A Brief Review of Computational Gene Prediction Methods

With the development of genome sequencing for many organisms, more and more raw sequences need to be annotated. Gene prediction by computational methods for finding the location of protein coding regions is one of the essential issues in bioinformatics. Two classes of methods are generally adopted: similarity based searches and ab initio prediction. Here, we review the development of gene prediction methods, summarize the measures for evaluating predictor quality, highlight open problems in this area, and discuss future research directions

Quantitative Estimation of Urban PM2.5 Pollution Baseline and Meteorological Resource Endowment Using Machine Learning in Chinese Yangtze River Economic Belt

Considering the influence of baseline values, meteorological conditions, and human activities on PM2.5, quantifying them will facilitate the classification, control, and management of pollution. The machine learning model explained the PM2.5-meteorological nonlinear relationship between PM2.5 and meteorological factors in each city across the Yangtze River Economic Belt, China. Meteorological resource endowments (MRE) are used to quantify the variation on PM2.5 concentration caused by meteorological conditions. Contamination baseline (CB) is used to characterize the lowest limit of anthropogenic impact in PM2.5 contamination without meteorological interference. According to the values of MRE and CB, cities in the Yangtze River economic belt can be divided into four categories (Q1-4). The average value of MRE is −0.41 μg/m3. The average value of CB is 34.05 μg/m3, which is lower than the Chinese Grade II standard (GB 3095-2012). The additional emissions by humans resulted in an increase of 7 μg/m3 in concentration, while the meteorological factors led to a decrease of −0.41 μg/m3. In terms of city classification, Q1 is concentrated in the midstream, and PM2.5 is the most challenging pollutant to control. Q2 is concentrated downstream, with relatively high PM2.5 emissions but favorable meteorological conditions. Q3 is concentrated upstream, and there is surplus environmental capacity even with limited meteorological conditions. Cites in Q4 have the most suitable development potential and exhibit a discrete spatial distribution. The research distinguished various categories of pollution and provided insights into the different characteristics of pollution around the Yangtze River Economic Belt. This information has helped the government classify cities and implement specific policies based on their individual situations

Study on the evaluation of the clinical effects of traditional chinese medicine in heart failure by complex intervention: protocol of SECETCM-HF

<p>Abstract</p> <p>Background</p> <p>Experts in Traditional Chinese Medicine (TCM) have studied the TCM subject of the pathogenesis of heart failure (HF) for several decades. As a result, the general idea is <it>ben </it>deficiency and <it>biao </it>excess. However, the clinical evaluation system which combined the TCM and western medicine in HF has not been developed yet. The objective is to establish the evaluation index system for the integration of TCM and western medicine. The evaluation indexes which include TCM items will specify the research design and methods.</p> <p>Methods</p> <p>Nine medical centers in different cities in China will participate in the trial. A population of 340 patients with HF will be enrolled through a central randomized system for different test groups. Group A will be treated with only western medicine, while group B with western and Chinese medicine together. The study will last for 12 months from the date of enrollment. The cardiovascular death will be the primary outcome.</p> <p>Discussion</p> <p>By putting the protocol into practice, the clinical effects of TCM for HF will be identified scientifically, objectively as well as rationally. The proper index system which built in the study will be helpful for the clinical effect expression of HF by integrated medicine in future.</p> <p>Trial Registration</p> <p>ChiCTR-TRC-00000059</p

Measuring shape complexity of breast lesions on ultrasound images

ABSTRACT The shapes of malignant breast tumors are more complex than the benign lesions due to their nature of infiltration into surrounding tissues. We investigated the efficacy of shape features and presented a method using polygon shape complexity to improve the discrimination of benign and malignant breast lesions on ultrasound. First, 63 lesions (32 benign and 31 malignant) were segmented by K-way normalized cut with the priori rules on the ultrasound images. Then, the shape measures were computed from the automatically extracted lesion contours. A polygon shape complexity measure (SCM) was introduced to characterize the complexity of breast lesion contour, which was calculated from the polygonal model of lesion contour. Three new statistical parameters were derived from the local integral invariant signatures to quantify the local property of the lesion contour. Receiver operating characteristic (ROC) analysis was carried on to evaluate the performance of each individual shape feature. SCM outperformed the other shape measures, the area under ROC curve (AUC) of SCM was 0.91, and the sensitivity of SCM could reach 0.97 with the specificity 0.66. The measures of shape feature and margin feature were combined in a linear discriminant classifier. The resubstitution and leave-one-out AUC of the linear discriminant classifier were 0.94 and 0.92, respectively. The distinguishing ability of SCM showed that it could be a useful index for the clinical diagnosis and computer-aided diagnosis to reduce the number of unnecessary biopsies

Moisture Transport and Contribution to the Continental Precipitation

Understanding the water cycle change under a warming climate is essential, particularly the ocean to land moisture transport, which affects the precipitation over land areas and influences society and the ecosystem. Using ERA5 data from 1988 to 2020, the time series of moisture transport and the trend across the boundary of each continent, including Eurasia, Africa, North America, South America, Antarctic, Australia, and Greenland, have been investigated. The inflow and outflow sections of the moisture have been identified for each continent. The trends of moisture convergence over Eurasia, Africa, North America, and Antarctic are all positive, with the values of 2.59 &plusmn; 3.12, 2.60 &plusmn; 3.17, 12.98 &plusmn; 2.28, and 0.32 &plusmn; 0.47 (in 106 kg/s/decade), respectively, but only the trend over North America is statistically significant at a 0.1 significance level. The moisture convergence trend of &minus;0.59 &plusmn; 3.63 (in 106 kg/s/decade) over South America is negative but insignificant. The positive trend of 0.10 &plusmn; 0.35 (in 106 kg/s/decade) over Greenland is very weak. The precipitation, evaporation, and moisture convergence are well balanced at middle and low latitudes, but the combination of moisture convergence and evaporation is systematically lower than the precipitation over Antarctic and Greenland. Contributions of evaporation and moisture convergence (or transport) to the continental precipitation vary with the continent, but the moisture convergence dominates the precipitation variability over all continents, and the significant correlation coefficients between the anomaly time series of continental mean moisture convergence and precipitation are higher than 0.8 in all continents

