Arrayed in vivo barcoding for multiplexed sequence verification of plasmid DNA and demultiplexing of pooled libraries.

Sequence verification of plasmid DNA is critical for many cloning and molecular biology workflows. To leverage high-throughput sequencing, several methods have been developed that add a unique DNA barcode to individual samples prior to pooling and sequencing. However, these methods require an individual plasmid extraction and/or in vitro barcoding reaction for each sample processed, limiting throughput and adding cost. Here, we develop an arrayed in vivo plasmid barcoding platform that enables pooled plasmid extraction and library preparation for Oxford Nanopore sequencing. This method has a high accuracy and recovery rate, and greatly increases throughput and reduces cost relative to other plasmid barcoding methods or Sanger sequencing. We use in vivo barcoding to sequence verify >45 000 plasmids and show that the method can be used to transform error-containing dispersed plasmid pools into sequence-perfect arrays or well-balanced pools. In vivo barcoding does not require any specialized equipment beyond a low-overhead Oxford Nanopore sequencer, enabling most labs to flexibly process hundreds to thousands of plasmids in parallel.

Recycling of deep eutectic solvent in the extraction of ferulic acid from oil palm empty fruit bunch.

The study explored ferulic acid extraction from palm empty fruit bunch (EFB) fiber using deep eutectic solvent (DES) of chlorine chloride-acetic acid as the extraction medium and the way to recover and recycle the DES thereafter. Antisolvent was added to selectively precipitate the ferulic acid, which was recovered by filtration thereafter. Recycling the DES without further purification led to increased ferulic acid yield with each subsequent extraction, likely due to retained ferulic acid. The retained ferulic acid and other impurities could be removed by precipitation brought upon by the addition of a second antisolvent. 1H nuclear magnetic resonance revealed that there was no excess ferulic acid in the recycled DES-treated with two types of antisolvents (ethanol and water). The yield of ferulic acid increased from 0.1367-0.1856 g/g when treated with only one antisolvent to 0.1368-0.2897 g/g with two antisolvent treatments. Oil droplets were also observed in the DES upon the addition of antisolvent 2, with recovered oil ranging from 0.6% to 3%. The study emphasized the significance of using DES as an extraction medium for ferulic acid from oil palm EFB fiber and the method to recycle the DES for subsequent processes.

Suppressive stroma-immune prognostic signature impedes immunotherapy in ovarian cancer and can be reversed by PDGFRB inhibitors.

BACKGROUND: As the most lethal gynecologic cancer, ovarian cancer (OV) holds the potential of being immunotherapy-responsive. However, only modest therapeutic effects have been achieved by immunotherapies such as immune checkpoint blockade. This study aims to propose a generalized stroma-immune prognostic signature (SIPS) to identify OV patients who may benefit from immunotherapy. METHODS: The 2097 OV patients included in the study were significant with high-grade serous ovarian cancer in the III/IV stage. The 470 immune-related signatures were collected and analyzed by the Cox regression and Lasso algorithm to generalize a credible SIPS. Correlations between the SIPS signature and tumor microenvironment were further analyzed. The critical immunosuppressive role of stroma indicated by the SIPS was further validated by targeting the major suppressive stroma component (CAFs, Cancer-associated fibroblasts) in vitro and in vivo. With four machine-learning methods predicting tumor immune subtypes, the stroma-immune signature was upgraded to a 23-gene signature. RESULTS: The SIPS effectively discriminated the high-risk individuals in the training and validating cohorts, where the high SIPS succeeded in predicting worse survival in several immunotherapy cohorts. The SIPS signature was positively correlated with stroma components, especially CAFs and immunosuppressive cells in the tumor microenvironment, indicating the critical suppressive stroma-immune network. The combination of CAFs' marker PDGFRB inhibitors and frontline PARP inhibitors substantially inhibited tumor growth and promoted the survival of OV-bearing mice. The stroma-immune signature was upgraded to a 23-gene signature to improve clinical utility. Several drug types that suppress stroma-immune signatures, such as EGFR inhibitors, could be candidates for potential immunotherapeutic combinations in ovarian cancer. CONCLUSIONS: The stroma-immune signature could efficiently predict the immunotherapeutic sensitivity of OV patients. Immunotherapy and auxiliary drugs targeting stroma could enhance immunotherapeutic efficacy in ovarian cancer.

