Miracle-dz/UniFAR-FTUs huggingface dataset:
Multi-Omics Revealed Molecular Mechanisms Underlying Guard Cell Systemic Acquired Resistance

Systemic Acquired Resistance (SAR) improves immunity of plant systemic tissue after local exposure to a pathogen. Guard cells that form stomatal pores on leaf surfaces recognize bacterial pathogens via pattern recognition receptors, such as Flagellin Sensitive 2 (FLS2). However, how SAR affects stomatal immunity is not known. In this study, we aim to reveal molecular mechanisms underlying the guard cell response to SAR using multi-omics of proteins, metabolites and lipids. Arabidopsis plants previously exposed to pathogenic bacteria Pseudomonas syringae pv. tomato DC3000 (Pst) exhibit an altered stomatal response compared to control plants when they are later exposed to the bacteria. Reduced stomatal apertures of SAR primed plants lead to decreased number of bacteria in leaves. Multi-omics has revealed molecular components of SAR response specific to guard cells functions, including potential roles of reactive oxygen species (ROS) and fatty acid signaling. Our results show an increase in palmitic acid and its derivative in the primed guard cells. Palmitic acid may play a role as an activator of FLS2, which initiates stomatal immune response. Improved understanding of how SAR signals affect stomatal immunity can aid biotechnology and marker-based breeding of crops for enhanced disease resistance.
Biphasic Expression of Atypical Chemokine Receptor (ACKR) 2 and ACKR4 in Colorectal Neoplasms in Association with Histopathological Findings

Facilitating resolution of inflammation using atypical chemokine receptors (ACKR) as an anticancer strategy is considered but requires a deeper understanding of receptor role in carcinogenesis. We aimed at transcriptional analysis (RTqPCR) of ACKR2 and ACKR4 expression in colorectal adenoma-adenocarcinoma sequence in paired normal-neoplastic tissues from 96 polyps and 51 cancers. On average, ACKR2 was downregulated in neoplastic as compared to non-affected tissue in polyp (by 2.7-fold) and cancer (by 3.1-fold) patients. The maximal downregulation (by 8.2-fold) was observed in adenomas with the highest potential for malignancy and was gradually lessening through cancer stages I-IV, owing to increased receptor expression in tumors. On average, ACKR4 was significantly downregulated solely in adenocarcinomas (by 1.5-fold), less so in patients with lymph node metastasis, owing to a gradual decrease in ACKR4 expression among N0-N1-N2 cancers in non-affected tissue without changes in tumors. In adenomas, ACKR4 downregulation in neoplastic tissue increased with increasing potential for malignancy and contribution of villous growth pattern. ACKR4 expression increased in non-affected tissue with a concomitant decrease in pathological mucosa. In conclusion, the changes in ACKRs expression occur already in precancerous colorectal lesions, culminating in the adenomas with the highest potential for malignancy. Therefore, chemoprevention by manipulating ACKRs’ expression is worth exploration.
The Polarity of an Amino Acid at Position 1891 of Severe Fever with Thrombocytopenia Syndrome Virus L Protein Is Critical for the Polymerase Activity

Severe fever with thrombocytopenia syndrome virus subclone B7 shows strong plaque formation and cytopathic effect induction compared with other subclones and the parental strain YG1. Compared to YG1 and the other subclones, only B7 possesses a single substitution in the L protein at the amino acid position 1891, in which N is changed to K (N1891K). In this study, we evaluate the effects of this mutation on L protein activity via a cell-based minigenome assay. Substitutions of N with basic amino acids (K or R) enhanced polymerase activity, while substitutions with an acidic amino acid (E) decreased this activity. Mutation to other neutral amino acids showed no significant effect on activity. These results suggest that the characteristic of the amino acid at position 1891 of the L protein are critical for its function, especially with respect to the charge status. Our data indicate that this C-terminal domain of the L protein may be crucial to its functions in genome transcription and viral replication.
Completeness of Medical Records of Trauma Patients Admitted to the Emergency Unit of a University Hospital, Upper Egypt

