DeepBAM: a high-accuracy single-molecule CpG methylation detection tool for Oxford nanopore sequencing.

Recent nanopore sequencing system (R10.4) has enhanced base calling accuracy and is being increasingly utilized for detecting CpG methylation state. However, the robustness and universality of the methylation calling model in officially supplied Dorado remains poorly tested. In this study, we obtained heterogeneous datasets from human and plant sources to carry out comprehensive evaluations, which showed that Dorado performed significantly different across datasets. We therefore developed deep neural networks and implemented several optimizations in training a new model called DeepBAM. DeepBAM achieved superior and more stable performances compared with Dorado, including higher area under the ROC curves (98.47% on average and up to 7.36% improvement) and F1 scores (94.97% on average and up to 16.24% improvement) across the datasets. DeepBAM-based whole genome methylation frequencies have achieved >0.95 correlations with BS-seq on four of five datasets, outperforming Dorado in all instances. It enables unraveling allele-specific methylation patterns, including regions of transposable elements. The enhanced performance of DeepBAM paves the way for broader applications of nanopore sequencing in CpG methylation studies.

Proteomic Profiling of Muscular Adaptations to Short-Term Concentric Versus Eccentric Exercise Training in Humans.

The molecular mechanisms underlying muscular adaptations to concentric (CON) and eccentric (ECC) exercise training have been extensively explored. However, most previous studies have focused on specifically selected proteins, thus, unable to provide a comprehensive protein profile and potentially missing the crucial mechanisms underlying muscular adaptation to exercise training. We herein aimed to investigate proteomic profiles of human skeletal muscle in response to short-term resistance training. Twenty young males were randomly and evenly assigned to two groups to complete a 4-week either ECC or CON training program. Measurements of body composition and physiological function of the quadriceps femoris were conducted both before and after the training. Muscle biopsies from the vastus lateralis of randomly selected participants (five in ECC and four in CON) of both before and after the training were analyzed using the liquid-chromatography tandem mass spectrometry in combination with bioinformatics analysis. Neither group presented a significant difference in body composition or leg muscle mass; however, muscle peak torque, total work, and maximal voluntary contraction were significantly increased after the training in both groups. Proteomics analysis revealed 122 differentially abundant proteins (DAPs; p value < 0.05 & fold change >1.5 or <0.67) in ECC, of which the increased DAPs were mainly related to skeletal muscle contraction and cytoskeleton and enriched specifically in the pentose phosphate pathway, extracellular matrix-receptor interaction, and PI3K-Akt signaling pathway, whereas the decreased DAPs were associated with the mitochondrial respiratory chain. One hundred one DAPs were identified in CON, of which the increased DAPs were primarily involved in translation/protein synthesis and the mitochondria respiratory, whereas the decreased DAPs were related to metabolic processes, cytoskeleton, and de-ubiquitination. In conclusion, the 4-week CON and ECC training resulted in distinctly different proteomic profiles, especially in proteins related to muscular structure and metabolism.

The Role of Ferroptosis in Amyotrophic Lateral Sclerosis Treatment.

Amyotrophic lateral sclerosis (ALS) is a rare neurodegenerative disease with a challenging treatment landscape, due to its complex pathogenesis and limited availability of clinical drugs. Ferroptosis, an iron-dependent form of programmed cell death (PCD), stands distinct from apoptosis, necrosis, autophagy, and other cell death mechanisms. Recent studies have increasingly highlighted the role of iron deposition, reactive oxygen species (ROS) accumulation, oxidative stress, as well as systemic Xc- and glutamate accumulation in the antioxidant system in the pathogenesis of amyotrophic lateral sclerosis. Therefore, targeting ferroptosis emerges as a promising strategy for amyotrophic lateral sclerosis treatment. This review introduces the regulatory mechanism of ferroptosis, the relationship between amyotrophic lateral sclerosis and ferroptosis, and the drugs used in the clinic, then discusses the current status of amyotrophic lateral sclerosis treatment, hoping to provide new directions and targets for its treatment.

A New Perspective in the Treatment of Ischemic Stroke: Ferroptosis.

