Miracle-dz/UniFAR-FTUs huggingface dataset:
Rice SUT and SWEET Transporters

Sugar transporters play important or even indispensable roles in sugar translocation among adjacent cells in the plant. They are mainly composed of sucrose–proton symporter SUT family members and SWEET family members. In rice, 5 and 21 members are identified in these transporter families, and some of their physiological functions have been characterized on the basis of gene knockout or knockdown strategies. Existing evidence shows that most SUT members play indispensable roles, while many SWEET members are seemingly not so critical in plant growth and development regarding whether their mutants display an aberrant phenotype or not. Generally, the expressions of SUT and SWEET genes focus on the leaf, stem, and grain that represent the source, transport, and sink organs where carbohydrate production, allocation, and storage take place. Rice SUT and SWEET also play roles in both biotic and abiotic stress responses in addition to plant growth and development. At present, these sugar transporter gene regulation mechanisms are largely unclear. In this review, we compare the expressional profiles of these sugar transporter genes on the basis of chip data and elaborate their research advances. Some suggestions concerning future investigation are also proposed.
Coffeeberry Activates the CaMKII/CREB/BDNF Pathway, Normalizes Autophagy and Apoptosis Signaling in Nonalcoholic Fatty Liver Rodent Model

Nonalcoholic fatty liver disease (NAFLD) shows extensive liver cell destruction with lipid accumulation, which is frequently accompanied by metabolic comorbidities and increases mortality. This study aimed to investigate the effects of coffeeberry (CB) on regulating the redox status, the CaMKII/CREB/BDNF pathway, autophagy, and apoptosis signaling by a NAFLD rodent model senescence-accelerated mice prone 8 (SAMP8). Three-month-old male SAMP8 mice were divided into a control group and three CB groups (50, 100, and 200 mg/kg BW), and fed for 12 weeks. The results show that CB reduced hepatic malondialdehyde and carbonyl protein levels. CB significantly enhanced Ca2+/calmodulin-dependent protein kinase II (CaMKII) and brain-derived neurotrophic factor (BDNF) and reduced the phospho-cAMP response element-binding protein (p-CREB)/CREB ratio. In addition, CB increased the silent information regulator T1 level, promoted Beclin 1 and microtubule-associated protein light chain 3 II expressions, and reduced phosphorylated mammalian target of rapamycin and its downstream p-p70s6k levels. CB also inhibited the expressions of apoptosis-related factors poly (ADP-ribose) polymerase-1 and the apoptosis-inducing factor. In conclusion, CB might protect the liver by reducing oxidative stress, activating the CaMKII/CREB/BDNF pathway, and improving autophagic and apoptotic expressions in a dose-dependent manner.
Batch Manufacturing of Split-Actuator Micro Air Vehicle Based on Monolithic Processing Technology

Microrobots have a wide range of applications. The rigid–flexible composite stereoscopic technology based on ultraviolet laser cutting technology is primarily researched for the design and manufacture of microrobots and has been used to fabricate microscale motion mechanisms and robots. This paper introduces a monolithic processing technology based on the rigid–flexible composite stereoscopic process. Based on this process, a split-actuator micro flapping-wing air vehicle with a size of 15 mm × 2.5 mm × 30 mm was designed. We proposed a batch manufacturing method capable of processing multiple micro air vehicles at the same time. The main structure of 22 flapping-wing micro air vehicles can be processed at the same time within the processing range of the composite sheet with an area of 80 mm × 80 mm, and the processing effect is good.
Fermentation Supernatants of Pleurotus eryngii Mushroom Ameliorate Intestinal Epithelial Barrier Dysfunction in Lipopolysaccharide-Induced Caco-2 Cells via Upregulation of Tight Junctions

