An Empirical Bayesian Method for Detecting Differentially Expressed Genes Using EST Data

Detection of differentially expressed genes from expressed sequence tags (ESTs) data has received much attention. An empirical Bayesian method is introduced in which gene expression patterns are estimated and used to define detection statistics. Significantly differentially expressed genes can be declared given detection statistics. Simulation is done to evaluate the performance of proposed method. Two real applications are studied

Experimental Study of Smoke Spread in Titled Urban Traffic Tunnels Fires

AbstractMore and more urban traffic tunnels are built due to the heavy traffic in dense urban areas. Fire safety in tunnels is a concern due to the large traffic flow. Most of the urban tunnels have slope. Knowledge on smoke spread in titled tunnel is still limited. Experimental studies on the smoke spread in a titled tunnel are carried out by the reduced-scale tunnel model tests and will be discussed in this paper. Effects of the titled gradients and longitudinal ventilation speed on the temperature distribution and smoke stratification downstream from the fire along the tunnel will be studied The results show that the smoke spread upwards much faster with the slop gradient increasing, and a thick smoke layer was formed when smoke moved to the upward part of the tunnel and filled it up. The ventilation speed had a great influence on temperature distribution along the tunnel, and the smoke stratification will be distributed when the longitudinal ventilation speed becomes large. Lower ventilation speed should be adopted at the beginning to ensure the smoke downstream of the fire keep stratified to give the tunnel users more time to escape

Statistical methods for assays with limits of detection: Serum bile acid as a differentiator between patients with normal colons, adenomas, and colorectal cancer

In analytic chemistry a detection limit (DL) is the lowest measurable amount of an analyte that can be distinguished from a blank; many biomedical measurement technologies exhibit this property. From a statistical perspective, these data present inferential challenges because instead of precise measures, one only has information that the value is somewhere between 0 and the DL (below detection limit, BDL). Substitution of BDL values, with 0 or the DL can lead to biased parameter estimates and a loss of statistical power. Statistical methods that make adjustments when dealing with these types of data, often called left-censored data, are available in many commercial statistical packages. Despite this availability, the use of these methods is still not widespread in biomedical literature. We have reviewed the statistical approaches of dealing with BDL values, and used simulations to examine the performance of the commonly used substitution methods and the most widely available statistical methods. We have illustrated these methods using a study undertaken at the Vanderbilt-Ingram Cancer Center, to examine the serum bile acid levels in patients with colorectal cancer and adenoma. We have found that the modern methods for BDL values identify disease-related differences that are often missed, with statistically naive approaches

Accuracy of radiomics in the diagnosis and preoperative high-risk assessment of endometrial cancer: a systematic review and meta-analysis

BackgroundWith the increasing use of radiomics in cancer diagnosis and treatment, it has been applied by some researchers to the preoperative risk assessment of endometrial cancer (EC) patients. However, comprehensive and systematic evidence is needed to assess its clinical value. Therefore, this study aims to investigate the application value of radiomics in the diagnosis and treatment of EC.MethodsPubmed, Cochrane, Embase, and Web of Science databases were retrieved up to March 2023. Preoperative risk assessment of EC included high-grade EC, lymph node metastasis, deep myometrial invasion status, and lymphovascular space invasion status. The quality of the included studies was appraised utilizing the RQS scale.ResultsA total of 33 primary studies were included in our systematic review, with an average RQS score of 7 (range: 5–12). ML models based on radiomics for the diagnosis of malignant lesions predominantly employed logistic regression. In the validation set, the pooled c-index of the ML models based on radiomics and clinical features for the preoperative diagnosis of endometrial malignancy, high-grade tumors, lymph node metastasis, lymphovascular space invasion, and deep myometrial invasion was 0.900 (95%CI: 0.871–0.929), 0.901 (95%CI: 0.877–0.926), 0.906 (95%CI: 0.882–0.929), 0.795 (95%CI: 0.693–0.897), and 0.819 (95%CI: 0.705–0.933), respectively.ConclusionsRadiomics shows excellent accuracy in detecting endometrial malignancies and in identifying preoperative risk. However, the methodological diversity of radiomics results in significant heterogeneity among studies. Therefore, future research should establish guidelines for radiomics studies based on different imaging sources.Systematic review registrationhttps://www.crd.york.ac.uk/PROSPERO/display_record.php?RecordID=364320 identifier CRD42022364320

