Miracle-dz/UniFAR-FTUs huggingface dataset:
On the Influence of Structural Connectivity on the Correlation Patterns and Network Synchronization

Since brain structural connectivity is the foundation of its functionality, in order to understand brain abilities, studying the relation between structural and functional connectivity is essential. Several approaches have been applied to measure the role of the structural connectivity in the emergent correlation/synchronization patterns. In this study, we investigates the cross-correlation and synchronization sensitivity to coupling strength between neural regions for different topological networks. We model the neural populations by a neural mass model that express an oscillatory dynamic. The results highlight that coupling between neural ensembles leads to various cross-correlation patterns and local synchrony even on an ordered network. Moreover, as the network departs from an ordered organization to a small-world architecture, correlation patterns, and synchronization dynamics change. Interestingly, at a certain range of the synaptic strength, by fixing the structural conditions, different organized patterns are seen at the different input signals. This variety switches to a bifurcation region by increasing the synaptic strength. We show that topological variations is a major factor of synchronization behavior and lead to alterations in correlated local clusters. We found the coupling strength (between cortical areas) to be especially important at conversions of correlation and synchronization states. Since correlation patterns generate functional connections and transitions of functional connectivity have been related to cognitive operations, these diverse correlation patterns may be considered as different dynamical states corresponding to various cognitive tasks.
Atonal Music: Can Uncertainty Lead to Pleasure?

In recent years, the field of neuroaesthetics has gained considerable attention with music being a favored object of study. The majority of studies concerning music have, however, focused on the experience of Western tonal music (TM), which is characterized by tonal hierarchical organization, a high degree of consonance, and a tendency to provide the listener with a tonic as a reference point during the listening experience. We argue that a narrow focus on Western TM may have led to a one-sided view regarding the qualities of the aesthetic experience of music since Western art music from the 20th and 21st century like atonal music (AM) – while lacking a tonal hierarchical structure, and while being highly dissonant and hard to predict – is nevertheless enjoyed by a group of avid listeners. We propose a research focus that investigates, in particular, the experience of AM as a novel and compelling way with which to enhance our understanding of both the aesthetic appreciation of music and the role of predictive models in the context of musical pleasure. We use music theoretical analysis and music information retrieval methods to demonstrate how AM presents the listener with a highly uncertain auditory environment. Specifically, an analysis of a corpus of 100 musical segments is used to illustrate how tonal classical music and AM differ quantitatively in terms of both key and pulse clarity values. We then examine person related, extrinsic and intrinsic factors, that point to potential mechanisms underlying the appreciation and pleasure derived from AM. We argue that personality traits like “openness to experience,” the framing of AM as art, and the mere exposure effect are key components of such mechanisms. We further argue that neural correlates of uncertainty estimation could represent a central mechanism for engaging with AM and that such contexts engender a comparatively weak predictive model in the listener. Finally we argue that in such uncertain contexts, correct predictions may be more subjectively rewarding than prediction errors since they signal to the individual that their predictive model is improving.
Improving the Cryotolerance of Wine Yeast by Interspecific Hybridization in the Genus Saccharomyces

Fermentations carried out at low temperatures (10–15°C) enhance the production and retention of flavor volatiles, but also increase the chances of slowing or arresting the process. Notwithstanding, as Saccharomyces cerevisiae is the main species responsible for alcoholic fermentation, other species of the genus Saccharomyces, such as cryophilic species Saccharomyces eubayanus, Saccharomyces kudriavzevii and Saccharomyces uvarum, are better adapted to low-temperature fermentations during winemaking. In this work, a Saccharomyces cerevisiae × S. uvarum hybrid was constructed to improve the enological features of a wine S. cerevisiae strain at low temperature. Fermentations of white grape musts were performed, and the phenotypic differences between parental and hybrid strains under different temperature conditions were examined. This work demonstrates that hybridization constitutes an effective approach to obtain yeast strains with desirable physiological features, like low-temperature fermentation capacity, which genetically depend on the expression of numerous genes (polygenic character). As this interspecific hybridization approach is not considered a GMO, the genetically improved strains can be quickly transferred to the wine industry.
Stent-Jailing Technique Reduces Aneurysm Recurrence More Than Stent-Jack Technique by Causing Less Mechanical Forces and Angiogenesis and Inhibiting TGF-β/Smad2,3,4 Signaling Pathway in Intracranial Aneurysm Patients

