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1.  KEGGscape: a Cytoscape app for pathway data integration 
F1000Research  2014;3:144.
In this paper, we present KEGGscape a pathway data integration and visualization app for Cytoscape ( KEGG is a comprehensive public biological database that contains large collection of human curated pathways. KEGGscape utilizes the database to reproduce the corresponding hand-drawn pathway diagrams with as much detail as possible in Cytoscape. Further, it allows users to import pathway data sets to visualize biologist-friendly diagrams using the Cytoscape core visualization function (Visual Style) and the ability to perform pathway analysis with a variety of Cytoscape apps. From the analyzed data, users can create complex and interactive visualizations which cannot be done in the KEGG PATHWAY web application. Experimental data with Affymetrix E. coli chips are used as an example to demonstrate how users can integrate pathways, annotations, and experimental data sets to create complex visualizations that clarify biological systems using KEGGscape and other Cytoscape apps.
PMCID: PMC4141640  PMID: 25177485
2.  Salvage therapy using FLT3 inhibitors may improve long-term outcome of relapsed or refractory AML in patients with FLT3-ITD 
British journal of haematology  2013;161(5):659-666.
To determine the long-term efficacy of FLT3 inhibitors (FLT3i) in the salvage setting for relapsed and refractory (rel/ref) acute myeloid leukemia (AML) with FLT3 internal tandem duplication (AML FLT3-ITD), we conducted a retrospective study of 120 patients with rel/ref AML FLT3-ITD who received salvage therapy with either FLT3i-containing regimen (FLT3i group, N = 45) or conventional cytotoxic regimen (conventional group, N = 75). The median overall survival (OS) after the first salvage in the FLT3i group was 6.9 vs. 4.6 months in the conventional group (P = 0.17). The OS was better in the FLT3i group among patients with initial complete remission (CR) duration ≤12 months or with primary refractory disease (6.9 vs. 3.7 months; P < 0.01). The OS was better when FLT3i was combined with cytotoxic agents versus monotherapy (17 vs. 4.8 months; P = 0.017). Multivariate analysis revealed that the use of FLT3i was an independent predictor of OS (hazard ratio 0.58; 95% confidence interval, 0.38–0.88). Incorporating FLT3i into salvage strategies may improve long-term outcome of patients with AML FLT3-ITD. Prospective studies to validate this conclusion are warranted.
PMCID: PMC4068703  PMID: 23530930
AML; FLT3 inhibitors; FLT3-ITD
3.  Emerging patterns of somatic mutations in cancer 
Nature reviews. Genetics  2013;14(10):703-718.
The advance in technological tools for massively parallel, high-throughput sequencing of DNA has enabled the comprehensive characterization of somatic mutations in large number of tumor samples. Here, we review recent cancer genomic studies that have assembled emerging views of the landscapes of somatic mutations through deep sequencing analyses of the coding exomes and whole genomes in various cancer types. We discuss the comparative genomics of different cancers, including mutation rates, spectrums, and roles of environmental insults that influence these processes. We highlight the developing statistical approaches used to identify significantly mutated genes, and discuss the emerging biological and clinical insights from such analyses as well as the challenges ahead translating these genomic data into clinical impacts.
PMCID: PMC4014352  PMID: 24022702
4.  High Glucose Level Promotes Migration Behavior of Breast Cancer Cells through Zinc and Its Transporters 
PLoS ONE  2014;9(2):e90136.
The diabetes patients have been associated with an increased risk of mortality by breast cancer and there are difference between the breast cancer patients with diabetes, and their nondiabetic counterparts in the regimen choice and effects of breast cancer treatment. However, the pathophysiological relationships of diabetes and breast cancer have not yet been elucidated in detail. In this study, we investigate the breast cancer cell line, MCF-7 motility, which linked to invasion and metastasis, in high glucose level corresponding to hyperglycemia and the role of Zn and its transporter.