Table_5_Polycystic ovary syndrome: Identification of novel and hub biomarkers in the autophagy-associated mRNA-miRNA-lncRNA network.xlsx

IntroductionPolycystic ovary syndrome (PCOS) is a common metabolic and endocrine disorder prevalent among women of reproductive age. Recent studies show that autophagy participated in the pathogenesis of PCOS, including anovulation, hyperandrogenism, and metabolic disturbances. This study was designed to screen autophagy-related genes (ATGs) that may play a pivotal role in PCOS, providing potential biomarkers and identifying new molecular subgroups for therapeutic intervention.MethodsGene expression profiles of the PCOS and control samples were obtained from the publicly available Gene Expression Omnibus database. The gene lists of ATGs from databases were integrated. Then, the weighted gene co-expression network analysis was conducted to obtain functional modules and construct a multifactorial co-expression network. Gene Ontology and KEGG pathway enrichment analyses were performed for further exploration of ATG's function in the key modules. Differentially expressed ATGs were identified and validated in external datasets with the Limma R package. To provide guidance on PCOS phenotyping, the dysfunction module consists of a co-expression network mapped to PCOS patients. A PCOS-Autophagy-related co-expression network was established using Cytoscape, followed by identifying molecular subgroups using the Limma R package. ps. RNA-sequencing analysis was used to confirm the differential expression of hub ATGs, and the diagnostic value of hub ATGs was assessed by receiver operating characteristic curve analysis.ResultsThree modules (Brown, Turquoise, and Green) in GSE8157, three modules (Blue, Red, and Green) in GSE43264, and four modules (Blue, Green, Black, and Yellow) in GSE106724 were identified to be PCOS-related by WGCNA analysis. 29 ATGs were found to be the hub genes that strongly correlated with PCOS. These hub ATGs were mainly enriched in autophagy-related functions and pathways such as autophagy, endocytosis, apoptosis, and mTOR signaling pathways. The mRNA-miRNA-lncRNA multifactorial network was successfully constructed. And three new molecular subgroups were identified via the K-means algorithm.DiscussionWe provide a novel insight into the mechanisms behind autophagy in PCOS. BRCA1, LDLR, MAP1B, hsa-miR-92b-3p, hsa-miR-20b-5p, and NEAT1 might play a considerably important role in PCOS dysfunction. As a result, new potential biomarkers can be evaluated for use in PCOS diagnosis and treatment in the future.</p

Review of the Observed Energy Flow in the Earth System

The energy budget imbalance at the top of the atmosphere (TOA) and the energy flow in the Earth’s system plays an essential role in climate change over the global and regional scales. Under the constraint of observations, the radiative fluxes at TOA have been reconstructed prior to CERES (Clouds and the Earth’s Radiant Energy System) between 1985 and 2000. The total atmospheric energy divergence has been mass corrected based on ERA5 (the fifth generation ECMWF ReAnalysis) atmospheric reanalysis by a newly developed method considering the enthalpy removing of the atmospheric water vapor, which avoids inconsistencies due to the residual lateral total mass flux divergence in the atmosphere, ensuring the balances of the freshwater fluxes at the surface. The net surface energy flux (Fs) has been estimated using the residual method based on energy conservation, which is the difference between the net TOA radiative flux and the atmospheric energy tendency and divergence. The Fs is then verified directly and indirectly with observations, and results show that the estimated Fs in North Atlantic is superior to those from model simulations. This paper gives a brief review of the progress in the estimation of the observed energy flow in the Earth system, discusses some caveats of the existing method, and provides some suggestions for the improvements of the aforementioned data sets

A multicenter randomized phase II trial of hyperthermia combined with TPF induction chemotherapy compared with TPF induction chemotherapy in locally advanced resectable oral squamous cell carcinoma

Background Hyperthermia has been reported to cause cancer stage regression, thus providing surgical opportunities in patients with unresectable tumors and improving the quality of life of patients by preserving certain organs. Methods A prospective open-label phase II trial was conducted to evaluate the efficacy of hyperthermia combined with induction chemotherapy in patients with locally advanced resectable oral squamous cell carcinoma (OSCC). Patients received hyperthermia combined with two cycles of 5-fluorouracil, cisplatin, and docetaxel (TPF) induction chemotherapy regimens or TPF induction chemotherapy alone, followed by radical surgery with postoperative radiotherapy. The primary endpoint was the clinical response rate of the induction chemotherapy. The secondary endpoints were overall survival (OS), disease-free survival (DFS), and toxicity. Results A total of 120 patients were enrolled, and 115 patients were included in the clinical response analysis. The clinical response rate was significantly higher in the experimental arm than in the control arm (65.45% vs. 40.00%, p = 0.0088). There were no unexpected toxicities, and hyperthermia and induction chemotherapy did not increase the perioperative morbidity rate. Moreover, there was a significant improvement in DFS, but no significant difference in OS between the two arms. In the subgroup analysis, increased OS and DFS rates were associated with patients with favorable clinical response after induction chemotherapy in the total population, experimental arm, and control arm. Conclusions Our study demonstrates that hyperthermia combined with induction chemotherapy is associated with a high response rate and provides a new treatment option for patients with resectable stage III or IVA OSCC