Miracle-dz/UniFAR-FTUs huggingface dataset:
Ovine prenatal growth-restriction and sex influence fetal adipose tissue phenotype and impact postnatal lipid metabolism and adiposity in vivo from birth until adulthood

Adipose tissue development begins in utero and is a key target of developmental programming. Here the influence of nutritionally-mediated prenatal growth-restriction on perirenal adipose tissue (PAT) gene expression and adipocyte phenotype in late fetal life was investigated in both sexes in an ovine model. Likewise circulating leptin concentrations and non-esterified fatty acid (NEFA) and glycerol responses to glucose challenge were determined in relation to offspring adiposity at key stages from birth to mid-adult life. In both studies’ singleton-bearing adolescent sheep were fed control or high nutrient intakes to induce normal or growth-restricted pregnancies, respectively. Fetal growth-restriction at day 130 of gestation (32% lighter) was characterised by greater body-weight-specific PAT mass and higher PAT expression of peroxisome proliferator-activated receptor gamma (PPARɤ), glycerol-3-phosphate dehydrogenase, hormone sensitive lipase (HSL), insulin-like growth factor 1 receptor, and uncoupling protein 1. Independent of prenatal growth, females had a greater body-weight-specific PAT mass, more multilocular adipocytes, higher leptin and lower insulin-like growth factor 1 mRNA than males. Growth-restricted offspring of both sexes (42% lighter at birth) were characterised by higher plasma NEFA concentrations across the life-course (post-fasting and after glucose challenge at 7, 32, 60, 85 and 106 weeks of age) consistent with reduced adipose tissue insulin sensitivity. Circulating plasma leptin correlated with body fat percentage (females>males) and restricted compared with normal females had more body fat and increased abundance of PPARɤ, HSL, leptin and adiponectin mRNA in PAT at necropsy (109 weeks). Therefore, prenatal nutrient supply and sex both influence adipose tissue development with consequences for lipid metabolism and body composition persisting throughout the life-course.
Biophysical techniques to distinguish ligand binding modes in cytochrome P450 monooxygenases.

The cytochrome P450 superfamily of heme monooxygenases catalyze important chemical reactions across nature. The changes in the optical spectra of these enzymes, induced by the addition of substrates or inhibitors, are critical for assessing how these molecules bind to the P450, enhancing or inhibiting the catalytic cycle. Here we use the bacterial CYP199A4 en-zyme (Uniprot ID; Q2IUO2), from Rhodopseudomonas palustris HaA2, and a range of substituted benzoic acids to investi-gate different binding modes. 4-Methoxybenzoic acid elicits an archetypal type I spectral response due to a 95% switch from the low- to high-spin state with concomitant dissociation of the sixth aqua ligand. 4-(Pyridin-3-yl)- and 4-(pyridin-2-yl)-benzoic acid induced different type II UV-vis spectral responses in CYP199A4. The former induced a greater red shift in the Soret wavelength (424 versus 422 nm) along with a larger overall absorbance change and other differences in the α-, β- and δ-bands. There were also variations in the ferrous UV-vis spectra of these two substrate-bound forms with a spectrum indicative of Fe-N bond formation with 4-(pyridin-3-yl)benzoic acid. The crystal structures of CYP199A4, with the pyridinyl com-pounds bound, revealed that while the nitrogen of 4-(pyridin-3-yl)benzoic acid is coordinated to the heme, with 4-(pyridin-2-yl)benzoic acid an aqua ligand remains. Continuous wave and pulse EPR data in frozen solution revealed that the sub-strates are bound in the active site in a form consistent with the crystal structures. The redox potential of each CYP199A4-substrate combination was measured, allowing correlation between binding modes, spectroscopic properties and the ob-served biochemical activity.
The Neural Dynamics of Individual Differences in Episodic Autobiographical Memory

