Miracle-dz/UniFAR-FTUs huggingface dataset:
Detection and differentiation of Salmonella Enteritidis and Salmonella Typhimurium by multiplex quantitative PCR from different poultry matrices

ABSTRACT 1. The aim of this study was to develop a multiplex quantitative polymerase chain reaction (qPCR) based molecular diagnostic kit for rapid diagnosis of Salmonella enterica serovar Enteritidis and S. enterica serovar Typhimurium serotypes, which are frequently isolated worldwide from poultry samples. 2. Detection and discrimination of S. Enteritidis and S. Typhimurium were performed by targeting the sdf and the STM4492 (putative cytoplasmic protein) gene, respectively. The invA (invasion protein) gene was used to detect Salmonella spp. as a target gene, since it is considered a standard. In this study, a total of 200 bacterial strains (178 Salmonella spp. strains and 22 other genera) were used to test the specificity and sensitivity of the developed kit. The limit of detection (LOD) of the assays was determined to be 100–101 cfu/25 g from chicken meat samples artificially contaminated by litter and 100–101 cfu/ml for cloacal swab samples. 3. The multiplex qPCR results were 100% compatible with conventional serotyping results while the specificity and sensitivity values were 100%. These findings indicated that the newly developed multiplex qPCR technique can provide an alternative method to conventional serotyping of S. Enteritidis and S. Typhimurium in laboratories lacking adequate infrastructure.
Melatonin ameliorates hepatic steatosis by inhibiting NLRP3 inflammasome in db/db mice

Introduction: Type 2 diabetes mellitus (T2DM) is commonly accompanied by obesity and non-alcoholic fatty liver disease (NAFLD), yet the mechanism underlying diabetes-related NAFLD is not fully understood. It has been reported that melatonin can regulate glucose and lipid metabolism. This study aims to investigate the actions and mechanisms of melatonin toward the development of diabetes-related NAFLD. Methods: Melatonin (bid, 30 mg/kg/day, i.p.) was administrated to db/db mice for 8 weeks, while saline was administrated to db/m mice. The metabolic parameters of mice were measured using an automatic biochemistry analyzer. The oxidative stress indexes and mitochondrial membrane potential (MMP) were determined with kits. Pathological assessment in liver tissues was used to analyze the effects of melatonin on hepatic steatosis. The levels of IL-1β and IL-18 were detected with ELISA kits. The mRNA levels of NLRP3 inflammasome were detected using quantitative real-time PCR assay, and protein expressions were estimated using Western blotting assay. Immunofluorescence staining was used to evaluate the caspase-1 expression in the liver. Results: Melatonin treatment significantly reduced blood glucose, serum insulin, body weight, related liver weight, serum lipids, and hepatic enzymes in db/db mice. Melatonin markedly corrected the NAFLD phenotypes, including lipid accumulation, steatohepatitis, fibrosis, and oxidative stress levels. Melatonin significantly improved the MMP level and decreased the serum IL-1β and IL-18 concentrations. The mRNA levels of the NLRP3 inflammasome could also be remarkably reversed by melatonin in the liver tissues. The activation of the NLRP3 inflammasome was also suppressed, evidenced by the downregulated proteins of NLRP3, caspase-1, IL-1β, and IL-18. The enhanced fluorescence intensity of caspase-1 in the liver tissues was also obviously weakened by the melatonin treatment. Conclusion: Our study concluded that melatonin could safeguard against NAFLD by improving hepatic steatosis in db/db mice, and this action could be associated with the regulation of the NLRP3 inflammasome activation.
Development of an Optimized Culture System for Generating Mouse Alveolar Macrophage–like Cells

