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Article ; Online: FluConvert and IniFlu

Chin-Rur Yang / Chwan-Chuen King / Li-Yu Daisy Liu / Chia-Chi Ku

BMC Bioinformatics, Vol 21, Iss 1, Pp 1-

a suite of integrated software to identify novel signatures of emerging influenza viruses with increasing risk

2020 Volume 14

Abstract: Abstract Background The pandemic threat of influenza has attracted great attention worldwide. To assist public health decision-makers, new suites of tools are needed to rapidly process and combine viral information retrieved from public-domain databases ... ...

Abstract	Abstract Background The pandemic threat of influenza has attracted great attention worldwide. To assist public health decision-makers, new suites of tools are needed to rapidly process and combine viral information retrieved from public-domain databases for a better risk assessment. Results Using our recently developed FluConvert and IniFlu software, we automatically processed and rearranged sequence data by standard viral nomenclature, determined the group-related consensus sequences, and identified group-specific polygenic signatures. The software possesses powerful ability to integrate viral, clinical, and epidemiological data. We demonstrated that both multiple basic amino acids at the cleavage site of the HA gene and also at least 11 more evidence-based viral amino acid substitutions present in global highly pathogenic avian influenza H5N2 viruses during the years 2009–2016 that are associated with viral virulence and human infection. Conclusions FluConvert and IniFlu are useful to monitor and assess all subtypes of influenza viruses with pandemic potential. These programs are implemented through command-line and user-friendly graphical interfaces, and identify molecular signatures with virological, epidemiological and clinical significance. FluConvert and IniFlu are available at https://apps.flutures.com or https://github.com/chinrur/FluConvert_IniFlu
Keywords	Highly pathogenic avian influenza viruses ; H5N2 ; Viral and immunological informatics ; Risk assessment ; Pandemic potential ; Computer applications to medicine. Medical informatics ; R858-859.7 ; Biology (General) ; QH301-705.5
Subject code	028
Language	English
Publishing date	2020-07-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The Ds1 Transposon Provides Messages That Yield Unique Profiles of Protein Isoforms and Acts Synergistically With Ds to Enrich Proteome Complexity via Exonization

Yuh-Chyang Charng / Lung-Hsin Hsu / Li-yu Daisy Liu

Evolutionary Bioinformatics, Vol

2017 Volume 13

Abstract: In exonization events, Ds1 may provide donor and/or acceptor sites for splicing after inserting into genes and be incorporated into new transcripts with new exon(s). In this study, the protein variants of Ds1 exonization yielding additional functional ... ...

Abstract	In exonization events, Ds1 may provide donor and/or acceptor sites for splicing after inserting into genes and be incorporated into new transcripts with new exon(s). In this study, the protein variants of Ds1 exonization yielding additional functional profile(s) were studied. Unlike Ds exonization, which creates new profiles mostly by incorporating flanking intron sequences with the Ds message, Ds1 exonization additionally creates new profiles through the presence or absence of Ds1 messages. The number of unique functional profiles harboring Ds1 messages is 1.3-fold more than that of functional profiles without Ds1 messages. The highly similar 11 protein isoforms at a single insertion site also contribute to proteome complexity enrichment by exclusively creating new profiles. Particularly, Ds1 exonization produces 459 unique profiles, of which 129 cannot be built by Ds. We thus conclude that Ds and Ds1 are independent but synergistic in their capacity to enrich proteome complexity through exonization.
Keywords	Biology (General) ; QH301-705.5
Language	English
Publishing date	2017-02-01T00:00:00Z
Publisher	SAGE Publishing
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Psychological distress of suicide attempters predicts one-year suicidal deaths during 2007–2016

Chia-Yi Wu / Ming-Been Lee / Shih-Cheng Liao / Chia-Ta Chan / Li-yu Daisy Liu / Chun-Yin Chen

Journal of the Formosan Medical Association, Vol 119, Iss 8, Pp 1306-

A population-based study

2020 Volume 1313

Abstract: Background/Purpose: Of the risk factors for suicide, prior attempt is regarded as one of the strongest for subsequent attempts or completed suicide. This large-scale cohort study aims to examine whether the distress level of individual mental symptoms ... ...

