Biomedical subjects

Yosuke Nishimura

Publications and source records attributed to Yosuke Nishimura.

14 recordsLinked to original sources

PubMed2026

VicMAG, an open-source tool for visualizing circular metagenome-assembled genomes highlighting bacterial virulence and antimicrobial resistance.

Bacterial pathogens spread in clinical and environmental settings, and mobile genetic elements (MGEs), such as plasmids and phages, mediate the transfer of virulence factor genes (VFGs) and antimicrobial resistance genes (ARGs) among bacterial communities. Metagenomic analysis of environmental and wastewater samples using highly accurate long-read sequencing technologies, such as Pacific Biosciences (PacBio) HiFi sequencing, provides valuable insights into monitoring the regional spread of VFGs and ARGs, including dissemination mediated by MGEs. No visualization tool is currently available for the comprehensive display of numerous resulting circular metagenome-assembled genomes (cMAGs) with functional gene annotations. Here, we developed visualization of circular metagenome-assembled genome (VicMAG), a visualization tool for highly complex cMAGs derived from long-read metagenome assemblies annotated using updated databases of VFGs, ARGs, and MGEs. Using 353 cMAGs from PacBio HiFi sequencing of a wastewater sample, we demonstrated the utility of VicMAG for metagenome visualization. VicMAG provides comprehensive, size-aware visualization of cMAGs representing bacterial chromosomes and plasmids, annotated with VFGs, ARGs, and phages. By simultaneously visualizing all cMAGs in a framework, VicMAG facilitates a holistic understanding of the distribution and genomic context of VFGs and ARGs across complex microbial communities. This tool supports integrated surveillance of bacteria associated with virulence and antimicrobial resistance across clinical, environmental, and One Health contexts.

Metagenome↗

PubMed2024

Double-stranded RNA sequencing reveals distinct riboviruses associated with thermoacidophilic bacteria from hot springs in Japan.

Metatranscriptome sequencing expanded the known diversity of the bacterial RNA virome, suggesting that additional riboviruses infecting bacterial hosts remain to be discovered. Here we employed double-stranded RNA sequencing to recover complete genome sequences of two ribovirus groups from acidic hot springs in Japan. One group, denoted hot spring riboviruses (HsRV), consists of viruses with distinct RNA-directed RNA polymerases (RdRPs) that seem to be intermediates between typical ribovirus RdRPs and viral reverse transcriptases. This group forms a distinct phylum, Artimaviricota, or even kingdom within the realm Riboviria. We identified viruses encoding HsRV-like RdRPs in marine water, river sediments and salt marshes, indicating that this group is widespread beyond extreme ecosystems. The second group, denoted hot spring partiti-like viruses (HsPV), forms a distinct branch within the family Partitiviridae. The genome architectures of HsRV and HsPV and their identification in bacteria-dominated habitats suggest that these viruses infect thermoacidophilic bacteria.

Hot Springs↗

PubMed2006

[Inflow cannula direct insertion into the true lumen of the ascending aorta for an acute aortic dissection patient with intraoperative malperfusion after aortic clamping].

A 47-year old woman, who was diagnosed as Stanford type A acute aortic dissection, underwent an emergent operation. Because of obesity and bleeding, it was impossible to find the right axillary artery. Only we could have for inflow line was the femoral line. After starting cardiopulmonary bypass (CPB) and crossclamping the ascending aorta, mean blood pressure of the right radial artery dropped to 15 mmHg, suggesting the occurrence of malperfusion. The ascending aorta was immediately transected, and the CPB was ceased. Inflow cannula was directly inserted into the true rumen of the ascending aorta, and resumed the CPB. The mean blood pressure rose up to 80 mmHg. Such procedure took about 10 minutes. Abnormal neurological findings were not apparent except for the transient postoperative delirium. The patient was discharged on the 48th day after operation. It is suggested that this method was useful and safe to have the new inflow line when emergently necessary.

