BMC Springer Open Data

Permanent URI for this collectionhttp://rportal.lib.ntnu.edu.tw/handle/20.500.12235/45016

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    The immediate effects of the severe acute respiratory syndrome (SARS) epidemic on childbirth in Taiwan
    (2005) Lee, Cheng-Hua; Huang, Nicole; Chang, Hong-Jen; Hsu, Yea-Jen; Wang, Mei-Chu; Chou, Yiing-Jenq
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    A search for a correlation between time change in transfer functions and seismic energy release in northern Taiwan
    (2006-09-16) Chen, Kuang-Jung; Chiu, Bonbbon; Lin, Cheng-Horng
    Abstract The geomagnetic data of the Lunping Geomagnetic Observatory from 1988 to 2000 are utilized for computing daily geomagnetic transfer functions. The method of analysis is based on the power spectrum analysis developed by Everett and Hyndman. Monthly means are statistically obtained from these daily values of transfer functions. In order to compare these time changes with seismic activity (seismicity), the earthquakes occurring within 150 km from Lunping, with a magnitude ML greater than 4.0, are located. The related energy releases by those earthquakes, summed month by month, are correlated to the transfer functions. After removing the seasonal effect, we find that the time changes of magnitude of Au and Bu (real parts of the transfer function) for frequencies of 2, 3, 4, and 6 cycles/hour seem to be strongly related to the energy release within the whole study period. Two significant precursors were found from the A and B values, 40 and 20 months before high seismicities, respectively.
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    A Learning State-Space Model for Image Retrieval
    (2007) Chiang, Cheng-Chieh; Hung, Yi-Ping; Lee, Greg C
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    Content-Based Object Movie Retrieval and Relevance Feedbacks
    (2007) Chiang, Cheng-Chieh; Chan, Li-Wei; Hung, Yi-Ping; Lee, Greg C
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    Molecular population genetics and gene expression analysis of duplicated CBF genes of Arabidopsis thaliana
    (2008) Lin, Yen-Heng; Hwang, Shih-Ying; Hsu, Po-Yen; Chiang, Yu-Chung; Huang, Chun-Lin; Wang, Chun-Neng; Lin, Tsan-Piao
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    Spinocerebellar ataxia type 8 larger triplet expansion alters histone modification and induces RNA foci
    (2009) Chen, I-Cheng; Lin, Hsuan-Yuan; Lee, Ghin-Chueh; Kao, Shih-Huan; Chen, Chiung-Mei; Wu, Yih-Ru; Hsieh-Li, Hsiu-Mei; Su, Ming-Tsan; Lee-Chen, Guey-Jen
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    Phylogeography of the Alcippe morrisonia (Aves: Timaliidae): long population history beyond late Pleistocene glaciations
    (2009-06-27) Song, Gang; Qu, Yanhua; Yin, Zuohua; Li, Shouhsien; Liu, Naifa; Lei, Fumin
    Abstract Background The role of Pleistocene glacial oscillations in current biodiversity and distribution patterns varies with latitude, physical topology and population life history and has long been a topic of discussion. However, there had been little phylogeographical research in south China, where the geophysical complexity is associated with great biodiversity. A bird endemic in Southeast Asia, the Grey-cheeked Fulvetta, Alcippe morrisonia, has been reported to show deep genetic divergences among its seven subspecies. In the present study, we investigated the phylogeography of A. morrisonia to explore its population structure and evolutionary history, in order to gain insight into the effect of geological events on the speciation and diversity of birds endemic in south China. Results Mitochondrial genes cytochrome b (Cytb) and cytochrome c oxidase I (COI) were represented by 1236 nucleotide sites from 151 individuals from 29 localities. Phylogenetic analysis showed seven monophyletic clades congruent with the geographically separated groups, which were identified as major sources of molecular variance (90.92%) by AMOVA. TCS analysis revealed four disconnected networks, and that no haplotype was shared among the geographical groups. The common ancestor of these populations was dated to 11.6 Mya and several divergence events were estimated along the population evolutionary history. Isolation by distance was inferred by NCPA to be responsible for the current intra-population genetic pattern and gene flow among geographical groups was interrupted. A late Pleistocene demographic expansion was detected in the eastern geographical groups, while the expansion time (0.2–0.4 Mya) was earlier than the Last Glacial Maximum. Conclusion It is proposed that the complicated topology preserves high genetic diversity and ancient lineages for geographical groups of A. morrisonia in China mainland and its two major islands, and restricts gene exchange during climate oscillations. Isolation by distance seems to be an important factor of genetic structure formation within geographical populations. Although glacial influence to population fluctuation was observed in late Pleistocene, it seems that populations in eastern China were more susceptible to climate change, and all geographical groups were growing stably through the Last Glacial Maximum. Coalescence analysis suggested that the ancestor of A. morrisonia might be traced back to the late Miocene, and the current phylogeographical structure of A. morrisonia is more likely to be attributable to a series geological events than to Pleistocene glacial cycles.
