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author:("Yamada, keio")
1.  Higher ventilatory responses during and after passive walking-like leg movement in older individuals 
Background
Minute ventilation (V·E) during walking has been shown to be higher in older individuals than in young individuals, but the mechanisms underlying the higher ventilatory response is unclear. Central command and peripheral neural reflex are important neural control mechanisms underlying ventilatory response during exercise. Passive leg movement has been used to exclude the influence of central command due to the lack of voluntary activation of muscles. The aim of the present study was to compare the ventilatory response during and after passive walking-like leg movement (PWM) in young and older individuals.
Methods
Eight young subjects (20 ± 2 years) and seven older subjects (70 ± 1 years) participated in this study. Subjects spent 7 minutes in a quiet standing (QS) position. Thereafter, they performed 14-minute rhythmic PWM at 1 Hz and this was followed by 7 minutes of QS.
Results
V·E values during pre-PWM QS were calculated as 1-minute averages using data obtained between 5 and 6 minutes. V·E values at pre-PWM QS in the young and older groups were 8.4 ± 2.1 and 7.5 ± 1.2 l/minute, respectively. V·E values increased significantly at the first minute of PWM to 11.4 ± 2.2 and 10.4 ± 2.5 l/minute in the young and older groups, respectively (P <0.001). In the young group, V·E at the last minute of PWM (9.2 ± 2.0 l/minute) was not significantly different from that at pre-PWM QS due to a decline in V·E, whereas V·E at the last minute of PWM in the older group (9.4 ± 2.2 l/minute) was still significantly higher (P <0.01). On the other hand, V·E at the first minute of post-PWM QS (7.2 ± 1.8 l/minute) was significantly lower than that during pre-PWM QS in the young group (P <0.05) but not in the older group.
Conclusions
Ventilatory response during and after PWM is higher in older individuals than in young individuals. This may be associated with a mechanism(s) other than central command. Our findings may explain part of the higher V·E response while walking in older individuals.
doi:10.1186/1880-6805-32-20
PMCID: PMC3831263  PMID: 24209769
Walking; Passive limb movement; Standing posture; Ventilation; Aging
2.  Wide Host Ranges of Herbivorous Beetles? Insights from DNA Bar Coding 
PLoS ONE  2013;8(9):e74426.
There are very few studies that have investigated host-specificity among tropical herbivorous insects. Indeed, most of the trophic interactions of herbivorous insects in Southeast Asian tropical rainforests remain unknown, and whether polyphagous feeding is common in the herbivores of this ecosystem has not been determined. The present study employed DNA bar coding to reveal the trophic associations of adult leaf-chewing chrysomelid beetles in a Bornean rainforest. Plant material ingested by the adults was retrieved from the bodies of the insects, and a portion of the chloroplast rbcL sequence was then amplified from this material. The plants were identified at the family level using an existing reference database of chloroplast DNA. Our DNA-based diet analysis of eleven chrysomelid species successfully identified their host plant families and indicated that five beetle species fed on more than two families within the angiosperms, and four species fed on several families of gymnosperms and/or ferns together with multiple angiosperm families. These findings suggest that generalist chrysomelid beetles associated with ecologically and taxonomically distant plants constitute a part of the plant-insect network of the Bornean rainforest.
doi:10.1371/journal.pone.0074426
PMCID: PMC3779210  PMID: 24073210
3.  Hybrid microincision vitrectomy surgery combined with 20-gauge silicone cannulas for use with 20-gauge horizontal scissors in diabetic tractional retinal detachment 
Purpose
To verify the utility and preliminary safety of a 20-gauge silicone cannula for use with 20-gauge horizontal scissors delamination during microincision vitrectomy surgery (MIVS).
Methods
Thirty-eight eyes in 35 consecutive patients with diabetic tractional retinal detachment, who underwent MIVS between April 2010 and March 2012 and were followed for 3–24 months, were retrospectively assessed using a chart review. Twenty-gauge scissors delamination through a silicone cannula, with an additional 20-gauge port as a hybrid, was primarily selected when treating thick and rigid fibrovascular membranes, including fluctuating vessels over the detached retina near the macula. The main outcome measures included the proportion of patients treated with this hybrid method, the postoperative visual acuity, and the incidence of complications.
