Miracle-dz/UniFAR-FTUs huggingface dataset:
Agaricus bisporus browning: a review

Agaricus bisporus browning is a common and economically detrimental phenomenon, in which melanogenic phenols are enzymically processed into quinones, which evolve eventually to melanins. This review deals with the two fundamental sides of this process, enzyme(s) and phenolic substrates. Mushroom tyrosinase, the main polyphenol oxidase encountered in the A. bisporus sporophore, is treated in the first part. Its overall molecular architecture, isoforms, primary sequence and genetic background are considered. The presentation of tyrosinase catalytic features, including enzyme assays, kinetic properties, substrates and inhibitors, is followed by a comprehensive description of the active site and reaction mechanisms. Because of their relevance for studies of mushroom browning during development and post-harvest storage, the occurrence and properties of latent enzyme forms, as well as the location of tyrosinase and variations of its activity during the A. bisporus life cycle, are also reviewed. The second part deals with the substrates, particularly γ-L-glutaminyl-4-hydroxybenzene (GHB) and its derivatives. Main data concerning the nature, obtention (by extraction or synthesis), spectrometric and chromatographic characteristics, chemical stabilities and biological properties of these typical Agaricaceae compounds are presented. Their distribution and levels according to the strains and flushes are described, as well as their variations during storage. Thirdly, the relationship between browning and the natural or pathogenic discolouration intensity is developed.
COVID-19: An Update about the Discovery Clinical Trial

Finding efficacious and safe treatments for COVID-19 emerges as a crucial need in order to control the spread of the pandemic. Whereas plasma therapy attracts much interest, the European project Discovery focuses on the potentialities of small molecules like remdesivir, the combination of lopinavir/ritonavir, hydroxychloroquine, and chloroquine. Results recently published on the clinical evaluation of those drugs are compiled in this brief report, although complete data are still impatiently awaited.
Intrasinusoidal HHV8-EBV–Positive Large B-Cell Lymphoma With Features of Germinotropic Lymphoproliferative Disorder

Germinotropic lymphoproliferative disorder (GLPD) is a poorly characterized lymphoproliferative entity, recently included in the World Health Organization classification of hematolymphoid neoplasms. The histological pattern of this disease comprises monotypic plasmablasts that involve the germinal centers of the lymphoid follicles (germinotrophism), forming confluent aggregates positive for both human herpes virus type 8 (HHV8) and Epstein-Barr virus. Currently, after 17 years of its first description, only 18 cases have been reported. In this article, we describe a case of a GLPD presenting in an immunocompetent 79-year-old woman with localized axillary lymphadenopathy, showing a prominent sinusoidal growth pattern, with no evidence of germinotrophism or extrasinusoidal spread. Stinking pleomorphism in tumor cells was also noted. An extension study has not revealed involvement of other groups of lymph nodes or extralymphoid sites. The patient is alive and has shown no relapse after 8 years follow-up (the longest follow-up reported period for this entity). This previously unrecognized pure sinusoidal growth pattern along with the striking pleomorphism in neoplastic cells closely mimics the appearance of an anaplastic large cell lymphoma. GLPD is not usually considered in such a setting, but it should be included in the differential diagnosis of sinusoidal proliferations. Our findings contribute to the expansion of the morphological spectrum of HHV8-associated lymphoproliferative lesions and aids in the characterization of the very infrequent GLPD entity.
Local PEComatosis of the Appendix: New Insights Into the Histogenesis of Nodular Granular Muscle Degeneration and Granular Cells/Granular Cell Lesions of the Appendix

