Prediction of protein structural class with Rough Sets

BACKGROUND: A new method for the prediction of protein structural classes is constructed based on Rough Sets algorithm, which is a rule-based data mining method. Amino acid compositions and 8 physicochemical properties data are used as conditional attributes for the construction of decision system. After reducing the decision system, decision rules are generated, which can be used to classify new objects. RESULTS: In this study, self-consistency and jackknife tests on the datasets constructed by G.P. Zhou (Journal of Protein Chemistry, 1998, 17: 729–738) are used to verify the performance of this method, and are compared with some of prior works. The results showed that the rough sets approach is very promising and may play a complementary role to the existing powerful approaches, such as the component-coupled, neural network, SVM, and LogitBoost approaches. CONCLUSION: The results with high success rates indicate that the rough sets approach as proposed in this paper might hold a high potential to become a useful tool in bioinformatics

Conservation of noncoding microsatellites in plants: implication for gene regulation

BACKGROUND: Microsatellites are extremely common in plant genomes, and in particular, they are significantly enriched in the 5' noncoding regions. Although some 5' noncoding microsatellites involved in gene regulation have been described, the general properties of microsatellites as regulatory elements are still unknown. To address the question of microsatellites associated with regulatory elements, we have analyzed the conserved noncoding microsatellite sequences (CNMSs) in the 5' noncoding regions by inter- and intragenomic phylogenetic footprinting in the Arabidopsis and Brassica genomes. RESULTS: We identified 247 Arabidopsis-Brassica orthologous and 122 Arabidopsis paralogous CNMSs, representing 491 CT/GA and CTT/GAA repeats, which accounted for 10.6% of these types located in the 500-bp regions upstream of coding sequences in the Arabidopsis genome. Among these identified CNMSs, 18 microsatellites show high conservation in the regulatory regions of both orthologous and paralogous genes, and some of them also appear in the corresponding positions of more distant homologs in Arabidopsis, as well as in other plants. A computational scan of CNMSs for known cis-regulatory elements showed that light responsive elements were clustered in the region of CT/GA repeats, as well as salicylic acid responsive elements in the (CTT)(n)/(GAA)(n )sequences. Patterns of gene expression revealed that 70–80% of CNMS (CTT)(n)/(GAA)(n )associated genes were regulated by salicylic acid, which was consistent with the prediction of regulatory elements in silico. CONCLUSION: Our analyses showed that some noncoding microsatellites were conserved in plants and appeared to be ancient. These CNMSs served as regulatory elements involved in light and salicylic acid responses. Our findings might have implications in the common features of the over-represented microsatellites for gene regulation in plant-specific pathways

Overexpression of lncRNA-MEG3 inhibits endometrial cell proliferation and invasion via miR-21–5p/DNMT3B/Twist

Recent studies have found that lncRNA-MEG3(MEG3) plays an important role in the development of EMs (Endometriosis), but the specific mechanism needs to be further explored. This study aimed to investigate the effect of MEG3 on the proliferation, invasion of EMs cells. The authors used RT-qPCR to detect the expression of MEG3 and miR-21–5p in EMs tissues and hESCs cells, MTT and Transwell to detect cell proliferation and invasion, western blotting assay to detect the expression of DNMT3B and Twist, MSP to detect the methylation of Twist. The present study's detection results showed that MEG3 was lowly expressed in EMs tissues and hESCs cells, and overexpression of MEG3 could down-regulate miR-21–5p and inhibit endometrial cell proliferation and invasion. In addition, overexpression of MEG3 upregulated the expression of DNMT3B and promoted the methylation of TWIST. In conclusion, the present findings suggest that MEG3 is downregulated in EMs tissues, and overexpression of MEG3 can promote the activity of DNA methyltransferase DNMT3B by downregulating miR-21–5p, thereby promoting the methylation of Twist, downregulating Twist level to inhibits hESCs cells proliferation and invasion

One-pot fabrication of magnetic fluorinated carbon nanotubes adsorbent for efficient extraction of perfluoroalkyl carboxylic acids and perfluoroalkyl sulfonic acids in environmental water samples

Abstract(#br)Efficient extraction of perfluoroalkyl carboxylic acids (PFCAs) and perfluoroalkyl sulfonic acids (PFSAs) is challenging due to their highly fluorinated property. Based on the particular characters of PFCAs and PFSAs, a new type of magnetic fluorinated carbon nanotubes adsorbent (MFCA) for magnetic solid phase extraction (MSPE) was fabricated facilely using one-pot hydrothermal approach. The morphology, structure and magnetic properties of the prepared MFCA were investigated by Fourier transform infrared spectroscopy, scanning electron microscopy, transmission electron microscopy and vibrating sample magnetometry. It was observed that the resultant adsorbent possessed satisfactory superparamagnetism and saturation magnetism. Furthermore, the MFCA exhibited excellent enrichment performance for target PFCAs and PFSAs by means of fluorous-fluorous, hydrophobic and hydrogen bonding interactions. Under the most favorable preparation and extraction conditions, the proposed MFCA/MSPE was combined with high performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) to quantify ultra trace target analytes in environmental water samples. The limits of detection (S/N = 3) of PFCAs and PFSAs were 0.010–0.036 ng/L and 0.024–0.50 ng/L, respectively. In addition, the introduced approach also displayed other features such as quick extraction procedure, wide linear dynamic ranges, excellent method precision and eco-friendliness. Finally, the concentrations of PFCAs and PFSAs in tap, river, lake and waste water samples were successfully measured by isotope internal standard calibration curve method

