Miracle-dz/UniFAR-FTUs huggingface dataset:
New insights into the evolution of host specificity of three Penicillium species and the pathogenicity of P. Italicum involving the infection of Valencia orange (Citrus sinensis)

ABSTRACT Blue and green molds, the common phenotypes of post-harvest diseases in fruits, are mainly caused by Penicillium fungal species, including P. italicum, P. digitatum, and P. expansum. We sequenced and assembled the genome of a P. italicum strain, which contains 31,034,623 bp with 361 scaffolds and 627 contigs. The mechanisms underlying the evolution of host specificity among the analyzed Penicillium species were associated with the expansion of protein families, genome restructuring, horizontal gene transfer, and positive selection pressure. A dual-transcriptome analysis following the infection of Valencia orange (Citrus sinensis) by P. italicum resulted in the annotation of 9,307 P. italicum genes and 24,591 Valencia orange genes. The pathogenicity of P. italicum may be due to the activation of effectors, including 51 small secreted cysteine-rich proteins, 110 carbohydrate-active enzymes, and 12 G protein-coupled receptors. Additionally, 211 metabolites related to the interactions between P. italicum and Valencia orange were identified by gas chromatography-time of flight mass spectrography, three of which were further confirmed by ultra-high performance liquid chromatography triple quadrupole mass spectrometry. A metabolomics analysis indicated that P. italicum pathogenicity is associated with the sphingolipid and salicylic acid signaling pathways. Moreover, a correlation analysis between the metabolite contents and gene expression levels suggested that P. italicum induces carbohydrate metabolism in Valencia orange fruits as part of its infection strategy. This study provides useful information regarding the genomic determinants that drive the evolution of host specificity in Penicillium species and clarifies the host-plant specificity during the infection of Valencia orange by P. italicum. IMPORTANCE P. italicum GL_Gan1, a local strain in Guangzhou, China, was sequenced. Comparison of the genome of P. italicum GL_Gan1 with other pathogenic Penicillium species, P. digitatum and P. expansum, revealed that the expansion of protein families, genome restructuring, HGT, and positive selection pressure were related to the host range expansion of the analyzed Penicillium species. Moreover, gene gains or losses might be associated with the speciation of these Penicillium species. In addition, the molecular basis of host-plant specificity during the infection of Valencia orange (Citrus sinensis) by P. italicum was also elucidated by transcriptomic and metabolomics analysis. The data presented herein may be useful for further elucidating the molecular basis of the evolution of host specificity of Penicillium species and for illustrating the host-plant specificity during the infection of Valencia orange by P. italicum.
Spatial Distribution and Mortality of Helicoverpa spp. Pupae (Lepidoptera: Noctuidae) under Field Crops on the Darling Downs, Queensland

The spatial distribution and mortality of Helicoverpa punctigera (Wallengren) and H. armigera (Hübner) pupae were investigated under field crops on the Darling Downs, Queensland. Mean pupal depth was 47.3 mm for H. punctigera and 46.2 mm for H. armigera. For each species, the mean depth of male pupae was significantly greater than that of female pupae. In rain‐grown crops where distinct ridges were not formed for the plant rows, pupae were evenly distributed across the inter‐row space. Average pupal survival was 36.6% (range 11.8–70.2). Parasitism averaged 37.0% (range 8.2–61.9). Seven primary parasitoids and four hyperparasitoids were recorded from pupae. Predation by Agrypnus sp. larvae was recorded under sorghum. More intensive sampling of non‐diapausing, overwintering and spring diapausing pupal populations are warranted to further investigate mortality factors.
Batch preparation of gold nanoparticles with highly uniform morphology and tunable plasmonic properties

