Miracle-dz/UniFAR-FTUs huggingface dataset:
Cell wall peroxidase against ferulic acid, lignin, and NaCl-reduced root growth of rice seedlings

Summary The changes in cell wall peroxidase activity against ferulic acid (FPOD) and lignin level in roots of NaCl-stressed rice seedlings and their correlation with root growth were investigated. Increasing concentrations of NaCl from 50 to 150 mmol L −1 progressively decreases root growth. The reduction of root growth by NaCl is closely correlated with the increase in FPOD activity extracted from the cell wall. In contrast, lignin level was reduced by NaCl. Since proline and ammonium accumulations are associated with root growth inhibition caused by NaCl, we determined the effect of proline or NH 4 Cl on root growth and FPOD in roots. Exogenous application of NH 4 Cl or proline markedly inhibited root growth and increased FPOD activity in rice seedlings in the absence of NaCl. An increase in FPOD activity in roots preceded inhibition of root growth caused either by NaCl, NH 4 Cl, or proline. Our results suggest that cell-wall stiffening catalyzed by FPOD may participate in the regulation of root growth reduction of rice seedlings caused by NaCl.
Amyloidogenic processing of amyloid β protein precursor (APP) is enhanced in the brains of alcadein α–deficient mice

Alzheimer's disease (AD) is a very common neurodegenerative disorder, chiefly caused by increased production of neurotoxic β-amyloid (Aβ) peptide generated from proteolytic cleavage of β-amyloid protein precursor (APP). Except for familial AD arising from mutations in the APP and presenilin (PSEN) genes, the molecular mechanisms regulating the amyloidogenic processing of APP are largely unclear. Alcadein α/calsyntenin1 (ALCα/CLSTN1) is a neuronal type I transmembrane protein that forms a complex with APP, mediated by the neuronal adaptor protein X11-like (X11L or MINT2). Formation of the ALCα–X11L–APP tripartite complex suppresses Aβ generation in vitro, and X11L-deficient mice exhibit enhanced amyloidogenic processing of endogenous APP. However, the role of ALCα in APP metabolism in vivo remains unclear. Here, by generating ALCα-deficient mice and using immunohistochemistry, immunoblotting, and co-immunoprecipitation analyses, we verified the role of ALCα in the suppression of amyloidogenic processing of endogenous APP in vivo. We observed that ALCα deficiency attenuates the association of X11L with APP, significantly enhances amyloidogenic β-site cleavage of APP, especially in endosomes, and increases the generation of endogenous Aβ in the brain. Furthermore, we noted amyloid plaque formation in the brains of human APP-transgenic mice in an ALCα-deficient background. These results unveil a potential role of ALCα in protecting cerebral neurons from Aβ-dependent pathogenicity in AD.
Glomerular Diseases Associated with Malignancies: Histopathological Pattern and Association with Circulating Autoantibodies

Aim: Glomerular diseases (GD) associated with malignancies (AM, GDAM) have unique features, which are important to recognize, in the light of the progress made in cancer therapy. We aimed to describe the clinical and histopathological characteristics of patients with GDAM in relation to the presence of circulating autoantibodies, pointing to potential immune pathogenic pathways connecting cancer to GD. Materials and Methods: The included patients were studied retrospectively on the basis of a kidney biopsy proving GD and a related biopsy to establish the diagnosis of AM. We recorded patients’ demographics, serological and laboratory parameters, histopathological findings, and the type of malignancy, GD, and therapy. Results: In total, 41 patients with GDAM, with a mean age of 63.1 (±10.7) years, were studied. In 28 (68.3%) cases, GD was associated with a solid tumor, and in 13 (31.7%) patients with a lymphoid malignancy. The most frequent histopathological pattern was membranous nephropathy (43.9%). Overall, at the time of GD diagnosis, 17% of the patients were positive for antinuclear antibodies (ANA), and 12.2% for antineutrophil cytoplasmic autoantibodies (ANCA), all against myeloperoxidase (MPO). In addition, 93.3% of the patients who had membranous nephropathy were negative for transmembrane glycoprotein M-type phospholipase A2 receptor (PLA2R) antibody. Sixteen patients (39.0%) presented with acute nephritic syndrome, of whom five (31.25%) developed rapidly progressive glomerulonephritis. In a mean follow-up time of 36.1 (±28.3) months, nine (21.95%) patients ended up with end-stage kidney disease, and eight (19.5%) died. Conclusion: We found that 3.2% of patients who underwent a native kidney biopsy in our institution during the past decade, for any reason, were identified as having some type of GD associated with a malignancy. Serology indicated a significant presence of ANA or MPO-ANCA antibodies in patients with nephritic syndrome and the absence of PLA2R antibodies in patients with membranous nephropathy.
Pharmacokinetic Analysis of Epithelial/Endothelial Cell Barriers in Microfluidic Bilayer Devices with an Air–Liquid Interface

