Miracle-dz/UniFAR-FTUs huggingface dataset:
Salivary Proinflammatory Cytokines IL-1β, IL-6 and TNF Decrease With Age

Objective to analyze salivary concentrations interleukin-1β (IL-1β), 6 (IL-6) and tumor necrosis factor (TNF) according to age in healthy subjects to determine baseline inflammatory state of the oral mucosa in elderly subjects, who are at higher risk of developing inflammation-related diseases. Materials and methods sixty-four healthy volunteers were divided into groups according to age: 20-39 (G1; n=20); 40-59 (G2; n=24); 60-80 years (G3; n=20). Their stomatognathic system and periodontal status were assessed; consumption of food sources of fatty acids (FA) was evaluated using a validated food frequency questionnaire. IL-1β, IL-6, and TNF salivary levels were determined (ELISA) in mixed unstimulated saliva. Kruskal Wallis and Spearman’s correlation tests were applied (p<0.05). Results salivary IL-1β and TNF levels were lower in G2 (p=0.001) and G3 (p<0.001) than in G1; IL-6 levels were lower in G3 than in G2 and G1 (p= <0.001). IL-1β showed the highest concentration in all groups (p<0.001). No statistically significant differences in salivary cytokine levels were observed on sex in any of the groups. Associations were observed between salivary cytokines and consumption of some foods containing FA. Conclusion salivary concentration of proinflammatory cytokines decreased with age. It could be influenced by ageing-related changes. In addtition, the baseline inflammatory state of the oral mucosa would appear to be influenced by dietary intake of sources of anti-inflammatory FA. Clinical relevance the knowledge about inflammatory state of the oral mucosa, as determined by salivary cytokine concentrations, could be useful for understanding and prevention of developing inflammation-related diseases.
Candidate Genes Underlying Wolbachia-Associated Plastic Recombination Revealed by Ovarian Transcriptomics of D. melanogaster

Phenotypic plasticity is prevalent in nature and can facilitate the acclimation of organisms to changing environments. Recombination rate is plastic in a diversity of organisms and under a variety of stressful conditions. However, the recent finding that Wolbachia pipientis induces plastic recombination in Drosophila melanogaster was surprising because Wolbachia is not strictly considered a stressor to this host. We investigate the molecular mechanisms of Wolbachia-associated plastic recombination by comparing the ovarian transcriptomes of D. melanogaster infected and uninfected with Wolbachia. Our data suggest that infection explains a small amount of transcriptional variation but specifically affects genes related to cell cycle, translation, and metabolism. We also find enrichment of cell division and recombination processes among genes with infection-associated differential expression. Broadly, the transcriptomic changes identified in this study provide insight for the mechanisms of microbe-mediated plastic recombination, an important but poorly understood facet of host-microbe dynamics. Significance Statement Though it is documented that Wolbachia is associated with increased recombination in D. melanogaster, the underlying mechanisms remain unknown. Here we use ovarian transcriptomics in Wolbachia-infected and uninfected flies to identify candidate genes underlying Wolbachia-associated plastic recombination. We find that infection alters ovarian gene expression in subtle ways, and also identify exciting candidate genes for functional analysis in subsequent work. These candidate genes may be the first step in determining the molecular mechanisms underlying Wolbachia-associated plastic recombination. Moreover, our data contribute to the growing body of knowledge surrounding how Wolbachia affects host gene expression, and highlights how context-dependent these effects are.
The Toll and Imd pathway, the complement system and lectins during immune response of the nemertean Lineus ruber

