information technology [keywords]
- Identification of differentially expressed genes implicated in peel color (red and green) of Dimocarpus confinis. [JOURNAL ARTICLE]
- Springerplus 2016; 5(1):1088.
Nowadays, there are few reports about regulatory genes implicated in peel color of longan. The basic genetic research of longan has been in stagnation for a long time as a lack of transcriptomic and genetic information. To predict candidate genes associated with peel color, Gene Functional Annotation and Coding Sequence prediction were used to perform functional annotation for our assembled unigenes and investigate differentially expressed genes (DEGs) of fruitlet peels from Longli (Dimocarpus confinis). Finally, a total of 24,044 (44.19 %) unigenes were annotated at least in one database after BLAST search to NCBI non-redundant protein sequence, NCBI non-redundant nucleotide sequences, Kyoto Encyclopedia of Genes and Genomes (KEGG) Ortholog, manually annotated and reviewed protein sequence database (Swiss-Prot), Protein family, Gene Ontology, euKaryotic Ortholog Groups databases. After searching against the KEGG-GENE protein database, a result of 6228 (11.45 %) unigenes were assigned to 245 KEGG pathways. Via comparing the distributions of expression value of all corresponding unigenes from red peel and green peel fruit, it could be intuitively concluded that high similarity was existed in the two distributions; however, on the whole, between two distributions of log RPKM expression value, some differences indicated that expression level in green-peel fruit group is slightly higher than values in red-peel fruit group. Finally, a total of 1349 unigenes were identified as DEGs after blasting the DEGs to public sequence databases, and 32 peel-color-related genes were identified in longan. Our results suggest that a number of unigenes involved in longan metabolic process, including anthocyanin biosynthesis. In addition, DRF, F3H, ANS, CYP75A1 and C1 may be the key ones. The study on key genes related to peel color will be contributed to revealing the molecular mechanisms of regulating peel color in woody plants.
- An emerging trend of equal authorship credit in major public health journals. [JOURNAL ARTICLE]
- Springerplus 2016; 5(1):1083.
This study aimed to identify the longitudinal trends and characteristics of the practice of explicitly giving equal credit to multiple authors of publications in public health journals. Manual searches were conducted to identify original research articles, published in five public health journals with the highest IFs according to the "2012 JCR Science Edition" between January 1, 2004 and December 31, 2013, which awarded equal credit to multiple authors (Epidemiologic Reviews, Environmental Health Perspectives, the International Journal of Epidemiology, Epidemiology, and the Annual Review of Public Health). The Instructions to Authors in the five journals were also examined with regard to information about giving equal credit to multiple authors.Statistically significant differences were noted in the annual prevalence in Environmental Health Perspectives, International Journal of Epidemiology, and Epidemiology (r = 0.753, P = 0.012; r = 0.894, P = 0.000; r = 0.522, P = 0.122, respectively). The first two authors listed in the by-line received equal credit in the majority of articles, but this practice was also extended to authors in nearly every position on the by-line in some publications. The authors given equal credit in articles appearing in Environmental Health Perspectives, International Journal of Epidemiology, and Epidemiology were primarily from European and North American countries. Finally, none of the journals provided specific guidance regarding this practice in their Instructions to Authors.An emerging trend of giving equal credit to multiple authors is observed in the public health journals. This practice should be better addressed in the guidance provided by journals to authors.
- Retinal Prosthesis System for Advanced Retinitis Pigmentosa: A Health Technology Assessment. [JOURNAL ARTICLE]
- Ont Health Technol Assess Ser 2016; 16(14):1-63.
Retinitis pigmentosa is a group of genetic disorders that involves the breakdown and loss of photoreceptors in the retina, resulting in progressive retinal degeneration and eventual blindness. The Argus II Retinal Prosthesis System is the only currently available surgical implantable device approved by Health Canada. It has been shown to improve visual function in patients with severe visual loss from advanced retinitis pigmentosa. The objective of this analysis was to examine the clinical effectiveness, cost-effectiveness, budget impact, and safety of the Argus II system in improving visual function, as well as exploring patient experiences with the system.We performed a systematic search of the literature for studies examining the effects of the Argus II retinal prosthesis system in patients with advanced retinitis pigmentosa, and appraised the evidence according to the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) Working Group criteria, focusing on visual function, functional outcomes, quality of life, and adverse events. We developed a Markov decision-analytic model to assess the cost-effectiveness of the Argus II system compared with standard care over a 10-year time horizon. We also conducted a 5-year budget impact analysis. We used a qualitative design and an interview methodology to examine patients' lived experience, and we used a modified grounded theory methodology to analyze information from interviews. Transcripts were coded, and themes were compared against one another.One multicentre international study and one single-centre study were included in the clinical review. In both studies, patients showed improved visual function with the Argus II system. However, the sight-threatening surgical complication rate was substantial. In the base-case analysis, the Argus II system was cost-effective compared with standard care only if willingness-to-pay was more than $207,616 per quality-adjusted life-year. The 5-year budget impact of funding the Argus II system ranged from $800,404 to $837,596. Retinitis pigmentosa significantly affects people's ability to navigate physical and virtual environments. Argus II was described as enabling the fundamental elements of sight. As such, it had a positive impact on quality of life for people with retinitis pigmentosa.Based on evidence of moderate quality, patients with advanced retinitis pigmentosa who were implanted with the Argus II retinal prosthesis system showed significant improvement in visual function, real-life functional outcomes, and quality of life, but there were complications associated with the surgery that could be managed through standard ophthalmologic treatments. The costs for the technology are high.
