Personalized medical care focuses on prediction of disease risk and response to medications. To build the risk models, access to both large-scale genomic resources and human genetic studies is ...required. The Taiwan Biobank (TWB) has generated high-coverage, whole-genome sequencing data from 1492 individuals and genome-wide SNP data from 103,106 individuals of Han Chinese ancestry using custom SNP arrays. Principal components analysis of the genotyping data showed that the full range of Han Chinese genetic variation was found in the cohort. The arrays also include thousands of known functional variants, allowing for simultaneous ascertainment of Mendelian disease-causing mutations and variants that affect drug metabolism. We found that 21.2% of the population are mutation carriers of autosomal recessive diseases, 3.1% have mutations in cancer-predisposing genes, and 87.3% carry variants that affect drug response. We highlight how TWB data provide insight into both population history and disease burden, while showing how widespread genetic testing can be used to improve clinical care.
This article presents a robust passivity-based control (PBC) strategy to mitigate the instability effect of the dc-dc boost power converter supplying a constant power load and a constant voltage load ...in dc microgrid systems. The control robustness of the PBC against both line and load variation is significantly improved by adding the nonlinear disturbance observer (NDO). Using the disturbance estimation technique, this observer works in parallel with the PBC strategy to compensate the disturbances of the system through a feed-forward compensation channel. Based on the dissipation property, the PBC strategy ensures the system stability, whereas the NDO guarantees global trajectory tracking to the reference voltage during disturbances. This control strategy not only ensures large-signal stability of the system, but also provides a fastest recovery performance during disturbances of the system as compared with other PBC strategies. The hardware-in-loop and real-hardware experimental results are provided to verify the control robustness of the proposed control strategy.
Autism spectrum disorder (ASD) is an early-onset neurodevelopmental disorder with complex genetic underpinning in its etiology. Copy number variations (CNVs) as one of the genetic factors associated ...with ASD have been addressed in recent genome-wide association studies (GWAS). However, the significance of CNV has not been well investigated in non-Caucasian ASD population.
To identify the pathogenic CNVs responsible for ASD in Han Chinese, we performed a segment-based GWAS of CNV in 335 ASD cases and 1093 healthy controls using Affymetrix single nucleotide polymorphism (SNP) array by focusing on case-specific CNVs. PARK2 was one of the important genes with several case-specific regions overlapped on it. The findings were validated in the initial screen sample set and replicated in another sample set by real-time quantitative PCR (qPCR).
A total of six CNVs at 6q26 that spanned different exons of PARK2 were identified. The PARK2 expression level was down-regulated at exon-dependent manner in cases with either deletion or duplication. The result revealed that the gene function might be disrupted by exonic deletion and duplication. We also observed that the ASD case with exonic duplication demonstrated a more severe interference of PARK2 expression and the clinical feature than the ones with deletion at the exons 2-4 of the PARK2 gene.
Our finding provides evidence to support that CNVs affecting PARK2 function might contribute to genetic etiology of a proportion of cases with ASD. The intriguing results of this work warrant further study on characterizing the functional impact of various exonic CNVs on the PARK2 gene.
ClinicalTrials.gov NCT00494754.
Full text
Available for:
IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
Selecting an appropriate substitution model and deriving a tree topology for a given sequence set are essential in phylogenetic analysis. However, such time consuming, computationally intensive tasks ...rely on knowledge of substitution model theories and related expertise to run through all possible combinations of several separate programs. To ensure a thorough and efficient analysis and avert tedious manipulations of various programs, this work presents an intuitive framework, the phylogenetic reconstruction with automatic likelihood model selectors (PALM), with convincing, updated algorithms and a best-fit model selection mechanism for seamless phylogenetic analysis.
As an integrated framework of ClustalW, PhyML, MODELTEST, ProtTest, and several in-house programs, PALM evaluates the fitness of 56 substitution models for nucleotide sequences and 112 substitution models for protein sequences with scores in various criteria. The input for PALM can be either sequences in FASTA format or a sequence alignment file in PHYLIP format. To accelerate the computing of maximum likelihood and bootstrapping, this work integrates MPICH2/PhyML, PalmMonitor and Palm job controller across several machines with multiple processors and adopts the task parallelism approach. Moreover, an intuitive and interactive web component, PalmTree, is developed for displaying and operating the output tree with options of tree rooting, branches swapping, viewing the branch length values, and viewing bootstrapping score, as well as removing nodes to restart analysis iteratively.