The plasmonic properties of individual metallic nanostructures are of great importance for application in surface science, materials science, and nanophotonics. Herein, being facilitated with a home-made flow device and pulsed laser irradiation, we proposed a batch preparation protocol towards spherical Au nanoparticles (Au NPs) and cage shell entrapped spherical core nanoparticles (Au@cAu NPs) with highly uniform morphology and a tunable size distribution. The Fano resonance behavior exhibited by the effective interaction between spherical Au NPs and the silicon surface has great potential for the design of ultrasensitive optical sensing devices. In comparison with the spherical Au NP, the individual Au@cAu NP displayed not only a red-shifted and broadened localized surface plasmon resonance (LSPR) scattering peak, but also a higher electromagnetic field enhancement. Therefore, the Au@cAu NPs offer a better choice for plasmonic enhancement-based applications in the red and near-infrared region. In general, the current work provides a new and easy method for the large-scale preparation of gold-based uniform nanostructures, and offers an avenue to understand the interference of different plasmon modes in plasmonic systems, which has potential applications in surface science.
Beta adrenoceptors mediate the catecholamine-induced stimulation of oxytocin secretion from cultured bovine granulosa cells

Bovine granulosa cells were treated in culture with alpha- and beta-adrenoceptor ligands to determine the receptor subtype mediating their response to catecholamines. The secretion of oxytocin by granulosa cells in serum-free medium was measured on the fourth day of culture (during the period of acquisition of a luteal phenotype). Cultures were performed in the presence of 0.5 mM ascorbic acid, which increased hormone output and potentiated the response to catecholamines. The effects of adrenaline and noradrenaline on oxytocin secretion were concentration-dependent; maximum stimulation was over 700% with adrenalin (EC50 92 nM) and 500% with noradrenaline (EC50 87 nM). The response to noradrenaline (10(-6) M) and adrenaline (10(-6) M) could be blocked by propranolol but not by phentolamine, suggesting that beta- rather than alpha-adrenoceptors were involved. Blockade by metoprolol and practolol (beta 1-adrenoceptor antagonists) was poor and dobutamine (beta 1-agonist) was weakly stimulatory. A concentration-dependent stimulatory response (EC50 200 nM) was obtained with salbutamol (beta 2-adrenoceptor agonist) and stimulation by adrenaline or salbutamol could be blocked by a selective beta 2-adrenoceptor antagonist (ICI 118,551). It is concluded that, during luteinization, the long-term response of bovine granulosa cells to stimulation induced by catecholamines is mediated through beta- rather than alpha-adrenoceptors. Although the beta 2-subtype is probably involved, the similar potencies of adrenaline and noradrenaline are uncharacteristic of beta 2-adrenoceptors and may be peculiar to the long-term response shown by these cells.
Management of SARS-CoV-2 infection: recommendations of the Polish Association of Epidemiologists and Infectiologists. Annex no. 2 as of October 13, 2020.

Diagnostic recommendations Preliminary remarks Testing of potentially infectious material (swabs from the upper or lower airways including pha‐ ryngeal, nasopharyngeal, and nasal swabs, sam‐ ples of sputum, saliva, and bronchopulmonary washing) regardless of the test used (molecular, antigen, or serological) should be performed in strict compliance with the epidemiological safety procedures to minimize the risk of transmitting infection to the staff. The results of molecular and antigen tests do not determine the repli‐ cation activity or infectivity of SARS ‐CoV ‐2, so the periods of infectivity should be defined on the basis of in vitro tests and not the results of diagnostic tests. There are no firm data available regarding the period of infectivity in immuno‐ deficient individuals and it may be prolonged.14
Serum Type XIX Collagen is Significantly Elevated in Non-Small Cell Lung Cancer: A Preliminary Study on Biomarker Potential

Type XIX collagen is a poorly characterized collagen associated with the basement membrane. It is abnormally regulated during breast cancer progression and the NC1 (XIX) domain has anti-tumorigenic signaling properties. However, little is known about the biomarker potential of collagen XIX in cancer. In this study, we describe a competitive ELISA, named PRO-C19, targeting the C-terminus of collagen XIX using a monoclonal antibody. PRO-C19 was measured in serum of patients with a range of cancer types and was elevated in non-small cell lung cancer (NSCLC) (p < 0.0001), small cell lung cancer (p = 0.0081), breast (p = 0.0005) and ovarian cancer (p < 0.0001) compared to healthy controls. In a separate NSCLC cohort, PRO-C19 was elevated compared to controls when evaluating adenocarcinoma (AD) (p = 0.0003) and squamous cell carcinoma (SCC) (p < 0.0001) patients but was not elevated in chronic obstructive pulmonary disease patients. SCC also had higher PRO-C19 levels than AD (p = 0.0457). PRO-C19 could discriminate between NSCLC and healthy controls (AUROC:0.749 and 0.826 for AD and SCC, respectively) and maintained discriminatory performance in patients of tumor stages I+II (AUROC:0.733 and 0.818 for AD and SCC, respectively). Lastly, we confirmed the elevated type XIX collagen levels using gene expression data from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) initiatives. In conclusion, type XIX collagen is released into circulation and is significantly elevated in the serum of cancer patients and PRO-C19 shows promise as a cancer biomarker.
Is ABO blood group a risk or prognostic factor for patients with endometrioid endometrial cancer? A retrospective analysis in Germany.

