Miracle-dz/UniFAR-FTUs huggingface dataset:
Dietary selenium sources differentially regulate selenium concentration, mRNA and protein expression of representative selenoproteins in various tissues of yellow catfish Pelteobagrus fulvidraco

Abstract The study was conducted to determine the effects of three dietary Se sources, such as sodium-selenite (S-S), seleno-yeast (S-Y) and seleno-methionine (S-M), on Se concentration, glutathione peroxidase (GPX) and TXNRD activities, and mRNA expression of fifteen representative selenoproteins, and protein expression of four endoplasmic reticulum-resided selenoproteins in a wide range of tissues of yellow catfish. Compared with S-S and S-M groups, dietary S-Y significantly decreased growth performance and feed utilisation of yellow catfish. Dietary Se sources significantly influenced Se contents in the spleen, dorsal muscle and the kidney, GPX activities in spleen, kidney, intestine, muscle and mesenteric fat, and TXNRD activities in the heart, intestine and mesenteric fat. Among ten tested tissues, dietary Se sources influenced mRNA expression of GPX4 and SELENOK in three tissues; GPX3, SELENOS and TXNRD2 in four tissues; SELENOF, SELENON and DIO2 in five tissues; SELENOM, GPX1/2 and TXNRD3 in six tissues; SELENOW in seven tissue and SELENOP and SELENOT in eight tissues. Based on these observations above, S-S and S-M seem to be suitable Se sources for improving growth performance and feed utilisation of yellow catfish. Dietary Se sources differentially influence the expression of selenoproteins in various tissues of yellow catfish. For the first time, we determined the expression of selenoproteins in fish in responses to dietary Se sources, which contributes to a better understanding of the functions and regulatory mechanisms of selenoporteins.
Chemical Constituent, Antimicrobial Activity, and Synergistic Effect of the Stem, Leaf, and Flower Essential Oil of the Artemisia fragrans Willd. from Khoy

Artemisia fragrans is commonly used as a folk medicine as antispasmodic, anti‐pyretic, anti‐inflammatory, and abortifacient agents. The villagers use its pungent odor to repel rodents, mites, and pests, as well as its essential oil and smoke after burning to treat lung infections after uprooting the plant. Herein, we extracted the essential oils (EOs) of different parts of the plant and analyzed their chemical compositions and antibacterial activities. The chemical analysis led to the identification of 73, 59, and 57 compounds in the EOs of the stem, leaf, and flower, respectively. All of the EOs exhibited antibacterial activities against both G+ and G− bacteria. The EOs of the leaf and flower were more effective against tested bacteria, except B. anthracis and P. aeruginosa, compared to that of the stem. The binary combination of the EOs (stem and flower) or (stem and leaf) showed a synergistic effect. Statistical analysis indicated EOs of leaf and flower are more potent than that of the stem. These findings suggest the application of leaf and flower of the plant, which not only can prevent its uprooting but also ensure better therapeutic function.
Monitoring the effect of environmental conditions on safety of fresh produce sold in Qatar’s wholesale market

ABSTRACT Fresh produce imported by Qatar are mostly sold at the wholesale produce market (WPM) located in open-air and near major animal markets and slaughterhouses. This study was the first in Qatar to monitor the effect of environmental conditions on the microbial quality and safety of fresh produce sold at the WPM over 1 year. The monitoring involved the collection of 540 produce samples along with samples of air, soil, and surface swabs. Samples were analyzed for total aerobic bacteria (TAB); generic Listeria spp. , Staphylococcus spp. , Salmonella spp. ; total coliforms and total fungi. Bacterial and fungal isolates were identified using 16S rRNA/ITS rRNA markers. Environmental/sanitary factors significantly impacted the prevalence of microorganisms in all samples tested. Produce quality was rated ‘poor’ during the months of November–February or May–August, with TAB and coliform counts exceeding 6 and 4 log10 CFU/g, respectively. Bacillus subtilus, Enterobacter cloacae, E. faecium, P. expansium, P. aurantiocandidum, and A. niger were the most abundant species with prevalence rate of 11–30%. The high microbial load of environmental samples indicates that the location of the WPM near livestock markets is likely impacting the microbial quality of fresh produce. Therefore, effective control measures need to be implemented at WPM to improve produce safety yearlong.
A Quantitative Metagenomic Sequencing Approach for High-Throughput Gene Quantification and Demonstration with Antibiotic Resistance Genes

