Unique features of conventional and nonconventional introns in Euglena gracilis.

BACKGROUND: Nuclear introns in Euglenida have been understudied. This study aimed to investigate nuclear introns in Euglenida by identifying a large number of introns in Euglena gracilis (E. gracilis), including cis-spliced conventional and nonconventional introns, as well as trans-spliced outrons. We also examined the sequence characteristics of these introns. RESULTS: A total of 28,337 introns and 11,921 outrons were identified. Conventional and nonconventional introns have distinct splice site features; the former harbour canonical GT/C-AG splice sites, whereas the latter are capable of forming structured motifs with their terminal sequences. We observed that short introns had a preference for canonical GT-AG introns. Notably, conventional introns and outrons in E. gracilis exhibited a distinct cytidine-rich polypyrimidine tract, in contrast to the thymidine-rich tracts observed in other organisms. Furthermore, the SL-RNAs in E. gracilis, as well as in other trans-splicing species, can form a recently discovered motif called the extended U6/5' ss duplex with the respective U6s. We also describe a novel type of alternative splicing pattern in E. gracilis. The tandem repeat sequences of introns in this protist were determined, and their contents were comparable to those in humans. CONCLUSIONS: Our findings highlight the unique features of E. gracilis introns and provide insights into the splicing mechanism of these introns, as well as the genomics and evolution of Euglenida.

Detection of circulating tumor DNA in plasma of patients with primary CNS lymphoma by digital droplet PCR.

BACKGROUND: Primary central nervous system lymphoma (PCNSL) are rare mature B-cell lymphoproliferative diseases characterized by a high incidence of MYD88 L265P and CD79B Y196 hotspot mutations. Diagnosis of PCNSL can be challenging. The aim of the study was to analyze the detection rate of the MYD88 L265P and CD79B Y196 mutation in cell free DNA (cfDNA) in plasma of patients with PCNSL. METHODS: We analyzed by digital droplet PCR (ddPCR) to determine presence of the MYD88 L265P and CD79B Y196 hotspot mutations in cfDNA isolated from plasma of 24 PCNSL patients with active disease. Corresponding tumor samples were available for 14 cases. Based on the false positive rate observed in 8 healthy control samples, a stringent cut-off for the MYD88 L265P and CD79B Y196 mutation were set at 0.3% and 0.5%, respectively. RESULTS: MYD88 L265P and CD79B Y196 mutations were detected in 9/14 (64%) and 2/13 (15%) tumor biopsies, respectively. In cfDNA samples, the MYD88 L265P mutation was detected in 3/24 (12.5%), while the CD79B Y196 mutation was not detected in any of the 23 tested cfDNA samples. Overall, MYD88 L265P and/or CD79B Y196 were detected in cfDNA in 3/24 cases (12.5%). The detection rate of the combined analysis did not improve the single detection rate for either MYD88 L265P or CD79B Y196. CONCLUSION: The low detection rate of MYD88 L265P and CD79B Y196 mutations in cfDNA in the plasma of PCNSL patients argues against its use in routine diagnostics. However, detection of MYD88 L265P by ddPCR in cfDNA in the plasma could be considered in challenging cases.

Effect of Reduced Graphene Oxide on Microwave Absorbing Properties of Al1.5Co4Fe2Cr High-Entropy Alloys.

The microwave absorption performance of high-entropy alloys (HEAs) can be improved by reducing the reflection coefficient of electromagnetic waves and broadening the absorption frequency band. The present work prepared flaky irregular-shaped Al1.5Co4Fe2Cr and Al1.5Co4Fe2Cr@rGO alloy powders by mechanical alloying (MA) at different rotational speeds. It was found that the addition of trace amounts of reduced graphene oxide (rGO) had a favorable effect on the impedance matching, reflection loss (RL), and effective absorbing bandwidth (EAB) of the Al1.5Co4Fe2Cr@rGO HEA composite powders. The EAB of the alloy powders prepared at 300 rpm increased from 2.58 GHz to 4.62 GHz with the additive, and the RL increased by 2.56 dB. The results showed that the presence of rGO modified the complex dielectric constant of HEA powders, thereby enhancing their dielectric loss capability. Additionally, the presence of lamellar rGO intensified the interfacial reflections within the absorber, facilitating the dissipation of electromagnetic waves. The effect of the ball milling speed on the defect concentration of the alloy powders also affected its wave absorption performance. The samples prepared at 350 rpm had the best wave absorption performance, with an RL of -16.23 and -17.28 dB for a thickness of 1.6 mm and EAB of 5.77 GHz and 5.43 GHz, respectively.

