Miracle-dz/UniFAR-FTUs huggingface dataset:
Variable Inhibition of Nitrous Oxide Reduction in Denitrifying Bacteria by Different Forms of Methanobactin

Herein, it was demonstrated that the different forms of methanobactin differentially enhance N2O emissions from Pseudomonas stutzeri strain DCP-Ps1 (harboring clade I nitrous oxide reductase) and Dechloromonas aromatica strain RCB (harboring clade II nitrous oxide reductase). This work contributes to our understanding of how aerobic methanotrophs compete with denitrifiers for the copper uptake and also suggests how MBs prevent copper collection by denitrifiers, thus downregulating expression of nitrous oxide reductase. ABSTRACT Aerobic methanotrophic activity is highly dependent on copper availability, and methanotrophs have developed multiple strategies to collect copper. Specifically, when copper is limiting (ambient concentrations less than 1 μM), some methanotrophs produce and secret a small modified peptide (less than 1,300 Da) termed methanobactin (MB) that binds copper with high affinity. As MB is secreted into the environment, other microbes that require copper for their metabolism may be inhibited as MB may make copper unavailable; e.g., inhibition of denitrifiers as complete conversion nitrate to dinitrogen involves multiple enzymes, some of which are copper-dependent. Of key concern is inhibition of the copper-dependent nitrous oxide reductase (NosZ), the only known enzyme capable of converting nitrous oxide (N2O) to dinitrogen. Herein, we show that different forms of MB differentially affect copper uptake and N2O reduction by Pseudomonas stutzeri strain DCP-Ps1 (that expresses clade I NosZ) and Dechloromonas aromatica strain RCB (that expresses clade II NosZ). Specifically, in the presence of MB from Methylocystis sp. strain SB2 (SB2-MB), copper uptake and nosZ expression were more significantly reduced than in the presence of MB from Methylosinus trichosporium OB3b (OB3b-MB). Further, N2O accumulation increased more significantly for both P. stutzeri strain DCP-Ps1 and D. aromatica strain RCB in the presence of SB2-MB versus OB3b-MB. These data illustrate that copper competition between methanotrophs and denitrifying bacteria can be significant and that the extent of such competition is dependent on the form of MB that methanotrophs produce. IMPORTANCE Herein, it was demonstrated that the different forms of methanobactin differentially enhance N2O emissions from Pseudomonas stutzeri strain DCP-Ps1 (harboring clade I nitrous oxide reductase) and Dechloromonas aromatica strain RCB (harboring clade II nitrous oxide reductase). This work contributes to our understanding of how aerobic methanotrophs compete with denitrifiers for the copper uptake and also suggests how MBs prevent copper collection by denitrifiers, thus downregulating expression of nitrous oxide reductase. This study provides critical information for enhanced understanding of microbe-microbe interactions that are important for the development of better predictive models of net greenhouse gas emissions (i.e., methane and nitrous oxide) that are significantly controlled by microbial activity.
Monoclonal Antibodies Targeting Surface-Exposed Epitopes of Candida albicans Cell Wall Proteins Confer In Vivo Protection in an Infection Model

Monoclonal antibody (mAb)-based immunotherapies targeting systemic and deep-seated fungal infections are still in their early stages of development, with no licensed antifungal mAbs currently being available for patients at risk. The cell wall glycoproteins of Candida albicans are of particular interest as potential targets for therapeutic antibody generation due to their extracellular location and key involvement in fungal pathogenesis. ABSTRACT Monoclonal antibody (mAb)-based immunotherapies targeting systemic and deep-seated fungal infections are still in their early stages of development, with no licensed antifungal mAbs currently being available for patients at risk. The cell wall glycoproteins of Candida albicans are of particular interest as potential targets for therapeutic antibody generation due to their extracellular location and key involvement in fungal pathogenesis. Here, we describe the generation of recombinant human antibodies specifically targeting two key cell wall proteins (CWPs) in C. albicans: Utr2 and Pga31. These antibodies were isolated from a phage display antibody library using peptide antigens representing the surface-exposed regions of CWPs expressed at elevated levels during in vivo infection. Reformatted human-mouse chimeric mAbs preferentially recognized C. albicans hyphal forms compared to yeast cells, and increased binding was observed when the cells were grown in the presence of the antifungal agent caspofungin. In J774.1 macrophage interaction assays, mAb pretreatment resulted in the faster engulfment of C. albicans cells, suggesting a role of the CWP antibodies as opsonizing agents during phagocyte recruitment. Finally, in a series of clinically predictive mouse models of systemic candidiasis, our lead mAb achieved improved survival (83%) and a several-log reduction of the fungal burden in the kidneys, similar to the levels achieved for the fungicidal drug caspofungin and superior to the therapeutic efficacy of any anti-Candida mAb reported to date.
Copy number and expression of CEP89, a protein required for ciliogenesis, are increased and predict poor prognosis in patients with ovarian cancer