Ischemic stroke is a common neurological disease. Currently, there are no Food and Drug Administration-approved drugs that can maximize the improvement in ischemic stroke-induced nerve damage. Hence, treating ischemic stroke remains a clinical challenge. Ferroptosis has been increasingly studied in recent years, and it is closely related to the pathophysiological process of ischemic stroke. Iron overload, reactive oxygen species accumulation, lipid peroxidation, and glutamate accumulation associated with ferroptosis are all present in ischemic stroke. This article focuses on describing the relationship between ferroptosis and ischemic stroke and summarizes the relevant substances that ameliorate ischemic stroke-induced neurological damage by inhibiting ferroptosis. Finally, the problems in the treatment of ischemic stroke targeting ferroptosis are discussed, hoping to provide a new direction for its treatment.

Molecular Mechanisms and Biological Characteristics of Botrytis cinerea Field Isolate Resistance to Pyrisoxazole in Liaoning Province.

Botrytis cinerea is a broad-host-range necrotrophic phytopathogen responsible for serious diseases in leading crops worldwide. The novel sterol 14α-demethylase inhibitor (DMI) pyrisoxazole was recently registered for the control of tomato gray mold caused by B. cinerea in China. One hundred fifty-seven isolates of B. cinerea were collected from tomato greenhouses in 14 cities of Liaoning Province from 2016 to 2021 and examined for sensitivity to pyrisoxazole, with a mean EC50 value of 0.151 µg/ml. Three highly resistant isolates, XD-5, DG-4, and GQ-3, were screened, and the EC50 values were 0.734, 0.606, and 0.639 µg/ml with corresponding resistance factors of 12.88, 10.63, and 11.21, respectively. Compared with field-sensitive strains, the highly resistant isolate XD-5 exhibited fitness defects in traits, including mycelial growth, conidial production, and pathogenicity, but DG-4 and GQ-3 did not experience fitness costs. Positive cross-resistance was observed only between pyrisoxazole and the DMIs tebuconazole and prochloraz but not between pyrisoxazole and the non-DMIs iprodione, procymidone, pyrimethanil, fludioxonil, fluazinam, and fluopyram. Sequence alignment of the CYP51 gene indicated that three point mutations were observed in the highly resistant mutant, namely, V24I in XD-5, G461S in GQ-3, and R464K in DG-4. When exposed to pyrisoxazole, the induced expression levels of the ABC transporter AtrD and MFS transporter Mfs1 increased in the resistant isolates compared with those in the sensitive isolates, whereas the expression level of the CYP51 gene did not change significantly. Molecular docking suggested that the G461S and R464K mutations both led to a decrease in the binding energy between CYP51 and pyrisoxazole, whereas no change was found with the V24I mutation. Thus, two point mutations in the CYP51 protein combined with induced expression of the Mfs1 and AtrD genes appeared to mediate the pyrisoxazole resistance of the highly resistant mutants DG-4 and GQ-3, while the overexpression of the Mfs1 and AtrD genes was responsible for the highly resistant mutant XD-5.

Polymer Dielectrics with Outstanding Dielectric Characteristics via Passivation with Oxygen Atoms through C-F Vacancy Carbonylation.

The development of advanced electrical equipment necessitates polymer dielectrics with a higher electric strength. Unfortunately, this bottleneck problem has yet to be solved because current material modification methods do not allow direct control of deep traps. Here, we propose a method for directly passivating deep traps. Measurements of nanoscale microregion charge characteristics and trap parameters reveal a significant reduction in the number of deep traps. The resulting polymer dielectric has an impressively high electrical strength, less surface charge accumulation, and a significantly increased flashover voltage and breakdown strength. In addition, the energy storage density is increased without sacrificing the charge-discharge efficiency. This reveals a new approach to increasing the energy storage density by reducing the trap energy levels at the electrode-dielectric interface. We further calculated and analyzed the microscopic physical mechanism of deep trap passivation based on density functional theory and characterized the contributions of orbital composition and orbital hybridization.

Research progress of microRNA in spinal cord injury.

Spinal cord injury (SCI) is a serious central nervous system disease with high disability and mortality rates and complex pathophysiologic mechanisms. MicroRNA (miRNA), as a kind of non-coding RNA, plays an important role in SCI. miRNA is involved in the regulation of inflammatory response, oxidative stress, axonal regeneration, and apoptosis after SCI, and interacts with long non-coding RNA (lncRNA) and circular RNA (circRNA) to regulate the pathophysiological process of SCI. This paper summarizes the changes in miRNA expression after SCI, and reviews the targeting mechanism of miRNA in SCI and the current research status of miRNA-targeted drugs to provide new targets and new horizons for basic and clinical research on SCI.