Perilla, sunflower, and tea seed oils as potential dietary supplements with anti-obesity effects by modulating the gut microbiota composition in mice fed a high-fat diet.

PURPOSE: Obesity has become a serious public health problem with its alarmingly increasing prevalence worldwide, prompting researchers to create and develop several anti-obesity drugs. Here, we aimed to investigate the protective effects of perilla seed oil (PSO), sunflower oil (SFO), and tea seed oil (TSO) against obesity through the modulation of the gut microbiota composition and related metabolic changes in mice fed a high-fat diet (HFD). METHODS: Mice were divided into six equal groups: ND (normal diet); HFD; ORL (HFD supplemented with 20 mg/kg body weight of orlistat); PSO, SFO, and TSO (HFD supplemented with 2 g/kg body weight of PSO, SFO, and TSO, respectively). RESULTS: Our findings showed that PSO, SFO, and TSO supplementation significantly reduced body weight, organ weight, blood glucose, lipopolysaccharides (LPS), insulin resistance, and improved serum lipid levels (TG, TC, LDL-C, and HDL-C). Meanwhile, the three treatments alleviated oxidative stress and hepatic steatosis and reduced liver lipid accumulation. Relative mRNA expression levels of inflammatory cytokines (TNF-α, IL-1ß, IL-6, and MCP-1) and lipid synthesis-related genes (PPAR-γ, FAS, and SREBP-1) were down-regulated, while ß-oxidation-related genes (PPAR-α, CPT1a, and CPT1b) were up-regulated in the liver tissue of treated mice. Besides, dietary oil supplementation alleviated HFD-induced gut microbiota dysbiosis by promoting gut microbiota richness and diversity, decreasing the Firmicutes-to-Bacteroidetes ratio, and boosting the abundance of some healthy bacteria, like Akkermansia. CONCLUSIONS: PSO, SFO, and TSO supplementation could alleviate inflammation, oxidative stress, and hepatic steatosis, likely by modulating the gut microbiota composition in HFD-fed mice.

Pyrite coupled with biochar alleviating the toxicity of silver nanoparticles on pollutants removal in constructed wetlands.

Silver nanoparticles (AgNPs) has been widely detected in the substrates of constructed wetlands (CWs), posing threaten to pollutants removal efficiency of CWs. However, the way to alleviate the toxicity of AgNPs on CWs is unclear. In this study, the gravel (GR), biochar (BC), pyrite (PY) and pyrite coupled with biochar matrix (PYBC) were selected as substrates to restore the pollutants removal efficiency of CWs under the exposure to the environment (0.2 mg/L) and accumulation (10 mg/L) concentration of AgNPs. Results showed that the BC and PY showed limited mitigation effects, while the PYBC alleviated the toxicity significantly. Especially in the exposure to the accumulation concentration of AgNPs, the removal of NH4+-N, TN, COD and TP in the PYBC were 10.2%, 8.3%, 9.4% and 10.7% higher than that in the GR, respectively. Mechanism analysis verified that AgNPs were transformed into Ag-Fe-S core shell aggregates (size >200 nm) decreasing bioavailability and the damage to cytomembrane. The PYBC restored the nitrogen removal efficiency by increasing the abundance of Nitrospira and Geothrix, which these bacteria were defined as nitrifiers and Feammox bacteria. This study provides a promising strategy to mitigate AgNPs' toxicity on the pollutant removal efficiency in CWs.