Trauma records in Egyptian hospitals are widely suspected to be inadequate for developing a practical and useful trauma registry, which is critical for informing both primary and secondary prevention. We reviewed archived paper records of trauma patients admitted to the Beni-Suef University Hospital in Upper Egypt for completeness in four domains: demographic data including contact information, administrative data tracking patients from admission to discharge, clinical data including vital signs and Glasgow Coma Scale scores, and data describing the causal traumatic event (mechanism of injury, activity at the time of injury, and location/setting). The majority of the 539 medical records included in the study had significant deficiencies in the four reviewed domains. Overall, 74.3% of demographic fields, 66.5% of administrative fields, 55.0% of clinical fields, and just 19.9% of fields detailing the causal event were found to be completed. Critically, oxygen saturation, arrival time, and contact information were reported in only 7.6%, 25.8%, and 43.6% of the records, respectively. Less than a fourth of the records provided any details about the cause of trauma. Accordingly, the current, paper-based medical record system at Beni-Suef University Hospital is insufficient for the development of a practical trauma registry. More efforts are needed to develop efficient and comprehensive documentation of trauma data in order to inform and improve patient care.
New Approaches to Assess Fertility in Domestic Animals: Relationship between Arterial Blood Flow to the Testicles and Seminal Quality

Simple Summary Reproduction is one of the most important economic factors at a production level. For that reason, the evaluation of the breeding soundness (BS) is of great relevance to secure high production rates. There is ongoing research to find new markers to bring closer breeding soundness examination (BSE) results to real fertility outcomes. Among the different methods to evaluate BS, ultrasonography is routinely used and it is the method of choice to evaluate the testicular parenchyma. Doppler mode allows the quantitative and qualitative evaluation of the irrigation of organs and can be used as an important diagnostic technique for evaluating the testicular irrigation. In humans and several animal species, a relationship between Doppler parameters of the testicular artery and seminal quality has been found. This suggests pulsed wave Doppler ultrasound measurements and indices could be proposed as objective parameters to evaluate testicular function. Abstract The early identification of infertile males improves reproduction efficiency at a production level and is essential to secure high production rates. Before entering a breeding program, males must pass an initial breeding soundness examination (BSE) which consist of several diagnostic exams whose end point is to estimate their future fertility. There is ongoing research to find new markers that allow better identification of fertile males. Doppler mode allows the quantitative and qualitative evaluation of the irrigation of organs. When evaluating the reproductive system, Doppler mode has been successfully used for the evaluation of the uterine and ovarian irrigation. In males, it is gaining relevance for the evaluation of testicular irrigation. Researchers have found a relationship between pulsed-wave Doppler velocimetric parameters and seminal quality in various domestic animal species. This suggests Doppler ultrasound parameters should be considered as objective parameters to evaluate testicular function. In this review, we analyze the results in the main domestic animal species and discuss the differences and similarities among the results. We also discuss the effect of the location of the measurements, breed, season and laterality in the measurement of Doppler velocimetric parameters as well as the impact and limitations of this method of assessing breeding soundness.
Finding the Ionospheric Fluctuations Reflection in the Pulsar Signals’ Characteristics Observed with LOFAR

Pulsars’ signals reaching the atmosphere can be considered being stable under certain assumptions. In such a case the ionosphere remains the main factor distorting signal from the extraterrestrial sources, particularly if we observe them at long radio waves. In this article we present the results of the analysis of relative peak flux changes for two selected pulsars: PSR J0332+5434 (B0329+54) and PSR J1509+5531 (B1508+55), observed with the long radio wave sensor (The PL612 Low Frequency Array (LOFAR) station in Bałdy), together with the analysis of Rate of TEC (ROT) parameter changes measured with the Global Navigation Satellite Systems (GNSS) sensor (IGS LAMA station (IGS: International GSSN Service)). The main objective of the work is to find if the rapid plasma density (observed with the Rate of Total Electron Content (TEC)) has a counterpart in the pulsar observation characteristics. This focuses the attention on ionosphere influence during pulsar investigations at low radio frequencies. Additionally, what was the aim of this work, our results give reasons for using pulsar signals from LOFAR together with GNSS data as multi instrumental ionosphere state probes. Our results show a clear anti-correlation between the ROT and the pulsar profile’s peak flux trends.
Production of Monoacylglycerols from Fully Hydrogenated Palm Oil Catalyzed by Hydrotalcite Loaded with K2CO3