Innate immunity is the first line of defense against pathogens. In animals, the Toll pathway, the Imd pathway, the complement system, and lectins are well-known mechanisms involved in innate immunity. Although these pathways and systems are well understood in vertebrates and arthropods, they are understudied in other invertebrates. In order to shed light on immunity in the nemertean Lineus ruber, we performed a transcriptomic survey and identified the main components of the Toll pathway (e.g. myD88, dorsal/dif/NFκB-p65), the Imd pathway (e.g. imd, relish/NFκB-p105/100), the complement system (e.g. C3, cfb) and some lectins (FreD-Cs and C-lectins). In situ hybridization showed that TLRβ1, TLRβ2 and imd and are expressed in the nervous system, the complement gene C3-1 is expressed in the gut and the lectins in the nervous system, the blood, and the gut. To reveal their potential role in defense mechanisms, we performed immune challenge experiments, in which Lineus ruber specimens were exposed to the gram-negative bacteria Vibrio diazotrophicus. Our results show the upregulation of specific components of the Toll pathway (TLRα3, TLRβ1, and TLRβ2), the complement system (C3-1), and lectins (c-lectin2 and fred-c5). Therefore, similarly to what occurs in other invertebrates, our study shows that components of the Toll pathway, the complement system and lectins are involved in the immune response in the nemertean Lineus ruber. The presence of these pathways and systems in Lineus ruber, but also in other spiralians, in protostomes and in deuterostomes suggest that these pathways and systems were involved in the immune response in the stem species of Bilateria.
Drosophila Keap1 oxidative/xenobiotic response factor interacts with B-type lamin to regulate nuclear lamina and heterochromatin

The essential function of the Keap1-Nrf2 pathway in mediating transcriptional response to xenobiotic and oxidative stimuli has been well established. However, the mechanisms whereby Keap1 and Nrf2 regulate developmental genes remains unclear. We hypothesized that Drosophila Keap1 (dKeap1) and Nrf2 (CncC) proteins regulate transcription through controlling high-order chromatin structure. Here, we describe evidence supporting that dKeap1 can regulate chromatin through interaction with lamin, the intermediate filament proteins that form nuclear lamina and organize the overall chromatin architecture. dKeap1 and lamin Dm0, the B-type lamin in Drosophila, interact with each other and form complexes in the nucleus. Overexpression of dKeap1 resulted in a redistribution of lamin Dm0 to the intra-nuclear area and consistently, caused a spreading of the heterochromatin marker H3K9me2 from the pericentromeric region to chromosome arms. Overexpression of dKeap1 fusion proteins in the dKeap1 null background significantly disrupted the nuclear lamina morphology, indicating that dKeap1 is required for the maintenance of a normal nuclear lamina. Knock down of dKeap1 partially rescued the lethality caused by lamin Dm0 overexpression, suggesting that dKeap1 and lamin Dm0 function in the same pathway during development. Taken together, these results support a model where dKeap1 regulates chromatin structure and developmental transcription through interaction with lamin proteins, revealing a novel epigenetic function of the Keap1 oxidative/xenobiotic response factor.
Bacterial lipopolysaccharide modulates immune response in the colorectal tumor microenvironment

Immune responses can have opposing effects in colorectal cancer (CRC), the balance of which may determine whether a cancer regresses, progresses, or potentially metastasizes. These effects are evident in CRC consensus molecular subtypes (CMS) where both CMS1 and CMS4 contain immune infiltrates yet have opposing prognoses. The microbiome has previously been associated with CRC and immune response in CRC but has largely been ignored in the CRC subtype discussion. We used CMS subtyping on surgical resections from patients and aimed to determine the contributions of the microbiome to the pleiotropic effects evident in immune-infiltrated subtypes. We integrated host gene-expression and meta-transcriptomic data to determine the link between immune characteristics and microbiome contributions in these subtypes and identified lipopolysaccharide (LPS) binding as a potential functional mechanism. We identified candidate bacteria with LPS properties that could affect immune response, and tested the effects of their LPS on cytokine production of peripheral blood mononuclear cells (PBMCs). We focused on Fusobacterium periodonticum and Bacteroides fragilis in CMS1, and Porphyromonas asaccharolytica in CMS4. Treatment of PBMCs with LPS isolated from these bacteria showed that F. periodonticum stimulates cytokine production in PBMCs while both B. fragilis and P. asaccharolytica had an inhibitory effect. Furthermore, LPS from the latter two species can inhibit the immunogenic properties of F. periodonticum LPS when co-incubated with PBMCs. We propose that different microbes in the CRC tumor microenvironment can alter the local immune activity, with important implications for prognosis and treatment response.
The localization of PHRAGMOPLAST ORIENTING KINESIN1 at the division site depends on the microtubule-binding proteins TANGLED1 and AUXIN-INDUCED IN ROOT CULTURES9 in Arabidopsis

