LoRaD: Marginal likelihood estimation with haste (but no waste).

The Lowest Radial Distance (LoRaD) method is a modification of the recently introduced Partition-Weighted Kernel method for estimating the marginal likelihood of a model, a quantity important for Bayesian model selection. For analyses involving a fixed tree topology, LoRaD improves upon the Steppingstone or Thermodynamic Integration (Path Sampling) approaches now in common use in phylogenetics because it requires sampling only from the posterior distribution, avoiding the need to sample from a series of ad hoc power posterior distributions, and yet is more accurate than other fast methods such as the Generalized Harmonic Mean (GHM) method. We show that the method performs well in comparison to the Generalized Steppingstone method on an empirical fixed-topology example from molecular phylogenetics involving 180 parameters. The LoRaD method can also be used to obtain the marginal likelihood in the variable-topology case if at least one tree topology occurs with sufficient frequency in the posterior sample to allow accurate estimation of the marginal likelihood conditional on that topology. [Bayesian; marginal likelihood; phylogenetics.].

Estimation of l0 Norm Penalized Models: A Statistical Treatment.

Fitting penalized models for the purpose of merging the estimation and model selection problem has become commonplace in statistical practice. Of the various regularization strategies that can be leveraged to this end, the use of the l0 norm to penalize parameter estimation poses the most daunting model fitting task. In fact, this particular strategy requires an end user to solve a non-convex NP-hard optimization problem irregardless of the underlying data model. For this reason, the use of the l0 norm as a regularization strategy has been woefully under utilized. To obviate this difficulty, a strategy to solve such problems that is generally accessible by the statistical community is developed. The approach can be adopted to solve l0 norm penalized problems across a very broad class of models, can be implemented using existing software, and is computationally efficient. The performance of the method is demonstrated through in-depth numerical experiments and through using it to analyze several prototypical data sets.

TAX1BP1 contributes to deoxypodophyllotoxin-induced glioma cell parthanatos via inducing nuclear translocation of AIF by activation of mitochondrial respiratory chain complex I.

Parthanatos is a type of programmed cell death initiated by over-activated poly (ADP-ribose) polymerase 1 (PARP1). Nuclear translocation of apoptosis inducing factor (AIF) is a prominent feature of parthanatos. But it remains unclear how activated nuclear PARP1 induces mitochondrial AIF translocation into nuclei. Evidence has shown that deoxypodophyllotoxin (DPT) induces parthanatos in glioma cells via induction of excessive ROS. In this study we explored the downstream signal of activated PARP1 to induce nuclear translocation of AIF in DPT-triggered glioma cell parthanatos. We showed that treatment with DPT (450 nM) induced PARP1 over-activation and Tax1 binding protein 1 (TAX1BP1) distribution to mitochondria in human U87, U251 and U118 glioma cells. PARP1 activation promoted TAX1BP1 distribution to mitochondria by depleting nicotinamide adenine dinucleotide (NAD+). Knockdown of TAX1BP1 with siRNA not only inhibited TAX1BP1 accumulation in mitochondria, but also alleviated nuclear translocation of AIF and glioma cell death. We demonstrated that TAX1BP1 enhanced the activity of respiratory chain complex I not only by upregulating the expression of ND1, ND2, NDUFS2 and NDUFS4, but also promoting their assemblies into complex I. The activated respiratory complex I generated more superoxide to cause mitochondrial depolarization and nuclear translocation of AIF, while the increased mitochondrial superoxide reversely reinforced PARP1 activation by inducing ROS-dependent DNA double strand breaks. In mice bearing human U87 tumor xenograft, administration of DPT (10 mg· kg-1 ·d-1, i.p., for 8 days) markedly inhibited the tumor growth accompanied by NAD+ depletion, TAX1BP1 distribution to mitochondria, AIF distribution to nuclei as well as DNA DSBs and PARP1 activation in tumor tissues. Taken together, these data suggest that TAX1BP1 acts as a downstream signal of activated PARP1 to trigger nuclear translocation of AIF by activation of mitochondrial respiratory chain complex I.