This study reports a new method of producing high-purity monoacylglycerols (MAGs) by glycerolysis of fully hydrogenated palm oil (FHPO) catalyzed by hydrotalcite loaded with K2CO3 (K2CO3/HT). The effects of reaction temperature, reaction time, catalyst (K2CO3/HT) loading, and mass ratio of FHPO to glycerol on glycerolysis were investigated. The selected conditions included a reaction temperature of 200°C, K2CO3/HT loading at 0.8 wt. % (FHPO mass), a 5:2 mass ratio of FHPO to glycerol, and a reaction time of 2 h. Under these selected conditions, the yield of MAGs in the acylglycerol phase reached 46.8 wt. %. A two-stage molecular distillation was introduced to purify MAGs, and the final MAG product was obtained with a purity of 96.6 wt. % and a recovery of 96.8%. Furthermore, the recycled K2CO3/HT was reactivated with restored catalytic efficiency through impregnation, carbonation, and recalcination.
"I Feel Like Less of a Mom": Experiences of Weight Stigma by Association among Mothers of Children with Overweight and Obesity.

Background: Parents of children with higher weight are blamed and shamed for their children's weight. However, parents' experiences of this form of stigma, termed weight stigma by association, are poorly understood. The objective of this study was to investigate the sources, forms, and impacts of weight stigma by association among mothers of children with overweight or obesity. Methods: In this qualitative study, mothers who reported concern about their children's weight participated in semistructured interviews administered by the research team. A coding scheme was developed and reliably applied to interview transcripts. Mothers' self-reported sociodemographic information, and height and weight were measured. Results: Thirty-four mothers (Mage: 43.4 years; 26.5% non-Hispanic Black or African American, 70.6% with obesity) participated in the study. Mothers reported that family members were a common source of negative comments about their children's weight; these comments were often critical of mothers' parenting and in some cases contributed to negative affect among mothers. Many mothers also reported negative experiences during children's physicians' visits as a result of their children's weight. Almost all mothers expressed guilt and sadness for their perceived role in their children's weight status, expressing regret that they did not parent differently. Conclusions: Mothers of children with overweight and obesity are frequently the target of weight stigma by association and experience negative cognitions and emotions regarding their perceived role in their children's weight. Continued research is needed to elucidate the impacts of stigma by association due to child weight on parents' health, the parent/child relationship, and children's health.
Targeting Cytokinin Homeostasis in Rapid Cycling Brassica rapa with Plant Growth Regulators INCYDE and TD-K

Modifying the cytokinin content in plants is a means of improving plant productivity. Here, we report the development and biological activity of compound TD-K (1-(furan-2-ylmethyl)-3-(1,2,3-thiadiazol-5-yl)urea)which is related to thidiazuron. TD-K—which exhibited extremely high antisenescence activity in the wheat leaf bioassay—and INCYDE (2-chloro-6-(3-methoxyphenyl)aminopurine)—a plant growth regulator reported to inhibit cytokinin oxidase/dehydrogenase (CKX), an enzyme involved in the degradation of the plant hormone cytokinin—were selected for investigation of their effects on the model plant Rapid Cycling Brassica rapa (RCBr). We monitored the expression of BrCKX and isopentenyl transferase (BrIPT), which codes for the key cytokinin biosynthesis enzyme, in developing leaves following INCYDE and TD-K application. Growth room experiments revealed that INCYDE increased RCBr seed yield per plant, but only when applied multiple times and when grown in 5 mM KNO3. Expression in control leaves showed transient, high levels of expression of BrCKX and BrIPT at true leaf appearance. Following INCYDE application, there was a rapid and strong upregulation of BrCKX3, and a transient downregulation of BrIPT1 and BrIPT3. Interestingly, the upregulation of BrCKX3 persisted in a milder form throughout the course of the experiment (16 days). TD-K also upregulated BrCKX3. However, in contrast to INCYDE, this effect disappeared after two days. These results suggest that both compounds (CKX inhibitor and cytokinin TD-K) influenced cytokinin homeostasis in RCBr leaves, but with different mechanisms.
Role of TGF-Beta and Smad7 in Gut Inflammation, Fibrosis and Cancer