Nodular granular muscle degeneration (NGMD) of the appendix is a rare histologic curiosity characterized by distinctive nests of polygonal epithelioid cells with abundant pale-pink eosinophilic granular cytoplasm, mostly distributed in the inner layer of the muscularis propria or submucosa of the appendix. Although the nature of the cells of interest in NGMD of the appendix has not been completely elucidated, it is believed that they denote degenerative smooth muscle cells of the appendiceal muscularis propria, a histologic finding described as granular cells/granular cell lesions of the appendix in the 1960s. In this article, we described a new case of NGMD of the appendix and documented for the first time that this peculiar lesion actually represents a form of perivascular epithelioid cell proliferation based on its dual immunopositivity for myogenic and melanocytic markers. We also analyzed the old medical literature on granular cells/granular cell lesions of the appendix to shed some light on this ill-defined morphologic finding and its relationship to NGMD of the appendix. Since NGMD of the appendix is a lesion of perivascular epithelioid cells, the term NGMD is a misnomer, and hence, the designation “local PEComatosis of the appendix” is proposed for this unusual phenomenon.
Correlation between the migration scale index and the number of new confirmed coronavirus disease 2019 cases in China

Abstract In late December 2019, patients of atypical pneumonia due to an unidentified microbial agent were reported in Wuhan, Hubei Province, China. Subsequently, a novel coronavirus was identified as the causative pathogen which was named SARS-CoV-2. As of 12 February 2020, more than 44 000 cases of SARS-CoV-2 infection have been confirmed in China and continue to expand. Provinces, municipalities and autonomous regions of China have launched first-level response to major public health emergencies one after another from 23 January 2020, which means restricting movement of people among provinces, municipalities and autonomous regions. The aim of this study was to explore the correlation between the migration scale index and the number of confirmed coronavirus disease 2019 (COVID-19) cases and to depict the effect of restricting population movement. In this study, Excel 2010 was used to demonstrate the temporal distribution at the day level and SPSS 23.0 was used to analyse the correlation between the migration scale index and the number of confirmed COVID-19 cases. We found that since 23 January 2020, Wuhan migration scale index has dropped significantly and since 26 January 2020, Hubei province migration scale index has dropped significantly. New confirmed COVID-19 cases per day in China except for Wuhan gradually increased since 24 January 2020, and showed a downward trend from 6 February 2020. New confirmed COVID-19 cases per day in China except for Hubei province gradually increased since 24 January 2020, and maintained at a high level from 24 January 2020 to 4 February 2020, then showed a downward trend. Wuhan migration scale index from 9 January to 22 January, 10 January to 23 January and 11 January to 24 January was correlated with the number of new confirmed COVID-19 cases per day in China except for Wuhan from 22 January to 4 February. Hubei province migration scale index from 10 January to 23 January and 11 January to 24 January was correlated with the number of new confirmed COVID-19 cases per day in China except for Hubei province from 22 January to 4 February. Our findings suggested that people who left Wuhan from 9 January to 22 January, and those who left Hubei province from 10 January to 24 January, led to the outbreak in the rest of China. The ‘Wuhan lockdown’ and the launching of the first-level response to this major public health emergency may have had a good effect on controlling the COVID-19 epidemic. Although new COVID-19 cases continued to be confirmed in China outside Wuhan and Hubei provinces, in our opinion, these are second-generation cases.
The Role of Foraging Mode in the Origin of Therapsids: Implications for the Origin of Mammalian Endothermy

Abstract The question of the adaptive basis for the origin of mammalian endothermy remains unresolved despite a great deal of research effort. Controversy continues over which physiological adaptations were of greatest importance in starting ectothermic nonmammalian synapsids of the Late Paleozoic on the path that culminated in modern endothermic mammals. Models of the selective basis for the origin of endothermy fall into two main categories: “thermoregulation first” and “aerobic capacity first. ” Studies of lizards show a dichotomy between a low-energy “sit-and-wait” (SW) foraging mode in Iguania and a more energy-intensive “widely foraging” (WF) mode in Autarchoglossa. It is proposed that in the transition from basal synapsids (“pelycosaurs”) to therapsids, a shift from the primitive SW mode to the WF mode put the ancestors of mammals on the path to increased aerobic capacity and the ability to sustain high levels of foraging activity. Selection for increased energy expenditure disproportionately increased the amount of food energy consumed, thus improving foraging efficiency. A shift from reliance on anaerobic muscle metabolism for short but rapid dashes to capture prey to a reliance on aerobic metabolism for active searching for prey necessitated improvements of the cardiovascular system and lungs for increased aerobic capacity and greater stamina. Over time, therapsids became locked into high food requirements, which selected for improvements in aerobic metabolism, locomotor and food-processing ability, and neurosensory/behavioral specializations. Evidence of a link between maximum activity metabolism and resting (basal) metabolism in anurans and rodents suggests that further increases in aerobic activity metabolism required an increased basal metabolic rate, which led to high body temperatures and, ultimately, homeothermy. Therapsids show adaptations for increased activity, greater food-getting and food-processing ability, and higher metabolic rates than basal synapsids (“pelycosaurs”). It is argued that the “foraging mode” model is preferable to the “parental care” model of Farmer and the “correlated progression” model of Kemp for understanding the origin of mammalian endothermy.
Non-thermal atmospheric gas plasma for decontamination of sliced cheese and changes in quality

