Multi-label feature selection based on HSIC and sparrow search algorithm.

Feature selection has always been an important topic in machine learning and data mining. In multi-label learning tasks, each sample in the dataset is associated with multiple labels, and labels are usually related to each other. At the same time, multi-label learning has the problem of "curse of dimensionality". Feature selection therefore becomes a difficult task. To solve this problem, this paper proposes a multi-label feature selection method based on the Hilbert-Schmidt independence criterion (HSIC) and sparrow search algorithm (SSA). It uses SSA for feature search and HSIC as feature selection criterion to describe the dependence between features and all labels, so as to select the optimal feature subset. Experimental results demonstrate the effectiveness of the proposed method.

Algorithm for frequency capture and rectification in a low-orbit satellite IoT communication network.

In satellite communication systems, due to relative motion between satellites and that between satellites and the ground, the resulting Doppler frequency offset adversely affects communication synchronization. In this research, Doppler frequency offset compensation and phase offset compensation method eliminate the influence of the Doppler effect on synchronization. The proposed algorithm divides frequency estimate into two steps, coarse and precision. Finally, the corresponding frequency offset and phase offset compensation are performed. The simulation results show that the demodulated output results after frequency offset and phase offset compensation agree well with the original modulation data, indicating that the algorithm is valid and accurate.

Recessive/dominant model: Alternative choice in case-control-based genome-wide association studies.

An additive genetic model is usually employed in case-control-based genome-wide association studies. The model usually encodes "AA", "Aa" and "aa" ("a" represents the minor allele) as three different numbers, implying the contribution of genotype "Aa" to the phenotype is different from "AA" and "aa". From the perspective of biological phenomena, the coding is reasonable since the phenotypes of lives are not "black and white". A case-control based study, however, has only two phenotypes, case and control, which means that the phenotypes are "black and white". It suggests that a recessive/dominant model may be an alternative to the additive model. In order to investigate whether the alternative is feasible, we conducted comparative experiments on several models used in those studies through chi-square test and logistic regression. Our simulation experiments demonstrate that a recessive model is better than the additive model. The area under the curve of the former has increased by 5% compared with the latter, the discrimination of identifying risk single nucleotide polymorphisms has been improved by 61%, and the precision has also reached 1.10 times that of the latter. Furthermore, the real data experiments show that the precision and area under the curve of the former are 16% and 20% higher than the latter respectively, and the area under the curve of dominant model of the former is 13% higher than the latter. The results indicate a recessive/dominant model may be an alternative to the additive model and suggest a new route for case-control-based studies.

coPLINK: A complementary tool to PLINK.

In genome-wide association studies (GWAS), a wide variety of analysis tools have been designed, leading to various formats of GWAS data. How to convert a dataset in non-PLINK format into PLINK format to use its powerful analysis performance, or to convert a dataset in PLINK format into the format of other analysis tools, is a problem that needs to be faced and solved. To address this issue, we developed a tool called coPLINK, a complementary tool to PLINK, to cooperate with PLINK to implement the conversions of GWAS data formats and to provide some additional functions, such as data files comparison. The tool can implement mutual conversions not only between an existing data format and PLINK PED/BED, but also between a user-defined data format and PLINK PED. The usage and performance of the tool are similar to PLINK. The characteristics of the conversions of existing data formats and user-defined formats make it be a good assistant to PLINK or other tools and, have good potential for GWAS studies or other works.

Provincial-level outcomes of China's 'Reducing maternal mortality and eliminating neonatal tetanus' program.

To determine whether the nationwide program 'Reducing maternal mortality and eliminating neonatal tetanus' contributed to the rapid decline in China's maternal mortality ratio (MMR) and neonatal tetanus elimination by enhancing hospital delivery, we compared MMR and neonatal tetanus incidence rate (NTR) reductions by province from 2000 to 2013. The difference-in-difference method was used to analyze the program effect. Long-term effects were analyzed relative to MMR and NTR in 2000 and 2002, respectively, while short-term effects in a given year were analyzed relative to MMR and NTR in the preceding year. The national program was associated with a faster decline in MMR in the long term. The rate of decline showed an inverse 'U' shape from 2000 to 2013, peaking in 2009. The program had a short-term effect in MMR reduction in 2005, 2007, and 2009. The program was also associated with faster decline in NTR in the short term at some time points, but this association was not consistent and was not found in the long term. In conclusion, the program accelerated decline of MMR from 2000 to 2013 but did not clearly reduce NTR at the province level. Therefore, this targeted program worked efficiently in resource-poor areas.