Activated SIRT1 contributes to DPT-induced glioma cell parthanatos by upregulation of NOX2 and NAT10.

Parthanatos is a type of programmed cell death dependent on hyper-activation of poly (ADP-ribose) polymerase 1 (PARP-1). SIRT1 is a highly conserved nuclear deacetylase and often acts as an inhibitor of parthanatos by deacetylation of PARP1. Our previous study showed that deoxypodophyllotoxin (DPT), a natural compound isolated from the traditional herb Anthriscus sylvestris, triggered glioma cell death via parthanatos. In this study, we investigated the role of SIRT1 in DPT-induced human glioma cell parthanatos. We showed that DPT (450 nmol/L) activated both PARP1 and SIRT1, and induced parthanatos in U87 and U251 glioma cells. Activation of SIRT1 with SRT2183 (10 µmol/L) enhanced, while inhibition of SIRT1 with EX527 (200 µmol/L) or knockdown of SIRT1 attenuated DPT-induced PARP1 activation and glioma cell death. We demonstrated that DPT (450 nmol/L) significantly decreased intracellular NAD+ levels in U87 and U251 cells. Further decrease of NAD+ levels with FK866 (100 µmol/L) aggravated, but supplement of NAD+ (0.5, 2 mmol/L) attenuated DPT-induced PARP1 activation. We found that NAD+ depletion enhanced PARP1 activation via two ways: one was aggravating ROS-dependent DNA DSBs by upregulation of NADPH oxidase 2 (NOX2); the other was reinforcing PARP1 acetylation via increase of N-acetyltransferase 10 (NAT10) expression. We found that SIRT1 activity was improved when being phosphorylated by JNK at Ser27, the activated SIRT1 in reverse aggravated JNK activation via upregulating ROS-related ASK1 signaling, thus forming a positive feedback between JNK and SIRT1. Taken together, SIRT1 activated by JNK contributed to DPT-induced human glioma cell parthanatos via initiation of NAD+ depletion-dependent upregulation of NOX2 and NAT10.

Multifocal primary amelanotic meningeal melanomas mimicking lymphoma: a case report and literature review.

Primary meningeal melanoma is a rare type of melanocytic cancer originating from the melanocytes of the leptomeninges. It commonly presents as a solitary mass, and multifocal amelanotic lesions were scarcely reported. Diagnosis of multifocal melanoma is particularly challenging, clinically and diagnostically, especially in the absence of cutaneous nevi and melanin pigment. Surgical biopsy result is the gold standard. In this case study, we present an uncommon case of multifocal primary amelanotic meningeal melanomas mimicking lymphomas in the skull base and near the Sylvian fissure, which serves to provide reference value to the clinical diagnosis. Physicians should be aware of the existence of this special type in the clinical work.

Clinical characteristics and risk factors for a prolonged length of stay of patients with asymptomatic and mild COVID-19 during the wave of Omicron from Shanghai, China.

