Miracle-dz/UniFAR-FTUs huggingface dataset:
Diversification of Aeonium Species Across Macaronesian Archipelagos: Correlations Between Genome-Size Variation and Their Conservation Status

The rich endemic flora of the Macaronesian Islands places these oceanic archipelagos among the top biodiversity hotspots worldwide. The radiations that have determined the evolution of many of these insular lineages resulted in a wealth of endemic species, many of which occur in a wide range of ecological niches, but show small distribution areas in each of them. Aeonium (Crassulaceae) is the most speciose lineage in the Canary Islands (ca. 40 taxa), and as such can be considered a good model system to understand the diversification dynamics of oceanic endemic floras. The present study aims to assess the genome size variation within Aeonium distribution, i.e., the Macaronesian archipelagos of Madeira, Canaries and Cabo Verde, and analyse it together with information on distribution (i.e., geography and conservation status), taxonomy (i.e., sections), morphological traits (i.e., growth-form), geological data (i.e., island's geological age), and environmental variables (i.e., altitude, annual mean temperature, and precipitation). Based on extensive fieldwork, a cytogeographic screening of 24 Aeonium species was performed. The conservation status of these species was assessed based on IUCN criteria. 61% of the taxa were found to be threatened (4% Endangered and 57% Vulnerable). For the first time, the genome size of a comprehensive sample of Aeonium across the Macaronesian archipelagos was estimated, and considerable differences in Cx-values were found, ranging from 0.984 pg (A. dodrantale) to 2.768 pg (A. gorgoneum). An overall positive correlation between genome size and conservation status was found, with the more endangered species having the larger genomes on average. However, only slight relationships were found between genome size, morphological traits, and environmental variables. These results underscore the importance of characterizing the cytogenomic diversity and conservation status of endemic plants found in Macaronesian Islands, providing, therefore, new data to establish conservation priorities.
Plant Glycan Metabolism by Bifidobacteria

Members of the genus Bifidobacterium, of which the majority have been isolated as gut commensals, are Gram-positive, non-motile, saccharolytic, non-sporulating, anaerobic bacteria. Many bifidobacterial strains are considered probiotic and therefore are thought to bestow health benefits upon their host. Bifidobacteria are highly abundant among the gut microbiota of healthy, full term, breast-fed infants, yet the relative average abundance of bifidobacteria tends to decrease as the human host ages. Because of the inverse correlation between bifidobacterial abundance/prevalence and health, there has been an increasing interest in maintaining, increasing or restoring bifidobacterial populations in the infant, adult and elderly gut. In order to colonize and persist in the gastrointestinal environment, bifidobacteria must be able to metabolise complex dietary and/or host-derived carbohydrates, and be resistant to various environmental challenges of the gut. This is not only important for the autochthonous bifidobacterial species colonising the gut, but also for allochthonous bifidobacteria provided as probiotic supplements in functional foods. For example, Bifidobacterium longum subsp. longum is a taxon associated with the metabolism of plant-derived poly/oligosaccharides in the adult diet, being capable of metabolising hemicellulose and various pectin-associated glycans. Many of these plant glycans are believed to stimulate the metabolism and growth of specific bifidobacterial species and are for this reason classified as prebiotics. In this review, bifidobacterial carbohydrate metabolism, with a focus on plant poly-/oligosaccharide degradation and uptake, as well as its associated regulation, will be discussed.
Complete CSN1S2 Characterization, Novel Allele Identification and Association With Milk Fatty Acid Composition in River Buffalo