The atmospheric-pressure non-thermal dielectric barrier discharge (DBD) plasma has recently emerged as an efficient decontamination method for the food safety enhancement. Thus the objective of this study was to evaluate the effectiveness of a simple DBD plasma treatment, with a relatively low-frequency power supply operating at 60 Hz, for microbial inactivation. A parametric study of operating conditions for bacterial inactivation was conducted using nutrient agar inoculated with Escherichia coli (2.28--6.28 log CFU/ml). The microbial log reduction was enhanced with increasing input power (30, 50, 70 W) and plasma exposure time (0, 1, 3, 5, 7 min). The inactivation effect was increased by decreasing inter-electrode gap (2, 1.5, 1 cm) and by reducing the initial microorganism concentration. Accordingly, a DBD plasma treatment at 50 W for 10 min could lead to complete killing of E. coli and partial inactivation of Listeria innocua on cheese (mean log reduction: 4.75 ± 0.02 and 0.72 ± 0.01, respectively). The decontamination efficacy of DBD plasma was affected by the types of microorganisms. The changes in hardness and color of cheese were unnoticeable after 10 min treatment with a power of 50 W. Overall, the results suggested that the DBD plasma can be potentially exploited to improve the food safety.
Probiotic Potential and Technological Properties of Bacteriocinogenic Lactococcus lactis Subsp. Lactis UTNGt28 from a Native Amazonian Fruit as a Yogurt Starter Culture

A native Lactococcus lactis subsp. lactis UTNGt28 (GenBank accession no: MG675576.1) isolated from Amazonian fruit of the tropical Caimitillo (Chrysophyllum oliviforme) tree and the commercial strain Lactococcus lactis subsp lactis ATCC11454 (LacAT) were targeted ex vitro in whole milk in combination with Streptococcus thermophilus ATCC19258 to obtain a fermented probiotic beverage. Concomitant with cell viability determination during storage (28 days), the pH, titratable acidity, syneresis, protein and fat were evaluated. The results indicated that neither UTNGt28 nor LacAT displayed a high capacity to ferment whole milk and survive during storage; a statistically significant difference (p < 0.05) in cell viability was registered for UTNGt28 compared with LacAT when inoculated alone or in combination with S. thermophilus. A principal component analysis showed a clear difference between the yogurt formulations at day 1 and 28 of storage. The PC 1 explained 46.8% of the total variance (day 28), was loaded in the negative (−) direction with titratable acidity (% lactic acid), while the PC 2 explained 22.5% (day 1) with pH. PC 1 was loaded in the positive (+) direction with pH, cell viability, syneresis, fat and protein. Overall results indicated that UTNGt28 has the technological properties for further development of a new probiotic product.
Opposing p53 and mTOR/AKT promote an in vivo switch from apoptosis to senescence upon telomere shortening in zebrafish

Progressive telomere shortening during lifespan is associated with restriction of cell proliferation, genome instability and aging. Apoptosis and senescence are the two major outcomes upon irreversible cellular damage. Here, we show a transition of these two cell fates during aging of telomerase deficient zebrafish. In young telomerase mutants, proliferative tissues exhibit DNA damage and p53-dependent apoptosis, but no senescence. However, these tissues in older animals display loss of cellularity and senescence becomes predominant. Tissue alterations are accompanied by a pro-proliferative stimulus mediated by AKT signaling. Upon AKT activation, FoxO transcription factors are phosphorylated and translocated out of the nucleus. This results in reduced SOD2 expression causing an increase of ROS and mitochondrial dysfunction. These alterations induce p15/16 growth arrest and senescence. We propose that, upon telomere shortening, early apoptosis leads to cell depletion and insufficient compensatory proliferation. Following tissue damage, the mTOR/AKT is activated causing mitochondrial dysfunction and p15/16-dependent senescence.
Habitat structure and egg distributions in the processionary caterpillar Ochrogaster lunifer: lessons for conservation and pest management

