Miracle-dz/UniFAR-FTUs huggingface dataset:
Insights into the Identification of the Specific Spoilage Organisms in Chicken Meat

Poultry meat deterioration is caused by environmental conditions, as well as proliferation of different bacterial groups, and their interactions. It has been proposed that meat spoilage involves two bacterial groups: one group that initiates the deterioration process, known as specific spoilage organisms (SSOs), and the other known as spoilage associated organisms (SAOs) which represents all bacteria groups recovered from meat samples before, during, and after the spoilage process. Numerous studies have characterized the diversity of chicken meat SAOs; nonetheless, the identification of the SSOs remains a long-standing question. Based on recent genomic studies, it is suggested that the SSOs should possess an extensive genome size to survive and proliferate in raw meat, a cold, complex, and hostile environment. To evaluate this hypothesis, we performed comparative genomic analyses in members of the meat microbiota to identify microorganisms with extensive genome size and ability to cause chicken meat spoilage. Our studies show that members of the Pseudomonadaceae family have evolved numerous biological features such as large genomic size, slow-growing potential, low 16S rRNA copy number, psychrotrophic, and oligotrophic metabolism to initiate the spoilage of poultry meat. Moreover, inoculation experiments corroborated that these biological traits are associated with the potential to cause chicken meat deterioration. Together, these results provide new insights into the identification of SSO. Further studies are in progress to elucidate the impact of the SSO on meat quality and microbiota diversity.
Factors Associated with the Leisure-Time Physical Activity (LTPA) during the First Trimester of the Pregnancy: The Cross-Sectional Study among Pregnant Women in Serbia

Background: The benefits of physical activity during pregnancy include lower maternal weight gain, a lower likelihood of gestational diabetes, low back pain, preeclampsia, preterm delivery, caesarian delivery, and macrosomia. This study aimed to examine the factors associated with insufficient leisure-time physical activity (LTPA) during the first trimester. Methods: A cross-sectional study was conducted at the Clinic for Obstetrics and Gynecology of Clinical Center of Serbia, Belgrade, between January and June of 2018. The final analyses included 162/175 pregnant women. The questionnaire was used to obtain social characteristics, pregnancy, and lifestyle characteristics (Pregnancy Risk Assessment Monitoring System—PRAMS), pre-pregnancy LTPA (International Physical Activity Questionnaire—IPAQ), and LTPA during the first trimester (Pregnancy Physical Activity Questionnaire—PPAQ). Women were classified into two groups of sufficient and insufficient LTPA during the first trimester based on the recommendations of the World Health Organization. Multivariate logistic regression analysis was applied. Results: A total of 27.2% of the women had insufficient LTPA during pregnancy. Insufficient LTPA during pregnancy was associated with <12 years of education (OR: 2.3, 95% CI: 1.05–5.04), self-rated financial status as poor (OR: 0.34, 95% CI: 0.14–0.79), and hours spent walking before pregnancy (OR: 0.87, 95% CI: 0.77–0.99). Conclusions: Our results can help direct health care professionals advice for women who are planning pregnancy towards walking as it seems to be sustained during pregnancy.
Pyrene Coating Transition Metal Disulfides as Protection from Photooxidation and Environmental Aging

Environmental degradation of transition metal disulfides (TMDs) is a key stumbling block in a range of applications. We show that a simple one-pot non-covalent pyrene coating process protects TMDs from both photoinduced oxidation and environmental aging. Pyrene is immobilized non-covalently on the basal plane of exfoliated MoS2 and WS2. The optical properties of TMD/pyrene are assessed via electronic absorption and fluorescence emission spectroscopy. High-resolution scanning transmission electron microscopy coupled with electron energy loss spectroscopy confirms extensive pyrene surface coverage, with density functional theory calculations suggesting a strongly bound stable parallel-stacked pyrene coverage of ~2–3 layers on the TMD surfaces. Raman spectroscopy of exfoliated TMDs while irradiating at 0.9 mW/4 μm2 under ambient conditions shows new and strong Raman bands due to oxidized states of Mo and W. Yet remarkably, under the same exposure conditions TMD/pyrene remain unperturbed. The current findings demonstrate that pyrene physisorbed on MoS2 and WS2 acts as an environmental barrier, preventing oxidative surface reactions in the TMDs catalyzed by moisture, air, and assisted by laser irradiation. Raman spectroscopy confirms that the hybrid materials stored under ambient conditions for two years remained structurally unaltered, corroborating the beneficial role of pyrene for not only hindering oxidation but also inhibiting aging.
Drug Flux Across RPE Cell Models: The Hunt for An Appropriate Outer Blood–Retinal Barrier Model for Use in Early Drug Discovery