Key Points GM-CSF, TGF-β, and rosiglitazone induced the generation of AM-like cells. AM-like cells serve as a tool for studies of AM differentiation and function. Alveolar macrophages (AMs) play critical roles in maintaining lung homeostasis and orchestrating the immune responses. Although the essential factors known for AM development have been identified, currently an optimal in vitro culture system that can be used for studying the development and functions of AMs is still lacking. In this study, we report the development of an optimized culture system for generating AM-like cells from adult mouse bone marrow and fetal liver cells on in vitro culture in the presence of a combination of GM-CSF, TGF-β, and peroxisome proliferator–activated receptor γ (PPAR-γ) agonist rosiglitazone. These AM-like cells expressed typical AM surface markers sialic acid–binding Ig-like lectin-F (Siglec-F), CD11c, and F4/80, and AM-specific genes, including carbonic anhydrase 4 (Car4), placenta-expressed transcript 1 (Plet1), eosinophil-associated RNase A family member 1 (Ear1), cell death–inducing DNA fragmentation factor A–like effector c (Cidec), and cytokeratin 19 (Krt19). Similar to primary AMs, the AM-like cells expressed alternative macrophage activation signature genes and self-renewal genes. Moreover, this culture system could be used for expansion of bronchoalveolar lavage fluid–derived AMs in vitro. The AM-like cells generated from bone marrow resembled the expanded bronchoalveolar lavage fluid–derived AMs in inflammatory responses and phagocytic activity. More importantly, these AM-like cells could be obtained in sufficient numbers that allowed genetic manipulation and functional analysis in vitro. Taken together, we provide a powerful tool for studying the biology of AMs.
Degradation of lignocellulosic matrix of oilseed cakes by solid state fermentation: fungi screening for enzymes production and antioxidants release.

BACKGROUND Vegetable oils are yearly produced in large amounts generating solid by-products, the oilseed cakes (OC). OC are lignocellulosic materials that have been used for animal feed with some limitations due to high fiber content from the plant cell walls. Biotechnological processes can help to overcome these limitations and contribute to up-grading such by-products, enhancing their nutritional value as feed ingredients. RESULTS All fungal species were able to decrease neutral detergent fiber and acid detergent fiber in all by-products. Additionally, relevant enzymes were produced by the three fungi studied resulting in an improved antioxidant capacity of all fermented OC. Aspergillus niger led to the highest activity of cellulase (109 U g-1 ), xylanase (692 U g-1 ) and protease (157 U g-1 ) per dry OC matter and to the recovery of an extract rich in antioxidants, with the highest scavenging potential of free radicals and superoxide anion, iron chelation ability and reducing power. Rhyzopus oryzae produced the highest activity of β-glucosidase (503 U g-1 ) and led to the highest liberation of total phenolic compounds (TPC). Principal components analysis showed that extracts with high antioxidant potential were obtained in SSF with high enzymatic activity. A positive correlation was established between the action of β-glucosidase and TPC. CONCLUSION Within the same bioprocess it was possible to improve the nutritional value of oilseed cakes and to obtain relevant bioactive compounds such as lignocellulosic enzymes and phenolic compounds with antioxidant potential, resulting in a significant improvement of already valuable by-products with commercial interest for animal feed. This article is protected by copyright. All rights reserved.
Tumor Targeting by Conditioned Medium Derived From Human Amniotic Membrane: New Insight in Breast Cancer Therapy

Objectives: Traditional breast cancer treatments have challenges including inefficiency, multidrug resistance, severe side effects, and targeting non-specifically. The development of alternative treatment strategies has attracted a great deal of interest. Using the amniotic membrane has become a promising and convenient new approach for cancer therapy. This study aimed to evaluate the anti-cancer ability of conditioned medium extracted from the human amniotic membrane (hAM-CM) on breast cancer cells. Methods: Conditioned medium was collected after 48 h incubation of hAM in epithelial up manner. MTT, cell cycle, apoptosis, colony formation, and sphere assays were used to determine the impact of hAM-CM on breast cancer cell lines. The effects of hAM-CM on the migration and invasion of breast cancer cells were determined using scratch wound healing and transwell assays, respectively. Results: Based on the results, cell viability was significantly decreased by hAM-CM in a dose-dependent manner. The hAM-CM remarkably induced apoptosis and necrosis of cancer cells. Moreover, cell migration and invasion potential of cancer cells decreased after the hAM-CM treatment. Further, both the number of colonies and their morphologies were affected by the treatment. In the treated group, a significant decrease in the number of colonies along with an obvious change in their morphologies from holoclone shape to a dominant paracolone structure was observed. Conclusion: Our results indicate that the conditioned medium derived from the human amniotic membrane able to inhibit proliferation and metastasis of tumor cells and can be considered a natural and valuable candidate for breast cancer therapy.
Maternal serum uric acid: a reliable prognostic indicator of foetal outcome among pre-eclamptic patients in a low resource setting

