Illumina and Nanopore sequencing in culture-negative samples from suspected lower respiratory tract infection patients.

Objective: To evaluate the diagnostic value of metagenomic sequencing technology based on Illumina and Nanopore sequencing platforms for patients with suspected lower respiratory tract infection whose pathogen could not be identified by conventional microbiological tests. Methods: Patients admitted to the Respiratory and Critical Care Medicine in Shanghai Ruijin Hospital were retrospectively studied from August 2021 to March 2022. Alveolar lavage or sputum was retained in patients with clinically suspected lower respiratory tract infection who were negative in conventional tests. Bronchoalveolar lavage fluid (BALF) samples were obtained using bronchoscopy. Sputum samples were collected, while BALF samples were not available due to bronchoscopy contraindications. Samples collected from enrolled patients were simultaneously sent for metagenomic sequencing on both platforms. Results: Thirty-eight patients with suspected LRTI were enrolled in this study, consisting of 36 parts of alveolar lavage and 2 parts of sputum. According to the infection diagnosis, 31 patients were confirmed to be infected with pathogens, while 7 patients were diagnosed with non-infectious disease. With regard to the diagnosis of infectious diseases, the sensitivity and specificity of Illumina and Nanopore to diagnose infection in patients were 80.6% vs. 93.5% and 42.9 vs. 28.6%, respectively. In patients diagnosed with bacterial, Mycobacterium, and fungal infections, the positive rates of Illumina and Nanopore sequencer were 71.4% vs. 78.6%, 36.4% vs. 90.9%, and 50% vs. 62.5%, respectively. In terms of pathogen diagnosis, the sensitivity and specificity of pathogens detected by Illumina and Nanopore were 55.6% vs. 77.8% and 42.9% vs. 28.6%, respectively. Among the patients treated with antibiotics in the last 2 weeks, 61.1% (11/18) and 77.8% (14/18) cases of pathogens were accurately detected by Illumina and Nanopore, respectively, among which 8 cases were detected jointly. The consistency between Illumina and diagnosis was 63.9% (23/36), while the consistency between Nanopore and diagnosis was 83.3% (30/36). Between Illumina and Nanopore sequencing methods, the consistency ratio was 55% (22/42) based on pathogen diagnosis. Conclusion: Both platforms play a certain value in infection diagnosis and pathogen diagnosis of CMT-negative suspected LRTI patients, providing a theoretical basis for clinical accurate diagnosis and symptomatic treatment. The Nanopore platform demonstrated potential advantages in the identification of Mycobacterium and could further provide another powerful approach for patients with suspected Mycobacterium infection.

New Hydroxyphenylacetic Acids and α-Pyrone Derivative from the Deep-Sea Cold Seep Sediment-Derived Fungus Penicillium corylophilum CS-682.

Two pairs of new enantiomeric hydroxyphenylacetic acid derivatives, (±)-corylophenols A and B ((±)-1 and (±)-2), a new α-pyrone analogue, corylopyrone A (3), and six andrastin-type meroterpenoids (4-9) were isolated and identified from the deep-sea cold-seep sediment-derived fungus Penicillium corylophilum CS-682. Their structures and stereo configurations were determined by detailed spectroscopic analysis of NMR and MS data, chiral HPLC analysis, J-based configuration analysis, and quantum chemical calculations of ECD, specific rotation, and NMR (with DP4+ probability analysis). Compound 3 showed inhibitory activity against some strains of pathogenic bacteria.

Palladium-catalyzed ring-opening [5+2] annulation of vinylethylene carbonates (VECs) and C5-substituted Meldrum's acids: rapid synthesis of 7-membered lactones.

A novel approach for the synthesis of unsaturated 7-membered lactones by Pd-catalyzed [5+2] dipolar cycloaddition of vinylethylene carbonates (VECs) and C5-substituted Meldrum's acid derivatives has been developed. Various Meldrum's acid derivatives worked well in this reaction under mild reaction conditions. A variety of 7-membered lactones can be accessed in a facile manner in moderate to good yields by employing easily prepared Meldrum's acid derivatives.

