Miracle-dz/UniFAR-FTUs huggingface dataset:
Ectopic Overexpression of Histone H3K4 Methyltransferase CsSDG36 from Tea Plant Decreases Hyperosmotic Stress Tolerance in Arabidopsis thaliana

Histone methylation plays an important regulatory role in the drought response of many plants, but its regulatory mechanism in the drought response of the tea plant remains poorly understood. Here, drought stress was shown to induce lower relative water content and significantly downregulate the methylations of histone H3K4 in the tea plant. Based on our previous analysis of the SET Domain Group (SDG) gene family, the full-length coding sequence (CDS) of CsSDG36 was cloned from the tea cultivar ‘Fuding Dabaicha’. Bioinformatics analysis showed that the open reading frame (ORF) of the CsSDG36 gene was 3138 bp, encoding 1045 amino acids and containing the conserved structural domains of PWWP, PHD, SET and PostSET. The CsSDG36 protein showed a close relationship to AtATX4 of the TRX subfamily, with a molecular weight of 118,249.89 Da, and a theoretical isoelectric point of 8.87, belonging to a hydrophilic protein without a transmembrane domain, probably located on the nucleus. The expression of CsSDG36 was not detected in the wild type, while it was clearly detected in the over-expression lines of Arabidopsis. Compared with the wild type, the over-expression lines exhibited lower hyperosmotic resistance by accelerating plant water loss, increasing reactive oxygen species (ROS) pressure, and increasing leaf stomatal density. RNA-seq analysis suggested that the CsSDG36 overexpression caused the differential expression of genes related to chromatin assembly, microtubule assembly, and leaf stomatal development pathways. qRT-PCR analysis revealed the significant down-regulation of stomatal development-related genes (BASL, SBT1.2(SDD1), EPF2, TCX3, CHAL, TMM, SPCH, ERL1, and EPFL9) in the overexpression lines. This study provides a novel sight on the function of histone methyltransferase CsSDG36 under drought stress.
Identification of Brain Electrical Activity Related to Head Yaw Rotations

Automatizing the identification of human brain stimuli during head movements could lead towards a significant step forward for human computer interaction (HCI), with important applications for severely impaired people and for robotics. In this paper, a neural network-based identification technique is presented to recognize, by EEG signals, the participant’s head yaw rotations when they are subjected to visual stimulus. The goal is to identify an input-output function between the brain electrical activity and the head movement triggered by switching on/off a light on the participant’s left/right hand side. This identification process is based on “Levenberg–Marquardt” backpropagation algorithm. The results obtained on ten participants, spanning more than two hours of experiments, show the ability of the proposed approach in identifying the brain electrical stimulus associate with head turning. A first analysis is computed to the EEG signals associated to each experiment for each participant. The accuracy of prediction is demonstrated by a significant correlation between training and test trials of the same file, which, in the best case, reaches value r = 0.98 with MSE = 0.02. In a second analysis, the input output function trained on the EEG signals of one participant is tested on the EEG signals by other participants. In this case, the low correlation coefficient values demonstrated that the classifier performances decreases when it is trained and tested on different subjects.
Decoding Brain Responses to Names and Voices across Different Vigilance States

Past research has demonstrated differential responses of the brain during sleep in response especially to variations in paralinguistic properties of auditory stimuli, suggesting they can still be processed “offline”. However, the nature of the underlying mechanisms remains unclear. Here, we therefore used multivariate pattern analyses to directly test the similarities in brain activity among different sleep stages (non-rapid eye movement stages N1-N3, as well as rapid-eye movement sleep REM, and wake). We varied stimulus salience by manipulating subjective (own vs. unfamiliar name) and paralinguistic (familiar vs. unfamiliar voice) salience in 16 healthy sleepers during an 8-h sleep opportunity. Paralinguistic salience (i.e., familiar vs. unfamiliar voice) was reliably decoded from EEG response patterns during both N2 and N3 sleep. Importantly, the classifiers trained on N2 and N3 data generalized to N3 and N2, respectively, suggesting similar processing mode in these states. Moreover, projecting the classifiers’ weights using a forward model revealed similar fronto-central topographical patterns in NREM stages N2 and N3. Finally, we found no generalization from wake to any sleep stage (and vice versa) suggesting that “processing modes” or the overall processing architecture with respect to relevant oscillations and/or networks substantially change from wake to sleep. However, the results point to a single and rather uniform NREM-specific mechanism that is involved in (auditory) salience detection during sleep.
Numerical Analysis of Thermal Radiative Maxwell Nanofluid Flow Over-Stretching Porous Rotating Disk