Methodology/Principal findings
We demonstrated the significant motility of MCF-7 cultured in hyperglycemic level (25 mM glucose) in comparison to normal physiological glucose level (5.5 mM glucose). The other hand, the osmotic control medium, 5.5 mM glucose with 19.5 mM mannitol or fructose had no effect on migratory, suggesting that high glucose level promotes the migration of MCF-7. Moreover, the activity of intracellular Zn2+ uptake significantly increased in high glucose-treated cells in comparison to 5.5 mM glucose, and the mRNA expression of zinc transporters, ZIP6 and ZIP10, was upregulated in 25 mM glucose-treated cells. The deficiency of ZIP6 or ZIP10 and intracellular Zn2+ significantly inhibited the high migration activity in 25 mM glucose medium, indicating that Zn2+ transported via ZIP6 and ZIP10 play an essential role in the promotion of cell motility by high glucose stimulation.
Zinc and its transporters, ZIP6 and ZIP10, are required for the motility stimulated with high glucose level. These findings provide the first evidence proposing the novel strategies for the diagnosis and therapy of breast cancer with hyperglycemia.
PMCID: PMC3938647  PMID: 24587242
5.  Acquisition of Cytogenetic Abnormalities in Patients with IPSS defined Lower-Risk Myelodysplastic Syndrome Is Associated with Poor Prognosis and Transformation to Acute Myelogenous Leukemia 
American journal of hematology  2013;88(10):831-837.
We hypothesized that the dynamic acquisition of cytogenetic abnormalities (ACA) during the follow up of myelodysplastic syndromes (MDS) could be associated with poor prognosis. We conducted a retrospective analysis of 365 patients with IPSS low or intermediate-1 risk MDS who had at least two consecutive cytogenetic analyses during the follow up. Acquisition of cytogenetic abnormalities was detected in 107 patients (29%). The most frequent alteration involved chromosome 7 in 21% of ACA cases. Median transformation-free and overall survival for patients with and without ACA were 13 vs. 52 months (P =0.01) and 17 vs. 62 months (P =0.01), respectively. By fitting ACA as a time-dependent covariate, multivariate Cox regression analysis showed that patients with ACA had increased risk of transformation (HR=1.40; P = 0.03) or death (HR=1.45; P = 0.02). Notably, female patients with therapy-related MDS (t-MDS) had an increased risk of developing ACA (OR= 5.26; P<0.0001), although subgroup analysis showed that prognostic impact of ACA was not evident in t-MDS. In conclusion, ACA occurs in close to one third of patients with IPSS defined lower risk MDS, more common among patients with t-MDS, but has a significant prognostic impact on de novo MDS.
PMCID: PMC3923606  PMID: 23760779
6.  Flexible and dynamic nucleosome fiber in living mammalian cells 
Nucleus  2013;4(5):349-356.
Genomic DNA is organized three dimensionally within cells as chromatin and is searched and read by various proteins by an unknown mechanism; this mediates diverse cell functions. Recently, several pieces of evidence, including our cryomicroscopy and synchrotron X-ray scattering analyses, have demonstrated that chromatin consists of irregularly folded nucleosome fibers without a 30-nm chromatin fiber (i.e., a polymer melt-like structure). This melt-like structure implies a less physically constrained and locally more dynamic state, which may be crucial for protein factors to scan genomic DNA. Using a combined approach of fluorescence correlation spectroscopy, Monte Carlo computer simulations, and single nucleosome imaging, we demonstrated the flexible and dynamic nature of the nucleosome fiber in living mammalian cells. We observed local nucleosome fluctuation (~50 nm movement per 30 ms) caused by Brownian motion. Our in vivo-in silico results suggest that local nucleosome dynamics facilitate chromatin accessibility and play a critical role in the scanning of genome information.