BACKGROUND A relationship is known to exist between gastric and pancreatic cancers and ABO antigens, caused by various immune modulations related to the ABO blood group of the patient. A similar relationship with regard to gynaecological cancers remains controversial. MATERIALS AND METHODS Patients who underwent surgery for endometrioid endometrial cancer in International Federation of Gynaecology and Obstetrics (FIGO) stage I, II, III or IV from 2006 to 2018 were identified. The research explored the existence of a relationship between the patients' blood group or Rhesus factor and the incidence of endometrial cancer, grade (G1, G2, G3), FIGO stage, nodal status, recurrence, menopausal status, parity, and body mass index. Statistical methods such as the chi-square test, analysis of variance and the Scheffé post-hoc test were used. RESULTS Two hundred and two patients with endometrioid endometrial cancer were included: 96 had blood group A, 19 blood group B, 75 blood group 0, and 12 had blood group AB. This distribution corresponds to the general blood group distribution in Germany. The vast majority of the dependent variables, such as grade, FIGO stage, nodal status or recurrence were not significantly associated with ABO blood group or Rhesus factor status. The relative frequencies of G1 and G3 endometrial cancers with respect to blood group were similar. Menopausal status, parity, and body mass index were not related to more advanced FIGO stages at initial diagnosis or to ABO blood group. DISCUSSION Blood group screening would probably not be helpful in the diagnosis of endometrioid endometrial carcinomas in early stages compared to the current gold standard. Furthermore, a specific blood group does not increase either the risk of recurrence or the risk of a dedifferentiated type of endometrial carcinoma.
Unregulated Sphingolipid Biosynthesis in Gene-Edited Arabidopsis ORM Mutants Results in Nonviable Seeds with Strongly Reduced Oil Content[OPEN]

Removing the regulation of sphingolipid biosynthesis by completely knocking out Orosomucoid-like protein (ORM) genes results in ceramide hyperaccumulation and nonviable seeds with strongly reduced oil content. Orosomucoid-like proteins (ORMs) interact with serine palmitoyltransferase (SPT) to negatively regulate sphingolipid biosynthesis, a reversible process critical for balancing the intracellular sphingolipid levels needed for growth and programmed cell death. Here, we show that ORM1 and ORM2 are essential for life cycle completion in Arabidopsis (Arabidopsis thaliana). Seeds from orm1−/− orm2−/− mutants, generated by crossing CRISPR/Cas9 knockout mutants for each gene, accumulated high levels of ceramide, indicative of unregulated sphingolipid biosynthesis. orm1−/− orm2−/− seeds were nonviable, displayed aberrant embryo development, and had >80% reduced oil content versus wild-type seeds. This phenotype was mimicked in Arabidopsis seeds expressing the SPT subunit LCB1 lacking its first transmembrane domain, which is critical for ORM-mediated regulation of SPT. We identified a mutant for ORM1 lacking one amino acid (Met-51) near its second transmembrane domain that retained its membrane topology. Expressing this allele in the orm2 background yielded plants that did not advance beyond the seedling stage, hyperaccumulated ceramides, and showed altered organellar structures and increased senescence- and pathogenesis-related gene expression. These seedlings also showed upregulated expression of genes for sphingolipid catabolic enzymes, pointing to additional mechanisms for maintaining sphingolipid homeostasis. ORM1 lacking Met-51 had strongly impaired interactions with LCB1 in a yeast (Saccharomyces cerevisiae) model, providing structural clues about regulatory interactions between ORM and SPT.
Tunnel geometry of the subterranean termite Reticulitermes grassei (Isoptera: Rhinotermitidae) in response to sand bulk density and the presence of food

