Miracle-dz/UniFAR-FTUs huggingface dataset:
Rhinovirus Infection Drives Complex Host Airway Molecular Responses in Children With Cystic Fibrosis

Early-life viral infections are responsible for pulmonary exacerbations that can contribute to disease progression in young children with cystic fibrosis (CF). The most common respiratory viruses detected in the CF airway are human rhinoviruses (RV), and augmented airway inflammation in CF has been attributed to dysregulated airway epithelial responses although evidence has been conflicting. Here, we exposed airway epithelial cells from children with and without CF to RV in vitro. Using RNA-Seq, we profiled the transcriptomic differences of CF and non-CF airway epithelial cells at baseline and in response to RV. There were only modest differences between CF and non-CF cells at baseline. In response to RV, there were 1,442 and 896 differentially expressed genes in CF and non-CF airway epithelial cells, respectively. The core antiviral responses in CF and non-CF airway epithelial cells were mediated through interferon signaling although type 1 and 3 interferon signaling, when measured, were reduced in CF airway epithelial cells following viral challenge consistent with previous reports. The transcriptional responses in CF airway epithelial cells were more complex than in non-CF airway epithelial cells with diverse over-represented biological pathways, such as cytokine signaling and metabolic and biosynthetic pathways. Network analysis highlighted that the differentially expressed genes of CF airway epithelial cells' transcriptional responses were highly interconnected and formed a more complex network than observed in non-CF airway epithelial cells. We corroborate observations in fully differentiated air–liquid interface (ALI) cultures, identifying genes involved in IL-1 signaling and mucin glycosylation that are only dysregulated in the CF airway epithelial response to RV infection. These data provide novel insights into the CF airway epithelial cells' responses to RV infection and highlight potential pathways that could be targeted to improve antiviral and anti-inflammatory responses in CF.
Zhen-Wu-Tang Protects IgA Nephropathy in Rats by Regulating Exosomes to Inhibit NF-κB/NLRP3 Pathway

Immunoglobulin A nephropathy (IgAN) is one of the most frequent kinds of primary glomerulonephritis characterized by IgA immune complexes deposition and glomerular proliferation. Zhen-wu-tang (ZWT), a well-known traditional Chinese formula has been reported to ameliorate various kidney diseases. However, its pharmacological mechanism remains unclear. Exosomes have been described in diverse renal diseases by mediating cellular communication but rarely in the IgAN. The purpose of the present study is to explore whether the underlying mechanisms of the effect of ZWT on IgAN is correlated to exosomes. Our results demonstrated that in human renal tubular epithelial cells (HK-2) stimulated by lipopolysaccharide, exosomes are obviously released after ZWT-containing serum treatment especially with 10% ZWT. In addition, once released, HK-2-derived exosomes were uptaked by human mesangial cells (HMC), which impeded the activation of NF-κB/NLRP3 signaling pathway to exert anti-inflammatory effects in a lipopolysaccharide induced proliferation model. Moreover, IgAN rat model was established by bovine serum albumin, CCL4 mixed solution and LPS. We found that 10% ZWT could significantly promote the release of exosomes from HK-2 and inhibit HMC proliferation to improve inflammation. Thus HK-2-derived exosomes treated with 10% ZWT (ZWT-EXO) were administered to the rats by tail vein injection. Our results showed that ZWT-EXO decreased the levels of 24 h proteinuria, urinary erythrocyte, IgA deposition in glomerulus and renal pathological injury which ameliorated the kidney damage. In addition, ZWT was able to dramatically promote secretion of exosomes in renal tissues while blocked NF-κB nuclear translocation as well as activation of NLRP3 inflammasome, leading to the inhibition of IL-1β and caspase-1. In conclusion, our study reveal that ZWT has protective effects on IgAN by regulating exosomes secretion to inhibit the activation of NF-κB/NLRP3 pathway, thereby attenuating the renal dysfunction. These findings may provide a new therapeutic target for the treatment of IgAN.
The Impact of Diffusive Water Vapor Transport on Snow Profiles in Deep and Shallow Snow Covers and on Sea Ice

