Miracle-dz/UniFAR-FTUs huggingface dataset:
Species Diversity, Molecular Phylogeny, and Ecological Habits of Fomitopsis (Polyporales, Basidiomycota)

Fomitopsis is a worldwide brown-rot fungal genus of Polyporales, which grows on different gymnosperm and angiosperm trees and has important ecological functions and economic values. In this study, species diversity, phylogenetic relationships, and ecological habits of Fomitopsis were investigated. A total of 195 specimens from 24 countries representing 29 species of Fomitopsis were studied. Based on the morphological characters and phylogenetic evidence of DNA sequences including the internal transcribed spacer (ITS) regions, the large subunit of nuclear ribosomal RNA gene (nLSU), the small subunit of nuclear ribosomal RNA gene (nSSU), the small subunit of mitochondrial rRNA gene (mtSSU), the translation elongation factor 1-α gene (TEF), and the second subunit of RNA polymerase II (RPB2), 30 species are accepted in Fomitopsis, including four new species: F. resupinata, F. srilankensis, F. submeliae and F. yimengensis. Illustrated descriptions of the novel species and the geographical locations of the Fomitopsis species are provided.
SLC38A10 Regulate Glutamate Homeostasis and Modulate the AKT/TSC2/mTOR Pathway in Mouse Primary Cortex Cells

Glutamate acts as a critical regulator of neurotransmitter balance, recycling, synaptic function and homeostasis in the brain and glutamate transporters control glutamate levels in the brain. SLC38A10 is a member of the SLC38 family and regulates protein synthesis and cellular stress responses. Here, we uncover the role of SLC38A10 as a transceptor involved in glutamate-sensing signaling pathways that control both the glutamate homeostasis and mTOR-signaling. The culture of primary cortex cells from SLC38A10 knockout mice had increased intracellular glutamate. In addition, under nutrient starvation, KO cells had an impaired response in amino acid-dependent mTORC1 signaling. Combined studies from transcriptomics, protein arrays and metabolomics established that SLC38A10 is involved in mTOR signaling and that SLC38A10 deficient primary cortex cells have increased protein synthesis. Metabolomic data showed decreased cholesterol levels, changed fatty acid synthesis, and altered levels of fumaric acid, citrate, 2-oxoglutarate and succinate in the TCA cycle. These data suggests that SLC38A10 may act as a modulator of glutamate homeostasis, and mTOR-sensing and loss of this transceptor result in lower cholesterol, which could have implications in neurodegenerative diseases.
A Novel Theanine Complex, Mg-L-Theanine Improves Sleep Quality via Regulating Brain Electrochemical Activity

L-Theanine is commonly used to improve sleep quality through inhibitory neurotransmitters. On the other hand, Mg2+, a natural NMDA antagonist and GABA agonist, has a critical role in sleep regulation. Using the caffeine-induced brain electrical activity model, here we investigated the potency of L-theanine and two novel Mg-L-theanine compounds with different magnesium concentrations on electrocorticography (ECoG) patterns, GABAergic and serotonergic receptor expressions, dopamine, serotonin, and melatonin levels. Furthermore, we evaluated the sleep latency and duration in the pentobarbital induced sleep model. We herein showed that L-theanine, particularly its various complexes with magnesium increases the expression of GABAergic, serotonergic, and glutamatergic receptors, which were associated with decreased ECoG frequency, increased amplitude, and enhanced delta wave powers. Besides increased dopamine, serotonin, and melatonin; decreased MDA and increased antioxidant enzyme levels were also observed particularly with Mg-complexes. Protein expression analyses also showed that Mg-L-theanine complexes decrease inducible nitric oxide synthase (iNOS) and endothelial nitric oxide synthase (eNOS) levels significantly. In accordance with these results, Mg complexes improved the sleep latency and duration even after caffeine administration. As a result, our data indicate that Mg-L-theanine compounds potentiate the effect of L-theanine on sleep by boosting slow-brain waves, regulating brain electrical activity, and increasing neurotransmitter and GABA receptor levels. Graphical Abstract The effects of Mg-L-Theanine on brain electrochemical activity, antioxidant enzymes and sleep. Mg-L-Theanine increases sleep duration, slow waves powers, GABAergic and serotonergic receptor expressions, dopamine, melatonin, and serotonin levels, and antioxidant enzyme activity.
Amelioration of Chromium-Induced Oxidative Stress by Combined Treatment of Selected Plant-Growth-Promoting Rhizobacteria and Earthworms via Modulating the Expression of Genes Related to Reactive Oxygen Species Metabolism in Brassica juncea