PMCID: PMC3899123  PMID: 23945462
nucleosome fiber (10-nm fiber); 30-nm chromatin fiber; fluorescence correlation spectroscopy (FCS); Monte Carlo computer simulations; single nucleosome imaging; nucleosome fluctuation; polymer-melt; irregular folding; interphase chromatin; mitotic chromosomes; transcriptional regulation
8.  Graphical representation of quality indicators based on medical service ontology 
SpringerPlus  2013;2:274.
For recent years, it has grown importance to evaluate medical service qualities of medical staffs and/or hospitals by using quality indicators. This paper introduces a representation system QI-RS of quality indicators. By using QI-RS, one can define quality indicators that satisfy understandability and formality, where “understandability” means that one can understand the calculation formula of a quality indicator easily and correctly, while “formality” means that the formula can be calculated to obtain the values of the indicator based on databases in a coherent manner.
PMCID: PMC3710578  PMID: 23888265
Quality indicator; Medical service; Quality assessment; Ontology; Graph representation
9.  Correction: Elevational Patterns in Archaeal Diversity on Mt. Fuji 
PLoS ONE  2013;8(6):10.1371/annotation/405cf97b-8e07-492d-aa4f-3ff0c2545292.
PMCID: PMC3731439
10.  How the timberline formed: altitudinal changes in stand structure and dynamics around the timberline in central Japan 
Annals of Botany  2012;109(6):1165-1174.
Background and Aims
Altitudinal timberlines are thought to move upward by global warming, a crucial topic in ecology. Tall tree species (the conifer Abies mariesii and the deciduous broad-leaved Betula ermanii) dominate the sub-alpine zone between 1600 and 2500 m a.s.l., the timberline, on Mount Norikura in central Japan. Dwarf pine Pinus pumila dominates above the timberline to near the summit (3026 m a.s.l.). This study evaluated how the timberline formed on Mount Norikura by examining altitudinal changes in stand structure and dynamics around the timberline.
One hundred and twenty-five plots of 10 m × 10 m were established around the timberline (2350–2600 m a.s.l.). Trunk diameter growth rate during 6 years was examined for A. mariesii, B. ermanii and P. pumila. Mortality during this period and mechanical damage scars on the trunks and branches due to strong wind and snow were examined for A. mariesii only.
Key Results
The density, maximum trunk height and diameter of A. mariesii in plots decreased with altitude. The maximum trunk height of B. ermanii decreased with altitude, but density and maximum trunk diameter did not decrease. In contrast, the density of P. pumila abruptly increased from around the timberline. A strong negative correlation was found between the densities of P. pumila and tall tree species, indicating their interspecific competition. Trunk diameter growth rates of A. mariesii and B. ermanii did not decrease with altitude, suggesting that these two tall tree species can grow at the timberline. The ratio of trees with mechanical damage scars increased with altitude for A. mariesii, a tendency more conspicuous for larger trees. The mortality of larger A. mariesii was also greater at higher altitude. Tall tree species may not increase their trunk height and survive around the timberline because of mechanical damage.
This study suggests that the altitudinal location of the timberline is mainly affected by mechanical damage due to strong wind and snow rather than by growth limitation due to low temperature. Therefore, the timberline would not move upward even under global warming if these growth and mortality characteristics do not change for a long time.
PMCID: PMC3336954  PMID: 22451598
Abies mariesii; Betula ermanii; climate change; disturbance; global warming; Pinus pumila; timberline
11.  A Quantitative Model of ERK MAP Kinase Phosphorylation in Crowded Media 
Scientific Reports  2013;3:1541.
Cytoplasm contains a large number of macromolecules at extremely high densities. How this striking nature of intracellular milieu called macromolecular crowding affects intracellular signaling remains uncharacterized. Here, we examined the effect of macromolecular crowding on ERK MAPK phosphorylation by MEK MAPKK. Addition of polyethylene glycol-6000 (PEG-6000) as a crowder to mimic intracellular environments, elicited a biphasic response to the overall ERK phosphorylation rate. Furthermore, probability of processive phosphorylation (processivity) of tyrosine and threonine residues within the activation loop on ERK increased non-linearly for increasing PEG-6000 concentration. Based on the experimental data, we developed for the first time a mathematical model integrating all of the effects of thermodynamic activity, viscosity, and processivity in crowded media, and found that ERK phosphorylation is transition-state-limited reaction. The mathematical model allows accurate estimation of the effects of macromolecular crowding on a wide range of reaction kinetics, from transition-state-limited to diffusion-limited reactions.