Abstract Background Pre-eclampsia is a major cause of maternal and fetal morbidity and mortality in both developed and developing countries. Hyperuricemia is often associated with pre-eclampsia and when this occurs, fetal outcome may become worse. We evaluated the role of maternal serum uric acid as a prognostic indicator of fetal outcome in pre-eclamptic mothers. Methods A prospective case-control study in which 55 eligible pre-eclamptic patients at term were matched in maternal age and gestational age with 55 consecutive normotensive pregnant women. Venous blood samples were obtained and analyzed for serum uric acid. Following delivery, the fetal outcomes in the pre-eclamptic group and controls were determined. Data analysis was carried out using SPSS (version 21) and the level of statistical significance was set at p-value <. 05. Results The mean serum uric acid levels of the pre-eclamptic subjects was significantly higher compared to their normotensive counterparts (12.7 ± 7.8 vs. 4.9 ± 1.2 mg/dL, p = .000). Babies with low birth weight, poor Apgar scores (at 1st and 5th minute of life) and those who required neonatal unit admission occurred more significantly among the pre-eclamptic women when compared with the controls (p = .000). However, the live birth rate of the case and control groups was comparable (94.5% vs. 100%, p = .079), Binary logistic regression analysis revealed a positive association between hyperuricemia and pre-eclampsia (OR = 18.8; 95% CI = 1.22–289.35, p = .035). Pre-eclamptic mothers with hyperuricemia had 4.41 odds of delivering babies with low birth weight when compared with pre-eclamptics without hyperuricemia (OR = 4.41; 95% CI = 0.76–25.5, p = .097); but Apgar scores and need for neonatal admission showed no association with maternal serum uric acid levels. Conclusion This study therefore suggests that hyperuricemia is a strong prognostic indicator of LBW babies among women with pre-eclampsia.
Perceived racial/ethnic discrimination among young adult college students: Prevalence rates and associations with mental health

Abstract Objective/Participants: In a large, diverse sample of college students (N = 2,230), this online study investigated racial/ethnic differences on type of discriminatory event experienced and perceived stress, and whether discrimination-related stress was associated with mental health symptoms. Methods: Prevalence of lifetime/past year discriminatory events was assessed and frequency of discrimination-related stress was compared across racial/ethnic groups. Correlations between discrimination-related stress and mental health symptoms were also examined. Results: All racial/ethnic groups reported experiencing all types of discriminatory events, though prevalence was lowest for White students. Racial/ethnic minority (i.e., Asian, Black, Latinx) students reported greater discrimination-related perceived stress compared to White, non-Hispanics. Across all racial/ethnic groups, discrimination-related stress was positively associated with negative mental health outcomes (e.g., anxiety/depressive symptoms). Conclusions: These results highlight the need to continue efforts to reduce discriminatory experiences of racial/ethnic minority students and to incorporate antiracism interventions in universities to mitigate the pervasive negative experiences of minority students.
Bibliometric and Altmetric Analyses of Publication Activity in the Field of Behcet's Disease in 2010–2019

Background Behcet's disease (BD) is a systemic vasculitis accompanied by oral-genital ulcers, ocular, cerebral, and gastrointestinal disorders. The aim of this study was to evaluate BD articles published between 2010–2019 bibliometrically and to provide up-to-date data. A secondary aim was to present a different perspective using altmetric assessments. Methods This bibliometric and altmetric research was performed with data obtained from the Web of Science database. The key terms “Behcet's disease,” “Behcet's syndrome,” and “Behcet” were used for listing the articles. The number of articles, citation data, and active countries were determined. Trend and correlation analyses were performed. Altmetric attention scores (AASs) and Mendeley readers count (MRC) of the articles were acquired for the altmetric evaluations. Results A total of 5,201 articles were listed. After the exclusion criteria, a total of 2,163 articles were obtained for further analysis. A significant and increasing trend was detected in the number of articles from 2010 to 2019 (P < 0.001). Turkey (28.24%), China (9.57%), South Korea (9.20%), Japan (6.38%), and Italy (5.64%) were the five most productive countries. France, the United States and, the United Kingdom were the top three countries in respect of the average number of citations per article. A weak significant correlation was detected between the number of citations and AAS (P < 0.001). The number of citations was significantly and strongly correlated with the MRC (P < 0.001). Conclusion An increasing trend was found in BD research productivity. Although the Silk Road countries were prominent in the number of articles, a similar ranking was not valid for the average number of citations per article.
Soil Candidate Phyla Radiation Bacteria Encode Components of Aerobic Metabolism and Co-occur with Nanoarchaea in the Rare Biosphere of Rhizosphere Grassland Communities