Synergistic action of indole-3-carbinol with membrane-active agents against multidrug-resistant Gram-negative bacteria.

The purpose of this study was to evaluate the antimicrobial activity of indole-3-carbinol (I3C) with membrane-active agents, namely carbonyl cyanide 3-chlorophenylhydrazone (CCCP) and ethylenediaminetetraacetic acid (EDTA) against multidrug-resistant (MDR) Gram-negative bacteria and bacterial persisters. The determination of minimal inhibitory concentration (MIC) showed that I3C was effective against Acinetobacter baumannii (3.13‒6.25 × 10-3 mol l-1), Klebsiella pneumoniae (8 × 10-3 mol l-1), Pseudomonas aeruginosa (6.25‒12.5 × 10-3 mol l-1), and Escherichia coli (6.25‒12.5 × 10-3 mol l-1). Our study demonstrated that EDTA synergistically enhanced the bactericidal activity of I3C against most MDR Gram-negative bacteria isolates and contributed to an 8- to 64-fold MIC reduction compared with that of I3C alone, yet CCCP only displayed synergy with I3C against P. aeruginosa and A. baumannii. The EDTA-I3C combination also significantly reduced the viable number of testing bacteria (P = 7.2E-05), effectively reduced bacterial persisters, and repressed bacterial growth compared with that the use of I3C alone. Our data demonstrate that use of EDTA as adjuvant molecules can effectively improve the antibacterial activity of I3C and may help to reduce the development of antimicrobial resistance.

Activating Transcription Factor 3 Diminishes Ischemic Cerebral Infarct and Behavioral Deficit by Downregulating Carboxyl-Terminal Modulator Protein.

Activating transcription factor 3 (ATF3) is a stress-induced transcription factor and a familiar neuronal marker for nerve injury. This factor has been shown to protect neurons from hypoxic insult in vitro by suppressing carboxyl-terminal modulator protein (CTMP) transcription, and indirectly activating the anti-apoptotic Akt/PKB cascade. Despite prior studies in vitro, whether this neuroprotective pathway also exists in the brain in vivo after ischemic insult remains to be determined. In the present study, we showed a rapid and marked induction of ATF3 mRNA throughout ischemia-reperfusion in a middle cerebral artery (MCA) occlusion model. Although the level of CTMP mRNA was quickly induced upon ischemia, its level showed only a mild increase after reperfusion. With the gain-of-function approach, both pre- and post-ischemic administration of Ad-ATF3 ameliorated brain infarct and neurological deficits. Whereas, with the loss-of-function approach, ATF3 knockout (KO) mice showed bigger infarct and worse functional outcome after ischemia. In addition, these congenital defects were rescued upon reintroducing ATF3 to the brain of KO mice. ATF3 overexpression led to a lower level of CTMP and a higher level of p-Akt(473) in the ischemic brain. On the contrary, ATF3 KO resulted in upregulation of CTMP and downregulation of p-Akt(473) instead. Furthermore, post-ischemic CTMP siRNA knockdown led to smaller infarct and better behaviors. CTMP siRNA knockdown increased the level of p-Akt(473), but did not alter the ATF3 level in the ischemic brain, upholding the ATF3→CTMP signal cascade. In summary, our proof-of-principle experiments support the existence of neuroprotective ATF3→CTMP signal cascade regulating the ischemic brain. Furthermore, these results suggest the therapeutic potential for both ATF3 overexpression and CTMP knockdown for stroke treatment.

Stepwise Evolution and Exceptional Conservation of ORF1a/b Overlap in Coronaviruses.