Long non-coding RNA MYOSLID functions as a competing endogenous RNA to regulate MCL-1 expression by sponging miR-29c-3p in gastric cancer.

OBJECTIVE: Long non-coding RNA (lncRNA) has become an important regulator of many human malignancies. However, the biological role and clinical significance of most lncRNA in gastric cancer (GC) remain unclear. METHODS: We investigate the biological function, mechanism of action and clinical expression of lncRNA MYOSLID in GC. First, we analysed the differential expression of lncRNA MYOSLID in GC tissues and non-cancerous tissues by analysing the sequencing data obtained from The Cancer Genome Atlas. Subsequently, we verified that lncRNA MYOSLID regulates the proliferation and apoptosis of GC cells by acting as a ceRNA against miR-29c-3p. The nude mouse xenograft was used to further confirm the functional significance of lncRNA MYOSLID in vivo. RESULTS: We found for the first time that the expression of lncRNA MYOSLID was significantly up-regulated in GC tissues, and the up-regulation of lncRNA MYOSLID in GC was correlated with tumour size, AJCC stage, depth of invasion and survival time. In addition, apoptosis and growth arrest can be induced in vitro after knockdown of lncRNA MYOSLID, which inhibits tumorigenesis in mouse xenografts in vivo. Further in-depth studies revealed that lncRNA MYOSLID acts as a ceRNA of miR-29c-3p, resulting in de-repression of its downstream target gene MCL-1. CONCLUSION: The lncRNA MYOSLID-miR-29c-3p-MCL-1 axis plays a key role in the development of GC. Our findings may provide potential new targets for the diagnosis and treatment of human GC.

Density distribution of gene expression profiles and evaluation of using maximal information coefficient to identify differentially expressed genes.

The hypothesis of data probability density distributions has many effects on the design of a new statistical method. Based on the analysis of a group of real gene expression profiles, this study reveal that the primary density distributions of the real profiles are normal/log-normal and t distributions, accounting for 80% and 19% respectively. According to these distributions, we generated a series of simulation data to make a more comprehensive assessment for a novel statistical method, maximal information coefficient (MIC). The results show that MIC is not only in the top tier in the overall performance of identifying differentially expressed genes, but also exhibits a better adaptability and an excellent noise immunity in comparison with the existing methods.

Maximal information coefficient applied to differentially expressed genes identification: A feasibility study.

BACKGROUND: The main obstacle encountered in microarray technology is how to mine the valuable information under the profiles and study the genes function. OBJECTIVE: Maximal information coefficient (MIC) is a novel, non-parametric statistic that has been successfully applied to genome-wide association studies and differentially gene and miRNA expression analysis. However, the data used in these applications are not gold standard but real data. METHODS: Therefore, this study attempts to test the feasibility of MIC for differentially expressed gene identification with simulation data. RESULTS: Our experiments indicate that, MIC perfermance is better than Limma always, which is almost the same level of SAM, ROTS or DESeq2. However, the count of AUC < 0.5 of MIC is significantly smaller than the three methods, and MIC does not exhibit an abnormal phenomenon in which the AUC increases as the noise increases. CONCLUSIONS: Compared to the existing methods, our experiments show that MIC is not only in the first tier in identifying differentially expressed genes and noise immunity, but also shows better robustness and stronger data/environment adaptability.

Analysis of connection networks among miRNAs differentially expressed in early gastric cancer for disclosing some biological features of disease development.