[Association between the structure of intestinal flora and inflammatory response in children with sepsis: a prospective cohort study]. / è„“æ¯’ç—‡æ‚£å„¿è‚ é“èŒç¾¤ç»“æž„ä¸Žç‚Žç—‡ååº”ç›¸å ³æ€§çš„å‰çž»æ€§é˜Ÿåˆ—ç ”ç©¶.

OBJECTIVES: To investigate the structural characteristics of intestinal flora in children with sepsis and its association with inflammatory response. METHODS: A prospective cohort study was conducted. The children with sepsis who were admitted from December 2021 to January 2023 were enrolled as the sepsis group, and the children with non-sepsis who were admitted during the same period were enrolled as the non-sepsis group. The two groups were compared in terms of the distribution characteristics of intestinal flora, peripheral white blood cell count (WBC), C reactive protein (CRP), and cytokines, and the correlation of the relative abundance of fecal flora with WBC, CRP, and cytokines was analyzed. RESULTS: At the genus level, compared with the non-sepsis group, the sepsis group had significantly lower relative abundance of Akkermansia, Ruminococcus, and Alistipes and significantly higher relative abundance of Enterococcus, Streptococcus, and Staphylococcus (P<0.05). At the phylum level, Proteobacteria was the dominant phylum (37.46%) in the group of children with a score of ≤70 from the Pediatric Critical Illness Score (PICS), and Firmicutes was the dominant phylum in the group of children with a score of 71-80 or 81-90 from the PICS (72.20% and 43.88%, respectively). At the genus level, among the 18 specimens, 5 had a relative abundance of >50% for a single flora. Compared with the non-sepsis group, the sepsis group had significant higher levels of WBC, CRP, interleukin-6 (IL-6), interleukin-10 (IL-10), and tumor necrosis factor-α (P<0.05). The Spearman's rank correlation analysis showed that at the genus level, the relative abundance of Ruminococcus, Alistipes, and Parasutterella in the sepsis group was negatively correlated with the levels of WBC, CRP, and IL-6 (P<0.05); the relative abundance of Enterococcus was positively correlated with the CRP level (P<0.01); the relative abundance of Streptococcus and Staphylococcus was positively correlated with the levels of CRP and IL-6 (P<0.05); the relative abundance of Streptococcus was positively correlated with WBC (P<0.05). CONCLUSIONS: Intestinal flora disturbance is observed in children with sepsis, and its characteristics vary with the severity of the disease. The structural changes of intestinal flora are correlated with inflammatory response in children with sepsis.

TRIM proteins in breast cancer: Function and mechanism.

Breast cancer is the most prevalent malignancy in the world, and despite tremendous progress in current treatment strategies, recurrence, metastasis and drug resistance of breast cancer remain the major causes of death in patients. Tripartite motif (TRIM) family proteins play a critical role in the tumor progression such as cell proliferation, migration, invasion, and metastasis. Accumulating evidence suggests that the TRIM protein family serve as cancer suppressor proteins or oncoproteins in breast cancer. This review focused on the roles and molecular mechanisms of TRIM protein in breast cancer. Importantly, it provides new insights that TRIM proteins may be ideal targets to treat breast cancer.

The feasibility of contrast-enhanced CT to identify the adhesive renal venous tumor thrombus of renal cell carcinoma.

OBJECTIVE: To identify adhesive renal venous tumor thrombus (RVTT) of renal cell carcinoma (RCC) by contrast-enhancement CT (CECT). MATERIALS AND METHODS: Our retrospective study included 53 patients who underwent preoperative CECT and pathologically confirmed RCC combined with RVTT. They were divided into two groups based on the intra-operative findings of RVTT adhesion to the venous wall, with 26 cases in the adhesive RVTT group (ARVTT) and 27 cases in the non-adhesive group (NRVTT). The location, maximum diameter (MD) and CT values of tumors, the maximum length (ML) and width (MW) of RVTT, and length of inferior vena cava tumor thrombus were compared between the two groups. The presence of renal venous wall involvement, renal venous wall inflammation, and enlarged retroperitoneal lymph node was compared between the two groups. A receiver operating characteristic curve was used to analyze the diagnostic performance. RESULTS: The MD of RCC and the ML and MW of the RVTT were all larger in the ARVTT group than in the NRVTT group (p = 0.042, p < 0.001, and p = 0.002). The proportion of renal vein wall involvement and renal vein wall inflammation were higher in the ARVTT group than in NRVTT groups (both p < 0.001). The multivariable model including ML and vascular wall inflammation to predict ARVTT could achieve the best diagnostic performance with the area under the curve, sensitivity, specificity, and accuracy of 0.91, 88.5%, 96.3%, and 92.5%, respectively. CONCLUSION: The multivariable model acquired by CECT images could be used to predict RVTT adhesion. CLINICAL RELEVANCE STATEMENT: For RCC patients with tumor thrombus, contrast-enhanced CT could noninvasively predict the adhesion of tumor thrombus, thus predicting the difficulty of surgery and contributing to the selection of an appropriate treatment plan. KEY POINTS: • The length and width of the tumor thrombus could be used to predict its adhesion to the vessel wall. • Adhesion of the tumor thrombus can be reflected by inflammation of the renal vein wall. • The multivariable model from CECT can well predict whether the tumor thrombus adhered to the vein wall.