Abstract The ability to mentally travel to specific events from one’s past, dubbed episodic autobiographical memory (E-AM), contributes to adaptive functioning. Nonetheless, the mechanisms underlying its typical interindividual variation remain poorly understood. To address this issue, we capitalize on existing evidence that successful performance on E-AM tasks draws on the ability to visualize past episodes and reinstate their unique spatiotemporal context. Hence, here, we test whether features of the brain’s functional architecture relevant to perceptual versus conceptual processes shape individual differences in both self-rated E-AM and laboratory-based episodic memory (EM) for random visual scene sequences (visual EM). We propose that superior subjective E-AM and visual EM are associated with greater similarity in static neural organization patterns, potentially indicating greater efficiency in switching, between rest and mental states relevant to encoding perceptual information. Complementarily, we postulate that impoverished subjective E-AM and visual EM are linked to dynamic brain organization patterns implying a predisposition towards semanticizing novel perceptual information. Analyses were conducted on resting state and task-based fMRI data from 329 participants (160 women) in the Human Connectome Project (HCP) who completed visual and verbal EM assessments, and an independent gender diverse sample (N = 59) who self-rated their E-AM. Interindividual differences in subjective E-AM were linked to the same neural mechanisms underlying visual, but not verbal, EM, in general agreement with the hypothesized static and dynamic brain organization patterns. Our results suggest that higher E-AM entails more efficient processing of temporally extended information sequences, whereas lower E-AM entails more efficient semantic or gist-based processing.
Estimating treatment effects under untestable assumptions with nonignorable missing data

Nonignorable missing data poses key challenges for estimating treatment effects because the substantive model may not be identifiable without imposing further assumptions. For example, the Heckman selection model has been widely used for handling nonignorable missing data but requires the study to make correct assumptions, both about the joint distribution of the missingness and outcome and that there is a valid exclusion restriction. Recent studies have revisited how alternative selection model approaches, for example estimated by multiple imputation (MI) and maximum likelihood, relate to Heckman‐type approaches in addressing the first hurdle. However, the extent to which these different selection models rely on the exclusion restriction assumption with nonignorable missing data is unclear. Motivated by an interventional study (REFLUX) with nonignorable missing outcome data in half of the sample, this article critically examines the role of the exclusion restriction in Heckman, MI, and full‐likelihood selection models when addressing nonignorability. We explore the implications of the different methodological choices concerning the exclusion restriction for relative bias and root‐mean‐squared error in estimating treatment effects. We find that the relative performance of the methods differs in practically important ways according to the relevance and strength of the exclusion restriction. The full‐likelihood approach is less sensitive to alternative assumptions about the exclusion restriction than Heckman‐type models and appears an appropriate method for handling nonignorable missing data. We illustrate the implications of method choice for inference in the REFLUX study, which evaluates the effect of laparoscopic surgery on long‐term quality of life for patients with gastro‐oseophageal reflux disease.
Phytate degradation cascade in pigs as affected by phytase supplementation and rapeseed cake inclusion in corn–soybean meal-based diets