The retinal pigment epithelial (RPE) cell monolayer forms the outer blood–retinal barrier and has a crucial role in ocular pharmacokinetics. Although several RPE cell models are available, there have been no systematic comparisons of their barrier properties with respect to drug permeability. We compared the barrier properties of several RPE secondary cell lines (ARPE19, ARPE19mel, and LEPI) and both primary (hfRPE) and stem-cell derived RPE (hESC-RPE) cells by investigating the permeability of nine drugs (aztreonam, ciprofloxacin, dexamethasone, fluconazole, ganciclovir, ketorolac, methotrexate, voriconazole, and quinidine) across cell monolayers. ARPE19, ARPE19mel, and hfRPE cells displayed a narrow Papp value range, with relatively high permeation rates (5.2–26 × 10−6 cm/s. In contrast, hESC-RPE and LEPI cells efficiently restricted the drug flux, and displayed even lower Papp values than those reported for bovine RPE-choroid, with the range of 0.4–32 cm−6/s (hESC-RPE cells) and 0.4–29 × 10−6 cm/s, (LEPI cells). Therefore, ARPE19, ARPE19mel, and hfRPE cells failed to form a tight barrier, whereas hESC-RPE and LEPI cells restricted the drug flux to a similar extent as bovine RPE-choroid. Therefore, LEPI and hESC-RPE cells are valuable tools in ocular drug discovery.
Design of Quad-Port Ultra-Wideband Multiple-Input-Multiple-Output Antenna with Wide Axial-Ratio Bandwidth

This article presents a compact, planar, quad-port ultra-wideband (UWB) multiple-input–multiple-output (MIMO) antenna with wide axial ratio bandwidth (ARBW). The proposed MIMO design consists of four identical square-shaped antenna elements, where each element is made up of a circular slotted ground plane and feed by a 50 Ω microstrip line. The circular polarization is achieved using a protruding hexagonal stub from the ground plane. The four elements of the MIMO antenna are placed orthogonally to each other to obtain high inter-element isolation. FR-4 dielectric substrate of size 45 × 45 × 1.6 mm3 is used for the antenna prototype, and a good agreement is noticed among the simulated and experimental results. The proposed MIMO antenna shows 3-dB ARBW of 52% (3.8–6.5 GHz) and impedance bandwidth (S11 ≤ −10 dB) of 144% (2.2–13.5 GHz).
Towards Low-Cost Hyperspectral Single-Pixel Imaging for Plant Phenotyping

Hyperspectral imaging techniques have been expanding considerably in recent years. The cost of current solutions is decreasing, but these high-end technologies are not yet available for moderate to low-cost outdoor and indoor applications. We have used some of the latest compressive sensing methods with a single-pixel imaging setup. Projected patterns were generated on Fourier basis, which is well-known for its properties and reduction of acquisition and calculation times. A low-cost, moderate-flow prototype was developed and studied in the laboratory, which has made it possible to obtain metrologically validated reflectance measurements using a minimal computational workload. From these measurements, it was possible to discriminate plant species from the rest of a scene and to identify biologically contrasted areas within a leaf. This prototype gives access to easy-to-use phenotyping and teaching tools at very low-cost.
Preeclampsia: The Interplay between Oxygen-Sensitive miRNAs and Erythropoietin

Changes in the oxygen partial pressure caused by a violation of uteroplacental perfusion are considered a powerful inducer of a cascade of reactions leading to the clinical manifestation of preeclampsia (PE). At the same time, the induction of oxygen-dependent molecule expression, in particular, miRNA and erythropoietin, is modulated. Therefore, the focus of our study was aimed at estimating the miRNA expression profile of placental tissue and blood plasma in pregnant women with preeclampsia using deep sequencing and quantitative RT-PCR, as well as determining the concentration of erythropoietin. The expression of miR-27b-3p, miR-92b-3p, miR-125b-5p, miR-181a-5p, and miR-186-5p, as regulated by hypoxia/reoxygenation, was significantly increased in blood plasma during early-onset preeclampsia. The possibility of detecting early PE according to the logistic regression model (miR-92b-3p, miR-125b-5p, and miR-181a-5p (AUC = 0.91)) was evaluated. Furthermore, the erythropoietin level, which is regulated by miR-125b-5p, was significantly increased. According to PANTHER14.1, the participation of these miRNAs in the regulation of pathways, such as the hypoxia’s response via HIF activation, oxidative stress response, angiogenesis, and the VEGF signaling pathway, were determined.
Mutant HTT (huntingtin) impairs mitophagy in a cellular model of Huntington disease