As the range of applications of organs-on-chips is broadening, the evaluation of aerosol-based therapies using a lung-on-a-chip model has become an attractive approach. Inhalation therapies are not only minimally invasive but also provide optimal pharmacokinetic conditions for drug absorption. As drug development evolves, it is likely that better screening through use of organs-on-chips can significantly save time and cost. In this work, bio-aerosols of various compounds including insulin were generated using a jet nebulizer. The aerosol flows were driven through microfluidic bilayer devices establishing an air–liquid interface to mimic the blood–air barrier in human small airways. The aerosol flow in the microfluidic devices has been characterized and adjusted to closely match physiological values. The permeability of several compounds, including paracellular and transcellular biomarkers, across epithelial/endothelial cell barriers was measured. Concentration–time plots were established in microfluidic devices with and without cells; the curves were then utilized to extract standard pharmacokinetic parameters such as the area under the curve, maximum concentration, and time to maximum concentration. The cell barrier significantly affected the measured pharmacokinetic parameters, as compound absorption through the barrier decreases with its increasing molecular size. Aerosolizing insulin can lead to the formation of fibrils, prior to its entry to the microfluidic device, with a substantially larger apparent molecular size effectively blocking its paracellular transport. The results demonstrate the advantage of using lung-on-a-chip for drug discovery with applications such as development of novel inhaled therapies.
Correlation of ride sharing service availability and decreased alcohol-related motor vehicle collision incidence and fatality

BACKGROUND Alcohol-related motor vehicle collisions (AR-MVCs) account for ~30% of all US traffic fatalities. Ride-sharing services (RSS) have existed since 2010, but few studies to date have investigated their impact on AR-MVCs. We hypothesized that the availability of RSS would be correlated with a decrease in AR-MVCs at an urban Level I trauma center. METHODS A retrospective chart review was conducted of all AR-MVC trauma activations at a Level I trauma center from 2012 to 2018. Additional data were gathered from regional governmental traffic and law enforcement databases, including crash incidence, fatalities, and demographics. Data were compared pre- and post-RSS and analyzed using an unpaired t test with p less than 0.05 considered significant. RESULTS There were 1,474 patients in AR-MVCs during the study period. There was a significant decrease in the annual average proportion of MVCs that were AR-MVCs pre- vs. post-RSS (39% vs. 29%, p = 0.02) as well as a decrease in the average annual incidence of fatal AR-MVCs (11.6 vs. 5, p = 0.02). Subset analysis showed a decrease in AR-MVC incidence in 18- to 29-year-olds (12.7% vs. 7.5%; p = 0.03), which was also demonstrated by data from a local law enforcement database. Availability of RSS was also correlated with a decreased proportion of nighttime AR-MVCs (14.7% vs. 7.6%, p = 0.03) and decreased number of driving while intoxicated (1198.0 ± 78.5 vs. 612.8 ± 137.6, p = <0.01). CONCLUSION We found that the incidence of both total AR-MVCs and fatal AR-MVCs presenting to our trauma center decreased after the introduction of RSS. Ride-sharing services may play a role in preventing AR-MVCs. Further research is needed to correlate AR-MVC incidence with granular proprietary RSS usage data and to account for any confounding factors. Future studies may identify ways to better utilize RSS availability as a targeted intervention for certain demographic groups to prevent AR-MVCs. LEVEL OF EVIDENCE Therapeutic/Care Management, Level IV.
Decay fungi from playground wood products in service using 28S rDNA sequence analysis

