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Search Results: 1 - 10 of 3398 matches for " Hirofumi Watanabe "
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Fragment Molecular Orbital Method: Application to Protein-Ligand Binding
Hirofumi Watanabe,Shigenori Tanaka
Interdisciplinary Bio Central , 2010,
Abstract: Fragment molecular orbital (FMO) method provides a novel tool for ab initio calculations of large biomolecules. This method overcomes the size limitation difficulties in conventional molecular orbital methods and has several advantages compared to classical force field approaches. While there are many features in this method, we here focus on explaining the issues related to protein-ligand binding: FMO method provides useful interaction-analysis tools such as IFIE, CAFI and FILM. FMO calculations can provide not only binding energies, which are well correlated with experimental binding affinity, but also QSAR descriptors. In addition, FMO-derived charges improve the descriptions of electrostatic properties and the correlations between docking scores and experimental binding affinities. These calculations can be performed by the ABINIT-MPX program and the calculation results can be visualized by its proper BioStation Viewer. The acceleration of FMO calculations on various computer facilities is ongoing, and we are also developing methods to deal with cytochrome P450, which belongs to the family of drug metabolic enzymes.
The p-q theory for active filter control: some problems and solutions
Watanabe, Edson H.;Aredes, Maurício;Akagi, Hirofumi;
Sba: Controle & Automa??o Sociedade Brasileira de Automatica , 2004, DOI: 10.1590/S0103-17592004000100010
Abstract: the instantaneous active and reactive power theory or the p-q theory is widely used to design controllers for active filters. this paper deals with some problems due to the misinterpretations of this theory. a historical background of the theory is presented and the problem caused by distorted voltages at the point of common connection (pcc) is analyzed. in addition, the appearance of source current harmonic component not present in the load current (hidden current) caused by different filtering characteristics for the calculation of the oscillating real and imaginary power components is discussed. the problem caused by the voltage distortion can be solved using a phase locked loop (pll) circuit. for the hidden current, filters with similar characteristics can avoid them. these analysis and solutions are presented to clarify some aspects of the p-q theory not clear in the original approach of the theory.
Usefulness of Fractional Exhaled Nitric Oxide-Guided Treatment in Patients with Asthma-Chronic Obstructive Pulmonary Disease Overlap  [PDF]
Taisuke Akamatsu, Toshihiro Shirai, Yuko Tanaka, Hirofumi Watanabe, Yoshinari Endo, Yukiko Shimoda, Takahito Suzuki, Rie Noguchi, Mika Saigusa, Akito Yamamoto, Yuichiro Shishido, Takefumi Akita, Satoru Morita, Kazuhiro Asada
Open Journal of Respiratory Diseases (OJRD) , 2018, DOI: 10.4236/ojrd.2018.81001
Abstract:
Background: Some patients present clinical features of both asthma and chronic obstructive pulmonary disease (COPD), which has led to the recent proposal of asthma-COPD overlap (ACO) as a diagnosis. Fractional exhaled nitric oxide (FeNO) is a candidate biomarker to diagnose ACO. We assessed the effect of an add-on treatment with budesonide/formoterol (BUD/FM) combination in patients with ACO, which was diagnosed by FeNO. Methods: This was a prospective, single-arm, open-label, before and after comparison study. Subjects included 83 patients with COPD who attended outpatient clinics for routine checkups at Shizuoka General Hospital between June and November 2016. All patients fulfilled the GOLD definition of COPD and were receiving long-acting muscarinic antagonist (LAMA) or LAMA/long-acting β2 agonist (LABA) combinations. After an 8-week run-in period, BUD/FM was added to the patients with FeNO levels of ≥35 ppb, defined as having ACO. For patients receiving LAMA/LABA, BUD/FM was added after the discontinuation of LABA. The modified British Medical Research Council (mMRC) score, COPD assessment test (CAT) score, spirometric indices, forced oscillation parameters, and FeNO were assessed before and after 8 weeks of BUD/ FM add-on treatment. Results: Twenty-four patients (28.9%) had FeNO levels ≥ 35 ppb, and 17 patients completed the study (mean age: 73 years and GOLD I/II/III/IV, 5/10/1/1). The mean CAT scores significantly improved (9.2 to 5.4, p = 0.015) and 10 patients (58.8%) showed ≥2 points improvement, a minimal clinically important difference. The mean FeNO levels significantly decreased from 63.0 to 34.3 ppb (p < 0.006). However, there were no changes in mMRC scores, spirometric indices, or forced oscillation parameters. Conclusions: FeNO-guided treatment with BUD/FM improves symptoms in patients with ACO.