Mildly elevated serum bilirubin and its correlations with lipid levels among male patients undergoing health checkups.

BACKGROUND: Bilirubin's ability to lower lipid levels was confirmed by several studies, but those studies mainly focused on total bilirubin (TBil). The present study aimed to elucidate the correlations of the two subtypes of bilirubin with lipid levels. METHODS: A total of 1732 male patients undergoing health checkups were categorized into three groups according to the levels of direct bilirubin (DBil) and indirect bilirubin (IBil). The differences in medical characteristics among the three groups were analysed. RESULTS: Subjects in the elevated DBil group had the lowest serum alanine aminotransferase (ALT), total cholesterol (TC), blood urea nitrogen (BUN), γ-glutamyl transpeptidase (γ-GT), fasting blood glucose (FBG), haemoglobin (HGB), and triglyceride (TG) levels in contrast to the other groups (P < 0.01), while subjects in the elevated IBil group had the highest ALT, γ-GT, BUN, serum creatinine (SCR), HGB, TC, and TG levels among the three groups (P < 0.01). DBil levels exhibited a significant negative correlation with TC (r = -0.777, P < 0.01) and TG (r = -0.397, P < 0.01) levels, while IBil levels exhibited a significant positive correlation with TC (r = 0.790, P < 0.01) and TG (r = 0.302, P < 0.01) levels. The frequencies of abnormal TC, TG, HGB and BUN levels were the lowest in the elevated DBil group, while the levels of these four variables were the highest in the elevated IBil group. Mildly elevated DBil levels were related to lower TG (OR = 0.112, 95% CI = 0.027-0.458) and TC (OR = 0.097, 95% CI = 0.013-0.700), and mildly elevated IBil levels were connected with increased TC (OR = 3.436, 95% CI = 2.398-4.924) and TG (OR = 1.636, 95% CI = 1.163-2.303). DBil was an independent protective factor against increased TC (OR = 0.702, 95% CI = 0.602-0.817, P < 0.01) and TG (OR = 0.632, 95% CI = 0.541-0.739, P < 0.01) levels, and IBil was an independent risk factors for increased TC (OR = 1.251, 95% CI = 1.176-1.331, P < 0.01). CONCLUSIONS: DBil was an independent protective factor against high TC and TG levels. IBil was an independent risk factors for elevated TC levels. The prognostic value of IBil levels warrants further attention.

Evaluation of the immune protective effects of rEmMIC2 and rEmMIC3 from Eimeria magna in rabbits.

Eimeria magna is a common pathogen in rabbits, which results in lethargy, weight loss, diarrhea, and even death in severe cases after infection. The current method for preventing rabbit coccidiosis is to add anticoccidial drugs to the diet. However, there are many concerns about drug resistance and drug residues. In our study, the rEmMIC2 and rEmMIC3 proteins were cloned and expressed to evaluate potential as recombinant subunit vaccine candidate antigens. The protective effects of rEmMIC2 and rEmMIC3 were evaluated by the relative weight gain ratio, oocyst decrease rate, anticoccidial index, feed conversion ratio, pathological alterations, clinical symptoms, specific IgG antibody, and cytokine levels in rabbits. The molecular weights of rEmMIC2 and rEmMIC3 were 18.69 kDa and 17.47 kDa, respectively. After the coccidia challenge, the control groups showed anorexia and soft poop, whereas the experimental group showed few anorexia symptoms. Significantly different from the control group, the relative weight gain ratios of the immunized rEmMIC2 and rEmMIC3 groups were 78.37% and 75.29%, respectively, and the oocyst reduction was 77.95% and 76.09%, respectively, and the anticoccidial index was 171.12 and 169.29, respectively. IgG antibody, IFN-γ, IL-4, IL-10, and IL-17 levels were significantly increased in the experimental group. The results showed that rEmMIC2 and rEmMIC3 have potential as vaccine candidate antigens.

