Miracle-dz/UniFAR-FTUs huggingface dataset:
Monocyte and CD4+ T cell antiviral and innate responses associated with HIV-1 inflammation and cognitive impairment.

OBJECTIVE Mechanisms underlying immune activation and HIV-associated neurocognitive disorders (HAND) in untreated chronic infection remain unclear. The objective of this study was to identify phenotypic and transcriptional changes in blood monocytes and CD4+ T cells in HIV-1-infected and uninfected individuals and elucidate processes associated with neurocognitive impairment. DESIGN A group of chronically HIV-1-infected Thai individuals (n = 19) were selected for comparison with healthy donor controls (n = 10). Infected participants were further classified as cognitively normal (CN, n = 10) or with HAND (n = 9). Peripheral monocytes and CD4+ T cells were phenotyped by flow cytometry and simultaneously isolated for multiplex qPCR targeted gene expression profiling directly ex vivo. The frequency of HIV-1 RNA-positive cells was estimated by limiting dilution cell sorting. RESULTS Expression of genes and proteins involved in cellular activation and proinflammatory immune responses was increased in monocytes and CD4+ T cells from HIV-1-infected relative to uninfected individuals. Gene expression profiles of both CD4+ T cells and monocytes correlated with soluble markers of inflammation in the periphery (p < 0.05). By contrast, only modest differences in gene programs were observed between CN and HAND cases. These included increased monocyte surface CD169 protein expression relative to CN (p = 0.10), decreased surface CD163 expression relative to uninfected (p = 0.02) and CN (p = 0.06), and downregulation of EMR2 (p = 0.04) and STAT1 (p = 0.02) relative to CN. CONCLUSIONS Our data support a model of highly activated monocytes and CD4+ T cells associated with inflammation in chronic HIV-1 infection, but impaired monocyte anti-inflammatory responses in HAND compared to CN.
Individualization of computed tomography protocols for suspected pulmonary embolism: a national investigation of routines

Objective Given the extensive use of computed tomography (CT) in radiation-sensitive patients such as pregnant and pediatric patients, and considering the importance of tailoring CT protocols to patient characteristics for both the radiation dose and image quality, this study was performed to investigate the extent to which individualization of CT protocols is practiced across Norway. Methods This cross-sectional study involved collection of CT protocols and administration of a mini-questionnaire to obtain additional information about how CT examinations are individualized. All public hospitals performing CT to detect pulmonary embolism were invited, and 41% participated. Results Tailoring a standard protocol to different patient groups was more common than using dedicated protocols. Most of the available radiation dose-reduction approaches were used. However, implementation of these strategies was not systematic. Children and pregnant patients were examined without using dedicated CT protocols or by using protocol adjustments focusing on radiation dose reduction in 30% and 39% of the hospitals, respectively. Conclusion Practice optimization is needed, especially the development of dedicated CT protocols or guidelines that tailor the existing protocol to pediatric and pregnant patients. Practice might benefit from a more systematic approach to individualization of CT examinations, such as inserting tailoring instructions into CT protocols.
Neighbor-joining revealed.

It is nearly 20 years since the landmark paper (Saitou and Nei 1987) in Molecular Biology and Evolution introducing Neighbor-Joining (NJ). The method has become the most widely used method for building phylogenetic trees from distances, and the original paper has been cited about 13,000 times (Science Citation Index). Yet the question "what does the NJ method seek to do? " has until recently proved somewhat elusive, leading to some imprecise claims and misunderstanding. However, a rigorous answer to this question has recently been provided by further mathematical investigation, and the purpose of this note is to highlight these results and their significance for interpreting NJ. The origins of this story lie in a paper by Pauplin (2000) though its continuation has unfolded in more mathematically inclined literature. Our aim here is to make these findings more widely accessible.
Cloning and Functional Characterization of a Flavonoid Transport-Related MATE Gene in Asiatic Hybrid Lilies (Lilium spp.)