Background: Stent-jailing and stent-jack are used for stent-assisted coil embolism (SCE) in intracranial aneurysm (IA) therapy, and cause different incidences of IA recurrence. Angiogenesis strongly correlates with aneurysm accumulation. Stent-jack causes higher mechanical forces in cerebral vessels than stent-jailing. Mechanical forces, as well as TGF-β/Smad2,3,4 signaling pathway, may play an important factor in IA recurrence by affecting angiogenesis. Methods: We explored the effects of stent-jailing or stent-jack technique on IA recurrence by investigating mechanical forces, TGF-β/Smad2,3,4 signaling pathway and the incidence of angiogenesis in IA patients. One-hundred-eighty-one IA patients were assigned into stent-jailing (n = 93) and stent-jacket groups (n = 88). The clinical outcome was evaluated using Glasgow Outcome Score (GOS) and aneurysm occlusion grades. The percentage of CD34+EPCs (releasing pro-angiogenic cytokines) in peripheral blood was measured by flow cytometer. Endothelial cells were separated from cerebral aneurysm and malformed arteries via immunomagnetic cell sorting. Angiogenesis was measured by microvessel density (MVD) using anti-CD34 monoclonal antibody staining before using the stent, immediately after surgery and 2 years later. Meanwhile, the mechanical forces in cerebral vessels were determined by measuring endothelial shear stress (ESS) via a computational method. TGF-β and Smad2,3,4 were measured by real-time qPCR and Western Blot. Tube formation analysis was performed to test the relationship between angiogenesis and TGF-β, and the effects of different techniques on angiogenesis. Results: After a 2-year follow-up, 85 and 81 patients from stent-jailing and stent-jack groups, respectively, completed the experiment. Stent-jailing technique improved GOS and reduced aneurysm occlusion grades higher than the stent-jack technique (P < 0.05). The counts of CD34+EPCs and MVD values in the stent-jailing group were lower than the stent-jack group (P < 0.05). ESS values in sent-jailing group were lower than the stent-jack group (P < 0.05), and positively correlated with MVD values (P < 0.05). TGF-β and Smad2,3,4 levels in sent-jailing group were also lower than the stent-jack group (P < 0.05). TGF-β was associated with angiogenesis incidence and stent-jack caused angiogenesis incidence more than stent-jailing. Conclusion: Stent-jailing technique reduces IA recurrence more than stent-jack by causing less mechanical forces, angiogenesis and inhibiting TGF-β/Smad2,3,4 signaling in IA patients.
Early and Delayed Alteration of Atrial Electrograms Around Single Radiofrequency Ablation Lesion

Purpose: The acute effect of radiofrequency (RF) ablation includes local necrosis and oedema. We investigated the spatiotemporal change of atrial electrograms in the area surrounding the site of single standardized pulse of RF energy. Methods: The study enrolled 12 patients (45–67 years, 10 males) with paroxysmal atrial fibrillation (AF) undergoing ablation procedure with irrigated-tip ablation catheter and 3D navigation. The high-density mapping/remapping (129 ± 63 points) within the circular area with radius of ~10 mm, centered at the pre-specified posterior left pulmonary vein antrum ablation site was performed at baseline, immediately after single RF energy delivery (25 W, 30 s, 20 ml/min) and after 30 min waiting period. Bipolar voltages of atrial electrograms (A-EGM-biV) were averaged within the central and 12 adjacent left atrium segments and their relative change was studied. Results: After the ablation, overall A-EGM-biV within the mapping zone (3.51 ± 1.89 mV at baseline) reduced to 2.83 ± 1.77 mV (immediately) and to 2.68 ± 1.58 mV (after 30 min waiting period). In per-segment pair-wise comparison, we observed highly significant change in A-EGM-biV that extended up to the distance of 8.8 mm from the lesion core. The maximum early A-EGM-biV attenuation by 39–49% (P < 0.001) was registered in segments adjacent to pulmonary vein ostia. The subsequent (delayed) A-EGM-biV reduction by 17–24% (P < 0.05) was observed in opposite direction from the lesion center. Conclusions: Significant alteration of atrial electrograms was detectable rather distant from the central lesion. Spatiotemporal development of ablation lesion was eccentric/asymmetric. While acute A-EGM-biV reduction can be attributed predominantly to direct thermal injury, delayed effects are probably due to oedema progression.
Engineering Drought Resistance in Forest Trees