Bromodomain protein BRD8 regulates cell cycle progression in colorectal cancer cells through a TIP60-independent regulation of the pre-RC complex.

Bromodomain-containing protein 8 (BRD8) is a subunit of the NuA4/TIP60-histone acetyltransferase complex. Although BRD8 has been considered to act as a co-activator of the complex, its biological role remains to be elucidated. Here, we uncovered that BRD8 accumulates in colorectal cancer cells through the inhibition of ubiquitin-dependent protein degradation by the interaction with MRG domain binding protein. Transcriptome analysis coupled with genome-wide mapping of BRD8-binding sites disclosed that BRD8 transactivates a set of genes independently of TIP60, and that BRD8 regulates the expression of multiple subunits of the pre-replicative complex in concert with the activator protein-1. Depletion of BRD8 induced cell-cycle arrest at the G1 phase and suppressed cell proliferation. We have also shown that the bromodomain of BRD8 is indispensable for not only the interaction with histone H4 or transcriptional regulation but also its own protein stability. These findings highlight the importance of bromodomain as a therapeutic target.

Thirdhand tobacco smoke exposure increases the genetic background-dependent risk of pan-tumor development in Collaborative Cross mice.

Increasing evidence has shown that thirdhand smoke (THS) exposure is likely to induce adverse health effects. An important knowledge gap remains in our understanding of THS exposure related to cancer risk in the human population. Population-based animal models are useful and powerful in investigating the interplay between host genetics and THS exposure on cancer risk. Here, we used the Collaborative Cross (CC) mouse population-based model system, which recapitulates the genetic and phenotypic diversity observed in the human population, to assess cancer risk after a short period of exposure, between 4 and 9 weeks of age. Eight CC strains (CC001, CC019, CC026, CC036, CC037, CC041, CC042 and CC051) were included in our study. We quantified pan-tumor incidence, tumor burden per mouse, organ tumor spectrum and tumor-free survival until 18 months of age. At the population level, we observed a significantly increased pan-tumor incidence and tumor burden per mouse in THS-treated mice as compared to the control (p = 3.04E-06). Lung and liver tissues exhibited the largest risk of undergoing tumorigenesis after THS exposure. Tumor-free survival was significantly reduced in THS-treated mice compared to control (p = 0.044). At the individual strain level, we observed a large variation in tumor incidence across the 8 CC strains. CC036 and CC041 exhibited a significant increase in pan-tumor incidence (p = 0.0084 and p = 0.000066, respectively) after THS exposure compared to control. We conclude that early-life THS exposure increases tumor development in CC mice and that host genetic background plays an important role in individual susceptibility to THS-induced tumorigenesis. Genetic background is an important factor that should be taken into account when determining human cancer risk of THS exposure.

Case report: Clinical characteristics of two cases of pneumonia caused with different strains of Chlamydia psittaci.

Background: With the development of metagenomic sequencing technologies, more and more cases of pneumonia caused with Chlamydia psittaci (C. psittaci) have been reported. However, it remains unknown about the characteristics of patients with pneumonia caused by different strains of C. psittaci. Here, we shared the clinical characteristics of two cases of pneumonia caused with C. psittaci strains SZ18-2 and SZ15 which were rarely identified in humans. Case presentation: Case 1: A 69-year-old male farmer who fed ducks presented to hospital for cough, diarrhea and lethargy with the temperature of 39.8°C. Case 2: A 48-year-old male worker who slaughtered ducks was transferred to hospital for high fever, cough, myalgia, diarrhea and loss of appetite. Both patients did not take any protective measures (wearing face masks or gloves) while processing ducks. C. psittaci pneumonia was diagnosed by metagenomic next-generation sequencing and polymerase chain reaction. After treatment with doxycycline and azithromycin individually, they recovered well and discharged from hospital. Through OmpA sequencing, two different strains of SZ18-2 and SZ15 were identified in case 1 and case 2, respectively. Conclusions: Patients infected with different strains of C. psittaci may own different clinical manifestations. C. psittaci infection should be suspected when pneumonia appears, accompanied by digestive symptoms and multiple organ dysfunction, especially under the exposure of specific birds.

Performance evaluation and clinical validation of optimized nucleotide MALDI-TOF-MS for mycobacterial identification.