Water vapor transport has been highlighted as a critical process in Arctic snowpacks, shaping the snow cover structure in terms of density, thermal conductivity, and temperature profile among others. Here, we present an attempt to describe the thermally-induced vertical diffusion of water vapor in the snow cover and its effects of the snowpack structure using the SNOWPACK model. Convection, that may also constitute a significant part of vapor transport, is not addressed. Assuming saturated conditions at the upper boundary of the snowpack and as initial condition, the vapor flux between snow layers is expressed by a 1-dimensional transient diffusion equation, which is solved with a finite difference routine. The implications on the snowpack of this vertical diffusive flux, are analyzed using metrics such as the cumulative density change due to diffusive vapor transport, the degree of over- or undersaturation, the instantaneous snow density change rate, and the percentage of snow density change. We present results for four different regions sampling the space of natural snow cover variability: Alpine, Subarctic, Arctic, and Antarctic sea ice. The largest impact of diffusive water vapor transport is observed in snow on sea ice in the Weddell Sea and the shallow Arctic snowpack. The simulations show significant density reductions upon inclusion of diffusive water vapor transport: cumulative density changes from diffusive vapor transport can reach −62 and −66 kg m−3 for the bottom layer in the shallow Arctic snowpack and snow on sea ice, respectively. For comparison, in deeper snow covers, they rarely exceed −40 kg m−3. This leads to changes in density for shallow snowpacks at the soil-snow interface in the range of −5 to −21%. Mirroring the density decease at depth is a thicker deposition layer above it with increase in density around 7.5%. Similarly, for the sea ice, the density decreased at the sea ice-snow interface by −20%. We acknowledge that vapor transport by diffusion may in some snow covers—such as in thin tundra snow—be small compared to convective transport, which will have to be addressed in future work.
Intraspecific Variation in Drought Response of Three Populations of Cryptocarya alba and Persea lingue, Two Native Species From Mediterranean Central Chile

An increase in the severity of drought events on Mediterranean climates highlights the need of using plant material adapted to drought during restoration efforts. Thus, we investigated between-population morpho-physiological differences in Cryptocarya alba and Persea lingue, two native species from Mediterranean central Chile, for traits that could effectively discriminate population performance in response to water restriction (WR) testing. Three populations from each species were subjected to WR treatment and physiological, morphological, and growth parameters were assessed at the beginning and at the end of the experiment. In C. alba, the most xeric population displayed smaller plants with mesophyllous leaves and lower photosynthetic rates indicating a resource saving strategy. Moreover, the xeric population performed better during WR than the most mesic populations, exhibiting higher water use efficiency (iWUE) and maintenance of growth rates. All C. alba populations responded equally to WR in terms of morphology and biomass partitioning. In contrast, differences among P. lingue populations were subtle at the morpho-physiological level with no apparent relation to provenance environmental conditions, and no morphological traits were affected by WR. However, in response to WR application, the most mesic population was, as observed through reduction in relative growth rates, more affected than xeric populations. We attribute such discrete differences between P. lingue provenances to the lower distributional range of selected populations. Our results show that relative growth rates in both species, and iWUE only in C. alba, exhibited population specific responses upon WR imposition; these results correspond with the environmental conditions found at the origin of each populations. Both traits could further assist in the selection of populations for restoration according to their response to water stress.
Perceived Risk and Protection From Infection and Depressive Symptoms Among Healthcare Workers in Mainland China and Hong Kong During COVID-19

Psychological health among healthcare workers (HCWs) has become a major concern since the COVID-19 outbreak. HCWs perceived risks of contracting COVID-19, in relation to depression were investigated. It was hypothesized that perceived high risk of contracting COVID-19 (close contact with cases, inadequate provision of personal protective equipment, insufficient infection control training, and presence of symptoms) would be significant predictors of depression. Our cross-sectional survey was completed by HCWs across three regions (Hubei, Guangdong, Hong Kong) between March 9 to April 9 2020 using convenience sampling. Depression was assessed using the 9-item Patient Health Questionnaire (PHQ-9). Prevalence of depression was 50.4% (95% CI: 44.5-56.2), 15.1% (10.1-21.9) and 12.9% (10.3-16.2) for HCWs in Hong Kong, Hubei and Guangdong, respectively. The strongest significant risk factors for depression, after adjustment, were HCWs who reported the greatest extent of feeling susceptible to contracting COVID-19 and those who reported the greatest difficulty obtaining face masks. HCWs whose family/peers greatly encouraged face mask use had lower prevalence of depression. Access to adequate supplies of personal protective equipment is essential for the psychological health of HCWs working in stressful environments, through potentially easing their perceptions of vulnerability to COVID-19.
Resource Heterogeneity, Not Resource Quantity, Plays an Important Role in Determining Tree Species Diversity in Two Species-Rich Forests

