Unraveling the evolutionary patterns and phylogenomics of coronaviruses: A consensus network approach.

The COVID-19 pandemic emphasizes the significance of studying coronaviruses (CoVs). This study investigates the evolutionary patterns of 350 CoVs using four structural proteins (S, E, M, and N) and introduces a consensus methodology to construct a comprehensive phylogenomic network. Our clustering of CoVs into 4 genera is consistent with the current CoV classification. Additionally, we calculate network centrality measures to identify CoV strains with significant average weighted degree and betweenness centrality values, with a specific focus on RaTG13 in the beta genus and NGA/A116E7/2006 in the gamma genus. We compare the phylogenetics of CoVs using our distance-based approach and the character-based model with IQ-TREE. Both methods yield largely consistent outcomes, indicating the reliability of our consensus approach. However, it is worth mentioning that our consensus method achieves an approximate 5000-fold increase in speed compared to IQ-TREE when analyzing the data set of 350 CoVs. This improved efficiency enhances the feasibility of conducting large-scale phylogenomic studies on CoVs.

MSClustering: A Cytoscape Tool for Multi-Level Clustering of Biological Networks.

MSClustering is an efficient software package for visualizing and analyzing complex networks in Cytoscape. Based on the distance matrix of a network that it takes as input, MSClustering automatically displays the minimum span clustering (MSC) of the network at various characteristic levels. To produce a view of the overall network structure, the app then organizes the multi-level results into an MSC tree. Here, we demonstrate the package's phylogenetic applications in studying the evolutionary relationships of complex systems, including 63 beta coronaviruses and 197 GPCRs. The validity of MSClustering for large systems has been verified by its clustering of 3481 enzymes. Through an experimental comparison, we show that MSClustering outperforms five different state-of-the-art methods in the efficiency and reliability of their clustering.

Factors Related to Passive Social Withdrawal and Active Social Avoidance in Schizophrenia.

ABSTRACT: Social withdrawal in schizophrenia may be a result of "passive" motivation (reduced drive to engage) or "active" motivation (increased drive to avoid). We conducted a cross-sectional, between-subjects study using self-report measures and social cognition tasks to evaluate the relationships between motivational subtypes, social abilities, and social functioning in schizophrenia spectrum (n = 52, ages 19-34). Regression models showed significant differences in passive and active withdrawal. Passive, but not active, motivation predicted social functioning as measured by a clinical interview. This suggests that motivation, especially passive type, plays an important role in social withdrawal in schizophrenia. However, on a self-report measure of social functioning, neither passive nor active motivation predicted outcomes, suggesting a potential disconnect between observer versus self-report measures when assessing social motivation. Furthermore, performance on tasks of social abilities did not predict motivation, which supports the idea that motivation is distinct from social ability and should be specifically addressed in treatment.

Combining MRI and cognitive evaluation to classify concussion in university athletes.

Current methods of concussion assessment lack the objectivity and reliability to detect neurological injury. This multi-site study uses combinations of neuroimaging (diffusion tensor imaging and resting state functional MRI) and cognitive measures to train algorithms to detect the presence of concussion in university athletes. Athletes (29 concussed, 48 controls) completed symptom reports, brief cognitive evaluation, and MRI within 72 h of injury. Hierarchical linear regression compared groups on cognitive and neuroimaging measures while controlling for sex and data collection site. Logistic regression and support vector machine models were trained using cognitive and neuroimaging measures and evaluated for overall accuracy, sensitivity, and specificity. Concussed athletes reported greater symptoms than controls (∆R2 = 0.32, p < .001), and performed worse on tests of concentration (∆R2 = 0.07, p < .05) and delayed memory (∆R2 = 0.17, p < .001). Concussed athletes showed lower functional connectivity within the frontoparietal and primary visual networks (p < .05), but did not differ on mean diffusivity and fractional anisotropy. Of the cognitive measures, classifiers trained using delayed memory yielded the best performance with overall accuracy of 71%, though sensitivity was poor at 46%. Of the neuroimaging measures, classifiers trained using mean diffusivity yielded similar accuracy. Combining cognitive measures with mean diffusivity increased overall accuracy to 74% and sensitivity to 64%, comparable to the sensitivity of symptom report. Trained algorithms incorporating both MRI and cognitive performance variables can reliably detect common neurobiological sequelae of acute concussion. The integration of multi-modal data can serve as an objective, reliable tool in the assessment and diagnosis of concussion.