Results
Compared with the 26 eyes treated with MIVS only, 12 eyes (32%) required a hybrid technique with the use of 20-gauge instruments through a silicone cannula in addition to MIVS. Two patients underwent additional surgery. Temporary silicone oil tamponade was performed in one case of retinotomy and one case of schizophrenia. The mean visual acuity (logarithm of the minimum angle of resolution [logMAR]) improved from 1.43 ± 0.85 to 0.72 ± 0.47 at the last follow-up visit. No patients exhibited worsening of their visual acuity postoperatively. No sclerotomy-related complications were recorded during the intraoperative or postoperative periods.
Conclusion
Hybrid MIVS combined with a 20-gauge silicone cannula for use with 20-gauge horizontal scissors in diabetic tractional retinal detachment eyes is useful and safe due to the reduced risk of sclerotomy-related retinal breaks. This procedure is a reasonable option when performing complex surgery for diabetic vitrectomy.
doi:10.2147/OPTH.S46486
PMCID: PMC3738249  PMID: 23946642
small gauge vitrectomy; cannulated vitrectomy system; cutter delamination; scissor delamination; 20-gauge instruments; sclerotomy retinal tears
4.  Complete Genome Sequence of Bacillus cereus NC7401, Which Produces High Levels of the Emetic Toxin Cereulide 
Journal of Bacteriology  2012;194(17):4767-4768.
We report the complete and annotated genome sequence of Bacillus cereus NC7401, a representative of the strain group that causes emetic-type food poisoning. The emetic toxin, cereulide, is produced by a nonribosomal protein synthesis (NRPS) system that is encoded by a gene cluster on a large resident plasmid, pNCcld.
doi:10.1128/JB.01015-12
PMCID: PMC3415479  PMID: 22887669
5.  Expression of prostaglandin E receptor subtype EP4 in conjunctival epithelium of patients with ocular surface disorders: case-control study 
BMJ Open  2012;2(5):e001330.
Objectives
To confirm the downregulation of PTGER4 mRNA in the conjunctiva of Stevens-Johnson syndrome/toxic epidermal necrolysis (SJS/TEN) and ocular cicatricial pemphigoid (OCP) patients and to examine the expression of its EP4 protein in the conjunctival epithelium of patients with various ocular surface disorders.
Design
Case-control study.
Setting and participants
We performed quantitative reverse transcription-PCR (RT-PCR) analysis of PTGER4 mRNA in conjunctival tissue sections from patients with SJS/TEN and OCP to confirm the downregulation of PTGER4 mRNA expression. We also analysed EP4 immunohistologically in other ocular surface disorders. Conjunctival tissues were obtained from patients undergoing surgical reconstruction of the ocular surface due to chemical eye burns, subacute SJS/TEN or chronic SJS/TEN, chronic OCP, severe graft versus host disease (GVHD) and from patients with Mooren's ulcers treated by resection of the inflammatory conjunctiva.
Primary and secondary outcome measures
The expression of PTGER4 mRNA and EP4 protein assessed by quantitative RT-PCR assay and immunohistological methods.
Results
PTGER4 mRNA was significantly lower in conjunctival tissues from SJS and OCP patients than in the control conjunctivochalasis samples. EP4 protein was detected in conjunctival epithelium from patients with chemical eye burn and in control conjunctival epithelium from patients with conjunctivochalasis. Its expression varied in conjunctival epithelium from patients with Mooren's ulcer. We did not detect EP4 immunoreactivity in conjunctival epithelium from patients with subacute SJS/TEN, severe GVHD, chronic SJS/TEN or OCP.
Conclusions
The strong downregulation of EP4 expression in conjunctival epithelium from patients with OCP or SJS/TEN may be attributable to ocular surface inflammation.
doi:10.1136/bmjopen-2012-001330
PMCID: PMC3488701  PMID: 23065448
Ophthalmology
6.  Suppression of cardiocirculatory responses to orthostatic stress by passive walking-like leg movement in healthy young men 
Background
Although passive walking-like leg movement in the standing posture (PWM) has been used in the clinical field, the safety of PWM has not been fully determined despite the risks of orthostatic intolerance due to standing posture. The aim of the present study was to examine cardiocirculatory response during PWM in healthy young men.