In recent years, modulation of gut microbiota through prebiotics has garnered interest as a potential to ameliorate intestinal barrier dysfunction. The aim of the study was to examine the in vitro effect of fermentation supernatants (FSs) from rich in β-glucan Pleurotus eryngii mushrooms on the expression levels of tight junctions (TJs) genes in Caco-2 cells stimulated by bacterial lipopolysaccharides (LPS). Mushrooms were fermented using fecal inocula in an in vitro batch culture model. Caco-2 cells were subjected to LPS and FS treatment under three different conditions: pre-incubation with FS, co- and post-incubation. Reverse transcription PCR was applied to measure the expression levels of zonulin-1, occludin and claudin-1 genes. FSs from P. eryngii mushrooms led to a significant upregulation of the TJs gene expression in pre-incubation state, indicating potential preventive action. Down-regulation of all TJs gene expression levels was observed when the cells were challenged with LPS. The FS negative control (gut microbiota of each donor with no carbohydrate source) exhibited a significant upregulation of TJs expression levels compared to the cells that were challenged with LPS, for all three conditions. Overall, our data highlighted the positive and potential protective effects of P. eryngii mushrooms in upregulation of TJs’ genes.
Bacteria–Cancer Interface: Awaiting the Perfect Storm

Epidemiological evidence reveal a very close association of malignancies with chronic inflammation as a result of persistent bacterial infection. Recently, more studies have provided experimental evidence for an etiological role of bacterial factors disposing infected tissue towards carcinoma. When healthy cells accumulate genomic insults resulting in DNA damage, they may sustain proliferative signalling, resist apoptotic signals, evade growth suppressors, enable replicative immortality, and induce angiogenesis, thus boosting active invasion and metastasis. Moreover, these cells must be able to deregulate cellular energetics and have the ability to evade immune destruction. How bacterial infection leads to mutations and enriches a tumour-promoting inflammatory response or micro-environment is still not clear. In this review we showcase well-studied bacteria and their virulence factors that are tightly associated with carcinoma and the various mechanisms and pathways that could have carcinogenic properties.
Radiological and Physiological Predictors of IPF Mortality

Background and Objectives: Idiopathic pulmonary fibrosis (IPF) has a variable clinical course, which ranges from being asymptomatic to progressive respiratory failure. The purpose of this study was to evaluate the novel clinical parameters of IPF patients who receive an anti-fibrotic agent. Materials and Methods: From January 2011 to January 2021, we identified 39 IPF patients at Okinawa Chubu Hospital. Clinical information was obtained, such as laboratory data, pulmonary function test (PFT) results, and chest images, including of soft tissue thickness and the high-resolution computed tomography (HRCT) pattern at diagnosis. Results: The mean age was 72.9 ± 7.0 (53–85); 27 patients were men and 12 were women. The mean body mass index was 25.1 ± 3.9 (17.3–35). Twenty-four were active smokers and the median number of packs per year was 20. Regarding laboratory findings, mean white blood cell (WBC), lactate dehydrogenase (LDH), and Krebs Von den Lungen-6 (KL-6) values were 7816 ± 1859, 248 ± 47, and 1615 ± 1503, respectively. In PFT, the mean percent predicted FVC, percent predicted total lung capacity, percent predicted functional residual capacity (FRC), and percent predicted diffusion capacity of the lung for carbon monoxide (DLco) were 66.8 ± 14.9%, 71.8 ± 13.7%, 65 ± 39.6%, and 64.6 ± 27.9%, respectively. In chest radiological findings, soft tissue thickness at the right 9th rib was 26.4 ± 8.8 mm. Regarding chest HRCT patterns, 15 showed the definite usual interstitial pneumonia (UIP) pattern, 16 showed the probable UIP pattern, and eight showed the indeterminate for UIP pattern. In the treatment, 24 patients received pirfenidone and 15 patients took nintedanib. The mean observation period was 38.6 ± 30.6 months and 24 patients died. The median survival time was 32.4 months (0.9–142.5). Multivariate analysis adjusted for age showed that both soft tissue thickness [Hazard ratio (HR): 0.912, 95% confidence interval (CI): 0.859–0.979, p-value: 0.009] and percent FRC [HR: 0.980, 95% CI: 0.967–0.992, p-value: 0.002] were robust predictors of IPF mortality. Conclusions: In IPF patients treated with anti-fibrotic agents, both soft tissue thickness at the right 9th rib shown on the chest radiograph and %FRC can be novel predictors of IPF mortality.
Ultra-Processed Foods and Nutritional Dietary Profile: A Meta-Analysis of Nationally Representative Samples