Abstract Proper plant growth and development require spatial coordination of cell divisions. Two unrelated microtubule-binding proteins, TANGLED1 (TAN1) and AUXIN-INDUCED IN ROOT CULTURES9 (AIR9), are together required for normal growth and division plane orientation in Arabidopsis (Arabidopsis thaliana). The tan1 air9 double mutant has synthetic growth and division plane orientation defects, while single mutants lack obvious defects. Here we show that the division site-localized protein, PHRAGMOPLAST ORIENTING KINESIN1 (POK1), was aberrantly lost from the division site during metaphase and telophase in the tan1 air9 mutant. Since TAN1 and POK1 interact via the first 132 amino acids of TAN1 (TAN11–132), we assessed the localization and function of TAN11–132 in the tan1 air9 double mutant. TAN11–132 rescued tan1 air9 mutant phenotypes and localized to the division site during telophase. However, replacing six amino-acid residues within TAN11–132, which disrupted the POK1–TAN1 interaction in the yeast-two-hybrid system, caused loss of both rescue and division site localization of TAN11–132 in the tan1 air9 mutant. Full-length TAN1 with the same alanine substitutions had defects in phragmoplast guidance and reduced TAN1 and POK1 localization at the division site but rescued most tan1 air9 mutant phenotypes. Together, these data suggest that TAN1 and AIR9 are required for POK1 localization, and yet unknown proteins may stabilize TAN1–POK1 interactions.
Prostate Tumorigenesis Induced by PTEN Deletion Involves Prostate Tumorigenesis Induced by PTEN Deletion Involves Estrogen Receptor beta Repression Estrogen Receptor beta Repression

The role of ER b in prostate cancer is unclear, although loss of ER b is associated with aggressive disease. Given that mice deﬁcient in ER b do not develop prostate cancer, we hypothesized that ER b loss occurs as a consequence of tumorigenesis caused by other oncogenic mechanisms and that its loss is necessary for tumorigenesis. In support of this hypothesis, we found that ER b is targeted for repression in prostate cancer caused by PTEN deletion and that loss of ER b is important for tumor formation. ER b transcription is repressed by BMI-1, which is induced by PTEN deletion and important for prostate tumorigenesis. This ﬁnding provides a mechanism for how ER b expression is regulated in prostate cancer. Repression of ER b contributes to tumorigenesis because it enables HIF-1/VEGF signaling that sustains BMI-1 expression. These data reveal a positive feedback loop that is activated in response to PTEN loss and sustains BMI-1.
MHC Class I Molecules Presented by Contemporary Human and A Comparative Analysis of Viral Peptides

Kes¸mir* Genetic factors such as the MHC inﬂuence the immunocompetence of an individual. MHC genes are the most polymorphic genes in primates, which is often interpreted as an adaptation to establish good T cell responses to a wide range of (evolving) pathogens. Chimpanzee MHC (Patr) genes are less polymorphic than human MHC (HLA) genes, which is surprising because chimpanzee is the older species of the two and is therefore expected to display more variation. To quantify the effect of the reduced polymorphism, we compared the peptide binding repertoire of human and chimpanzee MHC molecules. Using a peptide-MHC binding predictor and proteomes of >900 mammalian viruses, we show that, at the population level, the total peptide binding repertoire of Patr-A molecules is ∼ 36% lower than that of their human counterparts, whereas the reduction of the peptide binding repertoire of the Patr-B locus is only 15%. In line with these results, different Patr-A molecules turn out to have largely overlapping peptide binding repertoires, whereas the Patr-B molecules are more distinct from each other. This difference is somewhat less apparent at the individual level, where we found that only 25% of the viruses are signiﬁcantly better presented by “simulated” humans with heterozygous HLA-A and -B loci. Taken together, our results indicate that the Patr-B molecules recovered more after the selective sweep, whereas the Patr-A locus shows the most signs of the selective sweep with regard to its peptide binding repertoire. The Journal of Immunology , 2011, 187: 5995–6001.
Solving Airline Crew-Scheduling Problem with imprecise service time using Genetic Algorithm