CEP89 (centrosomal protein 89) is required for ciliogenesis and mitochondrial metabolism, but its role in cancer has yet to be clarified. We report that CEP89 is overexpressed in ovarian cancer (OC) compared to normal ovaries. Likewise, its expression is higher in malignant ovarian tumors than in borderline ovarian tumors with low malignant potential. More than a quarter of patients with OC have copy number gains in the CEP89 gene, and patients with high expression have more than a year shorter overall survival compared to those with low expression. Moreover, we found that CEP89 can be considered as a prognostic marker for poor overall survival in patients with OC, after adjusting for tumor stage and residual tumor. Nine out of the top 10 protein interactors of CEP89 have the highest percentage of total copy number variation (CNV) events in OC among all other cancer types. Furthermore, CEP89 messenger RNA (mRNA) levels are higher in OC patients with disease recurrence compared to those with no recurrence. We also analyzed CEP89 levels in OC cell lines in terms of CNV, mRNA, and protein levels; and observed that the FUOV‐1 cell line has the highest levels among cell lines that originated from primary sites. Our study suggests that CEP89 may be a valuable prognostic predictor for the overall survival of patients with OC, and it could also be a novel therapeutic target in this malignancy.
Changes in a Mediterranean lifestyle during the COVID-19 pandemic among elderly Italians: an analysis of gender and socioeconomic inequalities in the “LOST in Lombardia” study

Abstract Little is known on potential socioeconomic and gender disparities in dietary changes during the COVID-19 pandemic. We conducted a telephone-based survey during fall 2020 on 4400 participants representative of the population aged 65–99 years living in Lombardy, Italy. Changes in a Mediterranean lifestyle were assessed retrospectively by scoring modifications in the consumption of nine food groups and five diet-related behaviours compared to 2019. A Mediterranean COVID-19 Pandemic Score (MedCovid-19 Score) was computed, reflecting changes during pandemic, with increasing values indicating improvements in line with a Mediterranean lifestyle. Predictors of favourable dietary changes (MedCovid-19 Score ≥ 1) were education (odds ratio [OR] = 1.52; 95% confidence interval 1.19–1.95 for postgraduate vs. lower), wealth (OR = 1.52; 1.14–2.02 for high vs. low) and skilled manual occupations (OR = 1.57; 1.28–1.92 vs. white collars). Women were more likely than men to move away from a Mediterranean lifestyle (OR = 1.86; 1.58–2.21). In conclusions, changes towards a Mediterranean lifestyle were disproportionately distributed across gender and socioeconomic strata.
Acid‐Responsive Dual‐Targeted Nanoparticles Encapsulated Aspirin Rescue the Immune Activation and Phenotype in Autism Spectrum Disorder

The treatment of autism spectrum disorder (ASD) is one of the most difficult challenges in neurodevelopmental diseases, because of the unclear pathogenesis research and low brain‐lesion targeting efficiency. Besides, maternal immune activation has been reported as the most mature and widely used model of ASD and aspirin‐triggered lipoxin A4 is a potent anti‐inflammatory mediator being involved in the resolution of neuroinflammation in ASD. Therefore, an aspirin encapsulated cascade drug delivery system (Asp@TMNPs) is established, which can successively target the blood–brain barrier (BBB) and microglial cells and response to the acid microenvironment in lysosome. As a result, the mitochondrial oxidative stress, DNA damage, and inflammation of microglial cells are prominently alleviated. After the treatment of Asp@TMNPs, the social interaction, stereotype behavior, and anxious condition of ASD mice are notably improved and the activation of microglial cells is inhibited. Overall, this system successively penetrates the BBB and targets microglial cells, therefore, it significantly enhances the intracephalic drug accumulation and improves anti‐neuroinflammatory efficacy of aspirin, providing a promising strategy for ASD treatment.
Purification and Characterization of the Isoprene Monooxygenase from Rhodococcus sp. Strain AD45