Aortic Dissection↗

PubMed2005

Surgical application for a prolapse of the anterior mitral leaflet by replacing artificial chordae with polytetrafluoroethylene grafts.

PURPOSE: There are an increasing number of reports concerning mitral valve repair by a reconstruction of the chordae tendinae using expanded polytetrafluoro-ethylene (PTFE) sutures. However, little information is available about extended application or results of this technique for an extended prolapse of the anterior mitral leaflets. METHODS: Between July 1991 and August 2003, 28 patients with moderate to severe mitral regurgitation as a result of a prolapse of anterior leaflets (age range, 15-73 years) underwent mitral valve repair by reconstruction of the artificial chordae with 4-CV expanded polytetrafluoroethylene sutures without a leaflet resection. Either Kay's suture technique or ring annuloplasty was also performed to correct annular dilatation in all patients. RESULTS: No operative death or late mortality was observed. The prolapsed segment, which was successfully repaired, was within 33% of the anterior mitral leaflet (AML) in 6 patients, from 33% to 50% in 5, from 50% to 99% in 11, and 100% in 6 patients. Before discharge, immediate postoperative echocardiography showed less than moderate mitral regurgitation in 28 of 28 patients. The follow-up, consisting of a clinical examination and serial echocardiograms, was complete in all cases and the mean follow-up period was 80.6 months (range, 12-146). There were two failures that required a reoperation because of a worsening mitral regurgitation and hemolytic anemia (elongation of anchored side of papillary muscle). The other two patients required mitral valve replacement due to a progressive regression of the left ventricular function, although the regurgitation worsened from a mild level to a moderate one. When the reoperated patients were excluded from the following data, the degree of mitral regurgitation, estimated by echocardiography performed at recent follow-up period, was none in 10 patients, trivial in 13 patients, and mild in 1 patient. In addition, the systolic and diastolic dimensions of the left ventricle decreased significantly (P < 0.01). CONCLUSIONS: The replacement of artificial chordae was not complicated and it seemed to help to preserve a good relationship among leaflet tissues, chordae, and papillary muscles. We therefore suggest that the extensive use of PTFE artificial chordae appears to be a promising procedure for the repair of all kinds of mitral lesions causing mitral regurgitation.

Adolescent↗

PubMed2005

Endothelin-1 receptor antagonist prevents deterioration of left ventricular function and coronary flow reserve in brain-dead canine heart.

BACKGROUND: Rapid hemodynamic deterioration is caused by induction of brain death, but the exact mechanism is still uncertain. The aim of this study was to investigate the contribution of endothelin-1 by using endothelin-1 receptor antagonist (TAK-044) in a canine brain-death model. METHODS: Dogs were divided into 2 groups: (1) the TAK group, in which TAK-044 was intravenously injected 30 minutes before brain-death induction at a dose of 3 mg/kg; and (2) the control group. Brain death was induced by rapid inflation of a sub-durally placed balloon catheter. Left ventricular function and coronary flow reserve was compared between the 2 groups. RESULTS: Brain death caused a transient hyperdynamic response followed by hemodynamic deterioration after 60 minutes in both groups. Left ventricular function, evaluated by the slope of the end-systolic pressure-volume relation was significantly decreased from 7.7 +/- 0.6 to 3.7 +/- 0.3 mm Hg/ml (p < 0.01) in the control group, but was not decreased in the TAK group (7.7 +/- 0.8 to 7.3 +/- 0.9 mm Hg/ml, p = 0.75). Coronary flow reserve, measured by direct injection of acetylcholine (3 microg) into the coronary artery, was significantly reduced at 60 minutes after brain death in the control group (264.8% to 176.6%, p < 0.01), but not in the TAK group (291.2% to 301.3%, p = 0.84). Exactly the same results were obtained when sodium nitroprusside (SNP; 100 microg) was administered. CONCLUSIONS: TAK-044 can prevent the deterioration of left ventricular function and coronary flow reserve that follows induction of brain death, suggesting that endothelin-1 could play an important role in hemodynamic deterioration by impairment of coronary microcirculation after brain death.