Heterologous expression and characterization of a malathion-hydrolyzing carboxylesterase from a thermophilic bacterium, Alicyclobacillus tengchongensis

A carboxylesterase gene from thermophilic bacterium, Alicyclobacillus tengchongensis, was cloned and expressed in Escherichia coli BL21 (DE3). The gene coded for a 513 amino acid protein with a calculated molecular mass of 57.82 kDa. The deduced amino acid sequence had structural features highly conserved among serine hydrolases, including Ser204, Glu325, and His415 as a catalytic triad, as well as type-B carboxylesterase serine active site (FGGDPENITIGGQSAG) and type-B carboxylesterase signature 2 (EDCLYLNIWTP). The purified enzyme exhibited optimum activity with β-naphthyl acetate at 60 °C and pH 7 as well as stability at 25 °C and pH 7. One unit of the enzyme hydrolyzed 5 mg malathion l(−1) by 50 % within 25 min and 89 % within 100 min. The enzyme strongly degraded malathion and has a potential use for the detoxification of malathion residues

Biochemical characterization of an acetylesterase from Bacillus subtilis and its application for 7-aminocephalosporanic acid deacetylation

Deacetyl-7-aminocephalosporanic acid (D-7-ACA), which could be converted from 7-aminocephalosporanic acid (7-ACA), is a crucial starting material that is used for synthesizing industrial semisynthetic β-lactam antibiotics. Enzymes involved in the conversion from 7-ACA to D-7-ACA present critical resources in the pharmaceutical industry. In the present study, a putative acetylesterase, EstSJ, identified from Bacillus subtilis KATMIRA1933, was first heterologously expressed in Escherichia coli BL21(DE3) cells and biochemically characterized. EstSJ belongs to carbohydrate esterase family 12 and is active on short-chain acyl esters from p-NPC2 to p-NPC6. Multiple sequence alignments showed that EstSJ was also an SGNH family esterase with a typical GDS(X) motif at its N-terminal end and a catalytic triad composed of Ser186-Asp354-His357. The purified EstSJ displayed the highest specific activity of 1,783.52 U mg–1 at 30°C and pH 8.0, and was stable within the pH range of 5.0–11.0. EstSJ can deacetylate the C3′ acetyl group of 7-ACA to generate D-7-ACA, and the deacetylation activity was 4.50 U mg–1. Based on the structural and molecular docking with 7-ACA, the catalytic active sites (Ser186-Asp354-His357) together with four substrate-binding residues (Asn259, Arg295, Thr355, and Leu356) of EstSJ are revealed. This study provided a promising 7-ACA deacetylase candidate that could be applied to produce D-7-ACA from 7-ACA in the pharmaceutical industry

Biological control of Fusarium crown rot of wheat with Chaetomium globosum 12XP1-2-3 and its effects on rhizosphere microorganisms

Chaetomium globosum is a common plant endophytic fungi that exhibits great biocontrol potential in plant disease. Fusarium crown rot (FCR) is an important disease in wheat that seriously threatens wheat production worldwide. The control effect of C. globosum against wheat FCR remains unclear. In this study, we introduced an identified C. globosum 12XP1-2-3 and tested its biological control potential against wheat FCR. The hypha and fermentation broth exhibited an antagonistic effect against Fusarium pseudograminearum. Results from indoor experiments showed that C. globosum 12XP1-2-3 might delay the onset of symptoms of brown stem base and significantly reduced the disease index (37.3%). Field trials showed that wheat seeds coated with a spore suspension of 12XP1-2-3 grew better than the control seeds, had control effects of 25.9–73.1% on FCR disease, and increased wheat yield by 3.2–11.9%. Analysis of rhizosphere microorganisms revealed that seeds coated with C. globosum (‘Cg’ treatment) had a greater effect on fungal rather than on bacterial alpha diversity and may improve the health state of rhizosphere microorganisms, as reflected by the significantly increased fungal Shannon index at Feekes 11 and the increased complexity of the bacterial co-occurrence network but decreased complexity of the fungal network. Moreover, the accumulation of beneficial bacteria such as Bacillus and Rhizobium at Feekes 3, and Sphingomonas at Feekes 7 in the ‘Cg’ treatment may be the important contributions to healthier wheat growth state, significantly reduced relative abundance of Fusarium at Feekes 11, and reduced occurrence of FCR disease. These results provide a basis for further research on the mechanism of action of C. globosum and its application in the biological control of FCR in the field