PMCID: PMC3607838  PMID: 23528948
12.  Transcutaneous Immunization System Using a Hydrotropic Formulation Induces a Potent Antigen-Specific Antibody Response 
PLoS ONE  2012;7(10):e47980.
Transcutaneous immunization (TCI) is a novel vaccination strategy, which is expected to have therapeutic applications. However, to develop effective TCI systems, a simple, non-invasive and safe transdermal formulation is required. This study developed a novel TCI system utilizing the co-administration of a liposoluble absorption enhancer, propylene glycol monocaprylate (PGMC) and hydrosoluble protein antigen without pretreatment of any typical adjuvants and disruption of the skin. Novel transdermal formulations were also prepared with sodium salicylate (NaSal) as a hydrotropic agent to improve the solubility of poorly water-soluble substances.
Methodology/Principal Findings
The TCI system, which used a transdermal formulation containing hen lysozyme (HEL) and PGMC, solubilized with NaSal, resulted in a substantial HEL-specific antibody response in an HEL dose-dependent manner even in the absence of potent adjuvants, such as cholera toxin (CT). We also investigated whether NaSal activates antigen-presenting cells in vitro to clarify the mechanisms of antibody production by the hydrotropic formulation. NaSal enhanced the expression of MHC class II molecules and increased the production of IL-12 and TNF-α in dendritic cells, which were stimulated by lipopolysaccharide in vitro, indicating that NaSal had an effective adjuvant-like property. Moreover, the use of NaSal in the TCI system did not induce an HEL-specific, IgE-dependent anaphylactic reaction.
Our TCI system using a hydrotropic formulation effectively and safely induced the intended immune response, and this system thus represents a new advantageous method that will result in improved TCI strategies.
PMCID: PMC3480500  PMID: 23110149
13.  Elevational Patterns in Archaeal Diversity on Mt. Fuji 
PLoS ONE  2012;7(9):e44494.
Little is known of how archaeal diversity and community ecology behaves along elevational gradients. We chose to study Mount Fuji of Japan as a geologically and topographically uniform mountain system, with a wide range of elevational zones. PCR-amplified soil DNA for the archaeal 16 S rRNA gene was pyrosequenced and taxonomically classified against EzTaxon-e archaeal database. At a bootstrap cut-off of 80%, most of the archaeal sequences were classified into phylum Thaumarchaeota (96%) and Euryarchaeota (3.9%), with no sequences classified into other phyla. Archaeal OTU richness and diversity on Fuji showed a pronounced ‘peak’ in the mid-elevations, around 1500 masl, within the boreal forest zone, compared to the temperate forest zone below and the alpine fell-field and desert zones above. Diversity decreased towards higher elevations followed by a subtle increase at the summit, mainly due to an increase in the relative abundance of the group I.1b of Thaumarchaeota. Archaeal diversity showed a strong positive correlation with soil NH4+, K and NO3−. Archaeal diversity does not parallel plant diversity, although it does roughly parallel bacterial diversity. Ecological hypotheses to explain the mid diversity bulge on Fuji include intermediate disturbance effects, and the result of mid elevations combining a mosaic of upper and lower slope environments. Our findings show clearly that archaeal soil communities are highly responsive to soil environmental gradients, in terms of both their diversity and community composition. Distinct communities of archaea specific to each elevational zone suggest that many archaea may be quite finely niche-adapted within the range of soil environments. A further interesting finding is the presence of a mesophilic component of archaea at high altitudes on a mountain that is not volcanically active. This emphasizes the importance of microclimate – in this case solar heating of the black volcanic ash surface – for the ecology of soil archaea.