Abstract	Background/Purpose: Of the risk factors for suicide, prior attempt is regarded as one of the strongest for subsequent attempts or completed suicide. This large-scale cohort study aims to examine whether the distress level of individual mental symptoms and general psychopathology measured at the index attempt can predict subsequent suicide death within one year. Methods: The participants were 104,441 suicide attempters first reported to the Taiwan National Suicide Surveillance System during 2007–2016, who completed the five-item Brief Symptom Rating Scale (BSRS-5) at the index attempt. Kaplan–Meier survival curve analysis with log-rank test and Cox regression model were used to examine whether the level of psychological distress could predict the cumulative incidence of re-attempted suicidal death in the following year. Results: In total, 1254 (1.2%) participants subsequently killed themselves within one year. Survival curves analysis and Cox regression modelling indicated that levels of distress of individual items (i.e., suicide ideation, depression, inferiority, anxiety, hostility and insomnia) and total BSRS-5 scores were significantly correlated with the incidence of subsequent suicidal death within one year for both genders. Conclusion: The study revealed that self-rated psychological distress was a significant and sustained predictor of re-attempted suicide death within one year after the index attempt. These results imply that suicide is not only an issue of acute crisis, but also a prolonged problem of lasting psychological distress. The BSRS-5 assessment could provide a symptom profile on which to develop a pertinent person-centered approach to prevent subsequent suicide attempts.
Keywords	Population-based study ; Psychological distress ; Suicide attempt ; Suicide death ; Medicine (General) ; R5-920
Subject code	310 ; 150
Language	English
Publishing date	2020-08-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Identifying gene set association enrichment using the coefficient of intrinsic dependence.

Chen-An Tsai / Li-Yu Daisy Liu

PLoS ONE, Vol 8, Iss 3, p e

2013 Volume 58851

Abstract: Gene set testing problem has become the focus of microarray data analysis. A gene set is a group of genes that are defined by a priori biological knowledge. Several statistical methods have been proposed to determine whether functional gene sets express ... ...

Abstract	Gene set testing problem has become the focus of microarray data analysis. A gene set is a group of genes that are defined by a priori biological knowledge. Several statistical methods have been proposed to determine whether functional gene sets express differentially (enrichment and/or deletion) in variations of phenotypes. However, little attention has been given to analyzing the dependence structure among gene sets. In this study, we have proposed a novel statistical method of gene set association analysis to identify significantly associated gene sets using the coefficient of intrinsic dependence. The simulation studies show that the proposed method outperforms the conventional methods to detect general forms of association in terms of control of type I error and power. The correlation of intrinsic dependence has been applied to a breast cancer microarray dataset to quantify the un-supervised relationship between two sets of genes in the tumor and non-tumor samples. It was observed that the existence of gene-set association differed across various clinical cohorts. In addition, a supervised learning was employed to illustrate how gene sets, in signaling transduction pathways or subnetworks regulated by a set of transcription factors, can be discovered using microarray data. In conclusion, the coefficient of intrinsic dependence provides a powerful tool for detecting general types of association. Hence, it can be useful to associate gene sets using microarray expression data. Through connecting relevant gene sets, our approach has the potential to reveal underlying associations by drawing a statistically relevant network in a given population, and it can also be used to complement the conventional gene set analysis.
Keywords	Medicine ; R ; Science ; Q
Subject code	612
Language	English
Publishing date	2013-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Heart rhythm complexity analysis in patients with inferior ST-elevation myocardial infarction

Shu-Yu Tang / Hsi-Pin Ma / Chen Lin / Men-Tzung Lo / Lian-Yu Lin / Tsung-Yan Chen / Cho-Kai Wu / Jiun-Yang Chiang / Jen-Kuang Lee / Chi-Sheng Hung / Li-Yu Daisy Liu / Yu-Wei Chiu / Cheng-Hsuan Tsai / Yen-Tin Lin / Chung-Kang Peng / Yen-Hung Lin

Scientific Reports, Vol 13, Iss 1, Pp 1-

2023 Volume 11

Abstract: Abstract Heart rhythm complexity (HRC), a subtype of heart rate variability (HRV), is an important tool to investigate cardiovascular disease. In this study, we aimed to analyze serial changes in HRV and HRC metrics in patients with inferior ST-elevation ...