Abstract Two experiments (Exp.) with ileally cannulated growing barrows were conducted. The concentrations of positional inositol phosphate (InsP) isomers in ileal digesta and feces were determined, as well as the prececal and total tract phytate (InsP6) hydrolysis, and digestibility of dry matter, P, Ca, nitrogen, and gross energy. Prececal amino acid (AA) digestibility and digestive enzyme activities in ileal digesta were also studied. In both Exp. , pigs had an initial body weight (BW) of 28 kg and were completely randomized to a Double Latin Square Design with eight pigs, four diets, and three periods of 12 d each. Feces and ileal digesta were collected for 5 d and 2 d, respectively. Pigs were housed individually in stainless steel metabolic units. Water was available ad libitum and feed was provided two times daily at an amount of 4% of mean BW. In Exp. 1, pigs received a corn–soybean meal (SBM)-based diet that was supplemented with 0, 750, 1,500, or 3,000 FTU of a microbial phytase/kg diet. In Exp. 2, pigs were allotted to a 2 × 2 arrangement of diets based on corn and SBM or an SBM-rapeseed cake (RSC) mix and phytase supplementation at 0 or 1,500 FTU/kg of diet. In ileal digesta of pigs fed without the phytase supplement, the dominating InsP isomers beside InsP6 were InsP5 isomers. The InsP pattern in ileal digesta changed with the inclusion of microbial phytase in both Exp. , as there was a remarkable increase in Ins(1,2,5,6)P4 concentration (P < 0.001). In both Exp. , the myo-inositol concentration in ileal digesta was greater upon phytase addition (P < 0.001). Without phytase supplementation, prececal and total tract P digestibility were low, whereas hardly any InsP6 was excreted in feces. There was no difference between prececal and total tract P digestibility values. For most AA studied in Exp. 2, prececal digestibility was lower (P < 0.01) when the diet contained RSC. However, phytase supplementation did not significantly affect prececal AA digestibility in both Exp. The present study showed that InsP6 disappearance by the end of the ileum can be increased up to around 90% in SBM- and SBM–RSC-based diets when microbial phytase is supplemented, but prececal P digestibility hardly exceeded 60%. The study confirms that pigs cannot benefit from a remarkable InsP6 degradation in the hindgut.
Viperin, through its radical‐SAM activity, depletes cellular nucleotide pools and interferes with mitochondrial metabolism to inhibit viral replication

Viperin (RSAD2) is an antiviral radical S‐adenosylmethionine (SAM) enzyme highly expressed in different cell types upon viral infection. Recently, it has been reported that the radical‐SAM activity of viperin transforms cytidine triphosphate (CTP) to its analogue 3′‐deoxy‐3′,4′‐didehydro‐CTP (ddhCTP). Based on biochemical studies and cell biological experiments, it was concluded that ddhCTP and its nucleoside form ddhC do not affect the cellular concentration of nucleotide triphosphates and that ddhCTP acts as replication chain terminator. However, our re‐evaluation of the reported data and new results indicate that ddhCTP is not an effective viral chain terminator but depletes cellular nucleotide pools and interferes with mitochondrial activity to inhibit viral replication. Our analysis is consistent with a unifying view of the antiviral and radical‐SAM activities of viperin.
Emerging entities in NUTM1‐rearranged neoplasms

Structural alterations of NUTM1 were originally thought to be restricted to poorly differentiated carcinomas with variable squamous differentiation originating in the midline organs of children and adolescents. Termed NUT carcinomas (NCs), they were defined by a t(15;19) chromosomal rearrangement that was found to result in a BRD4‐NUTM1 gene fusion. However, the use of DNA and RNA‐based next‐generation sequencing has recently revealed a multitude of new NUTM1 fusion partners in a diverse array of neoplasms including sarcoma‐like tumors, poromas, and acute lymphoblastic leukemias (ALLs) that we propose to call NUTM1‐rearranged neoplasms (NRNs). Intriguingly, the nosology of NRNs often correlates with the functional classification of the fusion partner, suggesting different oncogenic mechanisms within each NRN division. Indeed, whereas NCs are characterized by their aggressiveness and intransigence to standard therapeutic measures, the more positive clinical outcomes seen in some sarcoma and ALL NRNs may reflect these mechanistic differences. Here we provide a broad overview of the molecular, nosological, and clinical features in these newly discovered neoplastic entities. We describe how aberrant expression of NUTM1 due to fusion with an N‐terminal DNA/chromatin‐binding protein can generate a potentially powerful chromatin modifier that can give rise to oncogenic transformation in numerous cellular contexts. We also conclude that classification, clinical behavior, and therapeutic options may be best defined by the NUTM1 fusion partner rather than by tumor morphology or immunohistochemical profile.
N-Acetylaspartate Is an Important Brain Osmolyte