Objective: To evaluate the performance and validate the diagnostic value of a nucleotide matrix-assisted laser desorption time-of-flight mass spectrometry (MALDI-TOF-MS) with the analysis process optimized in identification of mycobacterium species. Methods: The optimized analysis process was used for mycobacterial identification in the nucleic MALDI-TOF-MS. 108 samples were used for assessing the performance of nucleic MALDI-TOF-MS, including 25 reference standards, 37 clinical isolates, 37 BALF, and 9 plasmids. The BALF of 38 patients suspected of pulmonary mycobacterial infection was collected for validation. Clinical etiological diagnosis was used as the gold standard to evaluate the diagnostic value of nucleotide MALDI-TOF-MS. Results: The sensitivity, specificity, and accuracy of the nucleotide MALDI-TOF-MS in mycobacterial identification were 96.91%, 100% and 97.22%, respectively, and the limit of detection for mycobacterium tuberculosis (MTB) was 50 bacteria/mL. Among 38 patients suspected of pulmonary mycobacterial infection, 33 were diagnosed with pulmonary tuberculosis infection, and 5 with non-mycobacterial infection. In clinical validation, the positive rates of MALDI-TOF-MS, Xpert MTB/RIF, culture and AFS in BALF of patients diagnosed with tuberculosis infection were 72.7%, 63.6%, 54.5% and 27.3%, respectively. The sensitivity/specificity of MALDI-TOF-MS, Xpert, culture and AFS in diagnosing MTB were 72.7%/100%, 63.6%/100%, 54.5%/100%, 27.3%/100%, with the areas under the curve of 0.864, 0.818, 0.773, and 0.636, respectively. Conclusion: Optimized nucleotide MALDI-TOF-MS has satisfactory sensitivity, specificity and low LOD in the identification of mycobacteria, which may serve as a potential assay for mycobacterial identification.

SARS-CoV-2 Spike triggers barrier dysfunction and vascular leak via integrins and TGF-ß signaling.

Severe COVID-19 is associated with epithelial and endothelial barrier dysfunction within the lung as well as in distal organs. While it is appreciated that an exaggerated inflammatory response is associated with barrier dysfunction, the triggers of vascular leak are unclear. Here, we report that cell-intrinsic interactions between the Spike (S) glycoprotein of SARS-CoV-2 and epithelial/endothelial cells are sufficient to induce barrier dysfunction in vitro and vascular leak in vivo, independently of viral replication and the ACE2 receptor. We identify an S-triggered transcriptional response associated with extracellular matrix reorganization and TGF-ß signaling. Using genetic knockouts and specific inhibitors, we demonstrate that glycosaminoglycans, integrins, and the TGF-ß signaling axis are required for S-mediated barrier dysfunction. Notably, we show that SARS-CoV-2 infection caused leak in vivo, which was reduced by inhibiting integrins. Our findings offer mechanistic insight into SARS-CoV-2-triggered vascular leak, providing a starting point for development of therapies targeting COVID-19.

Discovery of SARS-CoV-2 antiviral synergy between remdesivir and approved drugs in human lung cells.

SARS coronavirus 2 (SARS-CoV-2) has caused an ongoing global pandemic with significant mortality and morbidity. At this time, the only FDA-approved therapeutic for COVID-19 is remdesivir, a broad-spectrum antiviral nucleoside analog. Efficacy is only moderate, and improved treatment strategies are urgently needed. To accomplish this goal, we devised a strategy to identify compounds that act synergistically with remdesivir in preventing SARS-CoV-2 replication. We conducted combinatorial high-throughput screening in the presence of submaximal remdesivir concentrations, using a human lung epithelial cell line infected with a clinical isolate of SARS-CoV-2. This identified 20 approved drugs that act synergistically with remdesivir, many with favorable pharmacokinetic and safety profiles. Strongest effects were observed with established antivirals, Hepatitis C virus nonstructural protein 5A (HCV NS5A) inhibitors velpatasvir and elbasvir. Combination with their partner drugs sofosbuvir and grazoprevir further increased efficacy, increasing remdesivir's apparent potency > 25-fold. We report that HCV NS5A inhibitors act on the SARS-CoV-2 exonuclease proofreader, providing a possible explanation for the synergy observed with nucleoside analog remdesivir. FDA-approved Hepatitis C therapeutics Epclusa® (velpatasvir/sofosbuvir) and Zepatier® (elbasvir/grazoprevir) could be further optimized to achieve potency and pharmacokinetic properties that support clinical evaluation in combination with remdesivir.