Excessive consumption of ultra-processed foods (UPFs), as described by the NOVA classification system, represents a potential threat to human health. The nutritional composition of UPFs may explain their observed adverse effects. The present study aimed to provide a quantitative meta-analysis of nationally representative surveys on the consumption of UPFs and the dietary/nutrient composition of respondents’ diets. A systematic search for relevant studies published prior to July 2021 was conducted via electronic databases. The studies that provided the dietary/nutrient composition of foods categorized according to the NOVA classification system were selected. The association between UPFs and other dietary variables was modelled using ordinary least squares linear regression based on aggregated data extracted from the selected articles. Consumption of UPFs represented up to 80% of total caloric intake in the US and Canada, with confectionery and sugar-sweetened beverages being the most consumed items. When considered in relation to other food groups, an inverse linear relation between UPFs and less-processed foods was evident. Increased UPF intake correlated with an increase in free sugars, total fats, and saturated fats, as well as a decrease in fiber, protein, potassium, zinc, and magnesium, and vitamins A, C, D, E, B12, and niacin. In conclusion, the data indicate that increased UPF consumption negatively affects the nutritional quality of diets.
Engineered Bacteriophage as a Delivery Vehicle for Antibacterial Protein, SASP

The difficulties in developing novel classes of antibacterials is leading to a resurgence of interest in bacteriophages as therapeutic agents, and in particular engineered phages that can be optimally designed. Here, pre-clinical microbiology assessment is presented of a Staphylococcus aureus phage engineered to deliver a gene encoding an antibacterial small acid soluble spore protein (SASP) and further, rendered non-lytic to give product SASPject PT1.2. PT1.2 has been developed initially for nasal decolonisation of S. aureus, including methicillin-resistant S. aureus. Time-kill curve assays were conducted with PT1.2 against a range of staphylococcal species, and serial passaging experiments were conducted to investigate the potential for resistance to develop. SASPject PT1.2 demonstrates activity against 100% of 225 geographically diverse S. aureus isolates, exquisite specificity for S. aureus, and a rapid speed of kill. The kinetics of S. aureus/PT1.2 interaction is examined together with demonstrating that PT1.2 activity is unaffected by the presence of human serum albumin. SASPject PT1.2 shows a low propensity for resistance to develop with no consistent shift in sensitivity in S. aureus cells passaged for up to 42 days. SASPject PT1.2 shows promise as a novel first-in-class antibacterial agent and demonstrates potential for the SASPject platform.
Immunoglobulin A, an Active Liaison for Host-Microbiota Homeostasis

Mucosal surfaces in the gastrointestinal tract are continually exposed to native, commensal antigens and susceptible to foreign, infectious antigens. Immunoglobulin A (IgA) provides dual humoral responses that create a symbiotic environment for the resident gut microbiota and prevent the invasion of enteric pathogens. This review features recent immunological and microbial studies that elucidate the underlying IgA and microbiota-dependent mechanisms for mutualism at physiological conditions. IgA derailment and concurrent microbiota instability in pathological diseases are also discussed in detail. Highlights of this review underscore that the source of IgA and its structural form can dictate microbiota reactivity to sustain a diverse niche where both host and bacteria benefit. Other important studies emphasize IgA insufficiency can result in the bloom of opportunistic pathogens that encroach the intestinal epithelia and disseminate into circulation. The continual growth of knowledge in these subjects can lead to the development of therapeutics targeting IgA and/or the microbiota to treat life threatening diseases.
Nationwide Data on the Characteristics of Linked-to-Care Chronic Hepatitis B in Korea

Linkage-to-care rate of chronic hepatitis B (CHB) is less well characterized. We aimed to evaluate the proportion, characteristics of CHB patients who are linked to care. We retrospectively analyzed insurance reimbursement claims data provided by the Korean National Health Insurance Service. CHB patients who had at least two clinic or hospital visits that were associated with a CHB diagnostic code during 2002–2006 were included. Those without a history of malignancy at baseline were followed up until 2018. Mean follow-up period was 14.5 ± 2.9 years. Among the participants, 553,085 patients (35.8%) were found to be linked to care. The rates were lower in men than women (35.7% vs. 36.0%, p = 0.006). By age, it was highest for the 40′s age group at 44.8% and lowest at 29.4% for the 20′s age group (All p < 0.0001). The linkage-to-care rate was higher in rural area than metropolitan area (p < 0.0001). The 15-year cumulative incidence of hepatocellular carcinoma and overall survival rates among linked-to-care CHB patients were 18.2% and 93.8%, respectively. Two thirds of CHB patients were not linked to care. Those who are male, dwelling in metropolitan areas, and not in life transition periods need to be targeted to improve the linkage-to-care rate in Korea.
Preparation of Acyclovir-Containing Solid Foam by Ultrasonic Batch Technology