Here, we investigated overlooked microbes in soil, candidate phyla radiation (CPR) bacteria and Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota (DPANN) archaea, by size fractionating small particles from soil, an approach typically used for the recovery of viral metagenomes. Concentration of these small cells (<0.2 μm) allowed us to identify these organisms as part of the rare soil biosphere and to sample genomes that were absent from non-size-fractionated metagenomes. ABSTRACT Candidate Phyla Radiation (CPR) bacteria and nanoarchaea populate most ecosystems but are rarely detected in soil. We concentrated particles of less than 0.2 μm in size from grassland soil, enabling targeted metagenomic analysis of these organisms, which are almost totally unexplored in largely oxic environments such as soil. We recovered a diversity of CPR bacterial and some archaeal sequences but no sequences from other cellular organisms. The sampled sequences include Doudnabacteria (SM2F11) and Pacearchaeota, organisms rarely reported in soil, as well as Saccharibacteria, Parcubacteria, and Microgenomates. CPR and archaea of the phyla Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota (DPANN) were enriched 100- to 1,000-fold compared to that in bulk soil, in which we estimate each of these organisms comprises approximately 1 to 100 cells per gram of soil. Like most CPR and DPANN sequenced to date, we predict these microorganisms live symbiotic anaerobic lifestyles. However, Saccharibacteria, Parcubacteria, and Doudnabacteria genomes sampled here also harbor ubiquinol oxidase operons that may have been acquired from other bacteria, likely during adaptation to aerobic soil environments. We conclude that CPR bacteria and DPANN archaea are part of the rare soil biosphere and harbor unique metabolic platforms that potentially evolved to live symbiotically under relatively oxic conditions. IMPORTANCE Here, we investigated overlooked microbes in soil, Candidate Phyla Radiation (CPR) bacteria and Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota (DPANN) archaea, by size fractionating small particles from soil, an approach typically used for the recovery of viral metagenomes. Concentration of these small cells (<0.2 μm) allowed us to identify these organisms as part of the rare soil biosphere and to sample genomes that were absent from non-size-fractionated metagenomes. We found that some of these predicted symbionts, which have been largely studied in anaerobic systems, have acquired aerobic capacity via lateral transfer that may enable adaptation to oxic soil environments. We estimate that there are approximately 1 to 100 cells of each of these lineages per gram of soil, highlighting that the approach provides a window into the rare soil biosphere and its associated genetic potential.
Effects of land‐use change in the Amazon on precipitation are likely underestimated

The Amazon forest enhances precipitation levels regionally as trees take up water from the soil and release it back into the atmosphere through transpiration. Therefore, land‐use changes in the Amazon affect precipitation patterns but to what extent remains unclear. Recent studies used hydrological and atmospheric models to estimate the contribution of tree transpiration to precipitation but assumed that precipitation decreases proportionally to the transpired portion of atmospheric moisture. Here, we relaxed this assumption by, first, relating observed hourly precipitation levels to atmospheric column water vapor in a relatively flat study area encompassing a large part of the Amazon. We found that the effect of column water vapor on hourly precipitation was strongly nonlinear, showing a steep increase in precipitation above a column water vapor content of around 60 mm. Next, we used published atmospheric trajectories of moisture from tree transpiration across the whole Amazon to estimate the transpiration component in column water vapor in our study area. Finally, we estimated precipitation reductions for column water vapor levels without this transpired moisture, given the nonlinear relationship we found. Although loss of tree transpiration from the Amazon causes a 13% drop in column water vapor, we found that it could result in a 55%–70% decrease in precipitation annually. Consequences of this nonlinearity might be twofold: although the effects of deforestation may be underestimated, it also implies that forest restoration may be more effective for precipitation enhancement than previously assumed.
Candidate Psychotropics against SARS – CoV – 2: A Narrative Review

