Public involvement in setting a national research agenda

<p>(A) Graphical map of the BLAST results showing nucleotide identity between <i>A</i>. <i>fasciata</i> mitogenome and 15 related species listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0136297#pone.0136297.t001" target="_blank">Table 1</a>, as generated by the CGView comparison tool (CCT). CCT arranges BLAST result in an order where sequence that is most similar to the reference (<i>A</i>. <i>fasciata</i>) is placed closer to the outer edge of the map. The rings labelled 1 to17 indicate BLAST results of <i>A</i>. <i>fasciata</i> mitogenome against <i>A</i>. <i>chrysaetos</i>, <i>N</i>. <i>nipalensis</i>, <i>N</i>. <i>alboniger</i>, <i>S</i>. <i>cheela</i>, <i>A</i>. <i>monachus</i>, <i>B</i>. <i>lagopus</i>, <i>B</i>. <i>buteo</i>, <i>B</i>. <i>buteo burmanicus</i>, <i>A</i>. <i>soloensis</i>, <i>A</i>. <i>virgatus</i>, <i>A</i>. <i>gentilis</i>, <i>A</i>. <i>nisus</i>, <i>P</i>. <i>haliaetus</i>, <i>S</i>. <i>serpentarius</i>, <i>C</i>. <i>aura</i>, <i>P</i>. <i>badius</i>, and <i>S</i>. <i>leptogrammica</i>, respectively. (B) Nucleotide-based phylogenetic tree of 16 Accipitriformes species, with two Strigiformes birds as outgroups. This analysis is based on 13PCGs. Both ML and Bayesian analyses produced identical tree topologies. The ML bootstrap and Bayesian posterior probability values for each node are indicated.</p

Improved Empirical Mode Decomposition Algorithm of Processing Complex Signal for IoT Application

Hilbert-Huang transform is widely used in signal analysis. However, due to its inadequacy in estimating both the maximum and the minimum values of the signals at both ends of the border, traditional HHT is easy to produce boundary error in empirical mode decomposition (EMD) process. To overcome this deficiency, this paper proposes an enhanced empirical mode decomposition algorithm for processing complex signal. Our work mainly focuses on two aspects. On one hand, we develop a technique to obtain the extreme points of observation interval boundary by introducing the linear extrapolation into EMD. This technique is simple but effective in suppressing the error-prone effects of decomposition. On the other hand, a novel envelope fitting method is proposed for processing complex signal, which employs a technique of nonuniform rational B-splines curve. This method can accurately measure the average value of instantaneous signal, which helps to achieve the accurate signal decomposition. Simulation experiments show that our proposed methods outperform their rivals in processing complex signals for time frequency analysis

An analysis of medication rule for HBeAg-positive chronic hepatitis B based on association rule and complex system entropy clustering

ObjectiveTo investigate the features of traditional Chinese medicine (TCM) and prescription rules in the treatment of HBeAg-positive chronic hepatitis B (CHB). MethodsA systematic search was performed for the articles on the TCM diagnosis and treatment of HBeAg-positive CHB, the information of TCM diagnosis and treatment in medical records were extracted, and a database was established after data standardization. The Traditional Chinese Medicine Inheritance Support System was used to investigate the medication rule. ResultsA total of 100 articles with 135 medical records were included in this study. A total of 220 types of Chinese materia medica were used, among which Bupleurum chinense, Salvia miltiorrhiza, Radix Glycyrrhizae, Atractylodes macrocephala Koidz., and Poria cocos were frequently used. As for the meridian entry of drugs, liver meridian, spleen meridian, and stomach meridian were commonly used. The analysis showed that the core drugs for HBeAg-positive CHB were Bupleurum chinense, Atractylodes macrocephala Koidz., Radix Paeoniae Alba, Radix Curcumae, Salvia miltiorrhiza, Radix Glycyrrhizae, Poria cocos, Polygonum cuspidatum, Astragalus membranaceus, Herba Artemisiae Scopariae, and Hedyotis diffusa. A total of 20 core drug combinations were deduced based on complex system entropy clustering, and 10 new prescriptions were obtained using unsupervised entropy hierarchical clustering. ConclusionIn this study, literature mining and inductive analysis show that the syndromes of stagnation of liver qi and spleen deficiency and liver and gallbladder damp-heat are common syndrome types of HBeAg-positive CHB. The medicine suits and prescriptions refined in this study can be used for reference in clinical practice