Effect of Brief Training to Identify Autism Spectrum Disorder During Toddler Well-Child Care Visits.

OBJECTIVE: To examine the effect of a brief Enhanced training using the information-motivation-behavior (IMB) change model on improving providers' surveillance rates and accuracy of autism spectrum disorder (ASD) detection. METHOD: Toddlers (n = 5,672) were screened for ASD during their pediatric well-child visits. Pediatric providers (n = 120) were randomized to receive Enhanced (incorporating components of the IMB model) or Control training. Providers indicated whether they had an ASD concern at each well-child visit. Toddlers who were positive on any screener and/or whose provider indicated ASD concern were invited for a diagnostic evaluation. Differences in provider-indicated ASD concerns before and after training were evaluated using log-linear analyses. RESULTS: The Enhanced training did not have a significant effect on provider-endorsed ASD concerns (p = 0.615) or accuracy of endorsing concerns (p = 0.619). Providers in the Control training showed a significant reduction in indicating whether or not they had concerns after the training (from 71.9% to 64.3%), which did not occur in the Enhanced group. The Enhanced training led to more frequent endorsements of language (χ2 = 8.772, p = 0.003) and restricted and repetitive behavior (χ2 = 7.918, p = 0.005) concerns for children seen after training. CONCLUSION: Provider training had limited impact on ASD surveillance, indicating the importance of using formal screening instruments that rely on parent report during well-child visits to complement developmental surveillance. Future research should examine whether providers who indicate specific concerns are more likely to accurately refer children for ASD evaluations.

Early and Repeated Screening Detects Autism Spectrum Disorder.

OBJECTIVE: To evaluate timing and accuracy of early and repeated screening for autism spectrum disorder (ASD) during well-child visits. STUDY DESIGN: Using a longitudinal study design, toddlers (n = 5784) were initially screened at 12 (n = 1504), 15 (n = 1228), or 18 (n = 3052) months during well-child visits, and rescreened at 18, 24, and 36 months. Of those screened, 368 toddlers attended an ASD evaluation after a positive screen and/or a provider concern for ASD at any visit. RESULTS: Screens initiated at 12 months yielded an ASD diagnosis significantly earlier than at 15 months (P = .003, d = 0.99) and 18 months (P < .001, d = 0.97). Cross-group overall sensitivity of the initial screen was .715 and specificity was .959. Repeat screening improves sensitivity (82.1%), without notably decreasing specificity (all >93.5%). Screening at 18 months resulted in significantly higher positive predictive value than at 12 months (X2 (1, n = 221) = 9.87, P = .002, OR = 2.60) and 15 months (X2 (1, n = 208) = 14.57, P < .001, OR = 3.67). With repeat screening, positive predictive value increased for all screen groups, but the increase was not significant. CONCLUSIONS: Screening as early as 12 months effectively identifies many children at risk for ASD. Children screened at 12 months receive a diagnosis of ASD significantly earlier than peers who are first screened at later ages, facilitating earlier intervention. However, as the sensitivity is lower for a single screen, screening needs to be repeated.

Hesperetin-5,7,3'-O-Trimethylether Dually Inhibits Phosphodiesterase 3/4 and Methacholine-Induced Airway Hyperresponsiveness in Sensitized and Challenged Mice.