Chromium (Cr) toxicity leads to the enhanced production of reactive oxygen species (ROS), which are extremely toxic to the plant and must be minimized to protect the plant from oxidative stress. The potential of plant-growth-promoting rhizobacteria (PGPR) and earthworms in plant growth and development has been extensively studied. The present study was aimed at investigating the effect of two PGPR (Pseudomonas aeruginosa and Burkholderia gladioli) along with earthworms (Eisenia fetida) on the antioxidant defense system in Brassica juncea seedlings under Cr stress. The Cr toxicity reduced the fresh and dry weights of seedlings, enhanced the levels of superoxide anion (O2•–), hydrogen peroxide (H2O2), malondialdehyde (MDA), and electrolyte leakage (EL), which lead to membrane as well as the nuclear damage and reduced cellular viability in B. juncea seedlings. The activities of the antioxidant enzymes, viz., superoxide dismutase (SOD), guaiacol peroxidase (POD), ascorbate peroxidase (APOX), glutathione peroxidase (GPOX), dehydroascorbate reductase (DHAR), and glutathione reductase (GR) were increased; however, a reduction was observed in the activity of catalase (CAT) in the seedlings under Cr stress. Inoculation of the PGPR and the addition of earthworms enhanced the activities of all other antioxidant enzymes except GPOX, in which a reduction of the activity was observed. For total lipid- and water-soluble antioxidants and the non-enzymatic antioxidants, viz., ascorbic acid and glutathione, an enhance accumulation was observed upon the inoculation with PGPR and earthworms. The supplementation of PGPR with earthworms (combined treatment) reduced both the reactive oxygen species (ROS) and the MDA content by modulating the defense system of the plant. The histochemical studies also corroborated that the combined application of PGPR and earthworms reduced O2•–, H2O2, lipid peroxidation, and membrane and nuclear damage and improved cell viability. The expression of key antioxidant enzyme genes, viz., SOD, CAT, POD, APOX, GR, DHAR, and GST showed the upregulation of these genes at post-transcriptional level upon the combined treatment of the PGPR and earthworms, thereby corresponding to the improved plant biomass. However, a reduced expression of RBOH1 gene was noticed in seedlings supplemented under the effect of PGPR and earthworms grown under Cr stress. The results provided sufficient evidence regarding the role of PGPR and earthworms in the amelioration of Cr-induced oxidative stress in B. juncea.
Seamless Gene Correction in the Human Cystic Fibrosis Transmembrane Conductance Regulator Locus by Vector Replacement and Vector Insertion Events

Background: Gene correction via homology directed repair (HDR) in patient-derived induced pluripotent stem (iPS) cells for regenerative medicine are becoming a more realistic approach to develop personalized and mutation-specific therapeutic strategies due to current developments in gene editing and iPSC technology. Cystic fibrosis (CF) is the most common inherited disease in the Caucasian population, caused by mutations in the CF transmembrane conductance regulator (CFTR) gene. Since CF causes significant multi-organ damage and with over 2,000 reported CFTR mutations, CF patients could be one prominent population benefiting from gene and cell therapies. When considering gene-editing techniques for clinical applications, seamless gene corrections of the responsible mutations, restoring native “wildtype” DNA sequence without remnants of drug selectable markers or unwanted DNA sequence changes, would be the most desirable approach. Result: The studies reported here describe the seamless correction of the W1282X CFTR mutation using CRISPR/Cas9 nickases (Cas9n) in iPS cells derived from a CF patient homozygous for the W1282X Class I CFTR mutation. In addition to the expected HDR vector replacement product, we discovered another class of HDR products resulting from vector insertion events that created partial duplications of the CFTR exon 23 region. These vector insertion events were removed via intrachromosomal homologous recombination (IHR) enhanced by double nicking with CRISPR/Cas9n which resulted in the seamless correction of CFTR exon 23 in CF-iPS cells. Conclusion: We show here the removal of the drug resistance cassette and generation of seamless gene corrected cell lines by two independent processes: by treatment with the PiggyBac (PB) transposase in vector replacements or by IHR between the tandemly duplicated CFTR gene sequences.
Embodied Intelligence: Smooth Coping in the Learning Intelligent Decision Agent Cognitive Architecture