The programmed frameshift element (PFE) rerouting translation from ORF1a to ORF1b is essential for the propagation of coronaviruses. The combination of genomic features that make up PFE-the overlap between the two reading frames, a slippery sequence, as well as an ensemble of complex secondary structure elements-places severe constraints on this region as most possible nucleotide substitution may disrupt one or more of these elements. The vast amount of SARS-CoV-2 sequencing data generated within the past year provides an opportunity to assess the evolutionary dynamics of PFE in great detail. Here, we performed a comparative analysis of all available coronaviral genomic data available to date. We show that the overlap between ORF1a and ORF1b evolved as a set of discrete 7, 16, 22, 25, and 31 nucleotide stretches with a well-defined phylogenetic specificity. We further examined sequencing data from over 1,500,000 complete genomes and 55,000 raw read data sets to demonstrate exceptional conservation and detect signatures of selection within the PFE region.

The correlation between miR -34a-3p, miR -31, PLEK2 and the occurrence, development and prognosis of colorectal cancer.

The current study aimed to explore the correlation between Mir-34A-3p, Mir-31, PLEK2 and the occurrence, development and prognosis of colorectal cancer. For this paper, 120 patients with colorectal cancer were selected as the study group, and their adjacent normal tissues were selected as the control group. The quantitative real-time PCR (QRT-PCR) method was used to detect miR-34a-3p and miR-31 in tissues, and the immunohistochemistry EnVision two-step method was used to detect PLEK2 positive expression. The expressions of miR -34a-3p, miR -31, and PLEK2 in colon cancer tissues and normal cancer tissues were compared, and the correlation between miR -34a-3p, miR -31, and PLEK2 and clinic-pathological characteristics of colorectal cancer patients were analyzed. The results showed that expression of miR -34a-3p, miR -31 and positive expression rate of PLEK2 in colorectal cancer tissues were higher than those in normal adjacent tissues (P<0.05). The expression of miR -34a-3p was related to tumor size, degree of tissue differentiation, lymph node metastasis and TNM stage (P < 0.05). The 3-year survival rate of miR -34a-3p with low expression was lower than miR -34a-3p with high expression, which was a protective factor affecting the poor prognosis of colorectal cancer (P < 0.05). The expression of miR -31 was related to tumor size and TNM stage. The 3-year survival rate of the group with high expression of miR -31 was lower than the group with low expression of miR -31, which was a risk factor affecting the poor prognosis of colorectal cancer (P < 0.05). PLEK2 positive expression was associated with lymph node metastasis, and the 3-year survival rate of the PLEK2 positive group was lower than the PLEK2 low expression group, which was a risk factor for poor prognosis of colorectal cancer (P < 0.05). In general, miR -34a-3p, miR -31, and PLEK2 are closely associated with the occurrence and development of colorectal cancer, and they are all influential factors affecting the prognosis of patients with colorectal cancer, which can provide a basis for the evaluation and treatment of patients, and are worthy of widespread clinical application.

Body volume is the major determinant of worsening renal function in acutely decompensated heart failure with reduced left ventricular ejection fraction.

AIMS: Little is known about the relative importance of body volume and haemodynamic parameters in the development of worsening of renal function in acutely decompensated heart failure (ADHF). To study the relationship between haemodynamic parameters, body water content and worsening of renal function in patients with heart failure with reduced ejection fraction (HFrEF) hospitalised for ADHF. METHODS AND RESULTS: This prospective observational study involved 51 consecutive patients with HFrEF (age: 73±14 years, male: 60%, left ventricular ejection fraction: 33.3%±9.9%) hospitalised for ADHF. Echocardiographic-determined haemodynamic parameters and body volume determined using a bioelectric impedance analyser were serially obtained. All patients received intravenous furosemide 160 mg/day for 3 days. There was a mean weight loss of 3.95±2.82 kg (p<0.01), and brain natriuretic peptide (BNP) reduced from 1380±901 pg/mL to 797±738 pg/mL (p<0.01). Nonetheless serum creatinine (SCr) increased from 134±46 µmol/L to 151±53 µmol/L (p<0.01), and 35% of patients developed worsening of renal function. The change in SCr was positively correlated with age (r=0.34, p=0.017); and negatively with the ratio of extracellular water to total body water, a parameter of body volume status (r=-0.58, p<0.001); E:E' ratio (r=-0.36, p=0.01); right ventricular systolic pressure (r=-0.40, p=0.009); and BNP (r=-0.40, p=0.004). Counterintuitively, no correlation was observed between SCr and cardiac output, or total peripheral vascular resistance. Regression analysis revealed that normal body volume and lower BNP independently predicted worsening of renal function. CONCLUSIONS: Normal body volume and lower serum BNP on admission were associated with worsening of renal function in patients with HFrEF hospitalised for ADHF.