Six Thallus Surface Types of Coralline Algae with Descriptions of Two New Records of Amphiroa beauvoisii and Neogoniolithon setchellii in Sanya reef, China

Coralline algae are globally distributed calcifying species and play critical ecological roles to marine ecosystems by contributing significantly to their structural complexity and diversity. Thallus surface types of historical samples in Sanya coral reef reserve were studied based on the scanning electron microscope (SEM) method. Our results show six thallus surface types within the study area: Corallina-type, Jania-type, Leptophytum-type, Phymatolithon-type, Pneophyllum-type, and Spongites-type. The Phymatolithon-type is the dominant surface type in Sanya reefs. Two new record species in the region are described: Amphiroa beauvoisii and Neogoniolithon setchellii. Although thallus surface types provide useful diagnostics characters for distinguishing coralline algae at tribe or subfamily level, species identification needs to refer to the reproductive features. This is the first surface study of coralline algae in the South China Sea. This result provides the baseline data needed for the monitoring and management of reef-building organisms of coral reef in China

Look Beneath the Surface: Exploiting Fundamental Symmetry for Sample-Efficient Offline RL

Offline reinforcement learning (RL) offers an appealing approach to real-world tasks by learning policies from pre-collected datasets without interacting with the environment. However, the performance of existing offline RL algorithms heavily depends on the scale and state-action space coverage of datasets. Real-world data collection is often expensive and uncontrollable, leading to small and narrowly covered datasets and posing significant challenges for practical deployments of offline RL. In this paper, we provide a new insight that leveraging the fundamental symmetry of system dynamics can substantially enhance offline RL performance under small datasets. Specifically, we propose a Time-reversal symmetry (T-symmetry) enforced Dynamics Model (TDM), which establishes consistency between a pair of forward and reverse latent dynamics. TDM provides both well-behaved representations for small datasets and a new reliability measure for OOD samples based on compliance with the T-symmetry. These can be readily used to construct a new offline RL algorithm (TSRL) with less conservative policy constraints and a reliable latent space data augmentation procedure. Based on extensive experiments, we find TSRL achieves great performance on small benchmark datasets with as few as 1% of the original samples, which significantly outperforms the recent offline RL algorithms in terms of data efficiency and generalizability.Comment: The first two authors contributed equall

Information theory-based algorithm for in silico prediction of PCR products with whole genomic sequences as templates

BACKGROUND: A new algorithm for assessing similarity between primer and template has been developed based on the hypothesis that annealing of primer to template is an information transfer process. RESULTS: Primer sequence is converted to a vector of the full potential hydrogen numbers (3 for G or C, 2 for A or T), while template sequence is converted to a vector of the actual hydrogen bond numbers formed after primer annealing. The former is considered as source information and the latter destination information. An information coefficient is calculated as a measure for fidelity of this information transfer process and thus a measure of similarity between primer and potential annealing site on template. CONCLUSION: Successful prediction of PCR products from whole genomic sequences with a computer program based on the algorithm demonstrated the potential of this new algorithm in areas like in silico PCR and gene finding

Reassessment of Split-Leg Signs in Amyotrophic Lateral Sclerosis: Differential Involvement of the Extensor Digitorum Brevis and Abductor Hallucis Muscles

Background: The muscle patterns involved in the “split-leg” syndrome of amyotrophic lateral sclerosis (ALS) remains controversial. We sought to evaluate and reassess the pattern of the extensor digitorum brevis (EDB) and the abductor hallucis (AH) muscles' involvement in split-leg syndrome in ALS.Methods: We recruited 60 consecutive patients with ALS and 25 healthy controls (HCs). Compound muscle action potentials (CMAPs) and F-waves were recorded over the EDB and AH muscles in all subjects. For comparison, we classified patients into two categories based on the presence or absence of lower limbs symptoms.Results: The EDB/AH CMAP amplitude ratio was significantly reduced in patients with affected legs (0.33 ± 0.21, P = 0.007), whereas patients with unaffected legs had a ratio similar to that of the HCs. The EDB/AH ratios for the F-wave latencies, mean F-wave amplitude, mean F/M amplitude ratio, and the persistence of the total repeater F-wave shapes (index Freps) of the EDB-AH, were significantly increased in the affected leg group, whereas the EDB/AH ratio for F-wave persistence was significantly reduced. These findings indicated a greater loss of lower motor neurons (LMNs) innervating the EDB and dysfunction of spinal motoneurons innervating the EDB. In the unaffected leg group, the EDB, but not the AH, F-wave latencies, mean and maximal F/M amplitude ratios, and index Freps were significantly altered. Receiver operating characteristic curve analysis suggested that the EDB F-wave latencies, mean F/M amplitude ratios, and index Freqs (area under the curve [AUC] > 0.8) more strongly differentiated patients with ALS from the HCs compared to the EDB/AH CMAP amplitude ratio (AUC = 0.61). Notably, the EDB maximal F-wave latency and index Freqs reliably differentiated patients with unaffected legs (HCs), with AUCs of 0.83 (95% CI 0.76–0.91) and 0.81 (95% CI 0.72–0.89), sensitivities of 76 and 78%, and specificities of 76 and 78%, respectively.Conclusions: These results suggest preferential EDB compared to AH involvement in the split-leg syndrome of ALS. The EDB maximal F-wave latency and index Freqs robustly differentiated patients with ALS from HCs, which might facilitate an earlier identification of ALS