlying the SSC in Brassica napus shoots is still unclear. Here, quantitative trait loci (QTLs) for the SSC in B. napus shoots were investigated by performing linkage mapping using a recombinant inbred line population containing 189 lines. A germplasm set comprising 302 accessions was also used to conduct a genome-wide association study (GWAS). The QTL mapping revealed six QTLs located on chromosomes A01, A04, A08, and A09 in two experiments. Among them, two major QTLs, qSSC/21GY.A04-1 and qSSC/21NJ.A08-1, accounted for 12.92% and 10.18% of the phenotypic variance, respectively. In addition, eight single-nucleotide polymorphisms with phenotypic variances between 5.62% and 10.18% were identified by the GWAS method. However, no locus was simultaneously identified by QTL mapping and GWAS. We identified AH174 (7.55 °Brix and 7.9 °Brix), L166 (8.9 °Brix and 8.38 °Brix), and L380 (8.9 °Brix and 7.74 °Brix) accessions can be used as superior parents. These results provide valuable information that increases our understanding of the genetic control of SSC and will facilitate the breeding of high-SSC B. napus shoots.
Antibiotic Resistance of Staphylococci from Bulk-Tank Milk of Sheep Flocks: Prevalence, Patterns, Association with Biofilm Formation, Effects on Milk Quality, and Risk Factors

Simple Summary This work investigated the presence of staphylococci resistant to antibiotics in the raw milk produced in sheep farms, which is intended for human consumption, in an extensive study performed throughout Greece. In 31% of flocks, staphylococci resistant to at least one antibiotic were recovered; in 12% of flocks, staphylococci resistant to at least three different antibiotic classes were found. Factors potentially associated with recovery of resistant isolates were the lack of experience by farmers (<5 years), the period immediately post lambing, and the intensive management system applied in the flocks. Abstract The objectives of this work were to study prevalence and characteristics of resistance to antibiotics of staphylococcal isolates from the bulk-tank milk of sheep flocks across Greece, to assess possible associations of the presence of antibiotic resistance with the quality of milk in these flocks and to evaluate flock-related factors potentially associated with antibiotic resistance among these isolates. A cross-sectional study was performed in 325 sheep flocks in Greece. Bulk-tank milk samples were collected for bacteriological examination; staphylococcal isolates were evaluated for resistance to 20 antibiotics. Oxacillin-resistant staphylococcal isolates, isolates resistant to any antibiotic, and multi-resistant isolates were recovered from 8.0%, 30.5%, and 12.0% of flocks, respectively. Of 232 isolates, 11.6% were resistant to oxacillin, 46.1% were resistant to at least one antibiotic, and 16.4% were multi-resistant. Resistance was seen more frequently among coagulase-negative (50.6%) than among Staphylococcus aureus (31.5%) isolates. Resistance was more frequent against penicillin and ampicillin (34.1% of isolates), clindamycin (17.7%), and fosfomycin (14.2%). An association was found between biofilm formation by staphylococci and resistance to fosfomycin. For recovery of oxacillin-resistant isolates, the lack of experience by farmers emerged as a significant factor; respective factors for the isolation of staphylococci resistant to any antibiotic or multi-resistant isolates were the early stage of the lactation period (0th–1st month) and the intensive management system applied in the flocks, respectively.
Socioeconomic Status, Institutional Power, and Body Mass Index among Chinese Adults

Despite the vast literature on the socioeconomic status (SES) gradient of obesity among adult people, no study has investigated the relationship between institutional power and body mass index. Using national survey data from the “China Labor-force Dynamics Survey 2016” (CLDS 2016), multistage cluster-stratified probability proportional to size (PPS) sampling was employed to select cases from 29 provinces, cities, and autonomous regions in China. This study adopts an institutional approach to explore the influences of SES and institutional power on the state of being overweight or severely overweight (obese) among Chinese adults. It is shown that SES has a non-linear influence on being overweight or obese, higher education has a negative effect on being overweight or obese, income has an inverted U-shaped effect on being overweight or obese, and having a managerial or administrative job has a positive effect on being overweight but less so on obesity. These findings reveal that disparities in health outcome and risks are due to inequality in SES. The work unit is a stronger predictor of adults being overweight or obese than occupation. Working in the public sector has a positive effect on being overweight relative to working in the private sector, and only state institutions and government departments have a positive association with obesity. Our results indicate that institutional structure still has effects on individuals’ life chances in the era of China’s market transition.
Nutritional Metabolites of Red Pigmented Lettuce (Lactuca sativa) Germplasm and Correlations with Selected Phenotypic Characters