This paper deals with a special case of the well known airline crew-scheduling problem which has been formulated considering the day-to-day assignment of the technical crew members to their legal round-trip rotations for all the scheduled flights connecting only two cities that will minimize the overall service times (including rest times) of all the crews. In this problem, the service times of crews from their starting city to another city are imprecise in nature. This impreciseness is represented by intervals. For solving this problem, two different methods are proposed: (a) an elitist genetic algorithm (EGA) with interval valued fitness function and (b) EGA approach after converting it into a multi-objective assignment problem with crisp objectives considering the centre and width values of the corresponding intervals. However, for the second method, at first, the multi-objective assignment problem is transformed into a single objective optimization problem with the help of Global Criterion Method (GCM) and then the reformulated problem is solved by EGA. The experimental results of the proposed methods to a realistic airline crew-scheduling problem are compared. Finally, the effect of changes of different genetic parameters on success rate of both the methods, computation times and function evaluations is observed by sensitivity analysis taking one at a time.
ISSN: 2525-8761

Additive manufacturing, specifically 3D printing (3DP), is a trend of great relevance in industry 4.0. The objective of this work is presented as a systematic review of the available literature to define the main methods and standards towards analyzing the material properties, 3D printing filament extrusion variables, and polylactic acid (PLA) recycling. The research used the methodology of a mixed explanatory sequential review based on studies already published in books and journals. These data have relevant information to serve as a guide for the recycling, extrusion, and 3D printing of the PLA.
Posteroanterior Chest X-ray Image Classification with a Multilayer 1D Convolutional Neural Network-Based Classifier for Cardiomegaly Level Screening

Palpitations, chest tightness, and shortness of breath are early indications of cardiomegaly, which is an asymptomatic disease. Their causes and treatment strategies are different due to differing indications. Hence, early screening of cardiomegaly levels can be used to make a strategy for administering drugs and surgical treatments. In this study, we will establish a multilayer one-dimensional (1D) convolutional neural network (CNN)-based classifier for automatic cardiomegaly level screening based on chest X-ray (CXR) image classification in frontal posteroanterior view. Using two-round 1D convolutional processes in the convolutional pooling layer, two-dimensional (2D) feature maps can be converted into feature signals, which can enhance their characteristics for identifying normal condition and cardiomegaly levels. In the classification layer, a classifier based on gray relational analysis, which has a straightforward mathematical operation, is used to screen the cardiomegaly levels. Based on the collected datasets from the National Institutes of Health CXR image database, the proposed multilayer 1D CNN-based classifier with K-fold cross-validation has promising results for the intended medical purpose, with precision of 97.80%, recall of 98.20%, accuracy of 98.00%, and F1 score of 0.9799.
Texture Analysis in Diagnosing Skin Pigmented Lesions in Normal and Polarized Light—A Preliminary Report

The differential diagnosis of benign nevi (BN), dysplastic nevi (DN), and melanomas (MM) represents a considerable clinical problem. These lesions are similar in clinical examination but have different prognoses and therapeutic management techniques. A texture analysis (TA) is a mathematical and statistical analysis of pixel patterns of a digital image. This study aims to demonstrate the relationship between the TA of digital images of pigmented lesions under polarized and non-polarized light and their histopathological diagnosis. Ninety pigmented lesions of 76 patients were included in this study. We obtained 166 regions of interest (ROI) images for MM, 166 for DN, and 166 for BN. The pictures were taken under polarized and non-polarized light. Selected image texture features (entropy and difference entropy and long-run emphasis) of ROIs were calculated. Those three equations were used to construct the texture index (TI) and bone index (BI). All of the presented features distinguish melanomas, benign and dysplastic lesions under polarized light very well. In non-polarized images, only the long-run emphasis moment and both indices effectively differentiated nevi from melanomas. TA is an objective method of assessing pigmented lesions and can be used in automatic diagnostic systems.
A Scientometric Analysis of Predicting Methods for Identifying the Environmental Risks Caused by Landslides