Clinical value of metagenomic next-generation sequencing by Illumina and Nanopore for the detection of pathogens in bronchoalveolar lavage fluid in suspected community-acquired pneumonia patients.

At present, metagenomic next-generation sequencing (mNGS) based on Illumina platform has been widely reported for pathogen detection. There are few studies on the diagnosis of major pathogens and treatment regulation using mNGS based on Illumina versus Nanopore. We aim to evaluate the clinical value of metagenomic next-generation sequencing (mNGS) by Illumina and Nanopore for the detection of pathogens in bronchoalveolar lavage fluid (BALF) in suspected community-acquired pneumonia (CAP) patients. BALF samples collected from 66 suspected CAP patients within 48 hours of hospitalization were divided into two parts, one for conventional culture and the other for mNGS by two platforms (Illumina and Nanopore). The clinical value based on infection diagnosis, diagnostic performance for main pathogens and treatment guidance were assessed. More types of species were detected by Nanopore than Illumina, especially in viruses, fungus and mycobacterium. Illumina and Nanopore showed similar detectability in bacterium except for mycobacterium tuberculosis complex/nontuberculosis mycobacteria. Pathogenic infection was established or excluded in 53 of 66 patients. There was little difference in the coincidence rate between Illumina and Nanopore with the clinical diagnosis, but both were superior to the culture (57.81%, 59.38%, 25%, respectively). Compared with Illumina, the diagnostic area under the curve of Nanopore was higher in fungi, but lower in bacteria and Chlamydia psittaci. There was no statistically significant difference between Illumina and Nanopore in guiding drug treatment (56.1% vs. 50%, p=0.43), but both were superior to the culture (56.1% vs. 28.8%, p=0.01; 50% vs. 28.8%, p=0.01). Single inflammatory indicators could not be used to determine whether the patients with culture-negative BALF were established or excluded from infection. The species detected at 1 h and 4 h by Nanopore were consistent to some extent, and its turn-around time (TAT) was significantly shorter than Illumina (p<0.01). Illumina and Nanopore both have its own advantages in pathogenic diagnosis and play similar roles in infection diagnosis and guiding clinical treatment. Nanopore has a relatively short TAT, which may be promising in rapid etiological diagnosis of acute and critically ill patients.

A Conceptual Study on the Peripheral Clearance of Brain-Derived α-Synuclein in Humans.

BACKGROUND: Abnormal intracellular expression and aggregation of α-synuclein (α-syn) is the histopathological hallmark of several neurodegenerative diseases especially Parkinson's disease. However, safe and efficient approaches to clear α-syn remain unavailable. OBJECTIVE: This study aimed to investigate the process of peripheral catabolism of brain-derived α-syn. METHODS: Thirty patients with atrioventricular reentrant tachycardia (AVRT) (left accessory pathways) who underwent radiofrequency catheter ablation (RFCA) were enrolled in this study. Blood was collected via catheters from superior vena cava (SVC), inferior vena cava (IVC) proximal to the hepatic vein (HV), the right femoral vein (FV), and femoral artery (FA) simultaneously during RFCA. Plasma α-syn levels of AVRT patients and soluble α-syn levels of the brain samples were measured using enzyme-linked immunosorbent assay kits. RESULTS: The α-syn concentrations in different locations of veins were divided by time-matched arterial α-syn concentrations to generate the venous/arterial (V/A) ratio. The V/A ratio of α-syn from the SVC was 1.204 (1.069-1.339, 95% CI), while the V/A ratio of α-syn from IVC was 0.831 (0.734-0.928, 95% CI), suggesting that brain-derived α-syn in the arterial blood was physiologically cleared while going through the peripheral organs and tissues. And it was estimated that about half of brain soluble α-syn could efflux and be cleared in the periphery. Moreover, the glomerular filtration rate was found correlated with V-A difference (FA-ICV) (p = 0.0272). CONCLUSION: Under physiological conditions, brain-derived α-syn could efflux into and be catabolized by the peripheral system. The kidney may play a potential role in the clearance of α-syn.