Animals↗

PubMed2004

The low resistance strategy for the perioperative management of the Norwood procedure.

BACKGROUND: Postoperative course of the Norwood procedure is fragile because of an unstable pulmonary to systemic blood flow ratio caused by fluctuation of systemic and pulmonary vascular resistance. METHODS: Twenty-seven patients with hypoplastic left heart syndrome who underwent the Norwood procedure from June 1998 to February 2002 were managed with the following low-resistance strategy. Intraoperative high-flow and low-resistance cardiopulmonary bypass was achieved with total avoidance of circulatory arrest and a large dose of chlorpromazine. In weaning from the bypass, pulmonary vascular resistance was maximally decreased by inspired oxygen fraction (100%), inhaled nitric oxide (20 ppm), and nitroglycerin (2 to 4 microg/kg/min). Then pulmonary blood flow was determined by adjusting the systemic to pulmonary shunt. Postoperatively, with continuous infusion of chlorpromazine and nitroglycerin as a systemic and pulmonary vasodilator, the inspired oxygen fraction and inhaled nitric oxide were tapered as the arterial oxygen saturation improved. RESULTS: In most patients, inhaled nitrous oxide and inspired oxygen fraction were weaned within 3 days. The postoperative course was stable with minimum changes in circulatory and respiratory status for the survivors. Patients were extubated on a median of 6 postoperative days. Early mortality was 11.1% (3 of 27), and none of the patients died of hemodynamic deterioration. CONCLUSIONS: The low resistance strategy is a simple and useful method for perioperative management of the Norwood procedure, minimizing fluctuation in both pulmonary and systemic vascular resistance and maintaining stable circulatory and respiratory status.

Cardiac Surgical Procedures↗

PubMed2004

Extensive use of polytetrafluoroethylene artificial grafts for prolapse of posterior mitral leaflet.

BACKGROUND: There are an increasing number of reports concerning mitral valve repair by means of reconstruction of the chordae tendinae with expanded polytetrafluoroethylene (e-PTFE) sutures. However little information is available about extended application or results of this technique for extended prolapse of posterior mitral leaflets. METHODS: Between March 1994 and December 2000, 22 patients with moderate-to-severe mitral regurgitation (MR) as the result of a prolapse of posterior leaflets (age range, 39-73 years) underwent mitral valve repair by means of reconstruction of artificial chordae with 4-CV e-PTFE sutures without leaflet resection. Either Kay's suture or ring annuloplasty was also performed to correct annular dilatation in all patients. RESULTS: No operative death or late mortality was observed. Before discharge immediate postoperative echocardiography indicated less than moderate MR in 20 out of 22 patients. The follow-up was complete in all cases by clinical examination and serial echocardiograms and the median follow-up period was 87 months (range 24-108). There were two failures that required reoperation because of unsuccessful repair and worsening MR (elongation of the anchored side of the papillary muscle). When the reoperated patients were excluded from the follow-up data, the degree of MR, estimated by echocardiography that was performed at a recent follow-up period, was nonexistent in 6 patients, trivial in 10 patients, and mild in 4 patients. The systolic and diastolic dimensions of the left ventricle decreased significantly (p < 0.01). CONCLUSIONS: Replacement of the artificial chordae was not complicated and seemed to preserve favorable relationships among leaflet tissues, chordae, and papillary muscles. We therefore suggest that the extensive use of PTFE artificial chordae seems to be a promising procedure regarding the repair of many kinds of mitral lesions causing MR.

Adult↗

PubMed2004

Endothelial activation through brain death?

