Modeling the fear effect in the predator-prey dynamics with an age structure in the predators

We incorporate the fear effect and the maturation period of predators into a diffusive predator-prey model. Local and global asymptotic stability for constant steady states as well as uniform persistence of the solution are obtained. Under some conditions, we also exclude the existence of spatially nonhomogeneous steady states and the steady state bifurcation bifurcating from the positive constant steady state. Hopf bifurcation analysis is carried out by using the maturation period of predators as a bifurcation parameter, and we show that global Hopf branches are bounded. Finally, we conduct numerical simulations to explore interesting spatial-temporal patterns

cDNA sequences reveal considerable gene prediction inaccuracy in the Plasmodium falciparum genome

<p>Abstract</p> <p>Background</p> <p>The completion of the <it>Plasmodium falciparum </it>genome represents a milestone in malaria research. The genome sequence allows for the development of genome-wide approaches such as microarray and proteomics that will greatly facilitate our understanding of the parasite biology and accelerate new drug and vaccine development. Designing and application of these genome-wide assays, however, requires accurate information on gene prediction and genome annotation. Unfortunately, the genes in the parasite genome databases were mostly identified using computer software that could make some erroneous predictions.</p> <p>Results</p> <p>We aimed to obtain cDNA sequences to examine the accuracy of gene prediction <it>in silico</it>. We constructed cDNA libraries from mixed blood stages of <it>P. falciparum </it>parasite using the SMART cDNA library construction technique and generated 17332 high-quality expressed sequence tags (EST), including 2198 from primer-walking experiments. Assembly of our sequence tags produced 2548 contigs and 2671 singletons <it>versus </it>5220 contigs and 5910 singletons when our EST were assembled with EST in public databases. Comparison of all the assembled EST/contigs with predicted CDS and genomic sequences in the PlasmoDB database identified 356 genes with predicted coding sequences fully covered by EST, including 85 genes (23.6%) with introns incorrectly predicted. Careful automatic software and manual alignments found an additional 308 genes that have introns different from those predicted, with 152 new introns discovered and 182 introns with sizes or locations different from those predicted. Alternative spliced and antisense transcripts were also detected. Matching cDNA to predicted genes also revealed silent chromosomal regions, mostly at subtelomere regions.</p> <p>Conclusion</p> <p>Our data indicated that approximately 24% of the genes in the current databases were predicted incorrectly, although some of these inaccuracies could represent alternatively spliced transcripts, and that more genes than currently predicted have one or more additional introns. It is therefore necessary to annotate the parasite genome with experimental data, although obtaining complete cDNA sequences from this parasite will be a formidable task due to the high AT nature of the genome. This study provides valuable information for genome annotation that will be critical for functional analyses.</p

Joint analysis of two microarray gene-expression data sets to select lung adenocarcinoma marker genes

BACKGROUND: Due to the high cost and low reproducibility of many microarray experiments, it is not surprising to find a limited number of patient samples in each study, and very few common identified marker genes among different studies involving patients with the same disease. Therefore, it is of great interest and challenge to merge data sets from multiple studies to increase the sample size, which may in turn increase the power of statistical inferences. In this study, we combined two lung cancer studies using micorarray GeneChip(®), employed two gene shaving methods and a two-step survival test to identify genes with expression patterns that can distinguish diseased from normal samples, and to indicate patient survival, respectively. RESULTS: In addition to common data transformation and normalization procedures, we applied a distribution transformation method to integrate the two data sets. Gene shaving (GS) methods based on Random Forests (RF) and Fisher's Linear Discrimination (FLD) were then applied separately to the joint data set for cancer gene selection. The two methods discovered 13 and 10 marker genes (5 in common), respectively, with expression patterns differentiating diseased from normal samples. Among these marker genes, 8 and 7 were found to be cancer-related in other published reports. Furthermore, based on these marker genes, the classifiers we built from one data set predicted the other data set with more than 98% accuracy. Using the univariate Cox proportional hazard regression model, the expression patterns of 36 genes were found to be significantly correlated with patient survival (p < 0.05). Twenty-six of these 36 genes were reported as survival-related genes from the literature, including 7 known tumor-suppressor genes and 9 oncogenes. Additional principal component regression analysis further reduced the gene list from 36 to 16. CONCLUSION: This study provided a valuable method of integrating microarray data sets with different origins, and new methods of selecting a minimum number of marker genes to aid in cancer diagnosis. After careful data integration, the classification method developed from one data set can be applied to the other with high prediction accuracy