Previous studies have suggested that multidrug and toxic compound extrusion (MATE) proteins might be involved in flavonoid transportation. However, whether MATE proteins are involved in anthocyanin accumulation in Lilium is unclear. Here, a flavonoid transport-related MATE candidate gene, LhDTX35, was cloned from the Asiatic hybrid lily cultivar ‘Tiny Padhye’ by rapid amplification of 5’ and 3’ cDNA ends (RACE) and found to encode 507 amino acids. BLASTx results indicated that LhDTX35 showed high homology to the DTX35 genes of other species. Bioinformatics analysis predicted that the protein encoded by LhDTX35 possessed 12 typical transmembrane segments and had functional domains typical of the MATE-like superfamily. Phylogenetic analysis grouped LhDTX35 in the same clade as the DTX35 of other species. Notably, the expression pattern of LhDTX35 was positively correlated with floral anthocyanin accumulation in ‘Tiny Padhye’. A subcellular localization assay showed that the protein encoded by LhDTX35 was plasmalemma localized but not nuclear, indicating that the LhDTX35 gene may function as a carrier protein to transport anthocyanins in Lilium. Functional complementation of the Arabidopsis DTX35 gene demonstrated that LhDTX35 could restore silique-infertility and the anthocyaninless phenotype of an Arabidopsis DTX35 mutant. These results indicated that LhDTX35 might be involved in anthocyanin accumulation in Lilium.
Effects of Presence and Challenge Variations on Emotional Engagement in Immersive Virtual Environments

Serious games and immersive virtual reality promote emotional engagement during learning tasks, mostly by providing (1) skill-adapted challenges with performance feedback (for trial and error learning) and (2) enhanced presence (further reactions to multimodal stimuli), respectively. However, it is still unclear how each of these two strategies independently influence emotional states to engage subjects to a task. This study assessed the dimensions of emotion (valence-arousal-dominance) of 87 healthy subjects in a virtual game, assigned to 2 groups that were exposed to a different set of 5 trials: Group A experienced game variations by virtual factors affecting user’s presence, whereas group B experienced levels of difficulty, affecting challenge. Emotional reports and 26 features extracted from physiological signals were statistically analyzed. Results showed that presence-based experimental conditions were able to modify the sense of arousal, whereas valence and dominance responded to challenge variation, i.e. were positively correlated with game score. Arousal is likely to increase with low sense of coexistence (social presence) and decrease with low scenario realism (physical presence). Faster breathing and higher skin conductance (SC) were detected at high challenge, whereas heart rate variability and SC increased with higher arousal. The evidence from this study suggests that both strategies can be used to separately influence dimensions of emotion, pointing out the customization of presence-based factors as a promising method to adjust emotional engagement by impacting arousal. Further research should be undertaken to identify the independent effect of single presence factors on emotional states.
Distinct defensive activity of phenolics and phenylpropanoid pathway genes in different cotton varieties toward chewing pests

ABSTRACT Identifying the maximum level of inherent defense against harmful insects in natural variation among wild lineages of crop plants may result in high yield tolerant varieties and reducing use of chemical insecticides. However, knowledge of natural cotton genotypes with high insect‐resistance is still indistinguishable at the biochemical or molecular level. In the present study, different cultivated Gossypium hirsutum varieties were evaluated for their inherent insect-tolerance against two major cottons chewing pests. The insect bio-assay identified two tolerant and one susceptible cotton varieties. The study demonstrates difference in phenolic acids, proanthocyanidin and tannin accumulation in tolerant and susceptible varieties. The post–infestation of chewing pests increases transcript level of the phenylpropanoid pathway genes were detected in tolerant varieties as compared to the susceptible varieties. Altogether, chewing pest-tolerance level in cotton varieties is the cumulative effect of enhanced phenylpropanoid pathway genes expression and secondary metabolite leading to defense responses to conventional host plant.
Aflatoxin M1-Binding Ability of Selected Lactic Acid Bacteria Strains and Saccharomyces boulardii in the Experimentally Contaminated Milk Treated with Some Biophysical Factors.