Abstract Since few therapeutic options are clinically accessible for coronavirus disease 2019 (COVID-19), effective, safe, and globally available pharmaceuticals need to be urgently developed to prevent severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) and alleviate the severity of COVID-19. In this regard, the present paper is intended to provide an extensive review of the clinical and preclinical evidence on the psychotropics’ anti-SARS-CoV-2 effects, giving an insight into their potential applications for patients with a proven or high likelihood of COVID-19 pneumonia. The results showed that psychotropic drugs such as melatonin, lithium carbonate, valproate, olanzapine, quetiapine, clozapine, fluoxetine, escitalopram, fluvoxamine, and cannabidiol could help lower the mortality due to SARS-CoV-2 infection. According to these medications’ direct immunomodulatory actions against the destructive cytokine storm, as well as other direct/indirect mechanisms (e. g., the endolysosomal pathway modulation, interactions with specific receptors, and membrane fusion), it was perceived that such drugs could effectively weaken the worsened immune response and avoid adult respiratory distress syndrome and acute lung injury. According to the author’s analysis of the currently available evidence, there is significant support for psychotropics as complementary interventions during SARS-CoV-2 infection. However, further studies need to be carried out to assess the effects of the above psychotropic drugs in vitro and clinical settings.
PHENOTYPIC CHARACTERIZATION OF TWO NOVEL CELL LINE MODELS OF CASTRATION RESISTANT PROSTATE CANCER

BACKGROUND Resistance to androgen deprivation therapies is a major driver of mortality in advanced prostate cancer. Therefore, there is a need to develop new pre-clinical models that allow the investigation of resistance mechanisms and the assessment of drugs for the treatment of castration resistant prostate cancer. METHODS We generated two novel cell line models (LAPC4-CR and VCaP-CR) which were derived by passaging LAPC4 and VCaP cells in vivo and in vitro under castrate conditions. We performed detailed transcriptomic (RNA-seq) and proteomic analyses (SWATH-MS) to delineate expression differences between castration-sensitive and castration-resistant cell lines. Furthermore, we characterized the in vivo and in vitro growth characteristics of the novel cell line models. RESULTS The two cell line derivatives LAPC4-CR and VCaP-CR showed castration resistant growth in vitro and in vivo which was only minimally inhibited by AR antagonists, enzalutamide and bicalutamide. High-dose androgen treatment resulted in significant growth arrest of VCaP-CR but not in LAPC4-CR cells. Both cell lines maintained AR expression, but exhibited distinct expression changes on the mRNA and protein level. Integrated analyses including data from LNCaP and the previously described castration resistant LNCaP-abl cells revealed an expression signature of castration resistance. CONCLUSIONS The two novel cell line models LAPC4-CR and VCaP-CR and their comprehensive characterization on the RNA and protein level represent important resources to study the molecular mechanisms of castration resistance.
Men have eating disorders too: an analysis of online narratives posted by men with eating disorders on YouTube

ABSTRACT Eating Disorders (ED) among men are still surrounded by stigma and gender stereotypes, with a common misconception that ED are an exclusively female condition. This study employed a gender-sensitive approach to uncover males’ critical needs for effective treatment and recovery. We qualitatively analyzed a sample of twenty-five videos posted on YouTube by men with ED, presenting personal stories of recovery and recovery in-progress. Through thematic analysis of the narratives, we identified three common factors increasing disordered eating behaviors in men: 1) bullying, 2) drive for muscularity, and 3) self-regulation. In addition, we found three major themes related to barriers preventing men from help-seeking: 1) shame and stigma, 2) lack of knowledge and information, and 3) low level of perceived doctor-patient communication. The findings of this study can contribute to the conceptualization of future interventions and recovery programs designed to prevent and treat ED in men.