Miracle-dz/UniFAR-FTUs huggingface dataset:
Emergence of Hypervirulent ST11-K64 Klebsiella pneumoniae Poses a Serious Clinical Threat in Older Patients

The carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKP) poses a severe therapeutic challenge to global public health, and research on CR-hvKP in older patients remain limited. In this study, we aimed to investigate the clinical and molecular characteristics and risk factors of CR-hvKP infections in older patients. We retrospectively investigated older patients with carbapenem-resistant Klebsiella pneumoniae (CRKP) infections in the intensive care unit (ICU) between January 2020 and December 2020. The clinical data, and microbiological data including antimicrobial susceptibility testing, phenotype experiment and detection of carbapenemases, string test, virulence genes, capsular serotype-specific (cps) genes, and multilocus sequence typing, of the CR-hvKP group defined by the presence of any one of the virulence genes, including rmpA, rmpA2, iucA, iroN, and peg-344 were compared with those of CR-non-hvKP strains. Of the 80 CRKP strains, 51 (63.8%) met the definition of CR-hvKP. The main mechanism of resistance to carbapenems was the presence of the blaKPC−2 gene. Sequence type (ST)11 (81.3%, 65/80) and ST15 (16.3%, 13/80) were the most common STs in CRKP strains. The minimum inhibitory concentration (MIC)50 values of the CR-hvKP group against the six tested antibiotics (ceftazidime, ceftazidime-avibactam, imipenem-avibactam, tigecycline, levofloxacin, and Cefoperazone-Sulbactam) exhibited elevated levels than the CR-non-hvKP group. Ceftazidime and imipenem by combining avibactam (4 μg/mL) significantly decreased the MIC90 values more than 16-fold than ceftazidime and imipenem alone against Klebsiella pneumoniae carbapenemase (KPC)-2-producing K. pneumoniae. Cardiovascular disease [odds ratio (OR) = 11.956] and ST11-K64 (OR = 8.385) appeared to be independent variables associated with CR-hvKP infection by multivariate analysis. In conclusion, higher MICs of the last line antibiotic agents (ceftazidime-avibactam, tigecycline) might be a critical consideration in the clinical management of older patients where the concentration of these toxic antibiotics matters because of underlying comorbidities. Caution regarding KPC-2-producing ST11-K64 CR-hvKP as being new significant “superbugs” is required as they are widespread, and infection control measures should be strengthened to curb further dissemination in nosocomial settings in China.
Characteristics of Exogenous Allergen in Breast Milk and Their Impact on Oral Tolerance Induction

Food allergy is a common health problem in childhood since its prevalence was estimated to range from 6. 5 to 24.6% in European countries. Recently, a lot of research has focused on the impact of breastfeeding on oral tolerance induction. Since it was found that breast milk contains immunologically active food antigens, it would be very helpful to clarify the factors of antigen shedding that promotes oral tolerance. This narrative review aimed to summarize the latest evidence from experimental and human studies regarding allergen characteristics in human milk that may influence oral tolerance induction. A literature search in PubMed, MEDLINE, and Google Scholar was conducted. The diet of the mother was found to have a direct impact on allergen amount in the breastmilk, while antigens had different kinetics in human milk between women and depending on the antigen. The mode of antigen consumption, such as the cooking of an antigen, may also affect the allergenicity of the antigen in human milk. The dose of the antigen in human milk is in the range of nanograms per milliliter; however, it was found to have a tolerogenic effect. Furthermore, the presence of antigen-specific immunoglobulins, forming immune complexes with antigens, was found more tolerogenic compared to free allergens in experimental studies, and this is related to the immune status of the mother. While examining available data, this review highlights gaps in knowledge regarding allergen characteristics that may influence oral tolerance.
Phenotypic and Methylome Responses to Salt Stress in Arabidopsis thaliana Natural Accessions