INTRODUCTION: Hesperetin-5,7,3'-O-trimethylether (HTME), a synthetic liposoluble hesperetin, has been reported to be a dual phosphodiesterase (PDE)3/4 inhibitor. We investigated its inhibitory effects on methacholine (MCh)-induced airway hyperresponsiveness (AHR) and its potential for treating atypical asthma and COPD. METHODS: FlexiVent system was used to determine AHR in ovalbumin (OVA) sensitized and challenged mice. Determination of cytokines was performed by using mouse T helper (Th)1/Th2 cytokine CBA kits, and of total immunoglobulin (Ig)E and OVA-specific IgE using ELISA kits. The number of inflammatory cells was counted using a hemocytometer. Xylazine/ketamine-induced anesthesia was to assess nausea, vomiting, and gastric hypersecretion in these mice. RESULTS: HTME dually and competitively inhibited PDE3/4 activities in the Lineweaver-Burk analysis. HTME (30 and 100 µmol/kg) dose-dependently and significantly decreased the airway resistance (RL) and increased lung dynamic compliance (Cdyn) values induced by MCh. It significantly suppressed numbers of total inflammatory cells and neutrophils, and levels of cytokines in bronchoalveolar lavage fluid (BALF). HTME dose-dependently and significantly inhibited total and OVA-specific IgE levels in the BALF and serum. However, HTME did not influence xylazine/ketamine-induced anesthesia. CONCLUSION: HTME exerted anti-inflammatory and bronchodilator effects and may be useful in treating chronic obstructive pulmonary disease and allergic atypical asthma with no gastrointestinal side effects.

SeQuery: an interactive graph database for visualizing the GPCR superfamily.

The rate at which new protein and gene sequences are being discovered has grown explosively in the omics era, which has increasingly complicated the efficient characterization and analysis of their biological properties. In this study, we propose a web-based graphical database tool, SeQuery, for intuitively visualizing proteome/genome networks by integrating the sequential, structural and functional information of sequences. As a demonstration of our tool's effectiveness, we constructed a graph database of G protein-coupled receptor (GPCR) sequences by integrating data from the UniProt, GPCRdb and RCSB PDB databases. Our tool attempts to achieve two goals: (i) given the sequence of a query protein, correctly and efficiently identify whether the protein is a GPCR, and, if so, define its sequential and functional roles in the GPCR superfamily; and (ii) present a panoramic view of the GPCR superfamily and its network centralities that allows users to explore the superfamily at various resolutions. Such a bottom-up-to-top-down view can provide the users with a comprehensive understanding of the GPCR superfamily through interactive navigation of the graph database. A test of SeQuery with the GPCR2841 dataset shows that it correctly identifies 99 out of 100 queried protein sequences. The developed tool is readily applicable to other biological networks, and we aim to expand SeQuery by including additional biological databases in the near future.

Butylidenephthalide facilitates contractions via nonspecific binding to receptors in isolated guinea-pig vas deferens.

Context: Butylidenephthalide (Bdph) has been reported to inhibit rat uterine contractions, but significantly potentiate the noradrenaline (NA)-induced contractions in guinea-pig vas deferens (GPVDs). Objective: The present study elucidates the binding specificity of Bdph in GPVD to potentiate contractions. Materials and methods: Electrical field stimulation (EFS, supramaximal voltage, 1 ms and 1 Hz) or exogenous NA (50 µM) was applied to the GPVD in Krebs or 1/10 Mg-Tyrode's solution, respectively. After the clonidine (10 nM)-induced twitch inhibition or the exogenous NA-induced contractions reached a constant, Bdph (50 µM) was added 2 min prior to the subsequent addition of NA (50 µM). Three experiments were performed. In the presence of Bdph (100 µM), the release of NA in the medium and remaining NA content in the tissues were determined after EFS-stimulation. Results: Bdph (100 µM) significantly antagonized the clonidine (10 nM)-induced twitch inhibition from 22.5 ± 2.1 to -11.4 ± 1.6% (n = 6) and dibutyryl-cAMP (300 µM) from 25.7 ± 3.2 to 7.9 ± 4.0% (n = 8). Bdph (100 µM) significantly increased the electrically stimulated release of NA from 393.0 ± 109.5 to 1000.0 ± 219.1 ng/g (n = 6). Bdph (50 µM) potentiated the exogenous NA (50 µM)-induced contractions from 3.0 ± 0.06 to 3.9 ± 0.06 g (n = 3), but after washout of Bdph, the response to NA gradually curtailed. Discussion and conclusions: Bdph action may be through the nonspecific binding of the butylidene group to prejunctional α2- and postjunctional α1-adrenoceptors to reversibly block K+ channels, and irreversibly block VDCCs on the smooth muscle cell membrane, respectively.