In recent years, the application of solid foams has become widespread. Solid foams are not only used in the aerospace field but also in everyday life. Although foams are promising dosage forms in the pharmaceutical industry, their usage is not prevalent due to decreased stability of the solid foam structure. These special dosage forms can result in increased bioavailability of drugs. Low-density floating formulations can also increase the gastric residence time of drugs; therefore, drug release will be sustained. Our aim was to produce a stable floating formula by foaming. Matrix components, PEG 4000 and stearic acid type 50, were selected with the criteria of low gastric irritation, a melting range below 70 °C, and well-known use in oral drug formulations. This matrix was melted at 54 °C in order to produce a dispersion of active substance and was foamed by different gases at atmospheric pressure using an ultrasonic homogenizer. The density of the molded solid foam was studied by the pycnometer method, and its structure was investigated by SEM and micro-CT. The prolonged drug release and mucoadhesive properties were proved in a pH 1.2 buffer. According to our experiments, a stable foam could be produced by rapid homogenization (less than 1 min) without any surfactant material.
Structure, Activity, and Function of the Protein Lysine Methyltransferase G9a

G9a is a lysine methyltransferase catalyzing the majority of histone H3 mono- and dimethylation at Lys-9 (H3K9), responsible for transcriptional repression events in euchromatin. G9a has been shown to methylate various lysine residues of non-histone proteins and acts as a coactivator for several transcription factors. This review will provide an overview of the structural features of G9a and its paralog called G9a-like protein (GLP), explore the biochemical features of G9a, and describe its post-translational modifications and the specific inhibitors available to target its catalytic activity. Aside from its role on histone substrates, the review will highlight some non-histone targets of G9a, in order gain insight into their role in specific cellular mechanisms. Indeed, G9a was largely described to be involved in embryonic development, hypoxia, and DNA repair. Finally, the involvement of G9a in cancer biology will be presented.
Streptococcus suis Isolates—Serotypes and Susceptibility to Antimicrobials in Terms of Their Use on Selected Repopulated Czech Pig Farms

Streptococcus suis represents a primary health problem (such as meningitis, septicemia and arthritis in piglets and fatteners) in the swine industry worldwide and also an emerging zoonotic pathogen. In the Czech Republic, many pig farms repopulated their herds over the past decades to reduce morbidity and minimize treatment. The study analysed serotypes, sequence types and antimicrobial susceptibility in 39 S. suis isolates obtained from organs of diseased pigs from selected 16 repopulated farms with a history of S. suis-associated diseases and routine antimicrobial treatment with tulathromycin and/or amoxicillin. The analysis revealed diversity of collected isolates with regular occurrence of more than three serotypes per farm. The serotypes identified were 1/2 and 7, each in six isolates, followed by serotype 2 and 3 found in five isolates each, other serotypes were less frequent. Seven isolates were not typable by multiplex PCR and we also found sequence type of unknown type in thirteen isolates. The majority of S. suis isolates were resistant to clindamycin (n = 31), tetracycline (n = 29) and tilmicosin and tulathromycin (n = 28). On the other hand, with the exception of two isolates that were intermediately susceptible to penicillin and ampicillin, all isolates were susceptible to all three tested subgroups of beta-lactam antibiotics.
Biochar Amendments Improve Licorice (Glycyrrhiza uralensis Fisch.) Growth and Nutrient Uptake under Salt Stress

