Additional file 4: of CloneCNA: detecting subclonal somatic copy number alterations in heterogeneous tumor samples from whole-exome sequencing data

Simulated mixtures with combinations of four genomes. (XLS 26 kb

Additional file 2: of CLImAT-HET: detecting subclonal copy number alterations and loss of heterozygosity in heterogeneous tumor samples from whole-genome sequencing data

This file contains Supplementary Figures. (PDF 1702 kb

Additional file 3: Table S2. of CLImAT-HET: detecting subclonal copy number alterations and loss of heterozygosity in heterogeneous tumor samples from whole-genome sequencing data

This file contains Supplementary Table S2. (XLS 26 kb

The use of car safety seats for children in China: A questionnaire survey based on the theory of planned behavior

The purpose of this study was to analyze the psychological characteristics underlying Chinese parents’ behaviors in using child car seats and to understand their decision-making processes. Based on the theory of planned behavior (TPB), three extended variables of perceived accident severity, perceived benefits, and perceived barriers were introduced. From the perspective of social psychology, the psychological factors that influence parents’ use of child car seats and their interrelationships were explored. A questionnaire was designed to collect data, including information on demographic characteristics, basic components of the TPB, and relevant extension variables. Using on online survey, 585 valid questionnaires were collected. Structural equation modeling was used to calibrate the data, and multiple group analysis was performed on the demographic variables. The extended TPB can effectively explain and predict parents’ behaviors when using children’s car seats. The results of the model show that parents’ positive attitudes toward child safety seats (CSSs), others’ recognition of their own use and perceptual control of the use of CSSs increase their willingness to use CSSs. Parents’ willingness to use has a positive impact on the use of CSSs. Additionally, for the three extended variables introduced, perceived benefit significantly promoted parental intention and behavior to use CSS for children; perceived barriers significantly reduced parental use of CSS; and perceived accident severity had no significant effect on parental use of CSS. This study established the validity of the extended TPB model in predicting parents’ behaviors in using car seats for their children. In addition, the current findings may provide a theoretical basis for policy development to promote CSS use.</p

Closest relatives of sequenced <i>g20</i> clones from different paddy floodwaters at the amino acid level.

<p>Closest relatives of sequenced <i>g20</i> clones from different paddy floodwaters at the amino acid level.</p

Neighbor-joining phylogenetic tree showing the relationships of <i>g20</i> amino acid sequence from paddy floodwaters in NE China with from those from lake freshwaters (Dorigo et al. 2004; Short and Suttle 2005; Wilhelm et al. 2006; Zhong and Jacquet 2013; Yeo and Gin, unpublished data which were submitted in Jan 15, 2013), paddy floodwaters in Japan (Wang et al. 2010), paddy field soils in Japan (Wang et al. 2011) and marine waters (Fuller et al. 1998; Zhong et al. 2002; Marston and Sallee 2003; Wang and Chen 2004; Mann et al. 2005; Short and Suttle 2005; Li and Li, unpublished data which were submitted in Jun 16, 2013).

<p><i>Green triangles</i> and <i>blue circles</i> indicate <i>g20</i> clones obtained from lake freshwater and marine water, respectively; <i>Black</i> and <i>white square boxes</i> indicate <i>g20</i> clones obtained from paddy field soils in Japan and paddy floodwaters in Japan, respectively; <i>White triangles</i> indicate <i>g20</i> clones obtained from paddy floodwaters in NE China. The <i>number in parentheses</i> denotes the accession number of amino acid sequences in the NCBI website. Bootstrap values <50 are not shown. The scale bar represents the number of amino acid substitutions per residue.</p

Neighbor-joining phylogenetic tree showing the relationship of <i>g20</i> amino acid sequences from paddy floodwaters in NE China with those from Japanese paddy floodwaters (Wang et al. 2010) and paddy field soils (Wang et al.2011).

<p><i>Brown</i> and <i>white square boxes</i> indicate <i>g20</i> clones obtained from paddy field soils in Japan and paddy floodwaters in Japan, respectively; <i>green triangles</i> indicate <i>g20</i> clones obtained from paddy floodwaters in NE China; <i>JP</i> and <i>CN</i> represent Japan and China, respectively; <i>PFW</i> and <i>PFS</i> represent paddy floodwater and paddy field soil, respectively. Bootstrap values <50 are not shown. The scale bar represents the number of amino acid substitutions per residue.</p

Three-dimensional principal coordinate analysis of <i>g20</i> clone sequences of cyanophage communities obtained from paddy floodwaters in NE China (<i>dark green circles</i>) and from Japanese paddy floodwaters (<i>light green circles</i>) and paddy soils (<i>brown circles</i>).

<p>The <i>percentages</i> in the axis labels represent the percentage of variation explained by the principal coordinates.</p

Three-dimensional principal coordinate analysis of <i>g20</i> clone sequences of cyanophage communities obtained from marine waters (<i>blue circles</i>), lake freshwaters (<i>red circles</i>), and paddy fields (<i>green circles</i>).

<p>The <i>percentages</i> in the axis labels represent the percentages of variation explained by the principal coordinates.</p

Data_Sheet_1_Biocontrol efficacy of Bacillus velezensis strain YS-AT-DS1 against the root-knot nematode Meloidogyne incognita in tomato plants.docx

Root-knot nematodes (RKNs; Meloidogyne spp.), one of the most economically important plant-parasitic nematodes (PPNs), cause severe yield and quality losses in agriculture annually. The application of biological control agents is an environmentally safe and effective approach to control RKNs. Here, we report the genomic characteristics of a Bacillus velezensis strain YS-AT-DS1 (Bv-DS1) isolated from the tidal soil, revealing that it has a 4.73 Mb circular chromosome with an average GC-content of 46.43%, 3,977 genes, 86 tRNAs, and 27 rRNAs, and contains secondary metabolite clusters for producing antimicrobial compounds. In vitro assays indicated that Bv-DS1 has not only antagonistic activities against fungal pathogens, but also shows nematicidal activity, with a mortality rate of 71.62% mortality rates in second-stage juvenile (J2s) Meloidogyne incognita. We then focused on the biocontrol efficiency of Bv-DS1 against M. incognita in pot assays. Preinoculation with Bv-DS1 enhanced tomato growth, and significantly reduced the infection rate of J2s, and the number of galls and egg masses on tomato roots. The underlying mechanism in Bv-DS1-induced resistance to M. incognita was further investigated through split-root experiments, and analysing the expression of the genes related to jasmonic acid (JA), salicylic acid (SA), and the tonoplast intrinsic protein (TIP). The results indicated that Bv-DS1 could not activate host systemic-induced resistance (ISR) in the split-root system of tomatoes. Additionally, the expression of JA- (LOX D and MC) and SA- (PAL2 and PR) responsive genes did not change in Bv-DS1-pretreated plants at 3 and 14 days after nematode inoculation. The presented data showed that JA-and SA-dependent pathways were not required for the biocontrol action of the Bv-DS1 against RKN. The TIP genes, responsible for transport of water and small substrates in plants, have previously been shown to negatively regulate the parasitism of PPNs. Surprisingly, Bv-DS1 compromised the downregulation of TIP1.1 and TIP1.3 by M. incognita. Together, our data suggest that Bv-DS1 exhibits a dual effect on plant growth promotion and protection against RKN, possibly related to the regulation of water and solute transport via TIPs. Thus, the Bv-DS1 strain could be used as a biocontrol agent for RKN control in sustainable agriculture.</p