BACKGROUND: Brain death induces myocardial dysfunction and multifocal microscopic myocardial necrosis in dogs; however, the pathogenetic pathways between brain death and cardiac damage remain incompletely understood. We hypothesized that brain death might induce a propensity toward coronary vasospasms, possibly by endothelial dysfunction. We therefore studied the effect of serotonin and acetylcholine on tension generated by isolated coronary artery segments from control and brain dead dogs. METHODS: Coronary segments were isolated 1 hour after brain death that was induced by the inflation (15 ml saline) of an extradurally placed balloon or from sham-operated time-matched controls. Studied were the effect of serotonin on isometric tension, with and without pre-constriction with prostaglandin F(2alpha) (PGF(2alpha)), and the effect of acetylcholine after pre-constriction. RESULTS: Coronary segments from brain dead dogs exhibited severe vasoconstriction when serotonin (10(-7), 10(-6), and 10(-5) mol/liter) was administered, a reaction that was barely detectable in control segments. After pre-construction with PGF(2alpha), serotonin caused only significant vasodilation in a concentration of 10(-5) mol/liter, unlike in control segments where 10(-6) mol/liter had already induced a highly significant vasodilation. The reaction on acetylcholine was identical in both groups. CONCLUSION: Brain death induces changes in coronary vasoreactivity in dogs, with a highly increased sensitivity for the vasospastic effects of serotonin. It is, however, not merely caused by aspecific endothelial dysfunction, as evidenced by the normal reaction on acetylcholine. These alterations in coronary artery properties might contribute to the myocardial damage seen after brain death.

Acetylcholine↗

PubMed2004

Midterm surgical results of total cavopulmonary connection: clinical advantages of the extracardiac conduit method.

OBJECTIVE: We evaluated the midterm surgical outcomes of intra-atrial lateral tunnel and extracardiac conduit total cavopulmonary connection to clarify the clinical superiority. METHODS: Patients (n = 167) underwent total cavopulmonary connection (88 with lateral tunnel and 79 with extracardiac conduit) from November 1991 to March 1999. Survival, incidence of reoperation and late complications, exercise tolerance, hemodynamic variables, and plasma concentration of natriuretic peptide type A were compared. In the lateral tunnel group, time-related change in lateral tunnel size was investigated for its relationship to postoperative arrhythmias. RESULTS: The 8-year survival was 93.2% in the lateral tunnel group and 94.9% in the extracardiac conduit group. Seven reoperations were performed in the lateral tunnel group but none in the extracardiac conduit group. Supraventricular arrhythmias developed in 14 patients (15.9%) in the lateral tunnel group and in 4 patients (5.1%) in the extracardiac conduit group (P =.003). Freedom from cardiac-related events was 72.5% in the lateral tunnel group and 89.8% in the extracardiac conduit group at 8 years (P =.0098). Hemodynamic variables and exercise tolerance were similar in both groups but plasma natriuretic peptide type A concentration, a parameter of atrial wall tension, was higher in the lateral tunnel group. In the lateral tunnel group, intra-atrial tunnel size increased by 19.4% during the 44.2-month interval and the percent increase in tunnel size was an independent predictor of supraventricular arrhythmias. CONCLUSIONS: The midterm survival, hemodynamic variables, and exercise tolerance were similar and satisfactory in both lateral tunnel and extracardiac conduit groups; however, the incidence of cardiac-related events was significantly less frequent in the extracardiac conduit group. In the lateral tunnel group, careful observation is required to monitor the relationship of the dilating tendency of the intra-atrial tunnel and the development of late complications.

Atrial Natriuretic Factor↗

PubMed2003

Impairment of coronary flow reserve and left ventricular function in the brain-dead canine heart.