Characterization and biocontrol mechanism of Streptomyces olivoreticuli as a potential biocontrol agent against Rhizoctonia solani.

Rhizoctonia solani is a widespread and devastating plant pathogenic fungus that infects many important crops. This pathogen causes tobacco target spot, a disease that is widespread in many tobacco-growing countries and is destructive to tobacco. To identify antagonistic microorganisms with biocontrol potential against this disease, we isolated Streptomyces strains from forest inter-root soil and screened a promising biocontrol strain, ZZ-21. Based on in vitro antagonism assays, ZZ-21 showed a significant inhibitory effect on R. solani and various other phytopathogens. ZZ-21 was identified as Streptomyces olivoreticuli by its phenotypic, genetic, physiological and biochemical properties. Complete genome sequencing revealed that ZZ-21 harbored numerous antimicrobial biosynthesis gene clusters. ZZ-21 significantly reduced the lesion length in detached inoculated leaf assays and reduced the disease index under greenhouse and field conditions. Based on an in vitro antagonistic assay of ZZ-21 culture, the strain exhibited an antifungal activity against R. solani in a dose-dependent manner. The culture filtrate could impair membrane integrity, possibly through membrane lipid peroxidation. ZZ-21 could secrete multiple extracellular enzymes and siderophores. According to a series of antifungal assays, the extracellular metabolites of ZZ-21 contained antimicrobial bioactive compounds composed of proteins/peptides extracted using ammonium sulfate precipitation, which were stable under stress caused by high temperature and protease K. The EC50 value for ammonium sulfate precipitation was determined to be 21.11 µg/mL in this study. Moreover, the proteins/peptides also exhibited biocontrol ability and were observed to alter the plasma membrane integrity of R. solani which were evaluated by biocontrol efficacy assays on detached tobacco leaves and PI staining. Overall, strain ZZ-21 shows the potential to be developed into a biopesticide against tobacco target spot disease.

Fatalism and Suicidal Behaviors Among Chinese College Students: The Mediating Role of Depressive Symptoms and the Moderating Role of Coping Strategies.

The aim of this study was to investigate the relationship between fatalism and suicidal behaviors, the mediating role of depressive symptoms, and the moderating effect of coping strategies on the mediating process. A total of 519 participants completed the Multidimensional Fatalism Scale for General Life Events, the Center for Epidemiologic Studies-Depression scale, the Simplified Coping Style Questionnaire, and the Suicidal Behaviors Questionnaire-Revised. Results suggest that depressive symptoms partially mediated the relationship between fatalism and suicidal behaviors. Active coping moderated the mediating effect of depressive symptoms. The higher the active coping level, the weaker the mediating effect. The findings revealed that the mechanism of fatalism affecting suicidal behaviors, and had theoretical and empirical value for the prevention and intervention of suicide among college students.

Lipid-Polymer Hybrid "Particle-in-Particle" Nanostructure Gene Delivery Platform Explored for Lyophilizable DNA and mRNA COVID-19 Vaccines.

SARS-CoV-2 has led to a worldwide pandemic, catastrophically impacting public health and the global economy. Herein, a new class of lipid-modified polymer poly (ß-amino esters) (L-PBAEs) is developed via enzyme-catalyzed esterification and further formulation of the L-PBAEs with poly(d,l-lactide-coglycolide)-b-poly(ethylene glycol) (PLGA-PEG) leads to self-assembly into a "particle-in-particle" (PNP) nanostructure for gene delivery. Out of 24 PNP candidates, the top-performing PNP/C12-PBAE nanoparticles efficiently deliver both DNA and mRNA in vitro and in vivo, presenting enhanced transfection efficacy, sustained gene release behavior, and excellent stability for at least 12 months of storage at -20 °C after lyophilization without loss of transfection efficacy. Encapsulated with spike encoded plasmid DNA and mRNA, the lipid-modified polymeric PNP COVID-19 vaccines successfully elicit spike-specific antibodies and Th1-biased T cell immune responses in immunized mice even after 12 months of lyophilized storage at -20 °C. This newly developed lipid-polymer hybrid PNP nanoparticle system demonstrates a new strategy for both plasmid DNA and mRNA delivery with the capability of long-term lyophilized storage.