Quantile regression for nonignorable missing data with its application of analyzing electronic medical records.

Over the past decade, there has been growing enthusiasm for using electronic medical records (EMRs) for biomedical research. Quantile regression estimates distributional associations, providing unique insights into the intricacies and heterogeneity of the EMR data. However, the widespread nonignorable missing observations in EMR often obscure the true associations and challenge its potential for robust biomedical discoveries. We propose a novel method to estimate the covariate effects in the presence of nonignorable missing responses under quantile regression. This method imposes no parametric specifications on response distributions, which subtly uses implicit distributions induced by the corresponding quantile regression models. We show that the proposed estimator is consistent and asymptotically normal. We also provide an efficient algorithm to obtain the proposed estimate and a randomly weighted bootstrap approach for statistical inferences. Numerical studies, including an empirical analysis of real-world EMR data, are used to assess the proposed method's finite-sample performance compared to existing literature.

Analysis of secondary failure time responses in studies with response-dependent sampling schemes.

Response-dependent sampling is routinely used as an enrichment strategy in the design of family studies investigating the heritable nature of disease. In addition to the response of primary interest, investigators often wish to investigate the association between biomarkers and secondary responses related to possible comorbidities. Statistical analysis regarding genetic biomarkers and their association with the secondary outcome must address the biased sampling scheme involving the primary response. In this article, we develop composite likelihoods and two-stage estimation procedures for such secondary analyses in which the within-family dependence structure for the primary and secondary outcomes is modeled via a Gaussian copula. The dependence among responses within family members is modeled based on kinship coefficients. Auxiliary data from independent individuals are exploited by augmenting the composite likelihoods to increase precision of marginal parameter estimates and enhance the efficiency of estimators of the dependence parameters. Simulation studies are carried out to evaluate the finite sample performance of the proposed method, and an application to a motivating family study in psoriatic arthritis is given for illustration.

Pathogens in PICU before and during the SARS-CoV-2 pandemic in China: a multicenter retrospective study.

BACKGROUND: Nonpharmacological interventions for COVID-19 could reduce the incidence of children hospitalized in pediatric intensive care units (PICU) and the incidence of children with bacterial infections. This study aimed to evaluate changes in the bacterial profile of children in PICU before and during the COVID-19 pandemics. METHODS: This is a retrospective study, involving clinical data of children with positive bacterial cultures admitted to the PICU respectively in 2019 and 2021. RESULTS: In total 652 children were included in this study. The total number of hospitalized patients and the incidence of bacteria-positive children in 2021 were lower than those in 2019. There were no significant differences in the ratio of Gram-positive bacterial infection, Gram-negative bacteria infection or fungi infection between the two years. The rate of Streptococcus pneumoniae in 2021 was higher than that in 2019(p = 0.127). The incidence of Haemophilus influenzae in hospitalized patients decreased with a downward trend(p = 0.002). The distribution of previous underlying diseases in children admitted to PICU with different outcomes of bacterial infection between the two years were homogeneous (p > 0.05). CONCLUSION: After the implementation of COVID-19 isolation, prevention and control measures, the number of hospitalizations and bacterial infections in PICU decreased, which may be due to changes in population's behavior patterns. Meanwhile, the incidence of Haemophilus influenzae in hospitalized patients decreased with a downward trend.

Transcriptomic and genomic identification of spliceosomal genes from Euglena gracilis.