Reduced infiltration of regulatory T cells in tumours from mice fed daily with gamma-tocotrienol supplementation.

Gamma-tocotrienol (γT3) is an analogue of vitamin E with beneficial effects on the immune system, including immune-modulatory properties. This study reports the immune-modulatory effects of daily supplementation of γT3 on host T helper (Th) and T regulatory cell (Treg ) populations in a syngeneic mouse model of breast cancer. Female BALB/c mice were fed with either γT3 or vehicle (soy oil) for 2 weeks via oral gavage before they were inoculated with syngeneic 4T1 mouse mammary cancer cells (4T1 cells). Supplementation continued until the mice were euthanized. Mice (n = 6) were euthanized at specified time-points for various analysis (blood leucocyte, cytokine production and immunohistochemistry). Tumour volume was measured once every 7 days. Gene expression studies were carried out on tumour-specific T lymphocytes isolated from splenic cultures. Supplementation with γT3 increased CD4+ (p < 0.05), CD8+ (p < 0.05) T-cells and natural killer cells (p < 0.05) but suppressed Treg cells (p < 0.05) in peripheral blood when compared to animals fed with the vehicle. Higher interferon (IFN)-γ and lower transforming growth factor (TGF)-ꞵ levels were noted in the γT3 fed mice. Immunohistochemistry findings revealed higher infiltration of CD4+ cells, increased expression of interleukin-12 receptor-beta-2 (IL-12ꞵ2R), interleukin (IL)-24 and reduced expression of cells that express the forkhead box P3 (FoxP3) in tumours from the γT3-fed animals. Gene expression studies showed the down-regulation of seven prominent genes in splenic CD4+ T cells isolated from γT3-fed mice. Supplementation with γT3 from palm oil-induced T cell-dependent cell-mediated immune responses and suppressed T cells in the tumour microenvironment in a syngeneic mouse model of breast cancer.

Outbreak of vibriosis associated with Vibrio parahaemolyticus in the mud crab Scylla paramamosain cultured in China.

In this study, a Gram-negative bacterium was isolated from diseased Scylla paramamosain and tentatively named strain QX17. The bacterial isolate was identified as Vibrio parahaemolyticus based on morphological and biochemical characteristics and molecular identification with the 16S rRNA and HSP60 genes. In the challenge experiment, S. paramamosain injected intramuscularly with the V. parahaemolyticus isolate developed pathological signs similar to the naturally diseased mud crabs. The infection experiment also showed that the median lethal dosage (LD50) for QX17 was 4.79 × 102 CFU g-1 (crab weight). Histopathological analysis of the diseased mud crabs infected with V. parahaemolyticus showed deformation and basement membrane rupture of hepatopancreatic tubules in the hepatopancreas, and disordered and broken muscle fiber in the muscle. Antimicrobial susceptibility tests revealed that QX17 was highly sensitive to most of the tested aminoglycosides, tetracyclines, and quinolones. To the best of our knowledge, this is the first study reporting isolation and antibiotic sensitivities of V. parahaemolyticus from cultured mud crabs. The discovery of V. parahaemolyticus in cultured mud crabs not only adds to the growing list of emerging pathogens in crab aquaculture in China, but also highlights the necessity of developing early detection strategies and appropriate interventions to reduce the damage caused by V. parahaemolyticus in mud crab aquaculture.