BACKGROUND: This study aims to investigate the clinical characteristics and the length of hospital stay (LOS), as well as risk factors for prolonged LOS in a cohort of asymptomatic and mild COVID-19 patients infected with the Omicron variant. METHODS: A total of 1166 COVID-19 patients discharged from the inpatient ward of the largest makeshift hospital (May 8-10, 2022) in Shanghai, China, were included. The demographics, medical history, and the lowest and admission cycle threshold (Ct) values of the RT-PCR tests for SARS-CoV-2 genes of the open reading frame 1ab (Ct-ORF) and the nucleocapsid protein (Ct-N) during hospitalization were recorded. Patients with LOS > 7 days, or LOS ≤ 7 days were included in the Prolonged group or the Control group, separately. The clinical characteristics and LOS of the participants in the two groups were described and compared. Multivariate Logistic and linear regression analyses were applied to explore the risk factors for prolonged LOS. The diagnostic efficacy of the lowest and admission Ct values for the Prolonged group was tested via the receiver operating characteristic (ROC) curve analysis. RESULTS: The median LOS was 6 days in the total study population. The age was older (45.52 ± 14.78 vs. 42.54 ± 15.30, P = 0.001), while both the lowest and admission Ct-ORF (27.68 ± 3.88 vs. 37.00 ± 4.62, P < 0.001; 30.48 ± 5.03 vs. 37.79 ± 3.81, P < 0.001) and Ct-N (25.79 ± 3.60 vs. 36.06 ± 5.39, P < 0.001; 28.71 ± 4.95 vs. 36.95 ± 4.59, P < 0.001) values were significantly lower in the Prolonged group. There were more mild cases in the Prolonged group (23.8% vs. 11.5%, P < 0.001). The symptom spectrum differed between the two groups. In multivariate analyses, age, disease category, and the lowest Ct-N values were shown to be associated with prolonged LOS. Besides, both the lowest and admission Ct-ORF (AUC = 0.911 and 0.873) and Ct-N (AUC = 0.912 and 0.874) showed robust diagnostic efficacy for prolonged LOS. CONCLUSIONS: Our study firstly reports the clinical characteristics and risk factors for prolonged LOS during the wave of the Omicron epidemic in Shanghai, China. These findings provide evidence for the early identification of asymptomatic and mild COVID-19 patients at a high risk of prolonged hospitalization who may require early intervention, and long-term monitoring and management.

Twelve New Seco-Pregnane Glycosides from Cynanchum taihangense.

For our interest in the potential biologically active and structurally unique steroidal glycosides, continued phytochemical investigation of Cynanchum taihangense was carried out; twelve new seco-pregnane glycosides, cynataihosides I-L (1-4), M-T (7-14), and two known glycosides, glaucoside A (5) and atratcynoside F (6), were isolated from the 95% ethanol extract of Cynanchum taihangense. Two new aglycones were found among compounds 10, 11, 13, and 14. The structures of the glycosides were elucidated based on 1D and 2D NMR spectroscopic data, HR-ESI-MS analysis, and chemical evidence. The cytotoxicity of compounds against three human tumor cell lines (HL-60, THP-1, and PC-3) were evaluated by MTT assay. Compound 11 displayed significant cytotoxicity against THP-1 and PC-3 cell line with IC50 values of 5.08 and 22.75 µm, respectively. Compounds 3 and 14 exhibited moderate and selective cytotoxicity on HL-60 and THP-1 with IC50 values of 17.78 and 16.02 µm, respectively.

Diagnostic possibility of the combination of exhaled nitric oxide and blood eosinophil count for eosinophilic asthma.

BACKGROUND: Tests to identify reversible airflow limitation are important in asthma diagnosis, but they are time-consuming and it may be difficult for patients to cooperate. We aimed to evaluate whether the combination of fractional exhaled nitric oxide (FeNO) and blood eosinophil (B-Eos) can be used to distinguish some asthma patients who could avoid objective tests. METHODS: We conducted a retrospective cohort study on 7463 suspected asthma cases between January 2014 and December 2019 in Chongqing, China, and identified 2349 patients with complete FeNO, B-Eos count, and spirometry data. Asthma was diagnosed by clinicians by the criteria of recurrent respiratory symptoms and a positive bronchial-provocation or bronchodilation test (BPT, BPD). We evaluated the diagnostic accuracy of FeNO or B-Eos alone or both in combination for asthma using receiver operating characteristic (ROC) curve analysis. RESULTS: In this study, 824 patients were diagnosed with asthma. When FeNO and B-Eos counts were used in combination, the area under the ROC curve (AUC) for diagnosing asthma increased slightly (0.768 vs. 0.745 [FeNO] or 0.728 [B-Eos]; both P < 0.001). The odds ratio for having asthma increased progressively with a gradual increase in FeNO or B-Eos count (both P < 0.001; assessed using the Cochran-Armitage trend test). Further analysis of in-series combinations of different threshold values for these biomarkers indicated that moderately elevated biomarker levels (FeNO > 40 ppb and B-Eos > 300 cells/µl) support a diagnosis of asthma because diagnostic specificity was > 95% and the positive likelihood ratio (PLR) was > 10. This conclusion was verified when selecting the 2017-2019 data as the internal validation dataset. CONCLUSION: FeNO or B-Eos count alone is insufficient to accurately diagnose asthma. Patients with moderately elevated biomarkers (FeNO > 40 ppb and B-Eos > 300 cells/µl) could be diagnosed with asthma and avoid objective tests when such tests are not feasible.