This paper first identified differentially expressed miRNAs associated with early gastric cancer and then respectively constructed relevant connection networks among the identified differentially expressed miRNAs that corresponded to early gastric cancer and control tissues. Twenty-three differentially expressed miRNAs were identified, 18 of which were different with the related results on the same data, and they provide great discriminatory power between patients and controls. There are not only conserved unchangeable sub-networks but also different sub-networks between the two connection networks. From the consistency and differences between two connection networks, we disclosed several new biological features that promote early gastric cancer development. This study shows 23 miRNAs that are early gastric cancer-specific and are worthy to do further experimental studies. The revealed biological features for early gastric cancer will provide new insights into improved understanding of the molecular mechanisms of this disease.

Biocomputional construction of a gene network under acid stress in Synechocystis sp. PCC 6803.

Acid stress is one of the most serious threats that cyanobacteria have to face, and it has an impact at all levels from genome to phenotype. However, very little is known about the detailed response mechanism to acid stress in this species. We present here a general analysis of the gene regulatory network of Synechocystis sp. PCC 6803 in response to acid stress using comparative genome analysis and biocomputational prediction. In this study, we collected 85 genes and used them as an initial template to predict new genes through co-regulation, protein-protein interactions and the phylogenetic profile, and 179 new genes were obtained to form a complete template. In addition, we found that 11 enriched pathways such as glycolysis are closely related to the acid stress response. Finally, we constructed a regulatory network for the intricate relationship of these genes and summarize the key steps in response to acid stress. This is the first time a bioinformatic approach has been taken systematically to gene interactions in cyanobacteria and the elaboration of their cell metabolism and regulatory pathways under acid stress, which is more efficient than a traditional experimental study. The results also provide theoretical support for similar research into environmental stresses in cyanobacteria and possible industrial applications.

Combined effects of the ATP-sensitive potassium channel opener pinacidil and simvastatin on pulmonary vascular remodeling in rats with monocrotaline-induced pulmonary arterial hypertension.

The drugs that are currently used to treat pulmonary hypertension (PH) lack the ability to inhibit or reverse the pulmonary vascular remodeling that occurs during the course of the disease. We propose a novel method that combines the therapeutic powers of the potassium channel opener pinacidil and the statin drug simvastatin. These two drugs do not share similar mechanisms of treating PH. We used rats with monocrotaline (MCT)-induced pulmonary arterial hypertension (PAH) as a model and examined the combined effects of pinacidil and simvastatin on pulmonary vascular remodeling. A series of indicators, including those for pulmonary vascular obstruction, proliferation, and cell phenotype, pulmonary vascular matrix and pulmonary vascular smooth muscle cell phenotype were used to monitor changes in pulmonary structure over the course of disease and treatment in normal controls, untreated PAH rats, pinacidil-treated subjects, simvastatin-treated subjects, and combination-treated subjects. We found that levels of mPAP, right ventricle Fulton index, pulmonary arteriolar wall thickness and muscularization, cell growth rate, transforming growth factor beta (TGF-beta), lung tissue matrix metalloproteinase-2 (MMP-2), MMP-9 and lung tissue inhibitor of matrix metalloproteinase-1 (TIMP-1), vascular smooth muscle cell (VSMC) contractile protein SM-alpha-actin, and SM-alpha-actin mRNA of these different groups were all significantly lower in the combination-treated group than in the untreated group. Subjects in the combination-treated group also showed lower levels than those in either the pinacidil-treated or simvastatin-treated group. These results support our hypothesis and provide basis for a new, more effective therapeutic methods of treating PAH in human patients.

Interface enhancement of glass fiber/vinyl ester composites with carbon nanotubes synthesized from ethanol flames.

Multi-walled carbon nanotubes synthesized from ethanol flames (F-MWCNTs) and nanotubes functionalized by n-hexadecylamine (H-MWCNTs) were applied to the preparation of glass fiber/vinyl ester composites by overcoating the original glass fiber. Scanning electron microscopy of the composites containing multi-walled carbon nanotubes (MWCNTs) showed better bonding between the glass fiber and the resin matrix which may be attributed to the existence of a flexible interphase introduced by the nanotubes. It was found that the bonding in the composites treated with H-MWCNTs was much stronger. Moreover, the dynamic mechanical properties and impact strengths of the resulting composites were investigated. The results revealed that treating glass fiber with MWCNTs effectively improved the mechanical properties of the composite materials. Furthermore, the dynamic properties showed that H-MWCNTs have become integral parts of the crosslinked polymer structure, rather than acting as separate fillers.