Monitoring and comprehensive assessment of microbial risks in the environment require high-throughput gene quantification. The quantitative metagenomic NGS (qmNGS) approach developed in this study incorporated numerous xenobiotic and synthetic DNA internal standard fragments into metagenomic NGS workflow, which are used to determine a new parameter called sequencing yield that relates sequence base reads to absolute concentration of target genes in the environmental samples. ABSTRACT Comprehensive microbial risk assessment requires high-throughput quantification of diverse microbial risks in the environment. Current metagenomic next-generation sequencing approaches can achieve high-throughput detection of genes indicative of microbial risks but lack quantitative capabilities. This study developed and tested a quantitative metagenomic next-generation sequencing (qmNGS) approach. Numerous xenobiotic synthetic internal DNA standards were used to determine the sequencing yield (Yseq) of the qmNGS approach, which can then be used to calculate absolute concentration of target genes in environmental samples based on metagenomic sequencing results. The qmNGS approach exhibited excellent linearity as indicated by a strong linear correlation (r2 = 0.98) between spiked and detected concentrations of internal standards. High-throughput capability of the qmNGS approach was demonstrated with artificial Escherichia coli mixtures and cattle manure samples, for which 95 ± 3 and 208 ± 4 types of antibiotic resistance genes (ARGs) were detected and quantified simultaneously. The qmNGS approach was further compared with quantitative real-time PCR (qPCR) and demonstrated comparable levels of accuracy and less variation for the quantification of six target genes (16S, tetO, sulI, tetM, ermB, and qnrS). IMPORTANCE Monitoring and comprehensive assessment of microbial risks in the environment require high-throughput gene quantification. The quantitative metagenomic NGS (qmNGS) approach developed in this study incorporated numerous xenobiotic and synthetic DNA internal standard fragments into metagenomic NGS workflow, which are used to determine a new parameter called sequencing yield that relates sequence base reads to absolute concentration of target genes in the environmental samples. The qmNGS approach demonstrated excellent method linearity and comparable performance as the qPCR approach with high-throughput capability. This new qmNGS approach can achieve high-throughput and accurate gene quantification in environmental samples and has the potential to become a useful tool in monitoring and comprehensively assessing microbial risks in the environment.
Vitamin D in Basketball Players: Current Evidence and Future Directions

Context: Despite growing interest in quantifying and correcting vitamin D inadequacy in basketball players, a critical synthesis of these data is yet to be performed to overcome the low generalizability of findings from individual studies. Objective: To provide a comprehensive analysis of data in basketball pertaining to (1) the prevalence of vitamin D inadequacy; (2) the effects of vitamin D supplementation on 25-hydroxyvitamin D [25(OH)D] concentration (and its association with body composition), bone health, and performance; and (3) crucial aspects that warrant further investigation. Data Sources: PubMed, MEDLINE, ERIC, Google Scholar, SCIndex, and ScienceDirect databases were searched. Study Selection: After screening, 15 studies were included in the systematic review and meta-analysis. Study Design: Systematic review and meta-analysis. Level of Evidence: Level 3. Data Extraction: The prevalence of vitamin D inadequacy, serum 25(OH)D, body composition, stress fractures, and physical performance were extracted. Results: The pooled prevalence of vitamin D inadequacy for 527 basketball players in 14 studies was 77% (P < 0.001; 95% CI, 0.70-0.84). Supplementation with 4000 IU/d and 4000 IU/wk (absolute mean difference [AMD]: 25.39 nmol/L; P < 0.001; 95% CI, 13.44-37.33), as well as 10,000 IU/d (AMD: 100.01; P < 0.001; 95% CI, 70.39-129.63) vitamin D restored 25(OH)D to normal concentrations. Body composition data revealed inverse correlations between changes in serum 25(OH)D (from pre- to postsupplementation) and body fat (r = −0.80; very large). Data concerning positive impacts of vitamin D supplementation on bone health and physical performance remain sparse. Conclusion: The high proportion of vitamin D inadequacy underscores the need to screen for serum 25(OH)D in basketball players. Although supplementation restored vitamin D sufficiency, the beneficial effects on bone health and physical performance remain sparse. Adiposity can modulate 25(OH)D response to supplementation.
Korea Heart Disease Fact Sheet 2020: Analysis of Nationwide Data