Risk factors and prediction model for persistent breast-cancer-related lymphedema: a 5-year cohort study.

PURPOSE: Breast-cancer-related lymphedema (BCRL) can be a transient or persistent condition. The aims of this study were to (1) identify and weigh the risk factors for persistent lymphedema (PLE) among all patients with BCRL and (2) establish a prediction model for the occurrence of PLE. METHODS: A cohort of 342 patients with BCRL with a median follow-up of 5 years after the onset of swelling was analyzed. PLE was defined as a hardening of the subcutaneous tissue, the persistence of the circumferential difference (CD) between arms, or a flare-up of swelling during follow-up. Multiple logistic regression was used to identify risk factors for PLE, including tumors, treatments, and patient-related factors. The prediction accuracy of the model was assessed using the area under the receiver operating characteristic curve (AUC). RESULTS: Of the 342 patients with BCRL, 229 (67%) had PLE. Multiple logistic regression analysis revealed that the number of lymph node metastases (p = 0.012), the maximal CD between arms at the first occurrence of swelling (p < 0.001), and the largest difference during follow-up (p < 0.001) were significant predictors for PLE. The corresponding AUC was 0.908. Although inclusion of body weight gains (p = 0.008) and maximal CD at the latest follow-up (p = 0.002) increased the analytical accuracy (AUC = 0.920), the resulting AUC values (p = 0.113) were not significantly different. CONCLUSIONS: BCRL is persistent in two thirds of patients. Patients with more lymph node metastases, weight gain, and larger CD since the onset of swelling and during follow-up have an increased likelihood of developing PLE.

Mechanisms of butylidenephthalide for twitch facilitation in electrically stimulated mouse vas deferens.

CONTEXT: The rhizome of Ligusticum chuaxiong Hort. (Umbelliferae) has been used by Chinese for several thousand years. Its main constituent, butylidenephthalide (Bdph), was proved to be active in inhibiting rat uterine contractions induced by prostaglandin F2α and was reported to be a nonspecific antispamodic and a blocker of voltage-dependent Ca2+ channels (VDCCs). OBJECTIVES: The present study investigates the mechanisms of Bdph for twitch facilitation in ICR mouse vas deferens (MVD). MATERIALS AND METHODS: Electrical field stimulation (EFS, supramaximal voltage ranging from 60-90 V, 1 ms, 0.2 Hz) was applied to the isolated MVD in Krebs solution. Interactions between Bdph (50 µM) and calcium antagonist (verapamil, diltiazem or aspaminol) on the EFS-evoked twitch responses were determined. The number of experiments was 3-18. RESULTS: Bdph (50 µM)-induced twitch facilitations from 100 to 391.9% were unrelated to activation of postjunctional cholinergic or adrenergic receptors. Verapamil and Bdph unabolished the twitch facilitation each other. Diltiazem unabolished the Bdph-induced twitch facilitation. In contrast, Bdph abolished those induced by diltiazem. Aspaminol at 20 µM abolished the Bdph-induced twitch facilitation. In contrast, Bdph abolished those induced by aspaminol. Tetraethylammonium and 4-aminopyridine, the K+ channel blockers, significantly augmented the Bdph-induced twitch facilitation. DISCUSSION AND CONCLUSIONS: Bdph may bind to the different, more and same subtypes of VDCCs from verapamil, than diltiazem, and as aspaminol does on prejunctional membrane, respectively. Besides a blocker of VDCCs, Bdph may be a blocker of K+ channels on prejunctional membrane. Thus, Bdph depolarized the membrane and facilitated the cumulative Ca2+-induced twitch responses.

Long-range gamma phase synchronization as a compensatory strategy during working memory in high-performing patients with schizophrenia.

