Miracle-dz/UniFAR-FTUs huggingface dataset:
Dietary simple sugars alter microbial ecology in the gut and promote colitis in mice

High-sugar diet promotes the growth of mucolytic bacteria, leading to reduction of the mucus layer and predisposition to colitis in mice. Harmful sweetness Inflammatory bowel diseases (IBDs) include multiple disorders characterized by chronic gastrointestinal inflammation. Although the etiology of these diseases is mostly unknown, Western diet and lifestyle seem to be associated with higher IBD incidence. Here, Khan et al. studied the effect of high-sugar diet on colitis in rodent models and showed that a diet high in simple sugars aggravated colitis in mouse models when administered before or after colitis induction. The effect was mediated by alteration of gut microbiota, with an increase of mucolytic bacteria that facilitated gut mucus barrier degradation. The results suggest that high-sugar diet might promote gut microbiota dysfunction and IBD development. The higher prevalence of inflammatory bowel disease (IBD) in Western countries points to Western diet as a possible IBD risk factor. High sugar, which is linked to many noncommunicable diseases, is a hallmark of the Western diet, but its role in IBD remains unknown. Here, we studied the effects of simple sugars such as glucose and fructose on colitis pathogenesis in wild-type and Il10−/− mice. Wild-type mice fed 10% glucose in drinking water or high-glucose diet developed severe colitis induced by dextran sulfate sodium. High-glucose–fed Il10−/− mice also developed a worsened colitis compared to glucose-untreated Il10−/− mice. Short-term intake of high glucose or fructose did not trigger inflammatory responses in healthy gut but markedly altered gut microbiota composition. In particular, the abundance of the mucus-degrading bacteria Akkermansia muciniphila and Bacteroides fragilis was increased. Consistently, bacteria-derived mucolytic enzymes were enriched leading to erosion of the colonic mucus layer of sugar-fed wild-type and Il10−/− mice. Sugar-induced exacerbation of colitis was not observed when mice were treated with antibiotics or maintained in a germ-free environment, suggesting that altered microbiota played a critical role in sugar-induced colitis pathogenesis. Furthermore, germ-free mice colonized with microbiota from sugar-treated mice showed increased colitis susceptibility. Together, these data suggest that intake of simple sugars predisposes to colitis and enhances its pathogenesis via modulation of gut microbiota in mice.
The IMMENSE Study: The Interplay Between iMMune and ENdothelial Cells in Mediating Cardiovascular Risk in Systemic Lupus Erythematosus

Patients with systemic lupus erythematosus (SLE) have a significant increase in cardiovascular (CV) risk although they display a preserved number of circulating angiogenic CD3+CD31+CXCR4+ T cells (Tang), a subpopulation of T cells which promotes repair of damaged endothelium. This happens due to the concomitant expansion of a Tang subset with immunosenescent features, such as the loss of CD28. Therefore, the aim of this study was to elucidate the interplay between Tang subpopulations and endothelial cells in a group of young SLE patients without previous cardiovascular events. Twenty SLE female patients and 10 healthy controls (HCs) were recruited. Flow cytometric analysis of endothelial progenitor cells (EPCs) and Tang subsets were performed and serum levels of interleukin (IL)-6, -8, matrix metalloproteinase (MMP)-9 and interferon (IFN)-γ were measured. Human umbilical vein endothelial cells (HUVECs) proliferation and pro-inflammatory phenotype in response to subjects’ serum stimulation were also evaluated. Results showed that the percentage of Tang and EPC subsets was reduced in SLE patients compared with HCs, with a marked increase of senescent CD28null cells among Tang subset. SLE disease activity index-2000 (SLEDAI-2K) was inversed related to Tang cells percentage. Furthermore, IL-8 serum levels were directly correlated with the percentage of Tang and inversely related to the CD28null Tang subsets. We indirectly evaluated the role of the Tang subset on the endothelium upon stimulation with serum from subjects with a low percentage of Tang CD3+ cells in HUVECs. HUVECs displayed pro-inflammatory phenotype with up-regulation of mRNA for IL-6, intercellular adhesion molecule (ICAM)-1 and endothelial leukocyte adhesion molecule (ELAM)-1. Cell proliferation rate was directly related to IL-8 serum levels and EPC percentage. In highly selected young SLE patients without previous CV events, we found that the deterioration of Tang compartment is an early event in disease course, preceding the development of an overt cardiovascular disease and potentially mediated by SLE-specific mechanisms. The overcome of the CD28null subset exerts detrimental role over the Tang phenotype, where Tang could exert an anti-inflammatory effect on endothelial cells and might orchestrate via IL-8 the function of EPCs, ultimately modulating endothelial proliferation rate.
Modeling Propulsion of Soft Magnetic Nanowires