There is a growing concern regarding the recurrent observation of aflatoxins (AFs) in the milk of lactating animals. Regarding this, the present study was conducted to assess the aflatoxin M1 (AFM1)-binding ability of three species, namely Lactobacillus rhamnosus, L. plantarum, and Saccharomyces boulardii, inAFM1-contaminatedmilk. The mentioned species were administeredatthe concentrations of107 and 109 CFU/mLto skimmed milk contaminated with 0.5 and 0.75 ng/mL AFM1 within the incubation times of 30 and 90 min at 4°C and 37°C. Lactobacillus rhamnosus was found to have the best binding ability at the concentrations of 107 and 109 (CFU/ml), rendering 82% and 90% removal in the milk samples with 0.5 and 0.75 ng/ml AFM1, respectively. Accordingly, this value at 107 and 109 CFU/ml of L. plantarum was obtained 89% and 82% with 0.75 ng/ml of AFM1, respectively. For S. boulardii at 107 and 109 CFU/ml, the rates were respectively estimated at 75% and 90% with 0.75 ng/ml of AFM1. The best AFM1-binding levels for L. rhamnosus, L. plantarum, and S. boulardii were 91.82±10.9%, 89.33±0.58%, and 93.20±10.9, respectively, at the concentrations of 1×109, 1×107, and 1×107 CFU/ml at 37, 4, and 37°C, respectively. In this study, the maximum AFM1 binding (100.0±0.58) occurred while a combination of the aforementioned probiotics was employed at a concentration of 1×107 CFU/ml at 37°C with 0.5 ng/ml AFM1, followed by the combination of L. rhamnosus and L. plantarum (95.86±10.9) at a concentration of 1×109 CFU/ml at the same temperature with 0.75 ng/ml AFM1. It was concluded that the use of S. boulardii in combination with Lactobacillus rhamnosus and L. plantarum, which bind AFM1 in milk, can decrease the risk of AFM1 in dairy products.
Association of three beta-defensin gene (AvBD4, AvBD5, AvBD14) polymorphisms with carrier-state susceptibility to salmonella in chickens

ABSTRACT 1. Chicken salmonellosis is a common zoonotic infectious disease transmitted both vertically and horizontally. Avian beta-defensins (gallinacins) play an important role in the innate defence of the host and provide broad-spectrum immunity against multiple pathogens. 2. To detect the relationship between immune genes and salmonella carrier status and susceptibility to salmonellosis in chickens, polymorphisms with carrier-state susceptibility to salmonella and, hence, developing salmonellosis, were investigated in three avian beta-defensin genes (AvBD4, AvBD5, and AvBD14) in a Chinese local chicken breed, based on a case-control study. 3. Fifteen, twenty and nineteen SNPs were found in AvBD4, AvBD5 and AvBD14, respectively. Among the 54 total SNPs, four resulted in non-synonymous substitution of amino acid changes. Five SNPs in AvBD5 and four SNPs in AvBD14 were significantly associated with salmonellosis susceptibility (P < 0.05). Using the PHASE program, thirteen, ten and twelve major haplotypes were constructed in AvBD4, AvBD5 and AvBD14. Logistic regression analysis revealed that five haplotypes in AvBD5 and six haplotypes in AvBD14 were significantly associated with salmonellosis susceptibility, but no significant haplotype in AvBD4 was detected. A total of six strongly susceptible haplotypes with odds ratio (OR) values greater than 2.0 and four strongly resistant haplotypes with OR value less than 0.5 were revealed in the three genes examined. 4. These results suggested that the AvBD5 and AvBD14 genes may play an important role in the susceptibility to salmonellosis in chickens.
Iron Oxide and Iron Sulfide Films Prepared for Dye-Sensitized Solar Cells

In this paper, the prospects of iron oxide films and their sulfidation for dye-sensitized solar cells (DSSC) are reviewed. Iron oxide thin films were prepared by hollow cathode plasma jet (HCPJ) sputtering, with an admixture of oxygen in the argon working gas and with an iron nozzle as the sputtering target. The discharge was powered by a constant current source in continuous mode and by a constant voltage source in pulsed mode. Plasma composition was measured by an energy-resolved mass spectrometer. Moreover, secondary electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDX), absorption and Raman spectra of the films are presented. Strong correlation between the color of the iron oxide film and its phase composition was revealed. Iron oxide films were sulfided at 350 °C. A relatively clean pyrite phase was obtained from the magnetite, while the marcasite with admixture of the pyrite phase was obtained from the hematite. Low influence of sulfidation on the films’ microstructure was demonstrated.
Health-Related Physical Fitness Benefits in Sedentary Women Employees after an Exercise Intervention with Zumba Fitness®