Isoprene is a highly abundant climate-active gas and a carbon source for some bacteria. Analyses of the genes encoding isoprene monooxygenase (IsoMO) indicate this enzyme is a soluble diiron center monooxygenase in the same family of oxygenases as soluble methane monooxygenase, alkene monooxygenase, and toluene monooxygenase. ABSTRACT Isoprene (2-methyl-1,3-butadiene) is a climate-active gas released to the atmosphere in large quantities, comparable to methane in magnitude. Several bacteria have been isolated which can grow on isoprene as a sole carbon and energy source, but very little information is available about the degradation of isoprene by these bacteria at the biochemical level. Isoprene utilization is dependent on a multistep pathway, with the first step being the oxidation of isoprene to epoxy-isoprene. This is catalyzed by a four-component soluble diiron monooxygenase, isoprene monooxygenase (IsoMO). IsoMO is a six-protein complex comprising an oxygenase (IsoABE), containing the di-iron active site, a Rieske-type ferredoxin (IsoC), a NADH reductase (IsoF), and a coupling/effector protein (IsoD), homologous to the soluble methane monooxygenase and alkene/aromatic monooxygenases. Here, we describe the purification of the IsoMO components from Rhodococcus sp. AD45 and reconstitution of isoprene-oxidation activity in vitro. Some IsoMO components were expressed and purified from the homologous host Rhodococcus sp. AD45-ID, a Rhodococcus sp. AD45 strain lacking the megaplasmid which contains the isoprene metabolic gene cluster. Others were expressed in Escherichia coli and purified as fusion proteins. We describe the characterization of these purified components and demonstrate their activity when combined with Rhodococcus sp. AD45 cell lysate. Demonstration of IsoMO activity in vitro provides a platform for further biochemical and biophysical characterization of this novel soluble diiron center monooxygenase, facilitating new insights into the enzymatic basis for the bacterial degradation of isoprene. IMPORTANCE Isoprene is a highly abundant climate-active gas and a carbon source for some bacteria. Analyses of the genes encoding isoprene monooxygenase (IsoMO) indicate this enzyme is a soluble diiron center monooxygenase in the same family of oxygenases as soluble methane monooxygenase, alkene monooxygenase, and toluene monooxygenase. We report the initial biochemical characterization of IsoMO from Rhodococcus, the first from any bacterium, describing the challenging purification and reconstitution of in vitro activity of its four components. This study lays the foundation for future detailed mechanistic studies of IsoMO, a key enzyme in the global isoprene cycle.
Percent Agreement Between Immunohistochemistry and Next-Generation Sequencing in Testing Patients for Mismatch Repair Deficiency

The presence of mismatch repair deficiency is frequently assessed in gastrointestinal and gynecologic neoplasms by surgical pathologists using immunohistochemical methods. Targeted next-generation sequencing (NGS) covering some genes in the mismatch repair complex is used with increasing frequency, however, the percent positive and negative agreement of immunohistochemical methods and NGS of mismatch repair genes is not well-described in the literature. We sought to compare performance of immunohistochemistry (IHC) and NGS of mismatch repair genes on our institutional targeted panel. We evaluated the concordance of immunohistochemical and panel-based gene sequencing methods in a retrospective cohort study of patients evaluated at our center with both immunohistochemical and panel-based sequencing. Our NGS panel covers only MLH1 and MSH2, whereas our immunohistochemical panel assesses for expression of MLH1, PMS2, MSH2, and MSH6. We identified 68 unique patients with both immunohistochemical evaluation of mismatch repair protein expression and NGS panel sequencing, of which 67 were suitable for analysis given the patterns of immunohistochemical loss of expression observed. The percent positive agreement for NGS with IHC was 50%, albeit with very rare positive cases (n=2/4). Percent negative agreement was also high at 100% (n=63/63). One case with loss of MLH1, PMS2, and MSH6 expression by IHC and no pathogenic variants by NGS exhibited MLH1 promoter hypermethylation. Percent negative agreement between immunohistochemical and NGS gene sequencing is high, although firm conclusions regarding percent positive agreement between NGS and IHC are limited by low numbers of positive cases in our cohort. In general, we consider the findings to support continued use of immunohistochemical methods to screen for the presence of mismatch repair deficiency and consider additional testing by NGS likely to add little diagnostic value in the context of intact immunohistochemical expression of mismatch repair proteins.
Anatomical and histological investigation of the pineal gland in the lake van fish (Alburnus tarichi (Güldenstädt, 1814))