Calibrations of Low-Cost Air Pollution Monitoring Sensors for CO, NO2, O3, and SO2.

Pollutant gases, such as CO, NO2, O3, and SO2 affect human health, and low-cost sensors are an important complement to regulatory-grade instruments in pollutant monitoring. Previous studies focused on one or several species, while comprehensive assessments of multiple sensors remain limited. We conducted a 12-month field evaluation of four Alphasense sensors in Beijing and used single linear regression (SLR), multiple linear regression (MLR), random forest regressor (RFR), and neural network (long short-term memory (LSTM)) methods to calibrate and validate the measurements with nearby reference measurements from national monitoring stations. For performances, CO > O3 > NO2 > SO2 for the coefficient of determination (R2) and root mean square error (RMSE). The MLR did not increase the R2 after considering the temperature and relative humidity influences compared with the SLR (with R2 remaining at approximately 0.6 for O3 and 0.4 for NO2). However, the RFR and LSTM models significantly increased the O3, NO2, and SO2 performances, with the R2 increasing from 0.3-0.5 to >0.7 for O3 and NO2, and the RMSE decreasing from 20.4 to 13.2 ppb for NO2. For the SLR, there were relatively larger biases, while the LSTMs maintained a close mean relative bias of approximately zero (e.g., <5% for O3 and NO2), indicating that these sensors combined with the LSTMs are suitable for hot spot detection. We highlight that the performance of LSTM is better than that of random forest and linear methods. This study assessed four electrochemical air quality sensors and different calibration models, and the methodology and results can benefit assessments of other low-cost sensors.

Applications of packed and capillary supercritical fluid chromatography in the separation of tocochromanols.

Tocochromanols consisting of tocopherols and tocotrienols, is collectively known as vitamin E. Similarity in their structures, physical and chemical properties rendered the tocochromanols to be subject of chromatography interest. Supercritical fluid chromatography is a highly efficient tool for the separation and analysis of tocochromanols. Separation and analysis of tocochromanols using supercritical fluid chromatography had been carried out in the past using capillary or packed columns. Each of these techniques offer their own advantages and drawbacks. Besides being used for analysis, packed column supercritical fluid chromatography found applications as a purification and content enrichment tool. Emergence of new equipment and stationary phase technologies in recent years also helped in making supercritical fluid chromatography a highly efficient tool for the separation and analysis of tocochromanols. This paper gives an insight into the use of capillary and packed columns in supercritical fluid chromatography for the separation and/or analysis of tocochromanols. The types of stationary phase used, as well as chromatographic conditions are also discussed.

Preoperative biopsy and tumor recurrence of stage I adenocarcinoma of the lung.

PURPOSE: To evaluate whether preoperative biopsy affects the outcomes of patients undergoing at least lobectomy for stage I lung adenocarcinoma. METHODS: We reviewed the medical records of patients who underwent surgery for stage I lung adenocarcinoma between 2006 and 2013. Tumor recurrence and survival were compared between patients who underwent preoperative biopsy, including computed tomographic-guided needle biopsy and transbronchial biopsy, and those who underwent intraoperative frozen section. RESULTS: Among 509 patients, 229 patients (44.9%) underwent preoperative biopsy and 280 patients had lung adenocarcinoma diagnosed by intraoperative frozen section (reference group). Recurrence developed in 65 (12.8%) patients within a median follow-up period of 54.4 months. Multivariate analysis demonstrated that preoperative biopsy (OR 1.97, p = 0.045), radiological solid appearance (OR 5.43, p < 0.001), and angiolymphatic invasion (OR 2.48, p = 0.010) were independent predictors of recurrence. In the overall cohort, preoperative biopsy appeared to worsen 5-year disease-free and overall survival significantly (76.6% vs. 93.0%, p < 0.001; and 83.8% vs. 94.5%, p = 0.002, respectively) compared with the reference group. After propensity matching, multivariable logistic regression still identified preoperative biopsy as an independent predictor of overall recurrence (OR 2.21, p = 0.048) after adjusting for tumor characteristics. CONCLUSION: Preoperative biopsy might be considered a prognosticator of recurrence of stage I adenocarcinoma of the lungs in patients who undergo at least anatomic lobectomy without postoperative adjuvant chemotherapy.