Diverse splicing types in nuclear and chloroplast genes of protist Euglena gracilis have been recognized for decades. However, the splicing machinery responsible for processing nuclear precursor messenger RNA introns, including trans-splicing of the 5' terminal outron and spliced leader (SL) RNA, remains elusive. Here, we identify 166 spliceosomal protein genes and two snRNA genes from E. gracilis by performing bioinformatics analysis from a combination of next-generation and full-length transcriptomic RNA sequencing (RNAseq) data as well as draft genomic data. With the spliceosomal proteins we identified in hand, the insensitivity of E. gracilis to some splicing modulators is revealed at the sequence level. The prevalence of SL RNA-mediated trans-splicing is estimated to be more than 70% from our full-length RNAseq data. Finally, the splicing proteomes between E. gracilis and its three evolutionary cousins within the same Excavata group are compared. In conclusion, our study characterizes the spliceosomal components in E. gracilis and provides the molecular basis for further exploration of underlying splicing mechanisms.

Recent advances and potentiality of postbiotics in the food industry: Composition, inactivation methods, current applications in metabolic syndrome, and future trends.

Postbiotics are defined as "preparation of inanimate microorganisms and/or their components that confers a health benefit on the host". Postbiotics have unique advantages over probiotics, such as stability, safety, and wide application. Although postbiotics are research hotspots, the research on them is still very limited. This review provides comprehensive information on the scope of postbiotics, the preparation methods of inanimate microorganisms, and the application and mechanisms of postbiotics in metabolic syndrome (MetS). Furthermore, the application trends of postbiotics in the food industry are reviewed. It was found that postbiotics mainly include inactivated microorganisms, microbial lysates, cell components, and metabolites. Thermal treatments are the main methods to prepare inanimate microorganisms as postbiotics, while non-thermal treatments, such as ionizing radiation, ultraviolet light, ultrasound, and supercritical CO2, show great potential in postbiotic preparation. Postbiotics could ameliorate MetS through multiple pathways including the modulation of gut microbiota, the enhancement of intestinal barrier, the regulation of inflammation and immunity, and the modulation of hormone homeostasis. Additionally, postbiotics have great potential in the food industry as functional food supplements, food quality improvers, and food preservatives. In addition, the SWOT analyses showed that the development of postbiotics in the food industry exists both opportunities and challenges.

Semiparametric recurrent event vs time-to-first-event analyses in randomized trials: Estimands and model misspecification.

Insights regarding the merits of recurrent event and time-to-first-event analyses are needed to provide guidance on strategies for analyzing intervention effects in randomized trials involving recurrent event responses. Using established asymptotic results we introduce a framework for studying the large sample properties of estimators arising from semiparametric proportional rate function models and Cox regression under model misspecification. The asymptotic biases and power implications are investigated for different data generating models, and we study the impact of dependent censoring on these findings. Illustrative applications are given involving data from a cystic fibrosis trial and a carcinogenicity experiment, following which we summarize findings and discuss implications for clinical trial design.

Selection models for efficient two-phase design of family studies.

Family studies routinely employ biased sampling schemes in which individuals are randomly chosen from a disease registry and genetic and phenotypic data are obtained from their consenting relatives. We view this as a two-phase study and propose the use of an efficient selection model for the recruitment of families to form a phase II sample subject to budgetary constraints. Simple random sampling, balanced sampling and use of an approximately optimal selection model are considered where the latter is chosen to minimize the variance of parameters of interest. We consider the setting where family members provide current status data with respect to the disease and use copula models to address within-family dependence. The efficiency gains from the use of an optimal selection model over simple random sampling and balanced sampling schemes are investigated as is the robustness of optimal sampling to model misspecification. An application to a family study on psoriatic arthritis is given for illustration.

Inhibition of ER stress attenuates kidney injury and apoptosis induced by 3-MCPD via regulating mitochondrial fission/fusion and Ca2+ homeostasis.