Lettuce is an important dietary source of bioactive phytochemicals. Screening and identification of the health beneficial metabolites and evaluating the relationships with phenotypic characters can help consumers adjust their preferences for lettuce plant types. Thus, we explored the major health-beneficial individual metabolites and antioxidant potential of 113 red pigmented lettuce leaf samples. A UV–Vis spectrophotometer and UPLC-DAD-QTOF/MS (TQ/MS) instruments were used for the identification and quantification of metabolites and antioxidant activity accordingly. The metabolites were quantified against their corresponding external standards. The contents of metabolites varied significantly among lettuce samples. Cyanidin 3-O-(6″-O-malonyl)glucoside (4.7~5013.6 μg/g DW), 2,3-di-O-caffeoyltartaric acid (337.1~19,957.2 μg/g DW), and quercetin 3-O-(6″-O-malonyl)glucoside (45.4~31,121.0 μg/g DW) were the most dominant in red pigmented lettuce samples among anthocyanins, hydroxycinnamoyl derivatives, and flavonols, respectively. Lettuces with dark and very dark red pigmented leaves, circular leaf shape, a strong degree of leaf undulation, and highly dense leaf incisions were found to have high levels of flavonoids and hydroxycinnamoyl derivatives. Principal component analysis was used to investigate similarities and/or differences between samples, and the partial least square discriminant analysis classified them into known groups. The key variables that contributed highly were determined. Our report provides critical data on the bioactive constituents of red pigmented lettuce to breeders developing varieties with enhanced bioactive compounds and to nutraceutical companies developing nutrient dense foods and pharmaceutical formulations.
Autophagy and the Lysosomal System in Cancer

Autophagy and the lysosomal system, together referred to as the autophagolysosomal system, is a cellular quality control network which maintains cellular health and homeostasis by removing cellular waste including protein aggregates, damaged organelles, and invading pathogens. As such, the autophagolysosomal system has roles in a variety of pathophysiological disorders, including cancer, neurological disorders, immune- and inflammation-related diseases, and metabolic alterations, among others. The autophagolysosomal system is controlled by TFEB, a master transcriptional regulator driving the expression of multiple genes, including autophagoly sosomal components. Importantly, Reactive Oxygen Species (ROS) production and control are key aspects of the physiopathological roles of the autophagolysosomal system, and may hold a key for synergistic therapeutic interventions. In this study, we reviewed our current knowledge on the biology and physiopathology of the autophagolysosomal system, and its potential for therapeutic intervention in cancer.
Virus-Induced Tumorigenesis and IFN System

Simple Summary This review aims to collect recent studies on the complex relationship between the host innate response to oncogenic viruses (i.e., HPV, HTLV-1, MCPyV, JCPyV, Herpesviruses, HBV, HCV) and tumorigenic processes by focusing mainly on regulatory crosstalks between viral components and the type I IFN system. It is a picture of new mechanisms by which type I IFNs may be affected and, in turn, affect signaling pathways to mediate anti-proliferative and antiviral responses in virus-induced tumorigenic context. Studies on cellular and viral miRNAs machinery, as well as cellular communication and microenvironment modification via classical secretion mechanisms and extracellular vesicle-mediated delivery are described. Abstract Oncogenic viruses favor the development of tumors in mammals by persistent infection and specific cellular pathways modifications by deregulating cell proliferation and inhibiting apoptosis. They counteract the cellular antiviral defense through viral proteins as well as specific cellular effectors involved in virus-induced tumorigenesis. Type I interferons (IFNs) are a family of cytokines critical not only for viral interference but also for their broad range of properties that go beyond the antiviral action. In fact, they can inhibit cell proliferation and modulate differentiation, apoptosis, and migration. However, their principal role is to regulate the development and activity of most effector cells of the innate and adaptive immune responses. Various are the mechanisms by which IFNs exert their effects on immune cells. They can act directly, through IFN receptor triggering, or indirectly by the induction of chemokines, the secretion of further cytokines, or by the stimulation of cells useful for the activation of particular immune cells. All the properties of IFNs are crucial in the host defense against viruses and bacteria, as well as in the immune surveillance against tumors. IFNs may be affected by and, in turn, affect signaling pathways to mediate anti-proliferative and antiviral responses in virus-induced tumorigenic context. New data on cellular and viral microRNAs (miRNAs) machinery, as well as cellular communication and microenvironment modification via classical secretion mechanisms and extracellular vesicles-mediated delivery are reported. Recent research is reviewed on the tumorigenesis induced by specific viruses with RNA or DNA genome, belonging to different families (i.e., HPV, HTLV-1, MCPyV, JCPyV, Herpesviruses, HBV, HCV) and the IFN system involvement.