Field Evaluation of Low-Cost Particulate Matter Sensors in Beijing.

Numerous particulate matter (PM) sensors with great development potential have emerged. However, whether the current sensors can be used for reliable long-term field monitoring is unclear. This study describes the research and application prospects of low-cost miniaturized sensors in PM2.5 monitoring. We evaluated five Plantower PMSA003 sensors deployed in Beijing, China, over 7 months (October 2019 to June 2020). The sensors tracked PM2.5 concentrations, which were compared to the measurements at the national control monitoring station of the Ministry of Ecology and Environment (MEE) at the same location. The correlations of the data from the PMSA003 sensors and MEE reference monitors (R2 = 0.83~0.90) and among the five sensors (R2 = 0.91~0.98) indicated a high accuracy and intersensor correlation. However, the sensors tended to underestimate high PM2.5 concentrations. The relative bias reached -24.82% when the PM2.5 concentration was >250 µg/m3. Conversely, overestimation and high errors were observed during periods of high relative humidity (RH > 60%). The relative bias reached 14.71% at RH > 75%. The PMSA003 sensors performed poorly during sand and dust storms, especially for the ambient PM10 concentration measurements. Overall, this study identified good correlations between PMSA003 sensors and reference monitors. Extreme field environments impact the data quality of low-cost sensors, and future corrections remain necessary.

Histone deacetylases in stroke.

Stroke is the second leading cause of death and the leading cause of adult disability worldwide. Despite an impressive amount of neuroprotective agents that has been identified in experimental stroke, none of them proved efficient in clinical trials. There is a general consensus that an effective treatment requires the ability to interact with not one, but multiple pathophysiological cascades at different levels that induced by the insult - cocktail therapy. Luckily, recent progress in the field of epigenetics revealed that epigenetic modifications had influence on many known pathways involved in the complex course of ischemic disease development. The fact that epigenetic molecules, by altering transcriptional regulation, may simultaneously act on different levels of ischemic brain injury makes them promising candidates for clinical use. These modifications arise typically owing to deoxyribonucleic acid methylation and histone acetylation. The aim of this review is to give a comprehensive overview of current advances in stroke epigenetics, in particular, the physiological and pathological functions of the 11 classical histone deacetylases.

Diagnostic Method of Liver Cirrhosis Based on MR Image Texture Feature Extraction and Classification Algorithm.

In order to improve the accuracy of cirrhosis staging diagnosis based on MR images, a diagnostic method combining image texture feature extraction and classification algorithm is proposed. Firstly, the liver MR image is preprocessed, the region of interest (ROI) image patch is extracted therefrom, and the ROI image is quantized and compressed by the Lloyd algorithm. Then, the ROI image is filtered by a local binary pattern (LBP) operator, and then the texture feature of a 20-dimensional gray-level co-occurrence Matrix (GLCM) in four directions on the LBP image is extracted. Finally, MR image is classified by performing support vector machine (SVM) and the final diagnosis of liver cirrhosis is obtained. The experimental results show that the proposed method can accurately diagnose liver cirrhosis.

Interobserver and intraobserver variability in measuring the tortuosity of the thoracic aorta on computed tomography.