Salt stress threatens plant growth, development and crop yields, and has become a critical global environmental issue. Increasing evidence has suggested that the epigenetic mechanism such as DNA methylation can mediate plant response to salt stress through transcriptional regulation and transposable element (TE) silencing. However, studies exploring genome-wide methylation dynamics under salt stress remain limited, in particular, for studies on multiple genotypes. Here, we adopted four natural accessions of the model species Arabidopsis thaliana and investigated the phenotypic and genome-wide methylation responses to salt stress through whole-genome bisulfite sequencing (WGBS). We found that salt stress significantly changed plant phenotypes, including plant height, rosette diameter, fruit number, and aboveground biomass, and the change in biomass tended to depend on accessions. Methylation analysis revealed that genome-wide methylation patterns depended primarily on accessions, and salt stress caused significant methylation changes in ∼ 0.1% cytosines over the genomes. About 33.5% of these salt-induced differential methylated cytosines (DMCs) were located to transposable elements (TEs). These salt-induced DMCs were mainly hypermethylated and accession-specific. TEs annotated to have DMCs (DMC-TEs) across accessions were found mostly belonged to the superfamily of Gypsy, a type II transposon, indicating a convergent DMC dynamic on TEs across different genetic backgrounds. Moreover, 8.0% of salt-induced DMCs were located in gene bodies and their proximal regulatory regions. These DMCs were also accession-specific, and genes annotated to have DMCs (DMC-genes) appeared to be more accession-specific than DMC-TEs. Intriguingly, both accession-specific DMC-genes and DMC-genes shared by multiple accessions were enriched in similar functions, including methylation, gene silencing, chemical homeostasis, polysaccharide catabolic process, and pathways relating to shifts between vegetative growth and reproduction. These results indicate that, across different genetic backgrounds, methylation changes may have convergent functions in post-transcriptional, physiological, and phenotypic modulation under salt stress. These convergent methylation dynamics across accession may be autonomous from genetic variation or due to convergent genetic changes, which requires further exploration. Our study provides a more comprehensive picture of genome-wide methylation dynamics under salt stress, and highlights the importance of exploring stress response mechanisms from diverse genetic backgrounds.
Effect of Velocity and Contact Stress Area on the Dynamic Behavior of the Spinal Cord Under Different Testing Conditions

Knowledge of the dynamic behavior of the spinal cord under different testing conditions is critical for our understanding of biomechanical mechanisms of spinal cord injury. Although velocity and contact stress area are known to affect external mechanical stress or energy upon sudden traumatic injury, quantitative investigation of the two clinically relevant biomechanical variables is limited. Here, freshly excised rat spinal-cord–pia-arachnoid constructs were tested through indentation using indenters of different sizes (radii: 0.25, 0.50, and 1.00 mm) at various loading rates ranging from 0.04 to 0.20 mm/s. This analysis found that the ex vivo specimen displayed significant nonlinear viscoelasticity at <10% of specimen thickness depth magnitudes. At higher velocity and larger contact stress area, the cord withstood a higher peak load and exhibited more sensitive mechanical relaxation responses (i.e., increasing amplitude and speed of the drop in peak load). Additionally, the cord became stiffer (i.e., increasing elastic modulus) and softer (i.e., decreasing elastic modulus) at a higher velocity and larger contact stress area, respectively. These findings will improve our understanding of the real-time complex biomechanics involved in traumatic spinal cord injury.
Neutrophils Require Activation to Express Functional Cell-Surface Complement Receptor Immunoglobulin

