Antidiabetic and Antiobesity Effects of Artemether in db/db Mice

Directory of Open Access Journals (Sweden)

Yu Guo

2018-01-01

Full Text Available This study is designed to investigate the effect of artemether on type 2 diabetic db/db mice. The experiments consisted of three groups: normal control (NC, db/+, 1% methylcellulose, intragastric administration, diabetic control (DM, db/db, 1% methylcellulose, intragastric administration, and artemether treated (artemether, db/db, 200 mg/kg of artemether, intragastric administration. The treatment lasted for two weeks. The food intake, body weight, and fasting blood glucose of mice were measured every three days. At the start and end of the experiment, the intraperitoneal glucose tolerance test (IPGTT and insulin tolerance test (IPITT were performed. We determined the serum insulin and glucagon levels by ELISA kits and calculated insulin resistance index (HOME-IR. HE staining was used to observe the morphologies of pancreas and liver in mice. The damage of pancreatic beta cells was evaluated by TUNEL staining and immunofluorescence. We found the following: (1 compared with the DM group, the food intake and weight increase rate of artemether group significantly reduced (P<0.05; (2 compared with pretreatment, artemether significantly reduced the fasting blood glucose levels, and the areas under the curves (AUCs of IPGTT were decreased significantly, increasing the tolerance to glucose of db/db mice. (P<0.05; (3 artemether improved hyperinsulinemia and decreased the AUCs of IPITT and HOME-IR, increasing the insulin sensitivity of db/db mice. (4 Artemether significantly ameliorated islet vacuolar degeneration and hepatic steatosis in db/db mice. (5 Artemether reduced the apoptosis of pancreatic beta cells and increased insulin secretion in db/db mice compared with DM group (P<0.05. Our results indicated that artemether significantly improved glucose homeostasis and insulin resistance and had the potential activity to prevent obesity, reduced the severity of fatty liver, and protected pancreatic beta cells, promising to treat type 2 diabetes.

Magnolia officinalis Extract Contains Potent Inhibitors against PTP1B and Attenuates Hyperglycemia in db/db Mice

Directory of Open Access Journals (Sweden)

Jing Sun

2015-01-01

Full Text Available Protein tyrosine phosphatase 1B (PTP1B is an established therapeutic target for type 2 diabetes mellitus (T2DM and obesity. The aim of this study was to investigate the inhibitory activity of Magnolia officinalis extract (ME on PTP1B and its anti-T2DM effects. Inhibition assays and inhibition kinetics of ME were performed in vitro. 3T3-L1 adipocytes and C2C12 myotubes were stimulated with ME to explore its bioavailability in cell level. The in vivo studies were performed on db/db mice to probe its anti-T2DM effects. In the present study, ME inhibited PTP1B in a reversible competitive manner and displayed good selectivity against PTPs in vitro. Furthermore, ME enhanced tyrosine phosphorylation levels of cellular proteins, especially the insulin-induced tyrosine phosphorylations of insulin receptor β-subunit (IRβ and ERK1/2 in a dose-dependent manner in stimulated 3T3-L1 adipocytes and C2C12 myotubes. Meanwhile, ME enhanced insulin-stimulated GLUT4 translocation. More importantly, there was a significant decrease in fasting plasma glucose level of db/db diabetic mice treated orally with 0.5 g/kg ME for 4 weeks. These findings indicated that improvement of insulin sensitivity and hypoglycemic effects of ME may be attributed to the inhibition of PTP1B. Thereby, we pioneered the inhibitory potential of ME targeted on PTP1B as anti-T2DM drug discovery.

Heterocyclic Dications as a New Class of Telomeric G-Quadruplex Targeting Agents

Science.gov (United States)

Nanjunda, Rupesh; Musetti, Caterina; Kumar, Arvind; Ismail, Mohamed A.; Farahat, Abdelbasset A.; Wang, Siming; Sissi, Claudia; Palumbo, Manlio; Boykin, David W.; Wilson, W. David

2013-01-01

Small molecules that can induce and stabilize G-quadruplex DNA structures represent a novel approach for anti-cancer and anti-parasitic therapy and extensive efforts have been directed towards discovering lead compounds that are capable of stabilizing quadruplexes. The purpose of this study is to explore conformational modifications in a series of heterocyclic dications to discover structural motifs that can selectively bind and stabilize specific G-quadruplexes, such as those present in the human telomere. The G-quadruplex has various potential recognition sites for small molecules; however, the primary interaction site of most of these ligands is the terminal tetrads. Similar to duplex-DNA groove recognition, quadruplex groove recognition by small molecules offers the potential for enhanced selectivity that can be developed into a viable therapeutic strategy. The compounds investigated were selected based on preliminary studies with DB832, a bifuryl-phenyl diamidine with a unique telomere interaction. This compound provides a paradigm that can help in understanding the optimum compound-DNA interactions that lead to quadruplex groove recognition. DNA recognition by the DB832 derivatives was investigated by biophysical experiments such as thermal melting, circular dichroism, mass spectrometry and NMR. Biological studies were also performed to complement the biophysical data. The results suggest a complex binding mechanism which involves the recognition of grooves for some ligands as well as stacking at the terminal tetrads of the human telomeric G-quadruplex for most of the ligands. These molecules represent an excellent starting point for further SAR analysis for diverse modes of quadruplex recognition and subsequent structure optimization for drug development. PMID:22380518

Quantitative GC-MS assay of citric acid from humans and db/db mice blood serum to assist the diagnosis of diabetic nephropathy.

Science.gov (United States)

Gao, Haoxue; Yu, Xiaoyi; Sun, Runbin; Yang, Na; He, Jun; Tao, Mingxue; Gu, Huilin; Yan, Caixia; Aa, Jiye; Wang, Guangji

2018-03-01

The early diagnosis of diabetic nephropathy (DN) is rather challenging. Our previous study suggested that citric acid is a potential marker for the early diagnosis of diabetic nephropathy in db/db mice. For the first time, in this study, a surrogate analyte of 13 C 6 -citric acid was employed to generate calibration curves for the quantitative measurement of the endogenous citric acid in the sera of db/db mice and diabetic nephropathy patients by GC/MS after the analytes were extracted, methoximated and trimethylsilylated. The constant response factor of 13 C 6 -citric acid versus citric acid over the linear range indicated the identical ionization efficiency of these two compounds. The full validation assessments suggested that the method is sensitive, specific, reliable, reproducible and has acceptable parameters. Statistical analysis revealed cut-off citric acid concentrations of 29.24 μg/mL with a 95% confidence interval between 32.75 and 39.16 μg/mL in the diabetic nephropathy patients and 16.74 and 22.57 μg/mL in the normal controls. The areas under the receiver operating characteristic curves indicated accuracies of over 90% for the diagnoses of early diabetic nephropathy in both humans and db/db mice, which suggests that the serum citric acid level is potentially a biomarker that could assist in the diagnosis of diabetic nephropathy. Copyright © 2018 Elsevier B.V. All rights reserved.

MonetDB: Two Decades of Research in Column-oriented Database Architectures

NARCIS (Netherlands)

S. Idreos (Stratos); F.E. Groffen (Fabian); N.J. Nes (Niels); S. Manegold (Stefan); K.S. Mullender (Sjoerd); M.L. Kersten (Martin)

2012-01-01

textabstractMonetDB is a state-of-the-art open-source column-store database management system targeting applications in need for analytics over large collections of data. MonetDB is actively used nowadays in health care, in telecommunications as well as in scientific databases and in data management

MonetDB: Two Decades of Research in Column-oriented Database Architectures

NARCIS (Netherlands)

Idreos, S.; Groffen, F.; Nes, N.; Manegold, S.; Mullender, S.; Kersten, M.

2012-01-01

MonetDB is a state-of-the-art open-source column-store database management system targeting applications in need for analytics over large collections of data. MonetDB is actively used nowadays in health care, in telecommunications as well as in scientific databases and in data management research,

Impaired Muscle Regeneration in Ob/ob and Db/db Mice

Directory of Open Access Journals (Sweden)

Mai-Huong Nguyen

2011-01-01

Full Text Available In obesity and type 2 diabetes, efficient skeletal muscle repair following injury may be required, not only for restoring muscle structure and function, but also for maintaining exercise capacity and insulin sensitivity. The hypothesis of this study was that muscle regeneration would be impaired in ob/ob and db/db mice, which are common mouse models of obesity and type 2 diabetes. Muscle injury was produced by cardiotoxin injection, and regeneration was assessed by morphological and immunostaining techniques. Muscle regeneration was delayed in ob/ob and db/db mice, but not in a less severe model of insulin resistance – feeding a high-fat diet to wild-type mice. Angiogenesis, cell proliferation, and myoblast accumulation were also impaired in ob/ob and db/db mice, but not the high-fat diet mice. The impairments in muscle regeneration were associated with impaired macrophage accumulation; macrophages have been shown previously to be required for efficient muscle regeneration. Impaired regeneration in ob/ob and db/db mice could be due partly to the lack of leptin signaling, since leptin is expressed both in damaged muscle and in cultured muscle cells. In summary, impaired muscle regeneration in ob/ob and db/db mice was associated with reduced macrophage accumulation, angiogenesis, and myoblast activity, and could have implications for insulin sensitivity in the skeletal muscle of obese and type 2 diabetic patients.

DB Energie 2020. Implementation of sustainability strategy DB2020; DB Energie 2020. Die Umsetzung der Nachhaltigkeitsstrategie DB2020

Energy Technology Data Exchange (ETDEWEB)

Witschke, Hans-Juergen [DB Energie GmbH, Frankfurt am Main (Germany)

2013-06-15

As a worldwide provider of mobility and logistics services and one of the biggest employers in Germany, Deutsche Bahn (DB) bears a special responsibility for customers, its own staff, the environment and society as a whole. In order to meet this responsibility, it has made the consistent implementation of the DB Energie 2020 sustainability concept an essential element of its business strategy. Following this line of business provides DB with good opportunities on the one hand but also carries risks and challenges on the other. (orig.)

MELCOR DB Construction for the Severe Accident Analysis DB

International Nuclear Information System (INIS)

Song, Y. M.; Ahn, K. I.

2011-01-01

The Korea Atomic Energy Research Institute (KAERI) has been constructing a severe accident analysis database (DB) under a National Nuclear R and D Program. In particular, an MAAP (commercial code being widely used in industries for integrated severe accident analysis) DB for many scenarios including a station blackout (SBO) has been completed. This paper shows the MELCOR DB construction process with examples of SBO scenarios, and the results will be used for a comparison with the MAAP DB

MonetDB: Two Decades of Research in Column-oriented Database Architectures

OpenAIRE

Idreos, Stratos; Groffen, Fabian; Nes, Niels; Manegold, Stefan; Mullender, Sjoerd; Kersten, Martin

2012-01-01

textabstractMonetDB is a state-of-the-art open-source column-store database management system targeting applications in need for analytics over large collections of data. MonetDB is actively used nowadays in health care, in telecommunications as well as in scientific databases and in data management research, accumulating on average more than 10,000 downloads on a monthly basis. This paper gives a brief overview of the MonetDB technology as it developed over the past two decades and the main r...

Proteases in Plasma and Kidney of db/db Mice as Markers of Diabetes-Induced Nephropathy

Science.gov (United States)

Hadler-Olsen, E.; Winberg, J.-O.; Reinholt, F. P.; Larsen, T.; Uhlin-Hansen, L.; Jenssen, T.; Berg, E.; Kolset, S. O.

2011-01-01

Db/db mice are overweight, dyslipidemic and develop diabetic complications, relevant for similar complications in human type 2 diabetes. We have used db/db and db/+ control mice to investigate alterations in proteinase expression and activity in circulation and kidneys by SDS-PAGE zymography, electron microscopy, immunohistochemistry, Western blotting, and in situ zymography. Plasma from db/db mice contained larger amounts of serine proteinases compared to db/+ mice. Kidneys from the db/db mice had a significantly larger glomerular surface area and somewhat thicker glomerular basement membranes compared to the db/+ mice. Furthermore, kidney extracts from db/+ mice contained metalloproteinases with M r of approximately 92000, compatible with MMP-9, not observed in db/db mice. These results indicate that higher levels of serine proteinases in plasma may serve as potential markers for kidney changes in db/db mice, whereas a decrease in MMP-9 in the kidney may be related to the glomerular changes. PMID:22363890

Mastering MariaDB

CERN Document Server

Razzoli, Federico

2014-01-01

This book is intended for intermediate users who want to learn how to administrate a MariaDB server or a set of servers. It is aimed at MariaDB users, and hence working knowledge of MariaDB is a prerequisite.

Portulaca oleracea Ameliorates Diabetic Vascular Inflammation and Endothelial Dysfunction in db/db Mice

Science.gov (United States)

Lee, An Sook; Lee, Yun Jung; Lee, So Min; Yoon, Jung Joo; Kim, Jin Sook; Kang, Dae Gill; Lee, Ho Sub

2012-01-01

Type 2 diabetes is associated with significantly accelerated rates of micro- and macrovascular complications such as diabetic vascular inflammation and endothelial dysfunction. In the present study, we investigated the protective effect of the aqueous extract of Portulaca oleracea L. (AP), an edible plant used as a folk medicine, on diabetic vascular complications. The db/db mice were treated with AP (300 mg/kg/day, p.o.) for 10 weeks, and AP treatment markedly lowered blood glucose, plasma triglyceride, plasma level of LDL-cholesterol, and systolic blood pressure in diabetic db/db mice. Furthermore, AP significantly increased plasma level of HDL-cholesterol and insulin level. The impairment of ACh- and SNP-induced vascular relaxation of aortic rings were ameliorated by AP treatment in diabetic db/db mice. This study also showed that overexpression of VCAM-1, ICAM-1, E-selectin, MMP-2, and ET-1 were observed in aortic tissues of untreated db/db mice, which were significantly suppressed by treatment with AP. We also found that the insulin immunoreactivity of the pancreatic islets remarkably increased in AP treated db/db mice compared with untreated db/db mice. Taken together, AP suppresses hyperglycemia and diabetic vascular inflammation, and prevents the development of diabetic endothelial dysfunction for the development of diabetes and its vascular complications. PMID:22474522

Zinc Prevents the Development of Diabetic Cardiomyopathy in db/db Mice

Directory of Open Access Journals (Sweden)

Shudong Wang

2017-03-01

Full Text Available Diabetic cardiomyopathy (DCM is highly prevalent in type 2 diabetes (T2DM patients. Zinc is an important essential trace metal, whose deficiency is associated with various chronic ailments, including vascular diseases. We assessed T2DM B6.BKS(D-Leprdb/J (db/db mice fed for six months on a normal diet containing three zinc levels (deficient, adequate, and supplemented, to explore the role of zinc in DCM development and progression. Cardiac function, reflected by ejection fraction, was significantly decreased, along with increased left ventricle mass and heart weight to tibial length ratio, in db/db mice. As a molecular cardiac hypertrophy marker, atrial natriuretic peptide levels were also significantly increased. Cardiac dysfunction and hypertrophy were accompanied by significantly increased fibrotic (elevated collagen accumulation as well as transforming growth factor β and connective tissue growth factor levels and inflammatory (enhanced expression of tumor necrosis factor alpha, interleukin-1β, caspase recruitment domain family member 9, and B-cell lymphoma/leukemia 10, and activated p38 mitogen-activated protein kinase responses in the heart. All these diabetic effects were exacerbated by zinc deficiency, and not affected by zinc supplementation, respectively. Mechanistically, oxidative stress and damage, mirrored by the accumulation of 3-nitrotyrosine and 4-hydroxy-2-nonenal, was significantly increased along with significantly decreased expression of Nrf2 and its downstream antioxidants (NQO-1 and catalase. This was also exacerbated by zinc deficiency in the db/db mouse heart. These results suggested that zinc deficiency promotes the development and progression of DCM in T2DM db/db mice. The exacerbated effects by zinc deficiency on the heart of db/db mice may be related to further suppression of Nrf2 expression and function.

Ultrasonographic Characterization of the db/db Mouse: An Animal Model of Metabolic Abnormalities

Directory of Open Access Journals (Sweden)

Francesco Faita

2018-01-01

Full Text Available The availability of an animal model able to reliably mirror organ damage occurring in metabolic diseases is an urgent need. These models, mostly rodents, have not been fully characterized in terms of cardiovascular, renal, and hepatic ultrasound parameters, and only sparse values can be found in literature. Aim of this paper is to provide a detailed, noninvasive description of the heart, vessels, liver, and kidneys of the db/db mouse by ultrasound imaging. Sixteen wild type and thirty-four db/db male mice (11-week-old were studied. State-of-the-art ultrasound technology was used to acquire images of cardiovascular, renal, and hepatic districts. A set of parameters describing function of the selected organs was evaluated. db/db mice are characterized by systolic and diastolic dysfunction, confirmed by strain analysis. Abdominal aortic and carotid stiffness do not seem to be increased in diabetic rodents; furthermore, they are characterized by a smaller mean diameter for both vessels. Renal microcirculation is significantly compromised, while liver steatosis is only slightly higher in db/db mice than in controls. We offer here for the first time an in vivo detailed ultrasonographic characterization of the db/db mouse, providing a useful tool for a thoughtful choice of the right rodent model for any experimental design.

Adeno-associated virus-mediated expression of myostatin propeptide improves the growth of skeletal muscle and attenuates hyperglycemia in db/db mice.

Science.gov (United States)

Jiang, J G; Shen, G F; Li, J; Qiao, C; Xiao, B; Yan, H; Wang, D W; Xiao, X

2017-03-01

Inhibition of myostatin, a negative growth modulator for muscle, can functionally enhance muscle mass and improve glucose and fat metabolism in myostatin propeptide (MPRO) transgenic mice. This study was to investigate whether myostatin inhibition by adeno-associated virus (AAV)-mediated gene delivery of MPRO could improve muscle mass and achieve therapeutic effects on glucose regulation and lipid metabolism in the db/db mice and the mechanisms involved in that process. Eight-week-old male db/db mice were administered saline, AAV-GFP and AAV-MPRO/Fc vectors and monitored random blood glucose levels and body weight for 36 weeks. Body weight gain was not different during follow-up among the groups, but AAV-MPRO/Fc vectors resulted high level of MPRO in the blood companied by an increase in skeletal muscle mass and muscle hypertrophy. In addition, AAV-MPRO/Fc-treated db/db mice showed significantly lower blood glucose and insulin levels and significantly increased glucose tolerance and insulin sensitivity compared with the control groups (P<0.05). Moreover, these mice exhibited lower triglyceride (TG) and free fatty acid (FFA) content in the skeletal muscle, although no difference was observed in fat pad weights and serum TG and FFA levels. Finally, AAV-MPRO/Fc-treated mice had enhanced insulin signaling in the skeletal muscle. These data suggest that AAV-mediated MPRO therapy may provide an important clue for potential clinical applications to prevent type II diabetes, and these studies confirm that MPRO is a therapeutic target for type II diabetes.

Coordinate Transcriptomic and Metabolomic Effects of the Insulin Sensitizer Rosiglitazone on Fundamental Metabolic Pathways in Liver, Soleus Muscle, and Adipose Tissue in Diabetic db/db Mice

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Sabrina Le Bouter

2010-01-01

Full Text Available Rosiglitazone (RSG, developed for the treatment of type 2 diabetes mellitus, is known to have potent effects on carbohydrate and lipid metabolism leading to the improvement of insulin sensitivity in target tissues. To further assess the capacity of RSG to normalize gene expression in insulin-sensitive tissues, we compared groups of 18-day-treated db/db mice with increasing oral doses of RSG (10, 30, and 100 mg/kg/d with untreated non-diabetic littermates (db/+. For this aim, transcriptional changes were measured in liver, inguinal adipose tissue (IAT and soleus muscle using microarrays and real-time PCR. In parallel, targeted metabolomic assessment of lipids (triglycerides (TGs and free fatty acids (FFAs in plasma and tissues was performed by UPLC-MS methods. Multivariate analyses revealed a relationship between the differential gene expressions in liver and liver trioleate content and between blood glucose levels and a combination of differentially expressed genes measured in liver, IAT, and muscle. In summary, we have integrated gene expression and targeted metabolomic data to present a comprehensive overview of RSG-induced changes in a diabetes mouse model and improved the molecular understanding of how RSG ameliorates diabetes through its effect on the major insulin-sensitive tissues.

Instant InnoDB

CERN Document Server

Reid, Matt

2013-01-01

This book is a complete reference guide, designed to provide you with answers and solutions to all the common problems you encounter within InnoDB, helping you achieve higher performance and greater stability in your InnoDB databases.The ""InnoDB Quick Reference Guide"" features content for all skill levels of MySQL administrators, developers, and engineers.

The Synthesis of Dicationic Extended Bis-Benzimidazoles

OpenAIRE

Kang, Zhijan; Dykstra, Christine C.; Boykin, David W.

2004-01-01

The synthesis of extended dicationic bis-benzimidazoles starting from trans-1,2-bis(4-cyanophenyl)ethene and trans-1,2-bis(4-cyanophenyl)cyclopropane is reported. The target diamidines show significant in vitro activity against B. subtilis.

MongoDB high availability

CERN Document Server

Mehrabani, Afshin

2014-01-01

This book has a perfect balance of concepts and their practical implementation along with solutions to make a highly available MongoDB server with clear instructions and guidance. If you are using MongoDB in a production environment and need a solution to make a highly available MongoDB server, this book is ideal for you. Familiarity with MongoDB is expected so that you understand the content of this book.

Elevated Steroid Hormone Production in the db/db Mouse Model of Obesity and Type 2 Diabetes.

Science.gov (United States)

Hofmann, Anja; Peitzsch, Mirko; Brunssen, Coy; Mittag, Jennifer; Jannasch, Annett; Frenzel, Annika; Brown, Nicholas; Weldon, Steven M; Eisenhofer, Graeme; Bornstein, Stefan R; Morawietz, Henning

2017-01-01

Obesity and type 2 diabetes have become a major public health problem worldwide. Steroid hormone dysfunction appears to be linked to development of obesity and type 2 diabetes and correction of steroid abnormalities may offer new approaches to therapy. We therefore analyzed plasma steroids in 15-16 week old obese and diabetic db/db mice using liquid chromatography-tandem mass spectrometry. Lean db/+ served as controls. Db/db mice developed obesity, hyperglycemia, hyperleptinemia, and hyperlipidemia. Hepatic triglyceride storage was increased and adiponectin and pancreatic insulin were lowered. Aldosterone, corticosterone, 11-deoxycorticosterone, and progesterone were respectively increased by 3.6-, 2.9-, 3.4, and 1.7-fold in db/db mice compared to controls. Ratios of aldosterone-to-progesterone and corticosterone-to-progesterone were respectively 2.0- and 1.5-fold higher in db/db mice. Genes associated with steroidogenesis were quantified in the adrenal glands and gonadal adipose tissues. In adrenals, Cyp11b2 , Cyp11b1 , Cyp21a1 , Hsd3b1 , Cyp11a1 , and StAR were all significantly increased in db/db mice compared with db/+ controls. In adipose tissue, no Cyp11b2 or Cyp11b1 transcripts were detected and no differences in Cyp21a1 , Hsd3b1 , Cyp11a1 , or StAR expression were found between db/+ and db/db mice. In conclusion, the present study showed an elevated steroid hormone production and adrenal steroidogenesis in the db/db model of obesity and type 2 diabetes. © Georg Thieme Verlag KG Stuttgart · New York.

Low Voltage CMOS Fully Differential Current Feedback Amplifier with Controllable 3-dB Bandwidth

International Nuclear Information System (INIS)

Madian, A.H.; Mahmoud, S.A.; Ashour, M.A.; Soliman, A.M.

2008-01-01

This paper presents a new CMOS fully differential current feedback operational amplifier with controllable 3-dB bandwidth suitable for analog data processing and acquisition applications. The FDCFOA has the advantage of a wide range controllable 3-dB bandwidth (∼57 MHz to 500 MHz) without changing the feedback resistance this guarantee the stability of the circuit. The FDCFOA has a standby current of 320μA. PSpice simulations of the FDCFOA block were given using 0.25μm CMOS technology from AMI MOSIS and dual supply voltages ±0.75 V

Protective effects of astragaloside IV on db/db mice with diabetic retinopathy.

Directory of Open Access Journals (Sweden)

Yuzhi Ding

Full Text Available Diabetic retinopathy (DR is a common diabetic eye disease which is well-known as the result of microvascular retinal changes. Although the potential biological functions of astragaloside IV (AS IV have long been described in traditional system of medicine, its protective effect on DR remains unclear. This study aims to investigate the function and mechanism of AS IV on type 2 diabetic db/db mice.Db/db mice were treated with AS IV (4.5 mg/kg or 9 mg/kg or physiological saline by oral gavage for 20 weeks along with db/m mice. In each group, retinal ganglion cell (RGC function was measured by pattern electroretinogram (ERG and apoptosis was determined by Terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL staining. Blood and retina aldose reductase (AR activity were quantified by chemiluminescence analysis. The expressions of phosporylated-ERK1/2, NF-κB were determined by Western blot analysis. Furthermore, the expression of related downstream proteins were quantified by Label-based Mouse Antibody Array.Administration of AS IV significantly improved the amplitude in pattern ERG and reduced the apoptosis of RGCs.in db/db mice. Furthermore, downregulation of AR activity, ERK1/2 phosphorylation, NF-κB and related cytokine were observed in AS IV treatment group.Our study indicated that AS IV, as an inhibitor of AR, could prevent the activation of ERK1/2 phosporylation and NF-kB and further relieve the RGCs disfunction in db/db mice with DR. It has provided a basis for investigating the clinical efficacy of AR inhibitors in preventing DR.

Liver PPARα and UCP2 are involved in the regulation of obesity and lipid metabolism by swim training in genetically obese db/db mice

International Nuclear Information System (INIS)

Oh, Ki Sook; Kim, Mina; Lee, Jinmi; Kim, Min Jeong; Nam, Youn Shin; Ham, Jung Eun; Shin, Soon Shik; Lee, Chung Moo; Yoon, Michung

2006-01-01

Swim training for 6 weeks significantly decreased body weight gain, adipose tissue mass, and adipocyte size in both sexes of genetically obese db/db mice compared with their respective sedentary controls. Swim training also caused significant decreases in serum levels of free fatty acids, triglycerides, and total cholesterol in both sexes of obese mice. Concomitantly, hepatic mRNA levels of peroxisome proliferator-activated receptor α (PPARα) target enzymes responsible for mitochondrial and peroxisomal fatty acid β-oxidation were significantly increased by swim training. Moreover, mRNA levels of uncoupling protein 2 (UCP2) in liver were also markedly increased by swim training. In conclusion, these results suggest that swim training-induced transcriptional activation of hepatic PPARα target enzymes and UCP2 may effectively prevent body weight gain, adiposity, and lipid disorders caused by leptin receptor deficiency in both sexes of mice

Exendin-4 improves resistance to Listeria monocytogenes infection in diabetic db/db mice

OpenAIRE

Liu, Hsien Yueh; Chung, Chih-Yao; Yang, Wen-Chin; Liang, Chih-Lung; Wang, Chi-Young; Chang, Chih-Yu; Chang, Cicero Lee-Tian

2012-01-01

The incidence of diabetes mellitus is increasing among companion animals. This disease has similar characteristics in both humans and animals. Diabetes is frequently identified as an independent risk factor for infections associated with increased mortality. In the present study, homozygous diabetic (db/db) mice were infected with Listeria (L.) monocytogenes and then treated with the anti-diabetic drug exendin-4, a glucagon-like peptide 1 analogue. In aged db/db mice, decreased CD11b+ macroph...

Basalt aquifer identification, correlation and sampling activities. History of Wells DB-8, DB-9, DB-10 and DB-11

International Nuclear Information System (INIS)

Webster, C.T.

1979-07-01

Research core wells have been completed to assist in the characterization of the groundwater regime of the upper confined aquifers found within the basalts of the Hanford Site. These wells were drilled on the Hanford Site for the Long-Term Transuranic Defense Waste Program. They were constructed to assure the Department of Energy that waste management operations will not provide an avenue for offsite migration of radionuclides. This second report details results of confined aquifer drilling activities. The purpose of this report is to document the drilling history of the wells by presenting as-built well construction diagrams and tables listing hole history data, coring records and bit records. Four wells were cored to a maximum depth of 1100 feet and water samples were taken from selected confined aquifers. Full depth was reached on all wells and core recovery was 94% of all formations drilled. Well DB-8 was abandoned after a well screen was destroyed while setting it in the well. Two wells, DB-9 and DB-10 were screened in the Mabton interbed and water was produced from this interval in both wells. Well DB-11 was used to explore for artesian water from the Priest Rapids flow unit on the western edge of the Hanford Site. The water was found at a depth of 1045 feet and now produces makeup water for all Hanford drilling

Efficacy of Acetylshikonin in Preventing Obesity and Hepatic Steatosis in db/db Mice

Directory of Open Access Journals (Sweden)

Mei-Ling Su

2016-07-01

Full Text Available Zicao (Lithospermum erythrorhizon has been used in clinics as a traditional Chinese medicine for thousands of years. Acetylshikonin (AS is the main ingredient of Zicao, Xinjiang, China. The objective of this study was to investigate the anti-obesity and anti-nonalcoholic fatty liver disease (NAFLD efficacy of AS in a model of spontaneous obese db/db mice. Mice were divided into Wild Type (WT groups and db/db groups, which received no treatment or treatment with 100 mg/kg/day clenbuterol (CL hydrochloride or 540 mg/kg/day AS by oral gavage for eight weeks. The results provided the evidence that AS prevented obesity and NAFLD including reduction in body weight, food efficiency ratio, serum triglyceride (TG and free fatty acid (FFA levels in db/db mice. Administration of AS markedly suppressed the levels of hepatic alanine aminotransferase (ALT, aspartate aminotransferase (AST and pro-inflammatory cytokines in treated groups when compared with that of db/db groups. Further investigation of the lipid synthesis-related protein using Western blotting revealed that hepatic protein expression of sterol regulatory element-binding protein-1 (SREBP-1, fatty acid synthetase (FAS and 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMGCR were significantly downregulated by AS treatment. These findings suggest that AS exerts anti-obesity and anti-NAFLD effects through the regulation of lipid metabolism and anti-inflammatory effects.

Alkannin Inhibited Hepatic Inflammation in Diabetic Db/Db Mice

Directory of Open Access Journals (Sweden)

Wenhua Xue

2018-03-01

Full Text Available Background/Aims: The current study was designed to investigate the protective role of alkannin (ALK on liver injury in diabetic C57BL/KsJ-db/db mice and explore its potential mechanisms. Methods: An oral glucose tolerance test (OGTT was performed. The levels of insulin, alanine aminotransferase (ALT, aspartate aminotransaminase (AST, total cholesterol (TC and triglyceride (TG were determined by commercial kits. The pro-inflammatory cytokines interleukin (IL-1β, IL-6 and tumour necrosis factor (TNF-α were determined by ELISA. The levels of the ROCK/NF-κB pathway were determined by Western blotting. Results: The contents of pro-inflammatory cytokines interleukin (IL-1β, IL-6 and tumour necrosis factor (TNF-α were inhibited by ALK, metformin or fasudil in diabetic db/db mice. Further, Western blotting analysis showed that the expression of Rho, ROCK1, ROCK2, p-NF-κBp65, and p-IκBα was significantly reversed by ALK treatment. In human hepatic HepG2 cells, the hepatoprotective effects of ALK were further characterized. With response to palmitic acid-challenge, increased amounts of insulin, ALT, AST, TG, and TC were observed, whereas ALK pretreatment significantly inhibited their leakage in HepG2 cells without appreciable cytotoxic effects. The inflammation condition was recovered with ALK treatment as shown by changes of IL-1β, IL-6 and TNF-α. Further, Western blotting analysis also suggested that ALK improves hepatic inflammation in a Rho-kinase pathway. Conclusion: The present study successfully investigated the role of Rho-kinase signalling in diabetic liver injury. ALK exhibited hepatoprotective effects in diabetic db/db mice, and it might act through improving hepatic inflammation through the Rho-kinase pathway.

ZiBuPiYin recipe protects db/db mice from diabetes-associated cognitive decline through improving multiple pathological changes.

Directory of Open Access Journals (Sweden)

Jing Chen

Full Text Available Multiple organ systems, including the brain, which undergoes changes that may increase the risk of cognitive decline, are adversely affected by diabetes mellitus (DM. Here, we demonstrate that type 2 diabetes mellitus (T2DM db/db mice exhibited hippocampus-dependent memory impairment, which might associate with a reduction in dendritic spine density in the pyramidal neurons of brain, Aβ1-42 deposition in the prefrontal cortex (PFC and hippocampus, and a decreased expression of neurostructural proteins including microtubule-associated protein (MAP2, a marker of dendrites, and postsynaptic density 95 (PSD95, a marker of excitatory synapses. To investigate the effects of the ZiBuPiYin recipe (ZBPYR, a traditional Chinese medicine recipe, on diabetes-related cognitive decline (DACD, db/db mice received daily administration of ZBPYR over an experimental period of 6 weeks. We then confirmed that ZBPYR rescued learning and memory performance impairments, reversed dendritic spine loss, reduced Aβ1-42 deposition and restored the expression levels of MAP2 and PSD95. The present study also revealed that ZBPYR strengthened brain leptin and insulin signaling and inhibited GSK3β overactivity, which may be the potential mechanism or underlying targets of ZBPYR. These findings conclude that ZBPYR prevents DACD, most likely by improving dendritic spine density and attenuating brain leptin and insulin signaling pathway injury. Our findings provide further evidence for the effects of ZBPYR on DACD.

Validity of leptin receptor-deficiency (db/db) type 2 diabetes mellitus mice as a model of secondary osteoporosis

Science.gov (United States)

Huang, Le; You, Yong-Ke; Zhu, Tracy Y.; Zheng, Li-Zhen; Huang, Xiao-Ru; Chen, Hai-Yong; Yao, Dong; Lan, Hui-Yao; Qin, Ling

2016-06-01

This study aimed to evaluate the validation of the leptin receptor-deficient mice model for secondary osteoporosis associated with type 2 diabetes mellitus (T2DM) at bone micro-architectural level. Thirty three 36-week old male mice were divided into four groups: normal control (db/m) (n = 7), leptin receptor-deficient T2DM (db/db) (n = 8), human C-reactive protein (CRP) transgenic normal control (crp/db/m) (n = 7), and human CRP transgenic T2DM (crp/db/db) (n = 11). Lumber vertebrae (L5) and bilateral lower limbs were scanned by micro-CT to analyze trabecular and cortical bone quality. Right femora were used for three-point bending to analyze the mechanical properties. Trabecular bone quality at L5 was better in db/db or crp/db/db group in terms of bone mineral density (BMD), bone volume fraction, connectivity density, trabecular number and separation (all p  0.05). Maximum loading and energy yield in mechanical test were similar among groups while the elastic modulus in db/db and crp/db/db significantly lower than db/m. The leptin-receptor mice is not a proper model for secondary osteoporosis associated with T2DM.

Scaling CouchDB

CERN Document Server

Holt, Bradley

2011-01-01

This practical guide offers a short course on scaling CouchDB to meet the capacity needs of your distributed application. Through a series of scenario-based examples, this book lets you explore several methods for creating a system that can accommodate growth and meet expected demand. In the process, you learn about several tools that can help you with replication, load balancing, clustering, and load testing and monitoring. Apply performance tips for tuning your databaseReplicate data, using Futon and CouchDB's RESTful interfaceDistribute CouchDB's workload through load balancingLearn option

75 FR 35919 - Investment Company Advertising: Target Date Retirement Fund Names and Marketing

Science.gov (United States)

2010-06-23

... rule 34b-1 to require a statement in marketing materials to the effect that a target date retirement... in these marketing materials at times belies the fact that asset allocation strategies among target...: Target Date Retirement Fund Names and Marketing; Proposed Rule #0;#0;Federal Register / Vol. 75 , No. 120...

Perivascular adipose tissue control of insulin-induced vasoreactivity in muscle is impaired in db/db mice

DEFF Research Database (Denmark)

Meijer, Rick I; Bakker, Wineke; Alta, Caro-Lynn A F

2013-01-01

in muscle, the underlying mechanisms, and how obesity disturbs this vasodilation. Insulin-induced vasoreactivity of resistance arteries was studied with PVAT from C57BL/6 or db/db mice. PVAT weight in muscle was higher in db/db mice compared with C57BL/6 mice. PVAT from C57BL/6 mice uncovered insulin......-induced vasodilation; this vasodilation was abrogated with PVAT from db/db mice. Blocking adiponectin abolished the vasodilator effect of insulin in the presence of C57BL/6 PVAT, and adiponectin secretion was lower in db/db PVAT. To investigate this interaction further, resistance arteries of AMPKa2(+/+) and AMPKa2......-induced vasodilation in an adiponectin-dependent manner. In conclusion, PVAT controls insulin-induced vasoreactivity in the muscle microcirculation through secretion of adiponectin and subsequent AMPKa2 signaling. PVAT from obese mice inhibits insulin-induced vasodilation, which can be restored by inhibition of JNK....

XMetDB

DEFF Research Database (Denmark)

Spjuth, Ola; Rydberg, Patrik; Willighagen, Egon L

2016-01-01

Xenobiotic metabolism is an active research topic but the limited amount of openly available high-quality biotransformation data constrains predictive modeling. Current database often default to commonly available information: which enzyme metabolizes a compound, but neither experimental conditions...... nor the atoms that undergo metabolization are captured. We present XMetDB, an open access database for drugs and other xenobiotics and their respective metabolites. The database contains chemical structures of xenobiotic biotransformations with substrate atoms annotated as reaction centra...... is also available. The database is open for data deposition, and a curation scheme is in place for quality control. An extensive guide on how to enter experimental data into is available from the XMetDB wiki. XMetDB formalizes how biotransformation data should be reported, and the openly available...

TaDb: A time-aware diffusion-based recommender algorithm

Science.gov (United States)

Li, Wen-Jun; Xu, Yuan-Yuan; Dong, Qiang; Zhou, Jun-Lin; Fu, Yan

2015-02-01

Traditional recommender algorithms usually employ the early and recent records indiscriminately, which overlooks the change of user interests over time. In this paper, we show that the interests of a user remain stable in a short-term interval and drift during a long-term period. Based on this observation, we propose a time-aware diffusion-based (TaDb) recommender algorithm, which assigns different temporal weights to the leading links existing before the target user's collection and the following links appearing after that in the diffusion process. Experiments on four real datasets, Netflix, MovieLens, FriendFeed and Delicious show that TaDb algorithm significantly improves the prediction accuracy compared with the algorithms not considering temporal effects.

Inhibiting the NLRP3 Inflammasome Activation with MCC950 Ameliorates Diabetic Encephalopathy in db/db Mice

Directory of Open Access Journals (Sweden)

Yadong Zhai

2018-02-01

Full Text Available Diabetes is associated with a high risk of developing cognitive dysfunction and neuropsychiatric disabilities, and these disease symptomsare termed diabetic encephalopathy (DEP. Inflammation is involved in the development of DEP. The cleavage and maturation of the proinflammatory cytokine interleukin (IL-1β is regulated by the NLRP3 inflammasome. Obese and type 2 diabetic db/db mice show anxiety- and depression-like behaviors and cognitive disorders associated with hippocampal inflammation. The purpose of this study was to explore the role of NLRP3 inflammasome in DEP. Results showed that expression levels of inflammasome components including NLRP3, apoptosis-associated speck-like protein (ASC, and caspase-1, as well as IL-1β in the hippocampus of diabetic db/db mice were higher than those of non-diabetic db/m mice. Treatment of db/db mice with NLRP3 inflammasome inhibitor MCC950 ameliorated anxiety- and depression-like behaviors as well as cognitive dysfunction, and reversed increased NLRP3, ASC, and IL-1βexpression levels and caspase-1 activity in hippocampus. Moreover, MCC950 treatment significantly improved insulin sensitivity in db/db mice. These results demonstrate that inhibition of NLRP3 inflammasome activation may prove to be a potential therapeutic approach for DEP treatment.

Resistin production from adipose tissue is decreased in db/db obese mice, and is reversed by rosiglitazone.

Directory of Open Access Journals (Sweden)

Hongying Ye

Full Text Available OBJECTIVE: This study was designed to (1 investigate the expression profiles of resistin in db/db mice and its dynamic association with metabolic parameters; and (2 evaluate the effects of Rosiglitazone on production of resistin. METHODS: Db/db mice and their lean litter mates were used for this study. Epididymal fat tissue was excised from mice of different age (from 5 to 12 weeks for ex vivo incubation. Resistin,along with adiponectin,in serum and conditioned culture medium of epididymal fat pads were measured with immunoassays. The gene expression of resistin was determined by real-time PCR. Rosiglitazone or the vehicle (PBS was administered into db/db mice by daily intra-gastric gavage. Differentiated 3T3-L1 adipocytes were used for in vitro evaluation. RESULTS: The secretion of resistin from the fat pads in db/db mice was significantly lower than that in lean mice (P<0.01. The mRNA expression of the resistin gene in fat tissue of db/db mice at the age of 5 weeks was decreased by 60.5% compared to lean controls (p<0.05. Serum levels of resistin were comparable between the obese and lean groups, perhaps due to the increased total fat mass in db/db mice. Correlation analysis showed that serum resistin levels were positively correlated to resistin secretion from fat pads(r = 0.844,P = 0.000, while negatively associated with the body weight (r = -0.515, P = 0.000 and fasting glucose level (r = -0.357, P = 0.002. Notably, treatment with rosiglitazone increased the serum resistin levels by 66.4%(P<0.05in db/db mice. In 3T3-L1 adipocytes, Rosiglitazone (10 uM markedly enhanced the secretion of resistin by 120% (P<0.01 and its gene expression by 78.1% (P<0.05. CONCLUSION: Both resistin gene expression and its secretion from the epididymal adipose tissue were decreased in db/db obese mice, while the insulin-sensitizing drug rosiglitazone increased resistin production. Our results do not support the role of resistin as an

Scaling MongoDB

CERN Document Server

Chodorow, Kristina

2011-01-01

Create a MongoDB cluster that will to grow to meet the needs of your application. With this short and concise book, you'll get guidelines for setting up and using clusters to store a large volume of data, and learn how to access the data efficiently. In the process, you'll understand how to make your application work with a distributed database system. Scaling MongoDB will help you: Set up a MongoDB cluster through shardingWork with a cluster to query and update dataOperate, monitor, and backup your clusterPlan your application to deal with outages By following the advice in this book, you'l

RavenDB high performance

CERN Document Server

Ritchie, Brian

2013-01-01

RavenDB High Performance is comprehensive yet concise tutorial that developers can use to.This book is for developers & software architects who are designing systems in order to achieve high performance right from the start. A basic understanding of RavenDB is recommended, but not required. While the book focuses on advanced topics, it does not assume that the reader has a great deal of prior knowledge of working with RavenDB.

ProteomicsDB.

Science.gov (United States)

Schmidt, Tobias; Samaras, Patroklos; Frejno, Martin; Gessulat, Siegfried; Barnert, Maximilian; Kienegger, Harald; Krcmar, Helmut; Schlegl, Judith; Ehrlich, Hans-Christian; Aiche, Stephan; Kuster, Bernhard; Wilhelm, Mathias

2018-01-04

ProteomicsDB (https://www.ProteomicsDB.org) is a protein-centric in-memory database for the exploration of large collections of quantitative mass spectrometry-based proteomics data. ProteomicsDB was first released in 2014 to enable the interactive exploration of the first draft of the human proteome. To date, it contains quantitative data from 78 projects totalling over 19k LC-MS/MS experiments. A standardized analysis pipeline enables comparisons between multiple datasets to facilitate the exploration of protein expression across hundreds of tissues, body fluids and cell lines. We recently extended the data model to enable the storage and integrated visualization of other quantitative omics data. This includes transcriptomics data from e.g. NCBI GEO, protein-protein interaction information from STRING, functional annotations from KEGG, drug-sensitivity/selectivity data from several public sources and reference mass spectra from the ProteomeTools project. The extended functionality transforms ProteomicsDB into a multi-purpose resource connecting quantification and meta-data for each protein. The rich user interface helps researchers to navigate all data sources in either a protein-centric or multi-protein-centric manner. Several options are available to download data manually, while our application programming interface enables accessing quantitative data systematically. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Impairment of the vascular relaxation and differential expression of caveolin-1 of the aorta of diabetic +db/+db mice.

Science.gov (United States)

Lam, Tze Yan; Seto, Sai Wang; Lau, Yee Man; Au, Lai Shan; Kwan, Yiu Wa; Ngai, Sai Ming; Tsui, Kwong Wing

2006-09-28

In this study, we compared the endothelium-dependent and -independent relaxation of the isolated thoracic aorta of control (+db/+m) and diabetic (+db/+db) (C57BL/KsJ) mice. The gene expression (mRNA and protein) level of the muscarinic M(3) receptors, endothelial nitric oxide synthase (eNOS) and caveolin-1 of the aorta was also evaluated. Acetylcholine caused a concentration-dependent, N(G)-nitro-L-arginine methyl-ester (20 microM)-sensitive relaxation, with approximately 100% relaxation at 10 microM, in +db/+m mice. In +db/+db mice, the acetylcholine-induced relaxation was significantly smaller (maximum relaxation: approximately 80%). The sodium nitroprusside-mediated relaxation was slightly diminished in +db/+db mice, compared to +db/+m mice. However, there was no significant difference in the isoprenaline- and cromakalim-induced relaxation observed in both species. The mRNA and protein expression levels of caveolin-1 were significantly higher in the aorta of +db/+db mice. In contrast, there was no difference in the mRNA and protein expression levels of eNOS and muscarinic M(3) receptors between these mice. Our results demonstrate that the impairment of the acetylcholine-induced, endothelium-dependent aortic relaxation observed in +db/+db mice was probably associated with an enhanced expression of caveolin-1 mRNA and protein.

DBA2J db/db mice are susceptible to early albuminuria and glomerulosclerosis that correlate with systemic insulin resistance.

Science.gov (United States)

Østergaard, Mette V; Pinto, Vanda; Stevenson, Kirsty; Worm, Jesper; Fink, Lisbeth N; Coward, Richard J M

2017-02-01

Diabetic nephropathy (DN) is the leading cause of kidney failure in the world. To understand important mechanisms underlying this condition, and to develop new therapies, good animal models are required. In mouse models of type 1 diabetes, the DBA/2J strain has been shown to be more susceptible to develop kidney disease than other common strains. We hypothesized this would also be the case in type 2 diabetes. We studied db/db and wild-type (wt) DBA/2J mice and compared these with the db/db BLKS/J mouse, which is currently the most widely used type 2 DN model. Mice were analyzed from age 6 to 12 wk for systemic insulin resistance, albuminuria, and glomerular histopathological and ultrastructural changes. Body weight and nonfasted blood glucose were increased by 8 wk in both genders, while systemic insulin resistance commenced by 6 wk in female and 8 wk in male db/db DBA/2J mice. The urinary albumin-to-creatinine ratio (ACR) was closely linked to systemic insulin resistance in both sexes and was increased ~50-fold by 12 wk of age in the db/db DBA/2J cohort. Glomerulosclerosis, foot process effacement, and glomerular basement membrane thickening were observed at 12 wk of age in db/db DBA/2J mice. Compared with db/db BLKS/J mice, db/db DBA/2J mice had significantly increased levels of urinary ACR, but similar glomerular histopathological and ultrastructural changes. The db/db DBA/2J mouse is a robust model of early-stage albuminuric DN, and its levels of albuminuria correlate closely with systemic insulin resistance. This mouse model will be helpful in defining early mechanisms of DN and ultimately the development of novel therapies. Copyright © 2017 the American Physiological Society.

Bile acid sequestration reduces plasma glucose levels in db/db mice by increasing its metabolic clearance rate.

Directory of Open Access Journals (Sweden)

Maxi Meissner

Full Text Available AIMS/HYPOTHESIS: Bile acid sequestrants (BAS reduce plasma glucose levels in type II diabetics and in murine models of diabetes but the mechanism herein is unknown. We hypothesized that sequestrant-induced changes in hepatic glucose metabolism would underlie reduced plasma glucose levels. Therefore, in vivo glucose metabolism was assessed in db/db mice on and off BAS using tracer methodology. METHODS: Lean and diabetic db/db mice were treated with 2% (wt/wt in diet Colesevelam HCl (BAS for 2 weeks. Parameters of in vivo glucose metabolism were assessed by infusing [U-(13C]-glucose, [2-(13C]-glycerol, [1-(2H]-galactose and paracetamol for 6 hours, followed by mass isotopologue distribution analysis, and related to metabolic parameters as well as gene expression patterns. RESULTS: Compared to lean mice, db/db mice displayed an almost 3-fold lower metabolic clearance rate of glucose (p = 0.0001, a ∼300% increased glucokinase flux (p = 0.001 and a ∼200% increased total hepatic glucose production rate (p = 0.0002. BAS treatment increased glucose metabolic clearance rate by ∼37% but had no effects on glucokinase flux nor total hepatic or endogenous glucose production. Strikingly, BAS-treated db/db mice displayed reduced long-chain acylcarnitine content in skeletal muscle (p = 0.0317 but not in liver (p = 0.189. Unexpectedly, BAS treatment increased hepatic FGF21 mRNA expression 2-fold in lean mice (p = 0.030 and 3-fold in db/db mice (p = 0.002. CONCLUSIONS/INTERPRETATION: BAS induced plasma glucose lowering in db/db mice by increasing metabolic clearance rate of glucose in peripheral tissues, which coincided with decreased skeletal muscle long-chain acylcarnitine content.