Methods
The subjects (n = 13) spent 5 min in a sitting position and then 5 min in a quiet standing position to determine baseline levels. Thereafter, they underwent 25-min rhythmic PWM at 1 Hz while standing. In another bout, subjects experienced the same protocol except that they underwent 25-min quiet standing (QS) instead of 25-min PWM. Two subjects dropped out of the 25-min QS due to feeling of discomfort. Thus, data obtained in the remaining eleven subjects are presented.
Results
In the PWM trial, systolic arterial blood pressure (SAP) decreased from 112 ± 8 mmHg during the sitting baseline period to 107 ± 8 mmHg during the standing baseline period (p <0.05), while heart rate (HR) increased from 73 ± 9 bpm during the sitting baseline period to 84 ± 10 bpm during the standing baseline period (p <0.001). After the imposition of PWM, SAP increased from 107 ± 8 mmHg in the standing baseline period to 120 ± 6 mmHg (p <0.001), while HR decreased from 84 ± 10 bpm in the standing baseline period to 76 ± 9 bpm (p <0.05). In the QS trial, SAP, which had decreased during the standing baseline period compared to that during the sitting baseline period, remained lowered during the 25-min QS period, while HR, which had increased during the standing baseline period compared to that during the sitting baseline period, remained elevated during the 25-min QS period. In both bouts, HR showed almost mirror-image changes in the high-frequency component of HR variability, suggesting that the changes in HR were due to change in parasympathetic activation. Double product (HR × SAP), as a predictor of myocardial oxygen consumption, during the 25-min QS period tended to increase with time, but double product remained almost constant during the 25-min PWM period.
Conclusions
The results suggest that PWM is effective for suppressing cardiocirculatory responses to orthostatic stress.
doi:10.1186/1880-6805-31-24
PMCID: PMC3517532  PMID: 22971904
Standing posture; Orthostatic intolerance; Passive exercise; Rehabilitation
7.  Benefits of off-campus education for students in the health sciences: a text-mining analysis 
BMC Medical Education  2012;12:84.
Background
In Japan, few community-based approaches have been adopted in health-care professional education, and the appropriate content for such approaches has not been clarified. In establishing community-based education for health-care professionals, clarification of its learning effects is required. A community-based educational program was started in 2009 in the health sciences course at Gunma University, and one of the main elements in this program is conducting classes outside school. The purpose of this study was to investigate using text-analysis methods how the off-campus program affects students.
Methods
In all, 116 self-assessment worksheets submitted by students after participating in the off-campus classes were decomposed into words. The extracted words were carefully selected from the perspective of contained meaning or content. With the selected terms, the relations to each word were analyzed by means of cluster analysis.
Results
Cluster analysis was used to select and divide 32 extracted words into four clusters: cluster 1—“actually/direct,” “learn/watch/hear,” “how,” “experience/participation,” “local residents,” “atmosphere in community-based clinical care settings,” “favorable,” “communication/conversation,” and “study”; cluster 2—“work of staff member” and “role”; cluster 3—“interaction/communication,” “understanding,” “feel,” “significant/important/necessity,” and “think”; and cluster 4—“community,” “confusing,” “enjoyable,” “proactive,” “knowledge,” “academic knowledge,” and “class.”
Conclusions
The students who participated in the program achieved different types of learning through the off-campus classes. They also had a positive impression of the community-based experience and interaction with the local residents, which is considered a favorable outcome. Off-campus programs could be a useful educational approach for students in health sciences.
doi:10.1186/1472-6920-12-84
PMCID: PMC3479041  PMID: 22928985
Community-based education; School of health sciences; Early exposure; Role model; Text-mining methods
8.  Proteome driven re-evaluation and functional annotation of the Streptococcus pyogenes SF370 genome 
BMC Microbiology  2011;11:249.
Background
The genome data of Streptococcus pyogenes SF370 has been widely used by many researchers and provides a vast array of interesting findings. Nevertheless, approximately 40% of genes remain classified as hypothetical proteins, and several coding sequences (CDSs) have been unrecognized. In this study, we attempted a shotgun proteomic analysis with a six-frame database that was independent of genome annotation.
