Miracle-dz/UniFAR-FTUs huggingface dataset:
The prognostic value of toll-like receptor5 and programmed cell death-ligand1 in patients with peripheral T-cell non-Hodgkin lymphoma

Abstract TLR5 is expressed in a variety of tumors. However, the clinical impact of TLR5 in Peripheral T-cell non-Hodgkin lymphomas (PTCLs) remains unclear. We analyzed differentially expressed genes in PTCLs samples from Gene Expression Omnibus database. We examined TLR5 and programed cell death-ligand1 (PD-L1) expression by immunohistochemistry in PTCLs tissues. Gene expression profiling shown PD-L1 and TLR5 expression was higher in PTCLs than in normal samples. The rates of high TLR5 and PD-L1 expression were 12.5% and 45.8%. We found association between TLR5 and PD-L1 expression. Low TLR5 expression or high PD-L1 expression was correlated with shorter overall survival and inferior disease-free survival. Multivariate Cox regression analysis shown low TLR5 expression, high PD-L1 expression, gender, and high IPI score were prognostic factors (p < .05). PTCLs patients with low TLR5 expression and high PD-L1 expression had worse prognosis. TLR5 and PD-L1 may serve as potential therapeutic targets in PTCLs patients.
Cultures of conflict: Protests, violent repression, and community values

What are the cultural origins of societal conflicts that revolve around democratization, women's rights, and modern libertarian values? We propose that deep‐seated differences in community‐based collective values (at the micro‐level) may be related to why people support anti‐government protest and why they support repression of such protests (at the macro‐level). The hypothesis was examined among residents of Turkey (N = 500). Cultural values, measured at the individual level and community level with the community collectivism scale, correlated with political orientation and emotions, as well as with subsequent support for anti‐governmental protest or its repression. The main conclusions are that both support for protest and support for repression are related to the cultural values people hold and their subsequent political orientations and emotions. Micro‐level cultural values in local communities may thus play a role in explaining macro‐level socio‐political divides.
Strain‐specific altered nicotine metabolism in 3,3′‐diindolylmethane (DIM) exposed mice

Two indole compounds, indole‐3‐carbinol (I3C) and its acid condensation product, 3,3′‐diindolymethane (DIM), have been shown to suppress the expression of flavin‐containing monooxygenases (FMO) and to induce some hepatic cytochrome P450s (CYPs) in rats. In liver microsomes prepared from rats fed I3C or DIM, FMO‐mediated nicotine N‐oxygenation was decreased, whereas CYP‐mediated nicotine metabolism to nicotine iminium and subsequently to cotinine was unchanged. Therefore, it was hypothesized that in mice DIM would also suppress nicotine N‐oxygenation without affecting CYP‐mediated nicotine metabolism. Liver microsomes were produced from male and female C57BL/6 J and CD1 mice fed 2500 parts per million (ppm) DIM for 14 days. In liver microsomes from DIM‐fed mice, FMO‐mediated nicotine N‐oxygenation did not differ from the controls, but CYP‐mediated nicotine metabolism was significantly increased, with results varying by sex and strain. To confirm the effects of DIM in vivo, control and DIM‐fed CD1 male mice were injected subcutaneously with nicotine, and the plasma concentrations of nicotine, cotinine and nicotine‐N‐oxide were measured over 30 minutes. The DIM‐fed mice showed greater cotinine concentrations compared with the controls 10 minutes following injection. It is concluded that the effects of DIM on nicotine metabolism in vitro and in vivo differ between mice and rats and between mouse strains, and that DIM is an effective inducer of CYP‐mediated nicotine metabolism in commonly studied mouse strains.
Evaluation of Polyphenolic Compounds and Pharmacological Activities in Hairy Root Cultures of Ligularia fischeri Turcz. f. spiciformis (Nakai)