An intranasal ASO therapeutic targeting SARS-CoV-2.

The COVID-19 pandemic is exacting an increasing toll worldwide, with new SARS-CoV-2 variants emerging that exhibit higher infectivity rates and that may partially evade vaccine and antibody immunity. Rapid deployment of non-invasive therapeutic avenues capable of preventing infection by all SARS-CoV-2 variants could complement current vaccination efforts and help turn the tide on the COVID-19 pandemic. Here, we describe a novel therapeutic strategy targeting the SARS-CoV-2 RNA using locked nucleic acid antisense oligonucleotides (LNA ASOs). We identify an LNA ASO binding to the 5' leader sequence of SARS-CoV-2 that disrupts a highly conserved stem-loop structure with nanomolar efficacy in preventing viral replication in human cells. Daily intranasal administration of this LNA ASO in the COVID-19 mouse model potently suppresses viral replication (>80-fold) in the lungs of infected mice. We find that the LNA ASO is efficacious in countering all SARS-CoV-2 "variants of concern" tested both in vitro and in vivo. Hence, inhaled LNA ASOs targeting SARS-CoV-2 represents a promising therapeutic approach to reduce or prevent transmission and decrease severity of COVID-19 in infected individuals. LNA ASOs are chemically stable and can be flexibly modified to target different viral RNA sequences and could be stockpiled for future coronavirus pandemics.

Motile sperm domain containing 1 is upregulated by the Wnt/ß-catenin signaling pathway in colorectal cancer.

Aberrant activation of the Wnt/ß-catenin signaling pathway plays a crucial role in the development and progression of colorectal cancer. Previously, we identified a set of candidate genes that were regulated by this signaling pathway, and the present study focused on motile sperm domain containing 1 (MOSPD1). Immunohistochemical staining revealed that the expression of MOSPD1 was elevated in tumor cells from colorectal cancer tissues compared with in non-tumor cells. Using ChIP-seq data and the JASPAR database, the regulatory region(s) in the MOSPD1 gene as a target of the Wnt/ß-catenin signaling pathway were searched, and a region containing three putative TCF-binding motifs in the 3'-flanking region was identified. Additional analyses using reporter assay and ChIP-quantitative PCR suggested that this region harbors enhancer activity through an interaction with transcription factor 7 like 2 (TCF7L2) and ß-catenin. In addition, chromatin conformation capture assay revealed that the 3'-flanking region interacts with the MOSPD1 promoter. These data suggested that MOSPD1 was regulated by the ß-catenin/TCF7L2 complex through the enhancer element located in the 3'-flanking region. These findings may be helpful for future studies regarding the precise regulatory mechanisms of MOSPD1.

A Robust 3D-Convolutional Neural Network-Based Electroencephalogram Decoding Model for the Intra-Individual Difference.

The convolutional neural network (CNN) has emerged as a powerful tool for decoding electroencephalogram (EEG), which owns the potential use in the event-related potential-based brain-computer interface (ERP-BCI). However, the intra-individual difference of ERP makes the traditional learning models trained on static EEG data hard to decode when the EEG features vary along the time, which limits the long-time performance of the model. Addressing this problem, this study proposes a three-dimension CNN (3D-CNN)-based model to decode the ERPs dynamically. As input, the EEG is transformed into a brain topographic map stream along time. Then the 3D-CNN applies three-dimension kernels to capture the dynamical characteristic of spatial feature at several time points. Ten subjects participated in a cross-time task for 6 or 12[Formula: see text]h. The 3D-CNN shows higher accuracies and shorter computational cost than the baseline models of the 2D-CNN, the long short term memory (LSTM), the back propagation (BP), and the fisher linear discriminant analysis (FLDA) when detecting the ERPs. In addition, four schemes of the 3D-CNN are compared to explore the influence of the structure on the performance. This result demonstrates advanced robustness of the 3D-CNN kernel to the intra-individual EEG difference, helping to launch a more practical EEG decoding model for a long-time use.