Curcumin restores mitochondrial functions and decreases lipid peroxidation in liver and kidneys of diabetic db/db mice

Directory of Open Access Journals (Sweden)

María G Soto-Urquieta

2014-01-01

Full Text Available BACKGROUND: Nitrosative and oxidative stress play a key role in obesity and diabetes-related mitochondrial dysfunction. The objective was to investigate the effect of curcumin treatment on state 3 and 4 oxygen consumption, nitric oxide (NO synthesis, ATPase activity and lipid oxidation in mitochondria isolated from liver and kidneys of diabetic db/db mice. RESULTS: Hyperglycaemia increased oxygen consumption and decreased NO synthesis in liver mitochondria isolated from diabetic mice relative to the control mice. In kidney mitochondria, hyperglycaemia increased state 3 oxygen consumption and thiobarbituric acid-reactive substances (TBARS levels in diabetic mice relative to control mice. Interestingly, treating db/db mice with curcumin improved or restored these parameters to normal levels; also curcumin increased liver mitochondrial ATPase activity in db/db mice relative to untreated db/db mice. CONCLUSIONS: These findings suggest that hyperglycaemia modifies oxygen consumption rate, NO synthesis and increases TBARS levels in mitochondria from the liver and kidneys of diabetic mice, whereas curcumin may have a protective role against these alterations.

Resistin production from adipose tissue is decreased in db/db obese mice, and is reversed by rosiglitazone.

Science.gov (United States)

Ye, Hongying; Zhang, Herbert J; Xu, Aimin; Hoo, Ruby L C

2013-01-01

This study was designed to (1) investigate the expression profiles of resistin in db/db mice and its dynamic association with metabolic parameters; and (2) evaluate the effects of Rosiglitazone on production of resistin. Db/db mice and their lean litter mates were used for this study. Epididymal fat tissue was excised from mice of different age (from 5 to 12 weeks) for ex vivo incubation. Resistin,along with adiponectin,in serum and conditioned culture medium of epididymal fat pads were measured with immunoassays. The gene expression of resistin was determined by real-time PCR. Rosiglitazone or the vehicle (PBS) was administered into db/db mice by daily intra-gastric gavage. Differentiated 3T3-L1 adipocytes were used for in vitro evaluation. The secretion of resistin from the fat pads in db/db mice was significantly lower than that in lean mice (Plean controls (plean groups, perhaps due to the increased total fat mass in db/db mice. Correlation analysis showed that serum resistin levels were positively correlated to resistin secretion from fat pads(r = 0.844,P = 0.000), while negatively associated with the body weight (r = -0.515, P = 0.000) and fasting glucose level (r = -0.357, P = 0.002). Notably, treatment with rosiglitazone increased the serum resistin levels by 66.4%(Pproduction. Our results do not support the role of resistin as an etiological link between obesity and diabetes.

CouchDB the definitive guide

CERN Document Server

Anderson, J; Slater, Noah

2010-01-01

Three of CouchDB's creators show you how to use this document-oriented database as a standalone application framework or with high-volume, distributed applications. With its simple model for storing, processing, and accessing data, CouchDB is ideal for web applications that handle huge amounts of loosely structured data. That alone would stretch the limits of a relational database, yet CouchDB offers an open source solution that's reliable, scales easily, and responds quickly. CouchDB works with self-contained data that has loose or ad-hoc connections. It's a model that fits many real-world

Getting Started with CouchDB

CERN Document Server

Brown, MC

2012-01-01

CouchDB is a new breed of database for the Internet, geared to meet the needs of today's dynamic web applications. With this concise introduction, you'll learn how CouchDB's simple model for storing, processing, and accessing data makes it ideal for the type of data and rapid response users now demand from your applications-and how easy CouchDB is to set up, deploy, maintain, and scale. The code-packed examples in this book will help you learn how to work with documents, populate a simple database, replicate data from one database to another, and a host of other tasks. Install CouchDB on Lin

Getting started with MariaDB

CERN Document Server

Bartholomew, Daniel

2013-01-01

A practical, hands-on, beginner-friendly guide to installing and using MariaDB.Getting Started with MariaDB is for anyone who wants to learn more about databases in general or MariaDB in particular. No prior database experience is required. It is assumed that you have basic knowledge of software installation, editing files with a text editor, and using the command line and terminal.

Dioscorea Extract (DA-9801) Modulates Markers of Peripheral Neuropathy in Type 2 Diabetic db/db Mice.

Science.gov (United States)

Moon, Eunjung; Lee, Sung Ok; Kang, Tong Ho; Kim, Hye Ju; Choi, Sang Zin; Son, Mi-Won; Kim, Sun Yeou

2014-09-01

The purpose of this study was to investigate the therapeutic effects of DA-9801, an optimized extract of Dioscorea species, on diabetic peripheral neuropathy in a type 2 diabetic animal model. In this study, db/db mice were treated with DA-9801 (30 and 100 mg/kg, daily, p.o.) for 12 weeks. DA-9801 reduced the blood glucose levels and increased the withdrawal latencies in hot plate tests. Moreover, it prevented nerve damage based on increased nerve conduction velocity and ultrastructural changes. Decrease of nerve growth factor (NGF) may have a detrimental effect on diabetic neuropathy. We previously reported NGF regulatory properties of the Dioscorea genus. In this study, DA-9801 induced NGF production in rat primary astrocytes. In addition, it increased NGF levels in the sciatic nerve and the plasma of type 2 diabetic animals. DA-9801 also increased neurite outgrowth and mRNA expression of Tieg1/Klf10, an NGF target gene, in PC12 cells. These results demonstrated the attenuation of diabetic peripheral neuropathy by oral treatment with DA-9801 via NGF regulation. DA-9801 is currently being evaluated in a phase II clinical study.

Qing-Hua Granule induces GLP-1 secretion via bitter taste receptor in db/db mice.

Science.gov (United States)

Li, Junyan; Xu, Jie; Hou, Ruifang; Jin, Xin; Wang, Jingyi; Yang, Na; Yang, Li; Liu, Li; Tao, Feng; Lu, Hao

2017-05-01

Qing-Hua Granule (QHG), the modified formulation of a classical Chinese prescription named Gegen Qinlian Decoction, was clinically employed to treat type 2 diabetes mellitus (T2DM) through regulation of glucagon-like peptide-1 (GLP-1). However, the potential mechanism is unknown. We investigate whether QHG induces GLP-1 secretion via activation of bitter taste receptor (TAS2R) pathway in the gastrointestinal tract of db/db mice. The db/db mice were intragastrically (i.g.) administered QHG (low/medium/high dose) once daily for 8 weeks. GLP-1 secretion was evaluated. The bitter receptor signaling pathway, which regulates GLP-1 secretion, including TAS2R5 (a subtype of TAS2R), α-gustducin (Gαgust), 1-phosphatidylinositol-4, 5-bisphosphate phosphodiesterase beta-2 (PLCβ2), transient receptor potential cation channel subfamily M member 5 (TRPM5), was assessed by quantitative real-time polymerase chain reaction (qRT-PCR), Western blot and immunohistochemistry (IHC). The biochemical observations of ileum and pancreas tissue were detected histopathologically. Acquity Ultra Performance LCTM - Micromass ZQ 2000 (UPLC-MS) was used for the phytochemical analysis. QHG exhibited significant and dose-dependent effect on GLP-1 secretion in db/db mice, along with significant up-regulation of TAS2R5 mRNA level and activation of TAS2R pathway (p<0.05). In addition, QHG improved the histopathological structure of ileum and pancreatic tissue. Seventeen compounds were identified in QHG. In conclusion, QHG induces GLP-1 secretion in db/db mice, most likely through the bitter taste receptor pathway. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Telmisartan ameliorates insulin sensitivity by activating the AMPK/SIRT1 pathway in skeletal muscle of obese db/db mice

Directory of Open Access Journals (Sweden)

Shiota Asuka

2012-11-01

Full Text Available Abstract Background Telmisartan is a well-established angiotensin II type 1 receptor blocker that improves insulin sensitivity in animal models of obesity and insulin resistance, as well as in humans. Telmisartan has been reported to function as a partial agonist of the peroxisome proliferator-activated receptor (PPAR γ, which is also targeted by the nicotinamide adenine dinucleotide (NAD-dependent deacetylase (SIRT1. Here, we investigated the pathways through which telmisartan acts on skeletal muscle, in vitro as well as in vivo. Methods Nine-week-old male db/db mice were fed a 60% high-fat diet, with orally administrated either vehicle (carboxymethyl-cellulose, CMC, 5 mg/kg telmisartan, or 5 mg/kg telmisartan and 1 mg/kg GW9662, a selective irreversible antagonist of PPARγ, for 5 weeks. Effects of telmisartan on Sirt1 mRNA, AMPK phosphorylation, and NAD+/NADH ratio were determined in C2C12 cultured myocytes. Results and discussion Telmisartan treatment improved insulin sensitivity in obese db/db mice fed a high-fat diet and led to reduction in the size of hypertrophic pancreatic islets in these mice. Moreover, in vitro treatment with telmisartan led to increased expression of Sirt1 mRNA in C2C12 skeletal muscle cells; the increase in Sirt1 mRNA in telmisartan-treated C2C12 myoblasts occurred concomitantly with an increase in AMPK phosphorylation, an increase in NAD+/NADH ratio, and increases in the mRNA levels of PGC1α, FATP1, ACO, and GLUT4. Conclusions Our results indicate that telmisartan acts through a PPARγ-independent pathway, but at least partially exerts its effects by acting directly on skeletal muscle AMPK/SIRT1 pathways.

MongoDB and PHP

CERN Document Server

Francia, Steve

2012-01-01

What would happen if you optimized a data store for the operations application developers actually use? You'd arrive at MongoDB, the reliable document-oriented database. With this concise guide, you'll learn how to build elegant database applications with MongoDB and PHP. Written by the Chief Solutions Architect at 10gen-the company that develops and supports this open source database-this book takes you through MongoDB basics such as queries, read-write operations, and administration, and then dives into MapReduce, sharding, and other advanced topics. Get out of the relational database rut,

Effect of zinc nutriture on tissue zinc (Zn) in the diabetic C57BL/KsJ db/db mouse

International Nuclear Information System (INIS)

Donaldson, D.L.; Smith, C.C.; Walker, M.S.; Yunice, A.A.; Rennert, O.M.

1986-01-01

The genetically obese diabetic db/db mouse has been reported to have low serum (S) and femur (F) Zn concentrations. In order to examine whether this animal model is predisposed to dietary Zn deficiency, they measured tissue Zn concentrations (conc.) in db/db, heterozygous db/m, and homozygous m/m control mice fed either a zinc deficient diet (2 ppm Zn) ad libitum or a zinc adequate diet (20 ppm Zn) either ad libitum or in restricted amounts (equal to that consumed by mice on the 2 ppm Zn diet) for 12 wks. The results were analyzed by analysis of variance for a completely randomized 3X3 design. Similar clinical manifestations of Zn deficiency were seen in mice of all 3 genotypes after 8-10 weeks on 2 ppm Zn. S Zn(p=0.0001) and F Zn conc.(p=0.0001) and content(p=0.0001) of those 3 groups showed similar marked reductions. S Zn was not reduced in db/db mice fed 20 ppm Zn. F Zn conc. was mildly reduced in these mice but not to the extent observed in mice fed 2 ppm Zn. Liver (L) Zn conc. was not affected by either genotype or diet, but total L Zn(p=0.0001) was greater in db/db mice due to their larger L weight. Kidney (K) Zn conc.(p=0.0001) of db/db mice was slightly but significantly decreased, but their total K Zn content(p=0.0001) was increased due to their greater K weights. They conclude that, in spite of its having a decreased F Zn conc. and content, the db/db mouse does not appear to be particularly susceptible to dietary Zn deficiency

Antibodies against human cytochrome P-450db1 in autoimmune hepatitis type II.

Science.gov (United States)

Zanger, U M; Hauri, H P; Loeper, J; Homberg, J C; Meyer, U A

1988-11-01

In a subgroup of children with chronic active hepatitis, circulating autoantibodies occur that bind to liver and kidney endoplasmic reticulum (anti-liver/kidney microsome antibody type I or anti-LKM1). Anti-LKM1 titers follow the severity of the disease and the presence of these antibodies serves as a diagnostic marker for this autoimmune hepatitis type II. We demonstrate that anti-LKM1 IgGs specifically inhibit the hydroxylation of bufuralol in human liver microsomes. Using two assay systems with different selectivity for the two cytochrome P-450 isozymes catalyzing bufuralol metabolism in human liver, we show that anti-LKM1 exclusively recognizes cytochrome P-450db1. Immunopurification of the LKM1 antigen from solubilized human liver microsomes resulted in an electrophoretically homogenous protein that had the same molecular mass (50 kDa) as purified P-450db1 and an identical N-terminal amino acid sequence. Recognition of both purified P-450db1 and the immunoisolated protein on western blots by several monoclonal antibodies confirmed the identity of the LKM1 antigen with cytochrome P-450db1. Cytochrome P-450db1 has been identified as the target of a common genetic polymorphism of drug oxidation. However, the relationship between the polymorphic cytochrome P-450db1 and the appearance of anti-LKM1 autoantibodies as well as their role in the pathogenesis of chronic active hepatitis remains speculative.

AFM-based detection of glycocalyx degradation and endothelial stiffening in the db/db mouse model of diabetes.

Science.gov (United States)

Targosz-Korecka, Marta; Jaglarz, Magdalena; Malek-Zietek, Katarzyna E; Gregorius, Aleksandra; Zakrzewska, Agnieszka; Sitek, Barbara; Rajfur, Zenon; Chlopicki, Stefan; Szymonski, Marek

2017-11-21

Degradation of the glycocalyx and stiffening of endothelium are important pathophysiological components of endothelial dysfunction. However, to our knowledge, these events have not been investigated in tandem in experimental diabetes. Here, the mechanical properties of the glycocalyx and endothelium in ex vivo mouse aorta were determined simultaneously in indentation experiments with an atomic force microscope (AFM) for diabetic db/db and control db/+ mice at ages of 11-19 weeks. To analyze highly heterogeneous aorta samples, we developed a tailored classification procedure of indentation data based on a bi-layer brush model supplemented with Hertz model for quantification of nanomechanics of endothelial regions with and without the glycocalyx surface. In db/db mice, marked endothelial stiffening and reduced glycocalyx coverage were present already in 11-week-old mice and persisted in older animals. In contrast, reduction of the effective glycocalyx length was progressive and was most pronounced in 19-week-old db/db mice. The reduction of the glycocalyx length correlated with an increasing level of glycated haemoglobin and decreased endothelial NO production. In conclusion, AFM nanoindentation analysis revealed that stiffening of endothelial cells and diminished glycocalyx coverage occurred in early diabetes and were followed by the reduction of the glycocalyx length that correlated with diabetes progression.

Anti-diabetic and hypolipidemic effects of Sargassum yezoense in db/db mice

International Nuclear Information System (INIS)

Kim, Su-Nam; Lee, Woojung; Bae, Gyu-Un; Kim, Yong Kee

2012-01-01

Highlights: ► Sargassum yezoense (SY) treatment improved glucose and lipid impairment in vivo. ► This pharmacological action is associated with PPARα/γ dual activation. ► It decreases the expression of G6Pase for gluconeogenesis in liver. ► It increases the expression of UCP3 for lipid metabolism in adipose tissue. ► There are no significant side effects such as body weight gain and hepatomegaly. -- Abstract: Peroxisome proliferator-activated receptors (PPARs) have been considered to be desirable targets for metabolic syndrome, even though their specific agonists have several side effects including body weight gain, edema and tissue failure. Previously, we have reported in vitro effects of Sargassum yezoense (SY) and its ingredients, sargaquinoic acid (SQA) and sargahydroquinoic acid (SHQA), on PPARα/γ dual transcriptional activation. In this study, we describe in vivo pharmacological property of SY on metabolic disorders. SY treatment significantly improved glucose and lipid impairment in db/db mice model. More importantly, there are no significant side effects such as body weight gain and hepatomegaly in SY-treated animals, indicating little side effects of SY in liver and lipid metabolism. In addition, SY led to a decrease in the expression of G6Pase for gluconeogenesis in liver responsible for lowering blood glucose level and an increase in the expression of UCP3 in adipose tissue for the reduction of total and LDL-cholesterol level. Altogether, our data suggest that SY would be a potential therapeutic agent against type 2 diabetes and related metabolic disorders by ameliorating the glucose and lipid metabolism.

Chemical behaviour of a few atoms of rutherfordium (Rf, Z= 104) and of dubnium (Db, Z= 105) produced at Orsay

International Nuclear Information System (INIS)

Trubert, D.; Hussonnois, M.; Le Naour, C.; Brillard, L.; Monroy Guzman, F.; Le Du, J.F.; Servajean, V.

1998-01-01

The isotopes 261 Rf and 262 Db were produced by irradiation of a 248 Cm target with respectively 18 O and 19 F ions, at the MP Tandem accelerator of Orsay (France). These isotopes were isolated in HF medium, using he RACHEL setup. Moreover, the radioisotope 262 DB was produced by a nuclear reaction. (authors)

Sharing mutants and experimental information prepublication using FgMutantDb (https://scabusa.org/FgMutantDb).

Science.gov (United States)

Baldwin, Thomas T; Basenko, Evelina; Harb, Omar; Brown, Neil A; Urban, Martin; Hammond-Kosack, Kim E; Bregitzer, Phil P

2018-06-01

There is no comprehensive storage for generated mutants of Fusarium graminearum or data associated with these mutants. Instead, researchers relied on several independent and non-integrated databases. FgMutantDb was designed as a simple spreadsheet that is accessible globally on the web that will function as a centralized source of information on F. graminearum mutants. FgMutantDb aids in the maintenance and sharing of mutants within a research community. It will serve also as a platform for disseminating prepublication results as well as negative results that often go unreported. Additionally, the highly curated information on mutants in FgMutantDb will be shared with other databases (FungiDB, Ensembl, PhytoPath, and PHI-base) through updating reports. Here we describe the creation and potential usefulness of FgMutantDb to the F. graminearum research community, and provide a tutorial on its use. This type of database could be easily emulated for other fungal species. Published by Elsevier Inc.

dbEM: A database of epigenetic modifiers curated from cancerous and normal genomes

Science.gov (United States)

Singh Nanda, Jagpreet; Kumar, Rahul; Raghava, Gajendra P. S.

2016-01-01

We have developed a database called dbEM (database of Epigenetic Modifiers) to maintain the genomic information of about 167 epigenetic modifiers/proteins, which are considered as potential cancer targets. In dbEM, modifiers are classified on functional basis and comprise of 48 histone methyl transferases, 33 chromatin remodelers and 31 histone demethylases. dbEM maintains the genomic information like mutations, copy number variation and gene expression in thousands of tumor samples, cancer cell lines and healthy samples. This information is obtained from public resources viz. COSMIC, CCLE and 1000-genome project. Gene essentiality data retrieved from COLT database further highlights the importance of various epigenetic proteins for cancer survival. We have also reported the sequence profiles, tertiary structures and post-translational modifications of these epigenetic proteins in cancer. It also contains information of 54 drug molecules against different epigenetic proteins. A wide range of tools have been integrated in dbEM e.g. Search, BLAST, Alignment and Profile based prediction. In our analysis, we found that epigenetic proteins DNMT3A, HDAC2, KDM6A, and TET2 are highly mutated in variety of cancers. We are confident that dbEM will be very useful in cancer research particularly in the field of epigenetic proteins based cancer therapeutics. This database is available for public at URL: http://crdd.osdd.net/raghava/dbem.

Tangshen formula attenuates hepatic steatosis by inhibiting hepatic lipogenesis and augmenting fatty acid oxidation in db/db mice.

Science.gov (United States)

Kong, Qin; Zhang, Haojun; Zhao, Tingting; Zhang, Weiku; Yan, Meihua; Dong, Xi; Li, Ping

2016-12-01

Tangshen formula (TSF), a well-prescribed traditional Chinese formula, has been used in the treatment of diabetic nephropathy. However, whether TSF ameliorates dyslipidemia and liver injury associated with diabetes remains unclear. In this study, we examined the effects of TSF on lipid profiles and hepatic steatosis in db/db mice. For this purpose, 8‑week-old db/db mice were treated with TSF or saline for 12 weeks via gavage and db/m mice were used as controls. Body weight and blood glucose levels were monitored weekly and bi-weekly, respectively. Blood samples were obtained for the analysis of lipids and enzymes related to hepatic function, and liver tissues were analyzed by histology, immunohistochemistry and molecular examination. The results revealed that TSF markedly reduced body weight, liver index [liver/body weight (LW/BW)] and improved lipid profiles, hepatic function and steatosis in db/db mice. TSF induced the phosphoralation of AMP-activated protein kinase and inhibited the activity of sterol regulatory element-binding protein 1 together with the inhibition of the expression of genes involved in de novo lipogenesis (DNL) and gluconeogenesis, such as fatty acid synthase (FAS), acetyl-CoA carboxylase (ACC), stearoyl CoA desaturase 1 (SCD1), glucose-6-phosphatase (G6pc) and phosphoenolpyruvate carboxykinase 1 (Pck1). Additionally, the silent mating type information regulation 2 homolog 1 (Sirt1)/peroxisome proliferator-activated receptor α (PPARα)/malonyl-CoA decarboxylase (MLYCD) cascade was potently activated by TSF in the liver and skeletal muscle of db/db mice, which led to enhanced fatty acid oxidation. These findings demonstrated that TSF attenuated hepatic fat accumulation and steatosis in db/db mice by inhibiting lipogenesis and augmenting fatty acid oxidation.

Improved cerebral energetics and ketone body metabolism in db/db mice

DEFF Research Database (Denmark)

Andersen, Jens V; Christensen, Sofie K; Nissen, Jakob D

2017-01-01

It is becoming evident that type 2 diabetes mellitus is affecting brain energy metabolism. The importance of alternative substrates for the brain in type 2 diabetes mellitus is poorly understood. The aim of this study was to investigate whether ketone bodies are relevant candidates to compensate...... metabolism in type 2 diabetes mellitus. The increased hippocampal ketone body utilization and improved mitochondrial function in db/db mice, may act as adaptive mechanisms in order to maintain cerebral energetics during hampered glucose metabolism....

MongoDB the definitive guide

CERN Document Server

Chodorow, Kristina

2010-01-01

How does MongoDB help you manage a huMONGOus amount of data collected through your web application? With this authoritative introduction, you'll learn the many advantages of using document-oriented databases, and discover why MongoDB is a reliable, high-performance system that allows for almost infinite horizontal scalability. Written by engineers from 10gen, the company that develops and supports this open source database, MongoDB: The Definitive Guide provides guidance for database developers, advanced configuration for system administrators, and an overview of the concepts and use cases f

The db/db mouse: a useful model for the study of diabetic retinal neurodegeneration.

Directory of Open Access Journals (Sweden)

Patricia Bogdanov

Full Text Available BACKGROUND: To characterize the sequential events that are taking place in retinal neurodegeneration in a murine model of spontaneous type 2 diabetes (db/db mouse. METHODS: C57BLKsJ-db/db mice were used as spontaneous type 2 diabetic animal model, and C57BLKsJ-db/+ mice served as the control group. To assess the chronological sequence of the abnormalities the analysis was performed at different ages (8, 16 and 24 weeks. The retinas were evaluated in terms of morphological and functional abnormalities [electroretinography (ERG]. Histological markers of neurodegeneration (glial activation and apoptosis were evaluated by immunohistochemistry. In addition glutamate levels and glutamate/aspartate transporter (GLAST expression were assessed. Furthermore, to define gene expression changes associated with early diabetic retinopathy a transcriptome analyses was performed at 8 week. Furthermore, an additional interventional study to lower blood glucose levels was performed. RESULTS: Glial activation was higher in diabetic than in non diabetic mice in all the stages (p<0.01. In addition, a progressive loss of ganglion cells and a significant reduction of neuroretinal thickness were also observed in diabetic mice. All these histological hallmarks of neurodegeneration were less pronounced at week 8 than at week 16 and 24. Significant ERG abnormalities were present in diabetic mice at weeks 16 and 24 but not at week 8. Moreover, we observed a progressive accumulation of glutamate in diabetic mice associated with an early downregulation of GLAST. Morphological and ERG abnormalities were abrogated by lowering blood glucose levels. Finally, a dysregulation of several genes related to neurotransmission and oxidative stress such as UCP2 were found at week 8. CONCLUSIONS: Our results suggest that db/db mouse reproduce the features of the neurodegenerative process that occurs in the human diabetic eye. Therefore, it seems an appropriate model for investigating the

75 GHz InP DHBT power amplifier based on two-stacked transistors

DEFF Research Database (Denmark)

Squartecchia, Michele; Midili, Virginio; Johansen, Tom Keinicke

2017-01-01

In this paper we present the design and measurements of a two-stage 75-GHz InP Double Heterojunction Bipolar Transistor (DHBT) power amplifier (PA). An optimized two-stacked transistor power cell has been designed, which represents the building block in the power stage as well as in the driver st......, the power amplifier exhibits a small signal gain of G = 12.6 dB, output power at 1-dB compression of Pout, 1dB = 18.6 dBm and a saturated output power of Psat > 21.4 dBm....

An aqueous extract of Portulaca oleracea ameliorates diabetic nephropathy through suppression of renal fibrosis and inflammation in diabetic db/db mice.

Science.gov (United States)

Lee, An Sook; Lee, Yun Jung; Lee, So Min; Yoon, Jung Joo; Kim, Jin Sook; Kang, Dae Gill; Lee, Ho Sub

2012-01-01

Diabetic nephropathy is one of the most common microvascular complications of diabetes and the leading cause of end-stage renal disease. In the present study, we investigated the renoprotective effect of the aqueous extract of Portulaca oleracea (AP) on diabetic nephropathy accelerated by renal fibrosis and inflammation in type 2 diabetic db/db mice. The mice were treated with AP (300 mg/kg/day, p.o.) for ten weeks to examine the long-term effects on diabetic nephropathy and renal dysfunction. We found that AP treatment markedly lowered blood glucose to 412 ± 11.4 mg/dl and plasma creatinine level to 2.3 ± 0.8 mg/dl compared to db/db mice (p < 0.05, p < 0.01, respectively). This study also showed that treatment with AP significantly decreased water intake and urine volume in diabetic db/db mice (p < 0.05). In immunohistological study, the renal expression of transforming growth factor-β1 (TGF-β1), advanced glycation end products (AGE), and intercellular adhesion molecule (ICAM)-1 markedly increased in the renal cortex of untreated db/db mice (p < 0.01). In contrast, AP treatment significantly reduced these expressions to 50 ± 2.1%, 48 ± 2.8%, 61 ± 1.1%, respectively (p < 0.01). Furthermore, NF-κB p65 activation in renal tissues markedly increased in untreated db/db mice, which was significantly suppressed by AP treatment. Taken together, these findings suggest that AP attenuates diabetic nephropathy through inhibition of renal fibrosis and inflammation in db/db mice.

dbSNP

Data.gov (United States)

U.S. Department of Health & Human Services — dbSNP is a database of single nucleotide polymorphisms (SNPs) and multiple small-scale variations that include insertions/deletions, microsatellites, and...

Development of integrated D/B system for the safety-related structures in nuclear power plant

International Nuclear Information System (INIS)

Cho, M. S.; Song, Y. C.; Lee, J. S.; Choi, W. S.

2002-01-01

The integrated D/B system is developed for digitalizing the history of the safety-related structures of nuclear power plant. It have 5 database which are consist of Generals, Structural and Design, Materials, Construction, Aging and repair information D/B. For efficient operation of the system, we are to set up the outline of the system, find out data field for target structures, and develop utilities. Utilities will be the aging and repair data management program, the close examination management program, the data search engine with various options which help users to find the information quickly, and the data management program restoring, updating and exchanging input data. Development of the integrated D/B system of the safety-related structures will contribute to management of the structures of nuclear power plant with advanced technology

DPP-4 inhibitor des-F-sitagliptin treatment increased insulin exocytosis from db/db mice {beta} cells

Energy Technology Data Exchange (ETDEWEB)

Nagamatsu, Shinya, E-mail: shinya@ks.kyorin-u.ac.jp [Department of Biochemistry, Kyorin University School of Medicine, Mitaka, Tokyo 181-8611 (Japan); Ohara-Imaizumi, Mica; Nakamichi, Yoko; Aoyagi, Kyota; Nishiwaki, Chiyono [Department of Biochemistry, Kyorin University School of Medicine, Mitaka, Tokyo 181-8611 (Japan)

2011-09-09

Highlights: {yields} Anti-diabetic new drug, DPP-4 inhibitor, can affect the insulin exocytosis. {yields} DPP-4 inhibitor treatment altered syntaxin 1 expression. {yields} Treatment of db/db mice with DPP-4 inhibitor increased insulin release. -- Abstract: Incretin promotes insulin secretion acutely. Recently, orally-administered DPP-4 inhibitors represent a new class of anti-hyperglycemic agents. Indeed, inhibitors of dipeptidyl peptidase-IV (DPP-4), sitagliptin, has just begun to be widely used as therapeutics for type 2 diabetes. However, the effects of sitagliptin-treatment on insulin exocytosis from single {beta}-cells are yet unknown. We therefore investigated how sitagliptin-treatment in db/db mice affects insulin exocytosis by treating db/db mice with des-F-sitagliptin for 2 weeks. Perfusion studies showed that 2 weeks-sitagliptin treatment potentiated insulin secretion. We then analyzed insulin granule motion and SNARE protein, syntaxin 1, by TIRF imaging system. TIRF imaging of insulin exocytosis showed the increased number of docked insulin granules and increased fusion events from them during first-phase release. In accord with insulin exocytosis data, des-F-sitagliptin-treatment increased the number of syntaxin 1 clusters on the plasma membrane. Thus, our data demonstrated that 2-weeks des-F-sitagliptin-treatment increased the fusion events of insulin granules, probably via increased number of docked insulin granules and that of syntaxin 1 clusters.

A7DB: a relational database for mutational, physiological and pharmacological data related to the α7 nicotinic acetylcholine receptor

Directory of Open Access Journals (Sweden)

Sansom Mark SP

2005-01-01

Full Text Available Abstract Background Nicotinic acetylcholine receptors (nAChRs are pentameric proteins that are important drug targets for a variety of diseases including Alzheimer's, schizophrenia and various forms of epilepsy. One of the most intensively studied nAChR subunits in recent years has been α7. This subunit can form functional homomeric pentamers (α75, which can make interpretation of physiological and structural data much simpler. The growing amount of structural, pharmacological and physiological data for these receptors indicates the need for a dedicated and accurate database to provide a means to access this information in a coherent manner. Description A7DB http://www.lgics.org/a7db/ is a new relational database of manually curated experimental physiological data associated with the α7 nAChR. It aims to store as much of the pharmacology, physiology and structural data pertaining to the α7 nAChR. The data is accessed via web interface that allows a user to search the data in multiple ways: 1 a simple text query 2 an incremental query builder 3 an interactive query builder and 4 a file-based uploadable query. It currently holds more than 460 separately reported experiments on over 85 mutations. Conclusions A7DB will be a useful tool to molecular biologists and bioinformaticians not only working on the α7 receptor family of proteins but also in the more general context of nicotinic receptor modelling. Furthermore it sets a precedent for expansion with the inclusion of all nicotinic receptor families and eventually all cys-loop receptor families.

Tangshen Formula Attenuates Diabetic Nephropathy by Promoting ABCA1-Mediated Renal Cholesterol Efflux in db/db Mice.

Science.gov (United States)

Liu, Peng; Peng, Liang; Zhang, Haojun; Tang, Patrick Ming-Kuen; Zhao, Tingting; Yan, Meihua; Zhao, Hailing; Huang, Xiaoru; Lan, Huiyao; Li, Ping

2018-01-01

The commonly prescribed Tangshen Formula (TSF) is a traditional Chinese formulation that has been shown to reduce plasma lipid metabolism and proteinuria and improve the estimated glomerular filtration rate (eGFR) in patients with diabetic kidney disease. This study investigated the underlying mechanism whereby TSF regulates renal lipid accumulation and ameliorates diabetic renal injuries in spontaneous diabetic db/db mice and in vitro in sodium palmitate (PA)-stimulated and Abca1-SiRNA-transfected mouse tubular epithelial cells (mTECs). The results revealed that TSF treatment significantly ameliorated the renal injuries by lowering urinary albumin excretion and improving renal tissue injuries in diabetic (db/db) mice. Interestingly, the treatment with TSF also resulted in decreased cholesterol levels in the renal tissues of db/db mice, which was associated with increased expression of the peroxisome proliferator-activated receptor γ coactivator 1-α (PGC-1α), the Liver X receptors (LXR), and ATP-binding cassette subfamily A member 1 (ABCA1), suggesting that TSF might attenuate diabetic kidney injury via a mechanism associated with improving cholesterol efflux in the diabetic kidney. This was investigated in vitro in mTECs, and the results showed that TSF reduced the PA-stimulated cholesterol accumulation in mTECs. Mechanistically, the addition of TSF was capable of reversing PA-induced downregulation of PGC-1α, LXR, and ABCA1 expression and cholesterol accumulation in mTECs, suggesting that TSF might act the protection via the PGC-1α-LXR-ABCA1 pathway to improve the cholesterol efflux in the renal tissues of db/db mice. This was further confirmed by silencing ABCA1 to block the promotive effect of TSF on cholesterol efflux in vitro . In conclusion, TSF might ameliorate diabetic kidney injuries by promoting ABCA1-mediated renal cholesterol efflux.

ToxRefDB - Release user-friendly web-based tool for mining ToxRefDB

Science.gov (United States)

The updated URL link is for a table of NCCT ToxCast public datasets. The next to last row of the table has the link for the US EPA ToxCast ToxRefDB Data Release October 2014. ToxRefDB provides detailed chemical toxicity data in a publically accessible searchable format. ToxRefD...

Dicty_cDB: SLJ310 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available 5' similar to Arabidopsis thaliana sequence At1g48030 lipoamide dehydrogenase precursor see http://mips... At1g48030 lipoamide dehydrogenase precursor see http://mips.gsf.de/proj/thal/db/index.html, mRNA sequence.

Anti-diabetic and hypolipidemic effects of Sargassum yezoense in db/db mice

Energy Technology Data Exchange (ETDEWEB)

Kim, Su-Nam, E-mail: snkim@kist.re.kr [Natural Medicine Center, KIST Gangneung Institute, Gangneung 210-340 (Korea, Republic of); Lee, Woojung [Natural Medicine Center, KIST Gangneung Institute, Gangneung 210-340 (Korea, Republic of); Bae, Gyu-Un [College of Pharmacy, Sookmyung Women' s University, Seoul 140-742 (Korea, Republic of); Research Center for Cell Fate Control, Sookmyung Women' s University, Seoul 140-742 (Korea, Republic of); Kim, Yong Kee, E-mail: yksnbk@sookmyung.ac.kr [College of Pharmacy, Sookmyung Women' s University, Seoul 140-742 (Korea, Republic of)

2012-08-10

Highlights: Black-Right-Pointing-Pointer Sargassum yezoense (SY) treatment improved glucose and lipid impairment in vivo. Black-Right-Pointing-Pointer This pharmacological action is associated with PPAR{alpha}/{gamma} dual activation. Black-Right-Pointing-Pointer It decreases the expression of G6Pase for gluconeogenesis in liver. Black-Right-Pointing-Pointer It increases the expression of UCP3 for lipid metabolism in adipose tissue. Black-Right-Pointing-Pointer There are no significant side effects such as body weight gain and hepatomegaly. -- Abstract: Peroxisome proliferator-activated receptors (PPARs) have been considered to be desirable targets for metabolic syndrome, even though their specific agonists have several side effects including body weight gain, edema and tissue failure. Previously, we have reported in vitro effects of Sargassum yezoense (SY) and its ingredients, sargaquinoic acid (SQA) and sargahydroquinoic acid (SHQA), on PPAR{alpha}/{gamma} dual transcriptional activation. In this study, we describe in vivo pharmacological property of SY on metabolic disorders. SY treatment significantly improved glucose and lipid impairment in db/db mice model. More importantly, there are no significant side effects such as body weight gain and hepatomegaly in SY-treated animals, indicating little side effects of SY in liver and lipid metabolism. In addition, SY led to a decrease in the expression of G6Pase for gluconeogenesis in liver responsible for lowering blood glucose level and an increase in the expression of UCP3 in adipose tissue for the reduction of total and LDL-cholesterol level. Altogether, our data suggest that SY would be a potential therapeutic agent against type 2 diabetes and related metabolic disorders by ameliorating the glucose and lipid metabolism.

MIPS PlantsDB: a database framework for comparative plant genome research.

Science.gov (United States)

Nussbaumer, Thomas; Martis, Mihaela M; Roessner, Stephan K; Pfeifer, Matthias; Bader, Kai C; Sharma, Sapna; Gundlach, Heidrun; Spannagl, Manuel

2013-01-01

The rapidly increasing amount of plant genome (sequence) data enables powerful comparative analyses and integrative approaches and also requires structured and comprehensive information resources. Databases are needed for both model and crop plant organisms and both intuitive search/browse views and comparative genomics tools should communicate the data to researchers and help them interpret it. MIPS PlantsDB (http://mips.helmholtz-muenchen.de/plant/genomes.jsp) was initially described in NAR in 2007 [Spannagl,M., Noubibou,O., Haase,D., Yang,L., Gundlach,H., Hindemitt, T., Klee,K., Haberer,G., Schoof,H. and Mayer,K.F. (2007) MIPSPlantsDB-plant database resource for integrative and comparative plant genome research. Nucleic Acids Res., 35, D834-D840] and was set up from the start to provide data and information resources for individual plant species as well as a framework for integrative and comparative plant genome research. PlantsDB comprises database instances for tomato, Medicago, Arabidopsis, Brachypodium, Sorghum, maize, rice, barley and wheat. Building up on that, state-of-the-art comparative genomics tools such as CrowsNest are integrated to visualize and investigate syntenic relationships between monocot genomes. Results from novel genome analysis strategies targeting the complex and repetitive genomes of triticeae species (wheat and barley) are provided and cross-linked with model species. The MIPS Repeat Element Database (mips-REdat) and Catalog (mips-REcat) as well as tight connections to other databases, e.g. via web services, are further important components of PlantsDB.

Analysis of neuron–astrocyte metabolic cooperation in the brain of db/db mice with cognitive decline using 13C NMR spectroscopy

Science.gov (United States)

Zheng, Hong; Zheng, Yongquan; Wang, Dan; Cai, Aimin; Lin, Qiuting; Zhao, Liangcai; Chen, Minjiang; Deng, Mingjie; Ye, Xinjian

2016-01-01

Type 2 diabetes has been linked to cognitive impairment, but its potential metabolic mechanism is still unclear. The present study aimed to explore neuron–astrocyte metabolic cooperation in the brain of diabetic (db/db, BKS.Cg-m+/+ Leprdb/J) mice with cognitive decline using 13C NMR technique in combination with intravenous [2-13C]-acetate and [3-13C]-lactate infusions. We found that the 13C-enrichment from [2-13C]-acetate into tricarboxylic acid cycle intermediate, succinate, was significantly decreased in db/db mice with cognitive decline compared with wild-type (WT, C57BLKS/J) mice, while an opposite result was obtained after [3-13C]-lactate infusion. Relative to WT mice, db/db mice with cognitive decline had significantly lower 13C labeling percentages in neurotransmitters including glutamine, glutamate, and γ-aminobutyric acid after [2-13C]-acetate infusion. However, [3-13C]-lactate resulted in increased 13C-enrichments in neurotransmitters in db/db mice with cognitive decline. This may indicate that the disturbance of neurotransmitter metabolism occurred during the development of cognitive decline. In addition, a reduction in 13C-labeling of lactate and an increase in gluconeogenesis were found from both labeled infusions in db/db mice with cognitive decline. Therefore, our results suggest that the development of cognitive decline in type 2 diabetes may be implicated to an unbalanced metabolism in neuron–astrocyte cooperation and an enhancement of gluconeogenesis. PMID:26762505

Analysis of neuron-astrocyte metabolic cooperation in the brain of db/db mice with cognitive decline using 13C NMR spectroscopy.

Science.gov (United States)

Zheng, Hong; Zheng, Yongquan; Wang, Dan; Cai, Aimin; Lin, Qiuting; Zhao, Liangcai; Chen, Minjiang; Deng, Mingjie; Ye, Xinjian; Gao, Hongchang

2017-01-01

Type 2 diabetes has been linked to cognitive impairment, but its potential metabolic mechanism is still unclear. The present study aimed to explore neuron-astrocyte metabolic cooperation in the brain of diabetic (db/db, BKS.Cg-m +/+ Leprdb/J) mice with cognitive decline using 13 C NMR technique in combination with intravenous [2- 13 C]-acetate and [3- 13 C]-lactate infusions. We found that the 13 C-enrichment from [2- 13 C]-acetate into tricarboxylic acid cycle intermediate, succinate, was significantly decreased in db/db mice with cognitive decline compared with wild-type (WT, C57BLKS/J) mice, while an opposite result was obtained after [3- 13 C]-lactate infusion. Relative to WT mice, db/db mice with cognitive decline had significantly lower 13 C labeling percentages in neurotransmitters including glutamine, glutamate, and γ-aminobutyric acid after [2- 13 C]-acetate infusion. However, [3- 13 C]-lactate resulted in increased 13 C-enrichments in neurotransmitters in db/db mice with cognitive decline. This may indicate that the disturbance of neurotransmitter metabolism occurred during the development of cognitive decline. In addition, a reduction in 13 C-labeling of lactate and an increase in gluconeogenesis were found from both labeled infusions in db/db mice with cognitive decline. Therefore, our results suggest that the development of cognitive decline in type 2 diabetes may be implicated to an unbalanced metabolism in neuron-astrocyte cooperation and an enhancement of gluconeogenesis. © The Author(s) 2016.

Getting started with LevelDB

CERN Document Server

Dent, Andy

2013-01-01

The book is a concise guide for using LevelDB. It explains database concepts and the use of C++, ranging from the basics all the way to high level topics in an easy to follow, step-by-step format.The book is meant for developers who want an embedded database for their applications. Experienced programmers can pick up on the sophisticated data mapping patterns and tuning tips.Getting Started with LevelDB requires a minimal background in programming in C++ or Objective-C for OS/X or iOS and familiarity with XCode. Therefore it teaches enough C++ to use LevelDB without presuming any C++ knowledge

dbVar

Data.gov (United States)

U.S. Department of Health & Human Services — dbVar is a database of genomic structural variation. It accepts data from all species and includes clinical data. It can accept diverse types of events, including...

Flow cytometry analysis reveals different activation profiles of thrombin- or TRAP-stimulated platelets in db/db mice. The regulatory role of PAR-3.

Science.gov (United States)

Kassassir, Hassan; Siewiera, Karolina; Talar, Marcin; Przygodzki, Tomasz; Watala, Cezary

2017-06-01

Recent studies have shown that it may be the concentration of thrombin, which is discriminative in determining of the mechanism of platelet activation via protease activated receptors (PARs). Whether the observed phenomenon of differentiated responses of mouse platelets to various thrombin concentrations in non-diabetic db/+ and diabetic db/db mice depends upon the concerted action of various PARs, remains to be established. We found elevated reactivity of platelets, as well as the enhanced PAR-3 expression in response to both the used concentrations of AYPGKF in db/db mice, as compared to db/+ heterozygotes. At low concentration of thrombin platelets from diabetic mice demonstrated hyperreactivity, reflected by higher expression of PAR-3. For higher thrombin concentration, blood platelets from db/db mice appeared hyporeactive, compared to db/+ animals, while no significant differences in PAR-3 expression were observed between diabetic and non-diabetic mice. The novel and previously unreported finding resulting from our study is that the increased expression of PAR-3 in response to either TRAP for PAR-4 or low thrombin (when PAR-4 is not the efficient thrombin receptor) may be one of the key events contributing to higher reactivity of platelets in db/db mice. Copyright © 2017 Elsevier Inc. All rights reserved.

Night-time restricted feeding normalises clock genes and Pai-1 gene expression in the db/db mouse liver.

Science.gov (United States)

Kudo, T; Akiyama, M; Kuriyama, K; Sudo, M; Moriya, T; Shibata, S

2004-08-01

An increase in PAI-1 activity is thought to be a key factor underlying myocardial infarction. Mouse Pai-1 (mPai-1) activity shows a daily rhythm in vivo, and its transcription seems to be controlled not only by clock genes but also by humoral factors such as insulin and triglycerides. Thus, we investigated daily clock genes and mPai-1 mRNA expression in the liver of db/db mice exhibiting high levels of glucose, insulin and triglycerides. Locomotor activity was measured using an infrared detection system. RT-PCR or in situ hybridisation methods were applied to measure gene expression. Humoral factors were measured using measurement kits. The db/ db mice showed attenuated locomotor activity rhythms. The rhythmic expression of mPer2 mRNA was severely diminished and the phase of mBmal1 oscillation was advanced in the db/db mouse liver, whereas mPai-1 mRNA was highly and constitutively expressed. Night-time restricted feeding led to a recovery not only from the diminished locomotor activity, but also from the diminished Per2 and advanced mBmal1 mRNA rhythms. Expression of mPai-1 mRNA in db/db mice was reduced to levels far below normal. Pioglitazone treatment slightly normalised glucose and insulin levels, with a slight reduction in mPai-1 gene expression. We demonstrated that Type 2 diabetes impairs the oscillation of the peripheral oscillator. Night-time restricted feeding rather than pioglitazone injection led to a recovery from the diminished locomotor activity, and altered oscillation of the peripheral clock and mPai-1 mRNA rhythm. Thus, we conclude that scheduled restricted food intake may be a useful form of treatment for diabetes.

GC/TOFMS analysis of metabolites in serum and urine reveals metabolic perturbation of TCA cycle in db/db mice involved in diabetic nephropathy.

Science.gov (United States)

Li, Mengjie; Wang, Xufang; Aa, Jiye; Qin, Weisong; Zha, Weibin; Ge, Yongchun; Liu, Linsheng; Zheng, Tian; Cao, Bei; Shi, Jian; Zhao, Chunyan; Wang, Xinwen; Yu, Xiaoyi; Wang, Guangji; Liu, Zhihong

2013-06-01

Early diagnosis of diabetic nephropathy (DN) is difficult although it is of crucial importance to prevent its development. To probe potential markers and the underlying mechanism of DN, an animal model of DN, the db/db mice, was used and serum and urine metabolites were profiled using gas chromatography/time-of-flight mass spectrometry. Metabolic patterns were evaluated based on serum and urine data. Principal component analysis of the data revealed an obvious metabonomic difference between db/db mice and controls, and db/db mice showed distinctly different metabolic patterns during the progression from diabetes to early, medium, and later DN. The identified metabolites discriminating between db/db mice and controls suggested that db/db mice have perturbations in the tricarboxylic acid cycle (TCA, citrate, malate, succinate, and aconitate), lipid metabolism, glycolysis, and amino acid turnover. The db/db mice were characterized by acidic urine, high TCA intermediates in serum at week 6 and a sharp decline thereafter, and gradual elevation of free fatty acids in the serum. The sharp drop of serum TCA intermediates from week 6 to 8 indicated the downregulated glycolysis and insulin resistance. However, urinary TCA intermediates did not decrease in parallel with those in the serum from week 6 to 10, and an increased portion of TCA intermediates in the serum was excreted into the urine at 8, 10, and 12 wk than at 6 wk, indicating kidney dysfunction occurred. The relative abundances of TCA intermediates in urine relative to those in serum were suggested as an index of renal damage.

Getting started with OrientDB

CERN Document Server

Tesoriero, Claudio

2013-01-01

A standard tutorial aimed at making you an OrientDB expert, through the use of practical examples, explained in a step-by-step format.Getting Started with OrientDB 1.3.0 is great for database designers, developers, and systems engineers. It is assumed that you are familiar with NoSQL concepts, Java, and networking principles.

Flat ended steel wires, backscattering targets for calibrating over a large dynamic range

NARCIS (Netherlands)

Lubbers, Jaap; Graaff, Reindert

2006-01-01

A series of flat ended stainless steel wires was constructed and experimentally evaluated as point targets giving a calibrated backscattering over a large range (up to 72 dB) for ultrasound frequencies in the range 2 to 10 MHz. Over a range of 36 dB, theory was strictly followed (within 1 dB),

Overactivity of Liver-Related Neurons in the Paraventricular Nucleus of the Hypothalamus: Electrophysiological Findings in db/db Mice.

Science.gov (United States)

Gao, Hong; Molinas, Adrien J R; Miyata, Kayoko; Qiao, Xin; Zsombok, Andrea

2017-11-15

Preautonomic neurons in the paraventricular nucleus (PVN) of the hypothalamus play a large role in the regulation of hepatic functions via the autonomic nervous system. Activation of hepatic sympathetic nerves increases glucose and lipid metabolism and contributes to the elevated hepatic glucose production observed in the type 2 diabetic condition. This augmented sympathetic output could originate from altered activity of liver-related PVN neurons. Remarkably, despite the importance of the brain-liver pathway, the cellular properties of liver-related neurons are not known. In this study, we provide the first evidence of overall activity of liver-related PVN neurons. Liver-related PVN neurons were identified with a retrograde, trans-synaptic, viral tracer in male lean and db/db mice and whole-cell patch-clamp recordings were conducted. In db/db mice, the majority of liver-related PVN neurons fired spontaneously; whereas, in lean mice the majority of liver-related PVN neurons were silent, indicating that liver-related PVN neurons are more active in db/db mice. Persistent, tonic inhibition was identified in liver-related PVN neurons; although, the magnitude of tonic inhibitory control was not different between lean and db/db mice. In addition, our study revealed that the transient receptor potential vanilloid type 1-dependent increase of excitatory neurotransmission was reduced in liver-related PVN neurons of db/db mice. These findings demonstrate plasticity of liver-related PVN neurons and a shift toward excitation in a diabetic mouse model. Our study suggests altered autonomic circuits at the level of the PVN, which can contribute to autonomic dysfunction and dysregulation of neural control of hepatic functions including glucose metabolism. SIGNIFICANCE STATEMENT A growing body of evidence suggests the importance of the autonomic control in the regulation of hepatic metabolism, which plays a major role in the development and progression of type 2 diabetes mellitus

Mulberry (Morus alba L.) Fruit Extract Containing Anthocyanins Improves Glycemic Control and Insulin Sensitivity via Activation of AMP-Activated Protein Kinase in Diabetic C57BL/Ksj-db/db Mice.

