Miracle-dz/UniFAR-FTUs huggingface dataset:
The effects of allospecific mitochondrial genome on the fitness of northern redbelly dace (Chrosomus eos)

Abstract Instantaneous mitochondrial introgression events allow the disentangling of the effects of hybridization from those of allospecific mtDNA. Such process frequently occurred in the fish Chrosomus eos, resulting in cybrid individuals composed of a C. eos nuclear genome but with a C. neogaeus mtDNA. This provides a valuable model to address the fundamental question: How well do introgressed individuals perform in their native environment? We infer where de novo production of cybrids occurred to discriminate native environments from those colonized by cybrids in 25 sites from two regions (West‐Qc and East‐Qc) in Quebec (Canada). We then compared the relative abundance of wild types and cybrids as a measure integrating both fitness and de novo production of cybrids. According to mtDNA variation, 12 introgression events are required to explain the diversity of cybrids. Five cybrid lineages could not be associated with in situ introgression events. This includes one haplotype carried by 93% of the cybrids expected to have colonized West‐Qc. These cybrids also displayed a nearly complete allopatric distribution with wild types. We still inferred de novo production of cybrids at seven sites, that accounted for 70% of the cybrids in East‐Qc. Wild‐type and cybrid individuals coexist in all East‐Qc sites while cybrids were less abundant. Allopatry of cybrids restricted to the postglacial expansion suggests the existence of higher fitness for cybrids in specific conditions, allowing for the colonization of different environments and expanding the species’ range. However, allospecific mtDNA does not provide a higher fitness to cybrids in their native environment compared to wild types, making the success of an introgressed lineage uncertain.
Pyruvate dehydrogenase activation in inactive muscle during and after maximal exercise in men.

Pyruvate dehydrogenase activity (PDHa) and acetyl-group accumulation were examined in the inactive deltoid muscle in response to maximal leg exercise in men. Seven subjects completed three consecutive 30-s bouts of maximal isokinetic cycling, with 4-min rest intervals between bouts. Biopsies of the deltoid were obtained before exercise, after bouts 1 and 3, and after 15 min of rest recovery. Inactive muscle lactate (LA) and pyruvate (PYR) contents increased more than twofold ( P < 0.05) after exercise ( bout 3) and remained elevated after 15 min of recovery ( P < 0.05). Increased PYR accumulation secondary to LA uptake by the inactive deltoid was associated with greater PDHa, which progressively increased from 0.71 ± 0.23 mmol ⋅ min-1 ⋅ kg wet wt-1 at rest to a maximum of 1.83 ± 0.30 mmol ⋅ min-1 ⋅ kg wet wt-1 after bout 3( P < 0.05) and remained elevated after 15 min of recovery (1.63 ± 0.24 mmol ⋅ min-1 ⋅ kg wet wt-1; P < 0.05). Acetyl-CoA and acetylcarnitine accumulations were unaltered. Increased PDHa allowed and did not limit the oxidation of LA and PYR in inactive human skeletal muscle after maximal exercise.
Lipid standardization of serum fat-soluble antioxidant concentrations: the YALTA study.

BACKGROUND Blood lipids can influence fat-soluble antioxidant concentrations and confound their interpretation as indicators of antioxidant intake status and disease risk. OBJECTIVES The objectives were to identify lipoproteins that can confound the interpretation of serum fat-soluble antioxidants, to evaluate the amount of the confounding, and to recommend a method for standardizing blood concentrations of fat-soluble antioxidants. DESIGN Several methods of lipid standardization of fat-soluble antioxidants were evaluated in a large cohort of young adults with the use of both cross-sectional and longitudinal data analysis. RESULTS Tocopherol and carotenoid concentrations were associated with plasma total cholesterol and its components, LDL, HDL, and VLDL cholesterol (estimated as plasma total triacylglycerols/5), some of which were independent predictors for all of the fat-soluble antioxidants. Among supplement nonusers, the most amphipathic (polar) of the antioxidants (alpha-tocopherol, gamma-tocopherol, and zeaxanthin plus lutein) and lycopene were associated strongly with these lipid fractions (R(2) = 0.09, 0.40). Consistent with a causal association in which blood antioxidant concentrations change as blood lipid concentrations change, similar relations were found for changes in blood antioxidant and lipid concentrations over a 7-y period. Concentrations of the remaining carotenoids (beta-cryptoxanthin, alpha-carotene, and beta-carotene) had a weaker association with plasma lipoproteins (R(2) < 0.06). Similar relations were found for supplement users. CONCLUSIONS The simultaneous adjustment of the concentrations of tocopherols, zeaxanthin plus lutein, and lycopene for VLDL, HDL, and LDL cholesterol is recommended. This method is practical and can provide a basis for the standardization of carotenoid and tocopherol concentrations.
Protein metabolism in children with edematous malnutrition and acute lower respiratory infection.