The Association of Serum Neurofilament Light Chain and Acute Ischaemic Stroke Is Influenced by Effective Revascularization.

Objective: To explore associations of serum neurofilament light chain (sNfL) at admission with clinical deficits and the long-term prognosis of acute ischaemic stroke (AIS). Methods: We recruited 110 AIS patients with serum sampled at hospital arrival. The concentrations of sNfL were detected by a Simoa HD-1 analyser. We first investigated the determinants of sNfL levels at admission within the study population. Associations of sNfL levels with National Institutes of Health Stroke Scale (NIHSS) scores and modified Rankin Scale (mRS) scores were then tested. We further divided the patients into revascularized and nonrevascularized groups, and the associations of sNfL levels with NIHSS and mRS scores were assessed in these subgroups. Results: Age, sex, stroke history, and the time between the onset of illness and arrival at the hospital were independent influencing factors of sNfL levels within the study population. The sNfL levels at admission were correlated with the NIHSS scores 7 days after stroke (p = 0.004) across all subjects but showed no correlation with the NIHSS scores at admission (p = 0.293) or the mRS scores 6 months after stroke (p = 0.065). Further analysis revealed that in the nonrevascularized group of AIS patients, the sNfL levels at admission were positively correlated with NIHSS scores (NIHSS at admission, p = 0.005; NIHSS 7 days after stroke, p = 0.003) and negatively correlated with mRS scores (p = 0.011). Conclusion: sNfL levels at admission could be a potential biomarker for predicting clinical deficits and prognosis in the natural course of AIS.

Pollution Characteristics and Health Risk Assessment of Phthalate Esters in PSW Recycling Sites: A Typical Case Study.

The concentrations of six priority phthalate esters (PAEs) in 700 soil samples and 110 sediment samples from an area in China containing plastic solid waste (PSW) recycling sites were determined. The total concentrations of the six PAEs in soil and sediment were not detected - 274 and not detected - 597 mg kg-1, respectively, and the mean concentrations in soil and sediment were 14.4 and 31.7 mg kg-1, respectively. The dominant PAEs were di(2-ethylhexyl) phthalate and di-n-butyl phthalate. PAEs were detected in soil collected from the surface to 0.5 m below ground level around the PSW recycling sites, and the concentrations were markedly higher in these areas than at other polluted sites. PSW recycling is an important source of PAEs to soil and sediment. The di(2-ethylhexyl)phthalate concentrations in soil were higher than the relevant concentrations that pose environmental risks for sensitive land uses and non-sensitive land uses (42 and 121 mg kg-1, respectively), indicating emissions of PAEs from PSW recycling sites may pose environmental risks. The results indicate that PAE pollution at PSW sites needs to be better controlled and managed.

Assessment and establishment of a reference interval for Roche Cobas t 711 coagulation analyzer for a hospital in China.

INTRODUCTION: Due to the use of different detection reagents and methods, coagulation analyzers can produce different results. Therefore, detection instruments, reagents and methods are important factors affecting the results of coagulation test. Therefore, this paper aims to establish reference intervals applicable to our laboratory for the Roche Cobas t 711 for routine coagulation assays.Methods:We completed a preliminary evaluation of the analytical performance of the cobas t 711 before any experiment. Healthy volunteer recruitment and ostensibly healthy patients via physical examination were performed to collect individual reference samples. Data were grouped and compared according to age, and the Z test was used to determine whether there was a statistically significant difference between the mean values after grouping. RESULTS: The self-established PT, APTT and TT reference intervals were 8.4-10.2s, 26.8-42.3s and 14.5-17.1s, respectively. The reference ranges of FIB, AT and DD for people aged 50 years or below were 1.85-3.78 (g/l), 83.9-113.2 (%) and 0-0.45 (mg/l), respectively, and those for people older than 50 years were 2.22-3.86 (g/l), 76.0-112.0 (%) and 0-0.52 (mg/l), respectively. CONCLUSION: The self-built reference intervals for the Roche t 711 were basically consistent with those in the instructions, except the APTT ranges were slightly wider. Laboratories should establish applicable reference intervals according to their own conditions to provide guidance for the diagnosis, monitoring and prognosis of clinically related diseases.