There is still considerable debate about the relative importance of resource heterogeneity and resource quantity in the maintenance of species diversity in a community. The resource heterogeneity hypothesis proposes that spatial heterogeneity of limiting resources and inter-specific differences in resource requirements will determine species richness. In contrast, the resource quantity hypothesis predicts that average resource supply rates contribute to species richness by their effects on plant density and stochastic population dynamics. However, the evaluation of the two hypotheses in observational studies is associated with a major methodological challenge as average resource supply rate often covaries with resource heterogeneity. Using a novel approach derived from the relationships between average resource supply rate, resource heterogeneity (calculated as the standard deviation of environmental factors) and plant density in the resource hypotheses, we evaluated the relative importance of resource quantity and resource heterogeneity with a variation partitioning model in Gutianshan (GTS) forest plot, China, and Barro Colorado Island (BCI) forest plot, Central Panama. We found that resource quantity explained much less of the variation in species richness than resource heterogeneity in both GTS and BCI (44.5% vs. 4.9% in GTS and 20.4% vs. 0.8% in BCI at the 20 × 20 m scale, 57.5% vs. 3.4% in GTS at the 40 × 40 m scale, and 34.5% vs. 2.6% in BCI at the 50 × 50 m scale). We also found that resource heterogeneity governed species richness in GTS, whereas spatial processes dominated species diversity in BCI. Moreover, most of the effect of resource heterogeneity and resource quantity on species richness overlapped with that of spatial processes. This result indicates that most effects of resources could also be explained by spatial processes, such as dispersal limitation. Therefore, resource heterogeneity and spatial processes, but not resource quantity, played an important role in determining species diversity in these two old-growth forests. This is in contrast to the results of several manipulative studies, which found that resource quantity governed species diversity when one or a limited number of resources were considered. This suggests that the processes determining species richness along ecological gradients are complicated and determined by the interaction of various processes.
Failing Is Derailing: The Underperformance as a Stressor Model

Job performance and job stress are widely studied phenomena in occupational research. However, most literatures on the relationship between work stress and job performance conceptualize job stress as an antecedent of performance, in line with the stress-performance framework, and do not examine what happens to the well-being of the employees after the performance was appraised as poor. In the current theoretical paper, I argue that task underperformance is a source of stress (i.e., stressor) for the employee and, as such, can affect a wide range of employee outcomes. Task underperformance is conceptualized as comprised of two main types: acute/episodic underperformance, such as a mistake or an accident (e.g., medical error and service failure), and chronic task underperformance, such as not achieving the expected work products over time, with an interplay between these types. The source of the appraisal (objective, supervisor-rated, and self-rated underperformance) is also considered. Several disjoint literatures are then integrated in order to explain how underperformance is expected to result in subsequent decrements to employee well-being. At the chronic underperformance level, the following literatures are included: self-efficacy, negative effects of performance feedback, and stress experienced when the basic need for competency is frustrated or when underperformance presents a threat to the self-image. At the acute/episodic level, affective and cognitive outcomes are explored, and examples are drawn from several industries including service failures and medical errors. The interplay between the two types of underperformance, acute/episodic and chronic, is discussed, and then relevant moderators are offered. One notable moderator is the occupation-level consequences of error, which likely affects most if not all outcomes. Finally, the discussion includes potential theoretical and practical implications for this conceptualization, as well as some methodological considerations for future research in this area.
Changes in Lumbo-Pelvic Coordination of Individuals With and Without Low Back Pain When Wearing a Hip Orthosis