PMCID: PMC3435261  PMID: 22970233
14.  Assessment of EEG dynamical complexity in Alzheimer’s disease using multiscale entropy 
Multiscale entropy (MSE) is a recently proposed entropy-based index of physiological complexity, evaluating signals at multiple temporal scales. To test this method as an aid to elucidating the pathophysiology of Alzheimer’s disease (AD), we examined MSE in resting state EEG activity in comparison with traditional EEG analysis.
We recorded EEG in medication-free 15 presenile AD patients and 18 age- and sex-matched healthy control (HC) subjects. MSE was calculated for continuous 60-second epochs for each group, concurrently with power analysis.
The MSE results from smaller and larger scales were associated with higher and lower frequencies of relative power, respectively. Group analysis demonstrated that the AD group had less complexity at smaller scales in more frontal areas, consistent with previous findings. In contrast, higher complexity at larger scales was observed across brain areas in AD group and this higher complexity was significantly correlated with cognitive decline.
MSE measures identified an abnormal complexity profile across different temporal scales and their relation to the severity of AD.
These findings indicate that entropy-based analytic methods with applied at temporal scales may serve as a complementary approach for characterizing and understanding abnormal cortical dynamics in AD.
PMCID: PMC2914820  PMID: 20400371
Alzheimer’s disease (AD); Electroencephalogram (EEG); Complexity; Multiscale entropy (MSE); Mini-Mental State Examination (MMSE); Power analysis
15.  Experimental Adjustment on Drug Interactions through Intestinal CYP3A Activity in Rat: Impacts of Kampo Medicines Repeat Administered 
To provide the information that is necessary for making the proper use of kampo medicines, we have proposed the adequate methodology focused on the following issues: (i) kampo medicines emphasize the effects produced by the combination of herbal drugs rather than the individual effect of any single herb and (ii) Intestinal CYP3A has become a key factor for the bioavailability of orally administrated drugs. In the present study, we investigated both the in vivo and in vitro effects of Saireito and Hochuekkito (kampo formulas) on CYP3A activities. From our study, oral pre-treatment with Saireito or Hochuekkito did not affect the pharmacokinetics of nifedipine after intravenous administration to rats. When nifedipine was administered to rat intrajejunum, a significant decrease of AUC was showed by pre-treatment with both kampo formulas. Saireito pre-treatment led to 80% decrease in Cmax of nifedipine. Saireito caused significant increases in both protein expression and metabolic activity of CYP3A in intestinal microsome, whereas it had no effect on CYP3A in hepatic microsome. Our result also showed that this affect of Saireito can be gone by wash-out with 1 week. These findings demonstrated that Saireito may induce CYP3A activity of intestine but not of liver in rats. When resources for research are limited, well-designed scientific studies except clinical trials also have many advantages.
PMCID: PMC3139423  PMID: 19884115
16.  Antipsychotics reverse abnormal EEG complexity in drug-naïve schizophrenia: A multiscale entropy analysis 
NeuroImage  2010;51(1):173-182.