3-Chloro-1, 2-propanediol (3-MCPD) is a food-borne toxic substance well-known for more than 40 years that is mainly associated with nephrotoxicity. A better understanding of 3-MCPD nephrotoxicity is required to devise efficacious strategies to counteract its toxicity. In the present work, the role of endoplasmic reticulum (ER) stress along with its underlying regulatory mechanism in 3-MCPD-mediated renal cytotoxicity was investigated in vivo and in vitro. Our data indicated that 3-MCPD-stimulated ER stress response evidenced by sustained activation of PERK-ATF4-p-CHOP and IRE1 branches in Sprague Dawley (SD) rats and human embryonic kidney (HEK293) cells. Moreover, ER stress-associated specific apoptotic initiator, caspase 12, was over-expressed. Blocking ER stress with its antagonist, 4-phenylbutyric acid (4-PBA), improved the morphology and function of kidney effectively. 4-PBA also increased cell viability, relieved mitochondrial vacuolation, and inhibited cell apoptosis through regulating caspase-dependent intrinsic apoptosis pathways. Furthermore, the enhanced expressions of two mitochondrial fission proteins, DRP1/p-DRP1 and FIS1, and the relocation of DRP1 on mitochondria subjected to 3-MPCD were reversed by 4-PBA, while the expression of the fusion protein, MFN2, was restored. Moreover, cellular Ca2+ overload, the over-expression of CaMKK2, and the loss of mitochondria-associated membranes (MAM) were also relieved after 4-PBA co-treatment. Collectively, our data emphasized that ER stress plays critical role in 3-MCPD-mediated mitochondrial dysfunction and subsequent apoptosis as well as blockage of ER stress ameliorated kidney injury through improving mitochondrial fission/fusion and Ca2+ homeostasis. These findings provide a novel insight into the regulatory role of ER stress in 3-MCPD-associated nephropathy and a potential therapeutic strategy. Graphical Headlights 1. 4-PBA inhibits ER stress mainly through regulating PERK-ATF4-CHOP and IRE1-XBP1s branches. 2. Inhibition of ER stress by 4-PBA mitigates ER associated and mitochondrial apoptosis 3. Inhibition of ER stress by 4-PBA helps maintaining calcium homeostasis and mitochondrial dynamic.

Doping effect on the structure and properties of eight-electron silver nanoclusters.

The bimetallic M20 and M21 compounds, {[Cu3Ag17{S2P(OiPr)2}12]0.5 [Cu4Ag16{S2P(OiPr)2}12]0.5} ({[1a]0.5[1b]0.5}) and [Cu4Ag17{S2P(OiPr)2}12](PF6) (2), have been structurally characterized, in which the Cu(I) ions are randomly distributed on the eight outer positions capping the eight-electron [Ag13]5+ core. DFT calculations show that the statistical disorder results from the nearly neutral preference of copper to occupy any of the eight outer positions. Surprisingly, the UV-Vis absorption spectra of the M20 and M21 bimetallic nanoclusters display an almost identical absorption profile as that of their homometallic [Ag20{S2P(OiPr)2}12] and [Ag21{S2P(OiPr)2}12]+ relatives. This is rationalized by TD-DFT calculations, which show that the frontier orbitals of such eight-electron alloys are largely independent from the nature of the capping metal ions. A blue-shifted absorption is observed upon replacing by Au the central Ag atom in 2, forming the trimetallic compound [Cu4AuAg16{S2P(OiPr)2}12](PF6) (3).

A New Synthetic Methodology in the Preparation of Bimetallic Chalcogenide Clusters via Cluster-to-Cluster Transformations.

A decanuclear silver chalcogenide cluster, [Ag10(Se){Se2P(OiPr)2}8] (2) was isolated from a hydride-encapsulated silver diisopropyl diselenophosphates, [Ag7(H){Se2P(OiPr)2}6], under thermal condition. The time-dependent NMR spectroscopy showed that 2 was generated at the first three hours and the hydrido silver cluster was completely consumed after thirty-six hours. This method illustrated as cluster-to-cluster transformations can be applied to prepare selenide-centered decanuclear bimetallic clusters, [CuxAg10-x(Se){Se2P(OiPr)2}8] (x = 0-7, 3), via heating [CuxAg7-x(H){Se2P(OiPr)2}6] (x = 1-6) at 60 °C. Compositions of 3 were accurately confirmed by the ESI mass spectrometry. While the crystal 2 revealed two un-identical [Ag10(Se){Se2P(OiPr)2}8] structures in the asymmetric unit, a co-crystal of [Cu3Ag7(Se){Se2P(OiPr)2}8]0.6[Cu4Ag6(Se){Se2P(OiPr)2}8]0.4 ([3a]0.6[3b]0.4) was eventually characterized by single-crystal X-ray diffraction. Even though compositions of 2, [3a]0.6[3b]0.4 and the previous published [Ag10(Se){Se2P(OEt)2}8] (1) are quite similar (10 metals, 1 Se2-, 8 ligands), their metal core arrangements are completely different. These results show that different synthetic methods by using different starting reagents can affect the structure of the resulting products, leading to polymorphism.