The αs2-casein is one of the phosphoproteins secreted in all ruminants' milk, and it is the most hydrophilic of all caseins. However, this important gene (CSN1S2) has not been characterized in detail in buffaloes with only two alleles detected (reported as alleles A and B), and no association studies with milk traits have been carried out unlike what has been achieved for other species of ruminants. In this study, we sequenced the whole gene of two Mediterranean river buffalo homozygotes for the presence/absence of the nucleotide C (g.7539G>C) realized at the donor splice site of exon 7 and, therefore, responsible for the skipping of the same exon at mRNA level (allele B). A high genetic variability was found all over the two sequenced CSN1S2 alleles. In particular, 74 polymorphic sites were found in introns, six in the promoter, and three SNPs in the coding region (g.11072C>T, g.12803A>T, and g.14067A>G) with two of them responsible for amino acid replacements. Considering this genetic diversity, those found in the database and the SNP at the donor splice site of exon 7, it is possible to deduce at least eight different alleles (CSN1S2 A, B, B1, B2, C, D, E, and F) responsible for seven different possible translations of the buffalo αs2-casein. Haplotype data analysis suggests an evolutionary pathway of buffalo CSN1S2 gene consistent with our proposal that the published allele CSN1S2 A is the ancestral αs2-CN form, and the B2 probably arises from interallelic recombination (single crossing) between the alleles D and B (or B1). The allele CSN1S2 C is of new identification, while CSN1S2 B, B1, and B2 are deleted alleles because all are characterized by the mutation g.7539G>C. Two SNPs (g.7539G>C and g.14067A>G) were genotyped in 747 Italian buffaloes, and major alleles had a relative frequency of 0.83 and 0.51, respectively. An association study between these SNPs and milk traits including fatty acid composition was carried out. The SNP g.14067A>G showed a significant association (P < 0.05) on the content of palmitic acid in buffalo milk, thus suggesting its use in marker-assisted selection programs aiming for the improvement of buffalo milk fatty acid composition.
Aspirin Use on Incident Dementia and Mild Cognitive Decline: A Systematic Review and Meta-Analysis

Background: More people with cognitive dysfunction and dementia also fall into the category of high vascular risk, for which aspirin is one of the most frequently used drugs. However, previous studies reporting that aspirin buffers against mild cognitive decline (MCI) and dementia remain controversial. We thus conducted an updated systematic review and meta-analysis to evaluate the association of aspirin use with the risk of MCI and dementia in older adults. Methods: Data sources from PubMed, Embase, Web of Science, and the Cochrane Database for randomized controlled trails (RCTs) and cohort studies (published between January 1, 2000 and April 11, 2020). Relative risks (RRs) and 95% confidence intervals (95% CIs) were used to pool data on the occurrence of dementia and MCI with random-effects models. Results: Of 3,193 identified articles, 15 studies (12 cohort studies and three RCTs) were eligible and were included in our analysis, which involved a total of 100,909 participants without cognitive dysfunctions or dementia at baseline. In pooled cohort studies, aspirin use did not reduce the incidence of MCI and dementia (the pooled RR = 0.97; 95% CI = 0.85–1.11; Ifor heterogeneity2 = 65%) compared with non-users. However, low-dose aspirin (75–100 mg/day) was associated with a decreased likelihood of developing dementia or MCI (the pooled RR = 0.75; 95% CI = 0.63–0.9; Ifor heterogeneity2 = 50.5%). This association existed in studies including all-cause dementia (the pooled RR = 0.82; 95% CI = 0.71–0.96) and Alzheimer's disease (AD) (the pooled RR = 0.54; 95% CI = 0.33–0.89), but not in MCI (the pooled RR = 0.58; 95% CI = 0.31–1.08). In RCTs, low-dose aspirin use was not significantly associated with less prevalence of dementia or MCI (RR = 0.94; 95% CI = 0.84–1.05; Ifor heterogeneity2 = 0.0%). Conclusions: In cohort studies, we found that low-dose aspirin use had a higher likelihood of reducing the incidence of dementia, which was not supported by RCTs. The evidence was insufficient to fully evaluate the effect of aspirin on cognitive function and dementia. Well-designed studies and innovative approaches are therefore needed to clarify whether the use of aspirin improves cognitive function and reduces the risk of dementia.
Dynamic Control of Mitochondrial Ca2+ Levels as a Survival Strategy of Cancer Cells