Science.gov (United States)

Choi, Kyung Ha; Lee, Hyun Ah; Park, Mi Hwa; Han, Ji-Sook

2016-08-01

The effect of mulberry (Morus alba L.) fruit extract (MFE) on hyperglycemia and insulin sensitivity in an animal model of type 2 diabetes was evaluated. C57BL/Ksj-diabetic db/db mice were divided into three groups: diabetic control, rosiglitazone, and MFE groups. Blood glucose, plasma insulin, and intraperitoneal glucose were measured, and an insulin tolerance test was performed after MFE supplementation in db/db mice. In addition, the protein levels of various targets of insulin signaling were measured by western blotting. The blood levels of glucose and HbA1c were significantly lower in the MFE-supplemented group than in the diabetic control group. Moreover, glucose and insulin tolerance tests showed that MFE treatment increased insulin sensitivity. The homeostatic index of insulin resistance significantly decreased in the MFE-supplemented group relative to the diabetic control group. MFE supplementation significantly stimulated the levels of phosphorylated (p)-AMP-activated protein kinase (pAMPK) and p-Akt substrate of 160 kDa (pAS160) and enhanced the level of plasma membrane-glucose transporter 4 (GLUT4) in skeletal muscles. Further, dietary MFE significantly increased pAMPK and decreased the levels of glucose 6-phosphatase and phosphoenolpyruvate carboxykinase in the liver. MFE may improve hyperglycemia and insulin sensitivity via activation of AMPK and AS160 in skeletal muscles and inhibition of gluconeogenesis in the liver.

Version VI of the ESTree db: an improved tool for peach transcriptome analysis

Science.gov (United States)

Lazzari, Barbara; Caprera, Andrea; Vecchietti, Alberto; Merelli, Ivan; Barale, Francesca; Milanesi, Luciano; Stella, Alessandra; Pozzi, Carlo

2008-01-01

Background The ESTree database (db) is a collection of Prunus persica and Prunus dulcis EST sequences that in its current version encompasses 75,404 sequences from 3 almond and 19 peach libraries. Nine peach genotypes and four peach tissues are represented, from four fruit developmental stages. The aim of this work was to implement the already existing ESTree db by adding new sequences and analysis programs. Particular care was given to the implementation of the web interface, that allows querying each of the database features. Results A Perl modular pipeline is the backbone of sequence analysis in the ESTree db project. Outputs obtained during the pipeline steps are automatically arrayed into the fields of a MySQL database. Apart from standard clustering and annotation analyses, version VI of the ESTree db encompasses new tools for tandem repeat identification, annotation against genomic Rosaceae sequences, and positioning on the database of oligomer sequences that were used in a peach microarray study. Furthermore, known protein patterns and motifs were identified by comparison to PROSITE. Based on data retrieved from sequence annotation against the UniProtKB database, a script was prepared to track positions of homologous hits on the GO tree and build statistics on the ontologies distribution in GO functional categories. EST mapping data were also integrated in the database. The PHP-based web interface was upgraded and extended. The aim of the authors was to enable querying the database according to all the biological aspects that can be investigated from the analysis of data available in the ESTree db. This is achieved by allowing multiple searches on logical subsets of sequences that represent different biological situations or features. Conclusions The version VI of ESTree db offers a broad overview on peach gene expression. Sequence analyses results contained in the database, extensively linked to external related resources, represent a large amount of

Pitavastatin suppresses diethylnitrosamine-induced liver preneoplasms in male C57BL/KsJ-db/db obese mice

International Nuclear Information System (INIS)

Shimizu, Masahito; Tanaka, Takuji; Moriwaki, Hisataka; Yasuda, Yoichi; Sakai, Hiroyasu; Kubota, Masaya; Terakura, Daishi; Baba, Atsushi; Ohno, Tomohiko; Kochi, Takahiro; Tsurumi, Hisashi

2011-01-01

Obesity and related metabolic abnormalities, including inflammation and lipid accumulation in the liver, play a role in liver carcinogenesis. Adipocytokine imbalances, such as decreased serum adiponectin levels, are also involved in obesity-related liver tumorigenesis. In the present study, we examined the effects of pitavastatin - a drug used for the treatment of hyperlipidemia - on the development of diethylnitrosamine (DEN)-induced liver preneoplastic lesions in C57BL/KsJ-db/db (db/db) obese mice. Male db/db mice were administered tap water containing 40 ppm DEN for 2 weeks and were subsequently fed a diet containing 1 ppm or 10 ppm pitavastatin for 14 weeks. At sacrifice, feeding with 10 ppm pitavastatin significantly inhibited the development of hepatic premalignant lesions, foci of cellular alteration, as compared to that in the untreated group by inducing apoptosis, but inhibiting cell proliferation. Pitavastatin improved liver steatosis and activated the AMPK-α protein in the liver. It also decreased free fatty acid and aminotransferases levels, while increasing adiponectin levels in the serum. The serum levels of tumor necrosis factor (TNF)-α and the expression of TNF-α and interleukin-6 mRNAs in the liver were decreased by pitavastatin treatment, suggesting attenuation of the chronic inflammation induced by excess fat deposition. Pitavastatin is effective in inhibiting the early phase of obesity-related liver tumorigenesis and, therefore, may be useful in the chemoprevention of liver cancer in obese individuals

Dysregulation of the unfolded protein response in db/db mice with diet induced steatohepatitis

OpenAIRE

Rinella, Mary E.; Siddiqui, M. Shaddab; Gardikiotes, Konstantina; Gottstein, Jeanne; Elias, Marc; Green, Richard M.

2011-01-01

In humans with non-alcoholic fatty liver, diabetes is associated with more advanced disease. We have previously shown that diabetic db/db mice are highly susceptible to methionine choline deficient diet (MCD) induced hepatic injury. Since activation of the unfolded protein response (UPR) is an important adaptive cellular mechanism in diabetes, obesity and fatty liver, we hypothesized that dysregulation of the UPR may partially explain how diabetes could promote liver injury.

dbVOR: a database system for importing pedigree, phenotype and genotype data and exporting selected subsets.

Science.gov (United States)

Baron, Robert V; Conley, Yvette P; Gorin, Michael B; Weeks, Daniel E

2015-03-18

When studying the genetics of a human trait, we typically have to manage both genome-wide and targeted genotype data. There can be overlap of both people and markers from different genotyping experiments; the overlap can introduce several kinds of problems. Most times the overlapping genotypes are the same, but sometimes they are different. Occasionally, the lab will return genotypes using a different allele labeling scheme (for example 1/2 vs A/C). Sometimes, the genotype for a person/marker index is unreliable or missing. Further, over time some markers are merged and bad samples are re-run under a different sample name. We need a consistent picture of the subset of data we have chosen to work with even though there might possibly be conflicting measurements from multiple data sources. We have developed the dbVOR database, which is designed to hold data efficiently for both genome-wide and targeted experiments. The data are indexed for fast retrieval by person and marker. In addition, we store pedigree and phenotype data for our subjects. The dbVOR database allows us to select subsets of the data by several different criteria and to merge their results into a coherent and consistent whole. Data may be filtered by: family, person, trait value, markers, chromosomes, and chromosome ranges. The results can be presented in columnar, Mega2, or PLINK format. dbVOR serves our needs well. It is freely available from https://watson.hgen.pitt.edu/register . Documentation for dbVOR can be found at https://watson.hgen.pitt.edu/register/docs/dbvor.html .

Novel anti-diabetic effect of SCM-198 via inhibiting the hepatic NF-κB pathway in db/db mice.

Science.gov (United States)

Huang, Hui; Xin, Hong; Liu, Xinhua; Xu, Yajun; Wen, Danyi; Zhang, Yahua; Zhu, Yi Zhun

2012-04-01

There are reports of early evidence that suggest the involvement of chronic low-grade inflammation in the pathogenesis of Type 2 diabetes. Thus, substances that have effects in reducing inflammation could be potential drugs for Type 2 diabetes. Leonurine (4-guanidino-n-butyl syringate; SCM-198) is an alkaloid in HL (Herba leonuri), which was reported to possess anti-inflammatory properties. We hypothesize that SCM-198 may have beneficial effects on Type 2 diabetes. In the present study, we attempted to test this hypothesis by evaluating the anti-diabetic effect of SCM-198 and the possible underlying mechanisms of its effects in db/db mice. SCM-198 (50, 100 and 200 mg/kg of body weight), pioglitazone (50 mg/kg of body weight, as a positive control) or 1% CMC-Na (sodium carboxymethylcellulose) were administered to the db/db or db/m mice once daily for 3 weeks. After 3 weeks, SCM-198 (200 mg/kg of body weight) treatment significantly reduced the fasting blood glucose level and increased the plasma insulin concentration in the db/db mice, meanwhile it significantly lowered the plasma TAG (triacylglycerol) concentration and increased the HDL (high-density lipoprotein)-cholesterol concentration. Moreover, the dysregulated transcription of the hepatic glucose metabolic enzymes, including GK (glucokinase), G6Pase (glucose-6-phosphatase) and PEPCK (phosphoenolpyruvate carboxykinase), was recovered by an Akt-dependent pathway. The pro-inflammatory mediators {such as TNFα (tumour necrosis factor α), IL (interleukin)-6, IL-1β, degradation of IκB [inhibitor of NF-κB (nuclear factor-κB)] α and thereafter activation of NF-κB} were reversed by SCM-198 treatment in the db/db mice. The present study provides first evidence that SCM-198 exhibits anti-inflammatory activity and has an ameliorating effect on diabetic symptoms via inhibiting of NF-κB/IKK (IκB kinase) pathway. Consequently, we suggest that SCM-198 may be a prospective agent for prevention and

Pluronic L-81 ameliorates diabetic symptoms in db/db mice through transcriptional regulation of microsomal triglyceride transfer protein

Science.gov (United States)

Au, Wo-Shing; Lu, Li-Wei; Tam, Sidney; Ko, Otis King Hung; Chow, Billy KC; He, Ming-Liang; Ng, Samuel S; Yeung, Chung-Man; Liu, Ching-Chiu; Kung, Hsiang-Fu; Lin, Marie C

2009-01-01

AIM: To test whether oral L-81 treatment could improve the condition of mice with diabetes and to investigate how L-81 regulates microsomal triglyceride transfer protein (MTP) activity in the liver. METHODS: Genetically diabetic (db/db) mice were fed on chow supplemented with or without L-81 for 4 wk. The body weight, plasma glucose level, plasma lipid profile, and adipocyte volume of the db/db mice were assessed after treatment. Toxicity of L-81 was also evaluated. To understand the molecular mechanism, HepG2 cells were treated with L-81 and the effects on apolipoprotein B (apoB) secretion and mRNA level of the MTP gene were assessed. RESULTS: Treatment of db/db mice with L-81 significantly reduced and nearly normalized their body weight, hyperphagia and polydipsia. L-81 also markedly decreased the fasting plasma glucose level, improved glucose tolerance, and attenuated the elevated levels of plasma cholesterol and triglyceride. At the effective dosage, little toxicity was observed. Treatment of HepG2 cells with L-81 not only inhibited apoB secretion, but also significantly decreased the mRNA level of the MTP gene. Similar to the action of insulin, L-81 exerted its effect on the MTP promoter. CONCLUSION: L-81 represents a promising candidate in the development of a selective insulin-mimetic molecule and an anti-diabetic agent. PMID:19554651

Dapagliflozin Aggravates Renal Injury via Promoting Gluconeogenesis in db/db Mice.

Science.gov (United States)

Jia, Yingli; He, Jinzhao; Wang, Liang; Su, Limin; Lei, Lei; Huang, Wei; Geng, Xiaoqiang; Zhang, Shun; Meng, Xiaolu; Zhou, Hong; Yang, Baoxue

2018-01-01

A sodium-glucose co-transporter-2 inhibitor dapagliflozin is widely used for lowering blood glucose and its usage is limited in type 2 diabetes mellitus patients with moderate renal impairment. As its effect on kidney function is discrepant and complicated, the aim of this study is to determine the effect of dapagliflozin on the progression of diabetic nephropathy and related mechanisms. Twelve-week-old male C57BL/6 wild-type and db/db mice were treated with vehicle or 1 mg/kg dapagliflozin for 12 weeks. Body weight, blood glucose, insulin tolerance, glucose tolerance, pyruvate tolerance and 24-hour urine were measured every 4 weeks. At 24 weeks of age, renal function was evaluated by blood urea nitrogen level, creatinine clearance, urine output, urinary albumin excretion, Periodic Acid-Schiff staining, Masson's trichrome staining and electron microscopy. Changes in insulin signaling and gluconeogenic key regulatory enzymes were detected using Western blot analysis. Dapagliflozin did not alleviate but instead aggravated diabetic nephropathy manifesting as increased levels of microalbuminuria, blood urea nitrogen, and glomerular and tubular damage in db/db mice. Despite adequate glycemic control by dapagliflozin, urinary glucose excretion increased after administration before 24 weeks of age and was likely associated with renal impairment. Increased urinary glucose excretion was mainly derived from the disturbance of glucose homeostasis with elevated hepatic and renal gluconeogenesis induced by dapagliflozin. Although it had no effect on insulin sensitivity and glucose tolerance, dapagliflozin further induced the expression of gluconeogenic key rate-limiting enzymes through increasing the expression levels of FoxO1 in the kidney and liver. These experimental results indicate that dapagliflozin aggravates diabetes mellitus-induced kidney injury, mostly through increasing gluconeogenesis. © 2018 The Author(s). Published by S. Karger AG, Basel.

The antidiabetic effects of a dry powder of dietary vegetable and fruit mixtures in diabetic db/db mice

Directory of Open Access Journals (Sweden)

Chung-Man Yeung

2008-09-01

Full Text Available Chung-Man Yeung1, Yi Tan1, Sidney Tam2, Liwei Lu3, King-Hung Ko3, Pai-Hao Yang1,4, Hsiang-Fu Kung4, Marie C Lin11Department of Chemistry, Open Laboratory of Chemical Biology of the Institute of Molecular Technology, 2Clinical Biochemistry Unit, 3Department of Pathology, The University of Hong Kong, Hong Kong, China; 4Centre of Emerging Infectious Diseases, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, ChinaAbstract: We evaluated the antidiabetic effects of a mixed vegetable powder-formula I (MVP-FI, which is a dry powder mixture of over 65 kinds of vegetables and fruits, using the db/db type 2 diabetes mouse model. The db/db mice at 8–10 weeks of age were randomly divided into three groups: vehicle treatment, 1.575 g/kg MVP-FI treatment, and 3.15 g/kg MVP-FI treatment. During 12 days of treatment, we measured food intake and body weight changes, fasting blood glucose levels, and plasma lipid levels. Our results showed that the food intake and the body weight of MVP-FI-treated group were decreased gradually. Moreover, the fasting blood glucose level of the treated group was significantly dropped to a normal level comparable to that of the lean mice. Furthermore, we also found that the plasma triglyceride level in the treated group was dropped, whereas the high-density lipoprotein (HDL level was increased and total cholesterol/HDL-cholesterol ratio was decreased. Taken together, these results suggest that the diabetic conditions of the db/db mice have been improved after 12 days treatment with MVP-FI. The antihyperglycemic and antiobese activities of the MVP-FI, as demonstrated in the present study, may have important clinical implications for improving the management of type 2 diabetic patients.Keywords: traditional Chinese medicine (TCM, db/db mice, diabetes

Diet supplementation with green tea extract epigallocatechin gallate prevents progression to glucose intolerance in db/db mice

Directory of Open Access Journals (Sweden)

Ortsäter Henrik

2012-02-01

Full Text Available Abstract Background Green tea was suggested as a therapeutic agent for the treatment of diabetes more than 70 years ago, but the mechanisms behind its antidiabetic effect remains elusive. In this work, we address this issue by feeding a green tea extract (TEAVIGO™ with a high content of epigallocatechin gallate (EGCG or the thiazolidinedione PPAR-γ agonist rosiglitazone, as positive control, to db/db mice, an animal model for diabetes. Methods Young (7 week-old db/db mice were randomized and assigned to receive diets supplemented with or without EGCG or rosiglitazone for 10 weeks. Fasting blood glucose, body weight and food intake was measured along the treatment. Glucose and insulin levels were determined during an oral glucose tolerance test after 10 weeks of treatment. Pancreata were sampled at the end of the study for blinded histomorphometric analysis. Islets were isolated and their mRNA expression analyzed by quantitative RT-PCR. Results The results show that, in db/db mice, EGCG improves glucose tolerance and increases glucose-stimulated insulin secretion. EGCG supplementation reduces the number of pathologically changed islets of Langerhans, increases the number and the size of islets, and heightens pancreatic endocrine area. These effects occurred in parallel with a reduction in islet endoplasmic reticulum stress markers, possibly linked to the antioxidative capacity of EGCG. Conclusions This study shows that the green tea extract EGCG markedly preserves islet structure and enhances glucose tolerance in genetically diabetic mice. Dietary supplementation with EGCG could potentially contribute to nutritional strategies for the prevention and treatment of type 2 diabetes.

Oligonol, a low-molecular-weight polyphenol derived from lychee fruit, attenuates diabetes-induced renal damage through the advanced glycation end product-related pathway in db/db mice.

Science.gov (United States)

Park, Chan Hum; Yokozawa, Takako; Noh, Jeong Sook

2014-08-01

This study was conducted to examine whether oligonol, a low-molecular-weight polyphenol derived from lychee fruit, has an ameliorative effect on diabetes-induced alterations, such as advanced glycation end product (AGE) formation or apoptosis in the kidneys of db/db mice with type 2 diabetes. Oligonol [10 or 20 mg/(kg body weight · d), orally] was administered every day for 8 wk to prediabetic db/db mice, and its effect was compared with vehicle-treated db/db and normal control mice (m/m). The administration of oligonol decreased the elevated renal glucose concentrations and reactive oxygen species in db/db mice (P factor-α (P related variables, representing renoprotective effects against the development of diabetic complications in db/db mice with type 2 diabetes. © 2014 American Society for Nutrition.

RAId_DbS: mass-spectrometry based peptide identification web server with knowledge integration

Directory of Open Access Journals (Sweden)

Ogurtsov Aleksey Y

2008-10-01

Full Text Available Abstract Background Existing scientific literature is a rich source of biological information such as disease markers. Integration of this information with data analysis may help researchers to identify possible controversies and to form useful hypotheses for further validations. In the context of proteomics studies, individualized proteomics era may be approached through consideration of amino acid substitutions/modifications as well as information from disease studies. Integration of such information with peptide searches facilitates speedy, dynamic information retrieval that may significantly benefit clinical laboratory studies. Description We have integrated from various sources annotated single amino acid polymorphisms, post-translational modifications, and their documented disease associations (if they exist into one enhanced database per organism. We have also augmented our peptide identification software RAId_DbS to take into account this information while analyzing a tandem mass spectrum. In principle, one may choose to respect or ignore the correlation of amino acid polymorphisms/modifications within each protein. The former leads to targeted searches and avoids scoring of unnecessary polymorphism/modification combinations; the latter explores possible polymorphisms in a controlled fashion. To facilitate new discoveries, RAId_DbS also allows users to conduct searches permitting novel polymorphisms as well as to search a knowledge database created by the users. Conclusion We have finished constructing enhanced databases for 17 organisms. The web link to RAId_DbS and the enhanced databases is http://www.ncbi.nlm.nih.gov/CBBResearch/qmbp/RAId_DbS/index.html. The relevant databases and binaries of RAId_DbS for Linux, Windows, and Mac OS X are available for download from the same web page.

MiR-138 promotes smooth muscle cells proliferation and migration in db/db mice through down-regulation of SIRT1

Energy Technology Data Exchange (ETDEWEB)

Xu, Juan [Department of Gynecology, Changzhou Maternity and Children Health Hospital, Changzhou, Jiangsu 213003 (China); Li, Li; Yun, Hui-fang [Department of Anesthesiology, Changzhou No. 2 People' s Hospital, Changzhou, Jiangsu 213003 (China); Han, Ye-shan, E-mail: yeshanhan123@163.com [Department of Anesthesiology, Changzhou No. 2 People' s Hospital, Changzhou, Jiangsu 213003 (China)

2015-08-07

Background: Diabetic vascular smooth muscle cells (VSMCs) exhibit significantly increased rates of proliferation and migration, which was the most common pathological change in atherosclerosis. In addition, the study about the role for miRNAs in the regulation of VSMC proliferation is just beginning to emerge and additional miRNAs involved in VSMC proliferation modulation should be identified. Methods: The expression of miR-138 and SIRT1 were examined in SMCs separated from db/db mice and in SMC lines C-12511 exposed to high glucose with qRT-PCR and western blot. The regulation of miR-138 on the expression of SMCs was detected with luciferase report assay. VSMCs proliferation and migration assays were performed to examine the effect of miR-138 inhibitor on VSMCs proliferation and migration. Results: We discovered that higher mRNA level of miR-138 and reduced expression of SIRT1 were observed in SMCs separated from db/db mice and in SMC lines C-12511. Moreover, luciferase report assay showed that the activity of SIRT1 3′-UTR was highly increased by miR-138 inhibitor and reduced by miR-138 mimic. In addition, we examined that the up-regulation of NF-κB induced by high glucose in SMCs was reversed by resveratrol and miR-138 inhibitor. MTT and migration assays showed that miR-138 inhibitor attenuated the proliferation and migration of smooth muscle cells. Conclusion: In this study, we revealed that miR-138 might promote proliferation and migration of SMC in db/db mice through suppressing the expression of SIRT1. - Highlights: • Higher mRNA level of miR-138 was observed in SMCs from db/db mice. • The mRNA and protein level of SIRT1 in SMCs from db/db mice were greatly reduced. • miR-138 could regulate the expression of SIRT1 in SMCs. • SIRT1 overexpression reversed the up-regulation of acetylized p65 and NF-κB induced by high glucose. • MiR-138 inhibitor reversed VSMCs proliferation and migration induced by high glucose.

FungiDB: An Integrated Bioinformatic Resource for Fungi and Oomycetes

Directory of Open Access Journals (Sweden)

Evelina Y. Basenko

2018-03-01

Full Text Available FungiDB (fungidb.org is a free online resource for data mining and functional genomics analysis for fungal and oomycete species. FungiDB is part of the Eukaryotic Pathogen Genomics Database Resource (EuPathDB, eupathdb.org platform that integrates genomic, transcriptomic, proteomic, and phenotypic datasets, and other types of data for pathogenic and nonpathogenic, free-living and parasitic organisms. FungiDB is one of the largest EuPathDB databases containing nearly 100 genomes obtained from GenBank, Aspergillus Genome Database (AspGD, The Broad Institute, Joint Genome Institute (JGI, Ensembl, and other sources. FungiDB offers a user-friendly web interface with embedded bioinformatics tools that support custom in silico experiments that leverage FungiDB-integrated data. In addition, a Galaxy-based workspace enables users to generate custom pipelines for large-scale data analysis (e.g., RNA-Seq, variant calling, etc.. This review provides an introduction to the FungiDB resources and focuses on available features, tools, and queries and how they can be used to mine data across a diverse range of integrated FungiDB datasets and records.

Protective effects of SGLT2 inhibitor luseogliflozin on pancreatic β-cells in obese type 2 diabetic db/db mice

Energy Technology Data Exchange (ETDEWEB)

Okauchi, Seizo, E-mail: okauchi@med.kawasaki-m.ac.jp; Shimoda, Masashi; Obata, Atsushi; Kimura, Tomohiko; Hirukawa, Hidenori; Kohara, Kenji; Mune, Tomoatsu; Kaku, Kohei; Kaneto, Hideaki

2016-02-12

It is well known that Sodium-Glucose Co-transporter 2 (SGLT2) inhibitors, new hypoglycemic agents, improve glycemic control by increasing urine glucose excretion, but it remained unclear how they exert protective effects on pancreatic β-cells. In this study, we examined the effects of SGLT2 inhibitor luseogliflozin on β-cell function and mass using obese type 2 diabetic db/db mice. Ten-week-old male diabetic db/db mice were treated with luseogliflozin 0.0025% or 0.01% in chow (Luse 0.0025% or Luse 0.01%) or vehicle (control) for 4 weeks. Urinary glucose excretion was increased in Luse groups (0.0025% and 0.01%) compared to control mice 3 days after the intervention. Fasting blood glucose levels were significantly lower in mice treated with Luse compared to control mice. Fasting serum insulin concentrations were significantly higher in mice treated with Luse compared to control mice. Triglyceride levels tended to be lower in Luse groups compared to control mice. In immunohistochemical study using pancreas tissues, β-cell mass was larger in Luse groups compared to control group which was due to the increase of β-cell proliferation and decrease of β-cell apoptosis. Furthermore, in gene analysis using isolated islets, insulin 1, insulin 2, MafA, PDX-1 and GLUT2 gene expression levels were significantly higher in Luse groups compared to control group. In contrast, expression levels of fibrosis-related gene such as TGFβ, fibronectin, collagen I and collagen III were significantly lower in Luse groups. In conclusion, SGLT2 inhibitor luseogliflozin ameliorates glycemic control and thus exerts protective effects on pancreatic β-cell mass and function. - Highlights: • SGLT2 inhibitor luseogliflozin ameliorates glycemic control in db/db mice. • Luseogliflozin increases β-cell proliferation and decreases β-cell apoptosis. • Luseogliflozin preserves various β-cell-specific gene expression. • Luseogliflozin decreases various fibrosis-related factors in db/db

Protective effects of SGLT2 inhibitor luseogliflozin on pancreatic β-cells in obese type 2 diabetic db/db mice

International Nuclear Information System (INIS)

Okauchi, Seizo; Shimoda, Masashi; Obata, Atsushi; Kimura, Tomohiko; Hirukawa, Hidenori; Kohara, Kenji; Mune, Tomoatsu; Kaku, Kohei; Kaneto, Hideaki

2016-01-01

It is well known that Sodium-Glucose Co-transporter 2 (SGLT2) inhibitors, new hypoglycemic agents, improve glycemic control by increasing urine glucose excretion, but it remained unclear how they exert protective effects on pancreatic β-cells. In this study, we examined the effects of SGLT2 inhibitor luseogliflozin on β-cell function and mass using obese type 2 diabetic db/db mice. Ten-week-old male diabetic db/db mice were treated with luseogliflozin 0.0025% or 0.01% in chow (Luse 0.0025% or Luse 0.01%) or vehicle (control) for 4 weeks. Urinary glucose excretion was increased in Luse groups (0.0025% and 0.01%) compared to control mice 3 days after the intervention. Fasting blood glucose levels were significantly lower in mice treated with Luse compared to control mice. Fasting serum insulin concentrations were significantly higher in mice treated with Luse compared to control mice. Triglyceride levels tended to be lower in Luse groups compared to control mice. In immunohistochemical study using pancreas tissues, β-cell mass was larger in Luse groups compared to control group which was due to the increase of β-cell proliferation and decrease of β-cell apoptosis. Furthermore, in gene analysis using isolated islets, insulin 1, insulin 2, MafA, PDX-1 and GLUT2 gene expression levels were significantly higher in Luse groups compared to control group. In contrast, expression levels of fibrosis-related gene such as TGFβ, fibronectin, collagen I and collagen III were significantly lower in Luse groups. In conclusion, SGLT2 inhibitor luseogliflozin ameliorates glycemic control and thus exerts protective effects on pancreatic β-cell mass and function. - Highlights: • SGLT2 inhibitor luseogliflozin ameliorates glycemic control in db/db mice. • Luseogliflozin increases β-cell proliferation and decreases β-cell apoptosis. • Luseogliflozin preserves various β-cell-specific gene expression. • Luseogliflozin decreases various fibrosis-related factors in db/db

TransAtlasDB: an integrated database connecting expression data, metadata and variants

Science.gov (United States)

Adetunji, Modupeore O; Lamont, Susan J; Schmidt, Carl J

2018-01-01

Abstract High-throughput transcriptome sequencing (RNAseq) is the universally applied method for target-free transcript identification and gene expression quantification, generating huge amounts of data. The constraint of accessing such data and interpreting results can be a major impediment in postulating suitable hypothesis, thus an innovative storage solution that addresses these limitations, such as hard disk storage requirements, efficiency and reproducibility are paramount. By offering a uniform data storage and retrieval mechanism, various data can be compared and easily investigated. We present a sophisticated system, TransAtlasDB, which incorporates a hybrid architecture of both relational and NoSQL databases for fast and efficient data storage, processing and querying of large datasets from transcript expression analysis with corresponding metadata, as well as gene-associated variants (such as SNPs) and their predicted gene effects. TransAtlasDB provides the data model of accurate storage of the large amount of data derived from RNAseq analysis and also methods of interacting with the database, either via the command-line data management workflows, written in Perl, with useful functionalities that simplifies the complexity of data storage and possibly manipulation of the massive amounts of data generated from RNAseq analysis or through the web interface. The database application is currently modeled to handle analyses data from agricultural species, and will be expanded to include more species groups. Overall TransAtlasDB aims to serve as an accessible repository for the large complex results data files derived from RNAseq gene expression profiling and variant analysis. Database URL: https://modupeore.github.io/TransAtlasDB/ PMID:29688361

Access of vehicles to DB netz infrastructure; Zugang von Fahrzeugen zur DB-Netz-Infrastruktur

Energy Technology Data Exchange (ETDEWEB)

Resch, U. [DB Systemtechnik, Frankfurt am Main (Germany); Ruch, M. [DB Energie GmbH, Frankfurt am Main (Germany)

2003-05-01

For line access it is necessary to take into account and observe the requirements of the infrastructure. The requirements and certifications for the power supply system and pantograph-overhead contact line interaction are described in the DB guidelines 810.0241 and 810.0242. (orig.) [German] Fuer den Netzzugang muessen die Anforderungen der Infrastruktur beachtet und eingehalten werden. Die Anforderungen und die erforderlichen Nachweise fuer den Bereich Energieversorgung und Zusammenwirken von Stromabnehmer und Oberleitung sind in den Richtlinien 810.0241 und 810.0242 der DB enthalten. (orig.)

MannDB – A microbial database of automated protein sequence analyses and evidence integration for protein characterization

Directory of Open Access Journals (Sweden)

Kuczmarski Thomas A

2006-10-01

Full Text Available Abstract Background MannDB was created to meet a need for rapid, comprehensive automated protein sequence analyses to support selection of proteins suitable as targets for driving the development of reagents for pathogen or protein toxin detection. Because a large number of open-source tools were needed, it was necessary to produce a software system to scale the computations for whole-proteome analysis. Thus, we built a fully automated system for executing software tools and for storage, integration, and display of automated protein sequence analysis and annotation data. Description MannDB is a relational database that organizes data resulting from fully automated, high-throughput protein-sequence analyses using open-source tools. Types of analyses provided include predictions of cleavage, chemical properties, classification, features, functional assignment, post-translational modifications, motifs, antigenicity, and secondary structure. Proteomes (lists of hypothetical and known proteins are downloaded and parsed from Genbank and then inserted into MannDB, and annotations from SwissProt are downloaded when identifiers are found in the Genbank entry or when identical sequences are identified. Currently 36 open-source tools are run against MannDB protein sequences either on local systems or by means of batch submission to external servers. In addition, BLAST against protein entries in MvirDB, our database of microbial virulence factors, is performed. A web client browser enables viewing of computational results and downloaded annotations, and a query tool enables structured and free-text search capabilities. When available, links to external databases, including MvirDB, are provided. MannDB contains whole-proteome analyses for at least one representative organism from each category of biological threat organism listed by APHIS, CDC, HHS, NIAID, USDA, USFDA, and WHO. Conclusion MannDB comprises a large number of genomes and comprehensive protein

Mechanical Vibration Mitigates the Decrease of Bone Quantity and Bone Quality of Leptin Receptor-Deficient Db/Db Mice by Promoting Bone Formation and Inhibiting Bone Resorption.

Science.gov (United States)

Jing, Da; Luo, Erping; Cai, Jing; Tong, Shichao; Zhai, Mingming; Shen, Guanghao; Wang, Xin; Luo, Zhuojing

2016-09-01

Leptin, a major hormonal product of adipocytes, is involved in regulating appetite and energy metabolism. Substantial studies have revealed the anabolic actions of leptin on skeletons and bone cells both in vivo and in vitro. Growing evidence has substantiated that leptin receptor-deficient db/db mice exhibit decreased bone mass and impaired bone microstructure despite several conflicting results previously reported. We herein systematically investigated bone microarchitecture, mechanical strength, bone turnover and its potential molecular mechanisms in db/db mice. More importantly, we also explored an effective approach for increasing bone mass in leptin receptor-deficient animals in an easy and noninvasive manner. Our results show that deterioration of trabecular and cortical bone microarchitecture and decreases of skeletal mechanical strength-including maximum load, yield load, stiffness, energy, tissue-level modulus and hardness-in db/db mice were significantly ameliorated by 12-week, whole-body vibration (WBV) with 0.5 g, 45 Hz via micro-computed tomography (μCT), three-point bending, and nanoindentation examinations. Serum biochemical analysis shows that WBV significantly decreased serum tartrate-resistant acid phosphatase 5b (TRACP5b) and CTx-1 levels and also mitigated the reduction of serum osteocalcin (OCN) in db/db mice. Bone histomorphometric analysis confirmed that decreased bone formation-lower mineral apposition rate, bone formation rate, and osteoblast numbers in cancellous bone-in db/db mice were suppressed by WBV. Real-time PCR assays show that WBV mitigated the reductions of tibial alkaline phosphatase (ALP), OCN, Runt-related transcription factor 2 (RUNX2), type I collagen (COL1), BMP2, Wnt3a, Lrp6, and β-catenin mRNA expression, and prevented the increases of tibial sclerostin (SOST), RANK, RANKL, RANL/osteoprotegerin (OPG) gene levels in db/db mice. Our results show that WBV promoted bone quantity and quality in db/db mice with obvious

The Human Cytomegalovirus Strain DB Activates Oncogenic Pathways in Mammary Epithelial Cells

Directory of Open Access Journals (Sweden)

Amit Kumar

2018-04-01

Full Text Available Background: Human cytomegalovirus (HCMV establishes a persistent life-long infection and increasing evidence indicates HCMV infection can modulate signaling pathways associated with oncogenesis. Breast milk is an important route of HCMV transmission in humans and we hypothesized that mammary epithelial cells could be one of the main cellular targets of HCMV infection. Methods: The infectivity of primary human mammary epithelial cells (HMECs was assessed following infection with the HCMV-DB strain, a clinical isolate with a marked macrophage-tropism. The impact of HCMV-DB infection on expression of p53 and retinoblastoma proteins, telomerase activity and oncogenic pathways (c-Myc, Akt, Ras, STAT3 was studied. Finally the transformation of HCMV-DB infected HMECs was evaluated using soft agar assay. CTH cells (CMV Transformed HMECs were detected in prolonged cultures of infected HMECs. Tumor formation was observed in NOD/SCID Gamma (NSG mice injected with CTH cells. Detection of long non coding RNA4.9 (lncRNA4.9 gene was assessed in CTH cells, tumors isolated from xenografted NSG mice and biopsies of patients with breast cancer using qualitative and quantitative PCR. Results: We found that HCMV, especially a clinical strain named HCMV-DB, infects HMECs in vitro. The clinical strain HCMV-DB replicates productively in HMECs as evidenced by detection of early and late viral transcripts and proteins. Following infection of HMECs with HCMV-DB, we observed the inactivation of retinoblastoma and p53 proteins, the activation of telomerase activity, the activation of the proto-oncogenes c-Myc and Ras, the activation of Akt and STAT3, and the upregulation of cyclin D1 and Ki67 antigen. Colony formation was observed in soft agar seeded with HCMV-DB-infected HMECs. Prolonged culture of infected HMECs resulted in the development of clusters of spheroid cells that we called CTH cells (CMV Transformed HMECs. CTH cells when injected in NOD/SCID Gamma (NSG mice

Scalable Earth-observation Analytics for Geoscientists: Spacetime Extensions to the Array Database SciDB

Science.gov (United States)

Appel, Marius; Lahn, Florian; Pebesma, Edzer; Buytaert, Wouter; Moulds, Simon

2016-04-01

Today's amount of freely available data requires scientists to spend large parts of their work on data management. This is especially true in environmental sciences when working with large remote sensing datasets, such as obtained from earth-observation satellites like the Sentinel fleet. Many frameworks like SpatialHadoop or Apache Spark address the scalability but target programmers rather than data analysts, and are not dedicated to imagery or array data. In this work, we use the open-source data management and analytics system SciDB to bring large earth-observation datasets closer to analysts. Its underlying data representation as multidimensional arrays fits naturally to earth-observation datasets, distributes storage and computational load over multiple instances by multidimensional chunking, and also enables efficient time-series based analyses, which is usually difficult using file- or tile-based approaches. Existing interfaces to R and Python furthermore allow for scalable analytics with relatively little learning effort. However, interfacing SciDB and file-based earth-observation datasets that come as tiled temporal snapshots requires a lot of manual bookkeeping during ingestion, and SciDB natively only supports loading data from CSV-like and custom binary formatted files, which currently limits its practical use in earth-observation analytics. To make it easier to work with large multi-temporal datasets in SciDB, we developed software tools that enrich SciDB with earth observation metadata and allow working with commonly used file formats: (i) the SciDB extension library scidb4geo simplifies working with spatiotemporal arrays by adding relevant metadata to the database and (ii) the Geospatial Data Abstraction Library (GDAL) driver implementation scidb4gdal allows to ingest and export remote sensing imagery from and to a large number of file formats. Using added metadata on temporal resolution and coverage, the GDAL driver supports time-based ingestion of

Neurotrophin Receptors TrkA, p75NTR, and Sortilin Are Increased and Targetable in Thyroid Cancer.

Science.gov (United States)

Faulkner, Sam; Jobling, Philip; Rowe, Christopher W; Rodrigues Oliveira, S M; Roselli, Severine; Thorne, Rick F; Oldmeadow, Christopher; Attia, John; Jiang, Chen Chen; Zhang, Xu Dong; Walker, Marjorie M; Hondermarck, Hubert

2018-01-01

Neurotrophin receptors are emerging targets in oncology, but their clinicopathologic significance in thyroid cancer is unclear. In this study, the neurotrophin tyrosine receptor kinase TrkA (also called NTRK1), the common neurotrophin receptor p75 NTR , and the proneurotrophin receptor sortilin were analyzed with immunohistochemistry in a cohort of thyroid cancers (n = 128) and compared with adenomas and normal thyroid tissues (n = 62). TrkA was detected in 20% of thyroid cancers, compared with none of the benign samples (P = 0.0007). TrkA expression was independent of histologic subtypes but associated with lymph node metastasis (P = 0.0148), suggesting the involvement of TrkA in tumor invasiveness. Nerves in the tumor microenvironment were positive for TrkA. p75 NTR was overexpressed in anaplastic thyroid cancers compared with papillary and follicular subtypes (P Neurotrophin receptor expression was confirmed in a panel of thyroid cancer cell lines at the mRNA and protein levels. Functional investigations using the anaplastic thyroid cancer cell line CAL-62 found that siRNA against TrkA, p75 NTR , and sortilin decreased cell survival and cell migration through decreased SRC and ERK activation. Together, these data reveal TrkA, p75 NTR , and sortilin as potential therapeutic targets in thyroid cancer. Copyright © 2018 American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.

Molecular signatures database (MSigDB) 3.0.

Science.gov (United States)

Liberzon, Arthur; Subramanian, Aravind; Pinchback, Reid; Thorvaldsdóttir, Helga; Tamayo, Pablo; Mesirov, Jill P

2011-06-15

Well-annotated gene sets representing the universe of the biological processes are critical for meaningful and insightful interpretation of large-scale genomic data. The Molecular Signatures Database (MSigDB) is one of the most widely used repositories of such sets. We report the availability of a new version of the database, MSigDB 3.0, with over 6700 gene sets, a complete revision of the collection of canonical pathways and experimental signatures from publications, enhanced annotations and upgrades to the web site. MSigDB is freely available for non-commercial use at http://www.broadinstitute.org/msigdb.

StarDB: a large-scale DBMS for strings

KAUST Repository

Sahli, Majed

2015-08-01

Strings and applications using them are proliferating in science and business. Currently, strings are stored in file systems and processed using ad-hoc procedural code. Existing techniques are not flexible and cannot efficiently handle complex queries or large datasets. In this paper, we demonstrate StarDB, a distributed database system for analytics on strings. StarDB hides data and system complexities and allows users to focus on analytics. It uses a comprehensive set of parallel string operations and provides a declarative query language to solve complex queries. StarDB automatically tunes itself and runs with over 90% efficiency on supercomputers, public clouds, clusters, and workstations. We test StarDB using real datasets that are 2 orders of magnitude larger than the datasets reported by previous works.

Plant DB link - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available List Contact us PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods ...e Site Policy | Contact Us Plant DB link - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ...

NGSmethDB 2017: enhanced methylomes and differential methylation

Science.gov (United States)

Lebrón, Ricardo; Gómez-Martín, Cristina; Carpena, Pedro; Bernaola-Galván, Pedro; Barturen, Guillermo; Hackenberg, Michael; Oliver, José L.

2017-01-01

The 2017 update of NGSmethDB stores whole genome methylomes generated from short-read data sets obtained by bisulfite sequencing (WGBS) technology. To generate high-quality methylomes, stringent quality controls were integrated with third-part software, adding also a two-step mapping process to exploit the advantages of the new genome assembly models. The samples were all profiled under constant parameter settings, thus enabling comparative downstream analyses. Besides a significant increase in the number of samples, NGSmethDB now includes two additional data-types, which are a valuable resource for the discovery of methylation epigenetic biomarkers: (i) differentially methylated single-cytosines; and (ii) methylation segments (i.e. genome regions of homogeneous methylation). The NGSmethDB back-end is now based on MongoDB, a NoSQL hierarchical database using JSON-formatted documents and dynamic schemas, thus accelerating sample comparative analyses. Besides conventional database dumps, track hubs were implemented, which improved database access, visualization in genome browsers and comparative analyses to third-part annotations. In addition, the database can be also accessed through a RESTful API. Lastly, a Python client and a multiplatform virtual machine allow for program-driven access from user desktop. This way, private methylation data can be compared to NGSmethDB without the need to upload them to public servers. Database website: http://bioinfo2.ugr.es/NGSmethDB. PMID:27794041

Relax with CouchDB - Into the non-relational DBMS era of Bioinformatics

Science.gov (United States)

Manyam, Ganiraju; Payton, Michelle A.; Roth, Jack A.; Abruzzo, Lynne V.; Coombes, Kevin R.

2012-01-01

With the proliferation of high-throughput technologies, genome-level data analysis has become common in molecular biology. Bioinformaticians are developing extensive resources to annotate and mine biological features from high-throughput data. The underlying database management systems for most bioinformatics software are based on a relational model. Modern non-relational databases offer an alternative that has flexibility, scalability, and a non-rigid design schema. Moreover, with an accelerated development pace, non-relational databases like CouchDB can be ideal tools to construct bioinformatics utilities. We describe CouchDB by presenting three new bioinformatics resources: (a) geneSmash, which collates data from bioinformatics resources and provides automated gene-centric annotations, (b) drugBase, a database of drug-target interactions with a web interface powered by geneSmash, and (c) HapMap-CN, which provides a web interface to query copy number variations from three SNP-chip HapMap datasets. In addition to the web sites, all three systems can be accessed programmatically via web services. PMID:22609849

Comparing MongoDB to SQL Server, Replicated

NARCIS (Netherlands)

K. Azizi

2014-01-01

htmlabstractParker et al [1] studied the performance difference between MongoDB and Microsoft SQL Server on basis of a number of insert, update and select scenarios. As the result of their study, they conclude that MongoDB has got a better performance when it comes to insert, update and simple

SilkDB: a knowledgebase for silkworm biology and genomics

DEFF Research Database (Denmark)

Wang, Jing; Xia, Qingyou; He, Ximiao

2005-01-01

The Silkworm Knowledgebase (SilkDB) is a web-based repository for the curation, integration and study of silkworm genetic and genomic data. With the recent accomplishment of a approximately 6X draft genome sequence of the domestic silkworm (Bombyx mori), SilkDB provides an integrated representati....... SilkDB is publicly accessible at http://silkworm.genomics.org.cn. Udgivelsesdato: 2005-Jan-1...

Saccharomyces boulardii administration changes gut microbiota and reduces hepatic steatosis, low-grade inflammation, and fat mass in obese and type 2 diabetic db/db mice.

Science.gov (United States)

Everard, Amandine; Matamoros, Sébastien; Geurts, Lucie; Delzenne, Nathalie M; Cani, Patrice D

2014-06-10

Growing evidence shows that gut microbes are key factors involved in the regulation of energy homeostasis, metabolic inflammation, lipid metabolism, and glucose metabolism. Therefore, gut microbiota modulations caused by selectively fermented oligosaccharides or probiotic bacteria constitute an interesting target in the physiopathology of obesity. However, to date, no probiotic yeast has been investigated in this context. Therefore, our study aimed to evaluate the impact of the most-studied probiotic yeast (i.e., Saccharomyces boulardii Biocodex) on obesity and associated metabolic features, such as fat mass development, hepatic steatosis, and low-grade inflammation, in obese mice. S. boulardii was administered daily by oral gavage to leptin-resistant obese and type 2 diabetic mice (db/db) for 4 weeks. We found that S. boulardii-treated mice exhibited reduced body weight, fat mass, hepatic steatosis, and inflammatory tone. Interestingly, these effects of S. boulardii on host metabolism were associated with local effects in the intestine. S. boulardii increased cecum weight and cecum tissue weight but also induced dramatic changes in the gut microbial composition at the phylum, family, and genus levels. These gut microbiota changes in response to S. boulardii may also be correlated with the host metabolism response. In conclusion, this study demonstrates for the first time that S. boulardii may act as a beneficial probiotic treatment in the context of obesity and type 2 diabetes. To date, no probiotic yeast have been investigated in the context of obesity and type 2 diabetes. Here we found that type 2 diabetic and obese mice (db/db) treated with Saccharomyces boulardii exhibited reduced body weight, fat mass, hepatic steatosis, and inflammatory tone. These effects on host metabolism were associated with local effects in the intestine. Importantly, by using pyrosequencing, we found that S. boulardii treatment induces changes of the gut microbiota composition at the

Preclinical evaluation of destruxin B as a novel Wnt signaling target suppressing proliferation and metastasis of colorectal cancer using non-invasive bioluminescence imaging

Energy Technology Data Exchange (ETDEWEB)

Yeh, Chi-Tai [Graduate Institute of Clinical Medicine, Taipei Medical University, Taipei, Taiwan (China); Center of Excellence for Cancer Research, Taipei Medical University, Taipei, Taiwan (China); Department of Surgery, Taipei Medical University-Shuang Ho Hospital, Taipei, Taiwan (China); Rao, Yerra Koteswara [Institute of Biochemical Sciences and Technology, Chaoyang University of Technology, Taichung, Taiwan (China); Ye, Min [Department of Natural Medicine, School of Pharmaceutical Sciences, Peking University, Beijing (China); Wu, Wen-Shi [Department of Horticulture and Biotechnology, Chinese Culture University, Taipei, Taiwan (China); Chang, Tung-Chen [Department of Surgery, Taipei Medical University-Shuang Ho Hospital, Taipei, Taiwan (China); Wang, Liang-Shun [Graduate Institute of Clinical Medicine, Taipei Medical University, Taipei, Taiwan (China); Division of Thoracic Surgery, Department of Surgery, Shuang Ho Hospital, Taipei Medical University, Taipei, Taiwan (China); Wu, Chih-Hsiung [Center of Excellence for Cancer Research, Taipei Medical University, Taipei, Taiwan (China); Department of Surgery, Taipei Medical University-Shuang Ho Hospital, Taipei, Taiwan (China); Wu, Alexander T.H., E-mail: chaw1211@tmu.edu.tw [Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan (China); Department of Radiation Oncology, Taipei Medical University Hospital, Taipei, Taiwan (China); Tzeng, Yew-Min, E-mail: ymtzeng@cyut.edu.tw [Institute of Biochemical Sciences and Technology, Chaoyang University of Technology, Taichung, Taiwan (China)

2012-05-15

In continuation to our studies toward the identification of direct anti-cancer targets, here we showed that destruxin B (DB) from Metarhizium anisopliae suppressed the proliferation and induced cell cycle arrest in human colorectal cancer (CRC) HT29, SW480 and HCT116 cells. Additionally, DB induced apoptosis in HT29 cells by decreased expression level of anti-apoptotic proteins Bcl-2 and Bcl-xL while increased pro-apoptotic Bax. On the other hand, DB attenuated Wnt-signaling by downregulation of β-catenin, Tcf4 and β-catenin/Tcf4 transcriptional activity, concomitantly with decreased expression of β-catenin target genes cyclin D1, c-myc and survivin. Furthermore, DB affected the migratory and invasive ability of HT29 cells through suppressed MMPs-2 and -9 enzymatic activities. We also found that DB targeted the MAPK and/or PI3K/Akt pathway by reduced expression of Akt, IKK-α, JNK, NF-κB, c-Jun and c-Fos while increased that of IκBα. Finally, we demonstrated that DB inhibited tumorigenesis in HT29 xenograft mice using non-invasive bioluminescence technique. Consistently, tumor samples from DB-treated mice demonstrated suppressed expression of β-catenin, cyclin D1, survivin, and endothelial marker CD31 while increased caspase-3 expression. Collectively, our data supports DB as an inhibitor of Wnt/β-catenin/Tcf signaling pathway that may be beneficial in the CRC management. Highlights: ► Destruxin B (DB) inhibited colorectal cancer cells growth and induced apoptosis. ► MAPK and/or PI3K/Akt cascade cooperates in DB induced apoptosis. ► DB affected the migratory and invasive ability of HT29 cells through MMP-9. ► DB attenuated Wnt-signaling components β-catenin, Tcf4. ► DB attenuated cyclin D1, c-myc, survivin and tumorigenesis in HT29 xenograft mice.