Multiscale entropy (MSE) analysis is a novel entropy-based approach for measuring dynamical complexity in physiological systems over a range of temporal scales. To evaluate this analytic approach as an aid to elucidating the pathophysiologic mechanisms in schizophrenia, we examined MSE in EEG activity in drug-naïve schizophrenia subjects pre- and post-treatment with antipsychotics in comparison with traditional EEG analysis. We recorded eyes-closed resting state EEG from frontal, temporal, parietal and occipital regions in drug-naïve 22 schizophrenia and 24 age-matched healthy control subjects. Fifteen patients were re-evaluated within 2–8 weeks after the initiation of antipsychotic treatment. For each participant, MSE was calculated on one continuous 60 second epoch for each experimental session. Schizophrenia subjects showed significantly higher complexity at higher time scales (lower frequencies), than that of healthy controls in fronto-centro-temporal, but not in parieto-occipital regions. Post-treatment, this higher complexity decreased to healthy control subject levels selectively in fronto-central regions, while the increased complexity in temporal sites remained higher. Comparative power analysis identified spectral slowing in frontal regions in pre-treatment schizophrenia subjects, consistent with previous findings, whereas no antipsychotic treatment effect was observed. In summary, multiscale entropy measures identified abnormal dynamical EEG signal complexity in anterior brain areas in schizophrenia that normalized selectively in fronto-central areas with antipsychotic treatment. These findings show that entropy-based analytic methods may serve as a novel approach for characterizing and understanding abnormal cortical dynamics in schizophrenia, and elucidating the therapeutic mechanisms of antipsychotics.
PMCID: PMC2849166  PMID: 20149880
Drug-naïve schizophrenia; Electroencephalography (EEG); Complexity; Multiscale entropy (MSE); Antipsychotics
17.  Curdione Plays an Important Role in the Inhibitory Effect of Curcuma aromatica on CYP3A4 in Caco-2 Cells 
Curcuma aromatica is a plant belonging to genus Curcuma of family Zingiberaceae and is widely used as supplements in Japan. Rhizomes of C. aromatica have curcumin as a major yellow pigment and curdione as a main ingredient of essential oils. In this study, we investigated the affect of C. aromatica on CYP3A4 using 1α,25-(OH)2-D3-treated Caco-2 clone cells. Caco-2 cells were treated with methanol extract (0.1 mg ml−1), its hexane soluble fraction (0.1 mg ml−1), curcumin (4 μM) and curdione (20 μM) for 72 hours. Nifedipine was used as a substrate of CYP3A4. Methanol extract, hexane fraction and curdione inhibited the formation of oxidized nifedipine by 50–70%, and curcumin showed no effect. The IC50s of methanol extract, hexane fraction and curdione to oxidized nifedipine formation were 21, 14 and 3.9 μg ml−1 (16.9 μM), respectively. The content of curdione in methanol extract was 11.4%. Moreover, all of methanol extract, hexane fraction and curdione decreased CYP3A4 protein expression but had no affect on CYP3A4 mRNA expression. Our results showed that these drugs further decreased the CYP3A4 protein expression level after the protein synthesis was inhibited by cychroheximide. These findings suggest that curdione plays an important role in the CYP3A4 inhibitory activity of C. aromatica and curdione might inhibit the activity by accelerating the degradation of CYP3A4.
PMCID: PMC3137788  PMID: 21785639
18.  Age-related variation in EEG complexity to photic stimulation: A multiscale entropy analysis 
This study was intended to examine variations in electroencephalographic (EEG) complexity in response to photic stimulation (PS) during aging to test the hypothesis that the aging process reduces physiologic complexity and functional responsiveness.
Multiscale entropy (MSE), an estimate of time-series signal complexity associated with long-range temporal correlation, is used as a recently proposed method for quantifying EEG complexity with multiple coarse-grained sequences. We recorded EEG in 13 healthy elderly subjects and 12 healthy young subjects during pre-PS and post-PS conditions and estimated their respective MSE values.
For the pre-PS condition, no significant complexity difference was found between the groups. However, a significant MSE change (complexity increase) was found post-PS only in young subjects, thereby revealing a power-law scaling property, which means long-range temporal correlation.
Enhancement of long-range temporal correlation in young subjects after PS might reflect a cortical response to stimuli, which was absent in elderly subjects. These results are consistent with the general “loss of complexity/diminished functional response to stimuli” theory of aging.
Our findings demonstrate that application of MSE analysis to EEG is a powerful approach for studying age-related changes in brain function.