Results
Nine proteins encoded by novel ORFs were found by shotgun proteomic analysis, and their specific mRNAs were verified by reverse transcriptional PCR (RT-PCR). We also provided functional annotations for hypothetical genes using proteomic analysis from three different culture conditions that were separated into three fractions: supernatant, soluble, and insoluble. Consequently, we identified 567 proteins on re-evaluation of the proteomic data using an in-house database comprising 1,697 annotated and nine non-annotated CDSs. We provided functional annotations for 126 hypothetical proteins (18.9% out of the 668 hypothetical proteins) based on their cellular fractions and expression profiles under different culture conditions.
Conclusions
The list of amino acid sequences that were annotated by genome analysis contains outdated information and unrecognized protein-coding sequences. We suggest that the six-frame database derived from actual DNA sequences be used for reliable proteomic analysis. In addition, the experimental evidence from functional proteomic analysis is useful for the re-evaluation of previously sequenced genomes.
doi:10.1186/1471-2180-11-249
PMCID: PMC3224786  PMID: 22070424
9.  A New Microarray System to Detect Streptococcus pneumoniae Serotypes 
Streptococcus pneumoniae, one of the most common gram-positive pathogens to colonize the human upper respiratory tract, is responsible for many severe infections, including meningitis and bacteremia. A 23-valent pneumococcal vaccine is available to protect against the 23 S. pneumoniae serotypes responsible for 90% of reported bacteremic infections. Unfortunately, current S. pneumoniae serotype testing requires a large panel of expensive antisera, assay results may be subjective, and serotype cross-reactions are common. For this study, we designed an oligonucleotide-based DNA microarray to identify glycosyltransferase gene sequences specific to each vaccine-related serotype. Out of 56 isolates representing different serotypes, only one isolate, representing serotype 23A, was not detected correctly as it could not be distinguished from serotype 23F. Our data suggest that the microarray provides a more cost-effective and reliable way of monitoring pneumococcal capsular types.
doi:10.1155/2011/352736
PMCID: PMC3118663  PMID: 21716703
10.  Variations in amount of TSST-1 produced by clinical methicillin resistant Staphylococcus aureus (MRSA) isolates and allelic variation in accessory gene regulator (agr) locus 
BMC Microbiology  2009;9:52.
Background
Staphylococcus aureus (S. aureus) is an important pathogen associated with both nosocomial and community-acquired infections and its pathogenicity is attributed to its potential to produce virulence factors. Since the amount of toxin produced is related to virulence, evaluating toxin production should be useful for controlling S. aureus infection. We previously found that some strains produce relatively large amounts of TSST-1; however, no reports have described the amount of TSST-1 produced by clinical isolates.
Methods
Amounts of TSST-1 produced by clinical methicillin resistant S. aureus (MRSA) isolates were measured by Western blotting. We determined their accessory gene regulator (agr) class by PCR and investigated whether TSST-1 production correlates with variations in the class and structure of the agr.
Results
We found that 75% of surveyed MRSA isolates (n = 152) possessed the tst gene and that 96.7% belonged to agr class 2. The concentrations of TSST-1 secreted into culture supernatants by 34 strains measured by Western blotting differed 170-fold. Sequencing the entire agr locus (n = 9) revealed that some had allelic variations regardless of the amount of TSST-1 produced whereas sequencing the sar, sigma factor B and the tst promoter region revealed no significant changes.
Conclusion
The amounts of TSST-1 produced by clinical MRSA isolates varied. The present results suggest that TSST-1 production is not directly associated with the agr structure, but is instead controlled by unknown transcriptional/translational regulatory systems, or synthesized by multiple regulatory mechanisms that are interlinked in a complex manner.
doi:10.1186/1471-2180-9-52
PMCID: PMC2667389  PMID: 19272162
11.  A New Phylogenetic Cluster of Cereulide-Producing Bacillus cereus Strains▿  
Journal of Clinical Microbiology  2007;45(4):1274-1277.