Background: The protective properties of high physical fitness levels on health are manifest independently of age, sex, fatness, smoking, alcohol consumption, and other clinical factors. However, women are less active than men, which contributes to low physical fitness and a high risk of CVD. Thus, the objective of this study is to analyze the effect of two exercise interventions on health-related physical fitness in sedentary employed females. Methods: A total of 98 physically inactive adult women were randomly assigned to 3 study groups: the control group (CG) = 31, the endurance training group based on Zumba Fitness® classes (ET; n = 39), and the concurrent training group that had an extra muscle-strengthening workout after the Zumba Fitness® class (CnT; n = 28). Body composition (BMI, waist circumference), motor fitness (one-leg stand test), musculoskeletal fitness (shoulder–neck mobility, handgrip strength test, jump and reach test, and dynamic sit-up test), and cardiorespiratory fitness (2-km test and estimated VO2 max) were assessed with the ALPHA-Fit test battery for adults. Results: Both interventions showed a significant improvement in the majority of health-related fitness and body composition variables/test (waist circumference: ET = −2.275 ± 0.95, p = 0.02, CnT = −2.550 ± 1.13, p = 0.03; one-stand leg test: ET = 13.532 ± 2.65, p < 0.001; CnT = 11.656 ± 2.88, p < 0.001; shoulder–neck mobility: ET = 1.757 ± 0.44, p < 0.001, CnT = 2.123 ± 0.47, p < 0.001; handgrip test: 0.274 ± 0.08, p < 0.001, CnT = 0.352 ± 0.08, p < 0.001; dynamic sit-up: ET = 1.769 ± 0.45, p < 0.001, CnT = −1.836 ± 0.49, p < 0.001; 2-km test time: −1.280 ± 0.25, p < 0.001, CnT = −1.808 ± 0.28, p < 0.001; estimated VO2 max: ET = 1.306 ± 0.13, p < 0.001, CnT = 1.191 ± 0.15, p < 0.001). There were no significant differences after the intervention between the two exercise intervention groups. Conclusions: Exercise interventions based on Zumba fitness® or Zumba fitness® combined with an extra muscle-strengthening workout based on bodyweight training exercises are effective strategies to improve the health-related physical fitness in sedentary women employees.
Polymorphisms in Fatty Acid Desaturase 2 Gene Are Associated with Milk Production Traits in Chinese Holstein Cows

Simple Summary Searching for causative polymorphisms underlying the variability of milk production traits and then incorporating them into breeding programs are very effective ways to improve the efficiency and reliability of conventional dairy cattle breeding. Fatty acid desaturase 2 (FADS2) plays a pivotal role in the biosynthesis of polyunsaturated fatty acids. Previous studies provided evidence that FADS2 was one of the most downregulated genes during negative energy balance in the liver of postpartum dairy cattle. Genes involved in the energetic pathways may influence other production traits, such as protein, fat and milk yields. Therefore, in the present study, we investigated the common genetic variants of the FADS2 gene in Chinese Holstein cows. Our results provided direct evidence that FADS2 was an interesting candidate for selection to increase milk production and improve resistance against mastitis. Abstract This study investigated the single nucleotide polymorphisms (SNPs) of Fatty acid desaturase 2 (FADS2) gene and further explored their genetic effects on conventionally collected milk production traits in Chinese Holstein cows using 18,264 test-day records of 841 cows. One missense mutation c. 908 C > T (SNP site in the complementary DNA sequence), which caused an amino acid change from alanine to valine (294Ala > Val), and two 3’ untranslated region (UTR) SNPs, c.1571 G > A and c.2776 A > G were finally identified. The SNP c.908 C > T was significantly associated with test-day milk yield, fat percentage and 305-day milk, fat and protein yield. In particular, the T allele of the SNP c.908 C > T showed a significant association with decreased somatic cell score (SCS) in the investigated population. Significant relationship between the SNP c.1571 G > A and 305-day milk yield showed that genotype GG was linked to the highest milk yield. Substituting the allele G for A at the c.2776 A > G locus resulted in a decrease of protein percentage. Our results demonstrated that FADS2 was an interesting candidate for selection to increase milk production and improve resistance against mastitis.
System Approach for Building of Calcium-Binding Sites in Proteins

We introduce five new local metal cation (first of all, Ca2+) recognition units in proteins: Clampn,(n−2), Clampn,(n−1), Clampn,n, Clampn,(n+1) and Clampn,(n+2). In these units, the backbone oxygen atom of a residue in position “n” of an amino acid sequence and side-chain oxygen atom of a residue in position “n + i” (i = −2 to +2) directly interact with a metal cation. An analysis of the known “Ca2+-bound niches” in proteins has shown that a system approach based on the simultaneous use of the Clamp units and earlier proposed One-Residue (OR)/Three-Residue (TR) units significantly improves the results of constructing metal cation-binding sites in proteins.
A Meta-Analysis of the Effects of Slow-Release Urea Supplementation on the Performance of Beef Cattle