Cancer cells have increased energy requirements due to their enhanced proliferation activity. This energy demand is, among others, met by mitochondrial ATP production. Since the second messenger Ca2+ maintains the activity of Krebs cycle dehydrogenases that fuel mitochondrial respiration, proper mitochondrial Ca2+ uptake is crucial for a cancer cell survival. However, a mitochondrial Ca2+ overload induces mitochondrial dysfunction and, ultimately, apoptotic cell death. Because of the vital importance of balancing mitochondrial Ca2+ levels, a highly sophisticated machinery of multiple proteins manages mitochondrial Ca2+ homeostasis. Notably, mitochondria sequester Ca2+ preferentially at the interaction sites between mitochondria and the endoplasmic reticulum (ER), the largest internal Ca2+ store, thus, pointing to mitochondrial-associated membranes (MAMs) as crucial hubs between cancer prosperity and cell death. To investigate potential regulatory mechanisms of the mitochondrial Ca2+ uptake routes in cancer cells, we modulated mitochondria–ER tethering and the expression of UCP2 and analyzed mitochondrial Ca2+ homeostasis under the various conditions. Hence, the expression of contributors to mitochondrial Ca2+ regulation machinery was quantified by qRT-PCR. We further used data from The Cancer Genome Atlas (TCGA) to correlate these in vitro findings with expression patterns in human breast invasive cancer and human prostate adenocarcinoma. ER-mitochondrial linkage was found to support a mitochondrial Ca2+ uptake route dependent on uncoupling protein 2 (UCP2) in cancer cells. Notably, combined overexpression of Rab32, a protein kinase A-anchoring protein fostering the ER-mitochondrial tethering, and UCP2 caused a significant drop in cancer cells' viability. Artificially enhanced ER-mitochondrial tethering further initiated a sudden decline in the expression of UCP2, probably as an adaptive response to avoid mitochondrial Ca2+ overload. Besides, TCGA analysis revealed an inverse expression correlation between proteins stabilizing mitochondrial-ER linkage and UCP2 in tissues of human breast invasive cancer and prostate adenocarcinoma. Based on these results, we assume that cancer cells successfully manage mitochondrial Ca2+ uptake to stimulate Ca2+-dependent mitochondrial metabolism while avoiding Ca2+-triggered cell death by fine-tuning ER-mitochondrial tethering and the expression of UCP2 in an inversed manner. Disruption of this equilibrium yields cancer cell death and may serve as a treatment strategy to specifically kill cancer cells.
Acute Effects of Short-Term Warm Water Immersion on Arterial Stiffness and Central Hemodynamics

Warm water immersion (WWI) has a potentially favorable effect on vascular health. However, the effects of short-term WWI on vascular function and central hemodynamics remain unclear. The present study aimed to determine the acute effects of short-term WWI on arterial stiffness and central hemodynamics in healthy men. Ten healthy men (27–57 years, 44 ± 12 years of mean age) underwent 5-min WWI (40–41°C) at the heart level. Systemic hemodynamics and tympanic temperature were monitored during WWI. Furthermore, pulse wave velocity (PWV) and aortic hemodynamics were measured before and 10 min after WWI. Cardiac output (CO) (via the Modelflow method) increased (P = 0.037), whereas tympanic temperature did not change (P = 0.879) during WWI. After 5-min WWI, heart rate (HR) and brachial diastolic blood pressure (BP) were significantly decreased. Aortic and leg PWV were decreased by 7.5 and 3.1%, respectively (P = 0.006 and P = 0.040). Femoral arterial blood flow was increased by 45.9% (P = 0.002), and leg vascular resistance was decreased by 29.1% (P < 0.001). Regarding central hemodynamic variables (estimated by general transfer function), aortic BP and augmentation index (AIx) did not change significantly, but the subendocardial viability ratio (SEVR), an index of coronary perfusion, was increased (P = 0.049). Our results indicate that a short-term WWI acutely improves aortic and peripheral arterial stiffness and coronary perfusion. Further studies to determine the interaction between the residual effect of a single bout of short-term WWI and chronic change (e.g., adaptation) in arterial stiffness and central hemodynamics are needed.
Copper Ions Induce DNA Sequence Variation in Zygotic Embryo Culture-Derived Barley Regenerants