Much of our everyday, embodied action comes in the form of smooth coping. Smooth coping is skillful action that has become habituated and ingrained, generally placing less stress on cognitive load than considered and deliberative thought and action. When performed with skill and expertise, walking, driving, skiing, musical performances, and short-order cooking are all examples of the phenomenon. Smooth coping is characterized by its rapidity and relative lack of reflection, both being hallmarks of automatization. Deliberative and reflective actions provide the contrast case. In Dreyfus’ classic view, smooth coping is “mindless” absorption into action, being in the flow, and any reflective thought will only interrupt this flow. Building on the pragmatist account of Dewey, others, such as Sutton, Montero, and Gallagher, insist on the intelligent flexibility built into smooth coping, suggesting that it is not equivalent to automatization. We seek to answer two complementary challenges in this article. First, how might we model smooth coping in autonomous agents (natural or artificial) at fine granularity? Second, we use this model of smooth coping to show how we might implement smooth coping in artificial intelligent agents. We develop a conceptual model of smooth coping in LIDA (Learning Intelligent Decision Agent). LIDA is an embodied cognitive architecture implementing the global workspace theory of consciousness, among other psychological theories. LIDA’s implementation of consciousness enables us to account for the phenomenology of smooth coping, something that few cognitive architectures would be able to do. Through the fine granular analysis of LIDA, we argue that smooth coping is a sequence of automatized actions intermittently interspersed with consciously mediated action selection, supplemented by dorsal stream processes. In other words, non-conscious, automatized actions (whether learned or innate) often require occasional bursts of conscious cognition to achieve the skillful and flexible adjustments of smooth coping. In addition, never-conscious dorsal stream information and associated sensorimotor processes provide further online adjustments during smooth coping. To achieve smooth coping in LIDA we introduce a new module to the LIDA cognitive architecture the Automatized Action Selection sub-module. Our complex model of smooth coping borrows notions of “embodied intelligence” from enactivism and augments these by allowing representations and more detailed mechanisms of conscious control. We explore several extended examples of smooth coping, starting from basic activities like walking and scaling up to more complex tasks like driving and short-order cooking.
Prospective Comparison Between Shotgun Metagenomics and Sanger Sequencing of the 16S rRNA Gene for the Etiological Diagnosis of Infections

Bacteriological diagnosis is traditionally based on culture. However, this method may be limited by the difficulty of cultivating certain species or by prior exposure to antibiotics, which justifies the resort to molecular methods, such as Sanger sequencing of the 16S rRNA gene (Sanger 16S). Recently, shotgun metagenomics (SMg) has emerged as a powerful tool to identify a wide range of pathogenic microorganisms in numerous clinical contexts. In this study, we compared the performance of SMg to Sanger 16S for bacterial detection and identification. All patients’ samples for which Sanger 16S was requested between November 2019 and April 2020 in our institution were prospectively included. The corresponding samples were tested with a commercial 16S semi-automated method and a semi-quantitative pan-microorganism DNA- and RNA-based SMg method. Sixty-seven samples from 64 patients were analyzed. Overall, SMg was able to identify a bacterial etiology in 46.3% of cases (31/67) vs. 38.8% (26/67) with Sanger 16S. This difference reached significance when only the results obtained at the species level were compared (28/67 vs. 13/67). This study provides one of the first evidence of a significantly better performance of SMg than Sanger 16S for bacterial detection at the species level in patients with infectious diseases for whom culture-based methods have failed. This technology has the potential to replace Sanger 16S in routine practice for infectious disease diagnosis.
Dual Relationship Between Stromal Cells and Immune Cells in the Tumor Microenvironment