The phagocytosis-promoting complement receptor, Complement Receptor Immunoglobulin (CRIg), is exclusively expressed on macrophages. It has been demonstrated that expression in macrophages could be modulated by inflammatory mediators, including cytokines. This raised the possibility that a major phagocyte, the neutrophil, may also express CRIg following activation with inflammatory mediators. Here we show that resting peripheral blood neutrophil lysates subjected to protein analysis by Western blot revealed a 35 kDa CRIg isoform, consistent with the expression of CRIg mRNA by RT-PCR. By flow cytometry, CRIg was detected intracellularly and in very minor amounts on the cell surface. Interestingly, expression on the cell surface was significantly increased to functional levels after activation with inflammatory mediators/neutrophil activators; N-Formylmethionine-leucyl-phenylalanine, tumor necrosis factor (TNF), Granulocyte-Macrophage Colony stimulating Factor (GM-CSF), bacterial lipopolysaccharide, leukotriene B4 and phorbol myristate acetate. The increase in expression required p38 MAP kinase and protein kinase C activation, as well as intracellular calcium. Neutrophils which were defective in actin microfilament reorganization due to a mutation in ARPC1B or inhibition of its upstream regulator, Rac2 lose their ability to upregulate CRIg expression. Inhibition of another small GTPase, Rab27a, with pharmacological inhibitors prevented the increase in CRIg expression, suggesting a requirement for the actin cytoskeleton and exocytosis. Engagement of CRIg on TNF-primed neutrophils with an anti-CRIg monoclonal antibody increased the release of superoxide and promoted the activation of p38 but not ERK1/ERK2 or JNK MAP kinases. The TNF-induced increase in killing of Staphylococcus aureus was blocked by the anti-CRIg antibody. Adding to the anti-microbial role of CRIg, it was found that GM-CSF priming lead to the release of neutrophil extracellular traps. Interestingly in contrast to the above mediators the anti-inflammatory cytokine IL-10 caused a decrease in basal expression and GM-CSF induced increase in CRIg expression. The data demonstrate that neutrophils also express CRIg which is regulated by inflammatory mediators and cytokines. The findings show that the neutrophil antimicrobial function involving CRIg requires priming as a means of arming the cell strategically with microbial invasion of tissues and the bloodstream.
Investigating the Clinico-Molecular and Immunological Evolution of Lung Adenocarcinoma Using Pseudotime Analysis

Introduction As the molecular features of lung adenocarcinoma (LUAD) have been evaluated as a cross-sectional study, the course of tumor characteristics has not been modeled. The temporal evolution of the tumor immune microenvironment (TIME), as well as the clinico-molecular features of LUAD, could provide a precise strategy for immunotherapy and surrogate biomarkers for the course of LUAD. Methods A pseudotime trajectory was constructed in patients with LUAD from the Cancer Genome Atlas and non-small cell lung cancer radiogenomics datasets. Correlation analyses were performed between clinical features and pseudotime. Genes associated with pseudotime were selected, and gene ontology analysis was performed. F-18 fluorodeoxyglucose positron emission tomography images of subjects were collected, and imaging parameters, including standardized uptake value (SUV), were obtained. Correlation analyses were performed between imaging parameters and pseudotime. Correlation analyses were performed between the enrichment scores of various immune cell types and pseudotime. In addition, correlation analyses were performed between the expression of PD-L1, tumor mutation burden, and pseudotime. Results Pseudotime trajectories of LUAD corresponded to clinical stages. Molecular profiles related to cell division and natural killer cell activity were changed along the pseudotime. The maximal SUV of LUAD tumors showed a positive correlation with pseudotime. Type 1 helper T (Th1) cells showed a positive correlation, whereas M2 macrophages showed a negative correlation with pseudotime. PD-L1 expression showed a negative correlation, whereas tumor mutation burden showed a positive correlation with pseudotime. Conclusion The estimated pseudotime associated with the stage suggested that it could reflect the clinico-molecular evolution of LUAD. Specific immune cell types in the TIME as well as cell division and glucose metabolism were dynamically changed according to the progression of the pseudotime. As a molecular progression of LUAD, different cellular targets should be considered for immunotherapy.
Adjustment Processes After the First Wave of the COVID-19 Pandemic: A Grounded Theory Study Based on Clinical Psychologists’ Experience