The fluid flow over a rotating disk is critically important due to its application in a broad spectrum of industries and engineering and scientific fields. In this article, the traditional swirling flow of Von Karman is optimized for Maxwell fluid over a porous spinning disc with a consistent suction/injection effect. Buongiorno’s model, which incorporates the effect of both thermophoresis and Brownian motion, describes the Maxwell nanofluid nature. The dimensionless system of ordinary differential equations (ODEs) has been diminished from the system of modeled equations through a proper transformation framework. Which is numerically computed with the bvp4c method and for validity purposes, the results are compared with the RK4 technique. The effect of mathematical abstractions on velocity, energy, concentration, and magnetic power is sketched and debated. It is perceived that the mass transmission significantly rises with the thermophoresis parameter, while the velocities in angular and radial directions are reducing with enlarging of the viscosity parameter. Further, the influences of thermal radiation Rd and Brownian motion parameters are particularly more valuable to enhance fluid temperature. The fluid velocity is reduced by the action of suction effects. The suction effect grips the fluid particles towards the pores of the disk, which causes the momentum boundary layer reduction.
Fermentation of Jamaican Cherries Juice Using Lactobacillus plantarum Elevates Antioxidant Potential and Inhibitory Activity against Type II Diabetes-Related Enzymes

Jamaican cherry (Muntinga calabura Linn.) is tropical tree that is known to produce edible fruit with high nutritional and antioxidant properties. However, its use as functional food is still limited. Previous studies suggest that fermentation with probiotic bacteria could enhance the functional properties of non-dairy products, such as juices. In this study, we analyze the metabolite composition and activity of Jamaican cherry juice following fermentation with Lactobacillus plantarum FNCC 0027 in various substrate compositions. The metabolite profile after fermentation was analyzed using UPLC-HRMS-MS and several bioactive compounds were detected in the substrate following fermentation, including gallic acid, dihydrokaempferol, and 5,7-dihydroxyflavone. We also found that total phenolic content, antioxidant activities, and inhibition of diabetic-related enzymes were enhanced after fermentation using L. plantarum. The significance of its elevation depends on the substrate composition. Overall, our findings suggest that fermentation with L. plantarum FNCC 0027 can improve the functional activities of Jamaican cherry juice.
Preconcentration of Mo (II) by Chemically Converted Nano Graphene Sheets Adsorbed on Surfactant before Determination by FAAS

A simple, accurate and selective method for determination of trace amounts of Mo (II) in water samples is presented. A novel chemically-converted Nano graphene sheets solid-phase extraction adsorbent was synthesized by chemically-converted Nano graphene sheets. The stability of a chemically (CCG) especially in concentrated hydrochloric acid was studied which used as a recycling and pre-concentration reagent for further uses of (CCG). The method is based on (CCG) of Mo (II) on surfactant coated C18, modified with a chemically converted Nano graphene sheets (CCG). The retained ions were then eluted with 4 ml of 4 M nitric acid and determined by flame atomic absorption spectrometry (FAAS) at 283.3 nm for Mo. The influence of flow rates of sample and eluent solutions, pH, breakthrough volume, effect of foreign ions on chelation and recovery were investigated. 1.5 g of surfactant coated C18 adsorbs 40 mg of the Schiff's base which in turn can retain 15.2±0.8mg of each of the two ions. The limit of detection (3σ) for Mo (II) was found to be 3.20 ng l -1 . The enrichment factors for both ions are 100. The mentioned method was successfully applied on determination of Mo in different water samples.
Genetic and Genome-Wide Association Analysis of Yearling Weight Gain in Israel Holstein Dairy Calves