ABSTRACT The precise degradation of dysfunctional mitochondria by mitophagy is essential for maintaining neuronal homeostasis. HTT (huntingtin) can interact with numerous other proteins and thereby perform multiple biological functions within the cell. In this study, we investigated the role of HTT during mitophagy and analyzed the impact of the expansion of its polyglutamine (polyQ) tract. HTT is involved in different mitophagy steps, promoting the physical proximity of different protein complexes during the initiation of mitophagy and recruiting mitophagy receptors essential for promoting the interaction between damaged mitochondria and the nascent autophagosome. The presence of the polyQ tract in mutant HTT affects the formation of these protein complexes and determines the negative consequences of mutant HTT on mitophagy, leading to the accumulation of damaged mitochondria and an increase in oxidative stress. These outcomes contribute to general mitochondrial dysfunction and neurodegeneration in Huntington disease. Abbreviations: AMPK: AMP-activated protein kinase; ATG13: autophagy related 13; BECN1: beclin 1, autophagy related; BNIP3: BCL2/adenovirus E1B interacting protein 3; BNIP3L/Nix: BCL2/adenovirus E1B interacting protein 3-like; CCCP: carbonyl cyanide 3-chlorophenyl hydrazone; DMEM: Dulbecco’s modified eagle medium; EDTA: ethylene-diamine-tetra-acetic acid; EGFP: enhanced green fluorescent protein; EGTA: ethylene glycol bis(2-aminoethyl ether)tetraacetic acid; FUNDC1: FUN14 domain containing 1; HD: Huntington disease; HRP: horseradish peroxidase; HTT: huntingtin; LC3-II: lipidated form of MAP1LC3/LC3; mtDNA: mitochondrial deoxyribonucleic acid; MTDR: MitoTracker Deep Red; MTOR: mechanistic target of rapamycin kinase; MTORC1: mechanistic target of rapamycin kinase complex 1; NBR1: NBR1, autophagy cargo receptor; CALCOCO2/NDP52: calcium binding and coiled-coil domain 2; OCR: oxygen consumption rate; OPTN: optineurin; OXPHOS: oxidative phosphorylation; PIK3C3/VPS34: phosphatidylinositol 3-kinase catalytic subunit type 3; PIK3R4/VPS15: phosphoinositide-3-kinase regulatory subunit 4; PINK1: PTEN induced putative kinase 1; PLA: proximity ligation assay; PMSF: phenylmethylsulfonyl fluoride; polyQ: polyglutamine; PtdIns3K: phosphatidylinositol 3-kinase; ROS: reactive oxygen species; Rot: rotenone; SDS-PAGE: sodium dodecyl sulfate-polyacrylamide gel electrophoresis; SEM: standard error of the mean; SQSTM1/p62: sequestosome 1; TMRM: tetramethylrhodamine methyl ester; UB: ubiquitin; ULK1: unc-51 like kinase 1.
Occurrence, Diversity of Listeria spp. Isolates from Food and Food-Contact Surfaces and the Presence of Virulence Genes

This study evaluates the hazards posed by foodborne bacteria of the Listeria genus by analyzing the occurrence, diversity and virulence of Listeria spp.in food and food-manufacturing plants. Seventy-five isolates obtained from the routine analysis of 653 samples taken by three diagnostic laboratories in Northern Italy were genotypically differentiated by Repetitive Extragenic Palindrome (rep) PCR, with the GTG5 primer identified by sequencing the 16S rRNA gene and examined by specific PCR tests for the presence of L. monocytogenes virulence determinants occasionally found to occur in other species of the genus. Within this sample, 76% (n = 57) isolates were identified as L. innocua, 16% (n = 12) as L. monocytogenes, 6.6% (n = 5) as L. welshimeri and 1.3% (n = 1) as L. seeligeri. All L. monocytogenes isolates belonged to the serotype 1/2a and were predicted to be virulent for the presence of the inlJ internalin gene. Potentially virulent strains of L. innocua, L. seeligeri and L. welshimeri, carrying the L. monocytogenesinlA gene and/or hly gene, were identified, and most isolates were found to possess the toxin–antitoxin system mazEF for efficient adaptation to heat shock. Results indicated the need to reinforce food-contamination-prevention measures against all Listeria species by defining efficiently their environmental distribution.
Pharmacologic Therapies in Patients With Exacerbation of Chronic Obstructive Pulmonary Disease