Insights Into to the KX (X = Cl, Br, I) Adsorption-Assisted Stabilization of CsPbI2 Br Surface.

Despite the excellent optoelectronic properties, organic-inorganic hybrid perovskite solar cells (PSCs) still present significant challenges in terms of ambient stability. CsPbI2 Br, a member of all-inorganic perovskites, may respond to this challenge because of its inherent high stability against light, moisture, and heat, and therefore has gained tremendous attraction recently. However, the practical application of CsPbI2 Br is still impeded by the notorious phenomenon of photoinduced halide segregation. Herein, by applying first-principles calculations, the stability, electronic structure, defect properties, and ion-diffusion properties of the stoichiometric CsPbI2 Br (110) surface and that with the adsorption of KX (X = Cl, Br, I) are systematically investigated. It is found that the adsorbed KX can serve as an external substitute of the halogen vacancies on the surface, therefore inhibiting halogen segregation and improving the stability of the CsPbI2 Br surface. The KX can also eliminate deep-level defect states caused by antisites, thereby contributing to the promoted optoelectronic properties of CsPbI2 Br. The mechanistic understanding of surface passivation in this work can lay the foundation for the future design of CsPbI2 Br PSCs with optimized optoelectronic performance.

KIMI: Knockoff Inference for Motif Identification from molecular sequences with controlled false discovery rate.

MOTIVATION: The rapid development of sequencing technologies has enabled us to generate a large number of metagenomic reads from genetic materials in microbial communities, making it possible to gain deep insights into understanding the differences between the genetic materials of different groups of microorganisms, such as bacteria, viruses, plasmids, etc. Computational methods based on k-mer frequencies have been shown to be highly effective for classifying metagenomic sequencing reads into different groups. However, such methods usually use all the k-mers as features for prediction without selecting relevant k-mers for the different groups of sequences, i.e. unique nucleotide patterns containing biological significance. RESULTS: To select k-mers for distinguishing different groups of sequences with guaranteed false discovery rate (FDR) control, we develop KIMI, a general framework based on model-X Knockoffs regarded as the state-of-the-art statistical method for FDR control, for sequence motif discovery with arbitrary target FDR level, such that reproducibility can be theoretically guaranteed. KIMI is shown through simulation studies to be effective in simultaneously controlling FDR and yielding high power, outperforming the broadly used Benjamini-Hochberg procedure and the q-value method for FDR control. To illustrate the usefulness of KIMI in analyzing real datasets, we take the viral motif discovery problem as an example and implement KIMI on a real dataset consisting of viral and bacterial contigs. We show that the accuracy of predicting viral and bacterial contigs can be increased by training the prediction model only on relevant k-mers selected by KIMI. AVAILABILITYAND IMPLEMENTATION: Our implementation of KIMI is available at https://github.com/xinbaiusc/KIMI. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Sparse logistic regression revealed the associations between HBV PreS quasispecies and hepatocellular carcinoma.

BACKGROUND: Chronic infection with hepatitis B virus (HBV) has been proved highly associated with the development of hepatocellular carcinoma (HCC). AIMS: The purpose of the study is to investigate the association between HBV preS region quasispecies and HCC development, as well as to develop HCC diagnosis model using HBV preS region quasispecies. METHODS: A total of 104 chronic hepatitis B (CHB) patients and 117 HBV-related HCC patients were enrolled. HBV preS region was sequenced using next generation sequencing (NGS) and the nucleotide entropy was calculated for quasispecies evaluation. Sparse logistic regression (SLR) was used to predict HCC development and prediction performances were evaluated using receiver operating characteristic curves. RESULTS: Entropy of HBV preS1, preS2 regions and several nucleotide points showed significant divergence between CHB and HCC patients. Using SLR, the classification of HCC/CHB groups achieved a mean area under the receiver operating characteristic curve (AUC) of 0.883 in the training data and 0.795 in the test data. The prediction model was also validated by a completely independent dataset from Hong Kong. The 10 selected nucleotide positions showed significantly different entropy between CHB and HCC patients. The HBV quasispecies also classified three clinical parameters, including HBeAg, HBVDNA, and Alkaline phosphatase (ALP) with the AUC value greater than 0.6 in the test data. CONCLUSIONS: Using NGS and SLR, the association between HBV preS region nucleotide entropy and HCC development was validated in our study and this could promote the understanding of HCC progression mechanism.