Influences of obese (ob/ob and diabetes (db/db genotype mutations on lumber vertebral radiological and morphometric indices: Skeletal deformation associated with dysregulated systemic glucometabolism

Directory of Open Access Journals (Sweden)

Garris David R

2006-02-01

Full Text Available Abstract Background Both diabetes and obesity syndromes are recognized to promote lumbar vertebral instability, premature osteodegeneration, exacerbate progressive osteoporosis and increase the propensity towards vertebral degeneration, instability and deformation in humans. Methods The influences of single-gene missense mutations, expressing either diabetes (db/db or obese (ob/ob metabolic syndromes on vertebral maturation and development in C57BL/KsJ mice were evaluated by radiological and macro-morphometric analysis of the resulting variances in osteodevelopment indices relative to control parameters between 8 and 16 weeks of age (syndrome onset @ 4 weeks, and the influences of low-dose 17-B-estradiol therapy on vertebral growth expression evaluated. Results Associated with the indicative genotypic obesity and hyper-glycemic/-insulinemic states, both db/db and ob/ob mutants demonstrated a significant (P ≤ 0.05 elongation of total lumbar vertebrae column (VC regional length, and individual lumbar vertebrae (LV1-5 lengths, relative to control VC and LV parameters. In contrast, LV1-5 width indices were suppressed in db/db and ob/ob mutants relative to control LV growth rates. Between 8 and 16 weeks of age, the suppressed LV1-5 width indices were sustained in both genotype mutant groups relative to control osteomaturation rates. The severity of LV1-5 width osteosuppression correlated with the severe systemic hyperglycemic and hypertriglyceridemic conditions sustained in ob/ob and db/db mutants. Low-dose 17-B-estradiol therapy (E2-HRx: 1.0 ug/ 0.1 ml oil s.c/3.5 days, initiated at 4 weeks of age (i.e., initial onset phase of db/db and ob/ob expressions re-established control LV 1–5 width indices without influencing VC or LV lengths in db/db groups. Conclusion These data demonstrate that the abnormal systemic endometabolic states associated with the expression of db/db and ob/ob genomutation syndromes suppress LV 1–5 width osteomaturation

NGSmethDB 2017: enhanced methylomes and differential methylation.

Science.gov (United States)

Lebrón, Ricardo; Gómez-Martín, Cristina; Carpena, Pedro; Bernaola-Galván, Pedro; Barturen, Guillermo; Hackenberg, Michael; Oliver, José L

2017-01-04

The 2017 update of NGSmethDB stores whole genome methylomes generated from short-read data sets obtained by bisulfite sequencing (WGBS) technology. To generate high-quality methylomes, stringent quality controls were integrated with third-part software, adding also a two-step mapping process to exploit the advantages of the new genome assembly models. The samples were all profiled under constant parameter settings, thus enabling comparative downstream analyses. Besides a significant increase in the number of samples, NGSmethDB now includes two additional data-types, which are a valuable resource for the discovery of methylation epigenetic biomarkers: (i) differentially methylated single-cytosines; and (ii) methylation segments (i.e. genome regions of homogeneous methylation). The NGSmethDB back-end is now based on MongoDB, a NoSQL hierarchical database using JSON-formatted documents and dynamic schemas, thus accelerating sample comparative analyses. Besides conventional database dumps, track hubs were implemented, which improved database access, visualization in genome browsers and comparative analyses to third-part annotations. In addition, the database can be also accessed through a RESTful API. Lastly, a Python client and a multiplatform virtual machine allow for program-driven access from user desktop. This way, private methylation data can be compared to NGSmethDB without the need to upload them to public servers. Database website: http://bioinfo2.ugr.es/NGSmethDB. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Dipeptidyl peptidase-4 inhibitor, vildagliptin, inhibits pancreatic beta cell apoptosis in association with its effects suppressing endoplasmic reticulum stress in db/db mice.

Science.gov (United States)

Wu, Yan-ju; Guo, Xin; Li, Chun-jun; Li, Dai-qing; Zhang, Jie; Yang, Yiping; Kong, Yan; Guo, Hang; Liu, De-min; Chen, Li-ming

2015-02-01

Vildagliptin promotes beta cell survival by inhibiting cell apoptosis. It has been suggested that chronic ER (endoplasmic reticulum) stress triggers beta cell apoptosis. The objective of the study is to explore whether the pro-survival effect of vildagliptin is associated with attenuation of endoplasmic reticulum stress in islets of db/db mice. Vildagliptin was orally administered to db/db mice for 6 weeks, followed by evaluation of beta cell apoptosis by caspase3 activity and TUNEL staining method. Endoplasmic reticulum stress markers were determined with quantitative RT-PCR, immunohistochemistry and immunoblot analysis. After 6 weeks of treatment, vildagliptin treatment increased plasma active GLP-1 levels (22.63±1.19 vs. 11.69±0.44, Pvildagliptin treatment down-regulated several genes related to endoplasmic reticulum stress including TRIB3 (tribbles homolog 3) (15.9±0.4 vs. 33.3±1.7, ×10⁻³, PVildagliptin promoted beta cell survival in db/db mice in association with down-regulating markers of endoplasmic reticulum stress including TRIB3, ATF-4 as well as CHOP. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Real-Time processing of Big Data with ScyllaDB

CERN Multimedia

CERN. Geneva; Martinez Pedreira, Miguel

2018-01-01

ScyllaDB: achieving 1 million operations/sec with stable and consistent real time latencies This talk will present ScyllaDB, a highly available Real-time Big Data Database that can achieve high throughput without compromising latencies or availability. ScyllaDB is API-compatible with Apache Cassandra but employs a different internal architecture to make sure that operational capacity is increased while the maintenance burden is reduced. It provides everything that a new-world database must provide: horizontal (infinite) scaling, no single point of failure, high availability and excellent performance, while keeping a sensible amount of operational efforts. Some of the key points that make ScyllaDB very efficient are its fully asynchronous operations and the smart integration with the kernel and hardware. You will learn about what makes ScyllaDB special in the crowded space of NoSQL solutions and how it can be used to power a wide variety of workloads: from real time bidding to the experiment data from the ALI...

PRISMA/DB: A Parallel Main-Memory Relational DBMS

NARCIS (Netherlands)

Apers, Peter M.G.; Flokstra, Jan; van den Berg, Carel A.; Grefen, P.W.P.J.; Wilschut, A.N.; Kersten, Martin L.; van den Berg, C.A.

1992-01-01

PRISMA/DB, a full-fledged parallel, main memory relational database management system (DBMS) is described. PRISMA/DB's high performance is obtained by the use of parallelism for query processing and main memory storage of the entire database. A flexible architecture for experimenting with

High-fat, carbohydrate-free diet markedly aggravates obesity but prevents beta-cell loss and diabetes in the obese, diabetes-susceptible db/db strain.

Science.gov (United States)

Mirhashemi, Farshad; Kluth, Oliver; Scherneck, Stephan; Vogel, Heike; Kluge, Reinhart; Schurmann, Annette; Joost, Hans-Georg; Neschen, Susanne

2008-01-01

We have previously reported that a high-fat, carbohydrate-free diet prevents diabetes and beta-cell destruction in the New Zealand Obese (NZO) mouse strain. Here we investigated the effect of diets with and without carbohydrates on obesity and development of beta-cell failure in a second mouse model of type 2 diabetes, the db/db mouse. When kept on a carbohydrate-containing standard (SD; with (w/w) 5.1, 58.3, and 17.6% fat, carbohydrates and protein, respectively) or high-fat diet (HFD; 14.6, 46.7 and 17.1%), db/db mice developed severe diabetes (blood glucose >20 mmol/l, weight loss, polydipsia and polyurea) associated with a selective loss of pancreatic beta-cells, reduced GLUT2 expression in the remaining beta-cells, and reduced plasma insulin levels. In contrast, db/db mice kept on a high-fat, carbohydrate-free diet (CFD; with 30.2 and 26.4% (w/w) fat or protein) did not develop diabetes and exhibited near-normal, hyperplastic islets in spite of a morbid obesity (fat content >60%) associated with hyperinsulinaemia. These data indicate that in genetically different mouse models of obesity-associated diabetes, obesity and dietary fat are not sufficient, and dietary carbohydrates are required, for beta-cell destruction.

Disparate phospho-Smad2 levels in advanced type 2 diabetes patients with diabetic nephropathy and early experimental db/db mouse model

DEFF Research Database (Denmark)

Thomsen, Lise Høj; Fog-Tonnesen, Morten; Nielsen Fink, Lisbeth

2017-01-01

Uncontrolled activation of transforming growth factor beta (TGF-β) family members is hypothesized to participate in type 2 diabetes (T2D) dependent diabetic nephropathy (DN). We evaluated and compared downstream activation of the Smad2-signaling pathway in kidney samples from T2D patients...... to kidneys from the T2D model of leptin receptor deficient db/db mouse. Furthermore, expression of TGF-β family members was evaluated to elucidate molecular mechanisms in the mouse model. Kidney samples from patients with advanced stages of DN showed elevated pSmad2 staining whereas db/db mouse kidneys...... surprisingly showed a decrease in pSmad2 in the tubular compartment. Structurally, kidney tissue showed dilated tubules and expanded glomeruli, but no clear fibrotic pattern was found in the diabetic mice. Selective TGF-β family members were up-regulated at the mRNA level. Antagonists of bone morphogenetic...

ProOpDB: Prokaryotic Operon DataBase.

Science.gov (United States)

Taboada, Blanca; Ciria, Ricardo; Martinez-Guerrero, Cristian E; Merino, Enrique

2012-01-01

The Prokaryotic Operon DataBase (ProOpDB, http://operons.ibt.unam.mx/OperonPredictor) constitutes one of the most precise and complete repositories of operon predictions now available. Using our novel and highly accurate operon identification algorithm, we have predicted the operon structures of more than 1200 prokaryotic genomes. ProOpDB offers diverse alternatives by which a set of operon predictions can be retrieved including: (i) organism name, (ii) metabolic pathways, as defined by the KEGG database, (iii) gene orthology, as defined by the COG database, (iv) conserved protein domains, as defined by the Pfam database, (v) reference gene and (vi) reference operon, among others. In order to limit the operon output to non-redundant organisms, ProOpDB offers an efficient method to select the most representative organisms based on a precompiled phylogenetic distances matrix. In addition, the ProOpDB operon predictions are used directly as the input data of our Gene Context Tool to visualize their genomic context and retrieve the sequence of their corresponding 5' regulatory regions, as well as the nucleotide or amino acid sequences of their genes.

DB2 11 the ultimate database for cloud, analytics, and mobile

CERN Document Server

Campbell, John; Jones, Gareth; Parekh, Surekha; Yothers, Jay

2014-01-01

Building on the prior book ""DB2 11: The Database for Big Data and Analytics,"" published in 2013, this book is written particularly for new and existing DB2 for z/OS customers and users who want to learn as much as they can about the new software version before migrating their organizations to DB2 11 for z/OS. The book begins with a technical overview of DB2 11 features and explains how the new functions in DB2 11 can help enterprise customers address the challenges they face with the explosion of data and information. There has been rapid growth in the variety, volume, and velocity of dat

An Introduction to the DB Relational Database Management System

OpenAIRE

Ward, J.R.

1982-01-01

This paper is an introductory guide to using the Db programs to maintain and query a relational database on the UNIX operating system. In the past decade. increasing interest has been shown in the development of relational database management systems. Db is an attempt to incorporate a flexible and powerful relational database system within the user environment presented by the UNIX operating system. The family of Db programs is useful for maintaining a database of information that i...

BtoxDB: a comprehensive database of protein structural data on toxin-antitoxin systems.

Science.gov (United States)

Barbosa, Luiz Carlos Bertucci; Garrido, Saulo Santesso; Marchetto, Reinaldo

2015-03-01

Toxin-antitoxin (TA) systems are diverse and abundant genetic modules in prokaryotic cells that are typically formed by two genes encoding a stable toxin and a labile antitoxin. Because TA systems are able to repress growth or kill cells and are considered to be important actors in cell persistence (multidrug resistance without genetic change), these modules are considered potential targets for alternative drug design. In this scenario, structural information for the proteins in these systems is highly valuable. In this report, we describe the development of a web-based system, named BtoxDB, that stores all protein structural data on TA systems. The BtoxDB database was implemented as a MySQL relational database using PHP scripting language. Web interfaces were developed using HTML, CSS and JavaScript. The data were collected from the PDB, UniProt and Entrez databases. These data were appropriately filtered using specialized literature and our previous knowledge about toxin-antitoxin systems. The database provides three modules ("Search", "Browse" and "Statistics") that enable searches, acquisition of contents and access to statistical data. Direct links to matching external databases are also available. The compilation of all protein structural data on TA systems in one platform is highly useful for researchers interested in this content. BtoxDB is publicly available at http://www.gurupi.uft.edu.br/btoxdb. Copyright © 2015 Elsevier Ltd. All rights reserved.

Calcium dobesilate prevents the oxidative stress and inflammation induced by diabetes in the retina of db/db mice.

Science.gov (United States)

Bogdanov, Patricia; Solà-Adell, Cristina; Hernández, Cristina; García-Ramírez, Marta; Sampedro, Joel; Simó-Servat, Olga; Valeri, Marta; Pasquali, Christian; Simó, Rafael

2017-10-01

Calcium dobesilate (CaD) is beneficial in early stages of diabetic retinopathy (DR), but its mechanisms of action remains to be elucidated. The aim was to investigate the effect of CaD on proinflammatory cytokines and oxidative stress. db/db mice were randomly assigned to daily oral treatment with CaD (200mg/kg/day) or vehicle for 15days. Biomarkers of oxidative stress (dihydroethidium, malondialdehyde), NF-κB, and proinflammatory cytokines (IL-1β, IL-6, IL-8, TNF-α, MCP-1) were examined in the retina by immunohistochemical analysis. Cultures of human retinal endothelial cells (HRECs) were used for complementary experiments. CaD significantly reduced the biomarkers of oxidative stress in the retina of db/db mice. In addition, CaD prevented the increase of NF-κB, IL-6, IL-8, TNF-α and MCP-1 induced by diabetes. CaD inhibited the activation of NF-kβ induced by IL-1β by preventing IKKB-α phosphorylation in HRECs and reduced the upregulation of IL-6 and IL-18 induced by TNF-α in a dose-dependent manner. Our results suggest that antioxidant and antiinflammatory effects are crucial in accounting for the effectiveness of CaD for treating DR. Copyright © 2017 Elsevier Inc. All rights reserved.

IBM DB2 97 Advanced Administration Cookbook

CERN Document Server

Neagu, Adrian

2012-01-01

This cookbook has recipes written in a simple, easy to understand format, with lots of screenshots and insightful tips and hints. If you are a DB2 Database Administrator who wants to understand and get hands on with the underlying aspects of database administration, then this book is for you. This book assumes that you have a basic understanding of DB2 database concepts.

Serotonin- and Dopamine-Related Gene Expression in db/db Mice Islets and in MIN6 β-Cells Treated with Palmitate and Oleate

Directory of Open Access Journals (Sweden)

L. R. Cataldo

2016-01-01

Full Text Available High circulating nonesterified fatty acids (NEFAs concentration, often reported in diabetes, leads to impaired glucose-stimulated insulin secretion (GSIS through not yet well-defined mechanisms. Serotonin and dopamine might contribute to NEFA-dependent β-cell dysfunction, since extracellular signal of these monoamines decreases GSIS. Moreover, palmitate-treated β-cells may enhance the expression of the serotonin receptor Htr2c, affecting insulin secretion. Additionally, the expression of monoamine-oxidase type B (Maob seems to be lower in islets from humans and mice with diabetes compared to nondiabetic islets, which may lead to increased monoamine concentrations. We assessed the expression of serotonin- and dopamine-related genes in islets from db/db and wild-type (WT mice. In addition, the effect of palmitate and oleate on the expression of such genes, 5HT content, and GSIS in MIN6 β-cell was determined. Lower Maob expression was found in islets from db/db versus WT mice and in MIN6 β-cells in response to palmitate and oleate treatment compared to vehicle. Reduced 5HT content and impaired GSIS in response to palmitate (−25%; p<0.0001 and oleate (−43%; p<0.0001 were detected in MIN6 β-cells. In conclusion, known defects of GSIS in islets from db/db mice and MIN6 β-cells treated with NEFAs are accompanied by reduced Maob expression and reduced 5HT content.

PhilDB: the time series database with built-in change logging

Directory of Open Access Journals (Sweden)

Andrew MacDonald

2016-03-01

Full Text Available PhilDB is an open-source time series database that supports storage of time series datasets that are dynamic; that is, it records updates to existing values in a log as they occur. PhilDB eases loading of data for the user by utilising an intelligent data write method. It preserves existing values during updates and abstracts the update complexity required to achieve logging of data value changes. It implements fast reads to make it practical to select data for analysis. Recent open-source systems have been developed to indefinitely store long-period high-resolution time series data without change logging. Unfortunately, such systems generally require a large initial installation investment before use because they are designed to operate over a cluster of servers to achieve high-performance writing of static data in real time. In essence, they have a ‘big data’ approach to storage and access. Other open-source projects for handling time series data that avoid the ‘big data’ approach are also relatively new and are complex or incomplete. None of these systems gracefully handle revision of existing data while tracking values that change. Unlike ‘big data’ solutions, PhilDB has been designed for single machine deployment on commodity hardware, reducing the barrier to deployment. PhilDB takes a unique approach to meta-data tracking; optional attribute attachment. This facilitates scaling the complexities of storing a wide variety of data. That is, it allows time series data to be loaded as time series instances with minimal initial meta-data, yet additional attributes can be created and attached to differentiate the time series instances when a wider variety of data is needed. PhilDB was written in Python, leveraging existing libraries. While some existing systems come close to meeting the needs PhilDB addresses, none cover all the needs at once. PhilDB was written to fill this gap in existing solutions. This paper explores existing time

Targeting GRP75 improves HSP90 inhibitor efficacy by enhancing p53-mediated apoptosis in hepatocellular carcinoma.

Directory of Open Access Journals (Sweden)

Weiwei Guo

Full Text Available Heat shock protein 90 (HSP90 inhibitors are potential drugs for cancer therapy. The inhibition of HSP90 on cancer cell growth largely through degrading client proteins, like Akt and p53, therefore, triggering cancer cell apoptosis. Here, we show that the HSP90 inhibitor 17-AAG can induce the expression of GRP75, a member of heat shock protein 70 (HSP70 family, which, in turn, attenuates the anti-growth effect of HSP90 inhibition on cancer cells. Additionally, 17-AAG enhanced binding of GRP75 and p53, resulting in the retention of p53 in the cytoplasm. Blocking GRP75 with its inhibitor MKT-077 potentiated the anti-tumor effects of 17-AAG by disrupting the formation of GRP75-p53 complexes, thereby facilitating translocation of p53 into the nuclei and leading to the induction of apoptosis-related genes. Finally, dual inhibition of HSP90 and GRP75 was found to significantly inhibit tumor growth in a liver cancer xenograft model. In conclusion, the GRP75 inhibitor MKT-077 enhances 17-AAG-induced apoptosis in HCCs and increases p53-mediated inhibition of tumor growth in vivo. Dual targeting of GRP75 and HSP90 may be a useful strategy for the treatment of HCCs.

Relax with CouchDB--into the non-relational DBMS era of bioinformatics.

Science.gov (United States)

Manyam, Ganiraju; Payton, Michelle A; Roth, Jack A; Abruzzo, Lynne V; Coombes, Kevin R

2012-07-01

With the proliferation of high-throughput technologies, genome-level data analysis has become common in molecular biology. Bioinformaticians are developing extensive resources to annotate and mine biological features from high-throughput data. The underlying database management systems for most bioinformatics software are based on a relational model. Modern non-relational databases offer an alternative that has flexibility, scalability, and a non-rigid design schema. Moreover, with an accelerated development pace, non-relational databases like CouchDB can be ideal tools to construct bioinformatics utilities. We describe CouchDB by presenting three new bioinformatics resources: (a) geneSmash, which collates data from bioinformatics resources and provides automated gene-centric annotations, (b) drugBase, a database of drug-target interactions with a web interface powered by geneSmash, and (c) HapMap-CN, which provides a web interface to query copy number variations from three SNP-chip HapMap datasets. In addition to the web sites, all three systems can be accessed programmatically via web services. Copyright © 2012 Elsevier Inc. All rights reserved.

Transfusion of CXCR4-primed endothelial progenitor cells reduces cerebral ischemic damage and promotes repair in db/db diabetic mice.

Directory of Open Access Journals (Sweden)

Ji Chen

Full Text Available This study investigated the role of stromal cell-derived factor-1α (SDF-1α/CXC chemokine receptor 4 (CXCR4 axis in brain and endothelial progenitor cells (EPCs, and explored the efficacy of CXCR4 primed EPCs in treating ischemic stroke in diabetes. The db/db diabetic and db/+ mice were used in this study. Levels of plasma SDF-1α and circulating CD34+CXCR4+ cells were measured. Brain SDF-1α and CXCR4 expression were quantified at basal and after middle cerebral artery occlusion (MCAO. In in vitro study, EPCs were transfected with adenovirus carrying null (Ad-null or CXCR4 (Ad-CXCR4 followed with high glucose (HG treatment for 4 days. For pathway block experiments, cells were pre-incubated with PI3K inhibitor or nitric oxide synthase (NOS inhibitor for two hours. The CXCR4 expression, function and apoptosis of EPCs were determined. The p-Akt/Akt and p-eNOS/eNOS expression in EPCs were also measured. In in vivo study, EPCs transfected with Ad-null or Ad-CXCR4 were infused into mice via tail vein. On day 2 and 7, the cerebral blood flow, neurologic deficit score, infarct volume, cerebral microvascular density, angiogenesis and neurogenesis were determined. We found: 1 The levels of plasma SDF-1α and circulating CD34+CXCR4+ cells were decreased in db/db mice; 2 The basal level of SDF-1α and MCAO-induced up-regulation of SDF-1α/CXCR4 axis were reduced in the brain of db/db mice; 3 Ad-CXCR4 transfection increased CXCR4 expression in EPCs and enhanced EPC colonic forming capacity; 4 Ad-CXCR4 transfection prevented EPCs from HG-induced dysfunction (migration and tube formation and apoptosis via activation of PI3K/Akt/eNOS signal pathway; 4 Ad-CXCR4 transfection enhanced the efficacy of EPC infusion in attenuating infarct volume and promoting angiogenesis and neurogenesis. Our data suggest that Ad-CXCR4 primed EPCs have better therapeutic effects for ischemia stroke in diabetes than unmodified EPCs do.

The Extract of Litsea japonica Reduced the Development of Diabetic Nephropathy via the Inhibition of Advanced Glycation End Products Accumulation in db/db Mice

Directory of Open Access Journals (Sweden)

Eunjin Sohn

2013-01-01

Full Text Available Increasing evidence indicates that advanced glycation end products (AGEs contribute to the pathogenesis of diabetic nephropathy. The aim of this study was to investigate the protective effect of L. japonica extract (LJE against renal damage in the db/db mouse. LJE (100 or 250 mg/kg per day was given to diabetic mice for 12 weeks. Body weight, blood glucose levels, glycated hemoglobin (HbA1c levels, and proteinuria were examined. In in vitro assay of the inhibition of AGE formation, immunohistochemical analysis of podocyte loss and AGE accumulations were performed. In 20-week-old db/db mice, severe hyperglycemia developed, and proteinuria was significantly increased. Diabetes induced markedly morphological alterations to the renal glomerular cells. AGE accumulations and podocyte loss were detected in renal glomeruli. LJE treatment significantly reduced proteinuria and AGE accumulations in diabetic mice. Moreover, the loss of nephrin, an important slit diaphragm component in the kidneys, was restored by LJE treatment. Our studies suggest that LJE might be beneficial for the treatment of diabetic nephropathy. The ability of LJE to attenuate proteinuria and podocyte dysfunction may be mediated by the inhibition of AGE accumulation in the context of diabetic nephropathy in db/db mice.

RegaDB: Community-driven data management and analysis for infectious diseases

NARCIS (Netherlands)

Libin, P.; Beheydt, G.; Deforche, K.; Imbrechts, S.; Ferreira, F.; Van Laethem, K.; Theys, K.; Carvalho, A.P.; Cavaco-Silva, J.; Lapadula, G.; Torti, C.; Assel, M.; Wesner, S.; Snoeck, J.; Ruelle, J.; de Bel, A.; Lacor, P.; de Munter, P.; van Wijngaerden, E.; Zazzi, M.; Kaiser, R.; Ayouba, A.; Peeters, M.; de Oliveira, T.; Alcantara, L.C.J.; Grossman, Z.; Sloot, P.; Otelea, D.; Paraschiv, S.; Boucher, C.; Camacho, R.J.; Vandamme, A.-M.

2013-01-01

RegaDB is a free and open source data management and analysis environment for infectious diseases. RegaDB allows clinicians to store, manage and analyze patient data, including viral genetic sequences. Moreover, RegaDB provides researchers with a mechanism to collect data in a uniform format and

DB2 9 for Linux, Unix, and Windows database administration certification study guide

CERN Document Server

Sanders, Roger E

2007-01-01

In DB2 9 for Linux, UNIX, and Windows Database Administration Certification Study Guide, Roger E. Sanders-one of the world's leading DB2 authors and an active participant in the development of IBM's DB2 certification exams-covers everything a reader needs to know to pass the DB2 9 UDB DBA Certification Test (731).This comprehensive study guide steps you through all of the topics that are covered on the test, including server management, data placement, database access, analyzing DB2 activity, DB2 utilities, high availability, security, and much more. Each chapter contains an extensive set of p

Production and separation of no-carrier-added 73As and 75Se from 7Li irradiated germanium oxide target

International Nuclear Information System (INIS)

Mandal, A.; Lahiri, S.

2012-01-01

This work reports for the first time 7 Li-induced accelerator based production of 71,72,73,74 As, 75,76,77 Br and 73,75 Se radionuclides in their no-carrier-added (nca) state. After the decay of all short-lived radionuclides 75 Se and 73 As were only existing radionuclides in germanium oxide target, which were subsequently separated by liquid-liquid extraction (LLX) using trioctylamine (TOA) dissolved in cyclohexane as liquid ion exchanger. The presence of stable germanium in various fractions was examined by Inductively Coupled Plasma Optical Spectrometry (ICP-OES). At 0.1 M TOA and 10 M HCl concentration, 75 Se and stable Ge were extracted into the organic phase leaving 73 As in the aqueous phase. The bulk Ge was stripped back to the aqueous phase by 1 M NaOH, keeping 75 Se in the organic phase. Therefore complete separation between 73 As, 75 Se and bulk Ge was achieved. (orig.)

InterProScan Result: DB674426 [KAIKOcDNA[Archive

Lifescience Database Archive (English)

Full Text Available DB674426 DB674426_4_ORF1 4B0C8A5F848582EF PFAM PF04683 Proteasom_Rpn13 NA ? IPR006773 unintegrated Cellular... Component: nucleus (GO:0005634)|Cellular Component: cytoplasm (GO:0005737) ...

MariaDB cookbook

CERN Document Server

Bartholomew, Daniel

2014-01-01

A practical cookbook, filled with advanced recipes , and plenty of code and commands used for illustration,which will make your learning curve easy and quick.This book is for anyone who wants to learn more about databases in general or MariaDB in particular. Some familiarity with SQL databases is assumed, but the recipes are approachable to almost anyone with basic database skills.

Long-term treatment with the sodium glucose cotransporter 2 inhibitor, dapagliflozin, ameliorates glucose homeostasis and diabetic nephropathy in db/db mice.

Directory of Open Access Journals (Sweden)

Naoto Terami

Full Text Available Inhibition of sodium glucose cotransporter 2 (SGLT2 has been reported as a new therapeutic strategy for treating diabetes. However, the effect of SGLT2 inhibitors on the kidney is unknown. In addition, whether SGLT2 inhibitors have an anti-inflammatory or antioxidative stress effect is still unclear. In this study, to resolve these issues, we evaluated the effects of the SGLT2 inhibitor, dapagliflozin, using a mouse model of type 2 diabetes and cultured proximal tubular epithelial (mProx24 cells. Male db/db mice were administered 0.1 or 1.0 mg/kg of dapagliflozin for 12 weeks. Body weight, blood pressure, blood glucose, hemoglobin A1c, albuminuria and creatinine clearance were measured. Mesangial matrix accumulation and interstitial fibrosis in the kidney and pancreatic β-cell mass were evaluated by histological analysis. Furthermore, gene expression of inflammatory mediators, such as osteopontin, monocyte chemoattractant protein-1 and transforming growth factor-β, was evaluated by quantitative reverse transcriptase-PCR. In addition, oxidative stress was evaluated by dihydroethidium and NADPH oxidase 4 staining. Administration of 0.1 or 1.0 mg/kg of dapagliflozin ameliorated hyperglycemia, β-cell damage and albuminuria in db/db mice. Serum creatinine, creatinine clearance and blood pressure were not affected by administration of dapagliflozin, but glomerular mesangial expansion and interstitial fibrosis were suppressed in a dose-dependent manner. Dapagliflozin treatment markedly decreased macrophage infiltration and the gene expression of inflammation and oxidative stress in the kidney of db/db mice. Moreover, dapagliflozin suppressed the high-glucose-induced gene expression of inflammatory cytokines and oxidative stress in cultured mProx24 cells. These data suggest that dapagliflozin ameliorates diabetic nephropathy by improving hyperglycemia along with inhibiting inflammation and oxidative stress.

GigaDB: announcing the GigaScience database

Directory of Open Access Journals (Sweden)

Sneddon Tam P

2012-07-01

Full Text Available Abstract With the launch of GigaScience journal, here we provide insight into the accompanying database GigaDB, which allows the integration of manuscript publication with supporting data and tools. Reinforcing and upholding GigaScience’s goals to promote open-data and reproducibility of research, GigaDB also aims to provide a home, when a suitable public repository does not exist, for the supporting data or tools featured in the journal and beyond.

AOP-DB Frontend: A user interface for the Adverse Outcome Pathways Database.

Science.gov (United States)

The EPA Adverse Outcome Pathway Database (AOP-DB) is a database resource that aggregates association relationships between AOPs, genes, chemicals, diseases, pathways, species orthology information, ontologies. The AOP-DB frontend is a simple yet powerful AOP-DB user interface in...

Design, Implementation and Applications of 3d Web-Services in DB4GEO

Science.gov (United States)

Breunig, M.; Kuper, P. V.; Dittrich, A.; Wild, P.; Butwilowski, E.; Al-Doori, M.

2013-09-01

The object-oriented database architecture DB4GeO was originally designed to support sub-surface applications in the geo-sciences. This is reflected in DB4GeO's geometric data model as well as in its import and export functions. Initially, these functions were designed for communication with 3D geological modeling and visualization tools such as GOCAD or MeshLab. However, it soon became clear that DB4GeO was suitable for a much wider range of applications. Therefore it is natural to move away from a standalone solution and to open the access to DB4GeO data by standardized OGC web-services. Though REST and OGC services seem incompatible at first sight, the implementation in DB4GeO shows that OGC-based implementation of web-services may use parts of the DB4GeO-REST implementation. Starting with initial solutions in the history of DB4GeO, this paper will introduce the design, adaptation (i.e. model transformation), and first steps in the implementation of OGC Web Feature (WFS) and Web Processing Services (WPS), as new interfaces to DB4GeO data and operations. Among its capabilities, DB4GeO can provide data in different data formats like GML, GOCAD, or DB3D XML through a WFS, as well as its ability to run operations like a 3D-to-2D service, or mesh-simplification (Progressive Meshes) through a WPS. We then demonstrate, an Android-based mobile 3D augmented reality viewer for DB4GeO that uses the Web Feature Service to visualize 3D geo-database query results. Finally, we explore future research work considering DB4GeO in the framework of the research group "Computer-Aided Collaborative Subway Track Planning in Multi-Scale 3D City and Building Models".

Impaired Hippocampal Glutamate and Glutamine Metabolism in the db/db Mouse Model of Type 2 Diabetes Mellitus

DEFF Research Database (Denmark)

Andersen, Jens Velde; Nissen, Jakob Dahl; Christensen, Sofie Kjellerup

2017-01-01

Type 2 diabetes mellitus (T2DM) is a risk factor for the development of Alzheimer's disease, and changes in brain energy metabolism have been suggested as a causative mechanism. The aim of this study was to investigate the cerebral metabolism of the important amino acids glutamate and glutamine...... significantly reduced 13C labeling in glutamate, glutamine, GABA, citrate, and aspartate from metabolism of [U-13C]glutamate. Additionally, reduced 13C labeling were observed in GABA, citrate, and aspartate from [U-13C]glutamine metabolism in hippocampal slices of db/db mice when compared to controls. None...

High-speed electro-optic switch with -80 dB crosstalk

Science.gov (United States)

Pan, J. J.; Su, W. H.; Xu, J. Y.; Grove, C. H.

1992-01-01

Special device modeling, design and layout, and precision processing controls were employed to fabricate new balanced-bridge 2x2 and 4x4 switches on X-cut, Y-propagation LiNbO3 substrate using Ti indiffused optical waveguides. The best of these devices achieved extinction ratio and crosstalk isolation of better than 93 dB electrically (46.5 dB optically). The new switches demonstrate good reproducibility with electrical crosstalk less than -80 dB.

A > 4 MGy radiation tolerant 8 THzOhm transimpedance amplifier with 50 dB dynamic range

International Nuclear Information System (INIS)

Verbeeck, J; Steyaert, M; Leroux, P

2013-01-01

A 130 nm Transimpedance Amplifier has been developed with a 255 MHz bandwidth, 90 dBΩ transimpedance gain and a dynamic input range of 1:325 or 50 dB for a photo-diode capacitance of 0.75 pF. The equivalent integrated input noise is 160 nA - 25°C. The gain of the voltage amplifier, used in the transimpedance amplifier (TIA), degrades less than 3% over a temperature range from -40 °C up to 125 °C. The TIA and attenuator exhibit a radiation tolerance larger than 4 MGy, as evidenced by radiation assessment.

P³DB 3.0: From plant phosphorylation sites to protein networks.

Science.gov (United States)

Yao, Qiuming; Ge, Huangyi; Wu, Shangquan; Zhang, Ning; Chen, Wei; Xu, Chunhui; Gao, Jianjiong; Thelen, Jay J; Xu, Dong

2014-01-01

In the past few years, the Plant Protein Phosphorylation Database (P(3)DB, http://p3db.org) has become one of the most significant in vivo data resources for studying plant phosphoproteomics. We have substantially updated P(3)DB with respect to format, new datasets and analytic tools. In the P(3)DB 3.0, there are altogether 47 923 phosphosites in 16 477 phosphoproteins curated across nine plant organisms from 32 studies, which have met our multiple quality standards for acquisition of in vivo phosphorylation site data. Centralized by these phosphorylation data, multiple related data and annotations are provided, including protein-protein interaction (PPI), gene ontology, protein tertiary structures, orthologous sequences, kinase/phosphatase classification and Kinase Client Assay (KiC Assay) data--all of which provides context for the phosphorylation event. In addition, P(3)DB 3.0 incorporates multiple network viewers for the above features, such as PPI network, kinase-substrate network, phosphatase-substrate network, and domain co-occurrence network to help study phosphorylation from a systems point of view. Furthermore, the new P(3)DB reflects a community-based design through which users can share datasets and automate data depository processes for publication purposes. Each of these new features supports the goal of making P(3)DB a comprehensive, systematic and interactive platform for phosphoproteomics research.

Effect of Long-Term Dietary Arginyl-Fructose (AF on Hyperglycemia and HbA1c in Diabetic db/db Mice

Directory of Open Access Journals (Sweden)

Kwang-Hyoung Lee

2014-05-01

Full Text Available We have previously reported that Amadori compounds exert anti-diabetic effects by lowering sucrose-induced hyperglycemia in normal Sprague-Dawley rats. In the present study we extended our recent findings to evaluate whether α-glucosidase inhibitor arginyl-fructose (AF lowers blood glucose level in diabetic db/db mice, a genetic model for type 2 diabetes. The db/db mice were randomly assigned to high-carbohydrate diets (66.1% corn starch with and without AF (4% in the diet for 6 weeks. Changes in body weight, blood glucose level, and food intake were measured daily for 42 days. Dietary supplementation of AF resulted in a significant decrease of blood glucose level (p < 0.001 and body weight (p < 0.001. The level of HbA1c, a better indicator of plasma glucose concentration over prolonged periods of time, was also significantly decreased for 6-week period (p < 0.001. Dietary treatment of acarbose® (0.04% in diet, a positive control, also significantly alleviated the level of blood glucose, HbA1c, and body weight. These results indicate that AF Maillard reaction product improves postprandial hyperglycemia by suppressing glucose absorption as well as decreasing HbA1c level.

Dicty_cDB: VHL817 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available eading fra... 75 2e-12 AF134593_1( AF134593 |pid:none) Homo sapiens L-pipecolic acid oxid... 75 2e-12 AX8822...k... 108 1e-22 (Q29RU9) RecName: Full=Peroxisomal sarcosine oxidase; S... 75 1e-12 BC114006_1( BC114006 |pid...:none) Bos taurus L-pipecolic acid oxidas... 75 1e-12 AY892312_1( AY892312 |pid:n

Reduced sulfation of chondroitin sulfate but not heparan sulfate in kidneys of diabetic db/db mice.

Science.gov (United States)

Reine, Trine M; Grøndahl, Frøy; Jenssen, Trond G; Hadler-Olsen, Elin; Prydz, Kristian; Kolset, Svein O

2013-08-01

Heparan sulfate proteoglycans are hypothesized to contribute to the filtration barrier in kidney glomeruli and the glycocalyx of endothelial cells. To investigate potential changes in proteoglycans in diabetic kidney, we isolated glycosaminoglycans from kidney cortex from healthy db/+ and diabetic db/db mice. Disaccharide analysis of chondroitin sulfate revealed a significant decrease in the 4-O-sulfated disaccharides (D0a4) from 65% to 40%, whereas 6-O-sulfated disaccharides (D0a6) were reduced from 11% to 6%, with a corresponding increase in unsulfated disaccharides. In contrast, no structural differences were observed in heparan sulfate. Furthermore, no difference was found in the molar amount of glycosaminoglycans, or in the ratio of hyaluronan/heparan sulfate/chondroitin sulfate. Immunohistochemical staining for the heparan sulfate proteoglycan perlecan was similar in both types of material but reduced staining of 4-O-sulfated chondroitin and dermatan was observed in kidney sections from diabetic mice. In support of this, using qRT-PCR, a 53.5% decrease in the expression level of Chst-11 (chondroitin 4-O sulfotransferase) was demonstrated in diabetic kidney. These results suggest that changes in the sulfation of chondroitin need to be addressed in future studies on proteoglycans and kidney function in diabetes.

Data Container Study for Handling array-based data using Hive, Spark, MongoDB, SciDB and Rasdaman

Science.gov (United States)

Xu, M.; Hu, F.; Yang, J.; Yu, M.; Yang, C. P.

2017-12-01

Geoscience communities have come up with various big data storage solutions, such as Rasdaman and Hive, to address the grand challenges for massive Earth observation data management and processing. To examine the readiness of current solutions in supporting big Earth observation, we propose to investigate and compare four popular data container solutions, including Rasdaman, Hive, Spark, SciDB and MongoDB. Using different types of spatial and non-spatial queries, datasets stored in common scientific data formats (e.g., NetCDF and HDF), and two applications (i.e. dust storm simulation data mining and MERRA data analytics), we systematically compare and evaluate the feature and performance of these four data containers in terms of data discover and access. The computing resources (e.g. CPU, memory, hard drive, network) consumed while performing various queries and operations are monitored and recorded for the performance evaluation. The initial results show that 1) the popular data container clusters are able to handle large volume of data, but their performances vary in different situations. Meanwhile, there is a trade-off between data preprocessing, disk saving, query-time saving, and resource consuming. 2) ClimateSpark, MongoDB and SciDB perform the best among all the containers in all the queries tests, and Hive performs the worst. 3) These studied data containers can be applied on other array-based datasets, such as high resolution remote sensing data and model simulation data. 4) Rasdaman clustering configuration is more complex than the others. A comprehensive report will detail the experimental results, and compare their pros and cons regarding system performance, ease of use, accessibility, scalability, compatibility, and flexibility.

Dicty_cDB: VHK777 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available ... 75 2e-12 BC114006_1( BC114006 |pid:none) Bos taurus L-pipecolic acid oxidas.....ll open reading fra... 75 4e-12 AF134593_1( AF134593 |pid:none) Homo sapiens L-pipecolic acid oxid... 75 4e-

Nonlinearity and Phase Noise Tolerant 75-110 GHz Signal over Fiber System Using Phase Modulation Technique

DEFF Research Database (Denmark)

Deng, Lei; Pang, Xiaodan; Zhang, Xu

2013-01-01

We report on the transmission of 8 Gb/s 0 dB PAPR 16QAM-OFDM W-band (75-110 GHz) signals over 22.8km SMF without phase noise compensation by using a phase modulator in the optical heterodyne up-convertor....

Results of the experiment on chemical identification of Db as a decay product of element 115

International Nuclear Information System (INIS)

Dmitriev, S.N.; Oganesyan, Yu.Ts.; Utenkov, V.K.

2004-01-01

For the first time the chemical identification of Db as the terminal isotope of the decay element 115 produced via the 243 Am( 48 Ca, 3n) 288 115 reaction was realized. The experiment was performed on the U400 cyclotron of FLNR, JINR. The 243 Am target was bombarded with a beam dose of 3.4 · 10 18 48 Ca projectiles at an energy of 247 MeV in the center of the target. The reaction products were collected in the surface of a copper catcher block, which was removed with a lathe and then dissolved in concentrated HNO 3 . The group 5 elements were separated by sorption onto Dowex 50X8 cation-exchange resin with subsequent desorption using 1 M HF, which forms anionic fluoride complexes of group 5 elements. The eluant was evaporated onto 0.4 μm thick polyethylene foils which were placed between a pair of semiconductor detectors surrounded by 3 He neutron counters for measurement of α particles, fission fragments and neutrons. Over the course of the experiment, we observed 15 spontaneous fission events with T 1/2 = 32 -7 +11 h which we attribute to 268 Db. The production cross section for the 243 Am + 48 Ca reaction was 4.2 -1.2 + 1 .6 pb. These results agree with the original element 115 synthesis experiment where 268 Db was first observed as the terminal isotope following the five consecutive α decays from the 288 115 parent nucleus at the Dubna gas-filled separator. The data from the present experiment give independent evidence for the synthesis of element 115 as well as element 113 via the 243 Am + 48 Ca reaction

A 60-dB linear VGA with novel exponential gain approximation

International Nuclear Information System (INIS)

Zhou Jiaye; Tan Xi; Wang Junyu; Tang Zhangwen; Min Hao

2009-01-01

A CMOS variable gain amplifier (VGA) that adopts a novel exponential gain approximation is presented. No additional exponential gain control circuit is required in the proposed VGA used in a direct conversion receiver. A wide gain control voltage from 0.4 to 1.8 V and a high linearity performance are achieved. The three-stage VGA with automatic gain control (AGC) and DC offset cancellation (DCOC) is fabricated in a 0.18-μm CMOS technology and shows a linear gain range of more than 58-dB with a linearity error less than ±1 dB. The 3-dB bandwidth is over 8 MHz at all gain settings. The measured input-referred third intercept point (IIP3) of the proposed VGA varies from -18.1 to 13.5 dBm, and the measured noise figure varies from 27 to 65 dB at a frequency of 1 MHz. The dynamic range of the closed-loop AGC exceeds 56 dB, where the output signal-to-noise-and-distortion ratio (SNDR) reaches 20 dB. The whole circuit, occupying 0.3 mm 2 of chip area, dissipates less than 3.7 mA from a 1.8-V supply.

Klaim-DB: A Modeling Language for Distributed Database Applications

DEFF Research Database (Denmark)

Wu, Xi; Li, Ximeng; Lluch Lafuente, Alberto

2015-01-01

and manipulation of structured data, with integrity and atomicity considerations. We present the formal semantics of KlaimDB and illustrate the use of the language in a scenario where the sales from different branches of a chain of department stores are aggregated from their local databases. It can be seen......We present the modelling language, Klaim-DB, for distributed database applications. Klaim-DB borrows the distributed nets of the coordination language Klaim but essentially re-incarnates the tuple spaces of Klaim as databases, and provides high-level language abstractions for the access...... that raising the abstraction level and encapsulating integrity checks (concerning the schema of tables, etc.) in the language primitives for database operations benefit the modelling task considerably....

HTT-DB: horizontally transferred transposable elements database.

Science.gov (United States)

Dotto, Bruno Reis; Carvalho, Evelise Leis; Silva, Alexandre Freitas; Duarte Silva, Luiz Fernando; Pinto, Paulo Marcos; Ortiz, Mauro Freitas; Wallau, Gabriel Luz

2015-09-01

Horizontal transfer of transposable (HTT) elements among eukaryotes was discovered in the mid-1980s. As then, >300 new cases have been described. New findings about HTT are revealing the evolutionary impact of this phenomenon on host genomes. In order to provide an up to date, interactive and expandable database for such events, we developed the HTT-DB database. HTT-DB allows easy access to most of HTT cases reported along with rich information about each case. Moreover, it allows the user to generate tables and graphs based on searches using Transposable elements and/or host species classification and export them in several formats. This database is freely available on the web at http://lpa.saogabriel.unipampa.edu.br:8080/httdatabase. HTT-DB was developed based on Java and MySQL with all major browsers supported. Tools and software packages used are free for personal or non-profit projects. bdotto82@gmail.com or gabriel.wallau@gmail.com. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

dbCAN2: a meta server for automated carbohydrate-active enzyme annotation

DEFF Research Database (Denmark)

Zhang, Han; Yohe, Tanner; Huang, Le

2018-01-01

of plant and plant-associated microbial genomes and metagenomes being sequenced, there is an urgent need of automatic tools for genomic data mining of CAZymes. We developed the dbCAN web server in 2012 to provide a public service for automated CAZyme annotation for newly sequenced genomes. Here, dbCAN2...... (http://cys.bios.niu.edu/dbCAN2) is presented as an updated meta server, which integrates three state-of-the-art tools for CAZome (all CAZymes of a genome) annotation: (i) HMMER search against the dbCAN HMM (hidden Markov model) database; (ii) DIAMOND search against the CAZy pre-annotated CAZyme...

RoboDB: an application of Semantic Web Technologies to robotics

NARCIS (Netherlands)

Juarez, Alex; Hu, J.; Feijs, L.M.G.

2011-01-01

RoboDB is a knowledge acquisition system that gathers information about robots. RoboDB uses Semantic Web technologies and tools to help the user in creating semantic descriptions of robot embodiments and their capabilities, as well as in building an ontology of robotics projects, research

Clone DB: an integrated NCBI resource for clone-associated data

Science.gov (United States)

Schneider, Valerie A.; Chen, Hsiu-Chuan; Clausen, Cliff; Meric, Peter A.; Zhou, Zhigang; Bouk, Nathan; Husain, Nora; Maglott, Donna R.; Church, Deanna M.

2013-01-01

The National Center for Biotechnology Information (NCBI) Clone DB (http://www.ncbi.nlm.nih.gov/clone/) is an integrated resource providing information about and facilitating access to clones, which serve as valuable research reagents in many fields, including genome sequencing and variation analysis. Clone DB represents an expansion and replacement of the former NCBI Clone Registry and has records for genomic and cell-based libraries and clones representing more than 100 different eukaryotic taxa. Records provide details of library construction, associated sequences, map positions and information about resource distribution. Clone DB is indexed in the NCBI Entrez system and can be queried by fields that include organism, clone name, gene name and sequence identifier. Whenever possible, genomic clones are mapped to reference assemblies and their map positions provided in clone records. Clones mapping to specific genomic regions can also be searched for using the NCBI Clone Finder tool, which accepts queries based on sequence coordinates or features such as gene or transcript names. Clone DB makes reports of library, clone and placement data on its FTP site available for download. With Clone DB, users now have available to them a centralized resource that provides them with the tools they will need to make use of these important research reagents. PMID:23193260

DB2 10.1 fundamentals certification study guide

CERN Document Server

Sanders, Roger E

2014-01-01

Beginning with an explanation of the certification process and working through fundamental exam objectives, this guide gives test-takers all they need to know to pass IBM's DB2 10.1 Fundamentals certification exam (Exam 610). All the subjects covered on the exam are included: planning, security, data concurrency, working with databases and database objects, working with data using SQL and XQuery, working with DB2 tables, views, and indexes-and more. The book concludes with an

ChimerDB 3.0: an enhanced database for fusion genes from cancer transcriptome and literature data mining.