In vitro tissue culture could be exploited to study cellular mechanisms that induce sequence variation. Altering the metal ion composition of tissue culture medium affects biochemical pathways involved in tissue culture-induced variation. Copper ions are involved in the mitochondrial respiratory chain and Yang cycle. Copper ions may participate in oxidative mutations, which may contribute to DNA sequence variation. Silver ions compete with copper ions to bind to the complex IV subunit of the respiratory chain, thus affecting the Yang cycle and DNA methylation. The mechanisms underlying somaclonal variation are unknown. In this study, we evaluated embryo-derived barley regenerants obtained from a single double-haploid plant via embryo culture under varying copper and silver ion concentrations and different durations of in vitro culture. Morphological variation among regenerants and the donor plant was not evaluated. Methylation-sensitive Amplified Fragment Length Polymorphism analysis of DNA samples showed DNA methylation pattern variation in CG and CHG (H = A, C, or T) sequence contexts. Furthermore, modification of in vitro culture conditions explained DNA sequence variation, demethylation, and de novo methylation in the CHG context, as indicated by analysis of variance. Linear regression indicated that DNA sequence variation was related to de novo DNA methylation in the CHG context. Mediation analysis showed the role of copper ions as a mediator of sequence variation in the CHG context. No other contexts showed a significant sequence variation in mediation analysis. Silver ions did not act as a mediator between any methylation contexts and sequence variation. Thus, incorporating copper ions in the induction medium should be treated with caution.
Review on Stress Tolerance in Campylobacter jejuni

Campylobacter spp. are the leading global cause of bacterial colon infections in humans. Enteropathogens are subjected to several stress conditions in the host colon, food complexes, and the environment. Species of the genus Campylobacter, in collective interactions with certain enteropathogens, can manage and survive such stress conditions. The stress-adaptation mechanisms of Campylobacter spp. diverge from other enteropathogenic bacteria, such as Escherichia coli, Salmonella enterica serovar Typhi, S. enterica ser. Paratyphi, S. enterica ser. Typhimurium, and species of the genera Klebsiella and Shigella. This review summarizes the different mechanisms of various stress-adaptive factors on the basis of species diversity in Campylobacter, including their response to various stress conditions that enhance their ability to survive on different types of food and in adverse environmental conditions. Understanding how these stress adaptation mechanisms in Campylobacter, and other enteric bacteria, are used to overcome various challenging environments facilitates the fight against resistance mechanisms in Campylobacter spp. , and aids the development of novel therapeutics to control Campylobacter in both veterinary and human populations.
Rapid Microbial Quality Assessment of Chicken Liver Inoculated or Not With Salmonella Using FTIR Spectroscopy and Machine Learning

Chicken liver is a highly perishable meat product with a relatively short shelf-life and that can get easily contaminated with pathogenic microorganisms. This study was conducted to evaluate the behavior of spoilage microbiota and of inoculated Salmonella enterica on chicken liver. The feasibility of Fourier-transform infrared spectroscopy (FTIR) to assess chicken liver microbiological quality through the development of a machine learning workflow was also explored. Chicken liver samples [non-inoculated and inoculated with a four-strain cocktail of ca. 103 colony-forming units (CFU)/g Salmonella] were stored aerobically under isothermal (0, 4, and 8°C) and dynamic temperature conditions. The samples were subjected to microbiological analysis with concomitant FTIR measurements. The developed FTIR spectral analysis workflow for the quantitative estimation of the different spoilage microbial groups consisted of robust data normalization, feature selection based on extra-trees algorithm and support vector machine (SVM) regression analysis. The performance of the developed models was evaluated in terms of the root mean square error (RMSE), the square of the correlation coefficient (R2), and the bias (Bf) and accuracy (Af) factors. Spoilage was mainly driven by Pseudomonas spp. , followed closely by Brochothrix thermosphacta, while lactic acid bacteria (LAB), Enterobacteriaceae, and yeast/molds remained at lower levels. Salmonella managed to survive at 0°C and dynamic conditions and increased by ca. 1.4 and 1.9 log CFU/g at 4 and 8°C, respectively, at the end of storage. The proposed models exhibited Af and Bf between observed and predicted counts within the range of 1.071 to 1.145 and 0.995 to 1.029, respectively, while the R2 and RMSE values ranged from 0.708 to 0.828 and 0.664 to 0.949 log CFU/g, respectively, depending on the microorganism and chicken liver samples. Overall, the results highlighted the ability of Salmonella not only to survive but also to grow at refrigeration temperatures and demonstrated the significant potential of FTIR technology in tandem with the proposed spectral analysis workflow for the estimation of total viable count, Pseudomonas spp. , B. thermosphacta, LAB, Enterobacteriaceae, and Salmonella on chicken liver.
Anticancer Compounds Based on Isatin-Derivatives: Strategies to Ameliorate Selectivity and Efficiency