Yearling weight gain in male and female Israeli Holstein calves, defined as 365 × ((weight − 35)/age at weight) + 35, was analyzed from 814,729 records on 368,255 animals from 740 herds recorded between 1994 and 2021. The variance components were calculated based on valid records from 2008 through 2017 for each sex separately and both sexes jointly by a single-trait individual animal model analysis, which accounted for repeat records on animals. The analysis model also included the square root, linear, and quadratic effects of age at weight. Heritability and repeatability were 0.35 and 0.71 in the analysis of both sexes and similar in the single sex analyses. The regression of yearling weight gain on birth date in the complete data set was −0.96 kg/year. The complete data set was also analyzed by the same model as the variance component analysis, including both sexes and accounting for differing variance components for each sex. The genetic trend for yearling weight gain, including both sexes, was 1.02 kg/year. Genetic evaluations for yearling weight gain was positively correlated with genetic evaluations for milk, fat, protein production, and cow survival but negatively correlated with female fertility. Yearling weight gain was also correlated with the direct effect on dystocia, and increased yearling weight gain resulted in greater frequency of dystocia. Of the 1749 Israeli Holstein bulls genotyped with reliabilities >50%, 1445 had genetic evaluations. As genotyping of these bulls was performed using several single nucleotide polymorhphism (SNP) chip platforms, we included only those markers that were genotyped in >90% of the tested cohort. A total of 40,498 SNPs were retained. More than 400 markers had significant effects after permutation and correction for multiple testing (pnominal < 1 × 10−8). Considering all SNPs simultaneously, 0.69 of variance among the sires’ transmitting ability was explained. There were 24 markers with coefficients of determination for yearling weight gain >0.04. One marker, BTA-75458-no-rs on chromosome 5, explained ≈6% of the variance among the estimated breeding values for yearling weight gain. ARS-BFGL-NGS-39379 had the fifth largest coefficient of determination in the current study and was also found to have a significant effect on weight at an age of 13–14 months in a previous study on Holsteins. Significant genomic effects on yearling weight gain were mainly associated with milk production quantitative trait loci, specifically with kappa casein metabolism.
Membrane Interference Against HIV-1 by Intrinsic Antiviral Factors: The Case of IFITMs

HIV-1 is a complex retrovirus that is adapted to replicate in cells of the immune system. To do so, HIV-1, like other viruses, developed strategies to use several cellular processes to its advantage, but had also to come to terms with an arsenal of cellular innate defense proteins, or antiviral factors, that target more or less efficiently, virtually every step of the virus replicative cycle. Among antiviral restriction factors, the family of interferon-induced transmembrane proteins (IFITMs) has emerged as a crucial component of cellular innate defenses for their ability to interfere with both early and late phases of viral replication by inhibiting cellular and viral membranes fusion. Here, we review the enormous advances made since the discovery of IFITMs as interferon-regulated genes more than thirty years ago, with a particular focus on HIV-1 and on the elements that modulate its susceptibility or resistance towards members of this family. Given the recent advances of the field in the elucidation of the mechanism of IFITM inhibition and on the mechanism(s) of viral resistance, we expect that future years will bring novel insights into the definition of the multiple facets of IFITMs and on their possible use for novel therapeutical approaches.
Hamster Polyomavirus Research: Past, Present, and Future §

Hamster polyomavirus (Mesocricetus auratus polyomavirus 1, HaPyV) was discovered as one of the first rodent polyomaviruses at the end of the 1960s in a colony of Syrian hamsters (Mesocricetus auratus) affected by skin tumors. Natural HaPyV infections have been recorded in Syrian hamster colonies due to the occurrence of skin tumors and lymphomas. HaPyV infections of Syrian hamsters represent an important and pioneering tumor model. Experimental infections of Syrian hamsters of different colonies are still serving as model systems (e.g., mesothelioma). The observed phylogenetic relationship of HaPyV to murine polyomaviruses within the genus Alphapolyomavirus, and the exclusive detection of other cricetid polyomaviruses, i.e., common vole (Microtus arvalis polyomavirus 1) and bank vole (Myodes glareolus polyomavirus 1) polyomaviruses, in the genus Betapolyomavirus, must be considered with caution, as knowledge of rodent-associated polyomaviruses is still limited. The genome of HaPyV shows the typical organization of polyomaviruses with an early and a late transcriptional region. The early region encodes three tumor (T) antigens including a middle T antigen; the late region encodes three capsid proteins. The major capsid protein VP1 of HaPyV was established as a carrier for the generation of autologous, chimeric, and mosaic virus-like particles (VLPs) with a broad range of applications, e.g., for the production of epitope-specific antibodies. Autologous VLPs have been applied for entry and maturation studies of dendritic cells. The generation of chimeric and mosaic VLPs indicated the high flexibility of the VP1 carrier protein for the insertion of foreign sequences. The generation of pseudotype VLPs of original VP1 and VP2–foreign protein fusion can further enhance the applicability of this system. Future investigations should evaluate the evolutionary origin of HaPyV, monitor its occurrence in wildlife and Syrian hamster breeding, and prove its value for the generation of potential vaccine candidates and as a gene therapy vehicle.
Influence of Backfat Thickness and the Interval from Altrenogest Withdrawal to Estrus on Reproductive Performance of Gilts