The tumor microenvironment (TME) plays a critical role in tumorigenesis and is comprised of different components, including tumor cells, stromal cells, and immune cells. Among them, the relationship between each mediator involved in the construction of the TME can be understood by focusing on the secreting or expressing factors from each cells. Therefore, understanding the various interactions between each cellular component of the TME is necessary for precise therapeutic approaches. In carcinoma, stromal cells are well known to influence extracellular matrix (ECM) formation and tumor progression through multiple mediators. Immune cells respond to tumor cells by causing cytotoxicity or inflammatory responses. However, they are involved in tumor escape through immunoregulatory mechanisms. In general, anti-cancer therapy has mainly been focused on cancer cells themselves or the interactions between cancer cells and specific cell components. However, cancer cells directly or indirectly influence other TME partners, and members such as stromal cells and immune cells also participate in TME organization through their mutual communication. In this review, we summarized the relationship between stromal cells and immune cells in the TME and discussed the positive and negative relationships from the point of view of tumor development for use in research applications and therapeutic strategies.
Case Report: Immune Checkpoint Inhibitors as a Single Agent in the Treatment of Metastatic Cervical Cancer

The incidence of cervical cancer has decreased in recent years due to widespread vaccination and routine screenings. It can be treated successfully, and the prognosis is also excellent if detected early. However, the 5-year survival rate for patients with stage IV cervical cancer is only 17% even with aggressive systemic chemotherapy. With the Food and Drug Administration (FDA)’s approval of immunotherapy, the prognosis has improved. We present a patient with stage IV cervical cancer who could not tolerate platinum-based chemotherapy and bevacizumab, so she was started on an immune checkpoint inhibitor, as her tumor was 100% programmed cell death ligand-1 (PD-L1) positive. She survived more than 2 years since the diagnosis of stage IV cervical cancer without any significant side effects. Based on our patient’s response, the use of immune checkpoint inhibitors as a single agent needs further research and probably can be considered in patients with stage 4 cervical cancer who cannot tolerate standard chemotherapy.
Self-Hierarchy in Perceptual Matching: Variations in Different Processing Stages

People have three cognitive representations of the self, namely, the individual, relational, and collective selves (CS), which are indispensable components of selfhood but not necessarily given equal preference. Previous studies found that people displayed varied self-hierarchy in miscellaneous tasks involving different research materials that had pre-existing learned associations established over long periods of time. Therefore, this study tries to explore a purer self-hierarchy without the influence of research materials, using perceptual matching tasks. The behavioral and event-related potentials’ (ERPs) findings showed that people recognized information association with their individual self (IS) faster compared with their relational (RS) and CS. Smaller N2, stronger P3 and late positive complex (LPC) amplitudes were evoked during IS compared with RS and CS. However, the three selves evoked equal P2 amplitudes at the early processing stage. Moreover, CS showed a weaker advantage than RS, demonstrating a longer reaction time, lower d prime, and weaker P3 and LPC amplitudes in the parietal region. Overall, self-hierarchy during simple perceptual processing manifested as IS > RS > CS at the late processing stage but manifested as IS = RS = CS at the early processing stage. Self-hierarchy varies according to the processing stage, even without meaningful information and during the simple perception processing. This result provides direct evidence that all selves can be tagged with neutral actions, which would fit the idea of an organism attuned to self-survival at multiple processing levels.
Synthesis, Characterization, Biological Activity and Molecular Docking Studies of Novel Organotin(IV) Carboxylates