A DKP Cyclo(L-Phe-L-Phe) Found in Chicken Essence Is a Dual Inhibitor of the Serotonin Transporter and Acetylcholinesterase
Nobuo Tsuruoka, Yoshinori Beppu, Hirofumi Koda, Nobutaka Doe, Hiroshi Watanabe, Keiichi Abe
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0050824
Abstract: Diketopiperazines (DKPs) are naturally-occurring cyclic dipeptides with a small structure and are found in many organisms and in large amounts in some foods and beverages. We found that a chicken essence beverage, which is popular among Southeast Asians as a traditional remedy and a rich source of DKPs, inhibited the serotonin transporter (SERT) and suppressed serotonin uptake from rat brain synaptosomes, which prompted us to isolate and identify the active substance(s). We purified a SERT inhibitor from the chicken essence beverage and identified it as the DKP cyclo(L-Phe-L-Phe). Interestingly, it was a naturally occurring dual inhibitor that inhibited both SERT and acetylcholinesterase (AChE) in vitro. The DKP increased extracellular levels of the cerebral monoamines serotonin, norepinephrine, and dopamine in the medial prefrontal cortex and acetylcholine in the ventral hippocampus of freely moving rats when administered orally. Moreover, cyclo(L-Phe-L-Phe) significantly shortened escape latency in the water maze test in depressed mice previously subjected to a repeated open-space swimming task, which induces a depression-like state. Cyclo(L-Phe-L-Phe) also significantly improved accuracy rates in a radial maze test in rats and increased step-through latencies in a passive avoidance test in mice with scopolamine-induced amnesia. These animal test results suggest that cyclo(L-Phe-L-Phe), which is present abundantly in some foods such as chicken essence, may abrogate the onset of depression and, thus, contribute to preventing the development of Alzheimer’s disease and other dementia, because senile depression is a risk factor for dementia.
Purification and partial genome characterization of the bacterial endosymbiont Blattabacterium cuenoti from the fat bodies of cockroaches
Gaku Tokuda, Nathan Lo, Aya Takase, Akinori Yamada, Yoshinobu Hayashi, Hirofumi Watanabe
BMC Research Notes , 2008, DOI: 10.1186/1756-0500-1-118
Abstract: B. cuenoti cells were successfully purified from the fat bodies of the cockroach Panesthia angustipennis by a combination of slow- and fast-speed centrifugal fractionations, nylon-membrane filtration, and centrifugation with Percoll solutions. We performed pulse-field electrophoresis, diagnostic PCR and random sequencing of the shoutgun library. These experiments confirmed minimal contamination of host and mitochondrial DNA. The genome size and the G+C content of B. cuenoti were inferred to be 650 kb and 32.1 ± 7.6%, respectively.The present study showed successful purification and characterization of the genome of B. cuenoti. Our methodology should be applicable for future symbiont genome sequencing projects. An advantage of the present purification method is that each step is easily performed with ordinary microtubes and a microcentrifuge, and without DNase treatment.Many eukaryotes have developed symbiotic relationships with bacterial endocytosymbionts [1,2]. These symbioses typically involve provision of nutrients by the bacterial partner to its host, and/or manipulation by the bacterial partner of the hosts' reproductive system [3]. Prior to the recent genomic revolution, details of their metabolism and physiology of many of these bacteria remained unknown, in part due to the difficulty of culturing these bacteria. Genome analyses have provided a wealth of information that will be crucial for elucidating the biology of these endosymbionts. The focus has been on symbionts in the phylum proteobacteria [4-13], although a few representatives of the other phyla have recently been sequenced [14,15].A challenging step in sequencing symbiont genomes is purification of the bacterial cells. In some cases, bacterial DNA that was directly extracted from accumulated bacteriocytes was pure enough for sequencing analyses [5,9]. However, in other cases, it was necessary to remove contaminated DNA derived from host nuclei and/or mitochondria. For example, purification of Blochm