Simple Summary Altrenogest, also known as allyl trenbolone, is a steroidal progestin that is widely used in veterinary medicine to synchronize estrus in gilts. To achieve the target number of services per week, enough weaned sows and gilts are needed each week for breeding. A problem with progestogen-synchronized replacement gilts is the variation of the interval between last feeding of altrenogest and onset of estrus. In the present study, we found that gilt backfat thickness had a strong positive correlation with the interval between last feeding of altrenogest and onset of estrus. This result may come from a larger reservoir of altrenogest in adipose tissue in fatter gilts. Abstract Estrus synchronization of gilts can be achieved by feeding the orally active progestogen altrenogest (AT) to cycling gilts at 20 mg/day for 14 to 18 days with gilts usually returning to estrus 4 to 8 days after the last feeding. In practice, gilts failing to exhibit estrus by 6 days after AT withdrawal may compromise weekly breeding targets. The cause of prolonged intervals to estrus are unknown but may involve prolonged suppression due to the release of progesterone (P4), and by extension AT, from adipose tissues. The present study examined relationships between gilt P2 backfat depth (<13.5 mm, 14–16.5 mm, >17 mm groups), the AT withdrawal to estrus interval, and subsequent reproductive performance in gilts. We noted longer intervals to estrus in gilts with greater P2 backfat depths (p < 0.0001), and higher serum P4 concentrations on the last day of AT feeding and at estrus detection (p < 0.05). Total born litter sizes were unaffected by backfat depth, but pigs born alive progressively decreased with increasing backfat depth with the fattest gilts producing the fewest liveborn pigs (p < 0.05). Taken together, these data suggest that adipose tissues may provide a reservoir of steroid, with its release from fatter gilts having potential negative effects on their subsequent reproductive performance.
The Effects of Biochar on Indigenous Arbuscular Mycorrhizae Fungi from Agroenvironments

The effects of biochar on soil–plant–microorganisms systems are currently being extensively investigated. Considering that arbuscular mycorrhizal fungi (AMF) play an essential role in nutrient dynamics, the present study aims at understanding vine shoot-derived biochar effects on AMF activity and the impact of their multiplication in soils on water-stress resistance of plants. Three agronomic tests were performed in greenhouse pots. The first experiment evaluated the effects of three factors: final pyrolysis temperature for biochar production (400 °C and 600 °C), application rate (0 weight-wt.- % as a control, 1.5 wt. %, and 3.0 wt. %) and texture of the growing media (sandy-loam and clay-loam origin) on AMF, microbial communities and phosphatase activity. In the second experiment, an indigenous consortium of AMF was multiplied through the solid substrate method and sorghum as a trap plant with biochar addition. This process was compared to a control treatment without biochar. Obtained inocula were tested in a third experiment with lettuce plants under different water irrigation conditions. Results from the first experiment showed a general increase in AMF activity with the addition of the biochar produced at 400 °C in the sandy-loam texture substrate. Results of the second experiment showed that the biochar addition increased AMF root colonization, the number of AMF spores and AMF infective potential. Results of the third experiment showed that biochar-derived AMF inoculum increased AMF root colonization, AMF spores, dry biomass and the SPAD index in a lettuce crop under low-water irrigation conditions.
Enhanced Antitumor Effect of Trastuzumab and Duligotuzumab or Ipatasertib Combination in HER-2 Positive Gastric Cancer Cells