Author's summary The Korean Society of Cardiology has recently published the Korea Heart Disease Fact Sheet 2020 to provide overview of the cardiovascular disease (CVD) burden and its temporal changes. CVD mortality, hospitalization, and risk factor distributions were analyzed from nationwide databases. Over the last decade, CVD mortality and hospitalization have increased, while their age-standardized rates have declined. In addition, a considerable proportion of adults had multiple risk factors, which markedly increased with older age. Thus, concerted efforts should be continued to address the rising burden of CVD in Korea.
A comparison of the effect of X and gamma irradiation on red cell storage quality

Irradiation of red cell components is indicated for recipients at risk of transfusion‐associated graft vs. host disease. Current technologies available comprise of a gamma (γ) or an x source of radiation. The benefits of x vs. γ include non‐radioactivity and hence no decay of the source. We aimed to compare the effect of the two technologies on red cell component storage quality post‐irradiation.
Static Magnetic Field (0.2–0.4 T) Stimulates the Self‐Renewal Ability of Osteosarcoma Stem Cells Through Autophagic Degradation of Ferritin

Static magnetic field (SMF) can alter cell fate decisions in many ways. However, the effects of SMF on cancer stem cells (CSCs) are little‐known. In this particular study, we evaluate the biological effect of moderate‐intensity SMF on osteosarcoma stem cells (OSCs) and try to clarify the underlying mechanisms of action. First, we demonstrated that prolonged exposure to SMF induced the proliferation and tumorsphere formation in K7M2 and MG63 OSCs. Moreover, SMF promoted the release of ferrous iron (Fe2+) and provoked reactive oxygen species (ROS) in OSCs. Interestingly, SMF evidently triggered the autophagic degradation of ferritin, which is characterized by the activation of microtubule‐associated protein 1 light chain 3 (LC3) and nuclear receptor co‐activator 4 (NCOA4), and downregulation of ferritin heavy chain 1 (FTH1) in OSCs. Particularly, the colony‐forming ability of K7M2 OSCs promoted by SMF was obviously abolished by using a small interfering RNA (siRNA) against NCOA4. Finally, treatment of the tumor‐bearing mice with SMF did not affect the tumor volume or tumor mass, nor pulmonary metastasis of K7M2 OSCs, but the SMF‐treated K7M2 OSCs caused a preference of pulmonary metastasis in a mouse model, which suggested that SMF might induce the metastatic characteristic of OSCs. Consequently, this paper demonstrates for the first time that the cumulative SMF exposure promoted the self‐renewal ability of OSCs via autophagic degradation of ferritin, implying that ferritinophagy may be a potential molecular target for cancer. © 2021 Bioelectromagnetics Society.
“It's Been Negative for Us Just All the Way Across the Board”: Focus Group Study Exploring Parent Perceptions of Child Screen Time During the COVID-19 Pandemic

Background Child screen time (ST) has soared during the COVID-19 pandemic as lockdowns and restrictions have forced changes to regular family routines. It is important to investigate how families are navigating ST. Objective This study aimed to explore families’ experiences of ST during the COVID-19 pandemic. Methods Virtual focus group sessions were conducted between December 2020 and February 2021 in English and Spanish. Transcripts were analyzed using reflexive thematic analysis. Results In total, 48 parents (predominantly Hispanic) residing in California participated in 1 of 14 focus group sessions. Children were attending school remotely at the time of the study. A total of 6 themes and 1 subtheme were identified: (1) total ST has increased; (2) children are too attached to screens; (3) ST has advantages and disadvantages but parents perceive ST as mostly negative; (4) parents and children have limited options; (5) ST restrictions (subtheme: children react negatively when ST is restricted); and (6) parents are concerned that children are not getting enough exercise. Conclusions This study provides a cross-sectional insight into how family life has changed with regard to ST during the COVID-19 pandemic. Parents expressed concerns about total ST, the addictive nature of it, and lack of physical activity. It is important that future studies examine the long-term effects of heavy ST and preemptively introduce ways to redirect children’s ST habits as the country attempts to establish a new normal.
Risk Factors that Predict Levothyroxine Medication after Thyroid Lobectomy.