The pineal gland and melatonin secreted from the gland regulate the biological clock and adaptation to seasonal changes, glucose balance, nutrition and locomotor activities. In this study, the pineal gland of the Lake Van fish was examined anatomically and histologically. The melatonin level secreted from the pineal gland was determined in fish plasma sampled from both lakes and streams during reproduction migration. The pineal gland in the Lake Van fish, as in other teleost fish, is located in the head, under the translucent pineal window, which does not contain many pigment cells. The gland consists of pineal vesicle and pineal stalk parts on the dorsal sac in the Lake Van fish. It was determined that the pineal gland showed good vascularity. The presence of pinealocytes and different types of cells in the pineal organ was determined histologically. Pinealocytes were intensely localized in the lumen of the pineal vesicle. The plasma melatonin level increased in fish passing from lake to stream for reproductive migration.
Daily Variation in Nursing Home Staffing and Its Association With Quality Measures

Key Points Question Is daily variation in nursing home staffing associated with quality, and does it offer additional information to measures of average staffing levels? Findings This quality improvement study of 13 339 nursing homes found that daily variation of staffing was significantly associated with the 5-Star Survey and Quality Measures rankings. There was little agreement between the variation and the average staffing measures on quality decile rankings of nursing homes, suggesting that staffing variation provides new quality improvement information. Meaning These findings suggest that quality ranking of nursing homes and an understanding of the relationship between staffing and quality might be improved by adding daily variability measures to the Nursing Home Care Compare reports.
Melittin Prevents Metastasis of Epidermal Growth Factor-Induced MDA-MB-231 Cells through The Inhibition of The SDF-1α/CXCR4 Signaling Pathway

Objective Melittin is one of the natural components of bee venom (Apis mellifera), and its anticancer and antimetastatic properties have been well established, but the underlying mechanism remains elusive. The MDA-MB-231 is a triple- negative cell line that is highly aggressive and invasive. Besides, many critical proteins are involved in tumor invasion and metastasis. In this study, we investigated whether melittin inhibits the migration and metastasis of epidermal growth factor (EGF)-induced MDA-MB-231 cells via the suppression of SDF-1α/CXCR4 and Rac1-mediated signaling pathways. Materials and Methods In this experimental study, cells were treated with melittin (0.5-4 μg/ml), and the toxicity of melittin was assessed by the MTT assay. Afterward, the migration assay was conducted to measure the degree of the migration of EGF-induced cells. The western blot technique was performed to analyze the rate of Rac1, p-Rac1, SDF- 1α, and CXCR4 expression in different groups. Results The results demonstrated that melittin markedly suppressed the migration of EGF-induced cells and decreased the expression of p-Rac1, CXCR4, and SDF-1α proteins. Conclusion The results of the present study suggested that the anti-tumor properties of melittin could be through the blocking of the SDF-1α/CXCR4 signaling pathway, which is beneficial for the reduction of tumor migration and invasion.
Circulating renin‐angiotensin‐aldosterone system activity in cats with systemic hypertension or cardiomyopathy

Abstract Background Activity of the circulating renin‐angiotensin‐aldosterone system (RAAS) has not been comprehensively characterized in cats with systemic hypertension (SH) or cardiomyopathy (CM), and the effects of furosemide or amlodipine treatment on the RAAS have not been fully evaluated in cats. Hypothesis/Objectives To document RAAS activity in cats with SH or CM compared to healthy cats and determine how RAAS profiles change with furosemide or amlodipine treatment. Animals Sixty‐six client‐owned cats: 15 with SH (7 amlodipine‐treated, 8 untreated), 17 with advanced CM (7 furosemide‐treated, 10 not furosemide‐treated), and 34 healthy cats. Methods Equilibrium concentrations of RAAS peptides and aldosterone were quantified in serum samples by liquid chromatography‐mass spectrometry. Variables were compared between groups using Kruskal‐Wallis analysis with post hoc Holms‐corrected Dunn's testing. Results Compared with healthy cats, cats with CM had higher concentrations of angiotensin I, aldosterone, and plasma renin activity (all P < .01), and these differences remained significant (P < .03) after considering subgroups of untreated or furosemide‐treated cats. Compared with healthy cats, untreated cats with SH showed no differences in RAAS biomarkers, whereas amlodipine‐treated cats had higher concentrations of angiotensins I, II, III, IV, and 1‐7, aldosterone, and plasma renin activity (all P < .03). Multivariable analysis determined that furosemide and amlodipine treatments were independent predictors of increased RAAS biomarker concentrations. Conclusions and Clinical Importance Cats with CM had increased RAAS activity, whereas cats with untreated SH did not. Furosemide and amlodipine both led to nonspecific activation of both classical and alternative RAAS pathways in cats.
The anti-inflammatory effects of cinnamyl alcohol on sepsis-induced mice via the NLRP3 inflammasome pathway