Background Chronic obstructive pulmonary disease (COPD) is characterized by frequent exacerbations. Purpose To evaluate the comparative effectiveness and adverse events (AEs) of pharmacologic interventions for adults with exacerbation of COPD. Data Sources English-language searches of several bibliographic sources from database inception to 2 January 2019. Study Selection 68 randomized controlled trials that enrolled adults with exacerbation of COPD treated in out- or inpatient settings other than intensive care and compared pharmacologic therapies with placebo, "usual care," or other pharmacologic interventions. Data Extraction Two reviewers independently extracted data and rated study quality and strength of evidence (SOE). Data Synthesis Compared with placebo or management without antibiotics, antibiotics given for 3 to 14 days were associated with increased exacerbation resolution at the end of the intervention (odds ratio [OR], 2.03 [95% CI, 1.47 to 2.80]; moderate SOE) and less treatment failure at the end of the intervention (OR, 0.54 [CI, 0.34 to 0.86]; moderate SOE), independent of severity of exacerbations in out- and inpatients. Compared with placebo in out- and inpatients, systemic corticosteroids given for 9 to 56 days were associated with less treatment failure at the end of the intervention (OR, 0.01 [CI, 0.00 to 0.13]; low SOE) but also with a higher number of total and endocrine-related AEs. Compared with placebo or usual care in inpatients, other pharmacologic interventions (aminophyllines, magnesium sulfate, anti-inflammatory agents, inhaled corticosteroids, and short-acting bronchodilators) had insufficient evidence, showing either no or inconclusive effects (with the exception of the mucolytic erdosteine) or improvement only in lung function. Limitation Scant evidence for many interventions; several studies had unclear or high risk of bias and inadequate reporting of AEs. Conclusion Antibiotics and systemic corticosteroids reduce treatment failure in adults with mild to severe exacerbation of COPD. Primary Funding Source Agency for Healthcare Research and Quality. (PROSPERO: CRD42018111609).
Mating-Induced Differential Expression in Genes Related to Reproduction and Immunity in Spodoptera litura (Lepidoptera: Noctuidae) Female Moths

Abstract Mating promotes reproductive activity, which may impact immune performance. Paradoxically, mating frequently challenges females’ immunity (e.g., infections). Therefore, studies of postmating resource allocation between reproduction and survival are likely to shed new light on life-history trade-off and sexual selection. Here, we used RNAseq to test whether and how mating affected mRNA expression in genes related to reproduction and immunity in Spodoptera litura female moths. Results show a divergent change in the differentially expressed genes (DEGs) between reproduction and immunity: the immune response was largely downregulated shortly after mating (~6 h postmating), which has some recovery at 24 h postmating; reproductive response is trivial shortly after mating (~6 h postmating), but it largely upregulated at 24 h postmating (e.g., egg maturation related genes were highly upregulated). Considering the fact that most of the total DEGs downregulated from 0 to 6 h postmating (from 51/68 to 214/260) but most of the total DEGs upregulated at 24 h postmating (816/928), it is possible that trade-offs between reproduction and immunity occurred in mated females. For example, they may shut down immunity to favor sperm storage and save limited resources to support the increased energy required in reproduction (e.g., egg maturation and oviposition). Mating-induced infections should be trivial due to low polyandry in S. litura. A reduced immune defense may have no threat to S. litura survival but may benefit reproduction significantly. Furthermore, obvious expression changes were detected in genes related to hormone production, suggesting that endocrine changes could play important roles in postmating responses.
Sex-Sparing Robot-Assisted Radical Cystectomy with Intracorporeal Padua Ileal Neobladder in Female: Surgical Technique, Perioperative, Oncologic and Functional Outcomes