A considerable amount of bioactive compounds have been used for the biopharmaceutical engineering to help human health and nutrition. Hairy root culture (HRC) or transgenic root is a favourable alternative technique for phytochemical production. Ligularia fischeri is a significant source of pharmaceutically important active compounds with an enormous range of health care applications. HRC of L. fischeri was developed using Agrobacterium rhizogenes for the production of polyphenolic compounds with antioxidant, antimicrobial, antidiabetic, anticancer and anti-inflammatory pharmaceutical activities. Hairy roots (HRs) were selected by morphological assessment, genetic and molecular analyses. The maximum accumulation of fresh mass (94.15 g/L) and dry mass (9.45 g/L) was recorded in MS liquid medium supplemented with 30 g/L sucrose at 28 days. Furthermore, HRs successfully produced numerous polyphenolic compounds, including six hydroxycinnamic acids, seven flavonols, seven hydroxybenzoic acids, vanillin, resveratrol, pyrogallol, homogentisic, and veratric acids, which were identified by UHPLC analysis. HRs produced higher total phenolic (185.65 mg/g), and flavonoid (5.25 mg/g) contents than non-transformed roots (125.55 mg/g and 3.75 mg/g). As a result of these metabolic changes, pharmaceutical activities were found higher in HRs than non-transformed roots (NTRs). The present study indicates that HRC has the potential to increase the content of beneficial polyphenolic compounds with higher potential pharmaceutical activities. To the best of our knowledge, the present study is the first report on enhancing the production of polyphenolic compounds with pharmaceutical activities from the HRCs of L. fischeri.
Spheroid Culture of Mesenchymal Stromal Cells Results in Morphorheological Properties Appropriate for Improved Microcirculation

Human bone marrow mesenchymal stromal cells (MSCs) have been used in clinical trials for the treatment of systemic inflammatory diseases due to their regenerative and immunomodulatory properties. However, intravenous administration of MSCs is hampered by cell trapping within the pulmonary capillary networks. Here, we hypothesize that traditional twodimensional (2D) plastic-adherent cell expansion fails to result in appropriate morphorheological properties required for cell-circulation. To address this issue, we adapted a novel method to culture MSCs in non-adherent three-dimensional (3D) spheroids (mesenspheres). The biological properties of mesensphere-cultured MSCs remained identical to conventional 2D cultures. Morpho-rheological analyses revealed a smaller size and lower cell stiffness of mesensphere-derived MSCs compared to plastic-adherent MSCs, measured using real-time deformability cytometry (RT-DC) and atomic force microscopy, resulting in an increased ability to pass through micro-constrictions in an ex vivo microcirculation assay. This ability was confirmed in vivo by analysis of cell accumulation in various organ capillary networks after intravenous injection of mesensphere-derived MSCs in mouse. Our findings generally identify cellular morpho-rheological properties as attractive targets to improve microcirculation and specifically suggest mesensphere cultures as a promising approach for optimized MSC-based therapies.
Polymeric Materials: Surfaces, Interfaces and Bioapplications

This special issue “Polymeric Materials: Surfaces, Interfaces and Bioapplications” was proposed to cover all the aspects related to recent innovations on surfaces, interfaces and bioapplications of polymeric materials. The collected articles show the advances in polymeric materials, which have tremendous applications in agricultural films, food packaging, dental restoration, antimicrobial systems and tissue engineering. We hope that readers will be able to enjoy highly relevant topics that are related to polymers. Therefore, we hope to prove that plastics can be a solution and not a problem.
Experimental and Numerical Simulation of the Formation of Cold Seep Carbonates in Marine Sediments

Cold seep emissions of low temperature fluid from the marine sediment basins are mainly comprised of methane and other hydrocarbons. A series of biogeochemical processes related to methane lead to the formation of authigenic carbonate minerals. In this study, a self-built experimental device was used to study the formation process of carbonate minerals under cold seep conditions. The concentrations of pore water chemicals, HCO3− and Ca2+ at different heights of the reactor under flow conditions can be observed. According to the experimental results, the formation process of carbonate minerals under cold seep conditions was estimated, that 1 m carbonate growth needs 12,000 and 7000 years, respectively, under fast (5 mL·min−1) and slow emission (1 mL·min−1) conditions. Furthermore, TOUGHREACT was used to simulate the diagenesis process. A 1D unsteady react-transport model was developed, and the experimental data was used to constrain the simulation. The results of simulation show that the carbonates need 17,000 and 9700 years to grow 1 m under the condition of fast and slow flow scenarios, respectively. The results of this work will contribute to the study of foundation on the formation of authigenic minerals in cold seep areas, and for the physical properties of sedimentary media as well.
Acute effects of cannabinoids on addiction endophenotypes are moderated by genes encoding the CB1 receptor and FAAH enzyme