- Locating and navigation mechanism based on place-cell and grid-cell models. [JOURNAL ARTICLE]
- Cogn Neurodyn 2016 Aug; 10(4):353-360.
Extensive experiments on rats have shown that environmental cues play an important role in goal locating and navigation. Major studies about locating and navigation are carried out based only on place cells. Nevertheless, it is known that navigation may also rely on grid cells. Therefore, we model locating and navigation based on both, thus developing a novel grid-cell model, from which firing fields of grid cells can be obtained. We found a continuous-time dynamic system to describe learning and direction selection. In our simulation experiment, according to the results from physiology experiments, we successfully rebuild place fields of place cells and firing fields of grid cells. We analyzed the factors affecting the locating accuracy. Results show that the learning rate, firing threshold and cell number can influence the outcomes from various tasks. We used our system model to perform a goal navigation task and showed that paths that are changed for every run in one experiment converged to a stable one after several runs.
- Direction and viewing area-sensitive influence of EOG artifacts revealed in the EEG topographic pattern analysis. [JOURNAL ARTICLE]
- Cogn Neurodyn 2016 Aug; 10(4):301-314.
The influence of eye movement-related artifacts on electroencephalography (EEG) signals of human subjects, who were requested to perform a direction or viewing area dependent saccade task, was investigated by using a simultaneous recording with ocular potentials as electro-oculography (EOG). In the past, EOG artifact removals have been studied in tasks with a single fixation point in the screen center, with less attention to the sensitivity of cornea-retinal dipole orientations to the EEG head map. In the present study, we hypothesized the existence of a systematic EOG influence that differs according to coupling conditions of eye-movement directions with viewing areas including different fixation points. The effect was validated in the linear regression analysis by using 12 task conditions combining horizontal/vertical eye-movement direction and three segregated zones of gaze in the screen. In the first place, event-related potential topographic patterns were analyzed to compare the 12 conditions and propagation coefficients of the linear regression analysis were successively calculated in each condition. As a result, the EOG influences were significantly different in a large number of EEG channels, especially in the case of horizontal eye-movements. In the cross validation, the linear regression analysis using the appropriate dataset of the target direction/viewing area combination demonstrated an improved performance compared with the traditional methods using a single fixation at the center. This result may open a potential way to improve artifact correction methods by considering the systematic EOG influence that can be predicted according to the view angle such as using eye-tracker systems.
- Selectivity of stimulus induced responses in cultured hippocampal networks on microelectrode arrays. [JOURNAL ARTICLE]
- Cogn Neurodyn 2016 Aug; 10(4):287-299.
Sensory information can be encoded using the average firing rate and spike occurrence times in neuronal network responses to external stimuli. Decoding or retrieving stimulus characteristics from the response pattern generally implies that the corresponding neural network has a selective response to various input signals. The role of various spiking activity characteristics (e.g., spike rate and precise spike timing) for basic information processing was widely investigated on the level of neural populations but gave inconsistent evidence for particular mechanisms. Multisite electrophysiology of cultured neural networks grown on microelectrode arrays is a recently developed tool and currently an active research area. In this study, we analyzed the stimulus responses represented by network-wide bursts evoked from various spatial locations (electrodes). We found that the response characteristics, such as the burst initiation time and the spike rate, can be used to retrieve information about the stimulus location. The best selectivity in the response spiking pattern could be found for a small subpopulation of neurones (electrodes) at relatively short post-stimulus intervals. Such intervals were unique for each culture due to the non-uniform organization of the functional connectivity in the network during spontaneous development.
- Classifying four-category visual objects using multiple ERP components in single-trial ERP. [REVIEW, JOURNAL ARTICLE]
- Cogn Neurodyn 2016 Aug; 10(4):275-285.
Object categorization using single-trial electroencephalography (EEG) data measured while participants view images has been studied intensively. In previous studies, multiple event-related potential (ERP) components (e.g., P1, N1, P2, and P3) were used to improve the performance of object categorization of visual stimuli. In this study, we introduce a novel method that uses multiple-kernel support vector machine to fuse multiple ERP component features. We investigate whether fusing the potential complementary information of different ERP components (e.g., P1, N1, P2a, and P2b) can improve the performance of four-category visual object classification in single-trial EEGs. We also compare the classification accuracy of different ERP component fusion methods. Our experimental results indicate that the classification accuracy increases through multiple ERP fusion. Additional comparative analyses indicate that the multiple-kernel fusion method can achieve a mean classification accuracy higher than 72 %, which is substantially better than that achieved with any single ERP component feature (55.07 % for the best single ERP component, N1). We compare the classification results with those of other fusion methods and determine that the accuracy of the multiple-kernel fusion method is 5.47, 4.06, and 16.90 % higher than those of feature concatenation, feature extraction, and decision fusion, respectively. Our study shows that our multiple-kernel fusion method outperforms other fusion methods and thus provides a means to improve the classification performance of single-trial ERPs in brain-computer interface research.