OBJECTIVE: The mechanisms of cardiac dysfunction after brain death, which are thought to be mainly associated with massive catecholamine release, have not been fully elucidated, especially with respect to the coronary circulation. The aim of this study was to investigate the changes in function of the coronary artery and its contribution to hemodynamic deterioration in a canine brain death model. METHODS: Brain death was induced by rapid inflation of a subdurally placed balloon catheter. Hemodynamic measurements including assessment of left ventricular contractility using pressure-volume relations and biochemical analyses of blood samples were performed in seven dogs. Coronary flow reserve in the same brain death model was assessed by changes in coronary flow and resistance induced by administering a vasodilator directly into the coronary artery in another eight dogs. RESULTS: A hyperdynamic response was transiently observed after induction of brain death, followed by decreases in arterial pressure, cardiac output, and coronary blood flow. Parameters of left ventricular contractility as measured by pressure-volume relations had significantly deteriorated by 60 min after brain death. Percent changes in coronary flow by administration of acetylcholine and sodium nitroprusside were 272 and 209%, respectively, before brain death; these were decreased to 178 and 145% at 30 min after brain death, and to 192 and 153% at 60 min. Coronary resistance ratios were also significantly increased at 30 and 60 min after brain death. CONCLUSIONS: Impairment of coronary flow reserve was found in the brain-dead canine heart. This impaired coronary circulation may constitute a disadvantage of prevention and recovery of cardiac dysfunction after induction of brain death.

Animals↗

PubMed2003

Early and late results of cardiac and thoracic aortic surgery in octogenarians: comparison with high-risk younger patients.

Forty octogenarians (OCTO) undergoing a variety of cardiac and thoracic aortic surgeries using cardiopulmonary bypass (CPB) between 1994 and 2002 were retrospectively studied. The results were compared with those of high-risk younger patients aged less than 60 years (YOUNG) (n=89). All patients had an expected operative mortality of EuroSCORE 5 and over. The EuroSCORE score was 9.9+/-3.3 (range, 5-18) in the OCTO group and 6.8+/-2.3 (range, 5-16) in the YOUNG patients (p<0.0001). There were 4 (10%) and 10 (11%) hospital deaths, respectively (p>0.99). Major postoperative complications occurred in 50% of the OCTO and 36% of the YOUNG patients (p=0.17). There were 10 and 7 late deaths, respectively. Actuarial survival including hospital death was significantly lower in the OCTO group than in the YOUNG (p=0.033). Actuarial survival was significantly higher in female octogenarians than in male (p=0.046). The overall 3-year survival rate was 88+/-8% and 64+/-11%, respectively. Multivariate analysis showed that predictors of late death were male gender (p=0.0005) and a high EuroSCORE (p=0.0010). Cardiac and thoracic aortic surgery using CPB can be performed in octogenarians with an acceptable hospital mortality rate and gratifying medium-term survival results.

Aged↗

PubMed2003

Comparative study of the natural history and operative outcome in patients 75 years and older with thoracic aortic aneurysm.

Surgery for thoracic aortic aneurysm (TAA) in patients 75 years and older is a high risk, but data for their natural history are not available. In the present study the subjects were 62 patients with TAA aged on average 78 years (range, 75-85 years) enrolled between August 1994 and December 2001: 20 operatively treated patients (OPE) and 42 medically managed patients (MED). All of them had been included in the indication for TAA surgery at the time of consultation. Hospital mortality rates and survival rates (Kaplan-Meier method) were compared among emergency OPE, elective OPE, and MED. There were 136 total patient-years of follow-up. Actuarial survival in MED (ie, the natural history) was 83% at 1 year after consultation and 41% at 3 years. Hospital mortality rates in emergency and elective OPE were 27% (3/11) and 0% (0/9), respectively (p=0.22), and the corresponding 3-year survival rates were 44% and 83% (p=0.019). Actuarial survival in elective OPE was higher than that in MED (p=0.022), but that of emergency OPE was similar to that for MED (p=0.17). Patients aged 75 years and older with TAA should undergo an elective operation if the aneurysm diameter is larger than 6 cm and if the patient is asymptomatic and in good anatomicosurgical, physical, and social condition.