Abstract	Abstract Heart rhythm complexity (HRC), a subtype of heart rate variability (HRV), is an important tool to investigate cardiovascular disease. In this study, we aimed to analyze serial changes in HRV and HRC metrics in patients with inferior ST-elevation myocardial infarction (STEMI) within 1 year postinfarct and explore the association between HRC and postinfarct left ventricular (LV) systolic impairment. We prospectively enrolled 33 inferior STEMI patients and 74 control subjects and analyzed traditional linear HRV and HRC metrics in both groups, including detrended fluctuation analysis (DFA) and multiscale entropy (MSE). We also analyzed follow-up postinfarct echocardiography for 1 year. The STEMI group had significantly lower standard deviation of RR interval (SDNN), and DFAα2 within 7 days postinfarct (acute stage) comparing to control subjects. LF power was consistently higher in STEMI group during follow up. The MSE scale 5 was higher at acute stage comparing to control subjects and had a trend of decrease during 1-year postinfarct. The MSE area under scale 1–5 showed persistently lower than control subjects and progressively decreased during 1-year postinfarct. To predict long-term postinfarct LV systolic impairment, the slope between MSE scale 1 to 5 (slope 1–5) had the best predictive value. MSE slope 1–5 also increased the predictive ability of the linear HRV metrics in both the net reclassification index and integrated discrimination index models. In conclusion, HRC and LV contractility decreased 1 year postinfarct in inferior STEMI patients, and MSE slope 1–5 was a good predictor of postinfarct LV systolic impairment.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2023-11-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The emergence and successful elimination of SARS-CoV-2 dominant strains with increasing epidemic potential in Taiwan’s 2021 outbreak

Chin-Rur Yang / Sui-Yuan Chang / Yu-Nong Gong / Chung-Guei Huang / Tsung-Hua Tung / Wei Liu / Ta-Chien Chan / Kuo-Sheng Hung / Hung-Sheng Shang / Jih-Jin Tsai / Chuan-Liang Kao / Hui-Lin Wu / Li-Yu Daisy Liu / Wan-Yu Lin / Yi-Chin Fan / Chwan-Chuen King / Chia-Chi Ku

Heliyon, Vol 9, Iss 12, Pp e22436- (2023)

2023

Abstract: Taiwan’s experience with severe acute respiratory syndrome coronavirus (SARS-CoV) in 2003 guided its development of strategies to defend against SARS-CoV-2 in 2020, which enabled the successful control of Coronavirus disease 2019 (COVID-19) cases from ... ...

Abstract	Taiwan’s experience with severe acute respiratory syndrome coronavirus (SARS-CoV) in 2003 guided its development of strategies to defend against SARS-CoV-2 in 2020, which enabled the successful control of Coronavirus disease 2019 (COVID-19) cases from 2020 through March 2021. However, in late-April 2021, the imported Alpha variant began to cause COVID-19 outbreaks at an exceptional rate in Taiwan. In this study, we aimed to determine what epidemiological conditions enabled the SARS-CoV-2 Alpha variant strains to become dominant and decline later during a surge in the outbreak. In conjunction with contact-tracing investigations, we used our bioinformatics software, CoVConvert and IniCoV, to analyze whole-genome sequences of 101 Taiwan Alpha strains. Univariate and multivariable regression analyses revealed the epidemiological factors associated with viral dominance. Univariate analysis showed the dominant Alpha strains were preferentially selected in the surge’s epicenter (p = 0.0024) through intensive human-to-human contact and maintained their dominance for 1.5 months until the Zero-COVID Policy was implemented. Multivariable regression found that the epidemic periods (p = 0.007) and epicenter (p = 0.001) were two significant factors associated with the dominant virus strains spread in the community. These dominant virus strains emerged at the outbreak’s epicenter with frequent human-to-human contact and low vaccination coverage. The Level 3 Restrictions and Zero-COVID policy successfully controlled the outbreak in the community without city lockdowns. Our integrated method can identify the epidemiological conditions for emerging dominant virus with increasing epidemiological potential and support decision makers in rapidly containing outbreaks using public health measures that target fast-spreading virus strains.
Keywords	SARS-CoV-2 ; Viral variants ; Whole-genome sequencing ; Community outbreak ; Reproduction number ; Transmission ; Science (General) ; Q1-390 ; Social sciences (General) ; H1-99
Subject code	630 ; 610
Language	English
Publishing date	2023-12-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Microarray meta-analysis to explore abiotic stress-specific gene expression patterns in Arabidopsis

Shen, Po-chih / Ai-ling Hour / Li-yu Daisy Liu

Botanical studies. 2017 Dec., v. 58, no. 1

2017

Abstract: BACKGROUND: Abiotic stresses are the major limiting factors that affect plant growth, development, yield and final quality. Deciphering the underlying mechanisms of plants’ adaptations to stresses using few datasets might overlook the different aspects ... ...