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    Paraphyly of organelle DNAs in Cycas Sect. Asiorientales due to ancient ancestral polymorphisms
    (2009-07-10) Chiang, Yu-Chung; Hung, Kuo-Hsiang; Moore, Shann-Jye; Ge, Xue-Jun; Huang, Shong; Hsu, Tsai-Wen; Schaal, Barbara A; Chiang, TY
    Abstract Background This study addresses the apportionment of genetic diversity between Cycas revoluta and C. taitungensis, species that constitute the section Asiorientales and represent a unique, basal lineage of the Laurasian genus Cycas. Fossil evidence indicates divergence of the section from the rest of Cycas at least 30 million years ago. Geographically, C. taitungensis is limited to Taiwan whereas C. revoluta is found in the Ryukyu Archipelago and on mainland China. Results The phylogenies of ribosomal ITS region of mtDNA and the intergenic spacer between atpB and rbcL genes of cpDNA were reconstructed. Phylogenetic analyses revealed paraphyly of both loci in the two species and also in the section Asiorientales. The lack of reciprocal monophyly between these long isolated sections is likely due to persistent shared ancestral polymorphisms. Molecular dating estimated that mt- and cp DNA lineages coalesced to the most recent common ancestors (TMRCA) about 327 (mt) and 204 MYA (cp), corresponding with the divergence of cycad sections in the Mesozoic. Conclusion Fates of newly derived mutations of cycads follow Klopfstein et al.'s surfing model where the majority of new mutations do not spread geographically and remain at low frequencies or are eventually lost by genetic drift. Only successful 'surfing mutations' reach very high frequencies and occupy a large portion of a species range. These mutations exist as dominant cytotypes across populations and species. Geographical subdivision is lacking in both species, even though recurrent gene flow by both pollen and seed is severely limited. In total, the contrasting levels between historical and ongoing gene flow, large population sizes, a long lifespan, and slow mutation rates in both organelle DNAs have all likely contributed to the unusually long duration of paraphyly in cycads.
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    Examination of effects of GSK3β phosphorylation, β-catenin phosphorylation, and β-catenin degradation on kinetics of Wnt signaling pathway using computational method
    (2009-07-22) Sun, Ying-Chieh
    Abstract Background Recent experiments have explored effects of activities of kinases other than the well-studied GSK3β, in wnt pathway signaling, particularly at the level of β-catenin. It has also been found that the kinase PKA attenuates β-catenin degradation. However, the effects of these kinases on the level and degradation of β-catenin and the resulting downstream transcription activity remain to be clarified. Furthermore, the effect of GSK3β phosphorylation on the β-catenin level has not been examined computationally. In the present study, the effects of phosphorylation of GSK3β and of phosphorylations and degradation of β-catenin on the kinetics of the wnt signaling pathway were examined computationally. Methods The well-known computational Lee-Heinrich kinetic model of the wnt pathway was modified to include these effects. The rate laws of reactions in the modified model were solved numerically to examine these effects on β-catenin level. Results The computations showed that the β-catenin level is almost linearly proportional to the phosphorylation activity of GSK3β. The dependence of β-catenin level on the phosphorylation and degradation of free β-catenin and downstream TCF activity can be analyzed with an approximate, simple function of kinetic parameters for added reaction steps associated with effects examined, rationalizing the experimental results. Conclusion The phosphorylations of β-catenin by kinases other than GSK3β involve free unphorphorylated β-catenin rather than GSK3β-phosphorylated β-catenin*. In order to account for the observed enhancement of TCF activity, the β-catenin dephosphorylation step is essential, and the kinetic parameters of β-catenin phosphorylation and degradation need to meet a condition described in the main text. These findings should be useful for future experiments.