Context and Objective The risk of needing lifelong thyroid hormone supplementation is an important factor affecting treatment decisions for both patients and clinicians ahead thyroid lobectomy. The purposes of this study were to assess the predictive factors of levothyroxine medication after thyroid lobectomy. Methods We retrospectively reviewed 252 patients who had undergone lobectomy for benign thyroid nodules between April 2009 and April 2017. We conducted two independent analyses: patients who started taking levothyroxine after surgery were compared with those who did not, and patients who did not need levothyroxine at last follow-up were compared with those who required continued treatment. We investigated the correlations of patient clinicopathological characteristics and levothyroxine medication after lobectomy. Results Ninety-eight patients started levothyroxine after surgery. Of these, 34 patients successfully ceased medication and 64 patients continued treatment as of their last follow-up. In multivariate analysis, older age and preoperative TSH ≥2.0mIU/L were associated with levothyroxine initiation after surgery. In terms of continuity of levothyroxine, both older age and TSH ≥ 3.0mIU/L showed a significant correlation with continuous medication. We created a risk-scoring system to predict likelihood of starting and maintaining levothyroxine using the two significant factors in each comparison. A risk score of 3 or more indicated an increased risk of starting levothyroxine (specificity = 81.8%; sensitivity = 48.0%). A risk score of 3 or more indicated increased risk of continuous medication, (specificity = 94.2%; sensitivity = 35.9%). Conclusions Greater age and higher preoperative TSH levels correlated with initiation and continuity of levothyroxine medication after lobectomy.
In vitro Anti-colorectal Cancer Potential of the Medicinal Mushroom Ganoderma neo-japonicum Imazeki in Hyperglycemic Condition: Impact on Oxidative Stress, Cell Cycle and Apoptosis

Abstract Clinical efficacy of chemotherapy is often compromised by diabetogenic glucose on colorectal cancer (CRC). High glucose has been shown to diminish the cytotoxicity of anticancer drugs. The issue can potentially be addressed with natural products. Recently, we revealed that Ganoderma neo-japonicum exhibits inhibitory activities against human colonic carcinoma cells. In this study, the impacts of hexane fraction (Hex, sterol-enriched) and chloroform fraction (Chl, terpenoid-enriched) were further elucidated. The cellular responses, including oxidative stress, cell cycle, and apoptosis were compared between the presence of normal glucose (NG, 5.5 mM) and high glucose (HG, 25 mM). HG promoted cell viability with concomitant elevation of GSH level. Both Hex and Chl fractions stimulated NO production, in addition, induced cell cycle arrest. The apoptotic effect of Hex fraction was glucose-dependent, but Chl fraction triggered apoptosis with an equivalent extent in NG and HG conditions. Overall, the active fractions from G. neo-japonicum show therapeutic potential in managing hyperglycemia-associated CRC.
Outcomes of COVID-19 in Patients With Cancer: Report From the National COVID Cohort Collaborative (N3C)