Individuals with low back pain demonstrate an abnormal lumbo-pelvic coordination compared to back-healthy individuals. This abnormal coordination presents itself as a reduction in lumbar contributions and an increase in pelvic rotations during a trunk forward bending and backward return task. This study investigated the ability of a hip orthosis in correcting such an abnormal lumbo-pelvic coordination by restricting pelvic rotation and, hence increasing lumbar contributions. The effects of the hip orthosis on the lumbo-pelvic coordination were investigated in 20 low back pain patients and 20 asymptomatic controls. The orthosis reduced pelvic rotation by 12.7° and increased lumbar contributions by 11%. Contrary to our expectation, orthosis-induced changes in lumbo-pelvic coordination were smaller in patients; most likely because our relatively young patient group had smaller unrestricted pelvic rotations compared to asymptomatic individuals. Considering the observed capability of a hip orthosis in causing the expected changes in lumbo-pelvic coordination when there is a relatively large pelvic contribution to trunk motion, application of a hip orthosis may provide a promising method of correcting abnormal lumbo-pelvic coordination, particularly among patients who demonstrate larger pelvic rotation, that warrants further investigation.
Epigenetic Modifications of RASSF1A Gene through Chromatin Remodeling in Prostate Cancer

Purpose: The RAS-association domain family 1, isoform A (RASSF1A) gene is shown to be inactivated in prostate cancers. However, the molecular mechanism of silencing of the RASSFIA gene is not fully understood. The present study was designed to investigate the mechanisms of inactivation of the RASSF1A gene through the analysis of CpG methylation and histone acetylation and H3 methylation associated with the RASSF1A promoter region. Experimental Design: Methylation status of the RASSF1A gene was analyzed in 131 samples of prostate cancer, 65 samples of benign prostate hypertrophy (BPH), and human prostate cell lines using methylation-specific PCR. Histone acetylation (acetyl-H3, acetyl-H4) and H3 methylation (dimethyl-H3-K4, dimethyl-H3-K9) status associated with the promoter region in prostate cells were analyzed by chromatin immunoprecipitation (ChIP) assay. Results: Aberrant methylation was detected in 97 (74.0%) prostate cancer samples and 12 (18.5%) BPH samples. The methylation frequency of RASSF1A showed a significant increase with high Gleason sum and high stage. The ChIP assays showed enhancement of histone acetylation and dimethyl-H3-K4 methylation on the unmethylated RASSF1A promoter. TSA alone was unable to alter key components of the histone code. However, after 5-aza-2′-deoxy-cytidine treatment, there was a complete reversal of the histone components in the hypermethylated promoter. Levels of acetyl-H3, acetyl-H4, and dimethyl-H3-K4 became more enriched, whereas H3K9me2 levels were severely depleted. Conclusions: This is the first report suggesting that reduced histone acetylation or H3K4me2 methylation and increased dimethyl-H3-K9 methylation play a critical role in the maintenance of promoter DNA methylation–associated RASSF1A gene silencing in prostate cancer.
Presentation and Outcomes of Kawasaki Disease in Latin American Infants Younger Than 6 Months of Age: A Multinational Multicenter Study of the REKAMLATINA Network

Objective: To characterize the clinical presentation and outcomes of Kawasaki disease (KD) in infants <6 months of age as compared to those ≥6 months in Latin America. Methods: We evaluated 36 infants <6 months old and 940 infants ≥6 months old diagnosed with KD in Latin America. We compared differences in laboratory data, clinical presentation, treatment response, and coronary artery outcomes between the two cohorts. Results: The majority (78.1%) of infants and children ≥6 months of age were initially diagnosed with KD, as compared to only 38.2% of infants <6 months. Clinical features of KD were more commonly observed in the older cohort: oral changes (92 vs. 75%, P = 0.0023), extremity changes (74.6 vs. 57.1%, P = 0.029), and cervical lymphadenopathy (67.6 vs. 37.1%, P = 0.0004). Whether treated in the first 10 days of illness or after the 10th day, infants <6 months were at greater risk of developing a coronary artery aneurysm compared to KD patients ≥6 months treated at the same point in the course of illness [ ≤ 10 days (53.8 vs. 9.4%, P = 0.00012); >10 days (50 vs. 7.4%, P = 0.043)]. Conclusion: Our data show that despite treatment in the first 10 days of illness, infants <6 months of age in Latin America have a higher risk of developing a coronary artery aneurysm. Delay in the diagnosis leads to larger coronary artery aneurysms disproportionately in these infants. Thus, suspicion for KD should be high in this vulnerable population.
Soil Microbial Community and Litter Quality Controls on Decomposition Across a Tropical Forest Disturbance Gradient