PMCID: PMC2880484  PMID: 19231279
Multiscale entropy; Aging; Electroencephalography; Complexity; Long-range temporal correlation; Photic stimulation
19.  Cerebrospinal fluid leakage after radioisotope cisternography is not influenced by needle size at lumbar puncture in patients with intracranial hypotension 
Radioisotope (RI) cisternography is considered to be the most important examination for the final diagnosis of intracranial hypotension, typically indicating cerebrospinal fluid (CSF) leakage as RI parathecal activity. Early bladder filling (EBF) of RI is another important finding. However, whether EBF without parathecal activity represents real CSF leakage due to intracranial hypotension or only an epiphenomenon of lumbar puncture causing CSF leak through a needle hole has been questioned.
To address this issue, we performed quantitative analysis of RI cisternography on 171 patients with suspected intracranial hypotension using different needle sizes (22 G, 23 G and 25 G) and compared RI residual activity in the CSF at different time points after injection. We also analyzed occurrence of early bladder filling and post-lumbar puncture headache.
No significant difference in RI residual activity was identified between the 22 G, 23 G and 25 G groups. The incidence of parathecal activity and early bladder filling was not significantly different between groups. The 22 G and 23 G groups had a higher but non-significant incidence of post lumbar headache.
The results suggest that needle size, at least for 22–25 G, does not affect the results of RI cisternographic diagnostic tests for CSF leakage and bladder filling in intracranial hypotension.
PMCID: PMC2695415  PMID: 19470184
20.  Do Interspecific Differences in Sapling Growth Traits Contribute to the Co-dominance of Acer saccharum and Fagus grandifolia? 
Annals of Botany  2007;101(1):103-109.
Background and Aims
Acer saccharum and Fagus grandifolia are among the most dominant late-successional tree species in North America. The influence of sapling growth responses to canopy gaps on the co-dominance of the two species in an old-growth forest in southern Quebec, Canada was examined. Two predictions were evaluated: (a) F. grandifolia is more shade tolerant than A. saccharum due to greater sapling leaf area and net production per sapling in closed-canopy conditions; and (b) the height growth rate of A. saccharum in canopy gaps is greater than that of F. grandifolia due to increased net production per sapling.
Sapling crown allometry, net production and height growth rates were compared between and within the two species in closed canopy vs. canopy gaps. Standardized major axis regression was used to analyse differences in crown allometry.
Key Results
F. grandifolia had greater crown projection, sapling leaf area and net production rate per sapling than A. saccharum in closed-canopy conditions. In response to canopy gaps, net production per sapling increased to the same degree in both species. The net production per sapling of F. grandifolia thus was much greater than that of A. saccharum in both canopy gap and closed-canopy conditions. The height growth rate of both species increased in canopy gaps, but the degree of increase was greater in F. grandifolia than in A. saccharum.
F. grandifolia regenerated more successfully than A. saccharum in both closed-canopy conditions and canopy gaps, which indicates that the co-dominance of the two species cannot be maintained simply by interspecific differences in shade tolerance and growth in gaps. Previous research showed that although Fagus and Acer shared dominance at this site, their relative dominance shifted with edaphic conditions. This suggests that the widespread co-dominance of the two species in eastern North American forests is maintained by the joint influence of canopy disturbance and species-specific responses to the heterogeneity of moisture and fertility regimes within forested landscapes.
PMCID: PMC2701832  PMID: 17942590
American beech; crown architecture; crown allometry; height growth rate; net production rate; saplings; sugar maple
21.  Responses of Crown Development to Canopy Openings by Saplings of Eight Tropical Submontane Forest Tree Species in Indonesia: A Comparison with Cool-temperate Trees 
Annals of Botany  2006;97(4):559-569.
• Background and Aims Growth in trunk height in canopy openings is important for saplings. How saplings increase height growth in canopy openings may relate to crown architectural constraints. Responses of crown development to canopy openings in relation to trunk height growth were studied for saplings (0·2–2·5 m tall) of eight tropical submontane forest tree species in Indonesia. The results of this study were also compared with those of temperate trees in northern Japan.