Climatic stresses limit plant growth and productivity. In the past decade, tree improvement programs were mainly focused on yield but it is obvious that enhanced stress resistance is also required. In this review we highlight important drought avoidance and tolerance mechanisms in forest trees. Genomes of economically important trees species with divergent resistance mechanisms can now be exploited to uncover the mechanistic basis of long-term drought adaptation at the whole plant level. Molecular tree physiology indicates that osmotic adjustment, antioxidative defense and increased water use efficiency are important targets for enhanced drought tolerance at the cellular and tissue level. Recent biotechnological approaches focused on overexpression of genes involved in stress sensing and signaling, such as the abscisic acid core pathway, and down-stream transcription factors. By this strategy, a suite of defense systems was recruited, generally enhancing drought and salt stress tolerance under laboratory conditions. However, field studies are still scarce. Under field conditions trees are exposed to combinations of stresses that vary in duration and magnitude. Variable stresses may overrule the positive effect achieved by engineering an individual defense pathway. To assess the usability of distinct modifications, large-scale experimental field studies in different environments are necessary. To optimize the balance between growth and defense, the use of stress-inducible promoters may be useful. Future improvement programs for drought resistance will benefit from a better understanding of the intricate networks that ameliorate molecular and ecological traits of forest trees.
New mtDNA Association Model, MutPred Variant Load, Suggests Individuals With Multiple Mildly Deleterious mtDNA Variants Are More Likely to Suffer From Atherosclerosis

The etiology of common complex diseases is multifactorial, involving both genetic, and environmental factors. A role for mitochondrial dysfunction and mitochondrial DNA (mtDNA) variation has been suggested in the pathogenesis of common complex traits. The aim of this study was to investigate a potential role of mtDNA variants in the development of obesity, diabetes, and atherosclerosis in the Polish population. Whole mtDNA sequences from 415 Polish individuals representing three disease cohorts and a control group were obtained using high-throughput sequencing. Two approaches for the assessment of mtDNA variation were applied, traditional mitochondrial haplogroup association analysis and the mutational or variant load model using the MutPred pathogenicity prediction algorithm for amino acid substitutions in humans. We present a possible association between mildly deleterious mtDNA variant load and atherosclerosis that might be due to having more than one likely mildly deleterious non-synonymous substitution. Moreover, it seems largely dependent upon a few common haplogroup associated variants with MutPred score above 0.5.
Streptococcus infantis, Streptococcus mitis, and Streptococcus oralis Strains With Highly Similar cps5 Loci and Antigenic Relatedness to Serotype 5 Pneumococci