Biofeedback EEG can quantify abnormal phenomenon of EEG in psychology

TEEG (electroencephalography, EEG) is a kind of single which we know human brain function active.BT (Biofeedback Therapy, BT) is based the method of EEG technology, focusing on the studies of human thoughts and emotions activities. We shall study new points that the two kinds of EEG technology are used simultaneously, to find the BT can be quantified abnormal EEG activities in mental illness, to provide the certain reference value in clinical. We found that BT can quantify β wave, θ wave and some abnormal phenomenon of traditional EEG. Therefore, based on the conventional examination of the traditional EEG in clinical, we used BT to further check. The results show not only to quantify the advantages of traditional EEG brain waves specific values occur, such as the specific data of fatigue (θ wave) and anxiety (β wave), but also abnormal phenomenon. Quantized data would become more intuitive, and to assess the clinical efficacy of treatment more scientific and objectivity

Detection of genome-wide polymorphisms in the AT-rich Plasmodium falciparum genome using a high-density microarray

<p>Abstract</p> <p>Background</p> <p>Genetic mapping is a powerful method to identify mutations that cause drug resistance and other phenotypic changes in the human malaria parasite <it>Plasmodium falciparum</it>. For efficient mapping of a target gene, it is often necessary to genotype a large number of polymorphic markers. Currently, a community effort is underway to collect single nucleotide polymorphisms (SNP) from the parasite genome. Here we evaluate polymorphism detection accuracy of a high-density 'tiling' microarray with 2.56 million probes by comparing single feature polymorphisms (SFP) calls from the microarray with known SNP among parasite isolates.</p> <p>Results</p> <p>We found that probe GC content, SNP position in a probe, probe coverage, and signal ratio cutoff values were important factors for accurate detection of SFP in the parasite genome. We established a set of SFP calling parameters that could predict mSFP (SFP called by multiple overlapping probes) with high accuracy (≥ 94%) and identified 121,087 mSFP genome-wide from five parasite isolates including 40,354 unique mSFP (excluding those from multi-gene families) and ~18,000 new mSFP, producing a genetic map with an average of one unique mSFP per 570 bp. Genomic copy number variation (CNV) among the parasites was also cataloged and compared.</p> <p>Conclusion</p> <p>A large number of mSFP were discovered from the <it>P. falciparum </it>genome using a high-density microarray, most of which were in clusters of highly polymorphic genes at chromosome ends. Our method for accurate mSFP detection and the mSFP identified will greatly facilitate large-scale studies of genome variation in the <it>P. falciparum </it>parasite and provide useful resources for mapping important parasite traits.</p

Spatiotemporal patterns and driving mechanism of tourism ecological security in Guangxi, China

Tourism ecological security (TES) is an important index reflecting the sustainable development of the regional economy. The construction of the China and ASEAN Free Trade Area has increased the total tourist consumption of Guangxi province by 36.48%. Unfortunately, overconsumption of resources, air pollution, disturbance of indigenous life, and other environmental degradation problems emerged due to the significant increase in tourists. Measuring the resilience of the tourism ecosystem is an urgent need to promote the high-quality development of tourism in Guangxi. To explore the dynamic changes in TES and its driving mechanism, the DPSIR (driver–pressure–state–impact–response) model for the tourism ecosystem was developed. The dynamic changes in TES and its driving mechanism from 2010 to 2019 were analyzed using fuzzy matter-element analysis, Markov chains, Geodetector, and other methods. The results show that: (1) the TES value increased steadily by 72.73%; the improvement speed was Northeast &gt; Southwest &gt; Southeast &gt; Northwest; (2) TES was negatively correlated with location, 14 cities developed independently; (3) the TES has a smaller probability to shift the lower level; (4) urbanization, water consumption, green area, tourism revenue, and the number of students in colleges had significant effects on TES. Four policies were proposed to improve TES: (1) developing forest tourism; (2) implementing greening projects in abandoned mining areas; (3) increasing tourism technical personnel; and (4) reducing clearance time for inbound tourists