A Review of Key Technologies and Trends in the Development of Integrated Heating and Power Systems in Agriculture.

Petroleum agriculture, characterized by mechanization and chemistry, is developing rapidly in China. However, petroleum agriculture has not only brought food safety problems, but also caused great obstacles to the sustainable development of society. In view of the disadvantages of oil agriculture, we provide an upgrading plan for energy systems in agriculture. This work can help reduce carbon emissions and improve food security. We introduce the most advanced technologies in Chinese agricultural development and the technical scope includes new agricultural energy power generation, agricultural energy use and the safe operation of agricultural energy systems. We describe the detailed data of agricultural bioenvironmental and energy engineering to clarify the level of agricultural energy efficiency in China. The overall conclusion of this paper is that the deep integration of agriculture and energy internet has become the development trend of agricultural energy systems.

A Two-Electron Silver Superatom Isolated from Thermally Induced Internal Redox Reaction of A Silver(I) Hydride.

Rational syntheses under controllable reducing conditions in the preparation of superatoms with cluster electron number not exceeding two are challenging. Herein a dithiolate-stabilized two-electron silver nanocluster, Ag10 {S2 P(Oi Pr)2 }8 (1), is isolated via a self-redox reaction of Ag7 (H){S2 P(Oi Pr)2 }6 without adding extra reducing agents. The metal framework of Ag7 , a bicapped trigonal bipyramid, is highly correlated to that of Ag10 , suggesting Ag7 (H){S2 P(Oi Pr)2 }6 acts as both reducing agent and template in cluster growth. 1 is highly fluorescent at ambient temperature and TD-DFT calculations indicate that the emission is of 1Px →1S nature.

Different expression pattern of human cytomegalovirus-encoded microRNAs in circulation from virus latency to reactivation.

BACKGROUND: Human cytomegalovirus (HCMV) is a beta-hersvirinae that has a high latent infection rate worldwide and can cause serious consequences in immunocompromised patients when reactivation; however, the mechanism of how HCMV convert from latent to reactivation has rarely been investigated. In the present study, we aimed to perform a comprehensive analysis of the HCMV-encoded microRNA (miRNA) profile in serum of patients upon HCMV reactivation from latency and to further evaluate its clinical significance for the disease monitoring and preventing usefulness. METHODS: Serum samples from 59 viremia patients and 60 age-gender matched controls were enrolled in this study for screening and validation of different expression of HCMV miRNAs. Serum concentrations of 22 known HCMV miRNAs were determined by a hydrolysis probe-based stem-loop quantitative reverse transcription polymerase chain reaction (RT-qPCR) assay. HCMV DNA was measured by quantitative real-time PCR (qPCR) with the whole blood sample. Serum HCMV IgG and IgM were assessed using enzyme linked immunosorbent assay (ELISA). Another 47 samples from 5 patients at different time points were collected to evaluate the monitoring effectiveness and disease prediction ability of differential expression HCMV-miRNAs during the antiviral treatment. RESULTS: The RT-qPCR analysis revealed that the serum levels of 16 of the 22 examined HCMV miRNAs were elevated in HCMV viremia patients compared with controls, and a profile of 8 HCMV miRNAs including hcmv-miR-US25-2-3p, hcmv-miR-US4-5p, hcmv-miR-US25-2-5p, hcmv-miR-US25-1-3p, hcmv-miR-US25-1, hcmv-miR-UL36, hcmv-miR-UL148D, hcmv-miR-US29-3p were markedly elevated (fold change > 2, P < 0.01). Receiver operating characteristic curve (ROC) analysis were performed on the selected HCMV-miRNAs in all of the patients and controls that enrolled in this study, and which ranged from 0.72 to 0.80 in the autoimmune patients. In addition, hcmv-miR-US25-1-3p levels were significantly correlated with HCMV DNA load (r = 0.349, P = 0.007), and were obviously higher in the reactivation set than the latency set in the autoimmune patients, which could be a predictor for the monitoring of the antiviral treatment. CONCLUSIONS: HCMV miRNAs profile showed markedly shift-switch from latency to reactivation in circulation from HCMV infected patients and hcmv-miR-US25-1-3p may be served as a predictor for the switch upon reactivation from latency in patients suffered with autoimmune diseases.