Phenotypic and molecular studies have established that cereulide-producing strains of Bacillus cereus are a distinct and probably recently emerged clone within the Bacillus population. We analyzed a set of B. cereus strains, both cereulide producers and nonproducers, by multilocus sequence typing. Consistent with earlier reports, nonproducers demonstrated high heterogeneity. Most cereulide-producing strains and all flagellar antigen type H1 strains were allocated to the known sequence type of exclusively emetic B. cereus strains. Several cereulide-producing strains, however, were recovered at a new phylogenetic location, all of which were serotype H3 or H12. We hypothesize that the group of cereulide producers is diversifying progressively, probably by lateral transfer of the corresponding gene complex.
doi:10.1128/JCM.02224-06
PMCID: PMC1865805  PMID: 17314223
12.  Growth Phase-Dependent Effect of Clindamycin on Production of Exoproteins by Streptococcus pyogenes▿  
The administration of high-dose clindamycin plus benzylpenicillin has been recommended for the treatment of streptococcal toxic shock-like syndrome caused by Streptococcus pyogenes, and clindamycin has been found to be more effective than beta-lactams in retrospective analyses of human cases. Although therapeutic doses of clindamycin have also been shown to be effective against experimental infections and clindamycin has great efficacy against the production of bacterial exoproteins, we recently reported that the level of production of some exoproteins was unchanged or even increased by a subinhibitory dose of clindamycin when it is added upon the initiation of bacterial culture and the treated cultures were analyzed by two-dimensional gel electrophoresis. In this study we further examined the effect of clindamycin on the production of exoproteins by adding it to Streptococcus pyogenes cultures during various growth phases. We found that the levels of production of some proteins, NAD+ glycohydrolase, streptolysin O, and streptococcal inhibitor of complement, were increased when clindamycin was added at early-log-phase growth, which was the result that was seen when clindamycin was added at the beginning of culture. However, clindamycin inhibited the production of most types of proteins when it was administered to Streptococcus pyogenes cultures at mid-log-phase growth. In csrS- or mga-knockout bacterial strains, the increase in exoproteins seen in parental strains was considerably inhibited. Our study indicates that the in vitro effect of clindamycin on the production of exoproteins greatly depends on the growth phase of bacteria and some regulatory factors of Streptococcus pyogenes that are involved in this phenomenon.
doi:10.1128/AAC.00539-06
PMCID: PMC1797754  PMID: 17101685
13.  Comparative sequence analysis of leucine-rich repeats (LRRs) within vertebrate toll-like receptors 
BMC Genomics  2007;8:124.
Background
Toll-like receptors (TLRs) play a central role in innate immunity. TLRs are membrane glycoproteins and contain leucine rich repeat (LRR) motif in the ectodomain. TLRs recognize and respond to molecules such as lipopolysaccharide, peptidoglycan, flagellin, and RNA from bacteria or viruses. The LRR domains in TLRs have been inferred to be responsible for molecular recognition. All LRRs include the highly conserved segment, LxxLxLxxNxL, in which "L" is Leu, Ile, Val, or Phe and "N" is Asn, Thr, Ser, or Cys and "x" is any amino acid. There are seven classes of LRRs including "typical" ("T") and "bacterial" ("S"). All known domain structures adopt an arc or horseshoe shape. Vertebrate TLRs form six major families. The repeat numbers of LRRs and their "phasing" in TLRs differ with isoforms and species; they are aligned differently in various databases. We identified and aligned LRRs in TLRs by a new method described here.
Results
The new method utilizes known LRR structures to recognize and align new LRR motifs in TLRs and incorporates multiple sequence alignments and secondary structure predictions. TLRs from thirty-four vertebrate were analyzed. The repeat numbers of the LRRs ranges from 16 to 28. The LRRs found in TLRs frequently consists of LxxLxLxxNxLxxLxxxxF/LxxLxx ("T") and sometimes short motifs including LxxLxLxxNxLxxLPx(x)LPxx ("S"). The TLR7 family (TLR7, TLR8, and TLR9) contain 27 LRRs. The LRRs at the N-terminal part have a super-motif of STT with about 80 residues. The super-repeat is represented by STTSTTSTT or _TTSTTSTT. The LRRs in TLRs form one or two horseshoe domains and are mostly flanked by two cysteine clusters including two or four cysteine residue.