- Comparative Transcriptome Reconstruction of Four Hypericum Species Focused on Hypericin Biosynthesis. [JOURNAL ARTICLE]
- Front Plant Sci 2016.:1039.
Next generation sequencing technology rapidly developed research applications in the field of plant functional genomics. Several Hypericum spp. with an aim to generate and enhance gene annotations especially for genes coding the enzymes supposedly included in biosynthesis of valuable bioactive compounds were analyzed. The first de novo transcriptome profiling of Hypericum annulatum Moris, H. tomentosum L., H. kalmianum L., and H. androsaemum L. leaves cultivated in vitro was accomplished. All four species with only limited genomic information were selected on the basis of differences in ability to synthesize hypericins and presence of dark nodules accumulating these metabolites with purpose to enrich genomic background of Hypericum spp. H. annulatum was chosen because of high number of the dark nodules and high content of hypericin. H. tomentosum leaves are typical for the presence of only 1-2 dark nodules localized in the apical part. Both H. kalmianum and H. androsaemum lack hypericin and have no dark nodules. Four separated datasets of the pair-end reads were gathered and used for de novo assembly by Trinity program. Assembled transcriptomes were annotated to the public databases Swiss-Prot and non-redundant protein database (NCBI-nr). Gene ontology analysis was performed. Differences of expression levels in the marginal tissues with dark nodules and inner part of leaves lacking these nodules indicate a potential genetic background for hypericin formation as the presumed site of hypericin biosynthesis is in the cells adjacent to these structures. Altogether 165 contigs in H. annulatum and 100 contigs in H. tomentosum were detected as significantly differentially expressed (P < 0.05) and upregulated in the leaf rim tissues containing the dark nodules. The new sequences homologous to octaketide synthase and enzymes catalyzing phenolic oxidative coupling reactions indispensable for hypericin biosynthesis were discovered. The presented transcriptomic sequence data will improve current knowledge about the selected Hypericum spp. with proposed relation to hypericin biosynthesis and will provide a useful resource of genomic information for consequential studies in the field of functional genomics, proteomics and metabolomics.
- Abstract Mindsets Increase Believability of Spatially Distant Online Messages. [JOURNAL ARTICLE]
- Front Psychol 2016.:1056.
Growing evidence from online credibility research reveals that online users rely on heuristic processes to evaluate the credibility of online information. The current paper, which is based on the construal level theory (CLT), proposes that congruency between the psychological distance of a stimulus and the way it is mentally construed can act as a heuristic for believability. According to CLT, psychologically close (e.g., spatially, temporally, socially) stimuli are represented concretely whereas psychologically distant stimuli are represented abstractly. The level of mental construals and the psychological distance of information have been shown to influence people's truth judgments in oﬄine contexts. This study tests whether congruency between the construal level of people's mindsets (abstract vs. concrete) and the psychological distance implied in an online message (far vs. close) enhances message believability. By partially confirming CLT predictions, we found that believability of an online news item about a distant location increased when people maintained an abstract mindset rather than a concrete one. The effect of a concrete mindset on believability was not significant for the close psychological distance condition. Our findings provide initial evidence that congruency between the construal level of people's mindsets and psychological distance cues in online messages can act as a heuristic for believability. We discuss the potential of applying the CLT framework to the growing literature on online cognitive heuristics in the area of online information credibility.
- Brain Decoding-Classification of Hand Written Digits from fMRI Data Employing Bayesian Networks. [JOURNAL ARTICLE]
- Front Hum Neurosci 2016.:351.
We are frequently exposed to hand written digits 0-9 in today's modern life. Success in decoding-classification of hand written digits helps us understand the corresponding brain mechanisms and processes and assists seriously in designing more efficient brain-computer interfaces. However, all digits belong to the same semantic category and similarity in appearance of hand written digits makes this decoding-classification a challenging problem. In present study, for the first time, augmented naïve Bayes classifier is used for classification of functional Magnetic Resonance Imaging (fMRI) measurements to decode the hand written digits which took advantage of brain connectivity information in decoding-classification. fMRI was recorded from three healthy participants, with an age range of 25-30. Results in different brain lobes (frontal, occipital, parietal, and temporal) show that utilizing connectivity information significantly improves decoding-classification and capability of different brain lobes in decoding-classification of hand written digits were compared to each other. In addition, in each lobe the most contributing areas and brain connectivities were determined and connectivities with short distances between their endpoints were recognized to be more efficient. Moreover, data driven method was applied to investigate the similarity of brain areas in responding to stimuli and this revealed both similarly active areas and active mechanisms during this experiment. Interesting finding was that during the experiment of watching hand written digits, there were some active networks (visual, working memory, motor, and language processing), but the most relevant one to the task was language processing network according to the voxel selection.