Aged↗

PubMed2002

Extensive use of polytetrafluoroethylene artificial grafts for prolapse of bilateral mitral leaflets.

OBJECTIVES: There are an increasing number of reports concerning mitral valve repair by reconstruction of the chordae tendinae with the use of expanded polytetrafluoroethylene (PTFE) sutures. However, little information is available about the extended application or results of this technique for extended prolapse of bilateral mitral leaflets, which is considered to be difficult to repair. METHODS: Between October 1993 and May 1998, 17 patients (age range 16-74 years) who had from moderate to severe mitral regurgitation as the result of a prolapse of bilateral leaflets underwent mitral valve repair by reconstruction of artificial chordae with CV-4 expanded PTFE sutures. Either bilateral or unilateral Kay's suture annuloplasty was also performed to correct annular dilatation in all patients. RESULTS: No operative death or late mortality was observed. Before discharge, immediate postoperative echocardiography showed less than moderate mitral regurgitation in 16 of 17 patients. The follow-up was completed in all cases by a clinical examination and serial echocardiograms, and the median follow-up period was 52 months (range 27-82 months). There was one failure that required re-operation because of worsening mitral regurgitation (elongation of the anchored side of papillary muscle). When the re-operated patient was excluded from the following data, the degree of mitral regurgitation, estimated by echocardiography performed at recent follow-up, was none in four patients, trivial in eight patients, and mild in four patients. The systolic and diastolic dimensions of the left ventricle decreased significantly (P<0.01). CONCLUSIONS: Because replacement of artificial chordae was not complicated and seemed to preserve fine relationships among leaflet tissues, chordae, and papillary muscles, we therefore suggest that the extensive use of PTFE artificial chordae appears to be a promising procedure for the repair of all kinds of mitral lesions causing mitral regurgitation.

Adolescent↗

PubMed2002

Bilateral testicular tumors: a report of nine cases with long-term follow-up.

BACKGROUND: The incidence and clinical features of bilateral germ cell testicular tumor (GCTT) in the Japanese population are not fully characterized. We examined the incidence, clinical features, management and outcome, sexual status, hormonal environment, implication of androgen replacement, and human leukocyte antigen (HLA) typing of bilateral GCTT. METHODS: We treated nine consecutive patients with bilateral GCTT from 1980 through to 1999, and reviewed their hospital and clinic charts. Testosterone, luteinizing hormone, follicle stimulating hormone, dehydroepiandrosterone, and dehydroepiandrosterone-sulfate were measured in bilateral orchiectomized patients. Human leukocyte antigen typing was assessed with peripheral lymphocyte. RESULTS: The incidence of bilateral GCTT against the total number of patients with GCTT was 9/274 (3.3%). The median age of the first tumor was 29 (range 21-75) years. Three cases were synchronous and the remaining six cases were metachronous. In the case of metachronous tumor, the median interval between first and contralateral tumor was 8 (range 2-25) years. Standard treatment was defined as surveillance policy in stage I, chemotherapy for higher stages of non-seminoma, and radiotherapy for stage II seminoma. Human leukocyte antigen typing was examined for seven cases. Five cases were positive for HLA-A24. The incidence of HLA-A24 in bilateral GCTT was identical to that of the Japanese population. The relapsing incidence of stage I disease with surveillance policy was almost identical to unilateral GCTT. A 74-year-old patient with stage II seminoma died of the disease at 1.3 years. The other eight patients remained well without any evidence of recurrence at a median follow-up period of 78 (range 12-204) months. Four patients with bilateral orchiectomy did not require androgen replacement without easy fatigability. Sexual status was conserved using androgen replacement. CONCLUSIONS: Long-term follow-up, as long as 25 years, is recommended for contralateral relapse. Some patients with bilateral orchiectomy do not require androgen replacement. The significance of HLA-A24 for bilateral testicular tumor is equivocal in the Japanese population.

Adult↗