Secondary structural ensembles of the SARS-CoV-2 RNA genome in infected cells.

SARS-CoV-2 is a betacoronavirus with a single-stranded, positive-sense, 30-kilobase RNA genome responsible for the ongoing COVID-19 pandemic. Although population average structure models of the genome were recently reported, there is little experimental data on native structural ensembles, and most structures lack functional characterization. Here we report secondary structure heterogeneity of the entire SARS-CoV-2 genome in two lines of infected cells at single nucleotide resolution. Our results reveal alternative RNA conformations across the genome and at the critical frameshifting stimulation element (FSE) that are drastically different from prevailing population average models. Importantly, we find that this structural ensemble promotes frameshifting rates much higher than the canonical minimal FSE and similar to ribosome profiling studies. Our results highlight the value of studying RNA in its full length and cellular context. The genomic structures detailed here lay groundwork for coronavirus RNA biology and will guide the design of SARS-CoV-2 RNA-based therapeutics.

Ensemble of kernel ridge regression-based small molecule-miRNA association prediction in human disease.

MicroRNAs (miRNAs) play crucial roles in human disease and can be targeted by small molecule (SM) drugs according to numerous studies, which shows that identifying SM-miRNA associations in human disease is important for drug development and disease treatment. We proposed the method of Ensemble of Kernel Ridge Regression-based Small Molecule-MiRNA Association prediction (EKRRSMMA) to uncover potential SM-miRNA associations by combing feature dimensionality reduction and ensemble learning. First, we constructed different feature subsets for both SMs and miRNAs. Then, we trained homogeneous base learners based on distinct feature subsets and took the average of scores obtained from these base learners as SM-miRNA association score. In EKRRSMMA, feature dimensionality reduction technology was employed in the process of construction of feature subsets to reduce the influence of noisy data. Besides, the base learner, namely KRR_avg, was the combination of two classifiers constructed under SM space and miRNA space, which could make full use of the information of SM and miRNA. To assess the prediction performance of EKRRSMMA, we conducted Leave-One-Out Cross-Validation (LOOCV), SM-fixed local LOOCV, miRNA-fixed local LOOCV and 5-fold CV based on two datasets. For Dataset 1 (Dataset 2), EKRRSMMA got the Area Under receiver operating characteristic Curves (AUCs) of 0.9793 (0.8871), 0.8071 (0.7705), 0.9732 (0.8586) and 0.9767 ± 0.0014 (0.8560 ± 0.0027). Besides, we conducted four case studies. As a result, 32 (5-Fluorouracil), 19 (17ß-Estradiol), 26 (5-Aza-2'-deoxycytidine) and 11 (cyclophosphamide) out of top 50 predicted potentially associated miRNAs were confirmed by database or experimental literature. Above evaluation results demonstrated that EKRRSMMA is reliable for predicting SM-miRNA associations.

Computational Modeling of Aortic Stenosis With a Reduced Degree-of-Freedom Fluid-Structure Interaction Valve Model.

In this study, a novel reduced degree-of-freedom (rDOF) aortic valve model is employed to investigate the fluid-structure interaction (FSI) and hemodynamics associated with aortic stenosis. The dynamics of the valve leaflets are determined by an ordinary differential equation with two parameters and this rDOF model is shown to reproduce key features of more complex valve models. The hemodynamics associated with aortic stenosis is studied for three cases: a healthy case and two stenosed cases. The focus of the study is to correlate the hemodynamic features with the source generation mechanism of systolic murmurs associated with aortic stenosis. In the healthy case, extremely weak flow fluctuations are observed. However, in the stenosed cases, simulations show significant turbulent fluctuations in the ascending aorta, which are responsible for the generation of strong wall pressure fluctuations after the aortic root mostly during the deceleration phase of the systole. The intensity of the murmur generation increases with the severity of the stenosis, and the source locations for the two diseased cases studied here lie around 1.0 inlet duct diameters (Do) downstream of the ascending aorta.