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    Oxidative stress promotes autophagic cell death in human neuroblastoma cells with ectopic transfer of mitochondrial PPP2R2B (Bβ2)
    (2009-12-18) Cheng, Wan-Ting; Guo, Zhi-Xuan; Lin, Chia-An; Lin, Ming-Yi; Tung, Li-Chu; Fang, Kang
    Abstract Background The multifunctional protein phosphatase 2A (PP2A) is a heterotrimeric serine/threonine protein phosphatase composed of a scaffolding, catalytic and regulatory subunits. By modifying various downstream signal transducers, the aberrant expression of the brain-targeted regulatory subunit PPP2R2B is associated with the onset of a panel of neuronal disorders. The alternatively splicing of PPP2R2B encodes two regulatory subunit isoforms that determine cellular distribution of the neuron-specific holoenzyme to mitochondria (Bβ2) and cytoplasm (Bβ1), respectively. Results Human neuroblastoma cells were transfected with PPP2R2B constructs encoding the complete sequences of Bβ2 and Bβ1, respectively. The colonies with antibiotic resistance were selected as stable cell lines. Both ectopic Bβ1 and Bβ2 clones exhibited characteristics of autophagy. To test how cells respond to reactive oxygen species generators, the cells were treated with either hydrogen peroxide or t-butyl hydroperoxide and Bβ2 clones induced cell death. Suppression of autophagy using either RNA interference of the essential autophagy gene or pharmacological inhibitor rescued cell death caused by oxidative stress. Conclusions Cells with ectopically expressed mitochondria-targeted regulatory subunit PPP2R2B of the holoenzyme PP2A were shown predisposed to autophagy and oxidative stress induced cell death that is related to apoptosis. The results promised a model for studying the mechanism and function of aberrant PPP2R2B expression in neuronal cells. The work provided a new target for understanding and prevention of neuropathogenesis.
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    Evaluation of unilateral cage-instrumented fixation for lumbar spine
    (2010) Chang, Ti-Sheng; Chang, Jia-Hao; Wang, Chien-Shiung; Chen, Hung-Yi; Cheng, Ching-Wei
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    Historical spatial range expansion and a very recent bottleneck of Cinnamomum kanehiraeHay. (Lauraceae) in Taiwan inferred from nuclear genes
    (2010-04-30) Liao, Pei-Chun; Kuo, Dai-Chang; Lin, Chia-Chia; Ho, Kuo-Chieh; Lin, Tsan-Piao; Hwang, Shih-Ying
    Abstract Background Species in the varied geographic topology of Taiwan underwent obvious demographic changes during glacial periods. Cinnamomum kanehirae has been exploited for timber and to obtain medicinal fungi for the past 100 years. Understanding anthropogenic factors influencing the demography of this species after the last glacial maximum (LGM) is critically important for the conservation of this species. Results Populations of C. kanehirae were classified into four geographic regions: northwestern (NW), west-central (WC), southwestern (SW), and southeastern (SE). In total, 113 individuals from 19 localities were sampled, and variations in the chalcone synthase gene (Chs) intron and leafy (Lfy) intron-2 sequences of nuclear DNA were examined in order to assess phylogeographic patterns, the timescales of demographic and evolutionary events, and recent anthropogenic effects. In total, 210 Chs and 170 Lfy sequences, which respectively constituted 36 and 35 haplotypes, were used for the analyses. Estimates of the migration rate (M) through time revealed a pattern of frequent gene flow during previous and the present interglacials. The isolation-by-distance test showed that there generally was no significant correlation between genetic and geographic distances. The level of among-region genetic differentiation was significant when comparing eastern to western populations. However, no significant among-region genetic differentiation was found in comparisons among the four geographic regions. Moreover, essentially no genetic structuring was found for the three regions west of the CMR. A fit of spatial range expansion was found for pooled and regional samples according to the non-significant values of the sum of squared deviations. Using the Bayesian skyline plot (BSP) method, a recent bottleneck after the LGM expansion was detected in both regional and pooled samples. Conclusions Common haplotype distributions among geographic regions and the relatively shallow genetic structuring displayed are the result of historical gene flows. Southward dispersals in an earlier time frame from the NW region and in a later time frame from the SE region were inferred. The BSP analysis suggested a postglacial expansion event. Recent trends, however, refer to a bottleneck due to human interventions observed for both pooled and regional C. kanehirae samples.