Our aim was to illustrate our technique of sex-sparing (SS)-robot-assisted radical cystectomy (RARC) in female patients receiving an intracorporeal neobladder (iN). From January 2013 to June 2018, 11 female patients underwent SS-RARC-iN at a single tertiary referral center. Inclusion criteria were a cT ≤ 2 N0 M0 bladder tumor at baseline imaging (CT or MRI) and an absence of tumors in the bladder neck, trigone and urethra at TURB. Baseline, perioperative, and outcomes at one year were reported. The median operative time was 255 min and the median hospital stay was seven days. Low-grade Clavien complications occurred in four patients (36.3%), while high-grade complications were not observed in any. Seven patients (63.7%) had an organ-confined disease at the pathologic specimen; nodal involvement and positive surgical margins were not detected in any of the cases. At a median follow-up of 28 months (IQR 14–51), no patients developed new onset of chronic kidney disease stage 3b. After one year, daytime and nighttime continence rates were 90.9% and 86.4% respectively. Quality of life as well as physical and emotional functioning improved significantly over time (all p ≤ 0.04), while urinary symptoms and sexual function worsened at three months with a significant recovery taking place at one year (all p ≤ 0.04). Overall, 8 out of 11 patients (72.7%) were sexually active at the 12-month evaluation. In select female patients, SS-RARC-iN is an oncologically sound procedure associated with favorable perioperative and functional outcomes.
Adipose-derived mesenchymal stem cells-derived exosome-mediated microRNA-342-5p protects endothelial cells against atherosclerosis

Exosomes are reported to mediate several disease-related microRNAs (miRNAs) to affect the progression of diseases, including atherosclerosis. Here, we aimed to screen the atherosclerosis-associated miRNAs and preliminarily investigate the potential regulatory mechanism of atherosclerosis. First, the lesion model for human umbilical vein endothelial cells (HUVECs) was favorably constructed. Later, through RNA-sequencing and bioinformatics analyses, miR-342-5p was identified in lesion model for HUVECs. MiR-342-5p overexpression or knockdown evidently promoted or inhibited the apoptosis of HUVECs impaired by H2O2. Mechanistically, PPP1R12B was found to have great potential as a target of miR-342-5p in HUVECs impaired by H2O2, supported by RNA-sequencing and a series of bioinformatics analyses. Meanwhile, the effect of miR-342-5p on PPP1R12B expression in HUVECs’ lesion model was explored, revealing that miR-342-5p had an inhibitory role in PPP1R12B expression. Additionally, adipose-derived mesenchymal stem cells (ADSCs) in spindle-like shape and their derived exosomes with 30 to 150 nm diameter were characterized. Furthermore, results showed miR-342-5p was evidently decreased in the presence of ADSCs-derived exosomes. These findings indicated ADSCs-derived exosomes restrained the expression of miR-324-5p in lesion model. Collectively, this work demonstrates an atherosclerosis-associated miR-342-5p and reveals a preliminary possible mechanism in which miR-342-5p mediated by ADSCs-derived exosomes protects endothelial cells against atherosclerosis.
Molecular and Biological Characterization of a Cervidpoxvirus Isolated From Moose with Necrotizing Dermatitis

Cervidpoxvirus is one of the more recently designated genera within the subfamily Chordopoxvirinae, with Deerpox virus (DPV) as the only recognized species to date. In this study, the authors describe spontaneous disease and infection in the North American moose (Alces americanus) by a novel Cervidpoxvirus, here named Moosepox virus (MPV). Three 4-month-old moose calves developed a multifocal subacute-to-chronic, necrotizing, suppurative-to-granulomatous dermatitis that affected the face and the extremities. Ultrastructurally, all stages of MPV morphogenesis—that is, crescents, spherical immature particles, mature particles, and enveloped mature virus—were observed in skin tissue. In vitro infection with MPV confirmed that its morphogenesis was similar to that of the prototype vaccinia virus. The entire coding region, including 170 putative genes of this MPV, was sequenced and annotated. The sequence length was 164,258 bp with 98.5% nucleotide identity with DPV (strain W-1170-84) based on the whole genome. The genome of the study virus was distinct from that of the reference strain (W-1170-84) in certain genes, including the CD30-like protein (83.9% nucleotide, 81.6% amino acid), the endothelin precursor (73.2% nucleotide including some indels, 51.4% amino acid), and major histocompatibility class (MHC) class I–like protein (81.0% nucleotide, 68.2% amino acid). This study provides biological characterization of a new Cervidpoxvirus attained through in vivo and in vitro ultrastructural analyses. It also demonstrates the importance of whole-genome sequencing in the molecular characterization of poxviruses identified in taxonomically related hosts.