1. The spatial and temporal distribution of eggs laid by herbivorous insects is a crucial component of herbivore population stability, as it influences overall mortality within the population. Thus an ecologist studying populations of an endangered butterfly can do little to increase its numbers through habitat management without knowledge of its egg-laying patterns across individual host-plants under different habitat management regimes. At the other end of the spectrum, a knowledge of egg-laying behaviour can do much to control pest outbreaks by disrupting egg distributions that lead to rapid population growth. 2. The distribution of egg batches of the processionary caterpillar Ochrogaster lunifer on acacia trees was monitored in 21 habitats during 2 years in coastal Australia. The presence of egg batches on acacias was affected by host-tree 'quality' (tree size and foliar chemistry that led to increased caterpillar survival) and host-tree 'apparency' (the amount of vegetation surrounding host-trees). 3. In open homogeneous habitats, more egg batches were laid on high-quality trees, increasing potential population growth. In diverse mixed-species habitats, more egg batches were laid on low-quality highly apparent trees, reducing population growth and so reducing the potential for unstable population dynamics. The aggregation of batches on small apparent trees in diverse habitats led to outbreaks on these trees year after year, even when population levels were low, while site-wide outbreaks were rare. 4. These results predict that diverse habitats with mixed plant species should increase insect aggregation and increase population stability. In contrast, in open disturbed habitats or in regular plantations, where egg batches are more evenly distributed across high-quality hosts, populations should be more unstable, with site-wide outbreaks and extinctions being more common. 5. Mixed planting should be used on habitat regeneration sites to increase the population stability of immigrating or reintroduced insect species. Mixed planting also increases the diversity of resources, leading to higher herbivore species richness. With regard to the conservation of single species, different practices of habitat management will need to be employed depending on whether a project is concerned with methods of rapidly increasing the abundance of an endangered insect or concerned with the maintenance of a stable, established insect population that is perhaps endemic to an area. Suggestions for habitat management in these different cases are discussed. 6. Finally, intercropping can be highly effective in reducing pest outbreaks, although the economic gains of reduced pest attack may be outweighed by reduced crop yields in mixed-crop systems.
Personality traits of core self-evaluation as predictors on clinical decision-making in nursing profession

Core self-evaluation (CSE) is a theory that includes four personality dimensions: self-esteem, self-efficacy, locus of control and emotional stability. CSE proved to be a significant predictor of the research on cognitive, emotional and behavioral responses across various situations in the workplace. The aim of this study was to examine the relationship between personality traits of the core self-evaluation and clinical decision-making in nurses’ profession. A cross-sectional design was applied. Data was collected with standardized instruments: Core Self-Evaluation Scale and Clinical Decision-Making Nurses Scale, 584 nurses have participated in the study. Correlation and hierarchical regression analysis were used to test the relations and prediction of variables. The findings of the study revealed that there is a significant positive relationship between overall core self-evaluation and nurses’ clinical decision-making, and there is a significant contribution of self-esteem, self-efficacy and locus of control on all dimensions of clinical decision, especially in the area of canvassing of objectives and values. Nurses with high CSE have positive self-views and tend to be confident in their ability and they also feel in control while performing nursing interventions, whereas those with low CSE tend to have fewer accessible positive resources and are more prone to risk aversion.
Extended-Spectrum-β-Lactamase- and Plasmid AmpC-Producing Escherichia coli Causing Community-Onset Bloodstream Infection: Association of Bacterial Clones and Virulence Genes with Septic Shock, Source of Infection, and Recurrence