Science.gov (United States)

Lee, Myunggyo; Lee, Kyubum; Yu, Namhee; Jang, Insu; Choi, Ikjung; Kim, Pora; Jang, Ye Eun; Kim, Byounggun; Kim, Sunkyu; Lee, Byungwook; Kang, Jaewoo; Lee, Sanghyuk

2017-01-04

Fusion gene is an important class of therapeutic targets and prognostic markers in cancer. ChimerDB is a comprehensive database of fusion genes encompassing analysis of deep sequencing data and manual curations. In this update, the database coverage was enhanced considerably by adding two new modules of The Cancer Genome Atlas (TCGA) RNA-Seq analysis and PubMed abstract mining. ChimerDB 3.0 is composed of three modules of ChimerKB, ChimerPub and ChimerSeq. ChimerKB represents a knowledgebase including 1066 fusion genes with manual curation that were compiled from public resources of fusion genes with experimental evidences. ChimerPub includes 2767 fusion genes obtained from text mining of PubMed abstracts. ChimerSeq module is designed to archive the fusion candidates from deep sequencing data. Importantly, we have analyzed RNA-Seq data of the TCGA project covering 4569 patients in 23 cancer types using two reliable programs of FusionScan and TopHat-Fusion. The new user interface supports diverse search options and graphic representation of fusion gene structure. ChimerDB 3.0 is available at http://ercsb.ewha.ac.kr/fusiongene/. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

DB-PABP: a database of polyanion-binding proteins.

Science.gov (United States)

Fang, Jianwen; Dong, Yinghua; Salamat-Miller, Nazila; Middaugh, C Russell

2008-01-01

The interactions between polyanions (PAs) and polyanion-binding proteins (PABPs) have been found to play significant roles in many essential biological processes including intracellular organization, transport and protein folding. Furthermore, many neurodegenerative disease-related proteins are PABPs. Thus, a better understanding of PA/PABP interactions may not only enhance our understandings of biological systems but also provide new clues to these deadly diseases. The literature in this field is widely scattered, suggesting the need for a comprehensive and searchable database of PABPs. The DB-PABP is a comprehensive, manually curated and searchable database of experimentally characterized PABPs. It is freely available and can be accessed online at http://pabp.bcf.ku.edu/DB_PABP/. The DB-PABP was implemented as a MySQL relational database. An interactive web interface was created using Java Server Pages (JSP). The search page of the database is organized into a main search form and a section for utilities. The main search form enables custom searches via four menus: protein names, polyanion names, the source species of the proteins and the methods used to discover the interactions. Available utilities include a commonality matrix, a function of listing PABPs by the number of interacting polyanions and a string search for author surnames. The DB-PABP is maintained at the University of Kansas. We encourage users to provide feedback and submit new data and references.

Peripherally administered baclofen reduced food intake and body weight in db/db as well as diet-induced obese mice.

Science.gov (United States)

Sato, Ikuko; Arima, Hiroshi; Ozaki, Noriyuki; Ozaki, Nobuaki; Watanabe, Minemori; Goto, Motomitsu; Shimizu, Hiroshi; Hayashi, Masayuki; Banno, Ryouichi; Nagasaki, Hiroshi; Oiso, Yutaka

2007-10-16

Peripheral administration of baclofen significantly reduced food intake and body weight increase in both diabetic (db/db) and diet-induced obese mice for 5 weeks, whereas it had no significant effects on energy balance in their lean control mice. Despite the decreased body weight, neuropeptide Y expression in the arcuate nucleus was significantly decreased, whereas pro-opiomelanocortin expression was significantly increased by baclofen treatment. These data demonstrate that the inhibitory effects of baclofen on body weight in the obese mice were mediated via the arcuate nucleus at least partially, and suggest that GABA(B) agonists could be a new therapeutic reagent for obesity.

Transformasi Skema Basis Data Relasional Menjadi Model Data Berorientasi Dokumen pada MongoDB

Directory of Open Access Journals (Sweden)

I Gede Winaya

2016-01-01

Full Text Available MongoDB is a database that uses document-oriented data storage models. In fact, to  migrate from a relational database to NoSQL databases such as MongoDB is not an easy matter especially if the data are extremely complex. Based on the documentation that has been done by several global companies related to the use of MongoDB, it can be concluded that the process of migration from RDBMS to MongoDB require quite a long time. One process that takes quite a lot is transformation of relational database schema into a document-oriented data model on MongoDB.             This research discusses the development transformation system of relational database schema to the document oriented data model in MongoDB. The process of transformation is done by utilizing the structure and relationships between tables in the scheme as the main parameters of the modeling algorithm. In the process of the modeling documents, it necessary to adjustments the specifications of MongoDB document that formed document model can be implemented in MongoDB.             Document models are formed from transformation process can be a single document, embedded document, referenced document or combination of these. Document models are formed depending on the type, rules, and the value of the relationships cardinality between tables in the relational database schema.

MAT-DB - A database for nuclear energy related materials data

International Nuclear Information System (INIS)

Over, H.H.

2009-01-01

The web-enabled materials database (Mat-DB) of JRC-IE has a long-term history in storing materials test data resulting from European and international research projects. The database structure and the user-guidance has bee permanently updated improved and optimized. The database is implemented in the secure ODIN portal: https://odin.jrc.ec.europa.eu of JRC-IE. This architecture guarantees fast access to confidential and public data and documentation which are stored in an inter-related document management database (DoMa). It is a part of JRC's nuclear knowledge management. Mat-DB hosts the whole pool of IAEA surveillance data of reactor pressure vessel materials from different nuclear power plants of the member states. Mat-DB contains also thousands of European GEN IV reactor systems related R and D materials data which are an important basis for the evaluating and extrapolating design data for candidate materials and setting up design rules covering high temperature exposure, irradiation and corrosion. Those data and rules would match also fusion related components. Mat-DB covers thermo-mechanical and thermo-physical properties data of engineering alloys at low, elevated and high temperatures for base materials and joints, including irradiated materials for nuclear fission and fusion applications, thermal barrier coated materials for gas turbines and properties of corroded materials. The corrosion part refers to weight gain/loss data of high temperature exposed engineering alloys and ceramic materials. For each test type the database structure reflects international test standards and recommendations. Mat-DB features an extensive library of evaluation programs for web-enabled assessment of uniaxial creep, fatigue, crack growth and high temperature corrosion properties. Evaluations can be performed after data retrieval or independently of Mat-DB by transferring other materials data in a given format to the programs. The fast evaluation processes help the user to

Dicty_cDB: Contig-U06541-1 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available 1 ( CW927554 ) EDCBM45TF A. castellanii, 6-8 kb library from tot... 44 7.5 1 ( CL534328 ) trib011xa13.g1 T. reesei HindIII BAC librar...y Hypo... 44 7.5 1 ( CL531533 ) trib005xd13.b1 T. reesei HindIII BAC library...CCNP644_b1 Cowpea UCR 779 Mixed Tissue an... 44 7.5 1 ( DQ121376 ) Uncultured bacterium clone YC01G10, parti..., ge... 44 7.5 1 ( CW927722 ) EDCBN39TR A. castellanii, 6-8 kb library from tot... 44 7.5 ...4 7.5 1 ( DW476283 ) GH_RMIRS_002_B08_F Cotton Normalized Library rand... 44 7.5 1 ( DR951133 ) EST1142672 Aquilegia cDNA library

MonetDB/X100 - A DBMS in the CPU cache

NARCIS (Netherlands)

M. Zukowski (Marcin); P.A. Boncz (Peter); N.J. Nes (Niels); S. Héman (Sándor)

2005-01-01

textabstractX100 is a new execution engine for the MonetDB system, that improves execution speed and overcomes its main memory limitation. It introduces the concept of in-cache vectorized processing that strikes a balance between the existing column-at-a-time MIL execution primitives of MonetDB and

Analysis of neuron–astrocyte metabolic cooperation in the brain of db/db mice with cognitive decline using 13C NMR spectroscopy

OpenAIRE

Zheng, Hong; Zheng, Yongquan; Wang, Dan; Cai, Aimin; Lin, Qiuting; Zhao, Liangcai; Chen, Minjiang; Deng, Mingjie; Ye, Xinjian; Gao, Hongchang

2016-01-01

Type 2 diabetes has been linked to cognitive impairment, but its potential metabolic mechanism is still unclear. The present study aimed to explore neuron–astrocyte metabolic cooperation in the brain of diabetic (db/db, BKS.Cg-m+/+ Leprdb/J) mice with cognitive decline using 13C NMR technique in combination with intravenous [2-13C]-acetate and [3-13C]-lactate infusions. We found that the 13C-enrichment from [2-13C]-acetate into tricarboxylic acid cycle intermediate, succinate, was significant...

SpecDB: The AAVSO’s Public Repository for Spectra of Variable Stars

Science.gov (United States)

Kafka, Stella; Weaver, John; Silvis, George; Beck, Sara

2018-01-01

SpecDB is the American Association of Variable Star Observers (AAVSO) spectral database. Accessible to any astronomer with the capability to perform spectroscopy, SpecDB provides an unprecedented scientific opportunity for amateur and professional astronomers around the globe. Backed by the Variable Star Index, one of the most utilized variable star catalogs, SpecDB is expected to become one of the world leading databases of its kind. Once verified by a team of expert spectroscopists, an observer can upload spectra of variable stars target easily and efficiently. Uploaded spectra can then be searched for, previewed, and downloaded for inclusion in publications. Close community development and involvement will ensure a user-friendly and versatile database, compatible with the needs of 21st century astrophysics. Observations of 1D spectra are submitted as FITS files. All spectra are required to be preprocessed for wavelength calibration and dark subtraction; Bias and flat are strongly recommended. First time observers are required to submit a spectrum of a standard (non-variable) star to be checked for errors in technique or equipment. Regardless of user validation, FITS headers must include several value cards detailing the observation, as well as information regarding the observer, equipment, and observing site in accordance with existing AAVSO records. This enforces consistency and provides necessary details for follow up analysis. Requirements are provided to users in a comprehensive guidebook and accompanying technical manual. Upon submission, FITS headers are automatically checked for errors and any anomalies are immediately fed back to the user. Successful candidates can then submit at will, including multiple simultaneous submissions. All published observations can be searched and interactively previewed. Community involvement will be enhanced by an associated forum where users can discuss observation techniques and suggest improvements to the database.

Dicty_cDB: Contig-U00957-1 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available .. 46 0.71 3 ( J04943 ) Rat nucleolar protein B23.2 mRNA, complete cds, clo... 46 0.75 2 ( DL486166 ) Molecular Toxicology... Modeling. 46 0.75 2 ( DL002044 ) Methods for Molecular Toxicology Modeling. 46 0.75 2 ( DJ019...atocyte toxicity modeling. 46 0.75 2 ( DD041343 ) Molecular Toxicology Modeling. 46 0.75 2 ( BD390609 ) Meth...( DL002041 ) Methods for Molecular Toxicology Modeling. 46 2.5 1 ( DJ019204 ) Molecular Nephrotoxicology Mod...ecular Hepatotoxicology Modeling. 46 2.5 1 ( DD193521 ) Cardiotoxin Molecular Toxicology

Update History of This Database - dbQSNP | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us dbQSNP Update History of This Database Date Update contents 2017/02/16 dbQSNP English archiv...e Description Download License Update History of This Database Site Policy | Contact Us Update History of This Database - dbQSNP | LSDB Archive ... ...e site is opened. 2002/10/23 dbQSNP (http://qsnp.gen.kyushu-u.ac.jp/) is opened. About This Database Databas

The Development of the TPR-DB as Grounded Theory Method

DEFF Research Database (Denmark)

Carl, Michael; Schaeffer, Moritz

2018-01-01

and refine the emerging concepts and categories and to validate the developing theories, the TPR-DB has been extended with further translation studies in different languages and translation modes. In this respect, it shares many features with Grounded Theory Method. This method was discovered in 1967...... and used in qualitative research in social science ad many other research areas. We analyze the TPR-DB development as a Grounded Theory Method....... on quantitative assessment of well-defined research questions on cognitive processes in human translation production, the integration of the data into the TPR-DB allowed for broader qualitative and exploratory research which has led to new codes, categories and research themes. In a constant effort to develop...

Differential Proteomic Analysis of the Pancreas of Diabetic db/db Mice Reveals the Proteins Involved in the Development of Complications of Diabetes Mellitus

Directory of Open Access Journals (Sweden)

Victoriano Pérez-Vázquez

2014-05-01

Full Text Available Type 2 diabetes mellitus is characterized by hyperglycemia and insulin-resistance. Diabetes results from pancreatic inability to secrete the insulin needed to overcome this resistance. We analyzed the protein profile from the pancreas of ten-week old diabetic db/db and wild type mice through proteomics. Pancreatic proteins were separated in two-dimensional polyacrylamide gel electrophoresis (2D-PAGE and significant changes in db/db mice respect to wild type mice were observed in 27 proteins. Twenty five proteins were identified by matrix-assisted laser desorption/ionization (MALDI time-of-flight (TOF and their interactions were analyzed using search tool for the retrieval of interacting genes/proteins (STRING and database for annotation, visualization and integrated discovery (DAVID. Some of these proteins were Pancreatic α-amylase, Cytochrome b5, Lithostathine-1, Lithostathine-2, Chymotrypsinogen B, Peroxiredoxin-4, Aspartyl aminopeptidase, Endoplasmin, and others, which are involved in the metabolism of carbohydrates and proteins, as well as in oxidative stress, and inflammation. Remarkably, these are mostly endoplasmic reticulum proteins related to peptidase activity, i.e., they are involved in proteolysis, glucose catabolism and in the tumor necrosis factor-mediated signaling pathway. These results suggest mechanisms for insulin resistance, and the chronic inflammatory state observed in diabetes.

PharmDB-K: Integrated Bio-Pharmacological Network Database for Traditional Korean Medicine.

Directory of Open Access Journals (Sweden)

Ji-Hyun Lee

Full Text Available Despite the growing attention given to Traditional Medicine (TM worldwide, there is no well-known, publicly available, integrated bio-pharmacological Traditional Korean Medicine (TKM database for researchers in drug discovery. In this study, we have constructed PharmDB-K, which offers comprehensive information relating to TKM-associated drugs (compound, disease indication, and protein relationships. To explore the underlying molecular interaction of TKM, we integrated fourteen different databases, six Pharmacopoeias, and literature, and established a massive bio-pharmacological network for TKM and experimentally validated some cases predicted from the PharmDB-K analyses. Currently, PharmDB-K contains information about 262 TKMs, 7,815 drugs, 3,721 diseases, 32,373 proteins, and 1,887 side effects. One of the unique sets of information in PharmDB-K includes 400 indicator compounds used for standardization of herbal medicine. Furthermore, we are operating PharmDB-K via phExplorer (a network visualization software and BioMart (a data federation framework for convenient search and analysis of the TKM network. Database URL: http://pharmdb-k.org, http://biomart.i-pharm.org.

Dicty_cDB: Contig-U04605-1 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available . 46 2.2 1 ( DB766622 ) Apis mellifera head cDNA, RIKEN full-length enric... 46 2.2 1 ( FG291142 ) 1108793330728 New World... Screwworm Egg 9261 ESTs C... 46 2.2 1 ( FG290464 ) 1108793321772 New World... Screwworm Egg 9261 ESTs C... 46 2.2 1 ( FG288754 ) 1108793276247 New World Screwworm Egg 9261 ESTs ...C... 46 2.2 1 ( FG285961 ) 1108770710727 New World Screwworm Egg 9261 ESTs C... 46 2.2 1 ( CT030663 ) Mouse ..._142_D08_3APR2008_058 BN18DYSC Brassic... 44 8.7 1 ( FG286796 ) 1108770726415 New World

AtomDB Progress Report: Atomic data and new models for X-ray spectroscopy.

Science.gov (United States)

Smith, Randall K.; Foster, Adam; Brickhouse, Nancy S.; Stancil, Phillip C.; Cumbee, Renata; Mullen, Patrick Dean; AtomDB Team

2018-06-01

The AtomDB project collects atomic data from both theoretical and observational/experimental sources, providing both a convenient interface (http://www.atomdb.org/Webguide/webguide.php) as well as providing input to spectral models for many types of astrophysical X-ray plasmas. We have released several updates to AtomDB in response to the Hitomi data, including new data for the Fe K complex, and have expanded the range of models available in AtomDB to include the Kronos charge exchange models from Mullen at al. (2016, ApJS, 224, 2). Combined with the previous AtomDB charge exchange model (http://www.atomdb.org/CX/), these data enable a velocity-dependent model for X-ray and EUV charge exchange spectra. We also present a new Kappa-distribution spectral model, enabling plasmas with non-Maxwellian electron distributions to be modeled with AtomDB. Tools are provided within pyAtomDB to explore and exploit these new plasma models. This presentation will review these enhancements and describe plans for the new few years of database and code development in preparation for XARM, Athena, and (hopefully) Arcus.

Dicty_cDB: VHC785 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available -12 BC114006_1( BC114006 |pid:none) Bos taurus L-pipecolic acid oxidas... 75 1e-1...one) Homo sapiens full open reading fra... 75 2e-12 AF134593_1( AF134593 |pid:none) Homo sapiens L-pipecolic

Ortholog - MicrobeDB.jp | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available List Contact us MicrobeDB.jp Ortholog Data detail Data name Ortholog DOI 10.18908/lsdba.nbdc01181-010.V002 V...814 triples - About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Ortholog - MicrobeDB.jp | LSDB Archive ...

50 tips and tricks for MongoDB developers

CERN Document Server

Chodorow, Kristina

2011-01-01

Getting started with MongoDB is easy, but once you begin building applications with it, you'll face some complex issues. What are the tradeoffs between normalized and denormalized data? How do you handle replica set failure and failover? This collection of MongoDB tips, tricks, and hacks helps you resolve issues with everything from application design and implementation to data safety and monitoring. You get specific guidance in five topic areas directly from engineers at 10gen, the company that develops and supports this open source database: Application Design Tips: What to keep in mind wh

Development of degradation D/B system for the containment building of NPP

International Nuclear Information System (INIS)

Cho, M. S.; Song, Y. C.; Yim, J. H.; Kim, D. K.; Lee, J. S.

2001-01-01

The Degradation D/B System is developed for digitalizing the history of the Containment building of nuclear power plant. It have 6 D/B which are consist of General, Design drawing, Material, Construction, ISI·SIT·ILRT D/B. For efficient operation of the system, utilities are also developed such as the aging and repair data management program for concrete and steel structures, the data search engine with various options helping users find what they want, and the data exchange program restoring and updating input data

Dicty_cDB: VHI816 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available omal sarcosine oxidase; S... 75 3e-12 BC114006_1( BC114006 |pid:none) Bos taurus L-pipecolic acid oxidas... ...pid:none) Homo sapiens full open reading fra... 75 5e-12 AF134593_1( AF134593 |pid:none) Homo sapiens L-pipecoli

The IRPVM-DB database

International Nuclear Information System (INIS)

Davies, L.M.; Gillemot, F.; Yanko, L.; Lyssakov, V.

1997-01-01

The IRPVM-DB (International Reactor Pressure Vessel Material Database) initiated by the IAEA IWG LMNPP is going to collect the available surveillance and research data world-wide on RPV material ageing. This paper presents the purpose of the database; it summarizes the type and the relationship of data included; it gives information about the data access and protection; and finally, it summarizes the state of art of the database. (author). 1 ref., 2 figs

The IRPVM-DB database

Energy Technology Data Exchange (ETDEWEB)

Davies, L M [Davies Consultants, Oxford (United Kingdom); Gillemot, F [Atomic Energy Research Inst., Budapest (Hungary); Yanko, L [Minatom (Russian Federation); Lyssakov, V [International Atomic Energy Agency, Vienna (Austria)

1997-09-01

The IRPVM-DB (International Reactor Pressure Vessel Material Database) initiated by the IAEA IWG LMNPP is going to collect the available surveillance and research data world-wide on RPV material ageing. This paper presents the purpose of the database; it summarizes the type and the relationship of data included; it gives information about the data access and protection; and finally, it summarizes the state of art of the database. (author). 1 ref., 2 figs.

Dicty_cDB: Contig-U10656-1 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available 83 4e-75 EU128481_1( EU128481 |pid:none) Tanichthys albonubes beta-actin mR... 283 4e-75 BC045879_1( BC04587...icus beta-actin gen... 283 4e-75 EU128482_1( EU128482 |pid:none) Tanichthys albonube

DB2 9 for zOS Database Administration Certification Study Guide

CERN Document Server

Lawson, Susan

2008-01-01

In order to become an IBM Certified Database Administrator - DB2 9 DBA for z/OS, you must pass two exams: DB2 9 Fundamentals Exam (Exam 730), and DB2 9 Database Administrator for z/OS (Exam 732)-the primary focus focus of this book. Written by two members of the team who participated in the actual writing of the exam, this specialized study guide covers every topic that you will need to know to pass Exam 732, including database design and implementation, operation and recovery, security and auditing, performance, as well as installation and migration/upgrade. But that is only the beginning.

Dicty_cDB: VHD308 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available eroxisomal sarcosine oxidase; S... 75 9e-13 BC114006_1( BC114006 |pid:none) Bos taurus L-pipecolic acid oxid...7155 |pid:none) Homo sapiens full open reading fra... 75 1e-12 AF134593_1( AF134593 |pid:none) Homo sapiens L-pipecoli

CerealsDB 3.0: expansion of resources and data integration.

Science.gov (United States)

Wilkinson, Paul A; Winfield, Mark O; Barker, Gary L A; Tyrrell, Simon; Bian, Xingdong; Allen, Alexandra M; Burridge, Amanda; Coghill, Jane A; Waterfall, Christy; Caccamo, Mario; Davey, Robert P; Edwards, Keith J

2016-06-24

The increase in human populations around the world has put pressure on resources, and as a consequence food security has become an important challenge for the 21st century. Wheat (Triticum aestivum) is one of the most important crops in human and livestock diets, and the development of wheat varieties that produce higher yields, combined with increased resistance to pests and resilience to changes in climate, has meant that wheat breeding has become an important focus of scientific research. In an attempt to facilitate these improvements in wheat, plant breeders have employed molecular tools to help them identify genes for important agronomic traits that can be bred into new varieties. Modern molecular techniques have ensured that the rapid and inexpensive characterisation of SNP markers and their validation with modern genotyping methods has produced a valuable resource that can be used in marker assisted selection. CerealsDB was created as a means of quickly disseminating this information to breeders and researchers around the globe. CerealsDB version 3.0 is an online resource that contains a wide range of genomic datasets for wheat that will assist plant breeders and scientists to select the most appropriate markers for use in marker assisted selection. CerealsDB includes a database which currently contains in excess of a million putative varietal SNPs, of which several hundreds of thousands have been experimentally validated. In addition, CerealsDB also contains new data on functional SNPs predicted to have a major effect on protein function and we have constructed a web service to encourage data integration and high-throughput programmatic access. CerealsDB is an open access website that hosts information on SNPs that are considered useful for both plant breeders and research scientists. The recent inclusion of web services designed to federate genomic data resources allows the information on CerealsDB to be more fully integrated with the WheatIS network and

Dicty_cDB: VHD682 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available 29RU9) RecName: Full=Peroxisomal sarcosine oxidase; S... 75 3e-12 BC114006_1( BC114006 |pid:none) Bos taurus L-pipecoli...id:none) Homo sapiens L-pipecolic acid oxid... 75 5e-12 AX882278_1( AX882278 |pid:none) Sequence 17183 from

Flux Density through Guides with Microstructured Twisted Clad DB Medium

Directory of Open Access Journals (Sweden)

M. A. Baqir

2014-01-01

Full Text Available The paper deals with the study of flux density through a newly proposed twisted clad guide containing DB medium. The inner core and the outer clad sections are usual dielectrics, and the introduced twisted windings at the core-clad interface are treated under DB boundary conditions. The pitch angle of twist is supposed to greatly contribute towards the control over the dispersion characteristics of the guide. The eigenvalue equation for the guiding structure is deduced, and the analytical investigations are made to explore the propagation patterns of flux densities corresponding to the sustained low-order hybrid modes under the situation of varying pitch angles. The emphasis has been put on the effects due to the DB twisted pitch on the propagation of energy flux density through the guide.

Download - PGDBj - Ortholog DB | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available e Description Download License Update History of This Database Site Policy | Contact Us Download - PGDBj - Ortholog DB | LSDB Archive ... ...List Contact us PGDBj - Ortholog DB Download First of all, please read the license of this database. Data na...switchLanguage; BLAST Search Image Search Home About Archive Update History Data

AOP-DB Frontend: A user interface for the Adverse Outcome Pathways Database

Science.gov (United States)

The EPA Adverse Outcome Pathway Database (AOP-DB) is a database resource that aggregates association relationships between AOPs, genes, chemicals, diseases, pathways, species orthology information, ontologies. The AOP-DB frontend is a simple yet powerful user interface in the for...

Joint study on activation of international nuclear information use through implementation INIS DB server with IAEA

International Nuclear Information System (INIS)

Lee, H. C.; Yi, J. H.; Kim, T. W.; Chun, Y. C.; Yoo, A. N.

2003-03-01

In order to install the INIS DB host site in Korea, the Korea INIS national center has cooperated with KAERI and organizations concerned, contacted the INIS secretariat participated in the consultative meeting of INIS liaison officers, and strengthened the relationship with Asian and Oceanian countries. And KAERI staff and a maintenance engineer participated training seminar on INIS DB installation and maintenance. The Korea national center obtained the INIS DB server code and data by international cooperation activity. Based these code and data, hardware and software for INIS DB server are purchased. INIS DB server system was installed the software and INIS database(2,347,302) was constructed. In 2003 INIS host DB site started to provide web service in Korea. Also It enables the users in the member countries in Asia as well as domestic users to get quick information. It will also bring the active use of the domestic INIS DB and the increase of the productivity of domestic research activities

DB2 9 for Linux, Unix, and Windows database administration upgrade certification study guide

CERN Document Server

Sanders, Roger E

2007-01-01

Written by one of the world's leading DB2 authors who is an active participant in the development of the DB2 certification exams, this resource covers everything a database adminstrator needs to know to pass the DB2 9 for Linux, UNIX, and Windows Database Administration Certification Upgrade exam (Exam 736). This comprehensive study guide discusses all exam topics: server management, data placement, XML concepts, analyzing activity, high availability, database security, and much more. Each chapter contains an extensive set of practice questions along with carefully explained answers. Both information-technology professionals who have experience as database administrators and have a current DBA certification on version 8 of DB2 and individuals who would like to learn the new features of DB2 9 will benefit from the information in this reference guide.

Eukaryotic Pathogen Database Resources (EuPathDB)

Data.gov (United States)

U.S. Department of Health & Human Services — EuPathDB Bioinformatics Resource Center for Biodefense and Emerging/Re-emerging Infectious Diseases is a portal for accessing genomic-scale datasets associated with...

PlantNATsDB: a comprehensive database of plant natural antisense transcripts.

Science.gov (United States)

Chen, Dijun; Yuan, Chunhui; Zhang, Jian; Zhang, Zhao; Bai, Lin; Meng, Yijun; Chen, Ling-Ling; Chen, Ming

2012-01-01

Natural antisense transcripts (NATs), as one type of regulatory RNAs, occur prevalently in plant genomes and play significant roles in physiological and pathological processes. Although their important biological functions have been reported widely, a comprehensive database is lacking up to now. Consequently, we constructed a plant NAT database (PlantNATsDB) involving approximately 2 million NAT pairs in 69 plant species. GO annotation and high-throughput small RNA sequencing data currently available were integrated to investigate the biological function of NATs. PlantNATsDB provides various user-friendly web interfaces to facilitate the presentation of NATs and an integrated, graphical network browser to display the complex networks formed by different NATs. Moreover, a 'Gene Set Analysis' module based on GO annotation was designed to dig out the statistical significantly overrepresented GO categories from the specific NAT network. PlantNATsDB is currently the most comprehensive resource of NATs in the plant kingdom, which can serve as a reference database to investigate the regulatory function of NATs. The PlantNATsDB is freely available at http://bis.zju.edu.cn/pnatdb/.

Getting Started with GEO, CouchDB, and Nodejs

CERN Document Server

Thompson, Mick

2011-01-01

Today's mobile devices have GPS and standard APIs to give you access to coordinates-but what can you do with that data? With this concise book, application developers learn how to work with location data quickly and easily, using Node.js, CouchDB, and other open source tools and libraries. Node.js makes it simple to run event code on the Web, and the CouchDB document-oriented database lets you store location data and perform complex queries on it quickly. You'll learn how to get started with these tools, and then use them together to build an example project called MapChat, using HTML and Ja

A MongoDB-Based Management of Planar Spatial Data with a Flattened R-Tree

Directory of Open Access Journals (Sweden)

Longgang Xiang

2016-07-01

Full Text Available This paper addresses how to manage planar spatial data using MongoDB, a popular NoSQL database characterized as a document-oriented, rich query language and high availability. The core idea is to flatten a hierarchical R-tree structure into a tabular MongoDB collection, during which R-tree nodes are represented as collection documents and R-tree pointers are expressed as document identifiers. By following this strategy, a storage schema to support R-tree-based create, read, update, and delete (CRUD operations is designed and a module to manage planar spatial data by consuming and maintaining flattened R-tree structure is developed. The R-tree module is then seamlessly integrated into MongoDB, so that users could manipulate planar spatial data with existing command interfaces oriented to geodetic spatial data. The experimental evaluation, using real-world datasets with diverse coverage, types, and sizes, shows that planar spatial data can be effectively managed by MongoDB with our flattened R-tree and, therefore, the application extent of MongoDB will be greatly enlarged. Our work resulted in a MongoDB branch with R-tree support, which has been released on GitHub for open access.

Taxon (Viridiplantae) - PGDBj - Ortholog DB | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available of This Database Site Policy | Contact Us Taxon (Viridiplantae) - PGDBj - Ortholog DB | LSDB Archive ... ...List Contact us PGDBj - Ortholog DB Taxon (Viridiplantae) Data detail Data name Taxon (Viridiplantae) DOI 10...switchLanguage; BLAST Search Image Search Home About Archive Update History Data

Taxon (Cyanobacteria) - PGDBj - Ortholog DB | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available of This Database Site Policy | Contact Us Taxon (Cyanobacteria) - PGDBj - Ortholog DB | LSDB Archive ... ...List Contact us PGDBj - Ortholog DB Taxon (Cyanobacteria) Data detail Data name Taxon (Cyanobacteria) DOI 10...switchLanguage; BLAST Search Image Search Home About Archive Update History Data

Green tea extract with polyethylene glycol-3350 reduces body weight and improves glucose tolerance in db/db and high-fat diet mice.

Science.gov (United States)

Park, Jae-Hyung; Choi, Yoon Jung; Kim, Yong Woon; Kim, Sang Pyo; Cho, Ho-Chan; Ahn, Shinbyoung; Bae, Ki-Cheor; Im, Seung-Soon; Bae, Jae-Hoon; Song, Dae-Kyu

2013-08-01

Green tea extract (GTE) is regarded to be effective against obesity and type 2 diabetes, but definitive evidences have not been proven. Based on the assumption that the gallated catechins (GCs) in GTE attenuate intestinal glucose and lipid absorption, while enhancing insulin resistance when GCs are present in the circulation through inhibiting cellular glucose uptake in various tissues, this study attempted to block the intestinal absorption of GCs and prolong their residence time in the lumen. We then observed whether GTE containing the nonabsorbable GCs could ameliorate body weight (BW) gain and glucose intolerance in db/db and high-fat diet mice. Inhibition of the intestinal absorption of GCs was accomplished by co-administering the nontoxic polymer polyethylene glycol-3350 (PEG). C57BLKS/J db/db and high-fat diet C57BL/6 mice were treated for 4 weeks with drugs as follows: GTE, PEG, GTE+PEG, voglibose, or pioglitazone. GTE mixed with meals did not have any ameliorating effects on BW gain and glucose intolerance. However, the administration of GTE plus PEG significantly reduced BW gain, insulin resistance, and glucose intolerance, without affecting food intake and appetite. The effect was comparable to the effects of an α-glucosidase inhibitor and a peroxisome proliferator-activated receptor-γ/α agonist. These results indicate that prolonging the action of GCs of GTE in the intestinal lumen and blocking their entry into the circulation may allow GTE to be used as a prevention and treatment for both obesity and obesity-induced type 2 diabetes.

License - Plabrain DB | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data List Contact us Plabrain... Alike 2.1 Japan . If you use data from this database, please be sure attribute this database as follows: Plabrain...of this database (http://dbarchive.lifesciencedb.jp/english/en/plabrain-db/desc.html) in the article or pape...se Description Download License Update History of This Database Site Policy | Contact Us License - Plabrain DB | LSDB Archive ...

Anti-liver-kidney microsome antibody type 1 recognizes human cytochrome P450 db1.

Science.gov (United States)

Gueguen, M; Yamamoto, A M; Bernard, O; Alvarez, F

1989-03-15

Anti-liver-kidney microsome antibody type 1 (LKM1), present in the sera of a group of children with autoimmune hepatitis, was recently shown to recognize a 50 kDa protein identified as rat liver cytochromes P450 db1 and db2. High homology between these two members of the rat P450 IID subfamily and human P450 db1 suggested that anti-LKM1 antibody is directed against this human protein. To test this hypothesis, a human liver cDNA expression library in phage lambda GT-11 was screened using rat P450 db1 cDNA as a probe. Two human cDNA clones were found to be identical to human P450 db1 by restriction mapping. Immunoblot analysis using as antigen, the purified fusion protein from one of the human cDNA clones showed that only anti-LKM1 with anti-50 kDa reactivity recognized the fusion protein. This fusion protein was further used to develop an ELISA test that was shown to be specific for sera of children with this disease. These results: 1) identify the human liver antigen recognized by anti-LKM1 auto-antibodies as cytochrome P450 db1, 2) allow to speculate that mutation on the human P450 db1 gene could alter its expression in the hepatocyte and make it auto-antigenic, 3) provide a simple and specific diagnostic test for this disease.

Balanced PIN-TIA photoreceiver with integrated 3 dB fiber coupler for distributed fiber optic sensors

Science.gov (United States)

Datta, Shubhashish; Rajagopalan, Sruti; Lemke, Shaun; Joshi, Abhay

2014-06-01

We report a balanced PIN-TIA photoreceiver integrated with a 3 dB fiber coupler for distributed fiber optic sensors. This detector demonstrates -3 dB bandwidth >15 GHz and coupled conversion gain >65 V/W per photodiode through either input port of the 3 dB coupler, and can be operated at local oscillator power of +17 dBm. The combined common mode rejection of the balanced photoreceiver and the integrated 3 dB coupler is >20 dB. We also present measurement results with various optical stimuli, namely impulses, sinusoids, and pseudo-random sequences, which are relevant for time domain reflectometry, frequency domain reflectometry, and code correlation sensors, respectively.

Dicty_cDB: Contig-U16414-1 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available ( CB282081 ) BT0047 Blomia tropicalis cDNA library Blomia trop... 52 9e-19 4 ( EX370580 ) GQ03219.B7_O07 GQ032 - Shoot ti...on of useful proteins deri... 72 1e-29 5 ( DR930447 ) EST1121986 Aquilegia cDNA library...63 ) EST1191412 Aquilegia cDNA library Aquilegia formo... 88 5e-26 2 ( DB657321 ) Saccharomyces cere... 64 1e-21 4 ( DT739515 ) EST1173364 Aquilegia cDNA library Aquilegia formo... 70 1e-21 3 ( CF609239 ) INFIO01_000017 Grape Inflore... ( DT733254 ) EST1167104 Aquilegia cDNA library Aquilegia formo... 68 8e-21 5 ( FF717444 ) XABT35772.fwd Gateway compati

GenMapDB: a database of mapped human BAC clones

OpenAIRE

Morley, Michael; Arcaro, Melissa; Burdick, Joshua; Yonescu, Raluca; Reid, Thomas; Kirsch, Ilan R.; Cheung, Vivian G.

2001-01-01

GenMapDB (http://genomics.med.upenn.edu/genmapdb) is a repository of human bacterial artificial chromosome (BAC) clones mapped by our laboratory to sequence-tagged site markers. Currently, GenMapDB contains over 3000 mapped clones that span 19 chromosomes, chromosomes 2, 4, 5, 9–22, X and Y. This database provides positional information about human BAC clones from the RPCI-11 human male BAC library. It also contains restriction fragment analysis data and end sequen...

PlantDB – a versatile database for managing plant research

Directory of Open Access Journals (Sweden)

Gruissem Wilhelm

2008-01-01

Full Text Available Abstract Background Research in plant science laboratories often involves usage of many different species, cultivars, ecotypes, mutants, alleles or transgenic lines. This creates a great challenge to keep track of the identity of experimental plants and stored samples or seeds. Results Here, we describe PlantDB – a Microsoft® Office Access database – with a user-friendly front-end for managing information relevant for experimental plants. PlantDB can hold information about plants of different species, cultivars or genetic composition. Introduction of a concise identifier system allows easy generation of pedigree trees. In addition, all information about any experimental plant – from growth conditions and dates over extracted samples such as RNA to files containing images of the plants – can be linked unequivocally. Conclusion We have been using PlantDB for several years in our laboratory and found that it greatly facilitates access to relevant information.

WholeCellSimDB: a hybrid relational/HDF database for whole-cell model predictions.

Science.gov (United States)

Karr, Jonathan R; Phillips, Nolan C; Covert, Markus W

2014-01-01

Mechanistic 'whole-cell' models are needed to develop a complete understanding of cell physiology. However, extracting biological insights from whole-cell models requires running and analyzing large numbers of simulations. We developed WholeCellSimDB, a database for organizing whole-cell simulations. WholeCellSimDB was designed to enable researchers to search simulation metadata to identify simulations for further analysis, and quickly slice and aggregate simulation results data. In addition, WholeCellSimDB enables users to share simulations with the broader research community. The database uses a hybrid relational/hierarchical data format architecture to efficiently store and retrieve both simulation setup metadata and results data. WholeCellSimDB provides a graphical Web-based interface to search, browse, plot and export simulations; a JavaScript Object Notation (JSON) Web service to retrieve data for Web-based visualizations; a command-line interface to deposit simulations; and a Python API to retrieve data for advanced analysis. Overall, we believe WholeCellSimDB will help researchers use whole-cell models to advance basic biological science and bioengineering. http://www.wholecellsimdb.org SOURCE CODE REPOSITORY: URL: http://github.com/CovertLab/WholeCellSimDB. © The Author(s) 2014. Published by Oxford University Press.

Degradation of 2,4-DB in Argentinean agricultural soils with high humic matter content.

Science.gov (United States)

Cuadrado, Virginia; Merini, Luciano J; Flocco, Cecilia G; Giulietti, Ana M

2008-01-01

The dissipation of 4-(2,4-dichlorophenoxy) butyric acid (2,4-DB) in high-humic-matter-containing soils from agricultural fields of the Argentinean Humid Pampa region was studied, employing soil microcosms under different experimental conditions. The added herbicide was dissipated almost completely by soils with and without history of herbicide use by day 28. At 500 ppm, both soils showed the same degradation rates; but at 5-ppm concentration, the chronically exposed soil demonstrated a faster degradation of the herbicide. 2,4-DB addition produced increases in herbicide-degrading bacteria of three and 1.5 orders of magnitude in soils with and without history of herbicide use, respectively, in microcosms with 5 ppm. At 500-ppm concentration, the increase in 2,4-DB degraders was five orders of magnitude after 14 days, independent of the history of herbicide use. No differences were observed in either 2,4-DB degradation rates or in degrader bacteria numbers in the presence and absence of alfalfa plants, in spite of some differential characteristics in patterns of 2,4-DB metabolite accumulation. The main factor affecting 2,4-DB degradation rate would be the history of herbicide use, as a consequence of the adaptation of the indigenous microflora to the presence of herbicides in the field.

A Crude 1-DNJ Extract from Home Made Bombyx Batryticatus Inhibits Diabetic Cardiomyopathy-Associated Fibrosis in db/db Mice and Reduces Protein N-Glycosylation Levels

Directory of Open Access Journals (Sweden)

Qing Zhao

2018-06-01

Full Text Available The traditional Chinese drug Bombyx Batryticatus (BB, which is also named the white stiff silkworm, has been widely used in Chinese clinics for thousands of years. It is famous for its antispasmodic and blood circulation-promoting effects. Cardiomyocyte hypertrophy, interstitial cell hyperplasia, and myocardial fibrosis are closely related to the N-glycosylation of key proteins. To examine the alterations of N-glycosylation that occur in diabetic myocardium during the early stage of the disease, and to clarify the therapeutic effect of 1-Deoxynojirimycin (1-DNJ extracted from BB, we used the db/db (diabetic mouse model and an approach based on hydrophilic chromatography solid-phase extraction integrated with an liquid Chromatograph Mass Spectrometer (LC-MS identification strategy to perform a site-specific N-glycosylation analysis of left ventricular cardiomyocyte proteins. Advanced glycation end products (AGEs, hydroxyproline, connective tissue growth factor (CTGF, and other serum biochemical indicators were measured with enzyme-linked immunosorbent assays (ELISA. In addition, the α-1,6-fucosylation of N-glycans was profiled with lens culinaris agglutinin (LCA lectin blots and fluorescein isothiocyanate (FITC-labelled lectin affinity histochemistry. The results indicated that 1-DNJ administration obviously downregulated myocardium protein N-glycosylation in db/db mice. The expression levels of serum indicators and fibrosis-related cytokines were reduced significantly by 1-DNJ in a dose-dependent manner. The glycan α-1,6-fucosylation level of the db/db mouse myocardium was elevated, and the intervention effect of 1-DNJ administration on N-glycan α-1,6-fucosylation was significant. To verify this result, the well-known transforming growth factor-β (TGF-β/Smad2/3 pathway was selected, and core α-1,6-fucosylated TGF-β receptor II (TGFR-βII was analysed semi-quantitatively with western blotting. The result supported the conclusions obtained

Protein (Viridiplantae) - PGDBj - Ortholog DB | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available ase Description Download License Update History of This Database Site Policy | Contact Us Protein (Viridiplantae) - PGDBj - Ortholog DB | LSDB Archive ... ...List Contact us PGDBj - Ortholog DB Protein (Viridiplantae) Data detail Data name Protein (Viridiplantae) DO...switchLanguage; BLAST Search Image Search Home About Archive Update History Data

Fermentation of purple Jerusalem artichoke extract to improve the α-glucosidase inhibitory effect in vitro and ameliorate blood glucose in db/db mice.

Science.gov (United States)

Wang, Zhiqiang; Hwang, Seung Hwan; Lee, Sun Youb; Lim, Soon Sung

2016-06-01

Jerusalem artichoke has inhibitory activity against α-glucosidase and decreases fasting serum glucose levels, which may be related to its fructan content. The biological activity of fructan can be influenced by the degree of polymerization. Thus, in this study, the inhibitory effects of original and fermented purple Jerusalem artichoke (PJA) on α-glucosidase were compared in vitro. Additionally, the anti-diabetes effect of Lactobacillus plantarum-fermented PJA (LJA) was studied in a non-insulin-dependent diabetes mellitus animal model (C57BIKsJ db/db). The water extract of PJA was fermented by L. plantarum, and two strains of Bacillus subtilis to compare their anti-α-glucosidase activities in vitro by α-glucosidase assays. The anti-diabetes effect of LJA was studied in a non-insulin-dependent diabetes mellitus animal model (C57BIKsJ db/db) for seven weeks. During the experiment, food intake, body weight, and fasting blood glucose were measured every week. At the end of the treatment period, several diabetic parameters and the intestinal α-glucosidase activity were measured. The LJA showed the highest α-glucosidase inhibitory activity in vitro. In the in vivo study, it resulted in a significantly lower blood glucose concentration than the control. Serum insulin and HDL cholesterol levels were significantly higher and the concentrations of triglycerides, non-esterified fatty acids, and total cholesterol were significant lower in mice treated with LJA after seven weeks. In addition, the intestinal α-glucosidase activity was partially inhibited. These results suggested that LJA regulates blood glucose and has potential use as a dietary supplement.

RefDB: The Reference Database for CMS Monte Carlo Production

CERN Document Server

Lefébure, V

2003-01-01

RefDB is the CMS Monte Carlo Reference Database. It is used for recording and managing all details of physics simulation, reconstruction and analysis requests, for coordinating task assignments to world-wide distributed Regional Centers, Grid-enabled or not, and trace their progress rate. RefDB is also the central database that the workflow-planner contacts in order to get task instructions. It is automatically and asynchronously updated with book-keeping run summaries. Finally it is the end-user interface to data catalogues.

Protein (Cyanobacteria) - PGDBj - Ortholog DB | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available ut This Database Database Description Download License Update History of This Database Site Policy | Contact Us Protein (Cyanobacteria) - PGDBj - Ortholog DB | LSDB Archive ... ...List Contact us PGDBj - Ortholog DB Protein (Cyanobacteria) Data detail Data name Protein (Cyanobacteria) DO...switchLanguage; BLAST Search Image Search Home About Archive Update History Data

dbSMR: a novel resource of genome-wide SNPs affecting microRNA mediated regulation

Directory of Open Access Journals (Sweden)

Hariharan Manoj

2009-04-01

Full Text Available Abstract Background MicroRNAs (miRNAs regulate several biological processes through post-transcriptional gene silencing. The efficiency of binding of miRNAs to target transcripts depends on the sequence as well as intramolecular structure of the transcript. Single Nucleotide Polymorphisms (SNPs can contribute to alterations in the structure of regions flanking them, thereby influencing the accessibility for miRNA binding. Description The entire human genome was analyzed for SNPs in and around predicted miRNA target sites. Polymorphisms within 200 nucleotides that could alter the intramolecular structure at the target site, thereby altering regulation were annotated. Collated information was ported in a MySQL database with a user-friendly interface accessible through the URL: http://miracle.igib.res.in/dbSMR. Conclusion The database has a user-friendly interface where the information can be queried using either the gene name, microRNA name, polymorphism ID or transcript ID. Combination queries using 'AND' or 'OR' is also possible along with specifying the degree of change of intramolecular bonding with and without the polymorphism. Such a resource would enable researchers address questions like the role of regulatory SNPs in the 3' UTRs and population specific regulatory modulations in the context of microRNA targets.

The Kepler DB, a Database Management System for Arrays, Sparse Arrays and Binary Data

Science.gov (United States)

McCauliff, Sean; Cote, Miles T.; Girouard, Forrest R.; Middour, Christopher; Klaus, Todd C.; Wohler, Bill

2010-01-01

The Kepler Science Operations Center stores pixel values on approximately six million pixels collected every 30-minutes, as well as data products that are generated as a result of running the Kepler science processing pipeline. The Kepler Database (Kepler DB) management system was created to act as the repository of this information. After one year of ight usage, Kepler DB is managing 3 TiB of data and is expected to grow to over 10 TiB over the course of the mission. Kepler DB is a non-relational, transactional database where data are represented as one dimensional arrays, sparse arrays or binary large objects. We will discuss Kepler DB's APIs, implementation, usage and deployment at the Kepler Science Operations Center.

The Kepler DB: a database management system for arrays, sparse arrays, and binary data

Science.gov (United States)

McCauliff, Sean; Cote, Miles T.; Girouard, Forrest R.; Middour, Christopher; Klaus, Todd C.; Wohler, Bill

2010-07-01

The Kepler Science Operations Center stores pixel values on approximately six million pixels collected every 30 minutes, as well as data products that are generated as a result of running the Kepler science processing pipeline. The Kepler Database management system (Kepler DB)was created to act as the repository of this information. After one year of flight usage, Kepler DB is managing 3 TiB of data and is expected to grow to over 10 TiB over the course of the mission. Kepler DB is a non-relational, transactional database where data are represented as one-dimensional arrays, sparse arrays or binary large objects. We will discuss Kepler DB's APIs, implementation, usage and deployment at the Kepler Science Operations Center.

Long noncoding RNA TUG1 alleviates extracellular matrix accumulation via mediating microRNA-377 targeting of PPARγ in diabetic nephropathy.

Science.gov (United States)

Duan, Li-Jun; Ding, Min; Hou, Li-Jun; Cui, Yuan-Tao; Li, Chun-Jun; Yu, De-Min

2017-03-11

Long noncoding RNA taurine-upregulated gene 1 (lncRNA TUG1) has been reported to play a key role in the progression of diabetic nephropathy (DN). However, the role of lncRNA TUG1 in the regulation of diabetic nephropathy remains largely unknown. The aim of the present study is to identify the regulation of lncRNA TUG1 on extracellular matrix accumulation via mediating microRNA-377 targeting of PPARγ, and investigate the underlying mechanisms in progression of DN. Microarray was performed to screen differentially expressed miRNAs in db/db DN mice. Afterwards, computational prediction programs (TargetScan, miRanda, PicTar and miRGen) was applied to predict the target gene of miRNAs. The complementary binding of miRNA and lncRNA was assessed by luciferase assays. Protein and mRNA expression were detected by western blot and real time quantitate PCR. MiRNA-377 was screened by miRNA microarray and differentially up-regulated in db/db DN mice. PPARγ was predicted to be the target of miR-377 and the prediction was verified by luciferase assays. Expression of miR-377 was up-regulated in mesangial cell treated with high glucose (25 mM), and overexpression of miR-377 inhibited PPARγ expression and promoted PAI-1 and TGF-β1 expression. The expression of TUG1 antagonized the effect of miR-377 on the downregulation of its target PPARγ and inhibited extracellular matrix accumulation, including PAI-1, TGF-β1, fibronectin (FN) and collagen IV (Col IV), induced by high glucose. LncRNA TUG1 acts as an endogenous sponge of miR-377 and downregulates miR-377 expression levels, and thereby relieving the inhibition of its target gene PPARγ and alleviates extracellular matrix accumulation of mesangial cells, which provides a novel insight of diabetic nephropathy pathogenesis. Copyright © 2017 Elsevier Inc. All rights reserved.

The Molecular Signatures Database (MSigDB) hallmark gene set collection.