This study tested the hypothesis that wholebody protein kinetics remain low in children with edematous malnutrition and acute infection. Thirteen children with edematous malnutrition and acute infection (subjects) were compared with 14 uninfected children with edematous malnutrition early in recovery (control children). Protein kinetics were determined by using a primed, constant intravenous infusion of [13C]leucine and [15N2]urea in the postabsorptive state. Calculations of rates of whole-body protein synthesis and breakdown were based on the rate of leucine appearance; the rate of leucine oxidation was estimated from the rate of urea appearance. Protein synthesis and breakdown rates were lower in subjects than in control children (97 +/- 30 compared with 153 +/- 67, P < 0.01, and 103 +/- 30 compared with 160 +/- 67 mumol leucine.kg-1.h-1, P < 0.01). No difference was found between the two groups in the rate of urea appearance, but this analysis only had a statistical power of 54%. The absence of the expected increase in the rate of protein turnover during acute infection in edematous malnutrition implies that acute phase proteins are made with a corresponding depletion of muscle, hepatic, and other body proteins such as albumin, and that there may also be a blunting of the acute phase response.
Verbal Memory Performance and Reduced Cortical Thickness of Brain Regions Along the Uncinate Fasciculus in Young Adult Cannabis Users

Abstract Introduction: Memory impairment is one of the most commonly reported effects of cannabis use, especially among those who initiate use earlier, perhaps due to the effects of delta-9- tetrahydrocannabinol on cannabinoid (CB1) receptors in the brain. Studies have increasingly investigated whether cannabis use is associated with impairments in verbal memory, and with alterations in brain structures underlying verbal memory. The uncinate fasciculus (UF), a long-range white matter tract, connects regions with densely localized CB1 receptors that are important in verbal memory. This study investigated the impact of cannabis use on UF structures and its association with memory performance in young adult cannabis users (CU) and non-using controls (CON). Materials and Methods: Nineteen CU and 22 CON completed a verbal memory task and a neuroimaging protocol, in which diffusion tensor imaging and structural scans were collected. We compared memory performance, diffusion and tractography measures of the UF, and cortical thickness of regions connected by the UF, between CU and CON. In regions showing a significant group effect, we also examined associations between verbal memory performance, cortical thickness, and age of onset of cannabis use. Results: Compared to non-users, CU had worse memory performance, decreased fiber bundle length in the UF, and decreased cortical thickness of brain regions along the UF such as the entorhinal cortex and fusiform gyrus. Verbal memory performance was significantly associated with age of onset of cannabis use, indicating that those who initiated cannabis use at an earlier age performed worse. Cortical thickness of the entorhinal cortex was significantly correlated with age of first use and memory performance. Conclusion: This study provides evidence that cannabis use, especially when initiated at a young age, may be associated with worse verbal memory and altered neural development along the UF. Reductions in cortical thickness in regions implicated in memory processes may underlie weaknesses in verbal memory performance.
Effect of supplemental zinc on the growth and serum zinc concentrations of prepubertal children: a meta-analysis of randomized controlled trials.