Working memory deficits in schizophrenia may be associated with impairments in the integration of neural activity across a distributed network of cortical areas. However, evaluation of the contribution of this integration to working memory impairments in patients is severely confounded by behavioral performance. In the present multidimensional-neuroimaging study, measures of neural oscillations at baseline and during a working memory task, baseline gamma-aminobutyric acid (GABA) level in the left dorsolateral prefrontal cortex (DLPFC), and behavioral performance were obtained. Controlling behavioral performance by recruiting only "high-performing" patients with schizophrenia, we investigated whether the strength of cross-area communications differs between patients with schizophrenia and healthy participants under accurate and equivalent behavioral performance. Results of phase-locking value indicated that these high-performing patients recruited significantly more between frontal and occipital regions in the left hemisphere, t(13) = -2.16, p = .05, Cohen's d = -1.20, and between frontal and temporal regions in the right hemisphere, t(13) = -2.63, p = .02, Cohen's d = -1.46. These cross-area communication patterns may be associated with visuoverbal and visuospatial working memory networks of the left and right hemispheres, respectively. Moreover, correlations of patient's cross-area communication with in vivo GABA levels of the left DLPFC revealed a significant positive relationship (r = .77, p = .04), demonstrating that the critical role of GABA functions in gamma band oscillations may go beyond local neuronal assemblies in the left DLPFC. Altogether, these exploratory findings point to the heterogeneity among schizophrenia patients and highlight the notion that high-performing patients may engage in potential compensatory mechanisms and may represent a subgroup of patients that may be categorically or dimensionally divergent in psychopathology.

Effects of chronic ketamine on hippocampal cross-frequency coupling: implications for schizophrenia pathophysiology.

Disrupted neuronal oscillations have been identified as a potentially important biomarker for the perceptual and cognitive symptoms of schizophrenia. Emerging evidences suggest that interactions between different frequency bands, cross-frequency coupling (CFC), serve an important role in integrating sensory and cognitive information and may contribute to disease pathophysiology. In this study, we investigated the effects of 14-day consecutive administration of ketamine (30 mg/kg i.p.) vs. saline on alterations in amplitude and changes in the coupling of low-frequency (0-30 Hz) phase and high-frequency (30-115 Hz) amplitude in the CA1 hippocampus of Long Evans rats. Intracranial electrode recordings were conducted pre- and post-injection while the animals performed a foraging task on a four-arm rectangular maze. Permutation analysis of frequency band-specific change in amplitudes revealed between-group differences in theta (6-12 Hz) and slow gamma (25-50 Hz) but not fast gamma (65-100 Hz) bands at both slow and fast speeds. Chronic ketamine challenge resulted in decreased coupling (pre to post) at slow speeds but increased coupling at faster speeds, compared to either no or modest increased coupling in the saline group. These results demonstrate that chronic ketamine administration alters the interaction of low-frequency phase and high-frequency oscillations chronically and that such coupling varies as a function of locomotive speed. These findings provide evidence for the potential relevance of CFC to the pathophysiology of schizophrenia.

An algorithm for the split-feasibility problems with application to the split-equality problem.

In this paper, we study the split-feasibility problem in Hilbert spaces by using the projected reflected gradient algorithm. As applications, we study the convex linear inverse problem and the split-equality problem in Hilbert spaces, and we give new algorithms for these problems. Finally, numerical results are given for our main results.

Visualizing the GPCR Network: Classification and Evolution.

In this study, we delineate an unsupervised clustering algorithm, minimum span clustering (MSC), and apply it to detect G-protein coupled receptor (GPCR) sequences and to study the GPCR network using a base dataset of 2770 GPCR and 652 non-GPCR sequences. High detection accuracy can be achieved with a proper dataset. The clustering results of GPCRs derived from MSC show a strong correlation between their sequences and functions. By comparing our level 1 MSC results with the GPCRdb classification, the consistency is 87.9% for the fourth level of GPCRdb, 89.2% for the third level, 98.4% for the second level, and 100% for the top level (the lowest resolution level of GPCRdb). The MSC results of GPCRs can be well explained by estimating the selective pressure of GPCRs, as exemplified by investigating the largest two subfamilies, peptide receptors (PRs) and olfactory receptors (ORs), in class A GPCRs. PRs are decomposed into three groups due to a positive selective pressure, whilst ORs remain as a single group due to a negative selective pressure. Finally, we construct and compare phylogenetic trees using distance-based and character-based methods, a combination of which could convey more comprehensive information about the evolution of GPCRs.