Science.gov (United States)

Liberzon, Arthur; Birger, Chet; Thorvaldsdóttir, Helga; Ghandi, Mahmoud; Mesirov, Jill P; Tamayo, Pablo

2015-12-23

The Molecular Signatures Database (MSigDB) is one of the most widely used and comprehensive databases of gene sets for performing gene set enrichment analysis. Since its creation, MSigDB has grown beyond its roots in metabolic disease and cancer to include >10,000 gene sets. These better represent a wider range of biological processes and diseases, but the utility of the database is reduced by increased redundancy across, and heterogeneity within, gene sets. To address this challenge, here we use a combination of automated approaches and expert curation to develop a collection of "hallmark" gene sets as part of MSigDB. Each hallmark in this collection consists of a "refined" gene set, derived from multiple "founder" sets, that conveys a specific biological state or process and displays coherent expression. The hallmarks effectively summarize most of the relevant information of the original founder sets and, by reducing both variation and redundancy, provide more refined and concise inputs for gene set enrichment analysis.

Dicty_cDB: Contig-U05261-1 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available DN828913 ) KUCD01_04_F02_T3 WSWR cDNA library Triticum aesti... 48 0.49 1 ( DB872994 ) Lipochromis sp. 'matu...berosum cDNA, ... 50 0.13 1 ( CK261371 ) EST707449 potato abiotic stress cDNA library Sola... 50 0.13 1 ( BQ...pergillus niger mRNA for hypothetical protein, ... 44 7.7 1 ( AL111181 ) Botrytis cinerea strain T4 cDNA library...) Batrachochytrium dendrobatidis strain JAM059 vari... 48 0.49 1 ( AL112706 ) Botrytis cinerea strain T4 cDNA library...3 ) GH_MBb0070I15f GH_MBb Gossypium hirsutum genomic ... 48 0.49 1 ( AL424547 ) T3 end of clone XAZ0AA001A10 of library

Dicty_cDB: Contig-U15612-1 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available 2.1 3 ( DJ134199 ) Method for identification of useful proteins deri... 36 2.2 2 ( AL401410 ) T3 end of clone AS0AA027F03 of library...ana tabacum EST, clone nt002084085. 38 0.015 3 ( EX054863 ) BR039507 floral buds cDNA library KBFS Brassic....63 2 ( EX073063 ) BR057707 root cDNA library KBRT Brassica rapa sub... 40 0.67 2...27_A23_F.... 36 3.8 3 ( CV650372 ) GS0040 Chinese cabbage seedling library Brassica ... 40 3.8 2 ( DB662283 ) Saccharomyces cere.... 52 0.083 1 ( CB084704 ) hq20f02.b1 Hedyotis centranthoides flower - Stage... 52 0.083 1 ( CA853976 ) EST357 almond cDNA library

Dicty_cDB: VHL427 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available d:none) Dictyostelium discoideum chromoso... 33 7.5 AY698035_1( AY698035 |pid:none) Desmognathus marmoratus ...isolate 69... 33 7.5 AY612348_1( AY612348 |pid:none) Desmognathus quadramaculatus vouch... 33 9.8 AY698038_1...( AY698038 |pid:none) Desmognathus marmoratus isolate T0... 33 9.8 AY612344_1( AY612344 |pid:none) Desmog...nathus marmoratus voucher KH... 33 9.8 AY698041_1( AY698041 |pid:none) Desmognathus

Dicty_cDB: VHA227 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available um chromoso... 33 7.5 AY698035_1( AY698035 |pid:none) Desmognathus marmoratus isolate 69... 33 7.5 AY612348_...1( AY612348 |pid:none) Desmognathus quadramaculatus vouch... 33 9.9 AY698038_1( AY698038 |pid:none) Desmogna...thus marmoratus isolate T0... 33 9.9 AY612344_1( AY612344 |pid:none) Desmognathus... marmoratus voucher KH... 33 9.9 AY698041_1( AY698041 |pid:none) Desmognathus marmoratus isolate T0... 33 9.

Targeting VEGF-B as a novel treatment for insulin resistance and type 2 diabetes.

Science.gov (United States)

Hagberg, Carolina E; Mehlem, Annika; Falkevall, Annelie; Muhl, Lars; Fam, Barbara C; Ortsäter, Henrik; Scotney, Pierre; Nyqvist, Daniel; Samén, Erik; Lu, Li; Stone-Elander, Sharon; Proietto, Joseph; Andrikopoulos, Sofianos; Sjöholm, Ake; Nash, Andrew; Eriksson, Ulf

2012-10-18

The prevalence of type 2 diabetes is rapidly increasing, with severe socioeconomic impacts. Excess lipid deposition in peripheral tissues impairs insulin sensitivity and glucose uptake, and has been proposed to contribute to the pathology of type 2 diabetes. However, few treatment options exist that directly target ectopic lipid accumulation. Recently it was found that vascular endothelial growth factor B (VEGF-B) controls endothelial uptake and transport of fatty acids in heart and skeletal muscle. Here we show that decreased VEGF-B signalling in rodent models of type 2 diabetes restores insulin sensitivity and improves glucose tolerance. Genetic deletion of Vegfb in diabetic db/db mice prevented ectopic lipid deposition, increased muscle glucose uptake and maintained normoglycaemia. Pharmacological inhibition of VEGF-B signalling by antibody administration to db/db mice enhanced glucose tolerance, preserved pancreatic islet architecture, improved β-cell function and ameliorated dyslipidaemia, key elements of type 2 diabetes and the metabolic syndrome. The potential use of VEGF-B neutralization in type 2 diabetes was further elucidated in rats fed a high-fat diet, in which it normalized insulin sensitivity and increased glucose uptake in skeletal muscle and heart. Our results demonstrate that the vascular endothelium can function as an efficient barrier to excess muscle lipid uptake even under conditions of severe obesity and type 2 diabetes, and that this barrier can be maintained by inhibition of VEGF-B signalling. We propose VEGF-B antagonism as a novel pharmacological approach for type 2 diabetes, targeting the lipid-transport properties of the endothelium to improve muscle insulin sensitivity and glucose disposal.

MongoDB and Python Patterns and processes for the popular document-oriented database

CERN Document Server

O'Higgins, Niall

2011-01-01

Learn how to leverage MongoDB with your Python applications, using the hands-on recipes in this book. You get complete code samples for tasks such as making fast geo queries for location-based apps, efficiently indexing your user documents for social-graph lookups, and many other scenarios. This guide explains the basics of the document-oriented database and shows you how to set up a Python environment with it. Learn how to read and write to MongoDB, apply idiomatic MongoDB and Python patterns, and use the database with several popular Python web frameworks. You'll discover how to model your

Validation approach for a fast and simple targeted screening method for 75 antibiotics in meat and aquaculture products using LC-MS/MS.

Science.gov (United States)

Dubreil, Estelle; Gautier, Sophie; Fourmond, Marie-Pierre; Bessiral, Mélaine; Gaugain, Murielle; Verdon, Eric; Pessel, Dominique

2017-04-01

An approach is described to validate a fast and simple targeted screening method for antibiotic analysis in meat and aquaculture products by LC-MS/MS. The strategy of validation was applied for a panel of 75 antibiotics belonging to different families, i.e., penicillins, cephalosporins, sulfonamides, macrolides, quinolones and phenicols. The samples were extracted once with acetonitrile, concentrated by evaporation and injected into the LC-MS/MS system. The approach chosen for the validation was based on the Community Reference Laboratory (CRL) guidelines for the validation of screening qualitative methods. The aim of the validation was to prove sufficient sensitivity of the method to detect all the targeted antibiotics at the level of interest, generally the maximum residue limit (MRL). A robustness study was also performed to test the influence of different factors. The validation showed that the method is valid to detect and identify 73 antibiotics of the 75 antibiotics studied in meat and aquaculture products at the validation levels.

Writing and querying MapReduce views in CouchDB

CERN Document Server

Holt, Bradley

2011-01-01

If you want to use CouchDB to support real-world applications, you'll need to create MapReduce views that let you query this document-oriented database for meaningful data. With this short and concise ebook, you'll learn how to create a variety of MapReduce views to help you query and aggregate data in CouchDB's large, distributed datasets. You'll get step-by-step instructions and lots of sample code to create and explore several MapReduce views through the course of the book, using an example database you construct. To work with these different views, you'll learn how to use the Futon web a

Semantics based approach for analyzing disease-target associations.

Science.gov (United States)

Kaalia, Rama; Ghosh, Indira

2016-08-01

A complex disease is caused by heterogeneous biological interactions between genes and their products along with the influence of environmental factors. There have been many attempts for understanding the cause of these diseases using experimental, statistical and computational methods. In the present work the objective is to address the challenge of representation and integration of information from heterogeneous biomedical aspects of a complex disease using semantics based approach. Semantic web technology is used to design Disease Association Ontology (DAO-db) for representation and integration of disease associated information with diabetes as the case study. The functional associations of disease genes are integrated using RDF graphs of DAO-db. Three semantic web based scoring algorithms (PageRank, HITS (Hyperlink Induced Topic Search) and HITS with semantic weights) are used to score the gene nodes on the basis of their functional interactions in the graph. Disease Association Ontology for Diabetes (DAO-db) provides a standard ontology-driven platform for describing genes, proteins, pathways involved in diabetes and for integrating functional associations from various interaction levels (gene-disease, gene-pathway, gene-function, gene-cellular component and protein-protein interactions). An automatic instance loader module is also developed in present work that helps in adding instances to DAO-db on a large scale. Our ontology provides a framework for querying and analyzing the disease associated information in the form of RDF graphs. The above developed methodology is used to predict novel potential targets involved in diabetes disease from the long list of loose (statistically associated) gene-disease associations. Copyright © 2016 Elsevier Inc. All rights reserved.

The effective temperature of the DBV's, and the sensitivity of DB model atmospheres to input physics

International Nuclear Information System (INIS)

Thejll, P.; Delaware Univ., Newark, DE; Vennes, S.; Shipman, H.L.

1990-01-01

A new grid of DB models is applied to the problem of the DBV temperatures and the DB gap. It is found that the DBV instability strip lies lower than thought before. This has consequences for the calibration of mixing-length theories and the reality of the DB gap. The DBV GD358 is discussed in detail. (orig.)

Combination of active components of Xiexin decoction ameliorates renal fibrosis through the inhibition of NF-κB and TGF-β1/Smad pathways in db/db diabetic mice.

Directory of Open Access Journals (Sweden)

Jia-Sheng Wu

Full Text Available Xiexin decoction, a herbal therapeutic agent commonly used in traditional Chinese medicine, is recognized for its beneficial effects on diabetic nephropathy exerted through the combined action of multiple components, including Rhizoma Coptidis alkaloids (A, Radix et Rhizoma Rhei polysaccharides (P, and Radix Scutellaria flavones (F. Our previous studies have shown that a combination of A, P, and F (APF exhibits renoprotective effects against diabetic nephropathy. This study was aimed at determining the effects of APF on renal fibrosis in diabetic nephropathy and elucidating the underlying molecular mechanisms. To evaluate the effects of APF, in vivo, db/db diabetic mice were orally administered a low or high dose of APF (300 or 600 mg/kg, respectively once a day for 8 weeks. We evaluated the blood and urine indices of metabolic and renal function, renal tissue histopathology, renal inflammation, and fibrosis. APF treatment significantly ameliorated glucose and lipid metabolism dysfunction, decreased urinary albumin excretion, normalized creatinine clearance, and reduced the morphological changes in renal tissue. Additionally, APF administration in db/db diabetic mice reduced the elevated levels of renal inflammation mediators such as intercellular adhesion molecule-1, monocyte chemotactic protein-1, tumor necrosis factor-α, interleukin-1β, and active nuclear factor κB (NF-κB. APF treatment also reduced type I and IV collagen, transforming growth factor-β1 (TGF-β1, and TGF-β1 type II receptor expression levels, and decreased the phosphorylation of Smad2/3 in the kidneys of db/db diabetic mice. These results suggest that APF reduces renal fibrosis in diabetic nephropathy through the NF-κB and TGF-β1/Smad signaling pathways. In vitro, APF treatment reduced cell proliferation and protein expression of α-smooth muscle actin, collagen I, TGF-β1 and NF-κB in mesangial cells cultured with high glucose concentrations. Our findings indicate

Characterization of very high frequency transducers with wire target and hydrophone

International Nuclear Information System (INIS)

Huang Bin; Shung, K Kik

2004-01-01

In this paper, the wire-target technique will be shown to be a useful alternative for beam profile measurements in very high frequency range (30-60 MHz). A 9 cm long tungsten wire with a diameter of 8 μm was used as the pulse-echo target to measure the lateral beam profiles at the focal points of two transducers, a spherically focused 40 MHz Panametrics transducer with an aperture size of 6.35 mm and a geometrical focal length of 12.7 mm and a lense-focused in-house lithium niobate (LiNbO 3 ) 60 MHz transducer with an aperture size of 2 mm and a geometrical focal length around 6.5 mm. For comparison, measurements on the same transducers were performed by three small-aperture hydrophones. The first one is a polyvinylidene fluoride trifluoroethylene (PVDF-TrFE) membrane hydrophone developed by Hewlett-Packard, which has a geometric diameter of 37 μm, a measured effective diameter of less than 100 μm and a -3 dB bandwidth of more than 150 MHz. The second one is a needle-type PVDF hydrophone from Precision Acoustics, which has a 9 μm-thick PVDF element, a 40 μm geometrical aperture and a measured effective diameter of less than 100 μm. The third one is a needle-type PVDF hydrophone from Onda, which has a 150 μm geometrical aperture and an effective diameter of about 180 μm. Experimental results show that the -6 dB two-way beam widths measured by this 8 μm wire-target are in agreement with -3 dB transmitted beam widths measured by small-aperture hydrophones. Compared to small-aperture hydrophones, the wire-target technique is simpler and more cost-effective. Its major advantage however is in the frequency range above 100 MHz in which commercial hydrophones are not yet available

myPhyloDB: a local web server for the storage and analysis of metagenomic data.

Science.gov (United States)

Manter, Daniel K; Korsa, Matthew; Tebbe, Caleb; Delgado, Jorge A

2016-01-01

myPhyloDB v.1.1.2 is a user-friendly personal database with a browser-interface designed to facilitate the storage, processing, analysis, and distribution of microbial community populations (e.g. 16S metagenomics data). MyPhyloDB archives raw sequencing files, and allows for easy selection of project(s)/sample(s) of any combination from all available data in the database. The data processing capabilities of myPhyloDB are also flexible enough to allow the upload and storage of pre-processed data, or use the built-in Mothur pipeline to automate the processing of raw sequencing data. myPhyloDB provides several analytical (e.g. analysis of covariance,t-tests, linear regression, differential abundance (DESeq2), and principal coordinates analysis (PCoA)) and normalization (rarefaction, DESeq2, and proportion) tools for the comparative analysis of taxonomic abundance, species richness and species diversity for projects of various types (e.g. human-associated, human gut microbiome, air, soil, and water) for any taxonomic level(s) desired. Finally, since myPhyloDB is a local web-server, users can quickly distribute data between colleagues and end-users by simply granting others access to their personal myPhyloDB database. myPhyloDB is available athttp://www.ars.usda.gov/services/software/download.htm?softwareid=472 and more information along with tutorials can be found on our websitehttp://www.myphylodb.org. Database URL:http://www.myphylodb.org. Published by Oxford University Press 2016. This work is written by US Government employees and is in the public domain in the United States.

Dicty_cDB: Contig-U14247-1 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available 22555 ) Zebrafish DNA sequence from clone DKEY-19D21 in l... 44 7.5 1 ( BV440136 ) S237P6107RD7.T0 Portugu...eseWaterDog Canis familiar... 44 7.5 1 ( AC158364 ) Mus musculus BAC clone RP23-187

"Science means learning to say-I don′t know": An interview with Dr. Ashok D.B. Vaidya

Directory of Open Access Journals (Sweden)

Ravindra R Pandharinath

2011-01-01

Full Text Available Dr. Ashok D.B. Vaidya, the stalwart in the fields of Experimental Pharmacology, Clinical Pharmacology, and Reverse Pharmacology turns 75 on Nov, 27, 2011. A former Clinical Research Head of CIBA Geigy Research Centre, his name has been synonymous with the concept of the Golden Triangle for resurgence of Ayurveda and its reinterpretation in modern scientific terms. At a time when most fields are populated by intellectual dwarfs and unethical operators, he stands like a giant-a scientist, a philosopher, and an ardent fighter for ethical values. In this free-wheeling interview with Ravindra R.Pandharinath, he discusses the milestones in his life, his inspirations, and dreams for the confluence of modern science, modern medicine, and Ayurveda as the new health care model for the 21st century

Determination of DB10B values of single and mixed cultures of ...

African Journals Online (AJOL)

The survi-ving fraction of isolates decreased with increased irradiation doses. DB10B values of E. coli, S. aureus and S. parat-hyphi B were respectively 0.27, 0.33 and 0.44 kGy when inoculated as single cultures, and 0.24, 0.28 and 0.32 kGy respectively when inoculated as mixed cultures. DB10B values were lower for ...

Averrhoa carambola free phenolic extract ameliorates nonalcoholic hepatic steatosis by modulating mircoRNA-34a, mircoRNA-33 and AMPK pathways in leptin receptor-deficient db/db mice.

Science.gov (United States)

Pang, Daorui; You, Lijun; Zhou, Lin; Li, Tong; Zheng, Bisheng; Liu, Rui Hai

2017-12-13

The objective of the present study is to investigate the hepatic steatosis relieving effect of Averrhoa carambola free phenolic extract (ACF) on leptin receptor-deficient (db/db) mice and elucidate the modulation hepatic lipogenesis mechanisms. The serum alanine aminotransferase (ALT) and aspartate aminotransferase (AST) assays, accompanying hematoxylin and eosin (H&E) staining, were applied to identify the alleviation of liver histopathological changes. Serum and hepatic lipid assays, combined with oil red O staining, were used to investigate the amelioration of lipid accumulation. Further assessments by quantitative real-time PCR and western blot assays were used to elucidate the suppression of the fatty acid and triglyceride (TG) synthesis mechanisms underlying ACF protection. These results indicated that ACF treatment significantly reduced the liver TG of db/db mice (p < 0.05). The mechanisms are partly through phosphorylation of AMPK α and down-regulation of SREBP-1c expression, and further down-regulation of FAS and SCD1 (p < 0.05). In addition, the expression levels of mircoRNA-34a and mircoRNA-33, which modulate this signaling pathway, were significantly down-regulated by ACF treatment (p < 0.05). Collectively, these results revealed that ACF exhibited a potent hepatic steatosis relieving effect partly by inhibiting the signal transduction of hepatic lipogenesis.

From ISIS to CouchDB: Databases and Data Models for Bibliographic Records

Directory of Open Access Journals (Sweden)

Luciano Ramalho

2011-04-01

Full Text Available For decades bibliographic data has been stored in non-relational databases, and thousands of libraries in developing countries still use ISIS databases to run their OPACs. Fast forward to 2010 and the NoSQL movement has shown that non-relational databases are good enough for Google, Amazon.com and Facebook. Meanwhile, several Open Source NoSQL systems have appeared. This paper discusses the data model of one class of NoSQL products, semistructured, document-oriented databases exemplified by Apache CouchDB and MongoDB, and why they are well-suited to collective cataloging applications. Also shown are the methods, tools, and scripts used to convert, from ISIS to CouchDB, bibliographic records of LILACS, a key Latin American and Caribbean health sciences index operated by the Pan-American Health Organization.

About miRNAs, miRNA seeds, target genes and target pathways.

Science.gov (United States)

Kehl, Tim; Backes, Christina; Kern, Fabian; Fehlmann, Tobias; Ludwig, Nicole; Meese, Eckart; Lenhof, Hans-Peter; Keller, Andreas

2017-12-05

miRNAs are typically repressing gene expression by binding to the 3' UTR, leading to degradation of the mRNA. This process is dominated by the eight-base seed region of the miRNA. Further, miRNAs are known not only to target genes but also to target significant parts of pathways. A logical line of thoughts is: miRNAs with similar (seed) sequence target similar sets of genes and thus similar sets of pathways. By calculating similarity scores for all 3.25 million pairs of 2,550 human miRNAs, we found that this pattern frequently holds, while we also observed exceptions. Respective results were obtained for both, predicted target genes as well as experimentally validated targets. We note that miRNAs target gene set similarity follows a bimodal distribution, pointing at a set of 282 miRNAs that seems to target genes with very high specificity. Further, we discuss miRNAs with different (seed) sequences that nonetheless regulate similar gene sets or pathways. Most intriguingly, we found miRNA pairs that regulate different gene sets but similar pathways such as miR-6886-5p and miR-3529-5p. These are jointly targeting different parts of the MAPK signaling cascade. The main goal of this study is to provide a general overview on the results, to highlight a selection of relevant results on miRNAs, miRNA seeds, target genes and target pathways and to raise awareness for artifacts in respective comparisons. The full set of information that allows to infer detailed results on each miRNA has been included in miRPathDB, the miRNA target pathway database (https://mpd.bioinf.uni-sb.de).

EST Table: DB673368 [KAIKOcDNA[Archive

Lifescience Database Archive (English)

Full Text Available DB673368 E_FL_BmN-_27M22_F_0 10/09/28 86 %/190 aa ref|XP_002092788.1| GE14387 [Dros...ophila yakuba] gb|EDW92500.1| GE14387 [Drosophila yakuba] 10/09/01 86 %/190 aa FBpp0259397|DyakGE14387-PA 10

Metabolite signal identification in accurate mass metabolomics data with MZedDB, an interactive m/z annotation tool utilising predicted ionisation behaviour 'rules'

Directory of Open Access Journals (Sweden)

Snowdon Stuart

2009-07-01

Full Text Available Abstract Background Metabolomics experiments using Mass Spectrometry (MS technology measure the mass to charge ratio (m/z and intensity of ionised molecules in crude extracts of complex biological samples to generate high dimensional metabolite 'fingerprint' or metabolite 'profile' data. High resolution MS instruments perform routinely with a mass accuracy of Results Metabolite 'structures' harvested from publicly accessible databases were converted into a common format to generate a comprehensive archive in MZedDB. 'Rules' were derived from chemical information that allowed MZedDB to generate a list of adducts and neutral loss fragments putatively able to form for each structure and calculate, on the fly, the exact molecular weight of every potential ionisation product to provide targets for annotation searches based on accurate mass. We demonstrate that data matrices representing populations of ionisation products generated from different biological matrices contain a large proportion (sometimes > 50% of molecular isotopes, salt adducts and neutral loss fragments. Correlation analysis of ESI-MS data features confirmed the predicted relationships of m/z signals. An integrated isotope enumerator in MZedDB allowed verification of exact isotopic pattern distributions to corroborate experimental data. Conclusion We conclude that although ultra-high accurate mass instruments provide major insight into the chemical diversity of biological extracts, the facile annotation of a large proportion of signals is not possible by simple, automated query of current databases using computed molecular formulae. Parameterising MZedDB to take into account predicted ionisation behaviour and the biological source of any sample improves greatly both the frequency and accuracy of potential annotation 'hits' in ESI-MS data.

BioPepDB: an integrated data platform for food-derived bioactive peptides.

Science.gov (United States)

Li, Qilin; Zhang, Chao; Chen, Hongjun; Xue, Jitong; Guo, Xiaolei; Liang, Ming; Chen, Ming

2018-03-12

Food-derived bioactive peptides play critical roles in regulating most biological processes and have considerable biological, medical and industrial importance. However, a large number of active peptides data, including sequence, function, source, commercial product information, references and other information are poorly integrated. BioPepDB is a searchable database of food-derived bioactive peptides and their related articles, including more than four thousand bioactive peptide entries. Moreover, BioPepDB provides modules of prediction and hydrolysis-simulation for discovering novel peptides. It can serve as a reference database to investigate the function of different bioactive peptides. BioPepDB is available at http://bis.zju.edu.cn/biopepdbr/ . The web page utilises Apache, PHP5 and MySQL to provide the user interface for accessing the database and predict novel peptides. The database itself is operated on a specialised server.

Portability, Salary and Asset Price Risk: A Continuous-Time Expected Utility Comparison of DB and DC Pension Plans

Directory of Open Access Journals (Sweden)

An Chen

2015-03-01

Full Text Available This paper compares two different types of private retirement plans from the perspective of a representative beneficiary: a defined benefit (DB and a defined contribution (DC plan. While salary risk is the main common risk factor in DB and DC pension plans, one of the key differences is that DB plans carry portability risks, whereas DC plans bear asset price risk. We model these tradeoffs explicitly in this paper and compare these two plans in a utility-based framework. Our numerical analysis focuses on answering the question of when the beneficiary is indifferent between the DB and DC plan. Most of our results confirm the findings in the existing literature, among which, e.g., portability losses considerably reduce the relative attractiveness of the DB plan. However, we also find that the attractiveness of the DB plan can decrease in the level of risk aversion, which is inconsistent with the existing literature.

Cluster (Viridiplantae) - PGDBj - Ortholog DB | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available 0”. This cluster ID is uniquely-assigned by the PGDBj Ortholog Database. Cluster size Number of proteins aff...r About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Cluster (Viridiplantae) - PGDBj - Ortholog DB | LSDB Archive ... ...List Contact us PGDBj - Ortholog DB Cluster (Viridiplantae) Data detail Data name Cluster (Viridiplantae) DO...switchLanguage; BLAST Search Image Search Home About Archive Update History Data

Cluster (Cyanobacteria) - PGDBj - Ortholog DB | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available 3090”. This cluster ID is uniquely-assigned by the PGDBj Ortholog Database. Cluster size Number of proteins ...ster About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Cluster (Cyanobacteria) - PGDBj - Ortholog DB | LSDB Archive ... ...List Contact us PGDBj - Ortholog DB Cluster (Cyanobacteria) Data detail Data name Cluster (Cyanobacteria) DO...switchLanguage; BLAST Search Image Search Home About Archive Update History Data

A 1.2-V 165-μW 0.29-mm² Multibit Sigma-Delta ADC for Hearing Aids Using Nonlinear DACs and With Over 91 dB Dynamic-Range

DEFF Research Database (Denmark)

Custódio, José R.; Goes, João; Paulino, Nuno

2013-01-01

This paper describes the design and experimental evaluation of a multibit Sigma-Delta (ΣΔ) modulator (ΣΔM) with enhanced dynamic range (DR) through the use of nonlinear digital-to-analog converters (DACs) in the feedback paths. This nonlinearity imposes a trade-off between DR and distortion, which...... in a 130 nm digital CMOS technology, which includes the proposed modulator with nonlinear DACs and a modulator with conventional linear DACs, for comparison purposes. The measured results show that the ΣΔM using nonlinear DACs achieves an enhancement of the DR around 8.4 dB (to 91.4 dB). Power dissipation...... and silicon area are about the same for the two cases. The performance achieved is comparable to that of the best reported multibit ΣΔ ADCs, with the advantage of occupying less silicon area (7.5 times lower area when compared with the most energy efficient ΣΔM)....

SeeDB: Efficient Data-Driven Visualization Recommendations to Support Visual Analytics.

Science.gov (United States)

Vartak, Manasi; Rahman, Sajjadur; Madden, Samuel; Parameswaran, Aditya; Polyzotis, Neoklis

2015-09-01

Data analysts often build visualizations as the first step in their analytical workflow. However, when working with high-dimensional datasets, identifying visualizations that show relevant or desired trends in data can be laborious. We propose SeeDB, a visualization recommendation engine to facilitate fast visual analysis: given a subset of data to be studied, SeeDB intelligently explores the space of visualizations, evaluates promising visualizations for trends, and recommends those it deems most "useful" or "interesting". The two major obstacles in recommending interesting visualizations are (a) scale : evaluating a large number of candidate visualizations while responding within interactive time scales, and (b) utility : identifying an appropriate metric for assessing interestingness of visualizations. For the former, SeeDB introduces pruning optimizations to quickly identify high-utility visualizations and sharing optimizations to maximize sharing of computation across visualizations. For the latter, as a first step, we adopt a deviation-based metric for visualization utility, while indicating how we may be able to generalize it to other factors influencing utility. We implement SeeDB as a middleware layer that can run on top of any DBMS. Our experiments show that our framework can identify interesting visualizations with high accuracy. Our optimizations lead to multiple orders of magnitude speedup on relational row and column stores and provide recommendations at interactive time scales. Finally, we demonstrate via a user study the effectiveness of our deviation-based utility metric and the value of recommendations in supporting visual analytics.

TR32DB - Management of Research Data in a Collaborative, Interdisciplinary Research Project

Science.gov (United States)

Curdt, Constanze; Hoffmeister, Dirk; Waldhoff, Guido; Lang, Ulrich; Bareth, Georg

2015-04-01

The management of research data in a well-structured and documented manner is essential in the context of collaborative, interdisciplinary research environments (e.g. across various institutions). Consequently, set-up and use of a research data management (RDM) system like a data repository or project database is necessary. These systems should accompany and support scientists during the entire research life cycle (e.g. data collection, documentation, storage, archiving, sharing, publishing) and operate cross-disciplinary in interdisciplinary research projects. Challenges and problems of RDM are well-know. Consequently, the set-up of a user-friendly, well-documented, sustainable RDM system is essential, as well as user support and further assistance. In the framework of the Transregio Collaborative Research Centre 32 'Patterns in Soil-Vegetation-Atmosphere Systems: Monitoring, Modelling, and Data Assimilation' (CRC/TR32), funded by the German Research Foundation (DFG), a RDM system was self-designed and implemented. The CRC/TR32 project database (TR32DB, www.tr32db.de) is operating online since early 2008. The TR32DB handles all data, which are created by the involved project participants from several institutions (e.g. Universities of Cologne, Bonn, Aachen, and the Research Centre Jülich) and research fields (e.g. soil and plant sciences, hydrology, geography, geophysics, meteorology, remote sensing). Very heterogeneous research data are considered, which are resulting from field measurement campaigns, meteorological monitoring, remote sensing, laboratory studies and modelling approaches. Furthermore, outcomes like publications, conference contributions, PhD reports and corresponding images are regarded. The TR32DB project database is set-up in cooperation with the Regional Computing Centre of the University of Cologne (RRZK) and also located in this hardware environment. The TR32DB system architecture is composed of three main components: (i) a file-based data

Increasing Muscle Mass Improves Vascular Function in Obese (db/db) Mice

Science.gov (United States)

Qiu, Shuiqing; Mintz, James D.; Salet, Christina D.; Han, Weihong; Giannis, Athanassios; Chen, Feng; Yu, Yanfang; Su, Yunchao; Fulton, David J.; Stepp, David W.

2014-01-01

Background A sedentary lifestyle is an independent risk factor for cardiovascular disease and exercise has been shown to ameliorate this risk. Inactivity is associated with a loss of muscle mass, which is also reversed with isometric exercise training. The relationship between muscle mass and vascular function is poorly defined. The aims of the current study were to determine whether increasing muscle mass by genetic deletion of myostatin, a negative regulator of muscle growth, can influence vascular function in mesenteric arteries from obese db/db mice. Methods and Results Myostatin expression was elevated in skeletal muscle of obese mice and associated with reduced muscle mass (30% to 50%). Myostatin deletion increased muscle mass in lean (40% to 60%) and obese (80% to 115%) mice through increased muscle fiber size (PMyostatin deletion decreased adipose tissue in lean mice, but not obese mice. Markers of insulin resistance and glucose tolerance were improved in obese myostatin knockout mice. Obese mice demonstrated an impaired endothelial vasodilation, compared to lean mice. This impairment was improved by superoxide dismutase mimic Tempol. Deletion of myostatin improved endothelial vasodilation in mesenteric arteries in obese, but not in lean, mice. This improvement was blunted by nitric oxide (NO) synthase inhibitor l‐NG‐nitroarginine methyl ester (l‐NAME). Prostacyclin (PGI2)‐ and endothelium‐derived hyperpolarizing factor (EDHF)‐mediated vasodilation were preserved in obese mice and unaffected by myostatin deletion. Reactive oxygen species) was elevated in the mesenteric endothelium of obese mice and down‐regulated by deletion of myostatin in obese mice. Impaired vasodilation in obese mice was improved by NADPH oxidase inhibitor (GKT136901). Treatment with sepiapterin, which increases levels of tetrahydrobiopterin, improved vasodilation in obese mice, an improvement blocked by l‐NAME. Conclusions Increasing muscle mass by genetic deletion of

RavenDB 2.x beginner's guide

CERN Document Server

Tannir, Khaled

2013-01-01

Written in a friendly, example-driven Beginner's Guide format, there are plenty of step-by-step instructions and examples that are designed to help you get started with RavenDB. If you are a .NET developer, new to document-oriented databases, and you wish to learn how to build applications using NoSQL databases, then this book is for you. Experience with relational database systems will be helpful, but not necessary.

The effective fraction isolated from Radix Astragali alleviates glucose intolerance, insulin resistance and hypertriglyceridemia in db/db diabetic mice through its anti-inflammatory activity.

Science.gov (United States)

Hoo, Ruby Lc; Wong, Janice Yl; Qiao, Cf; Xu, A; Xu, Hx; Lam, Karen Sl

2010-08-24

Macrophage infiltration in adipose tissue together with the aberrant production of pro-inflammatory cytokines has been identified as the key link between obesity and its related metabolic disorders. This study aims to isolate bioactive ingredients from the traditional Chinese herb Radix Astragali (Huangqi) that alleviate obesity-induced metabolic damage through inhibiting inflammation. Active fraction (Rx) that inhibits pro-inflammatory cytokine production was identified from Radix Astragali by repeated bioactivity-guided high-throughput screening. Major constituents in Rx were identified by column chromatography followed by high-performance liquid chromatography (HPLC) and mass-spectrometry. Anti-diabetic activity of Rx was evaluated in db/db mice. Treatment with Rx, which included calycosin-7-β-D-glucoside (0.9%), ononin (1.2%), calycosin (4.53%) and formononetin (1.1%), significantly reduced the secretion of pro-inflammatory cytokines (TNF-α, IL-6 and MCP-1) in human THP-1 macrophages and lipopolysaccharide (LPS)-induced activation of NF-κB in mouse RAW-Blue macrophages in a dose-dependent manner. Chronic administration of Rx in db/db obese mice markedly decreased the levels of both fed and fasting glucose, reduced serum triglyceride, and also alleviated insulin resistance and glucose intolerance when compared to vehicle-treated controls. The mRNA expression levels of inflammatory cell markers CD68 and F4/80, and cytokines MCP-1, TNF-α and IL-6 were significantly reduced in epididymal adipose tissue while the alternatively activated macrophage marker arginase I was markedly increased in the Rx-treated mice. These findings suggest that suppression of the inflammation pathways in macrophages represents a valid strategy for high-throughput screening of lead compounds with anti-diabetic and insulin sensitizing properties, and further support the etiological role of inflammation in the pathogenesis of obesity-related metabolic disorders.

The effective fraction isolated from Radix Astragali alleviates glucose intolerance, insulin resistance and hypertriglyceridemia in db/db diabetic mice through its anti-inflammatory activity

Directory of Open Access Journals (Sweden)

Hoo Ruby LC

2010-08-01

Full Text Available Abstract Background Macrophage infiltration in adipose tissue together with the aberrant production of pro-inflammatory cytokines has been identified as the key link between obesity and its related metabolic disorders. This study aims to isolate bioactive ingredients from the traditional Chinese herb Radix Astragali (Huangqi that alleviate obesity-induced metabolic damage through inhibiting inflammation. Methods Active fraction (Rx that inhibits pro-inflammatory cytokine production was identified from Radix Astragali by repeated bioactivity-guided high-throughput screening. Major constituents in Rx were identified by column chromatography followed by high-performance liquid chromatography (HPLC and mass-spectrometry. Anti-diabetic activity of Rx was evaluated in db/db mice. Results Treatment with Rx, which included calycosin-7-β-D-glucoside (0.9%, ononin (1.2%, calycosin (4.53% and formononetin (1.1%, significantly reduced the secretion of pro-inflammatory cytokines (TNF-α, IL-6 and MCP-1 in human THP-1 macrophages and lipopolysaccharide (LPS-induced activation of NF-κB in mouse RAW-Blue macrophages in a dose-dependent manner. Chronic administration of Rx in db/db obese mice markedly decreased the levels of both fed and fasting glucose, reduced serum triglyceride, and also alleviated insulin resistance and glucose intolerance when compared to vehicle-treated controls. The mRNA expression levels of inflammatory cell markers CD68 and F4/80, and cytokines MCP-1, TNF-α and IL-6 were significantly reduced in epididymal adipose tissue while the alternatively activated macrophage marker arginase I was markedly increased in the Rx-treated mice. Conclusion These findings suggest that suppression of the inflammation pathways in macrophages represents a valid strategy for high-throughput screening of lead compounds with anti-diabetic and insulin sensitizing properties, and further support the etiological role of inflammation in the pathogenesis of

SiteDB: Marshalling people and resources available to CMS

Energy Technology Data Exchange (ETDEWEB)

Metson, S [H.H. Wills Physics Laboratory, Bristol (United Kingdom); Bonacorsi, D [University of Bologna and INFN Bologna (Italy); Ferreira, M Dias [SPRACE (Brazil); Egeland, R [University of Minnesota, Twin Cities (United States)

2010-04-01

In a collaboration the size of CMS (approx. 3000 users, and almost 100 computing centres of varying size) communication and accurate information about the sites it has access to is vital in co-ordinating the multitude of computing tasks required for smooth running. SiteDB is a tool developed by CMS to track sites available to the collaboration, the allocation to CMS of resources available at those sites and the associations between CMS members and the sites (as either a manager/operator of the site or a member of a group associated to the site). It is used to track the roles a person has for an associated site or group. SiteDB eases the coordination load for the operations teams by providing a consistent interface to manage communication with the people working at a site, by identifying who is responsible for a given task or service at a site and by offering a uniform interface to information on CMS contacts and sites. SiteDB provides api's and reports for other CMS tools to use to access the information it contains, for instance enabling CRAB to use 'user friendly' names when black/white listing CE's, providing role based authentication and authorisation for other web based services and populating various troubleshooting squads in external ticketing systems in use daily by CMS Computing operations.

SiteDB: Marshalling people and resources available to CMS

International Nuclear Information System (INIS)

Metson, S; Bonacorsi, D; Ferreira, M Dias; Egeland, R

2010-01-01

In a collaboration the size of CMS (approx. 3000 users, and almost 100 computing centres of varying size) communication and accurate information about the sites it has access to is vital in co-ordinating the multitude of computing tasks required for smooth running. SiteDB is a tool developed by CMS to track sites available to the collaboration, the allocation to CMS of resources available at those sites and the associations between CMS members and the sites (as either a manager/operator of the site or a member of a group associated to the site). It is used to track the roles a person has for an associated site or group. SiteDB eases the coordination load for the operations teams by providing a consistent interface to manage communication with the people working at a site, by identifying who is responsible for a given task or service at a site and by offering a uniform interface to information on CMS contacts and sites. SiteDB provides api's and reports for other CMS tools to use to access the information it contains, for instance enabling CRAB to use 'user friendly' names when black/white listing CE's, providing role based authentication and authorisation for other web based services and populating various troubleshooting squads in external ticketing systems in use daily by CMS Computing operations.

Web development with MongoDB and Node.js

CERN Document Server

Krol, Jason

2014-01-01

This book is designed for developers of any skill level that want to get up and running using Node.js and MongoDB to build full featured web applications. A basic understanding of JavaScript and HTML is the only requirement for this book.

SinEx DB: a database for single exon coding sequences in mammalian genomes.

Science.gov (United States)

Jorquera, Roddy; Ortiz, Rodrigo; Ossandon, F; Cárdenas, Juan Pablo; Sepúlveda, Rene; González, Carolina; Holmes, David S

2016-01-01

Eukaryotic genes are typically interrupted by intragenic, noncoding sequences termed introns. However, some genes lack introns in their coding sequence (CDS) and are generally known as 'single exon genes' (SEGs). In this work, a SEG is defined as a nuclear, protein-coding gene that lacks introns in its CDS. Whereas, many public databases of Eukaryotic multi-exon genes are available, there are only two specialized databases for SEGs. The present work addresses the need for a more extensive and diverse database by creating SinEx DB, a publicly available, searchable database of predicted SEGs from 10 completely sequenced mammalian genomes including human. SinEx DB houses the DNA and protein sequence information of these SEGs and includes their functional predictions (KOG) and the relative distribution of these functions within species. The information is stored in a relational database built with My SQL Server 5.1.33 and the complete dataset of SEG sequences and their functional predictions are available for downloading. SinEx DB can be interrogated by: (i) a browsable phylogenetic schema, (ii) carrying out BLAST searches to the in-house SinEx DB of SEGs and (iii) via an advanced search mode in which the database can be searched by key words and any combination of searches by species and predicted functions. SinEx DB provides a rich source of information for advancing our understanding of the evolution and function of SEGs.Database URL: www.sinex.cl. © The Author(s) 2016. Published by Oxford University Press.

MPD model for radar echo signal of hypersonic targets

Directory of Open Access Journals (Sweden)

Xu Xuefei

2014-08-01

Full Text Available The stop-and-go (SAG model is typically used for echo signal received by the radar using linear frequency modulation pulse compression. In this study, the authors demonstrate that this model is not applicable to hypersonic targets. Instead of SAG model, they present a more realistic echo signal model (moving-in-pulse duration (MPD for hypersonic targets. Following that, they evaluate the performances of pulse compression under the SAG and MPD models by theoretical analysis and simulations. They found that the pulse compression gain has an increase of 3 dB by using the MPD model compared with the SAG model in typical cases.

AtomDB: Expanding an Accessible and Accurate Atomic Database for X-ray Astronomy

Science.gov (United States)

Smith, Randall

Since its inception in 2001, the AtomDB has become the standard repository of accurate and accessible atomic data for the X-ray astrophysics community, including laboratory astrophysicists, observers, and modelers. Modern calculations of collisional excitation rates now exist - and are in AtomDB - for all abundant ions in a hot plasma. AtomDB has expanded beyond providing just a collisional model, and now also contains photoionization data from XSTAR as well as a charge exchange model, amongst others. However, building and maintaining an accurate and complete database that can fully exploit the diagnostic potential of high-resolution X-ray spectra requires further work. The Hitomi results, sadly limited as they were, demonstrated the urgent need for the best possible wavelength and rate data, not merely for the strongest lines but for the diagnostic features that may have 1% or less of the flux of the strong lines. In particular, incorporation of weak but powerfully diagnostic satellite lines will be crucial to understanding the spectra expected from upcoming deep observations with Chandra and XMM-Newton, as well as the XARM and Athena satellites. Beyond incorporating this new data, a number of groups, both experimental and theoretical, have begun to produce data with errors and/or sensitivity estimates. We plan to use this to create statistically meaningful spectral errors on collisional plasmas, providing practical uncertainties together with model spectra. We propose to continue to (1) engage the X-ray astrophysics community regarding their issues and needs, notably by a critical comparison with other related databases and tools, (2) enhance AtomDB to incorporate a large number of satellite lines as well as updated wavelengths with error estimates, (3) continue to update the AtomDB with the latest calculations and laboratory measurements, in particular velocity-dependent charge exchange rates, and (4) enhance existing tools, and create new ones as needed to

The DB gap and a new class of pulsating white dwarfs

Directory of Open Access Journals (Sweden)

Shibahashi H.

2013-03-01

Full Text Available The recent systematic surveys providing enormously massive datasets of white dwarfs show that there is still a deficit of a factor of 2.5 in the DA/non-DA ratio within the temperature range of 30 000 K < Teff < 45 000 K, which has been regarded as the “DB gap” meaning a range with almost no helium atmosphere white dwarfs. Since all white dwarfs have to evolve through this temperature range along almost the identical sequence on the color-magnitude diagram, this implies that most of the helium atmosphere DO stars once evolve into hydrogen atmosphere hot DA stars in the temperature range of the DB gap and then back to helium atmosphere DB stars. Possible scenarios for this chameleon-like disguises of white dwarfs with helium dominant atmospheres are described and a new class of pulsating white dwarfs, named the hot-DAV stars, is predicted from these scenarios. One pulsating DA white dwarf, being consistent with the prediction, has been discovered indeed.

A basic study on the international cooperation using international nuclear DB

International Nuclear Information System (INIS)

Yi, Ji Ho; Kim, T. W.; Oh, J. H. and others

2001-12-01

KAERI has collected the domestic data related to nuclear energy and sent the INIS a total of 1,296 items inputted according to the INIS bibliographic input rules. Korea inputted a total of 1,360 items to the IAEA INIS DB in 2000, and ranked 12th among the 103 INIS member countries in input amount. So Korea has reached to the level of advanced countries in input amount. In order to induce the INIS DB Mirror Site in Korea, the Korea INIS National Center has cooperated with KAERI and organizations concerned, contacted the INIS Secretariat and strengthened the relationship with Asian nations. As INIS liaison officers from each country agreed to induce the INIS DB Mirror Site in Korea, In 2002 the Mirror Site will be launched in Korea. The total records of our local OECD NEA documents are 2,742. KAERI will develop the OECD NEA documents retrival system and service will start. The KAERI has contributed to the improvement of domestic nuclear energy technology by inducing more OECD NEA computer codes from advanced countries and utilizing the codes

MetaMetaDB: a database and analytic system for investigating microbial habitability.

Directory of Open Access Journals (Sweden)

Ching-chia Yang

Full Text Available MetaMetaDB (http://mmdb.aori.u-tokyo.ac.jp/ is a database and analytic system for investigating microbial habitability, i.e., how a prokaryotic group can inhabit different environments. The interaction between prokaryotes and the environment is a key issue in microbiology because distinct prokaryotic communities maintain distinct ecosystems. Because 16S ribosomal RNA (rRNA sequences play pivotal roles in identifying prokaryotic species, a system that comprehensively links diverse environments to 16S rRNA sequences of the inhabitant prokaryotes is necessary for the systematic understanding of the microbial habitability. However, existing databases are biased to culturable prokaryotes and exhibit limitations in the comprehensiveness of the data because most prokaryotes are unculturable. Recently, metagenomic and 16S rRNA amplicon sequencing approaches have generated abundant 16S rRNA sequence data that encompass unculturable prokaryotes across diverse environments; however, these data are usually buried in large databases and are difficult to access. In this study, we developed MetaMetaDB (Meta-Metagenomic DataBase, which comprehensively and compactly covers 16S rRNA sequences retrieved from public datasets. Using MetaMetaDB, users can quickly generate hypotheses regarding the types of environments a prokaryotic group may be adapted to. We anticipate that MetaMetaDB will improve our understanding of the diversity and evolution of prokaryotes.

MetaMetaDB: a database and analytic system for investigating microbial habitability.

Science.gov (United States)

Yang, Ching-chia; Iwasaki, Wataru

2014-01-01

MetaMetaDB (http://mmdb.aori.u-tokyo.ac.jp/) is a database and analytic system for investigating microbial habitability, i.e., how a prokaryotic group can inhabit different environments. The interaction between prokaryotes and the environment is a key issue in microbiology because distinct prokaryotic communities maintain distinct ecosystems. Because 16S ribosomal RNA (rRNA) sequences play pivotal roles in identifying prokaryotic species, a system that comprehensively links diverse environments to 16S rRNA sequences of the inhabitant prokaryotes is necessary for the systematic understanding of the microbial habitability. However, existing databases are biased to culturable prokaryotes and exhibit limitations in the comprehensiveness of the data because most prokaryotes are unculturable. Recently, metagenomic and 16S rRNA amplicon sequencing approaches have generated abundant 16S rRNA sequence data that encompass unculturable prokaryotes across diverse environments; however, these data are usually buried in large databases and are difficult to access. In this study, we developed MetaMetaDB (Meta-Metagenomic DataBase), which comprehensively and compactly covers 16S rRNA sequences retrieved from public datasets. Using MetaMetaDB, users can quickly generate hypotheses regarding the types of environments a prokaryotic group may be adapted to. We anticipate that MetaMetaDB will improve our understanding of the diversity and evolution of prokaryotes.

ORF Sequence: ch_oct10_gene_aa_db [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available GTGMKSFLEKLDEATKEFETQYKKWINDRREAIKKQRENEKLQKWNEISNIFKSDGVELNRDAQTPCIPEHLVEGFEESNESEDLSEIDQIEQVMLNPKGRLNFV* ... ch_oct10_gene_aa_db Chro.50191 >Chro.50191 hypothetical protein MSNSFLRDLKFVGVSSFL

Modulation of hyperglycemia and TNFα-mediated inflammation by helichrysum and grapefruit extracts in diabetic db/db mice.

Science.gov (United States)

de la Garza, Ana Laura; Etxeberria, Usune; Palacios-Ortega, Sara; Haslberger, Alexander G; Aumueller, Eva; Milagro, Fermín I; Martínez, J Alfredo

2014-09-01

Type-2 diabetes is associated with a chronic low-grade systemic inflammation accompanied by an increased production of adipokines/cytokines by obese adipose tissue. The search for new antidiabetic drugs with different mechanisms of action, such as insulin sensitizers, insulin secretagogues and α-glucosidase inhibitors, has directed the focus on the potential use of flavonoids in the management of type-2 diabetes. Thirty six diabetic male C57BL/6J db/db mice were fed a standard diet and randomly assigned into four experimental groups: non-treated control, (n = 8); acarbose (5 mg per kg bw, n = 8); helichrysum (1 g per kg bw, n = 10) and grapefruit (0.5 g per kg bw, n = 10) for 6 weeks. The mRNA expression in pancreas, liver and epididymal adipose tissue was determined by RT-PCR. DNA methylation was quantified in epididymal fat using pyrosequencing. Mice supplemented with helichrysum and grapefruit extracts showed a significant decrease in fasting glucose levels (p helichrysum and grapefruit extracts improved hyperglycemia through the regulation of glucose metabolism in the liver and reduction of the expression of proinflammatory genes in the liver and visceral fat. The hypermethylation of TNFα in adipose tissue may contribute to reduce the inflammation associated with diabetes and obesity.