Abstract In order to establish integrated control strategies of wood degradation, a systematic survey of basidiomycete decay fungi colonizing various wood products in service is a prerequisite to increasing the service life of wood products. As a first step, we initiated a thorough survey of basidiomycete decay fungi colonizing playground wood products. For accurate fungal identification, traditional methods were complemented with molecular methods, including a BLAST search for large-subunit 28S rDNA sequences in Genbank and phylogenetic analysis. A total of 132 basidiomycete fungi, including 30 different fungal taxa, were isolated from 35 playgrounds in 15 different areas. Eight species, Bjerkandera adusta, Ceriporia lacerata, Gloeophyllum trabeum, Peniophora sp. , Phanerochaete sordida, Schizophyllum commune, Sisto-trema brinkmannii, and Trametes versicolor, were predominantly isolated. A combination of traditional and molecular tools allowed a more detailed identification and diversity.
Hollow-Core Photonic Crystal Fiber Gas Sensing

Fiber gas sensing techniques have been applied for a wide range of industrial applications. In this paper, the basic fiber gas sensing principles and the development of different fibers have been introduced. In various specialty fibers, hollow-core photonic crystal fibers (HC-PCFs) can overcome the fundamental limits of solid fibers and have attracted intense interest recently. Here, we focus on the review of HC-PCF gas sensing, including the light-guiding mechanisms of HC-PCFs, various sensing configurations, microfabrication approaches, and recent research advances including the mid-infrared gas sensors via hollow core anti-resonant fibers. This review gives a detailed and deep understanding of HC-PCF gas sensors and will promote more practical applications of HC-PCFs in the near future.
Identification of co-expression modules and hub genes of retinoblastoma via co-expression analysis and protein-protein interaction networks

Retinoblastoma is a common intraocular malignant tumor in children. However, the molecular and genetic mechanisms of retinoblastoma remain unclear. The gene expression dataset GSE110811 was retrieved from Gene Expression Omnibus. After preprocessing, coexpression modules were constructed by weighted gene coexpression network analysis (WGCNA), and modules associated with clinical traits were identified. In addition, functional enrichment analysis was performed for genes in the indicated modules, and protein-protein interaction (PPI) networks and subnetworks were constructed based on these genes. Eight coexpression modules were constructed through WGCNA. Of these, the yellow module had the highest association with severity and age (r=0.82 and P=3e-07; r=0.72 and P=3e-05). The turquoise module had the highest association with months (r=−0.63 and P=5e-04). The genes in the two modules participate in multiple pathways of retinoblastoma, and by combining the PPI network and subnetworks; 10 hub genes were identified in the two modules. The present study identified coexpression modules and hub genes associated with clinical traits of retinoblastoma, providing novel insight into retinoblastoma progression.
The Antibacterial Effect of Silver Nanoparticles on Staphylococcus Epidermidis Strains with Different Biofilm-Forming Ability

Among many infectious diseases, infections caused by pathogens of Staphylococcus species exert a substantial influence upon human health, mainly due to their continuous presence on human skin and mucous membranes. For that reason, an intensive search for new, effective anistaphyloccocal agents can currently be observed worldwide. In recent years, there has been growing interest in nanoparticles, as compounds with potential antibacterial effect. The antibacterial activity of silver containing substances has been well recognized, but thoughtful studies focused on the effect of silver nanoparticles on bacterial biofilm are scarce. The aim of this study was to assess the influence of silver nanoparticles (AgNPs) with particle sizes in the range between 10 and 100 nm, and a concentration range from 1 to 10 µg/mL, upon Staphylococcus epidermidis strains with different biofilm-forming abilities (BFAs). The studies revealed the highest level of antimicrobial activity for AgNPs in relation to S. epidermidis strains with BFA, and what is more, the observed effect was proportional to the increasing particles’ size, and strains not forming biofilm were more susceptible to silver nanoparticles with the smallest examined size, which was 10 nm.
Progesterone Attenuates Stress-Induced NLRP3 Inflammasome Activation and Enhances Autophagy Following Ischemic Brain Injury