In this review we compare and discuss results of compounds already reported as anticancer agents based on isatin-derivatives, metalated as well as non-metallated. Isatin compounds can be obtained from plants, marine animals, and is also found in human fluids as a metabolite of amino acids. Its derivatives include imines, hydrazones, thiosemicarbazones, among others, already focused on numerous anticancer studies. Some of them have entered in pre-clinical and clinical tests as antiangiogenic compounds or inhibitors of crucial proteins. As free ligands or coordinated to metal ions, such isatin derivatives showed promising antiproliferative properties against different cancer cells, targeting different biomolecules or organelles. Binding to metal ions usually improves its biological properties, indicating a modulation by the metal and by the ligand in a synergistic process. They also reveal diverse mechanisms of action, being able of binding DNA, generating reactive species that cause oxidative damage, and inhibiting selected proteins. Strategies used to improve the efficiency and selectivity of these compounds comprise structural modification of the ligands, metalation with different ions, syntheses of mononuclear and dinuclear species, and use of inserted or anchored compounds in selected drug delivery systems.
Acceleration of Fusion Plasma Turbulence Simulations using the Mixed-Precision Communication-Avoiding Krylov Method

The multi-scale full-f simulation of the next generation experimental fusion reactor ITER based on a five dimensional (5D) gyrokinetic model is one of the most computationally demanding problems in fusion science. In this work, a Gyrokinetic Toroidal 5D Eulerian code (GT5D) is accelerated by a new mixed-precision communication-avoiding (CA) Krylov method. The bottleneck of global collective communication on accelerated computing platforms is resolved using a CA Krylov method. In addition, a new FP16 preconditioner, which is designed using the new support for FP16 SIMD operations on A64FX, reduces both the number of iterations (halo data communication) and the computational cost. The performance of the proposed method for ITER size simulations with $\sim$0.1 trillion grids on 1,440 CPUs/GPUs on Fugaku and Summit shows 2.8× and 1.9× speedups respectively from the conventional non-CA Krylov method, and excellent strong scaling is obtained up to 5,760 CPUs/GPUs.
Metaphors: Where the neighborhood in which one resides interacts with (interpretive) diversity

The effect of semantic neighborhood density (SND) on metaphor interpretation was examined by asking participants to list features for both metaphors (e.g., “music is medicine”) and the individual words in the metaphors (e.g., the metaphor topic, “music” and the metaphor vehicle, “medicine”). Topic word SND was associated with greater interpretive diversity for individual words, but lesser interpretive diversity for metaphors. High-SND metaphor topics decreased in interpretive diversity when the topic was framed in a metaphor (compared to when presented alone) whereas for Low-SND topics, there was an increase in interpretive diversity when framed in a metaphor. We propose that the function of the vehicle differs depending on the nature of the metaphor topic. Vehicles convey or emphasize a select few relevant features of topic meaning when the topic has many close semantic associates, whereas they highlight many potentially relevant low-salience features for topic concepts with few close associates.
Three Different Compact Elliptical Slot Ultra -Wide band Antennas for Wireless Communication Applications

—From this current paper, 3 separate elliptical slotted ultrawide band (UWB) antennas are being proposed. These antennas have been designed with a standard PCB design process to be capable of integrating with radiofrequency or microwave circuitry. Two designs were presented in which the initial design comprised a half circular ring radiator and the remaining one considers a half elliptical ring radiator. The third design of the radiator is in the shape of a crescent. The impedance bandwidth of all these presented antenna designs varies from 2.5GHz and reaches to 14GHz with a S11 less than -10GHz. Here, every proposed antenna design also has a consistent radiation pattern across its frequency band of interest. The performance of the antenna is impressive for lower band frequency in UWB system, which differs in a range of 3.1GHz to 5.1GHz. Across the whole frequency band the antenna shows a 10db return loss bandwidth. The antenna is fabricated on RTduroid substrate and fed with 50 Ω coupled tappered transmission line.