BACKGROUND Multiple studies have been carried out to assess the effect of zinc supplementation on children's growth. The results of these studies are inconsistent, and the factors responsible for these varied outcomes are unknown. OBJECTIVE Meta-analyses of randomized controlled intervention trials were therefore completed to assess the effect of zinc supplementation on the physical growth and serum zinc concentrations of prepubertal children. DESIGN A total of 33 acceptable studies with appropriate data were identified by MEDLINE (National Library of Medicine, Bethesda, MD) searches and other methods. Weighted mean effect sizes (expressed in SD units) were calculated for changes in height, weight, weight-for-height, and serum zinc concentration by using random-effects models; factors associated with effect sizes were explored by meta-regression techniques. RESULTS Zinc supplementation produced highly significant, positive responses in height and weight increments, with effect sizes of 0.350 (95% CI: 0.189, 0.511) and 0.309 (0.178, 0.439), respectively. There was no significant effect of zinc on weight-for-height indexes [weighted mean effect size: -0.018 (-0.132, 0.097)]. Zinc supplementation caused a large increase in the children's serum zinc concentrations, with an effect size of 0.820 (0.499, 1.14). Growth responses were greater in children with low initial weight-for-age z scores and in those aged >6 mo with low initial height-for-age z scores. CONCLUSIONS Interventions to improve children's zinc nutriture should be considered in populations at risk of zinc deficiency, especially where there are elevated rates of underweight or stunting. The population mean serum zinc concentration is a useful indicator of the successful delivery and absorption of zinc supplements in children.
De-Regulation of JNK and JAK/STAT Signaling in ESCRT-II Mutant Tissues Cooperatively Contributes to Neoplastic Tumorigenesis

Multiple genes involved in endocytosis and endosomal protein trafficking in Drosophila have been shown to function as neoplastic tumor suppressor genes (nTSGs), including Endosomal Sorting Complex Required for Transport-II (ESCRT-II) components vacuolar protein sorting 22 (vps22), vps25, and vps36. However, most studies of endocytic nTSGs have been done in mosaic tissues containing both mutant and non-mutant populations of cells, and interactions among mutant and non-mutant cells greatly influence the final phenotype. Thus, the true autonomous phenotype of tissues mutant for endocytic nTSGs remains unclear. Here, we show that tissues predominantly mutant for ESCRT-II components display characteristics of neoplastic transformation and then undergo apoptosis. These neoplastic tissues show upregulation of c-Jun N-terminal Kinase (JNK), Notch, and Janus Kinase (JAK)/Signal Transducer and Activator of Transcription (STAT) signaling. Significantly, while inhibition of JNK signaling in mutant tissues partially inhibits proliferation, inhibition of JAK/STAT signaling rescues other aspects of the neoplastic phenotype. This is the first rigorous study of tissues predominantly mutant for endocytic nTSGs and provides clear evidence for cooperation among de-regulated signaling pathways leading to tumorigenesis.
IRT studies of many groups: the alignment method

Asparouhov and Muthén (2014) presented a new method for multiple-group confirmatory factor analysis (CFA), referred to as the alignment method. The alignment method can be used to estimate group-specific factor means and variances without requiring exact measurement invariance. A strength of the method is the ability to conveniently estimate models for many groups, such as with comparisons of countries. This paper focuses on IRT applications of the alignment method. An empirical investigation is made of binary knowledge items administered in two separate surveys of a set of countries. A Monte Carlo study is presented that shows how the quality of the alignment can be assessed.
Efficient Data Association in Images using Active Matching

In the feature matching tasks which form an integral part of visual tracking or SLAM, there are invariably priors available on the absolute and/or relative image locations of features of interest. Usually, these priors are used post-hoc in the process of resolving feature matches and obtaining final scen estimates, via ‘first get candidate matches, then resolve’ conse nsus algorithms such as RANSAC or JCBB. In this paper we show that the dramatically different approach of using priors dynamically to guide a feature by feature matching search can achieve global matching with much fewer image processing operations and lower overall computational cost. Essentially, we put image processing into the loop of the search for global consensus. In particular, our approach is able to cope with significant image ambiguity thanks to a dynamic mixture of Gaussians treatment. In our fully Bayesian algorithm, the choice of the most efficient search action at each step is guided intuitively and rigorously by expected Shannon information gain. We demonstrate the algorithm in feature matching as part of a sequential SLAM system for 3D camera tracking. Robust, real-time matching can be achieved even in the previously unmanageable case of jerky, rapid motion necessitating weak motion modelling.
Acidification increases abundances of Vibrionales and Planctomycetia associated to a seaweed-grazer system: potential consequences for disease and prey digestion efficiency