Four new carboxylates complexes with general formula R2SnL2 and R3SnL, where R = n-butyl (1, 3), methyl (2, 4) and L = 4-Chlorophenoxyacetate, were synthesized in significant yields. FT-IR analysis revealed a chelating (1 and 2) and a bridging bidentate (3 and 4) coordination modes for the carboxylate ligand in solid state which was further confirmed by the single crystal X-ray analysis of complex 4. The NMR data (1H, 13C and 119Sn) revealed a higher coordination number around the tin center in R2SnL2 (1 and 2) compared to R3SnL (3 and 4). A close matching was observed between the experimental and calculated structures (obtained at B3LYP/6-31G* + LANL2DZ basis set). Quantum chemical analysis indicates that the carboxylate moiety has the major contribution in the formation of filled and unfilled orbitals as well as in ligand to ligand intramolecular charge transfer during the electronic transitions. The cytotoxicity data of the screened compounds evaluated against lung cancer cell line (A549) and normal lung fibroblast cell line (MRC-5) revealed that 1, 3 and 4 have shown dose dependent cytotoxic effects while HL and 2 have shown steady and low cytotoxic activities. The antibacterial activity of complexes 1–4 is higher than that of HL. Molecular docking study showed an intercalation binding mode for complex 3 with DNA (docking score = −3.6005) involving four polar interactions. Complex 3 docking with tubulin (PDB ID 1SA0) with colchicine as a target protein resulted in three polar interactions (docking score −5.2957). Further, the docking analysis of the HL and 1–4 has shown an adequate interactions with the coronavirus SARS-CoV-2 spike protein, nucleocapsid protein and human angiotensin converting enzyme (ACE2).
(−)-Epicatechin Ameliorates Monosodium Urate-Induced Acute Gouty Arthritis Through Inhibiting NLRP3 Inflammasome and the NF-κB Signaling Pathway

Background: Gouty arthritis is a common and complex inflammatory disease that will reduce the life quality of human beings (−)-Epicatechin (EC) is famous for antioxidant and anti-inflammatory activities. Thus, the aim of this study was to investigate the therapeutic effect of EC on gouty arthritis and its mechanisms. Methods and results: EC was added into a monosodium urate (MSU)-stimulated THP-1 cell that was induced by phorbol 12-myristate 13-acetate and lipopolysaccharide (LPS) in advance to establish a gout model in vitro. The efficiency of EC on acute gouty arthritis mice induced by MSU was further investigated. The results showed that EC concentration-dependently improved the cell viability of LPS and MSU stimulated THP-1 cells, and significantly alleviated MSU-induced ankle edema in mice in a dose-dependent manner. In addition, EC inhibited the infiltration of inflammatory cells and local cascular congestion in ankle joint tissue. Furthermore, the secretion of inflammatory cytokines (IL-1β, IL-18, IL-6, and TNF-α) activation of NLRP3 inflammasome and NF-κB signaling pathway were markedly suppressed by EC in vitro and in vivo. Conclusion: These results indicated that EC could effectively improve MSU-induced acute gouty arthritis via inhibiting NLRP3 inflammasome and the NF-κB signaling pathway in vitro and in vivo, which suggested that EC might be a promising active ingredient for the prevention and treatment of gouty arthritis. Graphical Abstract
The Role of Analytical Geomechanics in Foundation Engineering

The role of modern geotechnical analysis in foundation design is reviewed, and analysis methods are classified into three categories, depending on their level of sophistication. The benefits of using a soundly-based theory to better understand foundation behavior are emphasized, with particular reference to the case of a laterally loaded pile. Two case histories are then studied in detail, in order to examine the sensitivity of performance predictions to the method of analysis used, the soil and pile parameters selected, and the idealization of the soil profile adopted. It is shown that the choice of the method of analysis is less significant than the selection of the strength and deformation parameters of the soil and their distribution with depth.
Research Progress of Gallium Nitride Microdisk Cavity Laser

Whispering gallery mode (WGM) cavities provide resonance configurations for light propagation through internal reflection, achieving high Q factors, low thresholds, and small mode volumes. GaN-based materials exhibit high freedom in band engineering and are highly compatible with contemporary semiconductor processing technology. Recently, lasers from artificial GaN microdisks, obtained by combining the excellent material properties of GaN with the advantages of WGM, have attracted considerable research attention. These have a wide application scope in optical communication, display, and optoelectronic integration. In this review, we summarize the recent advances in GaN-based WGM microlasers, including the fabrication methods for GaN microcavities, observations of optical pumped GaN microdisk lasing, lasing mechanisms, comparison of Q factors, lasing modes, and threshold properties, commonly used light field control techniques, and mode clipping methods. Furthermore, we introduce the recent advances in electrically driven GaN-based laser diodes, followed by research challenges and strategies for promising applications, such as electrically pumped lasers and optoelectronic chip integration.