The workflow of PALM is straightforward and coherent. Via a succinct, user-friendly interface, researchers unfamiliar with phylogenetic analysis can easily use this server to submit sequences, retrieve the output, and re-submit a job based on a previous result if some sequences are to be deleted or added for phylogenetic reconstruction. PALM results in an inference of phylogenetic relationship not only by vanquishing the computation difficulty of ML methods but also providing statistic methods for model selection and bootstrapping. The proposed approach can reduce calculation time, which is particularly relevant when querying a large data set. PALM can be accessed online at http://palm.iis.sinica.edu.tw.
Full text
Available for:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
In order to provide early selection indicators for the breeding of plants used for producing tea seed oil or harvesting tea, we investigated the relationships between flower morphology and fruit ...yields in tea plants. We analyzed 106 tea varieties to determine the relationships between flower morphological traits and fruit yields. Notably, the homogeneity of flower traits within the same tea plant variety was found to be very high. The average length and width measurements of certain phenotypic traits of tea plants, including pistil length, stamen length, stamen bundle inner width, stamen bundle outer width, and stigma width, were 11.8, 10.9, 2.5, 15.0, 3.7 mm, respectively. In this study, the flower traits that affect fruit yield appear to be related to the difficulty of pollination by insects (e.g., bees), in terms of their contacting the stigma. In 2013, three phenotypic trait variables showed significant effects on yield; namely, the stamen bundle outer width (negative), stigma width (positive), and stigma width minus the stamen bundle inner width (positive). In 2015, only the stamen bundle outer width had a significant negative effect on yield. Regarding pollen viability, in the TTC (2,3,5-triphenyl tetrazolium chloride) staining test, about 84% of the considered tea varieties presented pollen viability exceeding 70%. This indicates that most tea pollen has the ability to germinate normally after contact with the cross-pollinated stigma. The yields of all of the tea varieties exhibited a positively skewed distribution in 2013 and 2015. Although our results indicate that flowers in the anther superior group tend to produce fewer fruits than flowers in the stigma superior group in 2013, in the analysis of the effect of traits on yield, there were no significant differences in the relative positions of stigmas and anthers. In conclusion, we determined that the main trait affecting fruit yield is stamen bundle outer width, while the secondary trait affecting fruit yield is stigma width. However, the efficacy of the stigma width may also be affected by the position of the stigma relative to the anther and the stamen bundle inner width. These two traits have the potential to be used as reference indicators for early selection in future breeding programs.
Nucleic acid hybridization is an extensively adopted principle in biomedical research, in which the performance of any hybridization-based method depends on the specificity of probes to their ...targets. To determine the optimal probe(s) for detecting target(s) from a sample cocktail, we developed a novel algorithm, which has been implemented into a web platform for probe designing. This probe design workflow is now upgraded to satisfy experiments that require a probe designing tool to take the increasing volume of sequence datasets.
Algorithms and probe parameters applied in UPS 2.0 include GC content, the secondary structure, melting temperature (Tm), the stability of the probe-target duplex estimated by the thermodynamic model, sequence complexity, similarity of probes to non-target sequences, and other empirical parameters used in the laboratory. Several probe background options,Unique probe within a group,Unique probe in a specific Unigene set,Unique probe based on the pangenomic level, and Unique Probe in the user-defined genome/transcriptome, are available to meet the scenarios that the experiments will be conducted. Parameters, such as salt concentration and the lower-bound Tm of probes, are available for users to optimize their probe design query. Output files are available for download on the result page. Probes designed by the UPS algorithm are suitable for generating microarrays, and the performance of UPS-designed probes has been validated by experiments.
The UPS 2.0 evaluates probe-to-target hybridization under a user-defined condition to ensure high-performance hybridization with minimal chance of non-specific binding at the pangenomic and genomic levels. The UPS algorithm mimics the target/non-target mixture in an experiment and is very useful in developing diagnostic kits and microarrays. The UPS 2.0 website has had more than 1,300 visits and 360,000 sequences performed the probe designing task in the last 30 months. It is freely accessible at http://array.iis.sinica.edu.tw/ups/. Screen cast: http://array.iis.sinica.edu.tw/ups/demo/demo.htm.
Full text
Available for:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
•Nationality diversity analysis should take both the similarities and differences of assignee country and inventor country into consideration.•Domestic Proportion and Nationality Diversity indexes ...were applied to define the types of invention, Domestic-inventions, Domestic/International-inventions, and International-inventions.•From the inventive level point of view, there three types of nationality diversity, domestic-dominated, domestic-participated, and international-supported were identified based on the distributions of the granted inventions.•A visual spectrum technique was proposed to show the overall talents allocation for the organizations effectively.