Ocean acidification significantly affects marine organisms in several ways, with complex interactions. Seaweeds might benefit from rising CO2 through increased photosynthesis and carbon acquisition, with subsequent higher growth rates. However, changes in seaweed chemistry due to increased CO2 may change the nutritional quality of tissue for grazers. In addition, organisms live in close association with a diverse microbiota, which can also be influenced by environmental changes, with feedback effects. As gut microbiomes are often linked to diet, changes in seaweed characteristics and associated microbiome can affect the gut microbiome of the grazer, with possible fitness consequences. In this study, we experimentally investigated the effects of acidification on the microbiome of the invasive brown seaweed Sargassum muticum and a native isopod consumer Synisoma nadejda. Both were exposed to ambient CO2 conditions (380 ppm, pH 8.16) and an acidification treatment (1,000 ppm, pH 7.86) for three weeks. Microbiome diversity and composition were determined using high-throughput sequencing of the variable regions V5-7 of 16S rRNA. We anticipated that as a result of acidification, the seaweed-associated bacterial community would change, leading to further changes in the gut microbiome of grazers. However, no significant effects of elevated CO2 on the overall bacterial community structure and composition were revealed in the seaweed. In contrast, significant changes were observed in the bacterial community of the grazer gut. Although the bacterial community of S. muticum as whole did not change, Oceanospirillales and Vibrionales (mainly Pseudoalteromonas) significantly increased their abundance in acidified conditions. The former, which uses organic matter compounds as its main source, may have opportunistically taken advantage of the possible increase of the C/N ratio in the seaweed under acidified conditions. Pseudoalteromonas, commonly associated to diseased seaweeds, suggesting that acidification may facilitate opportunistic/pathogenic bacteria. In the gut of S. nadejda, the bacterial genus Planctomycetia increased abundance under elevated CO2. This shift might be associated to changes in food (S. muticum) quality under acidification. Planctomycetia are slow-acting decomposers of algal polymers that could be providing the isopod with an elevated algal digestion and availability of inorganic compounds to compensate the shifted C/N ratio under acidification in their food. In conclusion, our results indicate that even after only three weeks of acidified conditions, bacterial communities associated to ungrazed seaweed and to an isopod grazer show specific, differential shifts in associated bacterial community. These have potential consequences for seaweed health (as shown in corals) and isopod food digestion. The observed changes in the gut microbiome of the grazer seem to reflect changes in the seaweed chemistry rather than its microbial composition.
Airway surface fluid volume and Cl content in cystic fibrosis and normal bronchial xenografts.

We describe the use of an in vivo human bronchial xenograft model of cystic fibrosis (CF) and non-CF airways to investigate pathophysiological alterations in airway surface fluid (ASF) volume (Vs) and Cl content. Vs was calculated based on the dilution of an impermeable marker, [3H]inulin, during harvesting of ASF from xenografts with an isosmotic Cl-free solution. These calculations demonstrated that Vs in CF xenographs (28 ± 3.0 μl/cm2; n = 17) was significantly less than that of non-CF xenografts (35 ± 2.4 μl/cm2; n = 30). The Cl concentration of ASF ([Cl]s) was determined using a solid-state AgCl electrode and adjusted for dilution during harvesting using the impermeable [3H]inulin marker. Cumulative results demonstrate small but significant elevations ( P < 0.045) in [Cl]s in CF (125 ± 4 mM; n = 27) compared with non-CF (114 ± 4 mM; n = 48) xenografts. To investigate potential mechanisms by which CF airways may facilitate a higher level of fluid absorption yet retain slightly elevated levels of Cl, we sought to evaluate the capacity of CF and non-CF airways to absorb both 22Na and36Cl. Two consistent findings were evident from these studies. First, in both CF and non-CF xenografts,22Na and36Cl were always absorbed in an equal molar ratio. Second, CF xenografts hyperabsorbed (∼1.5-fold higher) both 22Na and36Cl compared with non-CF xenografts. These results substantiate previously documented findings of elevated Na absorption in CF airways and also suggest that the slightly elevated [Cl]s found in this study of CF xenograft epithelia does not occur through a mechanism of decreased apical permeability to Cl.
Dysfunction of cortical synapse-specific mitochondria in developing rats exposed to lead and its amelioration by ascorbate supplementation