Understanding genetic factors that contribute to cannabis use disorder (CUD) is important, but to date, findings have been equivocal. Single‐nucleotide polymorphisms (SNPs) in the cannabinoid receptor 1 gene (CNR1; rs1049353 and rs806378) and fatty acid amide hydrolase (FAAH) gene (rs324420) have been implicated in CUD. Their relationship to addiction endophenotypes such as cannabis‐related state satiety, the salience of appetitive cues, and craving after acute cannabinoid administration has not been investigated. Forty‐eight cannabis users participated in a double‐blind, placebo‐controlled, four‐way crossover experiment where they were administered treatments in a randomized order via vaporization: placebo, Δ9‐tetrahydrocannabinol (THC) (8 mg), THC + cannabidiol (THC + CBD) (8 + 16 mg), and CBD (16 mg). Cannabis‐related state satiety, appetitive cue salience (cannabis and food), and cannabis craving were assessed each day. Participants were genotyped for rs1049353, rs806378, and rs324420. Results indicated that CNR1 rs1049353 GG carriers showed increased state satiety after THC/THC + CBD administration in comparison with placebo and reduced the salience of appetitive cues after THC in comparison with CBD administration; A carriers did not vary on either of these measures indicative of a vulnerability to CUD. CNR1 rs806378 CC carriers showed greater salience to appetitive cues in comparison with T carriers, but there was no evidence for changes in state satiety. FAAH rs324420 A carriers showed greater bias to appetitive cues after THC, in comparison with CC carriers. FAAH CC carriers showed reduced bias after THC in comparison with CBD. No SNPs modulated craving. These findings identify candidate neurocognitive mechanisms through which endocannabinoid system genetics may influence vulnerability to CUD.
New Approach to Analysis of Selected Measurement and Monitoring Systems Solutions in Ship Technology

This paper is dedicated to certain types of measurement in ship systems, analyzed based on selected case studies. In the introductory part, a simplified structure of a modern cargo ship as an object of measurement and control is presented. Next, the role of measurement in the ship’s operation process is described and commented on, with focus on specifics of local and remote control, both manual and automatic. The key part of the paper is dedicated to a short overview of selected examples of measuring and monitoring systems. The basic criteria for the aforementioned selection are the vital role of the considered systems for safe and effective ship operation as well as documented innovative contribution of Gdynia Maritime University (GMU) in development of the state-of-the-art in the analysed area of measurement. Based on these criteria, the monitoring of operational parameters of main engine and temperature measurement in the ships hazardous areas have been chosen. The aforementioned measurement and monitoring systems are analysed, taking into account both innovation of technical solutions together with their ship technology environment conditions and related legal requirements. Finally, some concluding remarks are formulated.
Diurnal variation of human tear meniscus volume measured with tear strip meniscometry self-examination

Purpose Tear secretion is critical for maintenance of healthy ocular surface and vision. Most of normal subjects and dry eye patients feel worsening of ocular dryness in the afternoon, however, diurnal variation of tear meniscus volume has not been directly measured because there was no appropriate method. We used a simple, non-invasive technique, tear strip meniscometry (SM) by self-examination. Previous investigations indicated the values of SM correlated strongly with those of the Schirmer test, tests of tear break up time, and tear meniscus height measurement by anterior optical coherence tomography. The purpose of this study was to capture diurnal variation of aqueous availability at the tear meniscus by measuring wetted length using SM through self-examination. Methods Thirty-six medical personnel (mean age; 35.7 years) participated and SM self-examination was performed using a mirror seven times a day. The strip is applied for 5 seconds to the lateral side of the lower lid tear meniscus without touching the ocular surface. Results The measured SM value was the highest upon awakening (4.44 ± 3.14 mm) and gradually decreased in the evening; 3.81 ± 3.12 at 9:00, 3.31 ± 2.72* at 12:00, 2.89 ± 1.88* at 15:00, 2.92 ± 1.87* at 18:00, 2.78 ± 1.85* at 21:00, and 2.89 ± 1.75* at bedtime with statistical significance compared to the value upon awakening (*P < 0.05, Dunnett’s multiple comparison test). Proportion of number of subjects with low SM value (< 4 mm) to total number of subjects was 52.8% upon awakening and 83.3% at 21:00, and gradually increased toward evening. Conclusion Our results could identify diurnal variation of tear meniscus volume in the general population.
The long-non-coding RNA NEAT1 is a novel target for Alzheimer’s disease progression via miR-124/BACE1 axis