15N Natural Abundance of C3 and C4 Herbaceous Plants and Its Response to Climatic Factors along an Agro-Pastoral Zone of Northern China

The nitrogen isotope composition of plants (&delta;15N) can comprehensively reflect information on climate change and ecosystems&rsquo; nitrogen cycle. By collecting common herbs and soil samples along the 400 mm isoline of mean annual precipitation (MAP) in the agro-pastoral zone of North China (APZNC) and measuring their &delta;15N values, the statistical characteristics of foliar &delta;15N of herbs and the responses of foliar &delta;15N to the MAP and mean annual temperature (MAT) were analyzed. The results showed that: (1) the &delta;15N values of all herbs investigated varied from &minus;5.5% to 15.25%. Among them, the &delta;15N value range of C3 herbs (&minus;5.5~15.00%) was wider than that of C4 herbs (&minus;2.17~15.25%), but the average value (3.27%) of C3 herbs was significantly lower than that of C4 herbaceous plants (5.55%). This difference provides an important method for identifying plants of different photosynthetic types by nitrogen isotope technology. (2) Along the transect from northeast to southwest, the &delta;15N of both C3 and C4 herbs decreased with the increase in the MAP, but not significantly for C3 herbs. The inverse relationship between the nitrogen isotopic signatures of herbs and MAP is consistent with previous studies. However, the MAP in the APZNC is found to only explain a small amount of the observed variance in the &delta;15N herbs (C3 herbs: 10.40%; C4 herbs: 25.03%). (3) A strong negative relationship was found between &delta;15N of herbs and MAT across the transect (C3 herbs: &minus;0.368%/&deg;C; C4 herbs: &minus;0.381%/&deg;C), which was contrary to the global pattern and some regional patterns. There was no significant difference in the &delta;15N responses of two different photosynthetic herbs to temperature, but the effect of temperature on the variances of &delta;15N of C3 and C4 herbs was significantly greater than that of precipitation. This suggests that temperature is a key factor affecting foliar &delta;15N of herbs in this transect. The above findings may be of value to global change researchers studying the processes of the nitrogen cycle and gaining an insight into climate dynamics of the past

miRNAome expression profiles in the gonads of adult Melopsittacus undulatus

The budgerigar (Melopsittacus undulatus) is one of the most widely studied parrot species, serving as an excellent animal model for behavior and neuroscience research. Until recently, it was unknown how sexual differences in the behavior, physiology, and development of organisms are regulated by differential gene expression. MicroRNAs (miRNAs) are endogenous short non-coding RNA molecules that can post-transcriptionally regulate gene expression and play a critical role in gonadal differentiation as well as early development of animals. However, very little is known about the role gonadal miRNAs play in the early development of birds. Research on the sex-biased expression of miRNAs in avian gonads are limited, and little is known about M. undulatus. In the current study, we sequenced two small non-coding RNA libraries made from the gonads of adult male and female budgerigars using Illumina paired-end sequencing technology. We obtained 254 known and 141 novel miRNAs, and randomly validated five miRNAs. Of these, three miRNAs were differentially expressed miRNAs and 18 miRNAs involved in sexual differentiation as determined by functional analysis with GO annotation and KEGG pathway analysis. In conclusion, this work is the first report of sex-biased miRNAs expression in the budgerigar, and provides additional sequences to the avian miRNAome database which will foster further functional genomic research

Immunomodulatory activity of a novel polysaccharide from Lonicera japonica in immunosuppressed mice induced by cyclophosphamide.