Background Anxiety, depression, and post-traumatic stress have been reported among the general population during the first wave of the COVID-19 pandemic. However, the adjustment after the emergency phase remains under-investigated. This study aims to understand the adjustment processes of the population after the emergency phase of the pandemic. Methods We conducted a grounded theory based on the experience of 24 clinical psychologists who provided extensive support to the population during the pandemic in different Italian regions. Three online focus groups were conducted. The transcripts of the focus groups were analyzed through a process of open, axial, and selective coding. Data collection terminated once thematic saturation was reached. Results Repositioning emerged as the evolutionary task people were confronted with in the face of a New Reality. Repositioning meant dealing with and integrating unpleasant Emotional Experiences deriving from the lockdown and reopening (i.e., unsafety, emotional exhaustion, loneliness, uncertainty, loss, and disconnection) through different Coping Strategies. Repositioning was facilitated or hindered by contextual and individual Intervening Conditions and led to two Adjustment Outcomes: growth or block. Conclusion Results suggest that repositioning was the core task people had to face after the emergency phase of COVID-19. Proactive psychological interventions may support the population in repositioning in order to prevent maladjustment and encourage post-traumatic growth.
Clinical Outcomes of Negative Balloon-Assisted Enteroscopy for Obscure Gastrointestinal Bleeding: A Systematic Review and Meta-Analysis

Background For patients with obscure gastrointestinal bleeding (OGIB), finding the bleeding site is challenging. Balloon-assisted enteroscopy (BAE) has become the preferred diagnostic modality for OGIB. The long-term outcome of patients with negative BAE remains undefined. The present study aimed to evaluate the long-term outcomes of patients with negative BAE results for OGIB and to clarify the effect of further investigations at the time of rebleeding with a systematic review and meta-analysis of the available cohort studies. Methods Studies were searched through the PubMed, EMBASE, and Cochrane library databases. The following indexes were analyzed: rebleeding rate after negative BAE, rebleeding rate after different follow-up periods, the proportion of patients who underwent further evaluation after rebleeding, the percentage of patients with identified rebleeding sources, and the percentage of patients with rebleeding sources in the small intestine. Heterogeneity was assessed using the I2 test. Results Twelve studies that involved a total of 407 patients were included in the analysis. The pooled rebleeding rate after negative BAE for OGIB was 29.1% (95% CI: 17.2–42.6%). Heterogeneity was significant among the studies (I2 = 88%; p < 0.0001). The Chi-squared test did not show a difference in rebleeding rates between the short and long follow-up period groups (p = 0.142). The pooled proportion of patients who underwent further evaluation after rebleeding was 86.1%. Among the patients who underwent further evaluation, rebleeding sources were identified in 73.6% of patients, and 68.8% of the identified rebleeding lesions were in the small intestine. Conclusion A negative result of BAE in patients with OGIB indicates a subsequently low risk of rebleeding. Further evaluation should be considered after rebleeding.
Deep Genomic Divergence and Phenotypic Admixture of the Treefrog Dendropsophus elegans (Hylidae: Amphibia) Coincide With Riverine Boundaries at the Brazilian Atlantic Forest

The Atlantic Forest (AF) domain is one of the Earth’s biodiversity hotspots, known for its high levels of species diversity and endemism. Factors related to palaeoenvironmental dynamics, such as the establishment of vegetational refugia and river basins, have different impacts on biological communities and biodiversity patterns in this domain. Here, we sample genome-wide RADseq data from a widespread treefrog (Dendropsophus elegans), inhabiting natural and human-impacted ecosystems at the Brazilian AF to test the impact of riverine boundaries and climatic refugia on population structure and diversification. We estimate divergence times and migration rate across identified genetic breaks related to the rivers Doce, Paraíba do Sul, Ribeira de Iguape, and Paraguaçu, known to represent barriers to gene flow for other AF endemic species, and test the role of climatic refugia. Finally, we investigate the impact of spatio-temporal population history on morphological variation in this species. We recovered a phylogeographic history supporting three distinct clades separated into two geographically structured populations, corresponding to the north and south of AF. In addition, we identified an admixture zone between north and south populations in the latitude close to the Doce River. Our findings support a pattern of isolation-by-distance and the existence of a secondary contact zone between populations, which might have been promoted by gene flow during population expansion. Further, we found support for models considering migration parameters for all the tested rivers with different population divergence times. Based on the species history and the AF palaeoenvironmental dynamics, we corroborate the role of forest refugia impacting population structure for this species through recent range expansion after the Last Glacial Maximum (LGM). The Doce and Paraíba do Sul Rivers coincide with the main genetic breaks, suggesting they might also have played a role in the diversification processes. Finally, despite finding subtle correlations for phenotypic data among different populations, variation is not strongly detectable and does not seem associated with speciation-level processes that could warrant taxonomic changes. Such results can be explained by phenotypic plasticity of the evaluated traits and by recent divergence times, where there has been insufficient time and weak selective pressures to accumulate enough phenotypic differences.
Beyond English: Considering Language and Culture in Psychological Text Analysis