The human gastrointestinal tract contains the largest population of immune cells in the body and this is a reflection of the fact that it is continuously exposed to a myriad of dietary and bacterial antigens. Although these cells produce a variety of inflammatory cytokines that could potentially promote tissue damage, in normal conditions the mucosal immune response is tightly controlled by counter-regulatory factors, which help induce and maintain gut homeostasis and tolerance. One such factor is transforming growth factor (TGF)-β1, a cytokine produced by multiple lineages of leukocytes, stromal cells and epithelial cells, and virtually targets all the gut mucosal cell types. Indeed, studies in animals and humans have shown that defects in TGF-β1 production and/or signaling can lead to the development of immune-inflammatory pathologies, fibrosis and cancer in the gut. Here, we review and discuss the available evidence about the role of TGF-β1 and Smad7, an inhibitor of TGF-β1 activity, in gut inflammation, fibrosis and cancer with particular regard to the contribution of these two molecules in the pathogenesis of inflammatory bowel diseases and colon cancer.
Diminishing Uncertainty Within the Training Pool: Active Learning for Medical Image Segmentation

Active learning is a unique abstraction of machine learning techniques where the model/algorithm could guide users for annotation of a set of data points that would be beneficial to the model, unlike passive machine learning. The primary advantage being that active learning frameworks select data points that can accelerate the learning process of a model and can reduce the amount of data needed to achieve full accuracy as compared to a model trained on a randomly acquired data set. Multiple frameworks for active learning combined with deep learning have been proposed, and the majority of them are dedicated to classification tasks. Herein, we explore active learning for the task of segmentation of medical imaging data sets. We investigate our proposed framework using two datasets: 1. ) MRI scans of the hippocampus, 2. ) CT scans of pancreas and tumors. This work presents a query-by-committee approach for active learning where a joint optimizer is used for the committee. At the same time, we propose three new strategies for active learning: 1. ) increasing frequency of uncertain data to bias the training data set; 2. ) Using mutual information among the input images as a regularizer for acquisition to ensure diversity in the training dataset; 3. ) adaptation of Dice log-likelihood for Stein variational gradient descent (SVGD). The results indicate an improvement in terms of data reduction by achieving full accuracy while only using 22.69% and 48.85% of the available data for each dataset, respectively.
Natural Plant-Derived Chemical Compounds as Listeria monocytogenes Inhibitors In Vitro and in Food Model Systems

Listeria monocytogenes is a foodborne pathogen, sporadically present in various food product groups. An illness caused by the pathogen, named listeriosis, has high fatality rates. Even though L. monocytogenes is resistant to many environmental factors, e.g., low temperatures, low pH and high salinity, it is susceptible to various natural plant-derived antimicrobials (NPDA), including thymol, carvacrol, eugenol, trans-cinnamaldehyde, carvone S, linalool, citral, (E)-2-hexenal and many others. This review focuses on identifying NPDAs active against L. monocytogenes and their mechanisms of action against the pathogen, as well as on studies that showed antimicrobial action of the compounds against the pathogen in food model systems. Synergistic action of NDPA with other factors, biofilm inhibition and alternative delivery systems (encapsulation and active films) of the compounds tested against L. monocytogenes are also summarized briefly.
Selection of Reference Genes for Normalization of Gene Expression in Thermobia domestica (Insecta: Zygentoma: Lepismatidae)

Zygentoma occupies a key evolutionary position for understanding the evolution of insect metamorphosis but has received little attention in terms of genetic analysis. To develop functional genomic studies in this insect, we evaluated five candidate internal reference genes for quantitative RT-PCR (qPCR) studies from Thermobia domestica, a representative species of Zygentoma, including Actin 5C (Actin5C), Elongation factor-1 alpha (EF1A), Ribosome protein S26 (RPS26), Ribosome protein L32 (RPL32), and Superoxide dismutase 2 (SOD2), at different developmental stages, in various body parts, and under dsRNA microinjection and starvation stresses, using four algorithms (delta Ct, geNorm, NormFinder and BestKeeper) and a comparative algorithm (RefFinder). Specific suitable reference genes were recommended across specific experimental conditions, and the combination of RPS26 and RPL32 was appropriate for all tested samples. Employing our selected reference gene combination, we investigated the gene expression pattern of Myoglianin (Myo), a crucial gene-regulating insect metamorphosis, in ametabolous T. domestica, and demonstrated the efficiency of RNA interference (RNAi) in firebrat nymphs. This study provides a basis for reliable quantitative studies of genes and greatly benefits evolutionary and functional genomics studies in Zygentoma.
Impact of Surface Chemistry of Silicon Nanoparticles on the Structural and Electrochemical Properties of Si/Ni3.4Sn4 Composite Anode for Li-Ion Batteries