The effects of a landslide can represent a very big problem, including the death of people, damage to the land, environmental pollution and the loss of natural resources. Landslides are the most important medium for transferring sediments and polluting waterways by earth and organic materials. An excess of sediments reduces the quality of fish habitat and the potability of water. In order to understand landslides in depth, a thorough study was conducted using a scientometric analysis, as well as a thorough practical examination of landslide analysis and monitoring techniques. This review focused on methods used for landslide analysis, including physical models requiring easily prepared event-based landslide inventory, probabilistic methods which are useful for both shallow and earthquake-based landslides, and landslide monitoring performed by remote sensing techniques, which provide data helpful for prediction, monitoring and mapping. The fundamental principles of each method are described in terms of the method used, and its advantages, and limits. People and infrastructure are at danger from landslides caused by heavy rain, so this report highlights landslide-prone regions and considers the analysis methods for landslides used in these countries, with a view to identifying mitigation measures for coping with landslide risks in hilly areas. Furthermore, future landslide research possibilities, as well as possible modeling methods, are addressed. The report summarizes some landslide prediction and monitoring techniques used in landslide-prone countries which can help inform researchers seeking to protect the public from danger in landslide areas.
Responses of Cell Wall Components to Low Nitrogen in Rapeseed Roots

: Rapeseed ( Brassica napus L.) is a major oil crop in China, with the world’s largest planted area and total yield. Rapeseed has a high demand for nitrogen (N), and nitrogen deﬁciency in soil is an important limiting factor for rapeseed production. However, rapeseed responds to N deprivation by regulating its own morphology, structure, and physiology. We carried out the current experiment by utilizing low N (LN: 0.3 mM NO 3 − ) and normal N (CK: 6.0 mM NO 3 − ) treatments using Brassica napus as the experimental material. The study results showed that low N induced root elongation in rapeseed, and the root length of LN treatment was 2.37 times that of HN treatment. The dry matter of roots also signiﬁcantly increased due to low N treatment. Meanwhile, low N treatment decreased photosynthetic pigment (including chlorophyll a, chlorophyll b, and carotenoids) contents and dry mass accumulation of leaves. A higher root/shoot ratio and N physiological efﬁciency were observed under low N treatment. The changes in cell wall components (pectin, cellulose, hemicellulose, and lignin), related enzymes, and genes’ transcription levels in roots were determined and the results suggested that low N promoted the demethylation of ion-bound pectin (ISP) and covalently bound pectin (CSP), the content of CSP and cellulose. The promoted pectin methylesterase (PME) activity, inhibited pectin and cellulose degradation enzymes, and up/downregulation of related genes also conﬁrming the results of cell wall components. The low N-increased demethylation degree of pectin and content of pectin and cellulose in cell walls was conducive to cell wall loosening and cell wall synthesis during cell division and elongation, ultimately promoting root-adaptive elongation. The study revealed a possible mechanism in which the alteration of cell wall component content and structure participates in cell elongation and expansion, which directly induces root elongation under N deﬁciency. The successful implementation of this research may be conducive to facilitating the development of rapeseed cultivars with high N use efﬁciency through root-based genetic improvements and improving plant adaptability to low N.
Evaluating Changes in Mental Workload in Indoor and Outdoor Ultra-Distance Cycling

Whilst increasing mental workload has been shown to have a detrimental effect on cycling performance and more generally to increase the risk of harm, no studies have measured how mental workload changes as a function of ultra-distance cycling, indoors or outdoors. Our objective was to measure the difference in mental workload, as indicated by changes in EEG theta power, components of HRV and psychomotor vigilance and as reported using the ‘NASA Task Load Index questionnaire’, before and after a 5 h indoor ride and outdoor ride completed at 65% of functional threshold power. Results of the NASA-TLX indicated the mental demand of outdoor cycling to be significantly less than that of indoor cycling. There were significant differences in the PVT results between the pre and the post outdoor ride average and median response times. The slowest 10% PVT responses were significantly slower pre than post the indoor ride. There were significant differences in HRV between pre and post outdoor and indoor rides, specifically, in the average RR intervals, RMSSD (ms2), LFPower (ms2), NN50. There were modest changes in indicators of mental workload during an ultra-distance cycle ride. As such, mental workload during ultra-distance cycling is unlikely to be a contributory factor to decreases in performance or to an increased likelihood of accident and injury.