A Deep Learning Approach for Missing Data Imputation of Rating Scales Assessing Attention-Deficit Hyperactivity Disorder.

A variety of tools and methods have been used to measure behavioral symptoms of attention-deficit/hyperactivity disorder (ADHD). Missing data is a major concern in ADHD behavioral studies. This study used a deep learning method to impute missing data in ADHD rating scales and evaluated the ability of the imputed dataset (i.

Comparative genomic analysis of bacteriocin-producing Weissella cibaria 110.

Weissella cibaria 110 was isolated from plaa-som, a Thai fermented fish product, and known to produce the weissellicin 110 bacteriocin. We carried out comprehensive comparative genomic analysis of W. cibaria 110 with four other non-bacteriocin-producing W.

Unique clustering genes in the bacterial chromosome affecting the type-III secretion of enterohaemorrhagic Escherichia coli.

Bioinformatics analysis was used to search for unknown genes that might influence the phenotypic presentations of enterohaemorrhagic Escherichia coli (EHEC). By so doing and using the known genomic data from EHEC O157  : H7 and K-12, it has been deduced that genes Z4863 to Z4866 of EHEC do not exist in K-12 strains. These four gene sequences have low degrees of homology (18-40 % amino acid identities) to a set of genes in K-12, which have been known to encode fatty acid biosynthesis enzymes.

Lessons from the Largest Epidemic of Avian Influenza Viruses in Taiwan, 2015.

The largest epidemic of avian influenza (AI) in history attacked poultry and wild birds throughout Taiwan starting January 6, 2015. This study analyzed surveillance results, epidemiologic characteristics, and viral sequences by using government-released information, with the intention to provide recommendations to minimize future pandemic influenza. The H5 clade 2.

Exploring comprehensive within-motif dependence of transcription factor binding in Escherichia coli.

Modeling the binding of transcription factors helps to decipher the control logic behind transcriptional regulatory networks. Position weight matrix is commonly used to describe a binding motif but assumes statistical independence between positions. Although current approaches take within-motif dependence into account for better predictive performance, these models usually rely on prior knowledge and incorporate simple positional dependence to describe binding motifs.

Genome architecture of Lactobacillus plantarum PS128, a probiotic strain with potential immunomodulatory activity.

Background: Clinical and preclinical observations indicate that Lactobacillus plantarum has anti-inflammatory activity and may regulate the immune responses of its hosts when ingested. Recently, modification of teichoic acids (TAs) produced by L. plantarum was reported as a key to regulating the systemic immune response in mice.

Behavior training reverses asymmetry in hippocampal transcriptome of the cav3.2 knockout mice.

Homozygous Cav3.2 knockout mice, which are defective in the pore-forming subunit of a low voltage activated T-type calcium channel, have been documented to show impaired maintenance of late-phase long-term potentiation (L-LTP) and defective retrieval of context-associated fear memory. To investigate the role of Cav3.

Hierarchical clustering of breast cancer methylomes revealed differentially methylated and expressed breast cancer genes.

Oncogenic transformation of normal cells often involves epigenetic alterations, including histone modification and DNA methylation. We conducted whole-genome bisulfite sequencing to determine the DNA methylomes of normal breast, fibroadenoma, invasive ductal carcinomas and MCF7. The emergence, disappearance, expansion and contraction of kilobase-sized hypomethylated regions (HMRs) and the hypomethylation of the megabase-sized partially methylated domains (PMDs) are the major forms of methylation changes observed in breast tumor samples.

A17, the First Sequenced Strain of Lactococcus lactis subsp. cremoris with Potential Immunomodulatory Functions.

Lactococcus lactis subsp. cremoris A17, isolated from Taiwan fermented cabbage, is the first sequenced strain of L. lactis subsp.

Diagnostics for stochastic genome-scale modeling via model slicing and debugging.

Modeling of biological behavior has evolved from simple gene expression plots represented by mathematical equations to genome-scale systems biology networks. However, due to obstacles in complexity and scalability of creating genome-scale models, several biological modelers have turned to programming or scripting languages and away from modeling fundamentals. In doing so, they have traded the ability to have exchangeable, standardized model representation formats, while those that remain true to standardized model representation are faced with challenges in model complexity and analysis.

Microbial diversity analysis of fermented mung beans (Lu-Doh-Huang) by using pyrosequencing and culture methods.

In Taiwanese alternative medicine Lu-doh-huang (also called Pracparatum mungo), mung beans are mixed with various herbal medicines and undergo a 4-stage process of anaerobic fermentation. Here we used high-throughput sequencing of the 16S rRNA gene to profile the bacterial community structure of Lu-doh-huang samples. Pyrosequencing of samples obtained at 7 points during fermentation revealed 9 phyla, 264 genera, and 586 species of bacteria.

Draft Genome Sequence of Lactobacillus pobuzihii E100301T.

Lactobacillus pobuzihii E100301(T) is a novel Lactobacillus species previously isolated from pobuzihi (fermented cummingcordia) in Taiwan. Phylogenetically, this strain is closest to Lactobacillus acidipiscis, but its phenotypic characteristics can be clearly distinguished from those of L. acidipiscis.

Genome-wide PhoB binding and gene expression profiles reveal the hierarchical gene regulatory network of phosphate starvation in Escherichia coli.