• Methods The crown architecture differed among the eight tropical species, i.e. they had sparsely to highly developed branching structures. Crown allometry was compared among the eight species in each canopy condition (closed canopy or canopy openings), and between closed canopy and canopy openings within a species. A general linear regression model was used to analyse how each species increases height growth rate in canopy openings. Crown allometry and its plasticity were compared between tropical and temperate trees by a nested analysis of covariance.
• Key Results Tropical submontane trees had responses similar to cool-temperate trees, showing an increase in height in canopy openings, i.e. taller saplings of sparsely branched species increase height growth rates by increasing the sapling leaf area. Cool-temperate trees have a wider crown projection area and a smaller leaf area per crown projection area to avoid self-shading within a crown compared with tropical submontane trees. Plasticity of the crown projection area is greater in cool-temperate trees than in tropical submontane trees, probably because of the difference in leaf longevity.
• Conclusions This study concluded that interspecific variation in the responses of crown development to canopy openings in regard to increasing height related to the species' branching structure, and that different life-forms, such as evergreen and deciduous trees, had different crown allometry and plasticity.
PMCID: PMC2803653  PMID: 16399792
Cool-temperate trees; crown allometry; crown architecture; height growth; Indonesia; saplings; plasticity; tropical trees
22.  Outbreak of Cefozopran (Penicillin, Oral Cephems, and Aztreonam)-Resistant Neisseria gonorrhoeae in Japan 
Antimicrobial Agents and Chemotherapy  2001;45(12):3603-3606.
We have previously reported that the Neisseria gonorrhoeae isolates from clinical failure cases treated with cefdinir and aztreonam, β-lactams exhibited high MICs. These resistant isolates were clearly separated from the isolates exhibiting a low level of resistance to β-lactams as shown by the MIC distribution of cefozopran. Restriction fragment length polymorphism DNA typing revealed that the outbreak of cefozopran-resistant isolates in Kitakyushu, Japan, occurred as a result of clonal spread.
PMCID: PMC90878  PMID: 11709349
23.  Reduced Clinical Efficacy of Pazufloxacin against Gonorrhea Due to High Prevalence of Quinolone-Resistant Isolates with the GyrA Mutation 
Forty-two men with gonococcal urethritis were treated with an oral dosage of 200 mg of pazufloxacin, a new fluoroquinolone, three times daily for 3 days. Only 28 of the 42 men (66.7%) had negative culture results for Neisseria gonorrhoeae during follow-up. Of the 42 isolates, 41 could be recultured for antibiotic susceptibility testing and DNA sequencing. In 26 of the 41 isolates (63.4%), GyrA mutations with or without ParC mutations were identified. Among the 26 isolates, 23 contained a single GyrA mutation, 1 contained two GyrA mutations, and 2 contained three mutations including double GyrA and single ParC mutations. A single Ser-91-to-Phe mutation, which was detected in 14 of the 26 isolates, was the most common GyrA mutation, followed by an Ala-75 to Ser mutation and an Asp-95 to Asn or Gly mutation in GyrA. All three isolates with two or three mutations contained the Ser-91-to-Phe GyrA mutation. Eleven of the 14 isolates with the single Ser-91-to-Phe mutation within GyrA and all 3 isolates with two or three mutations persisted after pazufloxacin treatment. On the other hand, all 15 wild-type and 9 mutant isolates with a substitution at codon Ala-75 or Asp-95 were eradicated. The mean MIC of pazufloxacin for mutants with the single Ser-91-to-Phe mutation in GyrA was 66-fold higher than that for the wild type. The results obtained in this study suggest that a high prevalence of fluoroquinolone-resistant gonococcal isolates with the Ser-91-to-Phe mutation in GyrA reduced the efficacy of pazufloxacin as treatment for gonococcal urethritis.
PMCID: PMC105501  PMID: 9517935

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