The cryptic habits of subterranean termites restricts detailed analysis of their foraging patterns in situ, but the process is evidently dominated by tunnel constructions connecting the nest with woody resources discovered within the territory of each colony. In this study, tunnel formation and orientation were studied experimentally in the termite Reticulitermes grassei (Clément), using 2‐dimensional laboratory foraging arenas containing fine sand as the substratum. The building of exploratory tunnels over a 10‐day period and the geometry of the resulting network are described. Fractal analysis showed that tunnel geometry had a fractal dimension, regardless of the total length tunnelled whether foragers encountered the food source or not. The bulk density of the sand in the arenas affected the distances tunnelled, with higher density reducing construction, but did not affect tunnel geometry. Tunnels were not discernibly orientated with respect to the positioning of the food source, even in a situation where termites had failed to find the food source at a distance of less than 50 mm, suggesting that volatiles from wood are not attractants.
Clinical outcomes of nonvitamin K oral anticoagulants and acenocoumarol for stroke prevention in contemporary practice: A population‐based propensity‐weighted cohort study

Acenocoumarol is a vitamin‐K antagonist (VKA) primarily used in certain countries (e.g. India, Netherlands, Spain). The half‐life of acenocoumarol is similar to that of non‐VKA oral anticoagulants (NOAC), unlike warfarin, and this could affect comparative effectiveness and safety (CES). However, data on CES for NOAC come almost exclusively from studies using warfarin as the comparator. We aimed to assess outcomes of NOAC and acenocoumarol in people with non‐valvular atrial fibrillation (NVAF) in real‐world clinical practice.
Dissecting the cognitive phenotype of post‐stroke fatigue using computerized assessment and computational modeling of sustained attention

Post‐stroke fatigue (PSF) is prevalent among stroke patients, but its mechanisms are poorly understood. Many patients with PSF experience cognitive difficulties, but studies aiming to identify cognitive correlates of PSF have been largely inconclusive. With the aim of characterizing the relationship between subjective fatigue and attentional function, we collected behavioral data using the attention network test (ANT) and self‐reported fatigue scores using the fatigue severity scale (FSS) from 53 stroke patients. In order to evaluate the utility and added value of computational modeling for delineating specific underpinnings of response time (RT) distributions, we fitted a hierarchical drift diffusion model (hDDM) to the ANT data. Results revealed a relationship between fatigue and RT distributions. Specifically, there was a positive interaction between FSS score and elapsed time on RT. Group analyses suggested that patients without PSF increased speed during the course of the session, while patients with PSF did not. In line with the conventional analyses based on observed RT, the best fitting hDD model identified an interaction between elapsed time and fatigue on non‐decision time, suggesting an increase in time needed for stimulus encoding and response execution rather than cognitive information processing and evidence accumulation. These novel results demonstrate the significance of considering the sustained nature of effort when defining the cognitive phenotype of PSF, intuitively indicating that the cognitive phenotype of fatigue entails an increased vulnerability to sustained effort, and suggest that the use of computational approaches offers a further characterization of specific processes underlying behavioral differences.
Perceptions, Experiences, and Outcomes of Lactation Support in the Workplace: A Systematic Literature Review