The emergent interest in artificial nanostructures that can be remotely navigated a specific location in a fluidic environment is motivated by the enormous potential this technology offers to biomedical applications. Originally, bio-inspired micro-/nanohelices driven by a rotating magnetic field were proposed. However, fabrication of 3D helical nanostructures is complicated. One idea to circumvent complex microfabrication is to use 1D soft magnetic nanowires that acquire chiral shape when actuated by a rotating field. The paper describes the comprehensive numerical approach for modeling propulsion of externally actuated soft magnetic nanowires. The proposed bead-spring model allows for arbitrary filament geometry and flexibility and takes rigorous account of intra-filament hydrodynamic interactions. The comparison of the numerical predictions with the previous experimental results on propulsion of composite two-segment (Ni-Ag) nanowires shows an excellent agreement. Using our model we could substantiate and rationalize important and previously unexplained details, such as bidirectional propulsion of three-segment (Ni-Ag-Au) nanowires.
Eat1-Like Alcohol Acyl Transferases From Yeasts Have High Alcoholysis and Thiolysis Activity

Esters are important flavor and fragrance compounds that are present in many food and beverage products. Many of these esters are produced by yeasts and bacteria during fermentation. While ester production in yeasts through the alcohol acyl transferase reaction has been thoroughly investigated, ester production through alcoholysis has been completely neglected. Here, we further analyze the catalytic capacity of the yeast Eat1 enzyme and demonstrate that it also has alcoholysis and thiolysis activities. Eat1 can perform alcoholysis in an aqueous environment in vitro, accepting a wide range of alcohols (C2–C10) but only a small range of acyl donors (C2–C4). We show that alcoholysis occurs in vivo in several Crabtree negative yeast species but also in engineered Saccharomyces cerevisiae strains that overexpress Eat1 homologs. The alcoholysis activity of Eat1 was also used to upgrade ethyl esters to butyl esters in vivo by overexpressing Eat1 in Clostridium beijerinckii. Approximately 17 mM of butyl acetate and 0.3 mM of butyl butyrate could be produced following our approach. Remarkably, the in vitro alcoholysis activity is 445 times higher than the previously described alcohol acyl transferase activity. Thus, alcoholysis is likely to affect the ester generation, both quantitatively and qualitatively, in food and beverage production processes. Moreover, mastering the alcoholysis activity of Eat1 may give rise to the production of novel food and beverage products.
Concordance between IFNγ +874 A/T polymorphism and interferon-γ expression in a TB-endemic indigenous settingConcordance between IFNγ +874 A/T polymorphism and interferon-γ expression in a TB-endemic indigenous setting

Introduction: Interferon-γ (IFN-γ) plays a crucial role in resistance to mycobacterial diseases; accordingly, variants of the gene encoding this cytokine may be associated with elevated risk of contracting pulmonary tuberculosis (TB). Methods: Blood samples were collected from 135 Warao indigenous individuals with newly diagnosed sputum culture-positive TB. Of these, 24 were diagnosed with active tuberculosis (ATB). The study comprised 111 participants, who were grouped as follows: 1) 14 tuberculin skin test (TST)-positive Warao indigenous individuals and 4 that were QuantiFERON-TBGold In-Tube (QFT-IT) test-positive, collectively comprising the latent TB infection group (LTBI), n = 18), and 2) healthy controls who were QFT-ITand TST-negative, comprising the control group (CTRL, n = 93). Detection of the IFNG+874A/T polymorphism was performed via PCR and quantification of IFN-γ gene (IFNG) expression via qPCR. Results: Relative to indigenous and white Americans, ATB and CTRL groups had a higher frequency of the IFNG SNP (+874A): 23 (95.8%) and 108 (97.3%), respectively. Indigenous Warao individuals homozygous for the IFNG (+874) A allele exhibited 3.59-fold increased risk of developing TB (95% confidence interval, 2.60-4.96, p =0.0001). A decreased frequency of the AT genotype was observed in individuals with pulmonary TB (4.16%) and controls (0.90%). The frequency of the TT genotype was decreased among controls (1.80%); none of the patients with TB were found to have this genotype. The differences in IFNG expression between the groups, under unstimulated and stimulated conditions, were not statistically significant. Conclusions: Preliminary results demonstrate concordance between IFNG +874 A/A genotype and low expression of IFNG.
Reasoning With Conditionals About Everyday and Mathematical Concepts in Primary School