Testing the heritability and parent-of-origin hypotheses for ages at onset of psoriatic arthritis under biased sampling.

The heritability and parent-of-origin effect hypotheses for chronic diseases can be evaluated by estimating and conducting inference about the parameters that measure the within-family dependences in disease onset times. We model the within-family associations in these times using a Gaussian copula whose correlation matrix accommodates the different pairwise family relationships. We derive score-type statistics to test the heritability and parent-of-origin effect hypotheses when the families selection protocol induces a sampling bias. We illustrate the use of the developed methods through an application to a motivating family study in Psoriatic arthritis and provide strong evidence of excessive paternal transmission of risk.

PDLIM2 acts as a cancer suppressor gene in non-small cell lung cancer via the down regulation of NF-κB signaling.

PDZ and LIM domain containing protein 2 (PDLIM2) has been identified as a vital tumor-associated gene that is aberrantly expressed in various types of tumors. Yet, the involvement of PDLIM2 in non-small cell lung cancer (NSCLC) is currently undetermined. The design of the current study was to evaluate whether PDLIM2 plays a role in NSCLC. We found that PDLIM2 expression was commonly decreased in NSCLC tissues. Moreover, low expression of PDLIM2 was also detected in NSCLC cell lines and demethylation treatment restored PDLIM2 expression. The re-expression of PDLIM2 impeded the proliferative, colony-forming, and invasive capabilities of NCLCL cells. In contrast, depletion of PDLIM2 markedly enhanced the malignant behaviors of NSCLC cells. Notably, PDLIM2 overexpression downregulated the expression of nuclear factor (NF)-κB p65 subunit and repressed NF-κB transcription reporter activity in NSCLC cells. The overexpression of p65 significantly reversed PDLIM2-mediated antitumor effects in NSCLC cells. Additionally, the Xenograft tumor formation assay revealed that the overexpression of PDLIM2 markedly restricted the tumor growth of NSCLC in vivo. Overall, our study confirms that PDLIM2 acts as a tumor-inhibitor in NSCLC through the inactivation of NF-κB, suggesting PDLIM2 as a candidate therapeutic target for NSCLC.

The effect of omitted covariates in marginal and partially conditional recurrent event analyses.

There have been many advances in statistical methodology for the analysis of recurrent event data in recent years. Multiplicative semiparametric rate-based models are widely used in clinical trials, as are more general partially conditional rate-based models involving event-based stratification. The partially conditional model provides protection against extra-Poisson variation as well as event-dependent censoring, but conditioning on outcomes post-randomization can induce confounding and compromise causal inference. The purpose of this article is to examine the consequences of model misspecification in semiparametric marginal and partially conditional rate-based analysis through omission of prognostic variables. We do so using estimating function theory and empirical studies.

Augmented composite likelihood for copula modeling in family studies under biased sampling.

The heritability of chronic diseases can be effectively studied by examining the nature and extent of within-family associations in disease onset times. Families are typically accrued through a biased sampling scheme in which affected individuals are identified and sampled along with their relatives who may provide right-censored or current status data on their disease onset times. We develop likelihood and composite likelihood methods for modeling the within-family association in these times through copula models in which dependencies are characterized by Kendall's [Formula: see text] Auxiliary data from independent individuals are exploited by augmentating composite likelihoods to increase precision of marginal parameter estimates and consequently increase efficiency in dependence parameter estimation. An application to a motivating family study in psoriatic arthritis illustrates the method and provides some evidence of excessive paternal transmission of risk.