ABSTRACT Objectives: Long-non-coding RNAs (lncRNAs) have been involved in central nervous system recently. A number of studies have reported that lncRNA NEAT1 exerts critical roles in neurodegenerative disorder. Beta-site amyloid precursor protein cleaving enzyme 1 (BACE1) has been reported to exert function in the accumulation of amyloid-β (Aβ). Moreover, BACE1 acts as a target of miR-124 in the progression of AD. So far, the biological role and underlying mechanisms of NEAT1 and miR-124 in AD remains elusive. Methods: The relative NEAT1 and miR-124 expression was examined by qRT-PCR in the tissues and cells line of AD. Cell apoptosis was examined by FACS. Luciferase reporter assay was performed to verify that miR-124 is a direct target of NEAT1, and BACE1 is a downstream target of miR-124. qRT-PCR and western blot analysis were also performed to determinate the BACE1 and the phosphorylation of tau protein. Results: NEAT1 was notably up-regulated and miR-124 was remarkably down-regulated in AD mouse model. Knockdown of NEAT1 or overexpression of miR-124 showed the protective effects on cellular AD model induced by Aβ. Moreover, miR-124 expression could be up- and down-regulated by suppression or overexpression of NEAT1, respectively. In addition, the expression of BACE1 was the potential functional target of miR-124. These findings suggested that NEAT1 might play a vital role in the development of AD by regulating miR-124/BACE1 axis. Discussion: The present study showed that NEAT1 worked as a regulating factor to promote the development of AD via modulating miR-124/BACE1 axis, which might be considered as a novel target in AD treatment.
Diversification of Colonization Factors in a Multidrug-Resistant Escherichia coli Lineage Evolving under Negative Frequency-Dependent Selection

Infections with multidrug-resistant (MDR) strains of Escherichia coli are a significant global public health concern. To combat these pathogens, we need a deeper understanding of how they evolved from their background populations. By understanding the processes that underpin their emergence, we can design new strategies to limit evolution of new clones and combat existing clones. By combining population genomics with modelling approaches, we show that dominant MDR clones of E. coli are under the influence of negative frequency-dependent selection, preventing them from rising to fixation in a population. Furthermore, we show that this selection acts on genes involved in anaerobic metabolism, suggesting that this key trait, and the ability to colonize human intestinal tracts, is a key step in the evolution of MDR clones of E. coli. ABSTRACT Escherichia coli is a major cause of bloodstream and urinary tract infections globally. The wide dissemination of multidrug-resistant (MDR) strains of extraintestinal pathogenic E. coli (ExPEC) poses a rapidly increasing public health burden due to narrowed treatment options and increased risk of failure to clear an infection. Here, we present a detailed population genomic analysis of the ExPEC ST131 clone, in which we seek explanations for its success as an emerging pathogenic strain beyond the acquisition of antimicrobial resistance (AMR) genes. We show evidence for evolution toward separate ecological niches for the main clades of ST131 and differential evolution of anaerobic metabolism, key colonization, and virulence factors. We further demonstrate that negative frequency-dependent selection acting across accessory loci is a major mechanism that has shaped the population evolution of this pathogen. IMPORTANCE Infections with multidrug-resistant (MDR) strains of Escherichia coli are a significant global public health concern. To combat these pathogens, we need a deeper understanding of how they evolved from their background populations. By understanding the processes that underpin their emergence, we can design new strategies to limit evolution of new clones and combat existing clones. By combining population genomics with modelling approaches, we show that dominant MDR clones of E. coli are under the influence of negative frequency-dependent selection, preventing them from rising to fixation in a population. Furthermore, we show that this selection acts on genes involved in anaerobic metabolism, suggesting that this key trait, and the ability to colonize human intestinal tracts, is a key step in the evolution of MDR clones of E. coli.
Fruit and Vegetable Intake is Inversely Associated with Cancer Risk in Mexican-Americans