Streptococcus pneumoniae is a highly impactful bacterial pathogen on a global scale. The principal pneumococcal virulence factor and target of effective vaccines is its polysaccharide capsule, of which there are many structurally distinct forms. Here, we describe four distinct strains of three Mitis group commensal species (Streptococcus infantis, Streptococcus mitis, and Streptococcus oralis) recovered from upper respiratory tract specimens from adults in Kenya and the United States that were PCR-positive for the pneumococcal serotype 5 specific gene, wzy5. For each of the four strains, the 15 genes comprising the capsular polysaccharide biosynthetic gene cluster (cps5) shared the same order found in serotype 5 pneumococci, and each of the serotype 5-specific genes from the serotype 5 pneumococcal reference strain shared 76–99% sequence identity with the non-pneumococcal counterparts. Double-diffusion experiments demonstrated specific reactivity of the non-pneumococcal strains with pneumococcal serotype 5 typing sera. Antiserum raised against S. mitis strain KE67013 specifically reacted with serotype 5 pneumococci for a positive Quellung reaction and stimulated serotype 5 specific opsonophagocytic killing of pneumococci. Four additional commensal strains, identified using PCR serotyping assays on pharyngeal specimens, revealed loci highly homologous to those of pneumococci of serotypes 12F, 15A, 18C, and 33F. These data, in particular the species and strain diversity shown for serotype 5, highlight the existence of a broad non-pneumococcal species reservoir in the upper respiratory tract for the expression of capsular polysaccharides that are structurally related or identical to those corresponding to epidemiologically significant serotypes. Very little is known about the genetic and antigenic capsular diversity among the vast array of commensal streptococcal strains that represent multiple diverse species. The discovery of serotype 5 strains within three different commensal species suggests that extensive capsular serologic overlap exists between pneumococci and other members of the diverse Mitis group. These findings may have implications for our current understanding of naturally acquired immunity to S. pneumoniae and pneumococcal serotype distributions in different global regions. Further characterization of commensal strains carrying homologs of serotype-specific genes previously thought to be specific for pneumococci of known serotypes may shed light on the evolution of these important loci.
Effect of Acetic Acid and Lactic Acid at Low pH in Growth and Azole Resistance of Candida albicans and Candida glabrata

Successful colonization of the acidic vaginal niche by C. glabrata and C. albicans depends on their ability to cope with the presence of lactic and acetic acids produced by commensal microbiota. As such, the inhibitory effect of these acids at a low pH in growth of C. glabrata and C. albicans was investigated. The effect of the presence of these organic acids in tolerance of the two Candida species to azoles used in treatment of vaginal infections was also investigated including eventual synergistic effects. Under the different experimental conditions tested lactic acid exerted no significant inhibitory effect against C. albicans or C. glabrata, contrasting with the generalized impression that the production of this acid is on the basis of the protective effect exerted by vaginal lactobacilii. Differently, C. glabrata and C. albicans exhibited susceptibility to acetic acid, more prominent at lower pHs and stronger for the latter species. Synergism between acetic acid and azoles was observed both for C. albicans and C. glabrata, while lactic acid-azole synergism was only efficient against C. albicans. Altogether our in vitro results indicate that tolerance to acetic acid at a low pH may play a more relevant role than tolerance to lactic acid in determining competitiveness in the vaginal tract of C. albicans and C. glabrata including under azole stress. Treatment of vaginal candidiasis with azoles may depend on the level of acetic and lactic acids present and improvements could be achieved synergizing the azole with these acids.
How to Discover a Planet Orbiting a Distant Star

Recently, thousands of planets have been discovered orbiting distant stars. We call these far-away planets exoplanets. Most exoplanets have been found by looking for tiny changes in the brightness of stars. When exoplanets pass in between their star and the Earth, they block out a bit of starlight, causing a small dip in the star’s brightness. Transits of exoplanets have revealed that the most common planets orbiting Sun-like stars are a bit bigger than the Earth and smaller than Neptune—unlike any planet in our Solar System.
SIRT6 Suppresses NFATc4 Expression and Activation in Cardiomyocyte Hypertrophy