Value of deep learning reconstruction at ultra-low-dose CT for evaluation of urolithiasis.

OBJECTIVES: To determine the diagnostic accuracy and image quality of ultra-low-dose computed tomography (ULDCT) with deep learning reconstruction (DLR) to evaluate patients with suspected urolithiasis, compared with ULDCT with hybrid iterative reconstruction (HIR) by using low-dose CT (LDCT) with HIR as the reference standard. METHODS: Patients with suspected urolithiasis were prospectively enrolled and underwent abdominopelvic LDCT, followed by ULDCT if any urinary stone was observed. Radiation exposure, stone characteristics, image noise, signal-to-noise ratio (SNR), and subjective image quality on a 5-point Likert scale were evaluated and compared. RESULTS: The average effective radiation dose of ULDCT was significantly lower than that of LDCT (1.28 ± 0.34 vs. 5.49 ± 1.00 mSv, p < 0.001). According to the reference standard (LDCT-HIR), 148 urinary stones were observed in 85.0% (51/60) of patients. ULDCT-DLR detected 143 stones with a rate of 96.6%, and ULDCT-HIR detected 142 stones with a rate of 95.9%. The urinary stones that were not observed with ULDCT-DLR or ULDCT-HIR were renal calculi smaller than 3 mm. There were no significant differences in the detection of clinically significant calculi (≥ 3 mm) or stone size estimation among ULDCT-DLR, ULDCT-HIR, and LDCT-HIR. The image quality of ULDCT-DLR was better than that of ULDCT-HIR and LDCT-HIR with lower image noise, higher SNR, and higher average subjective score. CONCLUSIONS: ULDCT-DLR performed comparably to LDCT-HIR in urinary stone detection and size estimation with better image quality and decreased radiation exposure. ULDCT-DLR may have potential to be considered the first-line choice to evaluate urolithiasis in practice. KEY POINTS: • Ultra-low-dose computed tomography (ULDCT) has been investigated for diagnosis of urolithiasis, but stone evaluation may be adversely impacted by compromised image quality. • This study evaluated the value of novel deep learning reconstruction (DLR) at ULDCT by comparing the stone evaluation and image quality of ULDCT-DLR to the reference standard of low-dose CT (LDCT) with hybrid iterative reconstruction (HIR). • ULDCT-DLR performed comparably to LDCT-HIR in urinary stone detection and size estimation with better image quality and reduced radiation exposure.

Neiella holothuriorum sp. nov., isolated from the gut of a sea cucumber Apostichopus japonicus.

A Gram-stain negative, aerobic, rod-shaped bacterium, designated 126T, was isolated from the intestinal content of a sea cucumber, Apostichopus japonicus, in China. Strain 126T was found to grow optimally at 25-28 °C and pH 7.5-8.0 in marine 2216 E medium, with tolerance of 1-7% (w/v) NaCl. Strain 126T is motile by means of one to several polar flagella. The dominant fatty acids of strain 126T were identified as C16:1 ω7c/C16:1 ω6c (29.5%), C18:1 ω7c/C18:1 ω6c (19.8%) and C16:0 (16.7%). The respiratory quinone was found to be Q-8. The polar lipid profile was found to be mainly composed of phosphatidylglycerol and phosphatidylethanolamine. The total length of the draft genome is approximately 4.2 × 106 bp, encoding 3655 genes and 3576 coding sequences. The G + C content of the genomic DNA is 48.0%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 126T belongs to the genus Neiella and is closely related to Neiella marina J221T (96.5%). Genomic comparisons of 126T to N. marina J221T revealed that they had similar genome size, G + C content and complement of clusters of orthologous groups. However, average nucleotide identity and digital DNA-DNA hybridization values between strains126T and N. marina J221T was 75.5% and 19.7%, which could distinguish the strains. On the basis of these phenotypic and genotypic data, strain 126T is concluded to represent a novel species, for which the name Neiella holothuriorum sp. nov. is proposed. The type strain is 126T (= GDMCC 1.2530T = KCTC 82829T).