Abstract	BACKGROUND: Abiotic stresses are the major limiting factors that affect plant growth, development, yield and final quality. Deciphering the underlying mechanisms of plants’ adaptations to stresses using few datasets might overlook the different aspects of stress tolerance in plants, which might be simultaneously and consequently operated in the system. Fortunately, the accumulated microarray expression data offer an opportunity to infer abiotic stress-specific gene expression patterns through meta-analysis. In this study, we propose to combine microarray gene expression data under control, cold, drought, heat, and salt conditions and determined modules (gene sets) of genes highly associated with each other according to the observed expression data. RESULTS: By analyzing the expression variations of the Eigen genes from different conditions, we had identified two, three, and five gene modules as cold-, heat-, and salt-specific modules, respectively. Most of the cold- or heat-specific modules were differentially expressed to a particular degree in shoot samples, while most of the salt-specific modules were differentially expressed to a particular degree in root samples. A gene ontology (GO) analysis on the stress-specific modules suggested that the gene modules exclusively enriched stress-related GO terms and that different genes under the same GO terms may be alternatively disturbed in different conditions. The gene regulatory events for two genes, DREB1A and DEAR1, in the cold-specific gene module had also been validated, as evidenced through the literature search. CONCLUSIONS: Our protocols study the specificity of the gene modules that were specifically activated under a particular type of abiotic stress. The biplot can also assist to visualize the stress-specific gene modules. In conclusion, our approach has the potential to further elucidate mechanisms in plants and beneficial for future experiments design under different abiotic stresses.
Keywords	Arabidopsis ; abiotic stress ; cold ; data collection ; drought ; gene expression ; gene expression regulation ; gene ontology ; gene regulatory networks ; genes ; heat ; meta-analysis ; microarray technology ; plant growth ; stress tolerance
Language	English
Dates of publication	2017-12
Size	p. 22.
Publishing place	Springer Berlin Heidelberg
Document type	Article
ZDB-ID	2432110-2
ISSN	1999-3110 ; 1817-406X
ISSN (online)	1999-3110
ISSN	1817-406X
DOI	10.1186/s40529-017-0176-8
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Genome-Wide Survey of Ds Exonization to Enrich Transcriptomes and Proteomes in Plants

Li-yu Daisy Liu / Yuh-Chyang Charng

Evolutionary Bioinformatics, Vol 2012, Iss 8, Pp 575-

2012 Volume 587

Keywords	Biology (General) ; QH301-705.5
Language	English
Publishing date	2012-10-01T00:00:00Z
Publisher	SAGE Publishing
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Analysis of New Functional Profiles of Protein Isoforms Yielded by Ds Exonization in Rice

Yuh-Chyang Charng / Ting-Ying Chien / Li-yu Daisy Liu

Evolutionary Bioinformatics, Vol 2013, Iss 9, Pp 417-

2013 Volume 427

Keywords	Biology (General) ; QH301-705.5
Language	English
Publishing date	2013-10-01T00:00:00Z
Publisher	SAGE Publishing
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The association between heart rhythm complexity and the severity of abdominal aorta calcification in peritoneal dialysis patients

Cheng-Hsuan Tsai / Chen Lin / Yi-Heng Ho / Men-Tzung Lo / Li-Yu Daisy Liu / Chih-Ting Lin / Jenq-Wen Huang / Chung-Kang Peng / Yen-Hung Lin

Scientific Reports, Vol 8, Iss 1, Pp 1-

2018 Volume 10

Abstract: Abstract Abdominal aorta calcification (AAC) has been associated with clinical outcomes in peritoneal dialysis (PD) patients. Heart rhythm complexity analysis has been shown to be a promising tool to predict outcomes in patients with cardiovascular ... ...

Abstract	Abstract Abdominal aorta calcification (AAC) has been associated with clinical outcomes in peritoneal dialysis (PD) patients. Heart rhythm complexity analysis has been shown to be a promising tool to predict outcomes in patients with cardiovascular disease. In this study, we aimed to analyze the association between heart rhythm complexity and AAC in PD patients. We prospectively analyzed 133 PD patients. Heart rhythm complexity including detrended fluctuation analysis and multiscale entropy was performed. In linear analysis, the patients in the higher AAC group (AAC ≥15%) had a significantly lower standard deviation of normal RR intervals, very low frequency, low frequency, high frequency and low/high frequency ratio. In non-linear analysis, DFAα1, slope 1–5, scale 5 and area 6–20 were significantly lower in the patients with higher AAC. Receiver operating characteristic curve analysis showed that DFAα1 had the greatest discriminatory power to differentiate these two groups. Multivariate logistic regression analysis showed that DFAα1 and HbA1c were significantly associated with higher AAC ratio. Adding DFAα1 significantly improved the discriminatory power of the linear parameters in both net reclassification improvement and integrated discrimination improvement models. In conclusion, DFAα1 is highly associated with AAC and a potential cardiovascular marker in PD patients.
Keywords	Medicine ; R ; Science ; Q
Subject code	610
Language	English
Publishing date	2018-10-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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