Most of the human diseases related to various proteopathies are confined to the brain, which leads to the development of various forms of neurological disorders. The human brain consists of several osmolytic compounds, such as N-Acetylaspartate (NAA), myo-inositol (mI), glutamate (Glu), glutamine (Gln), creatine (Cr), and choline-containing compounds (Cho). Among these osmolytes, the level of NAA drastically decreases under neurological conditions, and, hence, NAA is considered to be one of the most widely accepted neuronal biomarkers in several human brain disorders. To date, no data are available regarding the effect of NAA on protein stability, and, therefore, the possible effect of NAA under proteopathic conditions has not been fully uncovered. To gain an insight into the effect of NAA on protein stability, thermal denaturation and structural measurements were carried out using two model proteins at different pH values. The results indicate that NAA increases the protein stability with an enhancement of structure formation. We also observed that the stabilizing ability of NAA decreases in a pH-dependent manner. Our study indicates that NAA is an efficient protein stabilizer at a physiological pH.
Synthesis and Cytotoxicity Studies on Ru and Rh Nanoparticles as Potential X-Ray Fluorescence Computed Tomography (XFCT) Contrast Agents

X-Ray fluorescence computed tomography (XFCT) is an emerging biomedical imaging technique, which demands the development of new contrast agents. Ruthenium (Ru) and rhodium (Rh) have spectrally attractive Kα edge energies, qualifying them as new XFCT bio-imaging probes. Metallic Ru and Rh nanoparticles are synthesized by polyol method, in the presence of a stabilizer. The effect of several reaction parameters, including reaction temperature time, precursor and stabilizer concentration, and stabilizer molecular weight, on the size of particles, were studied. Resultant materials were characterized in detail using XRD, TEM, FT-IR, DLS-zeta potential and TGA techniques. Ru particles in the size range of 1–3 nm, and Rh particles of 6–9 nm were obtained. At physiological pH, both material systems showed agglomeration into larger assemblies ranging from 12–104 nm for Ru and 25–50 nm for Rh. Cytotoxicity of the nanoparticles (NPs) was evaluated on macrophages and ovarian cancer cells, showing minimal toxicity in doses up to 50 μg/mL. XFCT performance was evaluated on a small-animal-sized phantom model, demonstrating the possibility of quantitative evaluation of the measured dose with an expected linear response. This work provides a detailed route for the synthesis, size control and characterization of two materials systems as viable contrast agents for XFCT bio-imaging.
Intermittent fasting and weight loss: Systematic review.

OBJECTIVE To examine the evidence for intermittent fasting (IF), an alternative to calorie-restricted diets, in treating obesity, an important health concern in Canada with few effective office-based treatment strategies. DATA SOURCES A MEDLINE and EMBASE search from January 1, 2000, to July 1, 2019, yielded 1200 results using the key words fasting, time restricted feeding, meal skipping, alternate day fasting, intermittent fasting, and reduced meal frequency. STUDY SELECTION Forty-one articles describing 27 trials addressed weight loss in overweight and obese patients: 18 small randomized controlled trials (level I evidence) and 9 trials comparing weight after IF to baseline weight with no control group (level II evidence). Studies were often of short duration (2 to 26 weeks) with low enrolment (10 to 244 participants); 2 were of 1-year duration. Protocols varied, with only 5 studies including patients with type 2 diabetes. SYNTHESIS All 27 IF trials found weight loss of 0.8% to 13.0% of baseline weight with no serious adverse events. Twelve studies comparing IF to calorie restriction found equivalent results. The 5 studies that included patients with type 2 diabetes documented improved glycemic control. CONCLUSION Intermittent fasting shows promise for the treatment of obesity. To date, the studies have been small and of short duration. Longer-term research is needed to understand the sustainable role IF can play in weight loss.
Parallel quorum-sensing system in Vibrio cholerae prevents signal interference inside the host