Lonicera japonica is a typical Chinese herbal medicine. We previously reported a method to isolate polysaccharides from Lonicera japonica (LJP). In this study, we first performed a qualitative analysis of LJP using the Fourier Transform Infrared Spectrometer (FT-IR) and explored the monosaccharide composition of LJP using the pre-column derivatization high performance liquid chromatography (HPLC) method. We then investigated the immunomodulatory function of LJP in cyclophosphamide (CTX)-induced immunosuppressed mouse models. The results showed that LJP had the characteristic absorption of typical polysaccharides consisting of 6 types of monosaccharides. In addition, LJP can increase significantly the organ index, splenic lymphocyte proliferation, macrophage phagocytosis, and natural killer (NK) cell activity in CTX-treated mice. LJP could also restore the levels of serum cytokines interleukin (IL-2), tumor necrosis factor (TNF-α) and Interferon-γ (IFN-γ) in the CTX-treated mice. Finally, the results on measuring the T-lymphocytes subsets of spleen also confirmed LJP-induced immunomodulatory activity in immunosuppressed mice from another perspective. Therefore, LJP could be used as a potential immunomodulatory agent

Gene expression profile analysis of human intervertebral disc degeneration

In this study, we used microarray analysis to investigate the biogenesis and progression of intervertebral disc degeneration. The gene expression profiles of 37 disc tissue samples obtained from patients with herniated discs and degenerative disc disease collected by the National Cancer Institute Cooperative Tissue Network were analyzed. Differentially expressed genes between more and less degenerated discs were identified by significant analysis of microarray. A total of 555 genes were significantly overexpressed in more degenerated discs with a false discovery rate of < 3%. Functional annotation showed that these genes were significantly associated with membrane-bound vesicles, calcium ion binding and extracellular matrix. Protein-protein interaction analysis showed that these genes, including previously reported genes such as fibronectin, COL2A1 and f-catenin, may play key roles in disc degeneration. Unsupervised clustering indicated that the widely used morphology-based Thompson grading system was only marginally associated with the molecular classification of intervertebral disc degeneration. These findings indicate that detailed, systematic gene analysis may be a useful way of studying the biology of intervertebral disc degeneration

Mitogenomic Codon Usage Patterns of Superfamily Certhioidea (Aves, Passeriformes): Insights into Asymmetrical Bias and Phylogenetic Implications

The superfamily Certhioidea currently comprises five families. Due to the rapid diversification, the phylogeny of Certhioidea is still controversial. The advent of next generation sequencing provides a unique opportunity for a mitogenome-wide study. Here, we first provided six new complete mitogenomes of Certhioidea (Certhia americana, C. familiaris, Salpornis spilonota, Cantorchilus leucotis, Pheugopedius coraya, and Pheugopedius genibarbis). We further paid attention to the genomic characteristics, codon usages, evolutionary rates, and phylogeny of the Certhioidea mitogenomes. All mitogenomes we analyzed displayed typical ancestral avian gene order with 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs, and one control region (CR). Our study indicated the strand-biased compositional asymmetry might shape codon usage preferences in mitochondrial genes. In addition, natural selection might be the main factor in shaping the codon usages of genes. Additionally, evolutionary rate analyses indicated all mitochondrial genes were under purifying selection. Moreover, MT-ATP8 and MT-CO1 were the most rapidly evolving gene and conserved genes, respectively. According to our mitophylogenetic analyses, the monophylies of Troglodytidae and Sittidae were strongly supported. Importantly, we suggest that Salpornis should be separated from Certhiidae and put into Salpornithidae to maintain the monophyly of Certhiidae. Our findings are useful for further evolutionary studies within Certhioidea

An automatic parathyroid recognition and segmentation model based on deep learning of near‐infrared autofluorescence imaging

Abstract Introduction Near‐infrared autofluorescence imaging (NIFI) can be used to identify parathyroid gland (PG) during surgery. The purpose of the study is to establish a new model, help surgeons better identify, and protect PGs. Methods Five hundred and twenty three NIFI images were selected. The PGs were recorded by NIFI and marked with artificial intelligence (AI) model. The recognition rate for PGs was calculated. Analyze the differences between surgeons of different years of experience and AI recognition, and evaluate the diagnostic and therapeutic efficacy of AI model. Results Our model achieved 83.5% precision and 57.8% recall in the internal validation set. The visual recognition rate of AI model was 85.2% and 82.4% on internal and external sets. The PG recognition rate of AI model is higher than that of junior surgeons (p < 0.05). Conclusions This AI model will help surgeons identify PGs, and develop their learning ability and self‐confidence