Background Lead (Pb) is a widespread environmental neurotoxin and its exposure even in minute quantities can lead to compromised neuronal functions. A developing brain is particularly vulnerable to Pb mediated toxicity and early-life exposure leads to permanent alterations in brain development and neuronal signaling and plasticity, culminating into cognitive and behavioral dysfunctions and elevated risk of neuropsychiatric disorders later in life. Nevertheless, the underlying biochemical mechanisms have not been completely discerned. Methods Because of their ability to fulfill high energy needs and to act as calcium buffers in events of high intensity neuronal activity as well as their adaptive regulatory capability to match the requirements of the dynamicity of synaptic signaling, synapse-specific or synaptic mitochondria (SM) are critical for synaptic development, function and plasticity. Our aim for the present study hence was to characterize the effects of early-life Pb exposure on the functions of SM of prepubertal rats. For this purpose, employing a chronic model of Pb neurotoxicity, we exposed rat pups perinatally and postnatally to Pb and used a plethora of colorimetric and fluorometric assays for assessing redox and bioenergetic properties of SM. In addition, taking advantage of its ability as an antioxidant and as a metal chelator, we employed ascorbic acid (vitamin C) supplementation as an ameliorative therapeutic strategy against Pb-induced neurotoxicity and dysfunction of SM. Results Our results suggest that early-life exposure to Pb leads to elevated oxidative stress in cortical SM with consequent compromises in its energy metabolism activity. Ascorbate supplementation resulted in significant recovery of Pb-induced oxidative stress and functional compromise of SM. Conclusion Alterations in redox status and bioenergetic properties of SM could potentially contribute to the synaptic dysfunction observed in events of Pb neurotoxicity. Additionally, our study provides evidence for suitability of ascorbate as a significant ameliorative agent in tacking Pb neurotoxicity.
Mechanism of prejunctional muscarinic receptor-mediated inhibition of neurogenic vasodilation in cerebral arteries.

Nitric oxide (NO) is a major transmitter in mediating cerebral neurogenic vasodilation in several species. Recent findings have suggested that acetylcholine, which is costored with NO in cerebral perivascular nerves, plays a role in modulating NO release, presumably by acting on muscarinic (M) receptors on nitric oxidergic nerve terminals. The present study was designed using an in vitro tissue bath technique to pharmacologically characterize the presynaptic muscarinic-receptor subtype(s) that mediate modulation of NO release and therefore neurogenic vasodilation and to investigate further the possible mechanisms involved in this presynaptic modulation in porcine basilar arteries. Transmural nerve stimulation (TNS) elicited a frequency-dependent, tetrodotoxin-sensitive relaxation. The relaxation was abolished by nitro-l-arginine (30 μM) and was completely reversed byl-arginine andl-citrulline, but not by their d-enantiomers. Atropine (0.01-1 μM), pirenzepine (an M1-receptor antagonist, 0.01-1 μM), and methoctramine (an M2-receptor antagonist, 0.01-1 μM), but not 4-DAMP (an M3-receptor antagonist) or tropicamide (an M4-receptor antagonist) at concentrations as high as 10 mM, significantly increased the TNS-elicited relaxation. This relaxation, on the other hand, was significantly attenuated by arecaidine but-2-ynyl ester tosylate (an M2-receptor agonist, 0.1 μM) but was not affected by McN-A-343 (an M1-receptor agonist, 1 μM). Double-labeling immunohistochemical study demonstrated that perivascular M2receptor-immunoreactive fibers were completely coincident with NADPH diaphorase fibers. Furthermore, the muscarinic receptor-mediated modulation of TNS-elicited relaxation was completely prevented by ω-conotoxin GVIA (0.1 μM), a specific N-type Ca2+ channel inhibitor, but was still observed in the presence of tetraethylammonium (1 mM), 8-bromo-cAMP (0.5 mM), and pertussis toxin. It is concluded that the presynaptic M2 receptors on porcine cerebral perivascular nitric oxidergic nerves mediate inhibition of NO release. The inhibition is due primarily to a decreased Ca2+ influx through N-type Ca2+ channels.