NOD-like receptor pyrin domain containing 3 (NLRP3) inflammasome inhibition and autophagy induction attenuate inflammation and improve outcome in rodent models of cerebral ischemia. However, the impact of chronic stress on NLRP3 inflammasome and autophagic response to ischemia remains unknown. Progesterone (PROG), a neuroprotective steroid, shows promise in reducing excessive inflammation associated with poor outcome in ischemic brain injury patients with comorbid conditions, including elevated stress. Stress primes microglia, mainly by the release of alarmins such as high-mobility group box-1 (HMGB1). HMGB1 activates the NLRP3 inflammasome, resulting in pro-inflammatory interleukin (IL)-1β production. In experiment 1, adult male Sprague-Dawley rats were exposed to social defeat stress for 8 days and then subjected to global ischemia by the 4-vessel occlusion model, a clinically relevant brain injury associated with cardiac arrest. PROG was administered 2 and 6 h after occlusion and then daily for 7 days. Animals were killed at 7 or 14 days post-ischemia. Here, we show that stress and global ischemia exert a synergistic effect in HMGB1 release, resulting in exacerbation of NLRP3 inflammasome activation and autophagy impairment in the hippocampus of ischemic animals. In experiment 2, an in vitro inflammasome assay, primary microglia isolated from neonatal brain tissue, were primed with lipopolysaccharide (LPS) and stimulated with adenosine triphosphate (ATP), displaying impaired autophagy and increased IL-1β production. In experiment 3, hippocampal microglia isolated from stressed and unstressed animals, were stimulated ex vivo with LPS, exhibiting similar changes than primary microglia. Treatment with PROG reduced HMGB1 release and NLRP3 inflammasome activation, and enhanced autophagy in stressed and unstressed ischemic animals. Pre-treatment with an autophagy inhibitor blocked Progesterone’s (PROG’s) beneficial effects in microglia. Our data suggest that modulation of microglial priming is one of the molecular mechanisms by which PROG ameliorates ischemic brain injury under stressful conditions.
Sex-Ratio Selection in Species with Helpers at the Nest: Some Extensions of the Repayment Model

Although in classical models of sex allocation parents accrue fitness solely from their sons' and daughters' reproduction, parents of species with male helpers at the nest accrue fitness through their sons' help, as well. As a consequence, the evolutionarily stable (ES) sex ratio may be biased toward males (Trivers and Hare 1976; Clark 1978; Gowaty and Lennartz 1985). Recently, Emlen et al. (1986a) have provided an analytical model that allows the calculation of ES sex ratios in species with helpers. Their elegant model is particularly welcome, since it allows the prediction of ES sex ratios from parameters that are readily measurable in the field, facilitating the testing of the model. Here we take their repayment model as a starting point and use it to derive a simpler alternative expression for the ES proportion of males, to show how the ES sex ratios depend on additional factors not considered by them (including the sex of helpers and their relationship with the helped adult), and to predict the ES sex ratio for red-cockaded woodpeckers Picoides borealis (Lennartz 1983; Gowaty and Lennartz 1985; Lennartz et al., in press).
The Nuclear Pore Complex: A Target for NS3 Protease of Dengue and Zika Viruses

During flavivirus infection, some viral proteins move to the nucleus and cellular components are relocated from the nucleus to the cytoplasm. Thus, the integrity of the main regulator of the nuclear-cytoplasmic transport, the nuclear pore complex (NPC), was evaluated during infection with dengue virus (DENV) and Zika virus (ZIKV). We found that while during DENV infection the integrity and distribution of at least three nucleoporins (Nup), Nup153, Nup98, and Nup62 were altered, during ZIKV infection, the integrity of TPR, Nup153, and Nup98 were modified. In this work, several lines of evidence indicate that the viral serine protease NS2B3 is involved in Nups cleavage. First, the serine protease inhibitors, TLCK and Leupeptin, prevented Nup98 and Nup62 cleavage. Second, the transfection of DENV and ZIKV NS2B3 protease was sufficient to inhibit the nuclear ring recognition detected in mock-infected cells with the Mab414 antibody. Third, the mutant but not the active (WT) protease was unable to cleave Nups in transfected cells. Thus, here we describe for the first time that the NS3 protein from flavivirus plays novel functions hijacking the nuclear pore complex, the main controller of the nuclear-cytoplasmic transport.
Cryptic Haploid Stages in the Life Cycle of Leathesia marina (Chordariaceae, Phaeophyceae) Under In Vitro Culture