Licorice (Glycyrrhiza uralensis Fisch.) is a salt and drought tolerant legume suitable for rehabilitating abandoned saline lands, especially in dry arid regions. We hypothesized that soil amended with maize-derived biochar might alleviate salt stress in licorice by improving its growth, nutrient acquisition, and root system adaptation. Experiments were designed to determine the effect of different biochar concentrations on licorice growth parameters, acquisition of C (carbon), nitrogen (N), and phosphorus (P) and on soil enzyme activities under saline and non-saline soil conditions. Pyrolysis char from maize (600 °C) was used at concentrations of 2% (B2), 4% (B4), and 6% (B6) for pot experiments. After 40 days, biochar improved the shoot and root biomass of licorice by 80 and 41% under saline soil conditions. However, B4 and B6 did not have a significant effect on shoot growth. Furthermore, increased nodule numbers of licorice grown at B4 amendment were observed under both non-saline and saline conditions. The root architectural traits, such as root length, surface area, project area, root volume, and nodulation traits, also significantly increased by biochar application at both B2 and B4. The concentrations of N and K in plant tissue increased under B2 and B4 amendments compared to the plants grown without biochar application. Moreover, the soil under saline conditions amended with biochar showed a positive effect on the activities of soil fluorescein diacetate hydrolase, proteases, and acid phosphomonoesterases. Overall, this study demonstrated the beneficial effects of maize-derived biochar on growth and nutrient uptake of licorice under saline soil conditions by improving nodule formation and root architecture, as well as soil enzyme activity.
Key to Life: Physiological Role and Clinical Implications of Progesterone

The most recent studies of progesterone research provide remarkable insights into the physiological role and clinical importance of this hormone. Although the name progesterone itself means “promoting gestation”, this steroid hormone is far more than a gestational agent. Progesterone is recognized as a key physiological component of not only the menstrual cycle and pregnancy but also as an essential steroidogenic precursor of other gonadal and non-gonadal hormones such as aldosterone, cortisol, estradiol, and testosterone. Based on current findings, progesterone and novel progesterone-based drugs have many important functions, including contraception, treatment of dysfunctional uterine bleeding, immune response, and prevention of cancer. Considering the above, reproduction and life are not possible without progesterone; thus, a better understanding of this essential molecule could enable safe and effective use of this hormone in many clinical conditions.
The Amyloid Forming Peptides Islet Amyloid Polypeptide and Amyloid β Interact at the Molecular Level

Epidemiological studies support a connection between the two common disorders, type-2 diabetes and Alzheimer’s disease. Both conditions have local amyloid formation in their pathogenesis, and cross-seeding between islet amyloid polypeptide (IAPP) and amyloid β (Aβ) could constitute the link. The bimolecular fluorescence complementation (BiFC) assay was used to investigate the occurrence of heterologous interactions between IAPP and Aβ and to compare the potential toxic effects of IAPP/Aβ, IAPP/IAPP, and Aβ/Aβ expression in living cells. Microscopy was used to confirm the fluorescence and determine the lysosomal, mitochondrial areas and mitochondrial membrane potential, and a FACS analysis was used to determine ROS production and the role for autophagy. Drosophila melanogaster expressing IAPP and Aβ was used to study their co-deposition and effects on longevity. We showed that the co-expression of IAPP and Aβ resulted in fluorophore reconstitution to the same extent as determined for homologous IAPP/IAPP or Aβ/Aβ expression. The BiFC(+)/BiFC(−) ratio of lysosomal area calculations increased in transfected cells independent of the vector combinations, while only Aβ/Aβ expression increased mitochondrial membrane potential. Expression combinations containing Aβ were necessary for the formation of a congophilic amyloid. In Drosophila melanogaster expressing IAPP/Aβ, co-deposition of the amyloid-forming peptides caused reduced longevity. The BiFC results confirmed a heterologous interaction between IAPP and Aβ, while co-deposits in the brain of Drosophila suggest mixed amyloid aggregates.
Autoinflammatory Diseases and Cytokine Storms—Imbalances of Innate and Adaptative Immunity

Innate and adaptive immune responses have a well-known link and represent the distinctive origins of several diseases, many of which may be the consequence of the loss of balance between these two responses. Indeed, autoinflammation and autoimmunity represent the two extremes of a continuous spectrum of pathologic conditions with numerous overlaps in different pathologies. A common characteristic of these dysregulations is represented by hyperinflammation, which is an exaggerated response of the immune system, especially involving white blood cells, macrophages, and inflammasome activation with the hyperproduction of cytokines in response to various triggering stimuli. Moreover, hyperinflammation is of great interest, as it is one of the main manifestations of COVID-19 infection, and the cytokine storm and its most important components are the targets of the pharmacological treatments used to combat COVID-19 damage. In this context, the purpose of our review is to provide a focus on the pathogenesis of autoinflammation and, in particular, of hyperinflammation in order to generate insights for the identification of new therapeutic targets and strategies.