Acute onset of intracranial subdural hemorrhage five days after spinal anesthesia for knee arthroscopic surgery: a case report
Tetsuo Hagino, Satoshi Ochiai, Yoshiyuki Watanabe, Shinya Senga, Masanori Saito, Hirofumi Naganuma, Eiichi Sato, Hirotaka Haro
Journal of Medical Case Reports , 2012, DOI: 10.1186/1752-1947-6-75
Abstract: We report the case of a 73-year-old Japanese woman who had acute onset of intracranial subdural hemorrhage five days after spinal anesthesia for knee arthroscopic surgery.This case highlights the need to pay attention to acute intracranial subdural hemorrhage as a complication after spinal anesthesia. If the headache persists even in a supine position or nausea occurs abruptly, computed tomography or magnetic resonance imaging of the brain should be conducted. An intracranial subdural hematoma may have a serious outcome and is an important differential diagnosis for headache after spinal anesthesia.Spinal (subarachnoid) anesthesia is a widely used general purpose anesthesia. However, serious complications, such as intracranial subdural hemorrhage, can rarely occur [1]. The incidence of intracranial subdural hemorrhage after spinal anesthesia has been reported to be one in 500,000 [2]. In a literature review, 35 cases were identified and most had a chronic course with onset after a postdural puncture headache [1]. We report a case of acute onset of an intracranial subdural hematoma without trauma five days after spinal anesthesia.A 73 year-old Japanese woman underwent arthroscopic surgery of the knee for a torn medial meniscus. She had a surgical history of excision of a right frontal meningioma 11 years ago. She was receiving medications for hypertension and hyperlipidemia. She had no history of trauma, headache or coagulation abnormalities.From around four years before presentation to our center, our patient started to experience right knee pain and was treated at her local hospital with intra-articular injections of hyaluronic acid and physical therapy. She was referred to our center because of deterioration of pain and a catching sensation on the medial side of her right knee joint. Examinations at presentation detected pain from the medial side to the popliteal region of her right knee joint, a restricted range of motion to -10 degree extension and 110 degree fl
Sod1 Loss Induces Intrinsic Superoxide Accumulation Leading to p53-Mediated Growth Arrest and Apoptosis
Kenji Watanabe,Shuichi Shibuya,Hirofumi Koyama,Yusuke Ozawa,Toshihiko Toda,Koutaro Yokote,Takahiko Shimizu
International Journal of Molecular Sciences , 2013, DOI: 10.3390/ijms140610998
Abstract: Oxidative damages induced by a redox imbalance cause age-related changes in cells and tissues. Superoxide dismutase (SOD) enzymes play a major role in the antioxidant system and they also catalyze superoxide radicals (O 2 · ?). Since the loss of cytoplasmic SOD (SOD1) resulted in aging-like phenotypes in several types of mouse tissue, SOD1 is essential for the maintenance of tissue homeostasis. To clarify the cellular function of SOD1, we investigated the cellular phenotypes of Sod1-deficient fibroblasts. We demonstrated that Sod1 deficiency impaired proliferation and induced apoptosis associated with O 2 · ? accumulation in the cytoplasm and mitochondria in fibroblasts. Sod1 loss also decreased the mitochondrial membrane potential and led to DNA damage-mediated p53 activation. Antioxidant treatments effectively improved the cellular phenotypes through suppression of both intracellular O 2 · ? accumulation and p53 activation in Sod1-deficient fibroblasts. In vivo experiments revealed that transdermal treatment with a vitamin C derivative significantly reversed the skin thinning commonly associated with the upregulated p53 action in the skin. Our findings revealed that intrinsic O 2 · ? accumulation promoted p53-mediated growth arrest and apoptosis as well as mitochondrial disfunction in the fibroblasts.