Conclusion
Each of the six major TLR families is characterized by their constituent LRR motifs, their repeat numbers, and their patterns of cysteine clusters. The central parts of the TLR1 and TLR7 families and of TLR4 have more irregular or longer LRR motifs. These central parts are inferred to play a key role in the structure and/or function of their TLRs. Furthermore, the super-repeat in the TLR7 family suggests strongly that "bacterial" and "typical" LRRs evolved from a common precursor.
doi:10.1186/1471-2164-8-124
PMCID: PMC1899181  PMID: 17517123
14.  Therapeutic Effect of ME1036 on Endocarditis Experimentally Induced by Methicillin-Resistant Staphylococcus aureus 
The efficacy of ME1036, a novel parenteral carbapenem, was compared with that of vancomycin by using a rabbit model of methicillin-resistant Staphylococcus aureus (MRSA) endocarditis. Compared with vancomycin, ME1036 reduced the bacterial counts in the vegetations at a lower dosage or over a shorter period of administration when it was used for the treatment of MRSA endocarditis.
doi:10.1128/AAC.49.8.3526-3528.2005
PMCID: PMC1196270  PMID: 16048975
15.  In Vitro Activities of ME1036 (CP5609), a Novel Parenteral Carbapenem, against Methicillin-Resistant Staphylococci 
ME1036, formerly CP5609, is a novel parenteral carbapenem with a 7-acylated imidazo[5,1-b]thiazole-2-yl group directly attached to the carbapenem moiety of the C-2 position. The present study evaluated the in vitro activities of ME1036 against clinical isolates of gram-positive and gram-negative bacteria. ME1036 displayed broad activity against aerobic gram-positive and gram-negative bacteria. Unlike other marketed β-lactam antibiotics, ME1036 maintained excellent activity against multiple-drug-resistant gram-positive bacteria, such as methicillin-resistant staphylococci and penicillin-resistant Streptococcus pneumoniae (PRSP). The MICs of this compound at which 90% of isolates were inhibited were 2 μg/ml for methicillin-resistant Staphylococcus aureus (MRSA), 2 μg/ml for methicillin-resistant coagulase-negative staphylococci, and 0.031 μg/ml for PRSP. In time-kill studies with six strains of MRSA, ME1036 at four times the MIC caused a time-dependent decrease in the numbers of viable MRSA cells. The activity of ME1036 against MRSA is related to its high affinity for penicillin-binding protein 2a, for which the 50% inhibitory concentration of ME1036 was approximately 300-fold lower than that of imipenem. In conclusion, ME1036 demonstrated a broad antibacterial spectrum and high levels of activity in vitro against staphylococci, including β-lactam-resistant strains.
doi:10.1128/AAC.48.8.2831-2837.2004
PMCID: PMC478537  PMID: 15273088
16.  Effect of cyclic bis(3′–5′)diguanylic acid and its analogs on bacterial biofilm formation 
Fems Microbiology Letters  2009;301(2):193-200.
Cyclic bis(3′–5′)diguanylic acid (cyclic-di-GMP) functions as a second messenger in diverse species of bacteria to trigger wide-ranging physiological changes. We measured cyclic-di-GMP and its structural analogs such as cyclic bis(3′–5′)guanylic/adenylic acid (cyclic-GpAp), cyclic bis(3′–5′)guanylic/inosinic acid (cyclic-GpIp) and monophosphorothioic acid of cyclic-di-GMP (cyclic-GpGps) for effects on the biofilm formation of Staphylococcus aureus and Pseudomonas aeruginosa. We constructed a knockout mutant of SA0701, which is a GGDEF motif protein relevant to diguanylate cyclase from S. aureus 2507. We confirmed that the biofilm formation of this mutant (MS2507ΔSA0701) was reduced. Cyclic-di-GMP corresponding to physiological intracellular levels given in the culture recovered the biofilm formation of MS2507ΔSA0701, whereas its analogs did not, indicating that unlike a previous suggestion, cyclic-di-GMP was involved in the positive regulation of the biofilm formation of S. aureus and its action was structurally specific. At a high concentration (200 μM), cyclic-di-GMP and its analogs showed suppression effects on the biofilm formation of S. aureus and P. aeruginosa, and according to the quantification study using costat analysis, the suppression potential was in the order of cyclic-di-GMP, cyclic-GpGps, cyclic-GpAp and cyclic-GpIp, suggesting that the suppression effect was not strictly specific and the change of base structure quantitatively affected the suppression activity.
doi:10.1111/j.1574-6968.2009.01825.x
PMCID: PMC2784870  PMID: 20169626
biofilm; cyclic-di-GMP; Staphylococcus aureus; Pseudomonas aeruginosa; regulation of biofilm formation; GdpS

Results 1-16 (16)