Embedding silicon nanoparticles in an intermetallic matrix is a promising strategy to produce remarkable bulk anode materials for lithium-ion (Li-ion) batteries with low potential, high electrochemical capacity and good cycling stability. These composite materials can be synthetized at a large scale using mechanical milling. However, for Si-Ni3Sn4 composites, milling also induces a chemical reaction between the two components leading to the formation of free Sn and NiSi2, which is detrimental to the performance of the electrode. To prevent this reaction, a modification of the surface chemistry of the silicon has been undertaken. Si nanoparticles coated with a surface layer of either carbon or oxide were used instead of pure silicon. The influence of the coating on the composition, (micro)structure and electrochemical properties of Si-Ni3Sn4 composites is studied and compared with that of pure Si. Si coating strongly reduces the reaction between Si and Ni3Sn4 during milling. Moreover, contrary to pure silicon, Si-coated composites have a plate-like morphology in which the surface-modified silicon particles are surrounded by a nanostructured, Ni3Sn4-based matrix leading to smooth potential profiles during electrochemical cycling. The chemical homogeneity of the matrix is more uniform for carbon-coated than for oxygen-coated silicon. As a consequence, different electrochemical behaviors are obtained depending on the surface chemistry, with better lithiation properties for the carbon-covered silicon able to deliver over 500 mAh/g for at least 400 cycles.
Comparison of Blood Flow Restriction Training versus Non-Occlusive Training in Patients with Anterior Cruciate Ligament Reconstruction or Knee Osteoarthritis: A Systematic Review

Patients undergoing anterior cruciate ligament (ACL) reconstruction and patients suffering from knee osteoarthritis (KOA) have been shown to have quadriceps muscle weakness and/or atrophy in common. The physiological mechanisms of blood flow restriction (BFR) training could facilitate muscle hypertrophy. The purpose of this systematic review is to investigate the effects of BFR training on quadriceps cross-sectional area (CSA), pain perception, function and quality of life on these patients compared to a non-BFR training. A literature research was performed using Web of Science, PEDro, Scopus, MEDLINE, Dialnet, CINAHL and The Cochrane Library databases. The main inclusion criteria were that papers were English or Spanish language reports of randomized controlled trials involving patients with ACL reconstruction or suffering from KOA. The initial research identified 159 publications from all databases; 10 articles were finally included. The search was conducted from April to June 2020. Four of these studies found a significant improvement in strength. A significant increase in CSA was found in two studies. Pain significantly improved in four studies and only one study showed a significant improvement in functionality/quality of life. Low-load training with BFR may be an effective option treatment for increasing quadriceps strength and CSA, but more research is needed.
The Dependence of the Diffusion Coefficient on the Proton Concentration in the Proton Exchange of LiNbO3.

The concentration-dependent diffusion coefficient for proton-lithium counter-diffusion is studied in this paper. Depth profiles of the proton concentration for proton-exchanged LiNbO3 were measured by secondary ion mass spectroscopy (SIMS). The concentration-dependent diffusion coefficient for the proton-lithium counter-diffusion was calculated by the Boltzmann-Matano method and the relationships between the diffusion coefficient, the proton-exchange process, and the crystal phases in proton-exchanged LiNbO3 were examined. To confirm the validity of the diffusion coefficient calculated from the SIMS data, the depth profiles of the proton concentrations were numerically computed with the calculated diffusion coefficient and the exponential dependence of the diffusion coefficient on the content of lithium benzoate for dilution was reproduced.