We evaluated the life cycle of Leathesia marina through molecular analyses, culture studies, morphological observations, and ploidy measurements. Macroscopic sporophytes were collected from two localities in Atlantic Patagonia and were cultured under long‐day (LD) and short‐day (SD) conditions. Molecular identification of the microscopic and macroscopic phases was performed through the cox3 and rbcL genes and the phylogeny was assessed on the basis of single gene and concatenated datasets. Nuclear ploidy of each phase was estimated from the DNA contents of individual nuclei through epifluorescence microscopy and flow cytometry. Molecular results confirmed the identity of the Argentinian specimens as L. marina and revealed their conspecificity with L. marina from New Zealand, Germany, and Japan. The sporophytic macrothalli (2n) released mitospores from plurilocular sporangia, which developed into globular microthalli (2n), morphologically similar to the sporophytes but not in size, constituting a generation of small diploid thalli, with a mean fluorescent nuclei cross‐sectional area of 3.21 ± 0.7 μm2. The unilocular sporangia released meiospores that developed two morphologically different types of microthalli: erect branched microthalli (n) with a nuclear area of 1.48 ± 0.07 µm2 that reproduces asexually, and prostrate branched microthalli (n) with a nuclear area of 1.24 ± 0.10 µm2 that reproduces sexually. The prostrate microthalli released gametes in LD conditions, which merged and produced macroscopic thalli with a nuclear cross‐sectional area of 3.45 ± 0.09 µm2. Flow cytometry confirmed that the erect and prostrate microthalli were haploid and that the globular microthalli and macrothalli were diploid.
Interaction of Deubiquitinase 2A-DUB/MYSM1 with DNA Repair and Replication Factors

The deubiquitination of histone H2A on lysine 119 by 2A-DUB/MYSM1, BAP1, USP16, and other enzymes is required for key cellular processes, including transcriptional activation, apoptosis, and cell cycle control, during normal hematopoiesis and tissue development, and in tumor cells. Based on our finding that MYSM1 colocalizes with γH2AX foci in human peripheral blood mononuclear cells, leukemia cells, and melanoma cells upon induction of DNA double-strand breaks with topoisomerase inhibitor etoposide, we applied a mass spectrometry-based proteomics approach to identify novel 2A-DUB/MYSM1 interaction partners in DNA-damage responses. Differential display of MYSM1 binding proteins significantly enriched after exposure of 293T cells to etoposide revealed an interacting network of proteins involved in DNA damage and replication, including factors associated with poor melanoma outcome. In the context of increased DNA-damage in a variety of cell types in Mysm1-deficient mice, in bone marrow cells upon aging and in UV-exposed Mysm1-deficient skin, our current mass spectrometry data provide additional evidence for an interaction between MYSM1 and key DNA replication and repair factors, and indicate a potential function of 2A-DUB/MYSM1 in DNA repair processes.
From Gene to Protein—How Bacterial Virulence Factors Manipulate Host Gene Expression During Infection

Bacteria evolved many strategies to survive and persist within host cells. Secretion of bacterial effectors enables bacteria not only to enter the host cell but also to manipulate host gene expression to circumvent clearance by the host immune response. Some effectors were also shown to evade the nucleus to manipulate epigenetic processes as well as transcription and mRNA procession and are therefore classified as nucleomodulins. Others were shown to interfere downstream with gene expression at the level of mRNA stability, favoring either mRNA stabilization or mRNA degradation, translation or protein stability, including mechanisms of protein activation and degradation. Finally, manipulation of innate immune signaling and nutrient supply creates a replicative niche that enables bacterial intracellular persistence and survival. In this review, we want to highlight the divergent strategies applied by intracellular bacteria to evade host immune responses through subversion of host gene expression via bacterial effectors. Since these virulence proteins mimic host cell enzymes or own novel enzymatic functions, characterizing their properties could help to understand the complex interactions between host and pathogen during infections. Additionally, these insights could propose potential targets for medical therapy.