Pemt Deficiency Ameliorates Endoplasmic Reticulum Stress in Diabetic Nephropathy
Mayu Watanabe, Atsuko Nakatsuka, Kazutoshi Murakami, Kentaro Inoue, Takahiro Terami, Chigusa Higuchi, Akihiro Katayama, Sanae Teshigawara, Jun Eguchi, Daisuke Ogawa, Eijiro Watanabe, Jun Wada, Hirofumi Makino
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0092647
Abstract: Phosphatidylethanolamine N-methyltransferase (Pemt) catalyzes the methylation of phosphatidylethanolamine (PE) to phosphatidylcholine (PC) mainly in the liver. Under an obese state, the upregulation of Pemt induces endoplasmic reticulum (ER) stress by increasing the PC/PE ratio in the liver. We targeted the Pemt gene in mice to explore the therapeutic impact of Pemt on the progression of diabetic nephropathy and diabetes, which was induced by the injection of streptozotocin (STZ). Although the blood glucose levels were similar in STZ-induced diabetic Pemt+/+ and Pemt?/?mice, the glomerular hypertrophy and albuminuria in Pemt?/? mice were significantly reduced. Pemt deficiency reduced the intraglomerular F4/80-positive macrophages, hydroethidine fluorescence, tubulointerstitial fibrosis and tubular atrophy. The expression of glucose-regulated protein-78 (GRP78) was enriched in the renal tubular cells in STZ-induced diabetic mice, and this was ameliorated by Pemt deficiency. In mProx24 renal proximal tubular cells, the treatment with ER-stress inducers, tunicamycin and thapsigargin, increased the expression of GRP78, which was reduced by transfection of a shRNA lentivirus for Pemt (shRNA-Pemt). The number of apoptotic cells in the renal tubules was significantly reduced in Pemt?/? diabetic mice, and shRNA-Pemt upregulated the phosphorylation of Akt and decreased the cleavage of caspase 3 and 7 in mProx24 cells. Taken together, these findings indicate that the inhibition of Pemt activity ameliorates the ER stress associated with diabetic nephropathy in a model of type 1 diabetes and corrects the functions of the three major pathways downstream of ER stress, i.e. oxidative stress, inflammation and apoptosis.
An autopsy case of granulocyte-colony-stimulating-factor-producing extrahepatic bile duct carcinoma
Satoru Matsuyama, Tomonori Shimonishi, Hirofumi Yoshimura, Kensaku Higaki, Kenji Nasu, Mariko Toyooka, Shigehisa Aoki, Keiko Watanabe and Hajime Sugihara
World Journal of Gastroenterology , 2008,
Abstract: A 79-year-old man was referred to this department due to the presence of extrahepatic bile duct carcinoma with a tumor at the left chest wall. The lesion was suspected to be a metastasis of bile duct carcinoma to the left wall, however, computed tomography (CT) revealed no regional lymph node or liver metastases. In addition, cytological and pathological examinations did not show malignancy. At the time of admission, the white blood cell count was 21 460 cells/μL (neutrophils, 18 240 cells/μL) and this elevated to 106 040 before death. In addition, serum granulocyte colony-stimulating factor (G-CSF) was elevated. At 28 d after admission, the patient died. An autopsy showed a poorly differentiated adenocarcinoma with sarcomatous change, which had slightly invaded into the pancreas around the bile duct, and was found in the distal bile duct with multiple metastases to the chest wall, lung, kidney, adrenal body, liver, mesentery, vertebra and mediastinal and para-aortic lymph nodes, without locoregional lymph node and liver metastasis. The cancer cells showed positive immunohistochemical staining for anti-G-CSF antibody. This is believed to be the first report of an extrahepatic bile duct carcinoma that produces G-CSF. Since G-CSF-producing carcinoma and sarcomatous change of the biliary tract leads to poor prognosis, early diagnosis and treatment are needed. When infection is ruled out, the G-CSF in serum should be examined. In addition, examinations such as bone scintigraphy and chest CT should also be considered for distant metastasis.
Time Constants of the Transition between Onset and Decay Reynolds Numbers for the Appearance of Taylor-Couette Flow  [PDF]
Takashi Watanabe
World Journal of Mechanics (WJM) , 2012, DOI: 10.4236/wjm.2012.22009
Abstract: We investigate the onset and the decay of Taylor-Couette flow in finite cylinders, and we report the estimated time scales in the azimuthal section of the flow state transition between the super-critical state and the sub-critical state by fitting the numerical result to the solution of the Stuart-Landau equation. The inner cylinder rotates, and the outer cylinder and both end walls of the cylinders are stationary. Near the end walls of the cylinders, the value of the time scale is small. In the inner region, the radial velocity component has a large time scale near the center of the vortices, while the axial velocity component has a large time scale between the vortices.
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