[Effect of polycythemia on hypoxia induced pulmonary hypertension and pulmonary vascular remodeling in rats].

OBJECTIVE: To investigate the effect of polycythemia on hypoxia induced pulmonary hypertension and pulmonary vascular remodeling in rats. METHODS: The healthy female Sprague-Dawley rats were randomly divided into 3 groups: normoxia control group (C group), hypoxia group (H group), hypoxia + different doses of human recombine hemopoietin (rEPO) group. All rats in hyoxia groups were exposed to hypoxia, 8 hours every day, for 21 days. The rEPO groups were injected sc with different doses of rEPO (300 U/kg, 600 U/kg, 900 U/kg, 1200 U/kg) thrice weekly. Blood samples were taken for the measurement of RBC, Hb, Hct, plasma EPO concentration, whole blood/plasma viscosities, the animals were then catheterized to record mean pulmonary arterial pressure (mPAP) and demised to calculate the ratio [RV/(LV+S)]. Percentage of vascular wall thickness and muscularization of non-muscular pulmonary arteriole were examined microscopically. RESULTS: (1) As the dosage of exogenous rEPO increased, blood concentration of EPO increased correspondingly, as RBC, Hb, Hct and whole blood/plasma viscosities increased in various degrees. (2) There was positive correlation between whole blood viscosity and Hct at both high and low shears and linear correlation between mPAP and whole blood viscosity at high shear. (3) The degree of pulmonary hypertension, reflected by mPAP increased in accordance to rEPO dosage increment. However, the extent of pulmonary vascular remodeling alleviated somehow as the rEPO dose increased and so did right ventricular hypertrophy. CONCLUSION: Polycythemia induced by exogenous EPO increases the blood viscosity and the pulmonary vascular resistance, which contributes to the formation of hypoxia induced pulmonary hypertension.

[Changes of MMP-2,9 and TIMP-1 expressions in rats with pulmonary arterial hypertension after captopril and losartan interventions].

OBJECTIVE: To determine the effect of captopril and losartan on the expressions of matrix metalloproteinase-2,9 (MMP-2,9) and metalloproteinase-1 (TIMP-1) in rats with pulmonary arterial hypertension, and the mechanisms of captopril and losartan in intervening the development of pulmonary arterial hypertension. METHODS: Forty male Spraque-Dawley rats were divided into 4 groups randomly: pulmonary arterial hypertension (created by pneumonectomy plus MCT injection) model group (PAH Model), PAH model treated with captopril [PAH+Cap 10 mg/(kg x d)], losartan group [PAH+Los 15 mg/(kg x d)] and normal control group(Control). The mPAP, weight ratio of RV to LV+S, neointima formation, relative thickness of small pulmonary arteries, and degree of muscularization of non-muscular arterioles were measured at day 35. The expression of SM-a-actin in the PASMC was determined by immunochemistry stain. The expressions of MMP-2, 9, TIMP-1 and MMP-2, 9, TIMP-1 mRNA in the pulmonary tissues were determined by immunohistochemistry and FQ-PCR respectively. The enzymatic activity of MMP-2, 9 was measured by Gelatin zymography. RESULTS: Pneumonectomy plus MCT injection induced severe pulmonary arterial hypertension characterized by neointimal formation. Captopril or losartan suppressed the increase of mPAP, right ventricle weight, thickness of small pulmonary arteries and muscularization of peripheral pulmonary arterioles in the rats with PAH (P < 0.05). The PAH model group had higher expressions of MMP-2, 9, TIMP-1 mRNA and enzymatic activity of MMP-2, 9 in lung tissue than the other groups (P < 0.05). Captopril intervention had similar effects as losartan intervention. CONCLUSION: The captopril and losartan induced attenuation of PAH and pulmonary vascular remodeling is likely to be associated with the regulation of the expressions of MMP-2, 9, TIMP-1.