A research link between conditional reasoning and mathematics has been reported only for late adolescents and adults, despite claims about the pivotal importance of conditional reasoning, i.e., reasoning with if–then statements, in mathematics. Secondary students’ problems with deductive reasoning in mathematics have been documented for a long time. However, evidence from developmental psychology shows that even elementary students possess some early conditional reasoning skills in familiar contexts. It is still an open question to what extent conditional reasoning with mathematical concepts differs from conditional reasoning in familiar everyday contexts. Based on Mental Model Theory (MMT) of conditional reasoning, we assume that (mathematical) content knowledge will influence the generation of models, when conditionals concern mathematical concepts. In a cross-sectional study, 102 students in Cyprus from grades 2, 4, and 6 solved four conditional reasoning tasks on each type of content (everyday and mathematical). All four logical forms, modus ponens (MP), modus tollens (MT), denial of the antecedent (DA), and affirmation of the consequent (AC), were included in each task. Consistent with previous findings, even second graders were able to make correct inferences on some logical forms. Controlling for Working Memory (WM), there were significant effects of grade and logical form, with stronger growth on MP and AC than on MT and DA. The main effect of context was not significant, but context interacted significantly with logical form and grade level. The pattern of results was not consistent with the predictions of MMT. Based on analyses of students’ chosen responses, we propose an alternative mechanism explaining the specific pattern of results. The study indicates that deductive reasoning skills arise from a combination of knowledge of domain-general principles and domain-specific knowledge. It extends results concerning the gradual development of primary students’ conditional reasoning with everyday concepts to reasoning with mathematical concepts adding to our understanding of the link between mathematics and conditional reasoning in primary school. The results inspire the development of educational interventions, while further implications and limitations of the study are discussed.
Improving Newborn Respiratory Outcomes With a Sustained Inflation: A Systematic Narrative Review of Factors Regulating Outcome in Animal and Clinical Studies

Respiratory support is critically important for survival of newborns who fail to breathe spontaneously at birth. Although there is no internationally accepted definition of a sustained inflation (SI), it has commonly been defined as a positive pressure inflation designed to establish functional residual capacity and applied over a longer time period than normally used in standard respiratory support (SRS). Outcomes vary distinctly between studies and to date there has been no comprehensive investigation of differences in SI approach and study outcome in both pre-clinical and clinical studies. A systematic literature search was performed and, after screening, identified 17 animal studies and 17 clinical studies evaluating use of a SI in newborns compared to SRS during neonatal resuscitation. Study demographics including gestational age, SI parameters (length, repetitions, pressure, method of delivery) and study outcomes were compared. Animal studies provide mechanistic understanding of a SI on the physiology underpinning the cardiorespiratory transition at birth. In clinical studies, there is considerable difference in study quality, delivery of SIs (number, pressure, length) and timing of primary outcome evaluation which limits direct comparison between studies. The largest difference is method of delivery, where the role of a SI has been observed in intubated animals, as the inflation pressure is directly applied to the lung, bypassing the obstructed upper airway in an apnoeic state. This highlights a potential limitation in clinical use of a SI applied non-invasively. Further research is required to identify if a SI may have greater benefits in subpopulations of newborns.
Commentary: Commentary on Reconstructing Four Centuries of Temperature-Induced Bleaching on the Great Barrier Reef by Hoegh-Guldberg et al. 2019 and DeCarlo 2020