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    Association of TNF-α gene with spontaneous deep intracerebral hemorrhage in the Taiwan population: a case control study
    (2010-06-10) Chen, Yi-Chun; Hu, Fen-Ju; Chen, Phoebe; Wu, Yih-Ru; Wu, Hsiu-Chuan; Chen, Sien-Tsong; Lee-Chen, Guey-Jen; Chen, Chiung-Mei
    Abstract Background Genetic factors may play a role in susceptibility to spontaneous deep intracerebral hemorrhage (SDICH). Previous studies have shown that TNF-α gene variation was associated with risks of subarachnoid hemorrhage in multiple ethnicities. The present case-control study tested the hypothesis that genetic variations of the TNF-α gene may affect the risk of Taiwanese SDICH. We examined the association of SDICH risks with four single nucleotide polymorphisms (SNPs) within the TNF-α gene promoter, namely T-1031C, C-863A, C-857T, and G-308A. Methods Genotyping was determined by PCR-based restriction and electrophoresis assay for 260 SDICH patients and 368 controls. Associations were tested by logistic regression or general linear models with adjusting for multiple covariables in each gender group, and then in combined. Multiplicative terms of gender and each of the four SNPs were applied to detect the interaction effects on SDICH risks. To account for the multiple testing, permutation testing of 1,000 replicates was performed for empirical estimates. Results In an additive model, SDICH risks were positively associated with the minor alleles -1031C and -308A in men (OR = 1.9, 95% CI 1.1 to 3.4, p = 0.03 and OR = 2.6, 95% CI 1.3 to 5.3, p = 0.005, respectively) but inversely associated with -863A in females (OR = 0.5, 95% CI 0.2 to 0.9, p = 0.03). There were significant interaction effects between gender and SNP on SDICH risks regarding SNPs T-1031C, C-863A, and G-308A (p = 0.005, 0.005, and 0.007, respectively). Hemorrhage size was inversely associated with -857T in males (p = 0.04). Conclusions In the Taiwan population, the associations of genetic variations in the TNF-α gene promoter with SDICH risks are gender-dependent.
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    A single sequence context cannot satisfy all non-AUG initiator codons in yeast†
    (2010-07-09) Chang, Chia-Pei; Chen, Shun-Jia; Lin, Chen-Huan; Wang, Tzu-Ling; Wang, Chien-Chia
    Abstract Background Previous studies in Saccharomyces cerevisiae showed that ALA1 (encoding alanyl-tRNA synthetase) and GRS1 (encoding glycyl-tRNA synthetase) respectively use ACG and TTG as their alternative translation initiator codons. To explore if any other non-ATG triplets can act as initiator codons in yeast, ALA1 was used as a reporter for screening. Results We show herein that except for AAG and AGG, all triplets that differ from ATG by a single nucleotide were able to serve as initiator codons in ALA1. Among these initiator codons, TTG, CTG, ACG, and ATT had ~50% initiating activities relative to that of ATG, while GTG, ATA, and ATC had ~20% initiating activities relative to that of ATG. Unexpectedly, these non-AUG initiator codons exhibited different preferences toward various sequence contexts. In particular, GTG was one of the most efficient non-ATG initiator codons, while ATA was essentially inactive in the context of GRS1. Conclusion This finding indicates that a sequence context that is favorable for a given non-ATG initiator codon might not be as favorable for another.
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    Fairness analysis of throughput and delay in WLAN environments with channel diversities
    (2011) Wang, Chiapin; Lo, Hao-Kai; Fang, Shih-Hau
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    Performance evaluation on an air-cooled heat exchanger for alumina nanofluid under laminar flow
    (2011) Teng, Tun-Ping; Hung, Yi-Hsuan; Teng, Tun-Chien; Chen, Jyun-Hong
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