Industrial logging and agricultural expansion are driving rapid transformations of tropical ecosystems, modifying patterns in above-ground plant and below-ground microbial communities. However, the extent to which these changes in biodiversity drive modifications of ecosystem process rates such as leaf litter decomposition is poorly understood. To determine the relative effects of changes to the chemical quality of litter and shifts in microbial decomposers on leaf litter decomposition rates, we performed a controlled, reciprocal transplant, litter decomposition experiment across a tropical land-use disturbance gradient. Litter mixtures and soils were collected from old growth forest, moderately logged forest, heavily logged forest, and oil palm plantation in Sabah, Malaysia, and combined in a fully crossed, factorial microcosm experiment maintained under controlled environmental conditions. We found that whilst litter quality was the most important predictor of litter mass loss, soil origin was also significant, explaining between 5.17 and 15.43% of total variation. Microbial decomposer communities from old growth forest had greater functional breadth relative to those from logged forests and oil palm plantation as all litter types decomposed faster when combined with old growth soil. The most chemically recalcitrant litter (lowest N, highest lignin, lignin:N, and C:N ratio) from moderate logged forest decomposed faster when combined with its “home” soil (Home-Field Advantage) whilst the most labile litter from oil palm decomposed slowest when combined with its “home” soil. This was correlated with lower total soil microbial biomass. Taken together, these findings demonstrate that whilst litter quality regulated rates of litter decomposition across the disturbance gradient, soil microbial decomposer communities were functionally dissimilar between land uses and explained a significant proportion of variation. The impact of disturbance on soil, including microbial community structure, should be considered alongside changes to plant communities when assessing effects on crucial ecosystem processes such as decomposition.
Improved COVID-19 Serology Test Performance by Integrating Multiple Lateral Flow Assays using Machine Learning

Mitigating transmission of SARS-CoV-2 has been complicated by the inaccessibility and, in some cases, inadequacy of testing options to detect present or past infection. Immunochromatographic lateral flow assays (LFAs) are a cheap and scalable modality for tracking viral transmission by testing for serological immunity, though systematic evaluations have revealed the low performance of some SARS-CoV-2 LFAs. Here, we re-analyzed existing data to present a proof-of-principle machine learning framework that may be used to inform the pairing of LFAs to achieve superior classification performance while enabling tunable False Positive Rates optimized for the estimated seroprevalence of the population being tested.
Exploring the Potential of Antibiotic Production From Rare Actinobacteria by Whole-Genome Sequencing and Guided MS/MS Analysis

Actinobacteria are well recognized for their production of structurally diverse bioactive secondary metabolites, but the rare actinobacterial genera have been underexploited for such potential. To search for new sources of active compounds, an experiment combining genomic analysis and tandem mass spectrometry (MS/MS) screening was designed to isolate and characterize actinobacterial strains from a mangrove environment in Macau. Fourteen actinobacterial strains were isolated from the collected samples. Partial 16S sequences indicated that they were from six genera, including Brevibacterium, Curtobacterium, Kineococcus, Micromonospora, Mycobacterium, and Streptomyces. The isolate sp.01 showing 99.28% sequence similarity with a reference rare actinobacterial species Micromonospora aurantiaca ATCC 27029T was selected for whole genome sequencing. Organization of its gene clusters for secondary metabolite biosynthesis revealed 21 clusters encoded to antibiotic production, which is higher than other Micromonospora species. Of the genome-predicted antibiotics, kanamycin was found through guided MS/MS analysis producible by the M. aurantiaca strain for the first time. The present study highlighted that genomic analysis combined with MS/MS screening is a promising method to discover potential of antibiotic production from rare actinobacteria.