SimShiftDB; local conformational restraints derived from chemical shift similarity searches on a large synthetic database

Energy Technology Data Exchange (ETDEWEB)

Ginzinger, Simon W. [Center of Applied Molecular Engineering, University of Salzburg, Department of Molecular Biology, Division of Bioinformatics (Austria)], E-mail: simon@came.sbg.ac.at; Coles, Murray [Max-Planck-Institute for Developmental Biology, Department of Protein Evolution (Germany)], E-mail: Murray.Coles@tuebingen.mpg.de

2009-03-15

We present SimShiftDB, a new program to extract conformational data from protein chemical shifts using structural alignments. The alignments are obtained in searches of a large database containing 13,000 structures and corresponding back-calculated chemical shifts. SimShiftDB makes use of chemical shift data to provide accurate results even in the case of low sequence similarity, and with even coverage of the conformational search space. We compare SimShiftDB to HHSearch, a state-of-the-art sequence-based search tool, and to TALOS, the current standard tool for the task. We show that for a significant fraction of the predicted similarities, SimShiftDB outperforms the other two methods. Particularly, the high coverage afforded by the larger database often allows predictions to be made for residues not involved in canonical secondary structure, where TALOS predictions are both less frequent and more error prone. Thus SimShiftDB can be seen as a complement to currently available methods.

SimShiftDB; local conformational restraints derived from chemical shift similarity searches on a large synthetic database

International Nuclear Information System (INIS)

Ginzinger, Simon W.; Coles, Murray

2009-01-01

We present SimShiftDB, a new program to extract conformational data from protein chemical shifts using structural alignments. The alignments are obtained in searches of a large database containing 13,000 structures and corresponding back-calculated chemical shifts. SimShiftDB makes use of chemical shift data to provide accurate results even in the case of low sequence similarity, and with even coverage of the conformational search space. We compare SimShiftDB to HHSearch, a state-of-the-art sequence-based search tool, and to TALOS, the current standard tool for the task. We show that for a significant fraction of the predicted similarities, SimShiftDB outperforms the other two methods. Particularly, the high coverage afforded by the larger database often allows predictions to be made for residues not involved in canonical secondary structure, where TALOS predictions are both less frequent and more error prone. Thus SimShiftDB can be seen as a complement to currently available methods

75 FR 73987 - Target Date Disclosure

Science.gov (United States)

2010-11-30

... principal strategies (including a general description of the types of assets held by the investment), and... information about TDFs that apply age or target retirement-based asset allocations, described in paragraph (e..., the description must satisfy three requirements. The first is an explanation of the asset allocation...

D77, one benzoic acid derivative, functions as a novel anti-HIV-1 inhibitor targeting the interaction between integrase and cellular LEDGF/p75

International Nuclear Information System (INIS)

Du Li; Zhao Yaxue; Chen, Jing; Yang Liumeng; Zheng Yongtang; Tang Yun; Shen Xu; Jiang Hualiang

2008-01-01

Integration of viral-DNA into host chromosome mediated by the viral protein HIV-1 integrase (IN) is an essential step in the HIV-1 life cycle. In this process, Lens epithelium-derived growth factor (LEDGF/p75) is discovered to function as a cellular co-factor for integration. Since LEDGF/p75 plays an important role in HIV integration, disruption of the LEDGF/p75 interaction with IN has provided a special interest for anti-HIV agent discovery. In this work, we reported that a benzoic acid derivative, 4-[(5-bromo-4-{[2,4-dioxo-3-(2-oxo-2-phenylethyl) -1,3-thiazolidin-5-ylidene]methyl}-2-ethoxyphenoxy)methyl]benzoic acid (D77) could potently inhibit the IN-LEDGF/p75 interaction and affect the HIV-1 IN nuclear distribution thus exhibiting antiretroviral activity. Molecular docking with site-directed mutagenesis analysis and surface plasmon resonance (SPR) binding assays has clarified possible binding mode of D77 against HIV-1 integrase. As the firstly discovered small molecular compound targeting HIV-1 integrase interaction with LEDGF/p75, D77 might supply useful structural information for further anti-HIV agent discovery

Top-level DB design for Big Data in ATLAS Experiment at CERN

CERN Document Server

Dimitrov, Gancho; The ATLAS collaboration

2017-01-01

This presentation describes a system that accumulates a set of key quantities for a very large number of particle collision events recorded by the ATLAS experiment at the LHC (Large Hadron Collider) at CERN. The main project requirements are the handling of tens of billions of rows per year with minimal DB resources, and providing outstanding performance for the fundamental use cases. Various challenges were faced in the process of project development, such as large data volume, large transactions (tens to hundreds of million of rows per transaction) requiring significant amount of undo, row duplication checks, adequate table statistics gathering, and SQL execution plan stability. Currently the system hosts about 120 billion rows as the data ingestion rate has gone beyond the initially foreseen 30 billion rows per year. The crucial DB schema design decisions and the Oracle DB features and techniques will be shared with the audience. By attending this session you will learn how big physics data can be organize...

Dicty_cDB: VHA372 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available and read from insert in 3'HPRT insertion targeting and chromosome engineering clo...ne MHPP142o16. 50 0.16 1 CR044130 |CR044130.1 Forward strand read from insert in 3'HPRT insertion targeting and chromosome engineerin...in 3'HPRT insertion targeting and chromosome engineering clone MHPP47e19. 50 0.16... 1 CR023465 |CR023465.1 Forward strand read from insert in 3'HPRT insertion targeting and chromosome engineering...insert in 3'HPRT insertion targeting and chromosome engineering clone MHPP414o21.

Dicty_cDB: SHI133 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available 044130 |CR044130.1 Forward strand read from insert in 3'HPRT insertion targeting and chromosome engineering ...Forward strand read from insert in 3'HPRT insertion targeting and chromosome engineering clone MHPP47e19. 50... 0.068 1 CR034434 |CR034434.1 Forward strand read from insert in 3'HPRT insertion targeting and chromosome engineering...ion targeting and chromosome engineering clone MHPP142o16. 50 0.068 1 BX990136 |B...X990136.1 Forward strand read from insert in 3'HPRT insertion targeting and chromosome engineering clone MHP

ProCarDB: a database of bacterial carotenoids.

Science.gov (United States)

Nupur, L N U; Vats, Asheema; Dhanda, Sandeep Kumar; Raghava, Gajendra P S; Pinnaka, Anil Kumar; Kumar, Ashwani

2016-05-26

Carotenoids have important functions in bacteria, ranging from harvesting light energy to neutralizing oxidants and acting as virulence factors. However, information pertaining to the carotenoids is scattered throughout the literature. Furthermore, information about the genes/proteins involved in the biosynthesis of carotenoids has tremendously increased in the post-genomic era. A web server providing the information about microbial carotenoids in a structured manner is required and will be a valuable resource for the scientific community working with microbial carotenoids. Here, we have created a manually curated, open access, comprehensive compilation of bacterial carotenoids named as ProCarDB- Prokaryotic Carotenoid Database. ProCarDB includes 304 unique carotenoids arising from 50 biosynthetic pathways distributed among 611 prokaryotes. ProCarDB provides important information on carotenoids, such as 2D and 3D structures, molecular weight, molecular formula, SMILES, InChI, InChIKey, IUPAC name, KEGG Id, PubChem Id, and ChEBI Id. The database also provides NMR data, UV-vis absorption data, IR data, MS data and HPLC data that play key roles in the identification of carotenoids. An important feature of this database is the extension of biosynthetic pathways from the literature and through the presence of the genes/enzymes in different organisms. The information contained in the database was mined from published literature and databases such as KEGG, PubChem, ChEBI, LipidBank, LPSN, and Uniprot. The database integrates user-friendly browsing and searching with carotenoid analysis tools to help the user. We believe that this database will serve as a major information centre for researchers working on bacterial carotenoids.

myPhyloDB: a local web server for the storage and analysis of metagenomics data

Science.gov (United States)

myPhyloDB is a user-friendly personal database with a browser-interface designed to facilitate the storage, processing, analysis, and distribution of metagenomics data. MyPhyloDB archives raw sequencing files, and allows for easy selection of project(s)/sample(s) of any combination from all availab...

Enhancement of single mode operation in coaxial optical waveguide using DB boundary conditions

Science.gov (United States)

Lohia, Pooja; Prajapati, Y.; Saini, J. P.; Rai, B. S.

2014-11-01

In this study, a competent numerical strategy to compute the dispersion of optical waveguides is presented and propagation of electromagnetic waves in a coaxial optical waveguide with DB boundary conditions is instigated. For this intend, cylindrical coordinates are here being used to derive the DB boundary conditions and to obtain field components for the modes. The propagation constant for the waveguide to be studied is determined by solving the Bessel and the modified Bessel functions. The cutoff frequencies for various lower order modes have been calculated and their dispersion characteristics are plotted correspondingly. The behavior of the coaxial optical waveguide under DB boundary conditions is shown to be significantly different from that of coaxial optical waveguide and conventional optical waveguide under traditional or tangential boundary conditions. Finally, the effect of waveguide dimensions on the mode cutoff frequencies and fabrication issues are also addressed.

Dicty_cDB: CHR728 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available Forward strand read from insert in 3'HPRT insertion targeting and chromosome engineering clone MHPP142o16. 5... targeting and chromosome engineering clone MHPP421e10. 50 0.14 1 CR044130 |CR044130.1 Forward strand read f...rom insert in 3'HPRT insertion targeting and chromosome engineering clone MHPP186g09. 50 0.14 1 CR017539 |CR...017539.1 Forward strand read from insert in 3'HPRT insertion targeting and chromosome engineering...nsertion targeting and chromosome engineering clone MHPP47e19. 50 0.14 1 dna update 2005.11.21 Homology vs P

Dicty_cDB: SHE226 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available n 3'HPRT insertion targeting and chromosome engineering clone MHPP186g09. 50 0.05...5 1 CR023465 |CR023465.1 Forward strand read from insert in 3'HPRT insertion targeting and chromosome engineering...targeting and chromosome engineering clone MHPP47e19. 50 0.055 1 CR034434 |CR0344...34.1 Forward strand read from insert in 3'HPRT insertion targeting and chromosome engineering clone MHPP47e1...9. 50 0.055 1 CR103667 |CR103667.1 Forward strand read from insert in 3'HPRT insertion targeting and chromosome engineering

Dicty_cDB: SHK443 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available ertion targeting and chromosome engineering clone MHPP142o16. 50 0.071 1 CR044130 |CR044130.1 Forward strand... read from insert in 3'HPRT insertion targeting and chromosome engineering clone ...MHPP186g09. 50 0.071 1 CR034434 |CR034434.1 Forward strand read from insert in 3'HPRT insertion targeting and chromosome engineering... 3'HPRT insertion targeting and chromosome engineering clone MHPP421e10. 50 0.071 1 CR017539 |CR017539.1 For...ward strand read from insert in 3'HPRT insertion targeting and chromosome engineering

The target landscape of clinical kinase drugs.

Science.gov (United States)

Klaeger, Susan; Heinzlmeir, Stephanie; Wilhelm, Mathias; Polzer, Harald; Vick, Binje; Koenig, Paul-Albert; Reinecke, Maria; Ruprecht, Benjamin; Petzoldt, Svenja; Meng, Chen; Zecha, Jana; Reiter, Katrin; Qiao, Huichao; Helm, Dominic; Koch, Heiner; Schoof, Melanie; Canevari, Giulia; Casale, Elena; Depaolini, Stefania Re; Feuchtinger, Annette; Wu, Zhixiang; Schmidt, Tobias; Rueckert, Lars; Becker, Wilhelm; Huenges, Jan; Garz, Anne-Kathrin; Gohlke, Bjoern-Oliver; Zolg, Daniel Paul; Kayser, Gian; Vooder, Tonu; Preissner, Robert; Hahne, Hannes; Tõnisson, Neeme; Kramer, Karl; Götze, Katharina; Bassermann, Florian; Schlegl, Judith; Ehrlich, Hans-Christian; Aiche, Stephan; Walch, Axel; Greif, Philipp A; Schneider, Sabine; Felder, Eduard Rudolf; Ruland, Juergen; Médard, Guillaume; Jeremias, Irmela; Spiekermann, Karsten; Kuster, Bernhard

2017-12-01

Kinase inhibitors are important cancer therapeutics. Polypharmacology is commonly observed, requiring thorough target deconvolution to understand drug mechanism of action. Using chemical proteomics, we analyzed the target spectrum of 243 clinically evaluated kinase drugs. The data revealed previously unknown targets for established drugs, offered a perspective on the "druggable" kinome, highlighted (non)kinase off-targets, and suggested potential therapeutic applications. Integration of phosphoproteomic data refined drug-affected pathways, identified response markers, and strengthened rationale for combination treatments. We exemplify translational value by discovering SIK2 (salt-inducible kinase 2) inhibitors that modulate cytokine production in primary cells, by identifying drugs against the lung cancer survival marker MELK (maternal embryonic leucine zipper kinase), and by repurposing cabozantinib to treat FLT3-ITD-positive acute myeloid leukemia. This resource, available via the ProteomicsDB database, should facilitate basic, clinical, and drug discovery research and aid clinical decision-making. Copyright © 2017 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

Dicty_cDB: SHE191 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available strand read from insert in 3'HPRT insertion targeting and chromosome engineering clone MHPP186g09. 50 0.063 ...sert in 3'HPRT insertion targeting and chromosome engineering clone MHPP47e19. 50 0.063 1 CR034434 |CR034434....1 Forward strand read from insert in 3'HPRT insertion targeting and chromosome engineering clone MHPP47e19....ion targeting and chromosome engineering clone MHPP142o16. 50 0.063 1 dna update 2006. 2.10 Homology vs Prot...1 CR023465 |CR023465.1 Forward strand read from insert in 3'HPRT insertion targeting and chromosome engine

Dicty_cDB: VHF123 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available 03667.1 Forward strand read from insert in 3'HPRT insertion targeting and chromosome engineering clone MHPP1...nsertion targeting and chromosome engineering clone MHPP186g09. 50 0.17 1 CR034434 |CR034434.1 Forward stran...d read from insert in 3'HPRT insertion targeting and chromosome engineering clone MHPP47e19. 50 0.17 1 CR023...465 |CR023465.1 Forward strand read from insert in 3'HPRT insertion targeting and chromosome engineering...3'HPRT insertion targeting and chromosome engineering clone MHPP47e19. 50 0.17 1 BX990136 |BX990136.1 Forwar

IL-22R Ligands IL-20, IL-22, and IL-24 Promote Wound Healing in Diabetic db/db Mice.

Science.gov (United States)

Kolumam, Ganesh; Wu, Xiumin; Lee, Wyne P; Hackney, Jason A; Zavala-Solorio, Jose; Gandham, Vineela; Danilenko, Dimitry M; Arora, Puneet; Wang, Xiaoting; Ouyang, Wenjun

2017-01-01

Diabetic foot ulcers (DFU) are one of the major complications in type II diabetes patients and can result in amputation and morbidity. Although multiple approaches are used clinically to help wound closure, many patients still lack adequate treatment. Here we show that IL-20 subfamily cytokines are upregulated during normal wound healing. While there is a redundant role for each individual cytokine in this subfamily in wound healing, mice deficient in IL-22R, the common receptor chain for IL-20, IL-22, and IL-24, display a significant delay in wound healing. Furthermore, IL-20, IL-22 and IL-24 are all able to promote wound healing in type II diabetic db/db mice. Mechanistically, when compared to other growth factors such as VEGF and PDGF that accelerate wound healing in this model, IL-22 uniquely induced genes involved in reepithelialization, tissue remodeling and innate host defense mechanisms from wounded skin. Interestingly, IL-22 treatment showed superior efficacy compared to PDGF or VEGF in an infectious diabetic wound model. Taken together, our data suggest that IL-20 subfamily cytokines, particularly IL-20, IL-22, and IL-24, might provide therapeutic benefit for patients with DFU.

Dicty_cDB: SHH320 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available in 3'HPRT insertion targeting and chromosome engineering clone MHPP142o16. 50 0....12 1 CR023465 |CR023465.1 Forward strand read from insert in 3'HPRT insertion targeting and chromosome engineering...targeting and chromosome engineering clone MHPP186g09. 50 0.12 1 CR017539 |CR0175...39.1 Forward strand read from insert in 3'HPRT insertion targeting and chromosome engineering clone MHPP47e1

The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services

Directory of Open Access Journals (Sweden)

Hanspers Kristina

2010-01-01

Full Text Available Abstract Background Many complementary solutions are available for the identifier mapping problem. This creates an opportunity for bioinformatics tool developers. Tools can be made to flexibly support multiple mapping services or mapping services could be combined to get broader coverage. This approach requires an interface layer between tools and mapping services. Results Here we present BridgeDb, a software framework for gene, protein and metabolite identifier mapping. This framework provides a standardized interface layer through which bioinformatics tools can be connected to different identifier mapping services. This approach makes it easier for tool developers to support identifier mapping. Mapping services can be combined or merged to support multi-omics experiments or to integrate custom microarray annotations. BridgeDb provides its own ready-to-go mapping services, both in webservice and local database forms. However, the framework is intended for customization and adaptation to any identifier mapping service. BridgeDb has already been integrated into several bioinformatics applications. Conclusion By uncoupling bioinformatics tools from mapping services, BridgeDb improves capability and flexibility of those tools. All described software is open source and available at http://www.bridgedb.org.

Identification of MHC class I H-2 Kb/Db-restricted immunogenic peptides derived from retinal proteins

DEFF Research Database (Denmark)

Wang, Mingjun; Bai, Fang; Pries, Mette

2006-01-01

PURPOSE: To identify H-2 Kb/Db-binding immunogenic peptides derived from retinal proteins. METHODS: Computer-based prediction was used to identify potentially H-2 Kb/Db-binding peptides derived from the interphotoreceptor retinol-binding protein (IRBP), soluble retinal antigen (S...... on day 21 after immunization with IRBP or IRBP and the immunogenic peptides. RESULTS: All the 21 predicted peptides were found to upregulate expression of H-2 Kb/Db on RMA-S cells. Five peptides, the two IRBP-derived peptides IRBP89-96 and IRBP(101-108), and the three PEDF-derived peptides, PEDF389....... The immunogenic peptides alone did not induce inflammation in the eyes, but they could enhance severity of uveitis induced by IRBP. CONCLUSIONS: Five of 21 H-2 Kb/Db-binding retinal protein-derived peptides were found to be immunogenic, suggesting that these peptides could function as autoantigenic epitopes...

Dicty_cDB: SHF561 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available sertion targeting and chromosome engineering clone MHPP186g09. 50 0.14 1 CR023465 |CR023465.1 Forward strand... read from insert in 3'HPRT insertion targeting and chromosome engineering clone ...MHPP421e10. 50 0.14 1 CR017539 |CR017539.1 Forward strand read from insert in 3'HPRT insertion targeting and chromosome engineering...'HPRT insertion targeting and chromosome engineering clone MHPP47e19. 50 0.14 1 d

75 FR 8902 - Funding Opportunity Title: Crop Insurance Education in Targeted States (Targeted States Program)

Science.gov (United States)

2010-02-26

... and Target Audience D. Maximum Award E. Project Period F. Description of Agreement Award--Awardee.... Location and Target Audience Targeted States serviced by RMA Regional Offices are listed below. Staff from... established farmers or ranchers who are converting production and marketing systems to pursue new markets. D...

License - dbQSNP | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...escription Download License Update History of This Database Site Policy | Contact Us License - dbQSNP | LSDB Archive ...

Dicty_cDB: SHK554 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available orward strand read from insert in 3'HPRT insertion targeting and chromosome engineering clone MHPP186g09. 50... 0.14 1 CR023465 |CR023465.1 Forward strand read from insert in 3'HPRT insertion targeting and chromosome engineering...om insert in 3'HPRT insertion targeting and chromosome engineering clone MHPP47e19. 50 0.14 1 CR034434 |CR03...4434.1 Forward strand read from insert in 3'HPRT insertion targeting and chromosome engineering clone MHPP47

Dicty_cDB: VHB863 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available insertion targeting and chromosome engineering clone MHPP142o16. 50 0.17 1 CR044130 |CR044130.1 Forward str...and read from insert in 3'HPRT insertion targeting and chromosome engineering clone MHPP186g09. 50 0.17 1 CR...034434 |CR034434.1 Forward strand read from insert in 3'HPRT insertion targeting and chromosome engineerin...n 3'HPRT insertion targeting and chromosome engineering clone MHPP421e10. 50 0.17 1 dna update 2007. 4.17 Ho

Dicty_cDB: SHI542 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available . 42 8.2 1 CR129751 |CR129751.1 Reverse strand read from insert in 5'HPRT insertion targeting and chromosome engineering...ion targeting and chromosome engineering clone MHPN147m24. 42 8.2 1 CR010531 |CR010531.1 Reverse strand read... from insert in 5'HPRT insertion targeting and chromosome engineering clone MHPN2...17j13. 42 8.2 1 CR103480 |CR103480.1 Reverse strand read from insert in 5'HPRT insertion targeting and chromosome engineering

Deformed potential energy of $^{263}Db$ in a generalized liquid drop model

CERN Document Server

Chen Bao Qiu; Zhao Yao Lin; 10.1088/0256-307X/20/11/009

2003-01-01

The macroscopic deformed potential energy for super-heavy nuclei /sup 263/Db, which governs the entrance and alpha decay channels, is determined within a generalized liquid drop model (GLDM). A quasi- molecular shape is assumed in the GLDM, which includes volume-, surface-, and Coulomb-energies, proximity effects, mass asymmetry, and an accurate nuclear radius. The microscopic single particle energies derived from a shell model in an axially deformed Woods- Saxon potential with a quasi-molecular shape. The shell correction is calculated by the Strutinsky method. The total deformed potential energy of a nucleus can be calculated by the macro-microscopic method as the summation of the liquid-drop energy and the Strutinsky shell correction. The theory is applied to predict the deformed potential energy of the experiment /sup 22/Ne+/sup 241/Am to /sup 263/Db* to /sup 259/Db+4 n, which was performed on the Heavy Ion Accelerator in Lanzhou. It is found that the neck in the quasi-molecular shape is responsible for t...

EvoSNP-DB: A database of genetic diversity in East Asian populations.

Science.gov (United States)

Kim, Young Uk; Kim, Young Jin; Lee, Jong-Young; Park, Kiejung

2013-08-01

Genome-wide association studies (GWAS) have become popular as an approach for the identification of large numbers of phenotype-associated variants. However, differences in genetic architecture and environmental factors mean that the effect of variants can vary across populations. Understanding population genetic diversity is valuable for the investigation of possible population specific and independent effects of variants. EvoSNP-DB aims to provide information regarding genetic diversity among East Asian populations, including Chinese, Japanese, and Korean. Non-redundant SNPs (1.6 million) were genotyped in 54 Korean trios (162 samples) and were compared with 4 million SNPs from HapMap phase II populations. EvoSNP-DB provides two user interfaces for data query and visualization, and integrates scores of genetic diversity (Fst and VarLD) at the level of SNPs, genes, and chromosome regions. EvoSNP-DB is a web-based application that allows users to navigate and visualize measurements of population genetic differences in an interactive manner, and is available online at [http://biomi.cdc.go.kr/EvoSNP/].

Update History of This Database - D-HaploDB | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available List Contact us D-HaploDB Update History of This Database Date Update contents 2016/12/13 Description of the.../orca.gen.kyushu-u.ac.jp/) is released. About This Database Database Description Download License Update History of This Database... Site Policy | Contact Us Update History of This Database - D-HaploDB | LSDB Archive ...

Dicty_cDB: SHG345 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available 3'HPRT insertion targeting and chromosome engineering clone MHPP142o16. 50 0.13 1 CR044130 |CR044130.1 Forwa...rd strand read from insert in 3'HPRT insertion targeting and chromosome engineering clone MHPP186g09. 50 0.1...3 1 CR034434 |CR034434.1 Forward strand read from insert in 3'HPRT insertion targeting and chromosome engineering...sert in 3'HPRT insertion targeting and chromosome engineering clone MHPP421e10. 50 0.13 1 dna update 2006. 3

Dicty_cDB: VHC307 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available uence. 34 0.12 3 CR103667 |CR103667.1 Forward strand read from insert in 3'HPRT insertion targeting and chromosome engineering...T insertion targeting and chromosome engineering clone MHPP186g09. 50 0.15 1 CR03...4434 |CR034434.1 Forward strand read from insert in 3'HPRT insertion targeting and chromosome engineering cl...one MHPP47e19. 50 0.15 1 CR023465 |CR023465.1 Forward strand read from insert in 3'HPRT insertion targeting and chromosome engineerin

SolveDB: Integrating Optimization Problem Solvers Into SQL Databases

DEFF Research Database (Denmark)

Siksnys, Laurynas; Pedersen, Torben Bach

2016-01-01

for optimization problems, (2) an extensible infrastructure for integrating different solvers, and (3) query optimization techniques to achieve the best execution performance and/or result quality. Extensive experiments with the PostgreSQL-based implementation show that SolveDB is a versatile tool offering much...

Results of the Experiment on Chemical Identification of Db as a Decay Product of Element 115

CERN Document Server

Dmitriev, S N; Utyonkov, V K; Shishkin, S V; Eremin, A V; Lobanov, Yu V; Tsyganov, Yu S; Chepigin, V I; Sokol, E A; Vostokin, G K; Aksenov, N V; Hussonnois, M; Itkis, M G; Aggeler, H W; Schumann, D; Bruchertseifer, H; Eichler, R; Shaughnessy, D A; Wilk, P A; Kenneally, J M; Stoyer, M A; Wild, J F

2004-01-01

For the first time the chemical identification of Db as the terminal isotope of the decay element 115 produced via the $^{243}{\\text{Am}}(^{48}{\\text{Ca}},3n)^{288}115$ reaction was realized. The experiment was performed on the U400 cyclotron of FLNR, JINR. The $^{243}$Am target was bombarded with a beam dose of $3.4\\cdot 10^{18}$ $^{48}$Ca projectiles at an energy of 247 MeV in the center of the target. The reaction products were collected in the surface of a copper catcher block, which was removed with a lathe and then dissolved in concentrated HNO$_3$. The group 5 elements were separated by sorption onto Dowex 50$\\times$8 cation-exchange resin with subsequent desorption using 1M HF, which forms anionic fluoride complexes of group 5 elements. The eluant was evaporated onto 0.4 $\\mu$m thick polyethylene foils which were placed between a pair of semiconductor detectors surrounded by $^3$He neutron counters for measurement of $\\alpha$ particles, fission fragments and neutrons. Over the course of the experiment...

Anti-Diabetic Activities of Jiaotaiwan in db/db Mice by Augmentation of AMPK Protein Activity and Upregulation of GLUT4 Expression

Directory of Open Access Journals (Sweden)

Na Hu

2013-01-01

Full Text Available Jiaotaiwan (JTW, which is composed of Coptis chinensis (CC and cinnamon (CIN, is one of the most well-known traditional Chinese medicines. In this study, we investigated the antidiabetic effects and mechanism of JTW in db/db mice. Results showed that JTW significantly decreased the level of fasting blood glucose and improved glucose and insulin tolerance better than CC or CIN alone. JTW also effectively protected the pancreatic islet shape, augmented the activation of AMP-activated protein kinase (AMPK in the liver, and increased the expression of glucose transporter 4 (GLUT4 protein in skeletal muscle and white fat. AMPK and GLUT4 contributed to glucose metabolism regulation and had an essential function in the development of diabetes mellitus (DM. Therefore, the mechanisms of JTW may be related to suppressing gluconeogenesis by activating AMPK in the liver and affecting glucose uptake in surrounding tissues through the upregulation of GLUT4 protein expression. These findings provided a new insight into the antidiabetic clinical applications of JTW and demonstrated the potential of JTW as a new drug candidate for DM treatment.

Dicty_cDB: SHA389 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available equence. 34 0.12 3 CR044130 |CR044130.1 Forward strand read from insert in 3'HPRT insertion targeting and chromosome engineering...PRT insertion targeting and chromosome engineering clone MHPP142o16. 50 0.13 1 CR...034434 |CR034434.1 Forward strand read from insert in 3'HPRT insertion targeting and chromosome engineering

PK/DB: database for pharmacokinetic properties and predictive in silico ADME models.

Science.gov (United States)

Moda, Tiago L; Torres, Leonardo G; Carrara, Alexandre E; Andricopulo, Adriano D

2008-10-01

The study of pharmacokinetic properties (PK) is of great importance in drug discovery and development. In the present work, PK/DB (a new freely available database for PK) was designed with the aim of creating robust databases for pharmacokinetic studies and in silico absorption, distribution, metabolism and excretion (ADME) prediction. Comprehensive, web-based and easy to access, PK/DB manages 1203 compounds which represent 2973 pharmacokinetic measurements, including five models for in silico ADME prediction (human intestinal absorption, human oral bioavailability, plasma protein binding, blood-brain barrier and water solubility). http://www.pkdb.ifsc.usp.br

Dicty_cDB: VHC109 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available RT insertion targeting and chromosome engineering clone MHPP142o16. 50 0.16 1 CR0...44130 |CR044130.1 Forward strand read from insert in 3'HPRT insertion targeting and chromosome engineering c... in 3'HPRT insertion targeting and chromosome engineering clone MHPP421e10. 50 0....lone MHPP186g09. 50 0.16 1 CR034434 |CR034434.1 Forward strand read from insert in 3'HPRT insertion targeting and chromosome engineer...ing clone MHPP47e19. 50 0.16 1 CR023465 |CR023465.1 Forward strand read from insert

Dicty_cDB: SHE452 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available ard strand read from insert in 3'HPRT insertion targeting and chromosome engineering clone MHPP186g09. 50 0....insert in 3'HPRT insertion targeting and chromosome engineering clone MHPP47e19. 50 0.14 1 CR034434 |CR03443...4.1 Forward strand read from insert in 3'HPRT insertion targeting and chromosome engineering...ineering clone MHPP421e10. 50 0.14 1 CR017539 |CR017539.1 Forward strand read from ...14 1 CR023465 |CR023465.1 Forward strand read from insert in 3'HPRT insertion targeting and chromosome eng

Drilling history of core hole DB-15

International Nuclear Information System (INIS)

Diediker, L.D.; Ledgerwood, R.K.

1980-09-01

This core hole was drilled to obtain hydrologic and chemical data on the permeable zones of the Saddle Mountains and Wanapum Formations. These data were obtained by testing the zones that were penetrated during drilling. This testing-as-drilled method reduced the potential problems of interflow and water contamination. This report summarizes the drilling and coring operations; geologic logging, hydrologic testing, and geophysical logging activities; and cementing operations of DB-15 during drilling. The successful completion of DB-15 demonstrated that hydrologic testing can be conducted during core drilling operations. More reliable head measurements and uncontaminated representative water samples from isolated permeable zones, which have not been exposed to potential open borehole cross-flow and head equilibration problems, were benefits derived from the testing-as-drilled method. Disadvantages of the technique were a longer time to complete the borehole caused by time required for testing and increased drilling costs due to rig standby time during testing. Extension of the testing-as-drilled method to the drilling of future core holes is recommended. An evaluation should be made of the required hydrologic data and expected borehole stratigraphy before and during drilling to allow uninterrupted drilling in zones of low permeability that can be tested after drilling is complete

FlavorDB: a database of flavor molecules.

Science.gov (United States)

Garg, Neelansh; Sethupathy, Apuroop; Tuwani, Rudraksh; Nk, Rakhi; Dokania, Shubham; Iyer, Arvind; Gupta, Ayushi; Agrawal, Shubhra; Singh, Navjot; Shukla, Shubham; Kathuria, Kriti; Badhwar, Rahul; Kanji, Rakesh; Jain, Anupam; Kaur, Avneet; Nagpal, Rashmi; Bagler, Ganesh

2018-01-04

Flavor is an expression of olfactory and gustatory sensations experienced through a multitude of chemical processes triggered by molecules. Beyond their key role in defining taste and smell, flavor molecules also regulate metabolic processes with consequences to health. Such molecules present in natural sources have been an integral part of human history with limited success in attempts to create synthetic alternatives. Given their utility in various spheres of life such as food and fragrances, it is valuable to have a repository of flavor molecules, their natural sources, physicochemical properties, and sensory responses. FlavorDB (http://cosylab.iiitd.edu.in/flavordb) comprises of 25,595 flavor molecules representing an array of tastes and odors. Among these 2254 molecules are associated with 936 natural ingredients belonging to 34 categories. The dynamic, user-friendly interface of the resource facilitates exploration of flavor molecules for divergent applications: finding molecules matching a desired flavor or structure; exploring molecules of an ingredient; discovering novel food pairings; finding the molecular essence of food ingredients; associating chemical features with a flavor and more. Data-driven studies based on FlavorDB can pave the way for an improved understanding of flavor mechanisms. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

New tools and methods for direct programmatic access to the dbSNP relational database.

Science.gov (United States)

Saccone, Scott F; Quan, Jiaxi; Mehta, Gaurang; Bolze, Raphael; Thomas, Prasanth; Deelman, Ewa; Tischfield, Jay A; Rice, John P

2011-01-01

Genome-wide association studies often incorporate information from public biological databases in order to provide a biological reference for interpreting the results. The dbSNP database is an extensive source of information on single nucleotide polymorphisms (SNPs) for many different organisms, including humans. We have developed free software that will download and install a local MySQL implementation of the dbSNP relational database for a specified organism. We have also designed a system for classifying dbSNP tables in terms of common tasks we wish to accomplish using the database. For each task we have designed a small set of custom tables that facilitate task-related queries and provide entity-relationship diagrams for each task composed from the relevant dbSNP tables. In order to expose these concepts and methods to a wider audience we have developed web tools for querying the database and browsing documentation on the tables and columns to clarify the relevant relational structure. All web tools and software are freely available to the public at http://cgsmd.isi.edu/dbsnpq. Resources such as these for programmatically querying biological databases are essential for viably integrating biological information into genetic association experiments on a genome-wide scale.

Dicty_cDB: SHJ732 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available (bits) Value N CR022830 |CR022830.1 Forward strand read from insert in 3'HPRT insertion targeting andchromosome engineering... read from insert in 3'HPRT insertion targeting and chromosome engineering clone MHPP10i04. 38 0.010 2 CR019...573 |CR019573.1 Forward strand read from insert in 3'HPRT insertion targeting and chromosome engineering clo

Dicty_cDB: SHH391 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available 7.1 Forward strand read from insert in 3'HPRT insertion targeting and chromosome engineering...tion targeting and chromosome engineering clone MHPP186g09. 50 0.13 1 CR034434 |CR034434.1 Forward strand re...ad from insert in 3'HPRT insertion targeting and chromosome engineering clone MHPP47e19. 50 0.13 1 dna updat

Dicty_cDB: SHD353 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available |CR103667.1 Forward strand read from insert in 3'HPRT insertion targeting and chromosome engineering clone M...HPP142o16. 50 0.12 1 CR044130 |CR044130.1 Forward strand read from insert in 3'HPRT insertion targeting and chromosome engineering...'HPRT insertion targeting and chromosome engineering clone MHPP47e19. 50 0.12 1 d

Dicty_cDB: VHF408 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available MTYF9_FA... 33 7.5 CP000568_3082( CP000568 |pid:none) Clostridium thermocellum ATCC 2... 33 9.8 AY698035_1(... AY698035 |pid:none) Desmognathus marmoratus isolate 69... 33 9.8 protein update 2009. 3. 3 PSORT psg: 0.69

Dicty_cDB: VHM533 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available num A3 str. L... 35 7.5 AB049544_1( AB049544 |pid:none) Porcine enterovirus 10 ge...ne for RN... 34 9.8 AF363453_1( AF363453 |pid:none) Porcine enterovirus 9 strain UKG/4... 34 9.8 protein upd

0.75 atoms improve the clock signal of 10,000 atoms

DEFF Research Database (Denmark)

Kruse, I.; Lange, K.; Peise, Jan

2017-01-01

Since the pioneering work of Ramsey, atom interferometers are employed for precision metrology, in particular to measure time and to realize the second. In a classical interferometer, an ensemble of atoms is prepared in one of the two input states, whereas the second one is left empty. In this case.......75 atoms to improve the clock sensitivity of 10,000 atoms by 2.05 dB. The SQL poses a significant limitation for today's microwave fountain clocks, which serve as the main time reference. We evaluate the major technical limitations and challenges for devising a next generation of fountain clocks based...... on atomic squeezed vacuum....

Dicty_cDB: SHC632 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available n 3'HPRT insertion targeting and chromosome engineering clone MHPP186g09. 50 0.12 1 CR023465 |CR023465.1 For...ward strand read from insert in 3'HPRT insertion targeting and chromosome engineering clone MHPP421e10. 50 0...insert in 3'HPRT insertion targeting and chromosome engineering clone MHPP47e19. 50 0.12 1 CR103667 |CR10366...7.1 Forward strand read from insert in 3'HPRT insertion targeting and chromosome engineering clone MHPP142o1...rgeting and chromosome engineering clone MHPP47e19. 50 0.12 1 CR034434 |CR034434.1 Forward strand read from

Dicty_cDB: VHB821 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available ence. 34 0.17 3 CR103667 |CR103667.1 Forward strand read from insert in 3'HPRT insertion targeting and chromosome engineering... read from insert in 3'HPRT insertion targeting and chromosome engineering clone MHPP186g09. 50 0.17 1 CR034...434 |CR034434.1 Forward strand read from insert in 3'HPRT insertion targeting and chromosome engineering clo

Dicty_cDB: SHH264 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available sertion targeting and chromosome engineering clone MHPP142o16. 50 0.13 1 CR023465 |CR023465.1 Forward strand... read from insert in 3'HPRT insertion targeting and chromosome engineering clone MHPP421e10. 50 0.13 1 CR044...130 |CR044130.1 Forward strand read from insert in 3'HPRT insertion targeting and chromosome engineering clo

Dietary abscisic acid ameliorates glucose tolerance and obesity-related inflammation in db/db mice fed high-fat diets.

Science.gov (United States)

Guri, Amir J; Hontecillas, Raquel; Si, Hongwei; Liu, Dongmin; Bassaganya-Riera, Josep

2007-02-01

Despite their efficacy in improving insulin sensitivity, thiazolidinediones (TZDs) are associated with a number of side effects (i.e. weight gain, hepatotoxicity, congestive heart failure) that have limited their use by millions of diabetic patients. We have investigated whether abscisic acid (ABA), a naturally occurring phytochemical with structural similarities to TZDs, could be used as an alternative to TZDs to improve glucose homeostasis. We first examined whether ABA, similar to TZDs, activates PPARgamma in vitro. We next determined the lowest effective dose of dietary ABA (100 mg/kg) and assessed its effect on glucose tolerance, obesity-related inflammation, and mRNA expression of PPARgamma and its responsive genes in white adipose tissue (WAT) of db/db mice fed high-fat diets. We found that ABA induced transactivation of PPARgamma in 3T3-L1 pre-adipocytes in vitro. Dietary ABA-supplementation for 36 days decreased fasting blood glucose concentrations, ameliorated glucose tolerance, and increased mRNA expression of PPARgamma and its responsive genes (i.e., adiponectin, aP2, and CD36) in WAT. We also found that adipocyte hypertrophy, tumor necrosis factor-alpha (TNF-alpha) expression, and macrophage infiltration in WAT were significantly attenuated in ABA-fed mice. These findings suggest that ABA could be used as a nutritional intervention against type II diabetes and obesity-related inflammation.

Efecto de la Aplicación Tópica de una Solución Comercial de Amitraz sobre el Cronotropismo y Dromotropismo Cardiacos en Ratas Anestesiadas y Perros Conscientes

DEFF Research Database (Denmark)

Zerpa, H.; Briceno, E.; Chacon, Tony

2009-01-01

Amitraz is a diamidine molecule widely used as an ectoparasiticide in Veterinary Medicine. Although amitraz is prescribed as a topical treatment, its toxicity has been reported in oral and intravenous administration. This investigation assessed the potential chronotropic and dromotropic effects o...

cuticleDB: a relational database of Arthropod cuticular proteins

Directory of Open Access Journals (Sweden)

Willis Judith H

2004-09-01

Full Text Available Abstract Background The insect exoskeleton or cuticle is a bi-partite composite of proteins and chitin that provides protective, skeletal and structural functions. Little information is available about the molecular structure of this important complex that exhibits a helicoidal architecture. Scores of sequences of cuticular proteins have been obtained from direct protein sequencing, from cDNAs, and from genomic analyses. Most of these cuticular protein sequences contain motifs found only in arthropod proteins. Description cuticleDB is a relational database containing all structural proteins of Arthropod cuticle identified to date. Many come from direct sequencing of proteins isolated from cuticle and from sequences from cDNAs that share common features with these authentic cuticular proteins. It also includes proteins from the Drosophila melanogaster and the Anopheles gambiae genomes, that have been predicted to be cuticular proteins, based on a Pfam motif (PF00379 responsible for chitin binding in Arthropod cuticle. The total number of the database entries is 445: 370 derive from insects, 60 from Crustacea and 15 from Chelicerata. The database can be accessed from our web server at http://bioinformatics.biol.uoa.gr/cuticleDB. Conclusions CuticleDB was primarily designed to contain correct and full annotation of cuticular protein data. The database will be of help to future genome annotators. Users will be able to test hypotheses for the existence of known and also of yet unknown motifs in cuticular proteins. An analysis of motifs may contribute to understanding how proteins contribute to the physical properties of cuticle as well as to the precise nature of their interaction with chitin.

Download - Plabrain DB | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data List Contact us Plabrain...s Database Database Description Download License Update History of This Database Site Policy | Contact Us Download - Plabrain DB | LSDB Archive ...

DrugMetZ DB: an anthology of human drug metabolizing Chytochrome P450 enzymes.

Science.gov (United States)

Antony, Tresa Remya Thomas; Nagarajan, Shanthi

2006-11-14

Understandings the basics of Cytochrome P450 (P450 or CYP) will help to discern drug metabolism. CYP, a super-family of heme-thiolate proteins, are found in almost all living organisms and is involved in the biotransformation of a diverse range of xenobiotics, therapeutic drugs and toxins. Here, we describe DrugMetZ DB, a database for CYP metabolizing drugs. The DB is implemented in MySQL, PHP and HTML. www.bicpu.edu.in/DrugMetZDB/

Targeting Virus-host Interactions of HIV Replication.

Science.gov (United States)

Weydert, Caroline; De Rijck, Jan; Christ, Frauke; Debyser, Zeger

2016-01-01

Cellular proteins that are hijacked by HIV in order to complete its replication cycle, form attractive new targets for antiretroviral therapy. In particular, the protein-protein interactions between these cellular proteins (cofactors) and viral proteins are of great interest to develop new therapies. Research efforts have led to the validation of different cofactors and some successes in therapeutic applications. Maraviroc, the first cofactor inhibitor approved for human medicinal use, provided a proof of concept. Furthermore, compounds developed as Integrase-LEDGF/p75 interaction inhibitors (LEDGINs) have advanced to early clinical trials. Other compounds targeting cofactors and cofactor-viral protein interactions are currently under development. Likewise, interactions between cellular restriction factors and their counteracting HIV protein might serve as interesting targets in order to impair HIV replication. In this respect, compounds targeting the Vif-APOBEC3G interaction have been described. In this review, we focus on compounds targeting the Integrase- LEDGF/p75 interaction, the Tat-P-TEFb interaction and the Vif-APOBEC3G interaction. Additionally we give an overview of currently discovered compounds presumably targeting cellular cofactor-HIV protein interactions.

CoBaltDB: Complete bacterial and archaeal orfeomes subcellular localization database and associated resources

Directory of Open Access Journals (Sweden)

Lucchetti-Miganeh Céline

2010-03-01

Full Text Available Abstract Background The functions of proteins are strongly related to their localization in cell compartments (for example the cytoplasm or membranes but the experimental determination of the sub-cellular localization of proteomes is laborious and expensive. A fast and low-cost alternative approach is in silico prediction, based on features of the protein primary sequences. However, biologists are confronted with a very large number of computational tools that use different methods that address various localization features with diverse specificities and sensitivities. As a result, exploiting these computer resources to predict protein localization accurately involves querying all tools and comparing every prediction output; this is a painstaking task. Therefore, we developed a comprehensive database, called CoBaltDB, that gathers all prediction outputs concerning complete prokaryotic proteomes. Description The current version of CoBaltDB integrates the results of 43 localization predictors for 784 complete bacterial and archaeal proteomes (2.548.292 proteins in total. CoBaltDB supplies a simple user-friendly interface for retrieving and exploring relevant information about predicted features (such as signal peptide cleavage sites and transmembrane segments. Data are organized into three work-sets ("specialized tools", "meta-tools" and "additional tools". The database can be queried using the organism name, a locus tag or a list of locus tags and may be browsed using numerous graphical and text displays. Conclusions With its new functionalities, CoBaltDB is a novel powerful platform that provides easy access to the results of multiple localization tools and support for predicting prokaryotic protein localizations with higher confidence than previously possible. CoBaltDB is available at http://www.umr6026.univ-rennes1.fr/english/home/research/basic/software/cobalten.

Dicty_cDB: VHA138 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available ert in 3'HPRT insertion targeting and chromosome engineering clone MHPP186g09. 50 0.17 1 CR034434 |CR034434....1 Forward strand read from insert in 3'HPRT insertion targeting and chromosome engineering...4 CR103667 |CR103667.1 Forward strand read from insert in 3'HPRT insertion targeting and chromosome engine...ering clone MHPP142o16. 50 0.17 1 CR044130 |CR044130.1 Forward strand read from ins

MultitaskProtDB: a database of multitasking proteins.

Science.gov (United States)

Hernández, Sergio; Ferragut, Gabriela; Amela, Isaac; Perez-Pons, JosepAntoni; Piñol, Jaume; Mozo-Villarias, Angel; Cedano, Juan; Querol, Enrique

2014-01-01

We have compiled MultitaskProtDB, available online at http://wallace.uab.es/multitask, to provide a repository where the many multitasking proteins found in the literature can be stored. Multitasking or moonlighting is the capability of some proteins to execute two or more biological functions. Usually, multitasking proteins are experimentally revealed by serendipity. This ability of proteins to perform multitasking functions helps us to understand one of the ways used by cells to perform many complex functions with a limited number of genes. Even so, the study of this phenomenon is complex because, among other things, there is no database of moonlighting proteins. The existence of such a tool facilitates the collection and dissemination of these important data. This work reports the database, MultitaskProtDB, which is designed as a friendly user web page containing >288 multitasking proteins with their NCBI and UniProt accession numbers, canonical and additional biological functions, monomeric/oligomeric states, PDB codes when available and bibliographic references. This database also serves to gain insight into some characteristics of multitasking proteins such as frequencies of the different pairs of functions, phylogenetic conservation and so forth.

EPConDB: a web resource for gene expression related to pancreatic development, beta-cell function and diabetes.

Science.gov (United States)

Mazzarelli, Joan M; Brestelli, John; Gorski, Regina K; Liu, Junmin; Manduchi, Elisabetta; Pinney, Deborah F; Schug, Jonathan; White, Peter; Kaestner, Klaus H; Stoeckert, Christian J

2007-01-01

EPConDB (http://www.cbil.upenn.edu/EPConDB) is a public web site that supports research in diabetes, pancreatic development and beta-cell function by providing information about genes expressed in cells of the pancreas. EPConDB displays expression profiles for individual genes and information about transcripts, promoter elements and transcription factor binding sites. Gene expression results are obtained from studies examining tissue expression, pancreatic development and growth, differentiation of insulin-producing cells, islet or beta-cell injury, and genetic models of impaired beta-cell function. The expression datasets are derived using different microarray platforms, including the BCBC PancChips and Affymetrix gene expression arrays. Other datasets include semi-quantitative RT-PCR and MPSS expression studies. For selected microarray studies, lists of differentially expressed genes, derived from PaGE analysis, are displayed on the site. EPConDB provides database queries and tools to examine the relationship between a gene, its transcriptional regulation, protein function and expression in pancreatic tissues.

Production of Xylanase by Recombinant Bacillus subtilis DB104 Cultivated in Agroindustrial Waste Medium

Directory of Open Access Journals (Sweden)

Is Helianti

2016-07-01

Full Text Available A recombinant Bacillus subtilis DB104 strain harbouring recombinant plasmid pSKE194 containing an Open Reading Frame (ORF of endoxylanase and its indigenous promoter from the wild-type B. subtilis AQ1 strain was constructed. This recombinant B. subtilis DB104 strain had higher endoxylanase activity than the nonrecombinant B. subtilis DB104 strain in standard media, such as Luria Bertani (LB and LB with xylan. The agroindustrial wastes corncobs and tofu liquid waste were chosen as cost-effective carbon and nitrogen sources, respectively, to test the economics of xylanase production using the recombinant B. subtilis DB104 at a larger scale. Submerged fermentation using a 4.5 L working volume fermentor with tofu liquid waste and 4% corncobs produced maximum xylanase activity of 1296 ± 1.2 U/mg (601.7 ± 0.6 U/mL after 48-hour fermentation at 37°C with 150 rpm agitation; this is more than twofold higher than the activity produced in an Erlenmeyer flask. This is the first report of high xylanase activity produced from recombinant B. subtilis using inexpensive medium. During fermentation, the xylanase degrades corncobs into xylooligosaccharides, showing its potential as an enzyme feed additive or in xylooligosaccharide production.