Background Sepsis is an excessive inflammatory response to an infection that fails to return to homeostasis. It occurs frequently in patients following a primary infection or injury and is one of the most common causes of mortality in hospitalized patients. However, there is currently no specific and effective therapy for the management of sepsis. Previous findings have suggested that cinnamon and cinnamon extracts have anti-inflammatory and anti-oxidative activities and therefore, may be effective in treating sepsis. Methods In the present study, Escherichia coli was injected into mice to induce sepsis. Hematoxylin and eosin staining was used to investigate the influence of cinnamyl alcohol on histological changes including heart, liver, lung, and kidney tissues. Western blotting and real-time polymerase chain reaction (RT-PCR) were applied to measure the levels of NLRP3 inflammasome. The levels of interleukin (IL)-1β and IL-18 in the serum were detected with enzyme-linked immunosorbent assay (ELISA) method. Results Administration of cinnamyl alcohol by gavage effectively reduced the mortality of septic mice (70% survival), compared to untreated septic mice (50% survival). The histological findings indicated that cinnamyl alcohol reduced the inflammatory reaction in the liver, heart, lungs, and kidneys of the septic mice. In the circulatory system, the concentrations of the inflammatory cytokines IL-1β and IL-18 were significantly decreased by cinnamyl alcohol administration compared to the untreated septic group. Western blot analysis and quantitative polymerase chain reaction (qPCR) demonstrated that cinnamyl alcohol decreased the expression of apoptosis-associated speck-like protein containing a C-terminal caspase recruitment domain (ASC), nucleotide-binding oligomerization domain-like receptor 3 (NLRP3), and caspase-1 in the liver, heart, lungs, and kidneys of the mice, suggesting that cinnamyl alcohol alleviated sepsis syndrome via the NLRP3 inflammasome pathway. Conclusions Cinnamyl alcohol may be a novel therapeutic candidate for the treatment of sepsis syndrome.
A qualitative exploration of the National Academy of medicine model of well‐being and resilience among healthcare workers during COVID‐19

The aim of this research was to explore factors affecting the well-being and resilience of healthcare workers (HCWs) during COVID-19. Qualitative content analysis of survey responses to a single, open-ended question. The study took place in June and July 2020 in the Mid-Atlantic United States. Qualitative data from 452 HCWs were analysed with deductive content analysis, using a National Academy of Medicine model of factors affecting clinician well-being and resilience. The study is reported according to the Standards for Reporting Qualitative Research and the Consolidated Criteria for Reporting Qualitative Research. The findings reflect each of the seven domains of the National Academy of Medicine model, demonstrating the diverse factors that have impacted the well-being and resilience of HCWs during the COVID-19 pandemic. The results of the study show that factors within the workplace have significantly impacted the well-being and resilience of HCWs during the pandemic, in particular, the practice environment and the rules and regulations implemented by healthcare organizations. At the same time, individual and even societal factors have also affected well-being during the pandemic, but not to the same degree as factors within the workplace. The research findings illustrate how multiple, diverse factors have influenced the well-being and resilience of HCWs during the pandemic. The study has practical relevance for healthcare leaders and important implications for future research. Health system leaders can address the well-being and resilience of healthcare workers by implementing solutions that address health system factors like the practice environment and the policies and procedures of the organization. Researchers should not only focus on individual factors associated with professional well-being but must also expand research and interventional studies to include the system and environmental factors that significantly affect clinicians.