Virulence of Japanese Encephalitis Virus Genotypes I and III, Taiwan.

The virulence of genotype I (GI) Japanese encephalitis virus (JEV) is under debate. We investigated differences in the virulence of GI and GIII JEV by calculating asymptomatic ratios based on serologic studies during GI- and GIII-JEV endemic periods. The results suggested equal virulence of GI and GIII JEV among humans.

Hesperetin-5,7,3'-O-triacetate suppresses airway hyperresponsiveness in ovalbumin-sensitized and challenged mice without reversing xylazine/ketamine-induced anesthesia in normal mice.

BACKGROUND: We recently reported that hesperetin-5,7,3'-O-triacetate (HTA) dually inhibited phosphodiesterase (PDE)3/4 with a therapeutic ratio of 20.8. The application and development of PDE4 inhibitors for treating asthma or COPD are limited by their side effects, such as nausea, vomiting and gastric hypersecretion. PDE4 inhibitors were reported to reverse xylazine/ketamine-induced anesthesia in rats and triggered vomiting in ferrets. Thus the reversing effect of HTA on xylazine/ketamine-induced anesthesia in mice was studied to assess emetic effect of HTA. The aim of this study was to prove the therapeutic effect of HTA without vomiting effect at an effective dose for treating COPD. METHODS: Ten female BALB/c mice in each group were sensitized by ovalbumin (OVA) on days 0 and 14. On day 21, these mice were emphasized the sensitization by Freund's complete adjuvant. Mice were challenged by 1% OVA nebulization on days 28, 29, and 30. Airway hyperresponsiveness (AHR) was assessed on day 32 in each group, using the FlexiVent system to determine airway resistance (RL) and lung dynamic compliance (Cdyn) in anesthetized ovalbumin (OVA)-sensitized and challenged mice. Each group was orally administered HTA (10 ~ 100 µmol/kg), roflumilast (1 and 5 mg/kg) or vehicles (controls) 2 h before and 6 and 24 h after OVA provocation. For comparison, sham-treated mice were challenged with saline instead of 1% OVA. The ability to reverse xylazine/ketamine-induced anesthesia by HTA or roflumilast for 3 h was determined in normal mice. We used roflumilast, a selective PDE4 inhibitor and bronchodilator for severe COPD approved by the US Food and Drug Administration, as a reference drug. RESULTS: In the results, HTA (100 µmol/kg, p.o.) or roflumilast (5 mg/kg, p.o.) significantly suppressed all RL values of MCh at 0.78 ~ 25 mg/mL and enhanced Cdyn values of MCh at 3.125 ~ 25 mg/mL compared to OVA-sensitized and -challenged control mice. Orally administered 1, 3 or 10 mg/kg roflumilast, but not 30 or 100 µmol/kg HTA, significantly reversed xylazine/ketamine-induced anesthesia. CONCLUSIONS: In contrast to roflumilast, HTA may ameliorate COPD but induce few side effects of nausea, vomiting and gastric hypersecretion at an effective dose for treating COPD, because HTA did not reverse xylazine/ketamine-induced anesthesia in mice.

Synchronization and Inter-Layer Interactions of Noise-Driven Neural Networks.

In this study, we used the Hodgkin-Huxley (HH) model of neurons to investigate the phase diagram of a developing single-layer neural network and that of a network consisting of two weakly coupled neural layers. These networks are noise driven and learn through the spike-timing-dependent plasticity (STDP) or the inverse STDP rules. We described how these networks transited from a non-synchronous background activity state (BAS) to a synchronous firing state (SFS) by varying the network connectivity and the learning efficacy. In particular, we studied the interaction between a SFS layer and a BAS layer, and investigated how synchronous firing dynamics was induced in the BAS layer. We further investigated the effect of the inter-layer interaction on a BAS to SFS repair mechanism by considering three types of neuron positioning (random, grid, and lognormal distributions) and two types of inter-layer connections (random and preferential connections). Among these scenarios, we concluded that the repair mechanism has the largest effect for a network with the lognormal neuron positioning and the preferential inter-layer connections.