Invasive infections due to extended-spectrum-β-lactamase- and pAmpC-producing Escherichia coli (ESBL/pAmpC-EC) are an important cause of morbidity, often caused by the high-risk clone sequence type (ST131) and isolates classified as extraintestinal pathogenic E. coli (ExPEC). The relative influence of host immunocompetence versus microbiological virulence factors in the acquisition and outcome of bloodstream infections (BSI) is poorly understood. Herein, we used whole-genome sequencing on 278 blood culture isolates of ESBL/pAmpC-EC from 260 patients with community-onset BSI collected from 2012 to 2015 in Stockholm to study the association of virulence genes, sequence types, and antimicrobial resistance with severity of disease, infection source, ESBL/pAmpC-EC BSI low-risk patients, and patients with repeated episodes. ABSTRACT Invasive infections due to extended-spectrum-β-lactamase- and pAmpC-producing Escherichia coli (ESBL/pAmpC-EC) are an important cause of morbidity, often caused by the high-risk clone sequence type (ST131) and isolates classified as extraintestinal pathogenic E. coli (ExPEC). The relative influence of host immunocompetence versus microbiological virulence factors in the acquisition and outcome of bloodstream infections (BSI) is poorly understood. Herein, we used whole-genome sequencing on 278 blood culture isolates of ESBL/pAmpC-EC from 260 patients with community-onset BSI collected from 2012 to 2015 in Stockholm to study the association of virulence genes, sequence types, and antimicrobial resistance with severity of disease, infection source, ESBL/pAmpC-EC BSI low-risk patients, and patients with repeated episodes. ST131 subclade C2 comprised 29% of all patients. Factors associated with septic shock in multivariable analysis were patient host factors (hematologic cancer or transplantation and reduced daily living activity), presence of the E. coli virulence factor iss (increased serum survival), absence of phenotypic multidrug resistance, and absence of the genes pap and hsp. Adhesins, particularly pap, were associated with urinary tract infection (UTI) source, while isolates from post-prostate biopsy sepsis had a low overall number of virulence operons, including adhesins, and commonly belonged to ST131 clades A, B, and subclade C1, ST1193, and ST648. ST131 was associated with recurrent episodes. In conclusion, the most interesting finding is the association of iss with septic shock. Adhesins are important for UTI pathogenesis, while otherwise low-pathogenic isolates from the microbiota can cause post-prostate biopsy sepsis.
Developing a Multilayered Integrated Numerical Model of Surface Physics – Growing Plants Interaction (MINoSGI)

This paper describes a Multilayered Integrated Numerical Model of Surface Physics – Growing Plants Interaction (MINoSGI), which represents interactions between the dynamics of forest ecosystems and microclimate. Aiming at a large‐scale study in the future, we describe forest dynamics by using area‐averaged prognostic equations for thedistributions of plant density and plant weight with respect to plant height classes, instead of individual‐based treatments for small‐scale forest patches. Growth and mortality of plants are modelled based on the carbon balance of each plant height class. The area‐averaged microclimate (e.g., light, wind speed, temperature, humidity, CO2 concentration) within the forest canopy is simulated by a one‐dimensional multilayer canopy model, which includes most of the physical and physiological processes that control the forest microclimate. Owing to its multilayered framework, a direct specification is possible for the difference in the growing environment among plants of different size and species. Given hourly meteorological conditions, the model outputs energy, water, CO2 and momentum fluxes to and from a forest, of which the structure changes through competition among plants. The model's performance was tested by comparing its outputs with observed data on the development of plant size distribution taken over a 5‐year period in an evergreen coniferous (Cryptomeria japonica) forest. The model produced realistic estimates of the total biomass increments during the period. The ratio of net primary production to gross primary production (=0.45) was consistent with previous estimates for temperate forests. The bimodal seasonal pattern in net ecosystem production was similar to the seasonal trend in the CO2 flux measured over a forest of the same species. Although some limitations due to the one‐dimensional representation of microclimate were noticeable, the model adequately simulated distributions of annual growth rate, plant weight and diameter across plant height classes. Since the basic equations can be extended to include the effect of spatial variability with marginal increase of computational costs, the present model framework is feasible for large‐scale studies.