NPA-Cu2+ Complex as a Fluorescent Sensing Platform for the Selective and Sensitive Detection of Glyphosate.

Glyphosate is a highly effective, low-toxicity, broad-spectrum herbicide, which is extensively used in global agriculture to control weeds and vegetation. However, glyphosate has become a potential threat to human and ecosystem because of its excessive usage and its bio-concentration in soil and water. Herein, a novel turn-on fluorescent probe, N-n-butyl-4-(3-pyridin)ylmethylidenehydrazine-1,8-naphthalimide (NPA), is proposed. It efficiently detected Cu2+ within the limit of detection (LOD) of 0.21 µM and displayed a dramatic turn-off fluorescence response in CH3CN. NPA-Cu2+ complex was employed to selectively and sensitively monitor glyphosate concentrations in real samples accompanied by a fluorescence turn-on mode. A good linear relationship between NPA and Cu2+ of glyphosate was found in the range of 10-100 µM with an LOD of 1.87 µM. Glyphosate exhibited a stronger chelation with Cu2+ than NPA and the system released free NPA through competitive coordination. The proposed method demonstrates great potential in quantitatively detecting glyphosate in tap water, local water from Songhua River, soil, rice, millet, maize, soybean, mung bean, and milk with mild conditions, and is a simple procedure with obvious consequences and no need for large instruments or pretreatment.

Enhanced Electrochemical Performance of Aprotic Li-CO2 Batteries with a Ruthenium-Complex-Based Mobile Catalyst.

Li-CO2 batteries are regarded as next-generation high-energy-density electrochemical devices. However, the greatest challenge arises from the formation of the discharge product, Li2 CO3 , which would accumulate and deactivate heterogenous catalysts to cause huge polarization. Herein, Ru(bpy)3 Cl2 was employed as a solution-phase catalyst for Li-CO2 batteries and proved to be the most effective one screened so far. Spectroscopy and electrochemical analyses elucidate that the RuII center could interact with both CO2 and amorphous Li2 C2 O4 intermediate, thus promoting electroreduction process and delaying carbonate transformation. As a result, the charge potential is reduced to 3.86 V and over 60 discharge/charge cycles are achieved with a fixed capacity of 1000 mAh g-1 at a current density of 300 mA g-1 . Our work provides a new avenue to improve the electrochemical performance of Li-CO2 batteries with efficient mobile catalysts.

Using arterial blood as a substitute for venous blood in routine biochemistry parameter examinations in rabbits.

BACKGROUND: It has been widely accepted that there is a significant difference in peripheral blood oxygen between arteries and veins. Therefore, arterial blood has been collected for blood gas analysis, and venous blood, because it is convenient to collect, has been used for most laboratory examinations. However, venous blood is always difficult to collect in rabbits; in contrast, arterial blood is easier to obtain, and research on whether arterial blood can be used instead of venous blood for routine biochemical parameter examination is rare. Therefore, the present study was designed to explore whether arterial blood can be used as a substitute for venous blood for routine biochemistry parameter examination in rabbits. RESULTS: Three venous blood samples with gross hemolysis were excluded. Venous and arterial blood samples were obtained from forty-two rabbits. Arterial blood samples correlate well with venous blood in alkaline phosphatase (ALP), aspartate aminotransferase (AST), alanine transaminase (ALT), gamma-glutamyl transpeptidase (GGT), total protein (TP), globulin (GLB), serum total cholesterol (TC), serum triglyceride (TG), high-density lipoprotein cholesterol (HDL), low-density lipoprotein cholesterol (LDL), urea (Ur) and creatinine (Cr) levels by Deming regression analysis with slopes ranging from 0.893 to 1.176 and intercepts ranging from - 4.886 to 5.835. Bland-Altman analysis showed that the two sample parameters had 93%-98% of the points within the 95% consistency limits. There were significant differences between venous blood and arterial blood in ALP, TP, TC, TG, HDL, LDL and Cr, while AST, ALT, GGT, GLB and Ur showed no significant differences. CONCLUSIONS: Arterial blood can be a substitute for venous blood in routine biochemistry parameter examinations in rabbits, especially in situations where venous blood is difficult to collect.