Citation: Kamenos NA and Hennige SJ (2020) Commentary: Commentary on Reconstructing Four Centuries of Temperature-Induced Bleaching on the Great Barrier Reef by Hoegh-Guldberg et al. 2019 and DeCarlo 2020. Front. Mar. Sci. 7:570620. doi: 10.3389/fmars.2020. 570620 Commentary: Commentary on Reconstructing Four Centuries of Temperature-Induced Bleaching on the Great Barrier Reef by Hoegh-Guldberg et al. 2019 and DeCarlo 2020
The Construction of Efficient Portfolios: A Verification of Risk Models for Investment Making

Various statistical models have been used in estimating inputs to mean-variance efficient portfolio construction since the mid-1960s. One can argue how many factors are necessary, but there appears to be substantial evidence that statistical models outperform fundamental models for several expected returns models, such as we test in this analysis. In this paper, we show that tracking portfolios constructed with expected return rankings based on earnings forecasting and price momentum composite alpha strategies produce statistically significant excess returns and increased Sharpe Ratios when optimized with 3-factor statistical risk model.
Information and cyber security maturity models: a systematic literature review

This paper aims to clarify the uncertainty reflected in the current state of information security maturity evaluation where it has not enough matured and converged so that a generic approach or many specfics approaches become the go-to choice. In fact, in the past decade, many secruity maturity models are still being produced and remain unproven regardless of the existence of ISO 21827. ,The authors have used the systematic literature review to summarize existing research, help identify gaps in the existing literature and provide background for positioning new research studies. ,The authors highlighted the prevalent influence of the ISO/IEC 27001/27002 standard but raised the necessity for an in-depth investigation of ISO 21827. The authors also made the implementation facet a central topic of our review. The authors found out that, compared to the number of proposed models, implementation experiments are lacking. This could be due to the arduous task of validation and it could also be the reason why specific models are dominant. ,While the research literature contains many experience reports and a few case studies on information security maturity evaluation, a systematic review and synthesis of this growing field of research is unavailable as far as the authors know. In fact, the authors only picked-up one bodywork [Maturity models in cyber security A systematic review (2017)] carrying out a literature review on security maturity models between 2012 and 2017, written in Spanish.
The role of ribose-5-phosphate isomerase A in the regulation of autophagy

Macroautophagy (hereafter: autophagy), cell signalling and cellular metabolism are tightly linked processes. Multiple examples of metabolites and metabolic enzymes have recently been found to regulate signalling pathways and autophagy. Metabolic reprogramming is one of the hallmarks of cancer and often mediated via aberrant signalling pathways, such as receptor tyrosine kinase (RTK) signalling. Growth factor receptor-bound protein 2 (Grb2) is a key RTK signalling adaptor and is involved in a number of downstream signalling cascades, such as mitogen-activated protein kinase (MAPK) or phosphoinositide 3-kinase (PI3K) pathways, which in turn regulate metabolism through alterations in gene expression or by directly modifying enzymatic activity. This study investigates the role of ribose-5-phosphate isomerase (RPIA), a key metabolic enzyme in the pentose phosphate pathway (PPP), in the regulation of autophagy and Grb2-mediated signalling. RPIA expression induces Grb2 translocation from an even cytoplasmic distribution to unknown sub-cellular structures, possibly through direct protein-protein interaction. Interestingly, this effect is independent of the catalytic activity of RPIA, suggesting a non-canonical role in signalling. Neither RPIA over-expression, transient knockdown or deletion by CRISPR/Cas9 genome editing resulted in differences in metabolic activity or the MAPK pathway as tested by extracellular signal–regulated kinases (ERK) 1/2 phosphorylation and MTT assay. Furthermore, knockdown of RPIA by shRNA or genomic deletion resulted in an increase of LC3 processing and LC3-positive autophagosomes, suggesting that endogenous RPIA is an inhibitor of basal autophagy. Data fromSaccharomyces cerevisiae, mass spectrometry of sugar phosphates and pharmacological treatment assays suggest that RPIA may inhibit autophagy through a non-canonical function. Although the molecular mechanisms by which RPIA acts on Grb2 signalling and how it contributes to the regulation of autophagy are currently not fully understood, this study presents some interesting observations that may have implications in the development of therapeutics that target cancer metabolism or aim to modulate autophagy.
Triacylglycérols de la matière grasse laitière enrichie en acides gras insaturés : structures cristallines et fonctionnalités