The phosphate starvation response in bacteria has been studied extensively for the past few decades and the phosphate-limiting signal is known to be mediated via the PhoBR two-component system. However, the global DNA binding profile of the response regulator PhoB and the PhoB downstream responses are currently unclear. In this study, chromatin immunoprecipitation for PhoB was combined with high-density tiling array (ChIP-chip) as well as gene expression microarray to reveal the first global down-stream responses of the responding regulator, PhoB in E.

Protein domain repetition is enriched in Streptococcal cell-surface proteins.

Tandem repetition of domain in protein sequence occurs in all three domains of life. It creates protein diversity and adds functional complexity in organisms. In this work, we analyzed 52 streptococcal genomes and found 3748 proteins contained domain repeats.

Highly conserved influenza A virus epitope sequences as candidates of H3N2 flu vaccine targets.

This study focused on identifying the conserved epitopes in a single subtype A (H3N2)-as candidates for vaccine targets. We identified a total of 32 conserved epitopes in four viral proteins [22 HA, 4PB1, 3 NA, 3 NP]. Evaluation of conserved epitopes in coverage during 1968-2010 revealed that (1) 12 HA conserved epitopes were highly present in the circulating viruses; (2) the remaining 10 HA conserved epitopes appeared with lower percentage but a significantly increasing trend after 1989 [p<0.

Proteomics characterization of cytoplasmic and lipid-associated membrane proteins of human pathogen Mycoplasma fermentans M64.

Mycoplasma fermentans is a potent human pathogen which has been implicated in several diseases. Notably, its lipid-associated membrane proteins (LAMPs) play a role in immunomodulation and development of infection-associated inflammatory diseases. However, the systematic protein identification of pathogenic M.

CAGO: a software tool for dynamic visual comparison and correlation measurement of genome organization.

CAGO (Comparative Analysis of Genome Organization) is developed to address two critical shortcomings of conventional genome atlas plotters: lack of dynamic exploratory functions and absence of signal analysis for genomic properties. With dynamic exploratory functions, users can directly manipulate chromosome tracks of a genome atlas and intuitively identify distinct genomic signals by visual comparison. Signal analysis of genomic properties can further detect inconspicuous patterns from noisy genomic properties and calculate correlations between genomic properties across various genomes.

Sequencing and comparative genome analysis of two pathogenic Streptococcus gallolyticus subspecies: genome plasticity, adaptation and virulence.

Streptococcus gallolyticus infections in humans are often associated with bacteremia, infective endocarditis and colon cancers. The disease manifestations are different depending on the subspecies of S. gallolyticus causing the infection.

T4-Like genome organization of the Escherichia coli O157:H7 lytic phage AR1.

We report the genome organization and analysis of the first completely sequenced T4-like phage, AR1, of Escherichia coli O157:H7. Unlike most of the other sequenced phages of O157:H7, which belong to the temperate Podoviridae and Siphoviridae families, AR1 is a T4-like phage known to efficiently infect this pathogenic bacterial strain. The 167,435-bp AR1 genome is currently the largest among all the sequenced E.

Common altered epigenomic domains in cancer cells: characterization and subtle variations.

We have previously identified large megabase-sized hypomethylated zones in the genome of the breast cancer cell line MCF-7 using the TspRI-ExoIII technique. In this report, we used a more convenient high throughput method for mapping the hypomethylated zones in a number of human tumor genomes simultaneously. The method was validated by the bisulfite sequencing of 39 randomly chosen sites in a demethylated domain and by bisulfite genome-wide sequencing of the MCF-7 genome.

Change of protein profiles in the induction of the viable but nonculturable state of Vibrio parahaemolyticus.

This work reports on the metabolic response in the induction of the viable but nonculturable (VBNC) state of the seafood enteropathogen Vibrio parahaemolyticus, as determined by analyzing the corresponding change in protein profiles. V. parahaemolyticus ST550 was incubated at 4 degrees C in the Morita mineral salt-0.

Characterization of a new plasmid-like prophage in a pandemic Vibrio parahaemolyticus O3:K6 strain.

Vibrio parahaemolyticus is a common food-borne pathogen that is normally associated with seafood. In 1996, a pandemic O3:K6 strain abruptly appeared and caused the first pandemic of this pathogen to spread throughout many Asian countries, America, Europe, and Africa. The role of temperate bacteriophages in the evolution of this pathogen is of great interest.

Multiple regulatory elements mediating neuronal-specific expression of zebrafish sodium channel gene, scn8aa.

Zebrafish scn8aa sodium channels mediate the majority of sodium conductance, which is essential for the embryonic locomotor activities. Here, we investigated the transcriptional regulation of scn8aa in developing zebrafish embryos by constructing a GFP reporter driven by a 15-kb fragment of scn8aa gene designed as scn8aa:GFP. GFP expression patterns of scn8aa:GFP temporally and spatially recapitulated the expression of endogenous scn8aa mRNA during zebrafish embryonic development, with one exception in the inner nuclear layer of the retina.

A common virulence plasmid in biotype 2 Vibrio vulnificus and its dissemination aided by a conjugal plasmid.

Strains of Vibrio vulnificus, a marine bacterial species pathogenic for humans and eels, are divided into three biotypes, and those virulent for eels are classified as biotype 2. All biotype 2 strains possess one or more plasmids, which have been shown to harbor the biotype 2-specific DNA sequences. In this study we determined the DNA sequences of three biotype 2 plasmids: pR99 (68.