The paper discusses the role of language and culture in the context of quantitative text analysis in psychological research. It reviews current automatic text analysis methods and approaches from the perspective of the unique challenges that can arise when going beyond the default English language. Special attention is paid to closed-vocabulary approaches and related methods (and Linguistic Inquiry and Word Count in particular), both from the perspective of cross-cultural research where the analytic process inherently consists of comparing phenomena across cultures and languages and the perspective of generalizability beyond the language and the cultural focus of the original investigation. We highlight the need for a more universal and flexible theoretical and methodological grounding of current research, which includes the linguistic, cultural, and situational specifics of communication, and we provide suggestions for procedures that can be implemented in future studies and facilitate psychological text analysis across languages and cultures.
The link between corporate governance and sustainability: Evidence from the oil and gas industry

This study sought to investigate the link between corporate governance and sustainability in oil and gas firms across two countries. Sustainability was conceptualized as including three firm obligations: (1) economic performance; (2) social responsiveness; and (3) environmental quality. Using archival data from 53 Australian and 65 Canadian oil and gas companies from 2004, we found that Australian firms were more socially responsive while Canadian firms demonstrated higher levels of environmental quality. Board size was a significant predictor of social responsiveness and environmental quality for Australian firms, whereas none of the corporate governance variables provided explanations for the sustainability levels of Canadian firms.
Experimental study of heat transfer and flow friction characteristics of automotive evaporators

An experimental study on two brazed aluminum serpentine evaporators was carried out in a forced-circulation wind tunnel These two heat exchangers were made of flat tubes with internal membranes and with louver fins on the air side. Although these serpentine evaporators have been widely used in the automotive industry, few performance data are available in the open literature. In the present investigation, the performance characteristics of the coils in the dimensionless Colburn j factor and the friction factor (f) are presented.
Predicting Regeneration in Appalachian Hardwood Stands Using the REGEN Expert System

A study was initiated to adapt the REGEN regeneration prediction model to the Appalachians of Virginia and West Virginia. REGEN generates predictions via expert created REGEN knowledge bases (RKBs) that contain competitive rankings and stochastic parameters for selected species and size classes of advance reproduction. We developed RKBs for four site productivity classes (xeric, subxeric, submesic, mesic), and tested two (subxeric and submesic) using field collected inventory data in this study. To test the model we collected data from 48 paired sites which contained a mature stand and an adjacent regenerating stand (clearcut) of similar site productivity harvested within the past 20 years. Across all 48 sites, model predictions were within 5% of measured values on average, and explained 32% (R 2 = 0.32) of the variation in species composition in regenerating stands. The species compositions of 41 of the paired stands on the Appalachian Plateau in West Virginia were further analyzed to compare species composition. Species composition was compared between the mature and regenerating stands in the subxeric and submesic site classes. A comparison of the upper canopy (dominant and codominant) species composition in regenerating stands to that of all stems ≥ 1.5 in dbh in the mature stands was conducted as well. Our results suggest that the future species composition of stands regenerating following clearcut harvests will likely differ from previous rotations with mesophytic, shade intolerant species being more numerous. Oaks will likely assume a smaller role as the clearcuts mature, particularly on the submesic sites.