NFATc4, a member from the Nuclear Factor of Activated T cells (NFATs) transcription factor family, plays a pivotal role in the development of cardiac hypertrophy. NFATc4 is dephosphorylated by calcineurin and translocated from the cytoplasm to the nucleus to regulate the expression of hypertrophic genes, like brain natriuretic polypeptide (BNP). The present study identified SIRT6, an important subtype of NAD+ dependent class III histone deacetylase, to be a negative regulator of NFATc4 in cardiomyocyte hypertrophy. In phenylephrine (PE)-induced hypertrophic cardiomyocyte model, overexpression of SIRT6 by adenovirus infection or by plasmid transfection repressed the protein and mRNA expressions of NFATc4, elevated its phosphorylation level, prevented its nuclear accumulation, subsequently suppressed its transcriptional activity and downregulated its target gene BNP. By contrast, mutant of SIRT6 without deacetylase activity (H133Y) did not demonstrate these effects, suggesting that the inhibitory effect of SIRT6 on NFATc4 was dependent on its deacetylase activity. Moreover, the effect of SIRT6 overexpression on repressing BNP expression was reversed by NFATc4 replenishment, whereas the effect of SIRT6 deficiency on upregulating BNP was recovered by NFATc4 silencing. Mechanistically, interactions between SIRT6 and NFATc4 might possibly facilitate the deacetylation of NFATc4 by SIRT6, thereby preventing the activation of NFATc4. In conclusion, the present study reveals that SIRT6 suppresses the expression and activation of NFATc4. These findings provide more evidences of the anti-hypertrophic effect of SIRT6 and suggest SIRT6 as a potential therapeutic target for cardiac hypertrophy.
Bacillus amyloliquefaciens Ameliorates Dextran Sulfate Sodium-Induced Colitis by Improving Gut Microbial Dysbiosis in Mice Model

Several Bacillus strains exert beneficial effects on the maintenance of intestinal homeostasis and host health. However, whether Bacillus amyloliquefaciens (BA) can improve gut microbial dysbiosis and ameliorate colitis is unknown. Therefore, we conducted the present study to investigate the effects of BA administration on intestinal morphology, inflammatory response, and colonic microbial composition in a mouse model of dextran sulfate sodium (DSS)-induced colitis. Results showed that BA administration significantly ameliorated body weight loss, decreased disease activity index, and improved colonic tissue morphology in DSS-treated mice. In addition, levels of immunoglobulins, as well as pro-inflammatory cytokines, were decreased after BA administration. Importantly, colonic microbiota profiling indicated a significant (p < 0.05) difference in beta-diversity between BA-administrated and DSS-treated mice, according to weighted principal coordinate analysis (PCoA) results. The relative abundance of the Firmicutes genus was increased, whereas that of Bacteroidetes was decreased by BA administration. Furthermore, phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analysis showed that the most significantly changed pathways between the four groups of mice were carbohydrate, lipid, and amino acid metabolism. In conclusion, our results showed that BA administration has beneficial effects on DSS-induced colitis, suggesting that this strategy might be useful for the treatment of dysbiosis during ulcerative colitis. Further, the changes in metabolism, especially amino acid metabolism, might contribute to the beneficial effects of BA on the amelioration of DSS-induced colitis.
Early Selection Enabled by the Implementation of Genomic Selection in Coffea arabica Breeding

Genomic Selection (GS) has allowed the maximization of genetic gains per unit time in several annual and perennial plant species. However, no GS studies have addressed Coffea arabica, the most economically important species of the genus Coffea. Therefore, this study aimed (i) to evaluate the applicability and accuracy of GS in the prediction of the genomic estimated breeding value (GEBV); (ii) to estimate the genetic parameters; and (iii) to evaluate the time reduction of the selection cycle by GS in Arabica coffee breeding. A total of 195 Arabica coffee individuals, belonging to 13 families in generation of F2, susceptible backcross and resistant backcross, were phenotyped for 18 agronomic traits, and genotyped with 21,211 SNP molecular markers. Phenotypic data, measured in 2014, 2015, and 2016, were analyzed by mixed models. GS analyses were performed by the G-BLUP method, using the RKHS (Reproducing Kernel Hilbert Spaces) procedure, with a Bayesian algorithm. Heritabilities and selective accuracies were estimated, revealing moderate to high magnitude for most of the traits evaluated. Results of GS analyses showed the possibility of reducing the cycle time by 50%, maximizing selection gains per unit time. The effect of marker density on GS analyses was evaluated. Genomic selection proved to be promising for C. arabica breeding. The agronomic traits presented high complexity for they are controlled by several QTL and showed low genomic heritabilities, evidencing the need to incorporate genomic selection methodologies to the breeding programs of this species.