Comprenant environ 65 % d’acides gras satures (AGS) reputes nefastes pour la sante, la matiere grasse laitiere (MGL), dont les triacylglycerols (esters de glycerol et d’acides gras) constituent la majeure partie, est presente dans de nombreux produits alimentaires. Sa composition et sa complexite structurale lui conferent des proprietes de cristallisation particulieres et des qualites organoleptiques appreciees dans divers produits : beurre, cremes, mousses, etc. L’enjeu majeur est de diminuer la proportion des AGS tout en conservant les proprietes culinaires de la MGL. L’objectif de cette these est de quantifier les proprietes physiques de MGL a teneur reduite en AGS par le biais de l’alimentation animale dans des matrices de complexite croissante : a l’etat anhydre, en emulsion (lait et emulsion modele) et dans des produits finis (beurre et fromage). Pour cela, une approche systemique a ete utilisee ; les echantillons ont ete etudies pour leur composition et leurs proprietes physiques a differentes echelles : moleculaire, microscopique et macroscopique. Ainsi, les cristaux formes par ces triacylglycerols modifies montrent des caracteristiques moleculaires liees directement a la nature de leurs acides gras. La stabilite thermique de ces cristaux est alteree : bien qu’ayant une plage de fusion globale conservee, ils ne se reorganisent pas dans la zone classique 0-20°C. Les proprietes de durete des triacylglycerols sont diminuees jusqu’a 30%. En emulsion, la taille des gouttelettes influe fortement sur le mecanisme de nucleation et la nature des cristaux de ces triacylglycerols complexes en melange.
Impact of Arachidonic and Docosahexaenoic Acid Supplementation on Neural and Immune Development in the Young Pig

Background: Human milk contains both arachidonic acid (ARA) and docosahexaenoic acid (DHA). Supplementation of infant formula with ARA and DHA results in fatty acid (FA) profiles, neurodevelopmental outcomes, and immune responses in formula-fed infants that are more like those observed in breastfed infants. Consequently, ARA and DHA have been historically added together to infant formula. This study investigated the impact of ARA or DHA supplementation alone or in combination on tissue FA incorporation, immune responses, and neurodevelopment in the young pig. Methods: Male pigs (N = 48 total) received one of four dietary treatments from postnatal day (PND) 2–30. Treatments targeted the following ARA/DHA levels (% of total FA): CON (0.00/0.00), ARA (0.80/0.00), DHA (0.00/0.80), and ARA+DHA (0.80/0.80). Plasma, red blood cells (RBC), and prefrontal cortex (PFC) were collected for FA analysis. Blood was collected for T cell immunophenotyping and to quantify a panel of immune outcomes. Myelin thickness in the corpus callosum was measured by transmission electron microscopy and pig movement was measured by actigraphy. Results: There were no differences in formula intake or growth between dietary groups. DHA supplementation increased brain DHA, but decreased ARA, compared with all other groups. ARA supplementation increased brain ARA compared with all other groups but did not affect brain DHA. Combined supplementation increased brain DHA levels but did not affect brain ARA levels compared with the control. Pigs fed ARA or ARA+DHA exhibited more activity than those fed CON or DHA. Diet-dependent differences in activity suggested pigs fed ARA had the lowest percent time asleep, while those fed DHA had the highest. No differences were observed for immune or myelination outcomes. Conclusion: Supplementation with ARA and DHA did not differentially affect immune responses, but ARA levels in RBC and PFC were reduced when DHA was provided without ARA. Supplementation of either ARA or DHA alone induced differences in time spent asleep, and ARA inclusion increased general activity. Therefore, the current data support the combined supplementation with both ARA and DHA in infant formula and raise questions regarding the safety and nutritional suitability of ARA or DHA supplementation individually.