Mobile talent brings different expertise, perspectives, knowledge, and experience into an organization. With a diversity of views, organizations can obtain new ideas that help improve research and development. National diversity can be deemed to represent the mobile talent within an organization, which might increase innovation. Organizations with national diversity are more innovative. Performance is generally based on collaboration between domestic and international talent, which provides the opportunity to capture benefits from the knowledge transfer effect. Most studies on national diversity generally take a headcount of countries on an organizational basis to calculate the National Diversity Index; however, this approach fails to reveal the contribution of knowledge transfer between domestic/international inventor team collaborations. In this study, the authors propose an index, which includes two parts, in which values are assigned based on domestic/international collaboration and international/international collaboration. The index can determine the level of national diversity. The authors further provided a mechanism for visualizing the diversity of inventor teams. An empirical analysis that focuses on the pharmaceutical industry was conducted to test the proposed model.
Full text
Available for:
GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Shaking the tea leaves is the key manipulation to making oolong tea. It contributes to the formation of flavor and fragrance in oolong tea. The dynamic variations of catechins and volatile organic ...compounds (VOCs) during the shaking process were investigated. The results showed that the contents of epicatechin, epigallocatechin, epicatechin gallate (ECG), and epigallocatechin gallate (EGCG) first decreased after the shaking and then increased to the initial value before the next shaking. Geraniol, linalool and its oxides, and phenylethyl alcohol showed similar variations. The contents of trans-β-ocimene, 1H-indole, and 3-hexenyl hexanoate increased after the second or third shaking (the late fermentation stage). However, the contents of aldehydes showed an opposite trend to other VOCs. The abundance of phenylethyl alcohol was positively related to the content of ECG and EGCG during fermentation, whereas the abundance of cis-3-hexenal was negatively related to the content of ECG. The correlations between catechin and VOCs indicated that shaking affected the chemical transformation of the compounds in oolong tea.
Display omitted
Full text
Available for:
DOBA, GEOZS, IJS, IMTLJ, IZUM, KILJ, KISLJ, NLZOH, NUK, OILJ, PILJ, PNG, SAZU, SBCE, SBJE, SIK, UILJ, UKNU, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
We examined the performance of solution-processed organic light emitting diodes (OLEDs) by modifying the hole injection layer (HIL), poly(3,4-ethylenedioxythiophene) polystyrene sulfonate (PEDOT: ...PSS). Atomic force microscopy (AFM) showed morphological changes with surface roughness (RRMS) of 1.47, 1.73, and 1.37 nm for pristine PEDOT: PSS, PEDOT: PSS modified with a 40 v% deionized water and with a 30 v% acetone, respectively. The surface hydrophobicity of the acetone modified PEDOT:PSS HIL layer was decreased by 34% as comparing with the water modified counterpart. Electrical conductivity was increased to two orders of magnitude for the water and acetone modified PEDOT:PSS as compared to pristine. We observed a low refractive index and high transmittance for the modified HILs. We fabricated and explored electroluminescent properties of bis2-(4,6-difluorophenyl)pyridinato-C2,N(picolinato)iridium(III) (FIrpic) based sky blue device by utilizing HIL with and without modification. The changes in electrical conductivity, surface roughness, refractive index, and transmittance of the modified HILs strongly influenced the performance of devices. By utilizing a 30% acetone modified HIL, the power efficiency was increased from 14.2 to 24.2 lm/W, an increment of 70% and the EQE from 8.5 to 13.1% at 100 cd/m2, an increment of 54%. The maximum luminance also increased from 11,780 to 18,190 cd/m2. The findings revealed herein would be helpful in designing and fabricating high efficiency solution processed OLEDs.
Display omitted
•Poly(3,4-ethylenedioxythiophene) polystyrene sulfonate (PEDOT: PSS) modified with optimized concentrations of deionized water (DI water) and acetone and fabricated sky blue OLED devices with modified PEDOT:PSS.•By utilizing a 30% acetone modified HIL, the power efficiency was increased from 14.2 to 24.2 lm/W, an increment of 70% and the EQE from 8.5 to 13.1% at 100 cd/m2, an increment of 54%. The maximum luminance also increased from 11,780 to 18,190 cd/m2.•The changes in electrical conductivity, surface roughness, refractive index and transmittance of modified HIL strongly influenced the performance of devices.
Full text
Available for:
GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
We implemented a statistical model into our protein interaction database for validation of two-hybrid assays of Helicobacter pylori, and prediction of putative protein interactions not yet discovered ...experimentally. To present the enormous amount of experimental and inferred protein interaction networking maps, the H.pylori Database of Protein Interactomes (hp-DPI) is developed with a succinct yet comprehensive visualization tool integrated with annotation from Genbank, GO, and KEGG. hp-DPI is first built with, but not limited to, H.pylori protein interactions and is expected to naturally include other organisms’ protein interacting relationships in the future. Availability: hp-DPI can be accessed at http://www.dpi.nhri.org.tw/hp/ Contact: cylin@nhri.org.tw
PDF