PURPOSE Variation in risk of adverse clinical outcomes in patients with cancer and COVID-19 has been reported from relatively small cohorts. The NCATS’ National COVID Cohort Collaborative (N3C) is a centralized data resource representing the largest multicenter cohort of COVID-19 cases and controls nationwide. We aimed to construct and characterize the cancer cohort within N3C and identify risk factors for all-cause mortality from COVID-19. METHODS We used 4,382,085 patients from 50 US medical centers to construct a cohort of patients with cancer. We restricted analyses to adults ≥ 18 years old with a COVID-19–positive or COVID-19–negative diagnosis between January 1, 2020, and March 25, 2021. We followed N3C selection of an index encounter per patient for analyses. All analyses were performed in the N3C Data Enclave Palantir platform. RESULTS A total of 398,579 adult patients with cancer were identified from the N3C cohort; 63,413 (15.9%) were COVID-19–positive. Most common represented cancers were skin (13.8%), breast (13.7%), prostate (10.6%), hematologic (10.5%), and GI cancers (10%). COVID-19 positivity was significantly associated with increased risk of all-cause mortality (hazard ratio, 1.20; 95% CI, 1.15 to 1.24). Among COVID-19–positive patients, age ≥ 65 years, male gender, Southern or Western US residence, an adjusted Charlson Comorbidity Index score ≥ 4, hematologic malignancy, multitumor sites, and recent cytotoxic therapy were associated with increased risk of all-cause mortality. Patients who received recent immunotherapies or targeted therapies did not have higher risk of overall mortality. CONCLUSION Using N3C, we assembled the largest nationally representative cohort of patients with cancer and COVID-19 to date. We identified demographic and clinical factors associated with increased all-cause mortality in patients with cancer. Full characterization of the cohort will provide further insights into the effects of COVID-19 on cancer outcomes and the ability to continue specific cancer treatments.
A catalog of tens of thousands of viruses from human metagenomes reveals hidden associations with chronic diseases

Significance Mechanisms of many human chronic diseases involve abnormal action of the immune system and/or altered metabolism. The microbiome, an important regulator of metabolic and immune-related phenotypes, has been shown to be associated with or participate in the development of a variety of chronic diseases. Viruses of bacteria (i.e., “phages”) are ubiquitous and mysterious, and several studies have shown that phages exert great control over the behavior—and misbehavior—of their host bacteria. This study uses techniques to discover and analyze over 45,000 viruses associated with human bodies. The abundance of over 2,000 specific phages is found to correlate with a variety of common chronic diseases. Despite remarkable strides in microbiome research, the viral component of the microbiome has generally presented a more challenging target than the bacteriome. This gap persists, even though many thousands of shotgun sequencing runs from human metagenomic samples exist in public databases, and all of them encompass large amounts of viral sequence data. The lack of a comprehensive database for human-associated viruses has historically stymied efforts to interrogate the impact of the virome on human health. This study probes thousands of datasets to uncover sequences from over 45,000 unique virus taxa, with historically high per-genome completeness. Large publicly available case-control studies are reanalyzed, and over 2,200 strong virus–disease associations are found.
Reply to Camporota et al.: The 4DPRR Index and Mechanical Power: A Step Ahead or 4 Steps Backward?

mechanical effects of PEEP on mortality hazard may be more complex. Indeed, although PEEP’s effect on total lung stress and strain will depend on multiple factors (e.g., baseline compliance, recruitability, and lung homogeneity), its amount is not indifferent to the outcome because PEEP can influence driving pressure (for a given VT) and dead space (and can indirectly influence the respiratory rate) as well as acting independently as a key component of the total mechanical energy delivered. The relevance of PEEP in determining total stress and strain of the respiratory system is, in one sense, intuitive: omitting PEEP from a calculation of energywould imply that applying 30 cmH2Oof PEEP to anindividualpatientaddsnoriskofVILIorotheradverseoutcomes.On the contrary, it is clear from the univariate, population-based models presented by Costa and colleagues (1) that PEEP, the static elastic component ofmechanical power and of total power, impactsmortality with an effect size of similar magnitude as respiratory rate and driving pressure. There are not sufficient data available to fully elucidate the effect of PEEP on outcome, but there is already evidence—some from the same authors—that mechanical power is associated to outcome in the same populations (4). Second, the simplicity of the bedside calculation of 4DPRR is not superiortothesimplicityof thebedsidecalculationofmechanicalpower through simplified formulas (5). In addition, the 4DPRR formulation obscures the conceptual understanding of the delivered mechanical energy. Therefore, we argue that moving from the physical and physiological model of mechanical power to a contrived expression based on statisticalmodels devoid of direct physical meaning may be a retrograde step.