Downregulation of Nuclear Protein H2B Induces Salicylic Acid Mediated Defense Against PVX Infection in Nicotiana benthamiana

Histone H2B protein is not only structurally important for chromosomal DNA packaging but is also involved in the regulation of gene expression, including the immune response of plants against pathogens. In this study, we show that the potato virus X (PVX) infection resulted in the reduced expression of H2B at both the mRNA and protein level in Nicotiana benthamiana. Tobacco rattle virus (TRV)-based virus-induced gene silencing (VIGS) was then used to down-regulate the expression of H2B in N. benthamiana and tests showed that the titre of TRV was similar in these plants to that in control treated plants. When these H2B-silenced plants were inoculated with PVX, the virus spread more slowly through the plant and there was a lower titre of PVX compared to non-silenced plants. Abnormal leaf development and stem necrosis were observed in the H2B-silenced plants, which were alleviated in H2B-silenced NahG transgenic plants suggesting the involvement of salicylic acid (SA) in the production of these symptoms. Indeed, quantitative reverse transcription (qRT)-PCR and liquid chromatography tandem mass spectroscopy (LC-MS) results showed that endogenous SA is increased in H2B-silenced N. benthamiana. Thus, downregulation of H2B induced the accumulation of endogenous SA, which was correlated with stem necrosis and a decreased accumulation of PVX in N. benthamiana

Improving the Efficacy of Conventional Therapy by Adding Andrographolide Sulfonate in the Treatment of Severe Hand, Foot, and Mouth Disease: A Randomized Controlled Trial

Background. Herb-derived compound andrographolide sulfonate (called Xiyanping injection) recommended control measure for severe hand, foot, and mouth disease (HFMD) by the Ministry of Health (China) during the 2010 epidemic. However, there is a lack of good quality evidence directly comparing the efficacy of Andrographolide Sulfonate combination therapy with conventional therapy. Methods. 230 patients were randomly assigned to 7–10 days of Andrographolide Sulfonate 5–10 mg/Kg/day and conventional therapy, or conventional therapy alone. Results. The major complications occurred less often after Andrographolide Sulfonate (2.6% versus 12.1%; risk difference [RD], 0.94; 95% CI, 0.28–1.61; P=0.006). Median fever clearance times were 96 hours (CI, 80 to 126) for conventional therapy recipients and 48 hours (CI, 36 to 54) for Andrographolide Sulfonate combination-treated patients (χ2=16.57, P<0.001). The two groups did not differ in terms of HFMD-cause mortality (P=1.00) and duration of hospitalization (P=0.70). There was one death in conventional therapy group. No important adverse event was found in Andrographolide Sulfonate combination therapy group. Conclusions. The addition of Andrographolide Sulfonate to conventional therapy reduced the occurrence of major complications, fever clearance time, and the healing time of typical skin or oral mucosa lesions in children with severe HFMD

Genomic insights into local adaptation and future climate-induced vulnerability of a keystone forest tree in East Asia

Assessment of population vulnerability and adaptive capacity under climate change is crucial for informing conservation strategies. Sang et al. assemble a reference genome for Populus koreana and combine population genomics and modelling to predict spatiotemporal responses to climate change.Rapid global climate change is posing a substantial threat to biodiversity. The assessment of population vulnerability and adaptive capacity under climate change is crucial for informing conservation and mitigation strategies. Here we generate a chromosome-scale genome assembly and re-sequence genomes of 230 individuals collected from 24 populations for Populus koreana, a pioneer and keystone tree species in temperate forests of East Asia. We integrate population genomics and environmental variables to reveal a set of climate-associated single-nucleotide polymorphisms, insertion/deletions and structural variations, especially numerous adaptive non-coding variants distributed across the genome. We incorporate these variants into an environmental modeling scheme to predict a highly spatiotemporal shift of this species in response to future climate change. We further identify the most vulnerable populations that need conservation priority and many candidate genes and variants that may be useful for forest tree breeding with special aims. Our findings highlight the importance of integrating genomic and environmental data to predict adaptive capacity of a key forest to rapid climate change in the future