Simple Summary The ToGA trial has demonstrated, in HER2-expressing patients, that unresectable and advanced gastric cancer, chemotherapy and trastuzumab in combination increase overall survival, even if it is still unclear why after one year the same patients are non-responsive to trastuzumab treatment. Here, we have demonstrated that in HER2-positive gastric cancer cell lines, the addition of duligotuzumab, targeting HER3 receptor, or ipatasertib, targeting AKT protein, enhances the antitumor effect of trastuzumab in vitro through a full inhibition of the membrane signals, on HER2 and HER3, and of downstream signaling, including AKT, and MAPK pathways. Hence, this study suggests a novel and biomarker-driven therapeutic strategy supporting further evaluation of the anti-tumor efficacy of these combinations in HER2 human gastric cancer patients. Abstract The anti-HER2 monoclonal antibody trastuzumab is a key drug for the treatment of HER2-positive gastric cancer (GC); however, its activity is often limited by the onset of resistance and mechanisms of resistance are still poorly understood. Several targeted agents showed synergistic activity by concomitant use with trastuzumab in vitro and are under clinical investigation. The aim of this study was to assess the antitumor activity of duligotuzumab, an anti HER3/EGFR antibody or ipatasertib, an AKT inhibitor, combined with trastuzumab in a panel of HER2-positive human gastric cancer cells (GCC), and the efficacy of such combinations in HER2-resistant cells. We have assessed the efficacy of duligotuzumab or ipatasertib and trastuzumab in combination, analyzing proliferation, migration and apoptosis and downstream intracellular signaling in vitro on human HER2-positive GCC (NCI-N87, OE33, OE19) and in negative HER2 GCC (MKN28). We observed a reduction of proliferation, migration and apoptotic rate in HER2-positive OE33, OE19 and N87 cell lines with the combination of duligotuzumab or ipatasertib plus trastuzumab. In particular, in OE33 and OE19 cell lines, the same combined treatment inhibited the activation of proteins downstream of HER2, HER3, AKT and MAPK pathways. Targeting both HER2 and HER3, or HER2 and AKT, results in an improved antitumor effect on HER2-positive GCC.
The Evolving Landscape of Chronic Lymphocytic Leukemia on Diagnosis, Prognosis and Treatment

The knowledge of chronic lymphocytic leukemia (CLL) has progressively deepened during the last forty years. Research activities and clinical studies have been remarkably fruitful in novel findings elucidating multiple aspects of the pathogenesis of the disease, improving CLL diagnosis, prognosis and treatment. Whereas the diagnostic criteria for CLL have not substantially changed over time, prognostication has experienced an expansion with the identification of new biological and genetic biomarkers. Thanks to next-generation sequencing (NGS), an unprecedented number of gene mutations were identified with potential prognostic and predictive value in the 2010s, although significant work on their validation is still required before they can be used in a routine clinical setting. In terms of treatment, there has been an impressive explosion of new approaches based on targeted therapies for CLL patients during the last decade. In this current chemotherapy-free era, BCR and BCL2 inhibitors have changed the management of CLL patients and clearly improved their prognosis and quality of life. In this review, we provide an overview of these novel advances, as well as point out questions that should be further addressed to continue improving the outcomes of patients.
Avian Influenza H7N9 Virus Adaptation to Human Hosts

Avian influenza virus A (H7N9), after circulating in avian hosts for decades, was identified as a human pathogen in 2013. Herein, amino acid substitutions possibly essential for human adaptation were identified by comparing the 4706 aligned overlapping nonamer position sequences (1–9, 2–10, etc.) of the reported 2014 and 2017 avian and human H7N9 datasets. The initial set of virus sequences (as of year 2014) exhibited a total of 109 avian-to-human (A2H) signature amino acid substitutions. Each represented the most prevalent substitution at a given avian virus nonamer position that was selectively adapted as the corresponding index (most prevalent sequence) of the human viruses. The majority of these avian substitutions were long-standing in the evolution of H7N9, and only 17 were first detected in 2013 as possibly essential for the initial human adaptation. Strikingly, continued evolution of the avian H7N9 virus has resulted in avian and human protein sequences that are almost identical. This rapid and continued adaptation of the avian H7N9 virus to the human host, with near identity of the avian and human viruses, is associated with increased human infection and a predicted greater risk of human-to-human transmission.