A Bayesian regularized mediation analysis with multiple exposures.

Mediation analysis assesses the effect of study exposures on an outcome both through and around specific mediators. While mediation analysis involving multiple mediators has been addressed in recent literature, the case of multiple exposures has received little attention. With the presence of multiple exposures, we consider regularizations that allow simultaneous effect selection and estimation while stabilizing model fit and accounting for model selection uncertainty. In the framework of linear structural-equation models, we analytically show that a two-stage approach regularizing regression coefficients does not guarantee a unimodal posterior distribution and that a product-of-coefficient approach regularizing direct and indirect effects tends to penalize excessively. We propose a regularized difference-of-coefficient approach that bypasses these limitations. Using the connection between regularizations and Bayesian hierarchical models with Laplace prior, we develop an efficient Markov chain Monte Carlo algorithm for posterior estimation and inference. Through simulations, we show that the proposed approach has better empirical performances compared to some alternatives. The methodology is illustrated using data from two epidemiological studies in human reproduction.

Polybrominated diphenyl ethers and incident pregnancy loss: The LIFE Study.

BACKGROUND: Polybrominated diphenyl ethers (PBDEs) have not been studied in relation to incident pregnancy loss in human populations, despite their ubiquitous exposure and purported reproductive toxicity. OBJECTIVES: To investigate the association between preconception serum PBDE concentrations and incident pregnancy loss. METHODS: A preconception cohort of 501 couples was followed while trying to become pregnant, and for whom serum concentrations of 10 PBDE congeners were measured using gas chromatography-high resolution mass spectrometry. Pregnancy was prospectively identified as a positive home pregnancy test on the day of expected menstruation. Incident pregnancy loss was defined for 344 singleton pregnancies as a conversion to a negative home pregnancy test, menses, or clinical diagnosis depending upon gestational age. Cox proportional hazards models were used to estimate the hazard ratios (HRs) and 95% confidence intervals (CIs) for individual and summed PBDEs and incident pregnancy loss, adjusting for relevant covariates and male partners' information. In sensitivity analyses, inverse probability weighting was used to account for couples not becoming pregnant and, thereby, not at risk for loss. RESULTS: The incidence of prospectively observed pregnancy loss was 28%, and the serum concentrations of PBDE congeners in females were consistently associated with a higher hazard of incident pregnancy loss. Specifically, statistically significant hazard ratios (HRs) for incident pregnancy loss were observed for lower brominated PBDE congeners: 17 (HR 1.23; CI: 1.07-1.42), 28 (HR 1.25; CI: 1.03-1.52), 66 (HR 1.23; CI: 1.07-1.42), and homolog triBDE (HR: 1.25; CI: 1.05-1.49). Findings were robust to various model specifications explored in sensitivity analyses. CONCLUSIONS: Maternal preconception serum concentrations of specific PBDE congeners may increase the hazard of incident pregnancy.

Three new tetralol analogs from soil-derived fungus Myrothecium verrucaria with anti-inflammatory activity.

Three new tetralol analogs, myrochromanols A-C (1-3), together with 11 known trichothecenes (4-14), were isolated from a soil fungus Myrothecium verrucaria HL-P-1. The structures of the three new compounds were elucidated by extensive spectroscopic analysis including HRESIMS, NMR, and ECD calculation. All of the new compounds were tested for their anti-inflammatory activity and cytotoxicity. Compounds 1 and 3 inhibited lipopolysaccharide (LPS)-induced NO production in BV2 cells with IC50 values of 26.04 and 25.80 µM, respectively.