OBJECTIVE: The variability in measuring the tortuosity of the thoracic aorta has not been previously studied. This study evaluated the interobserver and intraobserver variability of major methods used for measuring the tortuosity of the thoracic aorta in patients with aortic arch or descending thoracic aortic aneurysm. METHODS: This retrospective study enrolled 66 patients with aortic arch or descending thoracic aortic aneurysm who had undergone thoracic endovascular aortic repair. Two radiologists used preoperative computed tomography images to measure the tortuosity of the thoracic aorta at multiple segments by using the fitting circle diameter, tortuosity index, and centerline angle methods; these measurements were repeated after an interval of >28 days. The variability of the methods was analyzed for interobserver and intraobserver reliability and agreement. The estimated intraclass correlation coefficient (ICC) was used to analyze the reliability. The Bland-Altman plot was used to analyze the interobserver and intraobserver agreement. The association between aortic characteristics, including calcification, luminal irregularity, shape, and diameter, and the variability of the measurements was also analyzed. RESULTS: The interobserver ICC estimates for the tortuosity index at multiple aortic segments, centerline angle methods at the supra-aortic branch orifices, and fitting circle diameter on the greater and lesser curvature sides were 0.97 to 0.98, 0.39 to 0.75, and 0.82 to 0.84, respectively. The corresponding intraobserver ICC estimates were 0.98 to 1.00, 0.44 to 0.75, and 0.82 to 0.85, respectively. In the agreement analysis, the 95% limits of agreement for the tortuosity index, centerline angle, and fitting circle diameter were -5.5% to 5.6%, -10.9% to 10.9%, and -18.0% to 24.0%, respectively. The tortuosity index had the highest ICC estimate and narrowest 99.5% limits of agreement of the three methods. Aortic characteristics, including calcification, grade of atheroma, aneurysm shape, and diameter, were not associated with the variability of the tortuosity index method in the thoracic aorta. CONCLUSIONS: The tortuosity index method has low interobserver and intraobserver variability in measuring the tortuosity of the thoracic aorta in patients with thoracic aortic aneurysm. The characteristics of the aorta and aneurysm are not associated with the interobserver or intraobserver variability of the tortuosity index.

Diagnostic feasibility and safety of CT-guided core biopsy for lung nodules less than or equal to 8 mm: A single-institution experience.

OBJECTIVES: This retrospective study evaluated the diagnostic yield and safety of CT-guided core biopsy of pulmonary nodules ≤8 mm. METHODS: We determined the diagnostic yield and safety profile of CT-guided lung biopsies for 125 pulmonary nodules ≤8 mm. Pathological diagnoses were made by a combination of histopathological examination and imprint cytology. Results were compared with biopsy results for 134 pulmonary nodules >8 and ≤10 mm. RESULTS: Final diagnoses were established in 94 nodules ≤8 mm. The sensitivity, specificity and diagnostic accuracy of CT-guided core biopsy for nodules ≤8 mm were 87.1 % (61/70 nodules), 100 % (24/24) and 90.4 % (85/94), respectively. Diagnostic failure rates were comparable for nodules ≤8 mm and nodules >8 mm and ≤10 mm (9/94, 9.6 % and 7/111, 6.3 %, respectively, P=0.385). The rate of tube thoracostomy for nodules ≤8 mm was comparable to that for nodules >8 and ≤10 mm (1.6 % vs. 0.7 %, P=0.611). Nodules ≤6 mm had a higher non-diagnostic result rate of 15.4 % (6/39) than did nodules >8 and ≤10 mm (3.7 %, 5/134, P=0.017). CONCLUSIONS: CT-guided pulmonary biopsy is feasible for lung nodules ≤8 mm, especially those >6 mm, and has an acceptable diagnostic yield and safety profile. KEY POINTS: • CT-guided biopsy of lung nodules ≤8 mm has high diagnostic accuracy. • Safety profiles are similar between nodules ≤8 mm and 8-10 mm. • Nodules ≤6 mm have higher rates of non-diagnostic results in biopsy. • Non-subpleural nodules and old age are risk factors for higher grade haemorrhage. • Biopsy is feasible for diagnosing nodules >6 and ≤8 mm.