Abstract Objective: There is inconsistent evidence and limited data in the Hispanic population concerning fruit and vegetable intake and cancer risk. This study explored the effect of fruit and vegetable intake on cancer risk in Mexican-Americans. Methods: Participants in this cross-sectional study were drawn from the Cameron County Hispanic Cohort. Consumption of fruits and vegetables were assessed using a validated questionnaire. Cancer was self-reported by the participants based on being told by a health care provider that they had cancer. Results: Among 2,381 participants with available dietary data, 82 reported a diagnosis of cancer. Participants who met recommendations of five or more servings of fruit and vegetable per day had a significantly 86% lower risk for reported cancer compared with those who did not meet recommendations, after adjusting for other covariates. Every portion increment of total fruit and vegetable intake was significantly associated with the reduced cancer risk by 11% with the adjustment of other covariates. Conclusions: Fruit and vegetable intake was inversely associated with cancer risk in Mexican-Americans. Improving the consumption of fruit and vegetable might be an effective area for further research as part of a strategy for cancer prevention and control among Mexican-Americans independent of other factors.
Silicified cell walls as a defensive trait in diatoms

Diatoms contribute nearly half of the marine primary production. These microalgae differ from other phytoplankton groups in having a silicified cell wall, which is the strongest known biological material relative to its density. While it has been suggested that a siliceous wall may have evolved as a mechanical protection against grazing, empirical evidence of its defensive role is limited. Here, we experimentally demonstrate that grazing by adult copepods and nauplii on diatoms is approximately inversely proportional to their silica content, both within and among diatom species. While a sixfold increase in silica content leads to a fourfold decrease in copepod grazing, silicification provides no protection against protozoan grazers that directly engulf their prey. We also found that the wall provides limited protection to cells ingested by copepods, since less than 1% of consumed cells were alive in the faecal pellets. Moreover, silica deposition in diatoms decreases with increasing growth rates, suggesting a possible cost of defence. Overall, our results demonstrate that thickening of silica walls is an effective defence strategy against copepods. This suggests that the plasticity of silicification in diatoms may have evolved as a response to copepod grazing pressure, whose specialized tools to break silicified walls have coevolved with diatoms.
Metabolomics Profiling of Visceral Adipose Tissue: Results From MESA and the NEO Study

Background Identifying associations between serum metabolites and visceral adipose tissue (VAT) could provide novel biomarkers of VAT and insights into the pathogenesis of obesity‐related diseases. We aimed to discover and replicate metabolites reflecting pathways related to VAT. Methods and Results Associations between fasting serum metabolites and VAT area (by computed tomography or magnetic resonance imaging) were assessed with cross‐sectional linear regression of individual‐level data from participants in MESA (Multi‐Ethnic Study of Atherosclerosis; discovery, N=1103) and the NEO (Netherlands Epidemiology of Obesity) study (replication, N=2537). Untargeted 1H nuclear magnetic resonance metabolomics profiling of serum was performed in MESA, and metabolites were replicated in the NEO study using targeted 1H nuclear magnetic resonance spectroscopy. A total of 30 590 metabolomic spectral variables were evaluated. After adjustment for age, sex, race/ethnicity, socioeconomic status, smoking, physical activity, glucose/lipid‐lowering medication, and body mass index, 2104 variables representing 24 nonlipid and 49 lipid/lipoprotein subclass metabolites remained significantly associated with VAT (P=4.88×10−20–1.16×10−3). These included conventional metabolites, amino acids, acetylglycoproteins, intermediates of glucose and hepatic metabolism, organic acids, and subclasses of apolipoproteins, cholesterol, phospholipids, and triglycerides. Metabolites mapped to 31 biochemical pathways, including amino acid substrate use/metabolism and glycolysis/gluconeogenesis. In the replication cohort, acetylglycoproteins, branched‐chain amino acids, lactate, glutamine (inversely), and atherogenic lipids remained associated with VAT (P=1.90×10−35–8.46×10−7), with most associations remaining after additional adjustment for surrogates of VAT (glucose level, waist circumference, and serum triglycerides), reflecting novel independent associations. Conclusions We identified and replicated a metabolite panel associated with VAT in 2 community‐based cohorts. These findings persisted after adjustment for body mass index and appear to define a metabolic signature of visceral adiposity.