Simple Summary Plant-based feedstuffs, such as soybean meal and rapeseed meal are utilised to supply rumen degradable protein (RDP) and rumen undegradable protein (RUP) in the diets of ruminant animals (e.g., cattle, buffalo, sheep and goat). The RDP is utilised by rumen microbes for microbial protein synthesis. Microbial protein can contribute up to 80% of the protein requirement of ruminants. However, the use of plant protein sources in ruminant diets can be restricted based on their availability, costs and associated environmental impacts. Slow-release urea (SRU) is a non-protein nitrogen (NPN) source that allows for a partial replacement of vegetable RDP sources in ruminant diets by providing a sustained availability of ammonia for rumen microbial synthesis. Over the past three decades, extensive research has been conducted on the use of SRU in beef cattle diets. The current study analysed a combined dataset obtained from multiple research studies to derive quantitative and research-based evidence on the impact of a commercial SRU (Optigen®) on beef cattle performance. Results revealed that dietary supplementation of SRU improves the performance, profitability and environmental impacts of beef cattle production. Thus, this study demonstrates SRU as an effective NPN solution in beef cattle diets. Abstract Slow-release urea (SRU) is a coated non-protein nitrogen (NPN) source for ruminant nutrition. This study applied a meta-analytic technique to quantify the effect of a commercial SRU (Optigen®, Alltech Inc., Nicholasville, KY, USA) on the performance of beef cattle. Data were extracted from 17 experiments and analysed using the random-effects model to estimate the effect size of SRU on dry matter intake (DMI), crude protein intake (CPI), live weight gain (LWG) and feed efficiency (FE) of growing and finishing beef cattle. There was no effect of feeding SRU on the overall DMI and CPI of beef cattle. Dietary inclusion of SRU improved the overall LWG (+92 g/d/head) and FE (+12 g LWG/kg DMI/head) of beef cattle. Notably, SRU supplementation in growing cattle exhibited a better improvement on LWG (130 vs. 60 g/d/head) and FE (18 vs. 8 g LWG/kg DMI/head) compared with finishing cattle. Moreover, SRU showed consistent improvements on the LWG and FE of beef cattle under several study factors. Simulation analysis indicated that positive effects of SRU on LWG and FE improved profitability through reduction in feed cost and reduced the emission intensity of beef production. These results indicate that SRU is a sustainable NPN solution in beef cattle production.
Do Post-Translational Modifications Influence Protein Aggregation in Neurodegenerative Diseases: A Systematic Review

The accumulation of abnormal protein aggregates represents a universal hallmark of neurodegenerative diseases (NDDs). Post-translational modifications (PTMs) regulate protein structure and function. Dysregulated PTMs may influence the propensity for protein aggregation in NDD-proteinopathies. To investigate this, we systematically reviewed the literature to evaluate effects of PTMs on aggregation propensity for major proteins linked to the pathogenesis and/or progression of NDDs. A search of PubMed, MEDLINE, EMBASE, and Web of Science Core Collection was conducted to retrieve studies that investigated an association between PTMs and protein aggregation in seven NDDs: Alzheimer’s disease (AD), Parkinson’s disease (PD), Huntington’s disease (HD), amyotrophic lateral sclerosis (ALS), spinocerebellar ataxias, transmissible spongiform encephalopathy, and multiple sclerosis. Together, 1222 studies were identified, of which 69 met eligibility criteria. We identified that the following PTMs, in isolation or combination, potentially act as modulators of proteinopathy in NDDs: isoaspartate formation in Aβ, phosphorylation of Aβ or tau in AD; acetylation, 4-hydroxy-2-neonal modification, O-GlcNAcylation or phosphorylation of α-synuclein in PD; acetylation or phosphorylation of TAR DNA-binding protein-43 in ALS, and SUMOylation of superoxide dismutase-1 in ALS; and phosphorylation of huntingtin in HD. The potential pharmacological manipulation of these aggregation-modulating PTMs represents an as-yet untapped source of therapy to treat NDDs.
Chemosystematic evaluation of Amazonian freshwater sponges

Abstract Freshwater sponges can be considered a promising new source of bioactive compounds for the pharmaceutical industry; however, the research on their chemical composition is still in the incipient stage. We evaluated the most endemic Amazonian freshwater sponge species from the Drulia and Metania genera by untargeted metabolomic approaches, based on UHPCL-HRMS, in order to identify chemical markers and explore the diversity of specialized metabolites. The use of untargeted approaches allowed us to observe subsets of metabolites that enabled the characterization of, not only each genus, but also, of each species. Freshwater sponge species presented themselves as rich sources of fatty acids and sterols, which were putatively identified. These metabolites were suggested as chemical markers for further targeted metabolomic studies. Graphical Abstract