Many bacteria use quorum sensing (QS) to regulate virulence factor production in response to changes in population density. QS is mediated through the production, secretion, and detection of signaling molecules called autoinducers (AIs) to modulate population-wide behavioral changes. Four histidine kinases, LuxPQ, CqsS, CqsR and VpsS, have been identified in Vibrio cholerae as QS receptors to activate virulence gene expression at low cell density. Detection of AIs by these receptors leads to virulence gene repression at high cell density. The redundancy among these receptors is puzzling since any one of the four receptors is sufficient to support colonization of V. cholerae in the host small intestine. It is believed that one of the functions of such circuit architecture is to prevent interference on any single QS receptor. However, it is unclear what natural molecules can interfere V. cholerae QS and in what environment interference is detrimental. We show here mutants expressing only CqsR without the other three QS receptors are defective in colonizing the host large intestine. We identified ethanolamine, a common intestinal metabolite that can function as a chemical source of QS interference. Ethanolamine specifically interacts with the ligand-binding CACHE domain of CqsR and induces a premature QS response in V. cholerae mutants expressing only CqsR without the other three QS receptors. The effect of ethanolamine on QS gene expression and host colonization is abolished by mutations that disrupt CqsR signal sensing. V. cholerae defective in producing ethanolamine is still proficient in QS, therefore, ethanolamine functions only as an external cue for CqsR. Our findings suggest the inhibitory effect of ethanolamine on CqsR could be a possible source of QS interference but is masked by the presence of the other parallel QS pathways, allowing V. cholerae to robustly colonize the host.
Characterization and Antioxidant Activity Determination of Neutral and Acidic Polysaccharides from Panax Ginseng C. A. Meyer

Panax ginseng (P. ginseng) is the most widely consumed herbal plant in Asia and is well-known for its various pharmacological properties. Many studies have been devoted to this natural product. However, polysaccharide’s components of ginseng and their biological effects have not been widely studied. In this study, white ginseng neutral polysaccharide (WGNP) and white ginseng acidic polysaccharide (WGAP) fractions were purified from P. ginseng roots. The chemical properties of WGNP and WGAP were investigated using various chromatography and spectroscopy techniques, including high-performance gel permeation chromatography, Fourier-transform infrared spectroscopy, and high-performance liquid chromatography with an ultra-violet detector. The antioxidant, anti-radical, and hydrogen peroxide scavenging activities were evaluated in vitro and in vivo using Caenorhabditis elegans as the model organism. Our in vitro data by ABTS (2,2′-azino-bis-(3-ethylbenzothiazoline-6-sulfonic acid), reducing power, ferrous ion chelating, and hydroxyl radical scavenging activity suggested that the WGAP with significantly higher uronic acid content and higher molecular weight exhibits a much stronger antioxidant effect as compared to that of WGNP. Similar antioxidant activity of WGAP was also confirmed in vivo by evaluating internal reactive oxygen species (ROS) concentration and lipid peroxidation. In conclusion, WGAP may be used as a natural antioxidant with potent scavenging and metal chelation properties.
Health Literacy as a Shared Capacity: Does the Health Literacy of a Country Influence the Health Disparities among Immigrants?

Health literacy (HL) is an individual ability as well as a distributed resource available within an individual’s social network. We performed an explorative study assessing the role of HL as the country-level ecological variable in predicting the health disparities among immigrants. Country-level HL data were obtained from the publicly available first European Health Literacy Survey reports. Individual-level data on citizenship, perceived health status, body mass index, smoking habits, physical activity and attendance at breast and cervical cancer screening were extracted from the European Health Interview Survey of Eurostat. Data from both sources were obtained for Austria, Bulgaria, Greece, Poland and Spain. The country-specific odds ratio (OR) for the association between the participants’ citizenship and other individual health-relevant characteristics was pooled into summary OR using random-effects models. Meta-regression was used to explore whether the HL of a country could explain part of the between-countries heterogeneity. Results: For the perceived health status, nutritional status and attendance at cervical cancer screening, the lower was the country-level HL (as ecological variable), the higher were the health inequalities relating to citizenship. The results of our exploratory research suggest that improving the population HL may help mitigate health inequalities between residents and migrants.