Background Despite legislation requiring break time and a private space to express milk, variations exist in accommodations for breastfeeding employees in the United States. Research Aims We aimed to describe employee and employer perceptions of and experiences with workplace lactation support in the United States and to identify research needed to inform workplace lactation support programs. Methods We searched Academic Search Complete, Business Search Complete, CINAHL, MEDLINE, PubMed, and PsycInfo for peer-reviewed articles published from 2009 to 2019 (n = 1638). We included 27 articles. Studies were categorized into four non-exclusive themes: (a) employee perceptions of and experiences with workplace lactation support; (b) employer reports of workplace lactation support; (c) association between workplace lactation support and business outcomes; and (d) association between workplace lactation support and breastfeeding outcomes. Results Analyses of associations between lactation support at work and employee breastfeeding outcomes (n = 14, 52%), and employee perceptions of and experiences with lactation support at work (n = 14, 52%) were most common, followed by employer reports of lactation support (n = 3, 11%) and associations between lactation support at work and job satisfaction (n = 3, 11%). Results indicated that workplace lactation support varied by employer, and that employee perceptions of and experiences with workplace lactation support varied by demographic and employment characteristics. The use of cross-sectional designs, unvalidated instruments, and limited representation from women with low incomes and minorities were common study limitations. Conclusions More research is needed to learn about experiences of employers and low-income and minority women with workplace lactation support and associations with business-relevant outcomes.
Coping with adversity: physical activity as a moderator in adaption to bereavement.

BACKGROUND The adaption of individuals to adverse life events such as bereavement which reduce their subjective well-being is referred to as the hedonic treadmill. This study examined whether previous physical activity moderates the negative impact of bereavement on subjective well-being and how quickly such adaption occurs. METHODS The analysis uses data from 13 waves (1996-2015) of the German Socio-Economic Panel (n = 139 097). Subjective well-being is captured with respondents' life satisfaction. Individual fixed effects regression models with three-wave lagged effects and interaction effects for bereavement and previous physical activity were estimated for females and males. RESULTS The significant reduction in life satisfaction is partly offset for individuals who were physically active prior to the adversity, suggesting moderation effects of previous physical activity. These effects are larger in absolute value for females, but females also suffered more severely from bereavement. Males' partial adaption through previous physical activity is closer to the pre-event level, while females adapt earlier. More frequent previous physical activity allows both genders to partially adapt more. CONCLUSIONS Previous physical activity helps individuals suffering bereavement to partially adapt faster to such adversity, suggesting that physical activity accelerates the hedonic treadmill, though at a different pace for each gender.
The effect of protein level on the performance of dwarf and normal crossbred layers

Dwarf and normal crossbred layers from Australorp dams by White Leghorn sires that were heterozygous for a sex-linked recessive dwarfing gene were compared at four protein levels (15, 17, 18 and 19 per cent). Relative to normal birds, dwarfs laid 19.1 per cent fewer eggs at 11.2 per cent lighter egg weight to give a reduction of 28.0 per cent in average egg mass per bird. Dwarfs consumed 28.2 per cent less feed than their normal relatives but showed no difference in the conversion of feed to eggs. Analyses of the effect of protein level of the rations, which included a wider range of protein levels than those used in the comparison of dwarfs and normals, showed that both genotypes had similar responses to increased protein level with, in general, no significant responses in production characters past a level of about 17 per cent protein.
Impaired T cell responses in domestic pigs and wild boar upon infection with a highly virulent African swine fever virus strain.

Since African swine fever (ASF) first appeared in the Caucasus region in 2007, it has spread rapidly and is now present in numerous European and Asian countries. In Europe, mainly wild boar populations are affected and pose a risk for domestic pigs. In Asia, domestic pigs are almost exclusively affected. An effective and safe vaccine is not available, and correlates of protection are far from being understood. Therefore, research on immune responses, immune dysfunction, and pathogenesis is mandatory. It is acknowledged that T cells play a pivotal role. Thus, we investigated T cell responses of domestic pigs and wild boar upon infection with the highly virulent ASF virus (ASFV) strain "Armenia08". For this purpose, we used a flow cytometry-based multicolor analysis to identify T cell subtypes (cytotoxic T cells, T-helper cells, γʂ T cells) and their functional impairment in ASFV infected pigs. Domestic pigs showed lymphopenia and neither in the blood nor in the lymphoid organs was a proliferation of CD8+ effector cells observed. Furthermore, a T-bet-dependent activation of the remaining CD8 T cells did not occur. In contrast, a T cell response could be observed in wild boar at 5 days post inoculation in the blood and in tendency also in some organs. However, this cytotoxic response was not beneficial as all wild boars showed a severe acute lethal disease and a higher proportion died spontaneously or was euthanized at the humane endpoint.