2-Methyl-versiquinazoline C, a new fumiquinazoline-type alkaloid from the fungus Aspergillus flavipes PJ03-11.

A new fumiquinazoline-type alkaloid 2-methyl-versiquinazoline C (1), together with six known compounds (2-7), was isolated from Aspergillus flavipes PJ03-11 using OSMAC method. Their structures were elucidated on the basis of extensive spectroscopic analysis, and the absolute configuration of compound 1 was determined by the experimental and calculated ECD data. In addition, the cytotoxic activities against three human cancer cell lines (HL-60, THP-1, and PC-3) were evaluated.

Structure determination of two new C21 steroidal glycosides from Cynanchum komarovii.

Two new 13,14:14,15-disecopregnane-type C21 steroidal glycosides, namely komarosides R (1) and S (2), along with four known compounds (3-6), were obtained from the 95% ethanol extract of the whole herbs of Cynanchum komarovii Al.Iljinski (Asclepiadaceae). The structures of new compounds were elucidated on the basis of 1D, 2D NMR spectroscopic data and acid hydrolysis. Compounds 1 and 2 showed potent inhibitory activities against human leukemia cell line (HL-60) with IC50 values being 6.2 and 17.6 µM, respectively, compared to the positive control 5-fluorouracil (6.4 µM).

C21 steroidal glycosides from Cynanchum taihangense.

Two new C21 steroidal glycosides, cynataihosides E (1) and F (2), together with a known one, sublanceoside H2 (3), were isolated from Cynanchum taihangense. The aglycone of cynataihoside F (2) was also a new compound. Their structures were elucidated on the basis of NMR spectroscopic data, HR-ESI-MS analysis, and chemical evidence. Their cytotoxic activities against three human tumor cell lines (HL-60, THP1, and Caco2) were reported.

Estimating Bayesian Phylogenetic Information Content.

Measuring the phylogenetic information content of data has a long history in systematics. Here we explore a Bayesian approach to information content estimation. The entropy of the posterior distribution compared with the entropy of the prior distribution provides a natural way to measure information content. If the data have no information relevant to ranking tree topologies beyond the information supplied by the prior, the posterior and prior will be identical. Information in data discourages consideration of some hypotheses allowed by the prior, resulting in a posterior distribution that is more concentrated (has lower entropy) than the prior. We focus on measuring information about tree topology using marginal posterior distributions of tree topologies. We show that both the accuracy and the computational efficiency of topological information content estimation improve with use of the conditional clade distribution, which also allows topological information content to be partitioned by clade. We explore two important applications of our method: providing a compelling definition of saturation and detecting conflict among data partitions that can negatively affect analyses of concatenated data. [Bayesian; concatenation; conditional clade distribution; entropy; information; phylogenetics; saturation.].

Massilia buxea sp. nov., isolated from a rock surface.

A Gram-stain-negative, rod-shaped and motile bacterial strain, designated A9T, was isolated from the surface of rock collected from the shore of Nvshan lake in Mingguang, Anhui province, China. Phylogenetic analysis based on 16S rDNA sequence data showed that strain A9T was affiliated with the genus Massilia and showed the highest sequence similarities to Massilia plicata KCTC 12344T (98.8 %) and Massilia lurida CGMCC 1.10822T (97.9 %). The major fatty acids (>5 %) were summed feature 3 (C16 : 1ω7c and/or C15 : 0 iso 2-OH), C16 : 0 and C18 : 1ω7c. Strain A9T contained Q-8 as the predominant ubiquinone and diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminophospholipid as the predominant polar lipids. The DNA G+C content was 69.9 mol%. Mean DNA-DNA relatedness values between strain A9T and its closest phylogenetic relatives, M. plicata KCTC 12344T and M. lurida CGMCC 1.10822T, were 38.8 % and 23.23 %, respectively. On the basis of the results obtained in this study, strain A9T is considered to represent a novel species of the genus Massilia, for which the name Massilia buxea sp. nov. is proposed. The type strain is A9T (=DSM 103547T=CGMCC 1.15931T=KCTC 52429T).