Identification of Novel Drug Targets and Lead Compounds for Advanced Prostate Cancer through Genomic and Cheminformatic Analyses

Science.gov (United States)

2016-10-01

atomic probes to search the protein surface for suitable small molecule binding pockets20. Each pocket was scored based on its size/ deepness , solvent...D1035–41. [7] Liu T, Lin Y, Wen X, Jorissen RN, Gilson MK. BindingDB: a web-accessible database of experimentally determined protein–ligand binding...Liu P, Wen W, James M, Wang D, et al. Common human cancer genes discovered by integrated gene-expression analysis. PLoS ONE 2007;2:e1149. [75] Xiong

Dicty_cDB: SHC138 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available CR044130 |CR044130.1 Forward strand read from insert in 3'HPRT insertion targeting and chromosome engineering... Forward strand read from insert in 3'HPRT insertion targeting and chromosome engineering clone MHPP47e19. 5...neering clone MHPP142o16. 50 0.13 1 CR034434 |CR034434.1... clone MHPP186g09. 50 0.13 1 CR103667 |CR103667.1 Forward strand read from insert in 3'HPRT insertion targeting and chromosome engi

Dicty_cDB: CHR211 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available 'HPRT insertion targeting and chromosome engineering clone MHPN350f07. 50 0.13 1 ...BX965467 |BX965467.1 Forward strand read from insert in 5'HPRT insertion targeting and chromosome engineering

Dicty_cDB: SHG190 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available tion targeting and chromosome engineering clone MHPP186g09. 50 0.14 1 CR034434 |C...R034434.1 Forward strand read from insert in 3'HPRT insertion targeting and chromosome engineering clone MHP

Regarding the perturbed operating process of DB propellant rocket motor at extreme initial grain temperatures

Directory of Open Access Journals (Sweden)

Ioan ION

2012-03-01

Full Text Available Despite many decades of study, the combustion instability of several DB propellants is still of particular concern, especially at extreme grain temperature conditions of rocket motor operating. The purpose of the first part of the paper is to give an overview of our main experimental results on combustion instabilities and pressure oscillations in DB propellant segmented grain rocket motors (SPRM-01, large L/D ratio, working at extreme initial grain temperatures. Thus, we recorded some particular pressure-time traces with significant perturbed pressure signal that was FFT analysed. An updated mathematical model incorporating transient frequency-dependent combustion response, in conjunction with pressure-dependent burning, is applied to investigate and predict the DB propellant combustion instability phenomenon. The susceptibility of the tested motor SPRM-01 with DB propellant to get a perturbed working and to go unstable with pressure was evidenced and this risk has to be evaluated. In the last part of our paper we evaluated the influence of recorded perturbed thrust on the rocket behaviour on the trajectory. The study revealed that at firing-table initial conditions, this kind of perturbed motor operating may not lead to an unstable rocket flight, but the ballistic parameters would be influenced in an unacceptable manner.

Dicty_cDB: AFI889 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available 3'HPRT insertion targeting and chromosome engineering clone MHPP164a17. 46 1.3 1 CK255549 |CK255549.1 EST73...nd read from insert in 3'HPRT insertion targeting and chromosome engineering clon

CerealsDB 2.0: an integrated resource for plant breeders and scientists

Directory of Open Access Journals (Sweden)

Wilkinson Paul A

2012-09-01

Full Text Available Abstract Background Food security is an issue that has come under renewed scrutiny amidst concerns that substantial yield increases in cereal crops are required to feed the world’s booming population. Wheat is of fundamental importance in this regard being one of the three most important crops for both human consumption and livestock feed; however, increase in crop yields have not kept pace with the demands of a growing world population. In order to address this issue, plant breeders require new molecular tools to help them identify genes for important agronomic traits that can be introduced into elite varieties. Studies of the genome using next-generation sequencing enable the identification of molecular markers such as single nucleotide polymorphisms that may be used by breeders to identify and follow genes when breeding new varieties. The development and application of next-generation sequencing technologies has made the characterisation of SNP markers in wheat relatively cheap and straightforward. There is a growing need for the widespread dissemination of this information to plant breeders. Description CerealsDB is an online resource containing a range of genomic datasets for wheat (Triticum aestivum that will assist plant breeders and scientists to select the most appropriate markers for marker assisted selection. CerealsDB includes a database which currently contains in excess of 100,000 putative varietal SNPs, of which several thousand have been experimentally validated. In addition, CerealsDB contains databases for DArT markers and EST sequences, and links to a draft genome sequence for the wheat variety Chinese Spring. Conclusion CerealsDB is an open access website that is rapidly becoming an invaluable resource within the wheat research and plant breeding communities.

Indexing Bibliographic Database Content Using MariaDB and Sphinx Search Server

Directory of Open Access Journals (Sweden)

Arie Nugraha

2014-07-01

Full Text Available Fast retrieval of digital content has become mandatory for library and archive information systems. Many software applications have emerged to handle the indexing of digital content, from low-level ones such Apache Lucene, to more RESTful and web-services-ready ones such Apache Solr and ElasticSearch. Solr’s popularity among library software developers makes it the “de-facto” standard software for indexing digital content. For content (full-text content or bibliographic description already stored inside a relational DBMS such as MariaDB (a fork of MySQL or PostgreSQL, Sphinx Search Server (Sphinx is a suitable alternative. This article will cover an introduction on how to use Sphinx with MariaDB databases to index database content as well as some examples of Sphinx API usage.

Numerical benchmark for the deep-burn modular helium-cooled reactor (DB-MHR)

International Nuclear Information System (INIS)

Taiwo, T. A.; Kim, T. K.; Buiron, L.; Varaine, F.

2006-01-01

Numerical benchmark problems for the deep-burn concept based on the prismatic modular helium-cooled reactor design (a Very High Temperature Reactor (VHTR)) are specified for joint analysis by U.S. national laboratories and industry and the French CEA. The results obtained with deterministic and Monte Carlo codes have been inter-compared and used to confirm the underlying feature of the DB-MHR concept (high transuranics consumption). The results are also used to evaluate the impact of differences in code methodologies and nuclear data files on the code predictions for DB-MHR core physics parameters. The code packages of the participating organizations (ANL and CEA) are found to give very similar results. (authors)

Dicty_cDB: SHB243 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available R103667 |CR103667.1 Forward strand read from insert in 3'HPRT insertion targeting and chromosome engineering... in 3'HPRT insertion targeting and chromosome engineering clone MHPP186g09. 50 0.13 1 dna update 2005.12.21

Dicty_cDB: VHB614 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available rand read from insert in 3'HPRT insertion targeting and chromosome engineering clone MHPP142o16. 50 0.18 1 C...R044130 |CR044130.1 Forward strand read from insert in 3'HPRT insertion targeting and chromosome engineering

Dicty_cDB: SHD651 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available ead from insert in 3'HPRT insertion targeting and chromosome engineering clone MH...PP142o16. 50 0.13 1 CR044130 |CR044130.1 Forward strand read from insert in 3'HPRT insertion targeting and chromosome engineering

Dicty_cDB: SHL840 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available 3667 |CR103667.1 Forward strand read from insert in 3'HPRT insertion targeting and chromosome engineering... 3'HPRT insertion targeting and chromosome engineering clone MHPP186g09. 50 0.16 1 dna update 2007. 3.10 Hom

Dicty_cDB: CHR667 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available strand read from insert in 5'HPRT insertion targeting and chromosome engineering clone MHPN347m23. 46 0.19 ...2 CR052856 |CR052856.1 Reverse strand read from insert in 5'HPRT insertion targeting and chromosome engineering

Dicty_cDB: CHK838 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available 239074.1 Reverse strand read from insert in 5'HPRT insertion targeting and chromosome engineering clone MHPN...32g20. 42 8.1 1 CR020888 |CR020888.1 Reverse strand read from insert in 5'HPRT insertion targeting and chromosome engineering

Dicty_cDB: VHB619 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available Forward strand read from insert in 3'HPRT insertion targeting and chromosome engineering clone MHPP142o16. 5...0 0.17 1 CR044130 |CR044130.1 Forward strand read from insert in 3'HPRT insertion targeting and chromosome engineering

MRC5 and QU-DB bystander cells can produce bystander factors and induce radiation bystander effect

Directory of Open Access Journals (Sweden)

Mohammad Taghi Bahreyni Toossi

2014-01-01

Full Text Available Radiation damages initiated by radiation-induced bystander effect (RIBE are not limited to the first or immediate neighbors of the irradiated cells, but the effects have been observed in the cells far from the irradiation site. It has been postulated that bystander cells, by producing bystander factors, are actively involved in the propagation of bystander effect in the regions beyond the initial irradiated site. Current study was planned to test the hypothesis. MRC5 and QU-DB cell lines were irradiated, and successive medium transfer technique was performed to induce bystander effects in two bystander cell groups. Conditioned medium extracted from the target cells was transferred to the bystander cells (first bystander cells. After one hour, conditioned medium was substituted by fresh medium. Two hours later, the fresh medium was transferred to a second group of non-irradiated cells (second bystander cells. Micronucleated cells (MC were counted to quantify damages induced in the first and second bystander cell groups. Radiation effect was observed in the second bystander cells as well as in the first ones. Statistical analyses revealed that the number of MC in second bystander subgroups was significantly more than the corresponding value observed in control groups, but in most cases it was equal to the number of MC observed in the first bystander cells. MRC5 and QU-DB bystander cells can produce and release bystander signals in the culture medium and affect non-irradiated cells. Therefore, they may contribute to the RIBE propagation.

License - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available List Contact us PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods ...t list, Marker list, QTL list, Plant DB link & Genome analysis methods © Satoshi ... Policy | Contact Us License - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ...

CANGS DB: a stand-alone web-based database tool for processing, managing and analyzing 454 data in biodiversity studies

Directory of Open Access Journals (Sweden)

Schlötterer Christian

2011-06-01

Full Text Available Abstract Background Next generation sequencing (NGS is widely used in metagenomic and transcriptomic analyses in biodiversity. The ease of data generation provided by NGS platforms has allowed researchers to perform these analyses on their particular study systems. In particular the 454 platform has become the preferred choice for PCR amplicon based biodiversity surveys because it generates the longest sequence reads. Nevertheless, the handling and organization of massive amounts of sequencing data poses a major problem for the research community, particularly when multiple researchers are involved in data acquisition and analysis. An integrated and user-friendly tool, which performs quality control, read trimming, PCR primer removal, and data organization is desperately needed, therefore, to make data interpretation fast and manageable. Findings We developed CANGS DB (Cleaning and Analyzing Next Generation Sequences DataBase a flexible, stand alone and user-friendly integrated database tool. CANGS DB is specifically designed to organize and manage the massive amount of sequencing data arising from various NGS projects. CANGS DB also provides an intuitive user interface for sequence trimming and quality control, taxonomy analysis and rarefaction analysis. Our database tool can be easily adapted to handle multiple sequencing projects in parallel with different sample information, amplicon sizes, primer sequences, and quality thresholds, which makes this software especially useful for non-bioinformaticians. Furthermore, CANGS DB is especially suited for projects where multiple users need to access the data. CANGS DB is available at http://code.google.com/p/cangsdb/. Conclusion CANGS DB provides a simple and user-friendly solution to process, store and analyze 454 sequencing data. Being a local database that is accessible through a user-friendly interface, CANGS DB provides the perfect tool for collaborative amplicon based biodiversity surveys

GiSAO.db: a database for ageing research

Directory of Open Access Journals (Sweden)

Grillari Johannes

2011-05-01

Full Text Available Abstract Background Age-related gene expression patterns of Homo sapiens as well as of model organisms such as Mus musculus, Saccharomyces cerevisiae, Caenorhabditis elegans and Drosophila melanogaster are a basis for understanding the genetic mechanisms of ageing. For an effective analysis and interpretation of expression profiles it is necessary to store and manage huge amounts of data in an organized way, so that these data can be accessed and processed easily. Description GiSAO.db (Genes involved in senescence, apoptosis and oxidative stress database is a web-based database system for storing and retrieving ageing-related experimental data. Expression data of genes and miRNAs, annotation data like gene identifiers and GO terms, orthologs data and data of follow-up experiments are stored in the database. A user-friendly web application provides access to the stored data. KEGG pathways were incorporated and links to external databases augment the information in GiSAO.db. Search functions facilitate retrieval of data which can also be exported for further processing. Conclusions We have developed a centralized database that is very well suited for the management of data for ageing research. The database can be accessed at https://gisao.genome.tugraz.at and all the stored data can be viewed with a guest account.

KMeyeDB: a graphical database of mutations in genes that cause eye diseases.

Science.gov (United States)

Kawamura, Takashi; Ohtsubo, Masafumi; Mitsuyama, Susumu; Ohno-Nakamura, Saho; Shimizu, Nobuyoshi; Minoshima, Shinsei

2010-06-01

KMeyeDB (http://mutview.dmb.med.keio.ac.jp/) is a database of human gene mutations that cause eye diseases. We have substantially enriched the amount of data in the database, which now contains information about the mutations of 167 human genes causing eye-related diseases including retinitis pigmentosa, cone-rod dystrophy, night blindness, Oguchi disease, Stargardt disease, macular degeneration, Leber congenital amaurosis, corneal dystrophy, cataract, glaucoma, retinoblastoma, Bardet-Biedl syndrome, and Usher syndrome. KMeyeDB is operated using the database software MutationView, which deals with various characters of mutations, gene structure, protein functional domains, and polymerase chain reaction (PCR) primers, as well as clinical data for each case. Users can access the database using an ordinary Internet browser with smooth user-interface, without user registration. The results are displayed on the graphical windows together with statistical calculations. All mutations and associated data have been collected from published articles. Careful data analysis with KMeyeDB revealed many interesting features regarding the mutations in 167 genes that cause 326 different types of eye diseases. Some genes are involved in multiple types of eye diseases, whereas several eye diseases are caused by different mutations in one gene.

Incorporating AFEWC IMOM as an Instructional Asset for NPS Radar and Electronic Warfare Curricula

Science.gov (United States)

1992-09-01

Backlobe EL. dB down - 20 dB Backlobe AZ. dB down = 20 dB Ru - 400 km 215.983 nmi Scope Range = 200 km 107.991 nmi PRF = 375 Hz Pay = 600 W RCS = 10 sq m...10 dB Backlobe EL. dB down = 20 dB Backlobe AZ. dB down = 20 dB Ru = 400 km 215.983 nmi Scope Range = 400 km 215.983 nmi PRF = 375 Hz Pay = 93.75 W

Registered plant list - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available List Contact us PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods ...the Plant DB link list in simple search page) Genome analysis methods Presence or... absence of Genome analysis methods information in this DB (link to the Genome analysis methods information ...base Site Policy | Contact Us Registered plant list - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ...

Integrating XQuery and P2P in MonetDB/XQuery*

NARCIS (Netherlands)

Y. Zhang (Ying); P.A. Boncz (Peter); M. Arenas (Marcelo); J. Hidders

2007-01-01

textabstractMonetDB/XQuery* is a fully functional publicly available XML DBMS that has been extended with distributed and P2P data management functionality. Our (minimal) XQuery language extension XRPC adds the concept of RPC to XQuery, and exploits the set-at-a-time database processing model to

TcoF-DB v2: update of the database of human and mouse transcription co-factors and transcription factor interactions

KAUST Repository

Schmeier, Sebastian; Alam, Tanvir; Essack, Magbubah; Bajic, Vladimir B.

2016-01-01

Transcription factors (TFs) play a pivotal role in transcriptional regulation, making them crucial for cell survival and important biological functions. For the regulation of transcription, interactions of different regulatory proteins known as transcription co-factors (TcoFs) and TFs are essential in forming necessary protein complexes. Although TcoFs themselves do not bind DNA directly, their influence on transcriptional regulation and initiation, although indirect, has been shown to be significant, with the functionality of TFs strongly influenced by the presence of TcoFs. In the TcoF-DB v2 database, we collect information on TcoFs. In this article, we describe updates and improvements implemented in TcoF-DB v2. TcoF-DB v2 provides several new features that enables exploration of the roles of TcoFs. The content of the database has significantly expanded, and is enriched with information from Gene Ontology, biological pathways, diseases and molecular signatures. TcoF-DB v2 now includes many more TFs; has substantially increased the number of human TcoFs to 958, and now includes information on mouse (418 new TcoFs). TcoF-DB v2 enables the exploration of information on TcoFs and allows investigations into their influence on transcriptional regulation in humans and mice. TcoF-DB v2 can be accessed at http://tcofdb.org/.

TcoF-DB v2: update of the database of human and mouse transcription co-factors and transcription factor interactions

KAUST Repository

Schmeier, Sebastian

2016-10-17

Transcription factors (TFs) play a pivotal role in transcriptional regulation, making them crucial for cell survival and important biological functions. For the regulation of transcription, interactions of different regulatory proteins known as transcription co-factors (TcoFs) and TFs are essential in forming necessary protein complexes. Although TcoFs themselves do not bind DNA directly, their influence on transcriptional regulation and initiation, although indirect, has been shown to be significant, with the functionality of TFs strongly influenced by the presence of TcoFs. In the TcoF-DB v2 database, we collect information on TcoFs. In this article, we describe updates and improvements implemented in TcoF-DB v2. TcoF-DB v2 provides several new features that enables exploration of the roles of TcoFs. The content of the database has significantly expanded, and is enriched with information from Gene Ontology, biological pathways, diseases and molecular signatures. TcoF-DB v2 now includes many more TFs; has substantially increased the number of human TcoFs to 958, and now includes information on mouse (418 new TcoFs). TcoF-DB v2 enables the exploration of information on TcoFs and allows investigations into their influence on transcriptional regulation in humans and mice. TcoF-DB v2 can be accessed at http://tcofdb.org/.

Antidiabetic Effects of a Chinese Herbal Medicinal Compound Sangguayin Preparation via PI3K/Akt Signaling Pathway in db/db Mice

Directory of Open Access Journals (Sweden)

Qichang Xing

2018-01-01

Full Text Available Sangguayin (SGY, comprising four types of Chinese herbs, can be used as both food and medicine and has been clinically used to treat type 2 diabetes mellitus (T2DM for a long time. Our previous study demonstrated the antidiabetic effect of SGY in experimental T2DM rats fed with a high-fat diet and treated with a low dose of streptozotocin. However, its mechanism of action is questionable. In this study, we refined the traditional SGY decoction and investigated its antidiabetic activity in db/db mice. We evaluated the possible molecular mechanism using skeletal muscle tissues. The results show that the treatment with SGY preparation resulted in a decrease in the blood glucose, glycated serum protein, and blood lipid levels and an improvement in the glucose tolerance as well as insulin resistance. In addition, SGY preparation remarkably upregulated the expression of insulin receptor, insulin receptor substrate-1, phosphoinositide 3 kinase (PI3K, protein kinase B (Akt, and glucose transporter type 4 (GLUT4. Thus, SGY preparation is an effective agent for the treatment of T2DM, and its molecular mechanism may be related to the regulation of PI3K/Akt signaling in the skeletal muscle.

MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource for plant genomics

Science.gov (United States)

Schoof, Heiko; Ernst, Rebecca; Nazarov, Vladimir; Pfeifer, Lukas; Mewes, Hans-Werner; Mayer, Klaus F. X.

2004-01-01

Arabidopsis thaliana is the most widely studied model plant. Functional genomics is intensively underway in many laboratories worldwide. Beyond the basic annotation of the primary sequence data, the annotated genetic elements of Arabidopsis must be linked to diverse biological data and higher order information such as metabolic or regulatory pathways. The MIPS Arabidopsis thaliana database MAtDB aims to provide a comprehensive resource for Arabidopsis as a genome model that serves as a primary reference for research in plants and is suitable for transfer of knowledge to other plants, especially crops. The genome sequence as a common backbone serves as a scaffold for the integration of data, while, in a complementary effort, these data are enhanced through the application of state-of-the-art bioinformatics tools. This information is visualized on a genome-wide and a gene-by-gene basis with access both for web users and applications. This report updates the information given in a previous report and provides an outlook on further developments. The MAtDB web interface can be accessed at http://mips.gsf.de/proj/thal/db. PMID:14681437

Dicty_cDB: Contig-U04484-1 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available F04, complete se... 37 7.4 4 ( FG300472 ) 1108793371523 New World Screwworm Larvae 9387 EST... 35 7.4 3 ( AC...258-141F23, WORKING DRAFT... 39 7.5 3 ( FG293793 ) 1108770683019 New World Screww

Dicty_cDB: Contig-U11810-1 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available otein; Short=MT... 78 8e-13 S55598( S55598 ) tegument protein 03 - equine herpesv...( S55669 ) tegument protein 75 - equine herpesvirus 2 &U208... 61 1e-07 AE009950_198( AE009950 |pid:none) Py

HmtDB 2016: data update, a better performing query system and human mitochondrial DNA haplogroup predictor.

Science.gov (United States)

Clima, Rosanna; Preste, Roberto; Calabrese, Claudia; Diroma, Maria Angela; Santorsola, Mariangela; Scioscia, Gaetano; Simone, Domenico; Shen, Lishuang; Gasparre, Giuseppe; Attimonelli, Marcella

2017-01-04

The HmtDB resource hosts a database of human mitochondrial genome sequences from individuals with healthy and disease phenotypes. The database is intended to support both population geneticists as well as clinicians undertaking the task to assess the pathogenicity of specific mtDNA mutations. The wide application of next-generation sequencing (NGS) has provided an enormous volume of high-resolution data at a low price, increasing the availability of human mitochondrial sequencing data, which called for a cogent and significant expansion of HmtDB data content that has more than tripled in the current release. We here describe additional novel features, including: (i) a complete, user-friendly restyling of the web interface, (ii) links to the command-line stand-alone and web versions of the MToolBox package, an up-to-date tool to reconstruct and analyze human mitochondrial DNA from NGS data and (iii) the implementation of the Reconstructed Sapiens Reference Sequence (RSRS) as mitochondrial reference sequence. The overall update renders HmtDB an even more handy and useful resource as it enables a more rapid data access, processing and analysis. HmtDB is accessible at http://www.hmtdb.uniba.it/. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Dicty_cDB: SHD280 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available insert in 3'HPRT insertion targeting and chromosome engineering clone MHPP421e10....ineering clone MHPP186g09. 50 0.14 1 CR023465 |CR023465.1 Forward strand read from ...GRESS *** from clone. 38 0.13 8 CR044130 |CR044130.1 Forward strand read from insert in 3'HPRT insertion targeting and chromosome eng

Dicty_cDB: SHD671 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available rd strand read from insert in 3'HPRT insertion targeting and chromosome engineering...neering clone MHPP186g09. 50 0.13 1 dna update 2006. 2. 5 Homology vs Protein Score... clone MHPP142o16. 50 0.13 1 CR044130 |CR044130.1 Forward strand read from insert in 3'HPRT insertion targeting and chromosome engi

Dicty_cDB: CHO866 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available ** from clone. 48 0.072 1 CR224953 |CR224953.1 Reverse strand read from insert in 5'HPRT insertion targeting and chromosome engineeri...rse strand read from insert in 5'HPRT insertion targeting and chromosome engineering clone MHPN107i08. 36 0....ng clone MHPN106i08. 36 0.13 2 CR072681 |CR072681.1 Reve

Effect of dark sweet cherry powder consumption on the gut microbiota, short-chain fatty acids, and biomarkers of gut health in obese db/db mice

Directory of Open Access Journals (Sweden)

Jose F. Garcia-Mazcorro

2018-01-01

Full Text Available Cherries are fruits containing fiber and bioactive compounds (e.g., polyphenolics with the potential of helping patients with diabetes and weight disorders, a phenomenon likely related to changes in the complex host-microbiota milieu. The objective of this study was to investigate the effect of cherry supplementation on the gut bacterial composition, concentrations of caecal short-chain fatty acids (SCFAs and biomarkers of gut health using an in vivo model of obesity. Obese diabetic (db/db mice received a supplemented diet with 10% cherry powder (supplemented mice, n = 12 for 12 weeks; obese (n = 10 and lean (n = 10 mice served as controls and received a standard diet without cherry. High-throughput sequencing of the 16S rRNA gene and quantitative real-time PCR (qPCR were used to analyze the gut microbiota; SCFAs and biomarkers of gut health were also measured using standard techniques. According to 16S sequencing, supplemented mice harbored a distinct colonic microbiota characterized by a higher abundance of mucin-degraders (i.e., Akkermansia and fiber-degraders (the S24-7 family as well as lower abundances of Lactobacillus and Enterobacteriaceae. Overall this particular cherry-associated colonic microbiota did not resemble the microbiota in obese or lean controls based on the analysis of weighted and unweighted UniFrac distance metrics. qPCR confirmed some of the results observed in sequencing, thus supporting the notion that cherry supplementation can change the colonic microbiota. Moreover, the SCFAs detected in supplemented mice (caproate, methyl butyrate, propionate, acetate and valerate exceeded those concentrations detected in obese and lean controls except for butyrate. Despite the changes in microbial composition and SCFAs, most of the assessed biomarkers of inflammation, oxidative stress, and intestinal health in colon tissues and mucosal cells were similar in all obese mice with and without supplementation. This paper shows

Radiation-Force Assisted Targeting Facilitates Ultrasonic Molecular Imaging

Directory of Open Access Journals (Sweden)

Shukui Zhao

2004-07-01

Full Text Available Ultrasonic molecular imaging employs contrast agents, such as microbubbles, nanoparticles, or liposomes, coated with ligands specific for receptors expressed on cells at sites of angiogenesis, inflammation, or thrombus. Concentration of these highly echogenic contrast agents at a target site enhances the ultrasound signal received from that site, promoting ultrasonic detection and analysis of disease states. In this article, we show that acoustic radiation force can be used to displace targeted contrast agents to a vessel wall, greatly increasing the number of agents binding to available surface receptors. We provide a theoretical evaluation of the magnitude of acoustic radiation force and show that it is possible to displace micron-sized agents physiologically relevant distances. Following this, we show in a series of experiments that acoustic radiation force can enhance the binding of targeted agents: The number of biotinylated microbubbles adherent to a synthetic vessel coated with avidin increases as much as 20-fold when acoustic radiation force is applied; the adhesion of contrast agents targeted to αvβ3 expressed on human umbilical vein endothelial cells increases 27-fold within a mimetic vessel when radiation force is applied; and finally, the image signal-to-noise ratio in a phantom vessel increases up to 25 dB using a combination of radiation force and a targeted contrast agent, over use of a targeted contrast agent alone.

Dicty_cDB: Contig-U12980-1 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available ; ddbjgss68.seq; ddbjgss69.seq; ddbjgss7.seq; ddbjgss70.seq; ddbjgss71.seq; ddbjgss72.seq; ddbjgss73.seq; ddbjgss74.seq; ddbjgss7...5.seq; ddbjgss76.seq; ddbjgss77.seq; ddbjgss78.seq; ddbjgss7

Dicty_cDB: Contig-U14108-1 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available .seq; ddbjgss69.seq; ddbjgss7.seq; ddbjgss70.seq; ddbjgss71.seq; ddbjgss72.seq; ddbjgss73.seq; ddbjgss7...4.seq; ddbjgss75.seq; ddbjgss76.seq; ddbjgss77.seq; ddbjgss78.seq; ddbjgss79.seq; ddbj

Dicty_cDB: Contig-U07065-1 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available jgss68.seq; ddbjgss69.seq; ddbjgss7.seq; ddbjgss70.seq; ddbjgss71.seq; ddbjgss72.seq; ddbjgss7...3.seq; ddbjgss74.seq; ddbjgss75.seq; ddbjgss76.seq; ddbjgss77.seq; ddbjgss78.seq; ddbjgss79.seq

Dicty_cDB: Contig-U04485-1 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available q; ddbjgss68.seq; ddbjgss69.seq; ddbjgss7.seq; ddbjgss70.seq; ddbjgss71.seq; ddbjgss72.seq; ddbjgss73.seq; ddbjgss74.seq; ddbjgss7...5.seq; ddbjgss76.seq; ddbjgss77.seq; ddbjgss78.seq; ddbjgss7

Dicty_cDB: Contig-U03723-1 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available dbjgss68.seq; ddbjgss69.seq; ddbjgss7.seq; ddbjgss70.seq; ddbjgss71.seq; ddbjgss72.seq; ddbjgss73.seq; ddbjgss74.seq; ddbjgss7...5.seq; ddbjgss76.seq; ddbjgss77.seq; ddbjgss78.seq; ddbjgss79.s

Dicty_cDB: Contig-U14432-1 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available .seq; ddbjgss69.seq; ddbjgss7.seq; ddbjgss70.seq; ddbjgss71.seq; ddbjgss72.seq; ddbjgss73.seq; ddbjgss7...4.seq; ddbjgss75.seq; ddbjgss76.seq; ddbjgss77.seq; ddbjgss78.seq; ddbjgss79.seq; ddbj

DB90: A Fortran Callable Relational Database Routine for Scientific and Engineering Computer Programs

Science.gov (United States)

Wrenn, Gregory A.

2005-01-01

This report describes a database routine called DB90 which is intended for use with scientific and engineering computer programs. The software is written in the Fortran 90/95 programming language standard with file input and output routines written in the C programming language. These routines should be completely portable to any computing platform and operating system that has Fortran 90/95 and C compilers. DB90 allows a program to supply relation names and up to 5 integer key values to uniquely identify each record of each relation. This permits the user to select records or retrieve data in any desired order.

DB2 9 for Linux, UNIX, and Windows Advanced Database Administration Certification Certification Study Guide

CERN Document Server

Sanders, Roger E

2008-01-01

Database administrators versed in DB2 wanting to learn more about advanced database administration activities and students wishing to gain knowledge to help them pass the DB2 9 UDB Advanced DBA certification exam will find this exhaustive reference invaluable. Written by two individuals who were part of the team that developed the certification exam, this comprehensive study guide prepares the student for challenging questions on database design; data partitioning and clustering; high availability diagnostics; performance and scalability; security and encryption; connectivity and networking; a

Download - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available List Contact us PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods ...t_db_link_en.zip (36.3 KB) - 6 Genome analysis methods pgdbj_dna_marker_linkage_map_genome_analysis_methods_... of This Database Site Policy | Contact Us Download - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ...

Dicty_cDB: SHA814 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available rt in 5'HPRT insertion targeting and chromosome engineering clone MHPN313j15. 44 3.6 1 AG419904 |AG419904.1 ...1 CR220170 |CR220170.1 Forward strand read from insert in 5'HPRT insertion targeting and chromosome engine...ering clone MHPN355o20. 44 3.6 1 CR028932 |CR028932.1 Forward strand read from inse

AHCODA-DB: a data repository with web-based mining tools for the analysis of automated high-content mouse phenomics data.

Science.gov (United States)

Koopmans, Bastijn; Smit, August B; Verhage, Matthijs; Loos, Maarten

2017-04-04

Systematic, standardized and in-depth phenotyping and data analyses of rodent behaviour empowers gene-function studies, drug testing and therapy design. However, no data repositories are currently available for standardized quality control, data analysis and mining at the resolution of individual mice. Here, we present AHCODA-DB, a public data repository with standardized quality control and exclusion criteria aimed to enhance robustness of data, enabled with web-based mining tools for the analysis of individually and group-wise collected mouse phenotypic data. AHCODA-DB allows monitoring in vivo effects of compounds collected from conventional behavioural tests and from automated home-cage experiments assessing spontaneous behaviour, anxiety and cognition without human interference. AHCODA-DB includes such data from mutant mice (transgenics, knock-out, knock-in), (recombinant) inbred strains, and compound effects in wildtype mice and disease models. AHCODA-DB provides real time statistical analyses with single mouse resolution and versatile suite of data presentation tools. On March 9th, 2017 AHCODA-DB contained 650 k data points on 2419 parameters from 1563 mice. AHCODA-DB provides users with tools to systematically explore mouse behavioural data, both with positive and negative outcome, published and unpublished, across time and experiments with single mouse resolution. The standardized (automated) experimental settings and the large current dataset (1563 mice) in AHCODA-DB provide a unique framework for the interpretation of behavioural data and drug effects. The use of common ontologies allows data export to other databases such as the Mouse Phenome Database. Unbiased presentation of positive and negative data obtained under the highly standardized screening conditions increase cost efficiency of publicly funded mouse screening projects and help to reach consensus conclusions on drug responses and mouse behavioural phenotypes. The website is publicly

Dicty_cDB: Contig-U14358-1 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available ; ddbjgss67.seq; ddbjgss68.seq; ddbjgss69.seq; ddbjgss7.seq; ddbjgss70.seq; ddbjgss71.seq; ddbjgss72.seq; ddbjgss73.seq; ddbjgss7...4.seq; ddbjgss75.seq; ddbjgss76.seq; ddbjgss77.seq; ddbjgss78.seq; ddbjgss7

Dicty_cDB: Contig-U14623-1 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available dbjgss67.seq; ddbjgss68.seq; ddbjgss69.seq; ddbjgss7.seq; ddbjgss70.seq; ddbjgss71.seq; ddbjgss7...2.seq; ddbjgss73.seq; ddbjgss74.seq; ddbjgss75.seq; ddbjgss76.seq; ddbjgss77.seq; ddbjgss78.seq; ddbjgss7

Dicty_cDB: Contig-U13745-1 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available dbjgss67.seq; ddbjgss68.seq; ddbjgss69.seq; ddbjgss7.seq; ddbjgss70.seq; ddbjgss71.seq; ddbjgss7...2.seq; ddbjgss73.seq; ddbjgss74.seq; ddbjgss75.seq; ddbjgss76.seq; ddbjgss77.seq; ddbjgss78.seq; ddbjgss7

Dicty_cDB: Contig-U16081-1 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available 1291 |pid:none) Cyanothece sp. PCC 7424, comple... 81 4e-37 AJ535197_1( AJ535197 |pid:none) Propionibacterium freud...eumoniae 342, comp... 75 4e-32 AJ535196_1( AJ535196 |pid:none) Propionibacterium freudenreichii s... 72 4e-3

Dicty_cDB: SLF274 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available 5215 |pid:none) Lymphocytic choriomeningitis virus... 39 0.20 AE014187_324( AE014187 |pid:none) Plasmodium f...alciparum 3D7 chromo... 37 0.75 EU480452_2( EU480452 |pid:none) Lymphocytic choriomeningitis... virus... 36 1.3 AF325214_2( AF325214 |pid:none) Lymphocytic choriomeningitis virus... 36 1.7 ( P...09992 ) RecName: Full=Nucleoprotein; AltName: Full=Nucleocapsid... 35 2.2 Y16308_1( Y16308 |pid:none) Lymphocytic choriomeningitis

MoonDB — A Data System for Analytical Data of Lunar Samples

Science.gov (United States)

Lehnert, K.; Ji, P.; Cai, M.; Evans, C.; Zeigler, R.

2018-04-01

MoonDB is a data system that makes analytical data from the Apollo lunar sample collection and lunar meteorites accessible by synthesizing published and unpublished datasets in a relational database with an online search interface.

Database Description - D-HaploDB | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available 1-8. External Links: Article title: D-HaploDB: a database of definitive haplotypes determined by genotypin...(5):e1000468. External Links: Article title: A definitive haplotype map as determined by genotyping

GenderMedDB: an interactive database of sex and gender-specific medical literature.

Science.gov (United States)

Oertelt-Prigione, Sabine; Gohlke, Björn-Oliver; Dunkel, Mathias; Preissner, Robert; Regitz-Zagrosek, Vera

2014-01-01

Searches for sex and gender-specific publications are complicated by the absence of a specific algorithm within search engines and by the lack of adequate archives to collect the retrieved results. We previously addressed this issue by initiating the first systematic archive of medical literature containing sex and/or gender-specific analyses. This initial collection has now been greatly enlarged and re-organized as a free user-friendly database with multiple functions: GenderMedDB (http://gendermeddb.charite.de). GenderMedDB retrieves the included publications from the PubMed database. Manuscripts containing sex and/or gender-specific analysis are continuously screened and the relevant findings organized systematically into disciplines and diseases. Publications are furthermore classified by research type, subject and participant numbers. More than 11,000 abstracts are currently included in the database, after screening more than 40,000 publications. The main functions of the database include searches by publication data or content analysis based on pre-defined classifications. In addition, registrants are enabled to upload relevant publications, access descriptive publication statistics and interact in an open user forum. Overall, GenderMedDB offers the advantages of a discipline-specific search engine as well as the functions of a participative tool for the gender medicine community.

ORF Alignment: ch_oct10_gene_aa_db [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available ch_oct10_gene_aa_db Chro.60303 >1wicA 11 152 1 150 4e-26 ... gb|EAL37012.1| conserverd MSP-domain transme...mbrane protein [Cryptosporidium ... hominis] ... Length = 150 ... Query: 1 ... MSME...GAKLVRVHPEKALEFPLVLYSSVTTPLILENITSSTVAFKIKTTAPRGYLVRPSSG 60 ... MSMEGAKLVRVHPEKALEFPLVLYSSVTTPLIL...ENITSSTVAFKIKTTAPRGYLVRPSSG Sbjct: 1 ... MSMEGAKLVRVHPEKALEFPLVLYSSVTTPLILENITSSTVA

Exogenous Nitric Oxide Suppresses in Vivo X-ray-Induced Targeted and Non-Targeted Effects in Zebrafish Embryos

Directory of Open Access Journals (Sweden)

E.Y. Kong

2016-08-01

Full Text Available The present paper studied the X-ray-induced targeted effect in irradiated zebrafish embryos (Danio rerio, as well as a non-targeted effect in bystander naïve embryos partnered with irradiated embryos, and examined the influence of exogenous nitric oxide (NO on these targeted and non-targeted effects. The exogenous NO was generated using an NO donor, S-nitroso-N-acetylpenicillamine (SNAP. The targeted and non-targeted effects, as well as the toxicity of the SNAP, were assessed using the number of apoptotic events in the zebrafish embryos at 24 h post fertilization (hpf revealed through acridine orange (AO staining. SNAP with concentrations of 20 and 100 µM were first confirmed to have no significant toxicity on zebrafish embryos. The targeted effect was mitigated in zebrafish embryos if they were pretreated with 100 µM SNAP prior to irradiation with an X-ray dose of 75 mGy but was not alleviated in zebrafish embryos if they were pretreated with 20 µM SNAP. On the other hand, the non-targeted effect was eliminated in the bystander naïve zebrafish embryos if they were pretreated with 20 or 100 µM SNAP prior to partnering with zebrafish embryos having been subjected to irradiation with an X-ray dose of 75 mGy. These findings revealed the importance of NO in the protection against damages induced by ionizing radiations or by radiation-induced bystander signals, and could have important impacts on development of advanced cancer treatment strategies.

Dicty_cDB: Contig-U06926-1 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available ddbjgss68.seq; ddbjgss69.seq; ddbjgss7.seq; ddbjgss70.seq; ddbjgss71.seq; ddbjgss72.seq; ddbjgss73.seq; ddbjgss74.seq; ddbjgss7...5.seq; ddbjgss76.seq; ddbjgss77.seq; ddbjgss78.seq; ddbjgss79.seq; ddbjgss8.seq; ddbjgss

Dicty_cDB: Contig-U14004-1 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available seq; ddbjgss67.seq; ddbjgss68.seq; ddbjgss69.seq; ddbjgss7.seq; ddbjgss70.seq; ddbjgss71.seq; ddbjgss72.seq; ddbjgss73.seq; ddbjgss7...4.seq; ddbjgss75.seq; ddbjgss76.seq; ddbjgss77.seq; ddbjgss78.seq; ddbjgss7

Dicty_cDB: Contig-U10778-1 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available 75_1( AF399175 |pid:none) Eutintinnus pectinis clone Epec99a... 246 e-123 AM168471_1( AM168471 |pid:none) Di...one) Mallomonas papillosa clone H9 alph... 256 e-122 AF399172_1( AF399172 |pid:none) Eutintinnus pectinis cl

Project Plan Remote Target Fabrication Refurbishment Project

International Nuclear Information System (INIS)

Bell, Gary L.; Taylor, Robin D.

2009-01-01

In early FY2009, the DOE Office of Science - Nuclear Physics Program reinstated a program for continued production of 252 Cf and other transcurium isotopes at the Radiochemical Engineering Development Center (REDC) at Oak Ridge National Laboratory (ORNL). The FY2009 major elements of the workscope are as follows: (1) Recovery and processing of seven transuranium element targets undergoing irradiation at the High Flux Isotope Reactor (HFIR) at ORNL; (2) Development of a plan to manufacture new targets for irradiation beginning in early- to mid-FY10 to supply irradiated targets for processing Campaign 75 (TRU75); and (3) Refurbishment of the target manufacturing equipment to allow new target manufacture in early FY10 The 252 Cf product from processing Campaign 74 (recently processed and currently shipping to customers) is expected to supply the domestic demands for a period of approximately two years. Therefore it is essential that new targets be introduced for irradiation by the second quarter of FY10 (HFIR cycle 427) to maintain supply of 252 Cf; the average irradiation period is ∼10 HFIR cycles, requiring about 1.5 calendar years. The strategy for continued production of 252 Cf depends upon repairing and refurbishing the existing pellet and target fabrication equipment for one additional target production campaign. This equipment dates from the mid-1960s to the late 1980s, and during the last target fabrication campaign in 2005- 2006, a number of component failures and operations difficulties were encountered. It is expected that following the target fabrication and acceptance testing of the targets that will supply material for processing Campaign 75 a comprehensive upgrade and replacement of the remote hot-cell equipment will be required prior to subsequent campaigns. Such a major refit could start in early FY 2011 and would take about 2 years to complete. Scope and cost estimates for the repairs described herein were developed, and authorization for the work

MCAW-DB: A glycan profile database capturing the ambiguity of glycan recognition patterns.

Science.gov (United States)

Hosoda, Masae; Takahashi, Yushi; Shiota, Masaaki; Shinmachi, Daisuke; Inomoto, Renji; Higashimoto, Shinichi; Aoki-Kinoshita, Kiyoko F

2018-05-11

Glycan-binding protein (GBP) interaction experiments, such as glycan microarrays, are often used to understand glycan recognition patterns. However, oftentimes the interpretation of glycan array experimental data makes it difficult to identify discrete GBP binding patterns due to their ambiguity. It is known that lectins, for example, are non-specific in their binding affinities; the same lectin can bind to different monosaccharides or even different glycan structures. In bioinformatics, several tools to mine the data generated from these sorts of experiments have been developed. These tools take a library of predefined motifs, which are commonly-found glycan patterns such as sialyl-Lewis X, and attempt to identify the motif(s) that are specific to the GBP being analyzed. In our previous work, as opposed to using predefined motifs, we developed the Multiple Carbohydrate Alignment with Weights (MCAW) tool to visualize the state of the glycans being recognized by the GBP under analysis. We previously reported on the effectiveness of our tool and algorithm by analyzing several glycan array datasets from the Consortium of Functional Glycomics (CFG). In this work, we report on our analysis of 1081 data sets which we collected from the CFG, the results of which we have made publicly and freely available as a database called MCAW-DB. We introduce this database, its usage and describe several analysis results. We show how MCAW-DB can be used to analyze glycan-binding patterns of GBPs amidst their ambiguity. For example, the visualization of glycan-binding patterns in MCAW-DB show how they correlate with the concentrations of the samples used in the array experiments. Using MCAW-DB, the patterns of glycans found to bind to various GBP-glycan binding proteins are visualized, indicating the binding "environment" of the glycans. Thus, the ambiguity of glycan recognition is numerically represented, along with the patterns of monosaccharides surrounding the binding region. The

MicroRNA-214 Suppresses Gluconeogenesis by Targeting Activating Transcriptional Factor 4*

Science.gov (United States)

Li, Kai; Zhang, Jin; Yu, Junjie; Liu, Bin; Guo, Yajie; Deng, Jiali; Chen, Shanghai; Wang, Chunxia; Guo, Feifan

2015-01-01

Although the gluconeogenesis pathway is already a target for the treatment of type 2 diabetes, the potential role of microRNAs (miRNAs) in gluconeogenesis remains unclear. Here, we investigated the physiological functions of miR-214 in gluconeogenesis. The expression of miR-214 was suppressed by glucagon via protein kinase A signaling in primary hepatocytes, and miR-214 was down-regulated in the livers of fasted, high fat diet-induced diabetic and leptin receptor-mutated (db/db) mice. The overexpression of miR-214 in primary hepatocytes suppressed glucose production, and silencing miR-214 reversed this effect. Gluconeogenesis was suppressed in the livers of mice injected with an adenovirus expressing miR-214 (Ad-miR-214). Additionally, Ad-miR-214 alleviated high fat diet-induced elevation of gluconeogenesis and hyperglycemia. Furthermore, we found that activating transcription factor 4 (ATF4), a reported target of miR-214, can reverse the suppressive effect of miR-214 on gluconeogenesis in primary hepatocytes, and this suppressive effect was blocked in liver-specific ATF4 knock-out mice. ATF4 regulated gluconeogenesis via affecting forkhead box protein O1 (FOXO1) transcriptional activity. Finally, liver-specific miR-214 transgenic mice exhibited suppressed gluconeogenesis and reduced expression of ATF4, phosphoenolpyruvate carboxykinase, and glucose-6-phosphatase in liver. Taken together, our results suggest that the miR-214-ATF4 axis is a novel pathway for the regulation of hepatic gluconeogenesis. PMID:25657009

p75 Neurotrophin Receptor Suppresses the Proliferation of Human Gastric Cancer Cells

Directory of Open Access Journals (Sweden)

Haifeng Jin

2007-06-01

Full Text Available Identifying an effective therapeutic target is pivotal in the treatment of gastric cancer. In this study, we investigated the expression of p75 neurotrophin receptor (p75NTR in gastric cancer and the impact of its alteration on tumor growth. p75NTR expression was absent or significantly decreased in 212 cases of gastric cancers compared with the normal gastric mucosa (P < .05. Moreover, p75NTR expression was also lost or significantly decreased in various human gastric cancer cell lines. p75NTR inhibited in vitro growth activities and caused dramatic attenuation of tumor growth in animal models by induction of cell cycle arrest. Upregulation of p75NTR led to downregulation of cyclin A, cyclin D1, cyclin E, cyclin-dependent kinase 2, p-Rb, and PCNA, but to upregulation of Rb and p27 expressions. Conversely, downregulating p75NTR with specific siRNA yielded inverse results. The rescue of tumor cells from cell cycle progression by a death domain-deleted dominant-negative antagonist of p75NTR (Δp75NTR showed that the death domain transduced antiproliferative activity in a ligandindependent manner and further demonstrated the inhibitive effect of p75NTR on growth in gastric cancer. Therefore, we provided evidence that p75NTR was a potential tumor suppressor and may be used as a therapeutic target for gastric cancer.

Dim small targets detection based on self-adaptive caliber temporal-spatial filtering

Science.gov (United States)

Fan, Xiangsuo; Xu, Zhiyong; Zhang, Jianlin; Huang, Yongmei; Peng, Zhenming

2017-09-01

To boost the detect ability of dim small targets, this paper began by using improved anisotropy for background prediction (IABP), followed by target enhancement by improved high-order cumulates (HQS). Finally, on the basis of image pre-processing, to address the problem of missed and wrong detection caused by fixed caliber of traditional pipeline filtering, this paper used targets' multi-frame movement correlation in the time-space domain, combined with the scale-space theory, to propose a temporal-spatial filtering algorithm which allows the caliber to make self-adaptive changes according to the changes of the targets' scale, effectively solving the detection-related issues brought by unchanged caliber and decreased/increased size of the targets. Experiments showed that the improved anisotropic background predication could be loyal to the true background of the original image to the maximum extent, presenting a superior overall performance to other background prediction methods; the improved HQS significantly increased the signal-noise ratio of images; when the signal-noise ratio was lower than 2.6 dB, this detection algorithm could effectively eliminate noise and detect targets. For the algorithm, the lowest signal-to-noise ratio of the detectable target is 0.37.

Dicty_cDB: Contig-U15448-1 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available s66.seq; ddbjgss67.seq; ddbjgss68.seq; ddbjgss69.seq; ddbjgss7.seq; ddbjgss70.seq; ddbjgss71.seq; ddbjgss7...2.seq; ddbjgss73.seq; ddbjgss74.seq; ddbjgss75.seq; ddbjgss76.seq; ddbjgss77.seq; ddbjgss78.seq; ddbjgss7

Dicty_cDB: Contig-U01474-1 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available 68.seq; ddbjgss69.seq; ddbjgss7.seq; ddbjgss70.seq; ddbjgss71.seq; ddbjgss72.seq; ddbjgss73.seq; ddbjgss74.seq; ddbjgss7...5.seq; ddbjgss76.seq; ddbjgss77.seq; ddbjgss78.seq; ddbjgss79.seq; ddbjgss8.seq; ddbjgss80.seq;

Dicty_cDB: Contig-U00778-1 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available ss66.seq; ddbjgss67.seq; ddbjgss68.seq; ddbjgss69.seq; ddbjgss7.seq; ddbjgss70.seq; ddbjgss71.seq; ddbjgss72.seq; ddbjgss7...3.seq; ddbjgss74.seq; ddbjgss75.seq; ddbjgss76.seq; ddbjgss77.seq; ddbjgss78.seq; ddbjgss79.se

Dicty_cDB: Contig-U01684-1 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available ss66.seq; ddbjgss67.seq; ddbjgss68.seq; ddbjgss69.seq; ddbjgss7.seq; ddbjgss70.seq; ddbjgss7...1.seq; ddbjgss72.seq; ddbjgss73.seq; ddbjgss74.seq; ddbjgss75.seq; ddbjgss76.seq; ddbjgss77.seq; ddbjgss78.seq; ddbjgss7

Dicty_cDB: Contig-U15382-1 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available s66.seq; ddbjgss67.seq; ddbjgss68.seq; ddbjgss69.seq; ddbjgss7.seq; ddbjgss70.seq; ddbjgss71.seq; ddbjgss72.seq; ddbjgss7...3.seq; ddbjgss74.seq; ddbjgss75.seq; ddbjgss76.seq; ddbjgss77.seq; ddbjgss78.seq; ddbjgss79.seq

Dicty_cDB: Contig-U02918-1 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available 66.seq; ddbjgss67.seq; ddbjgss68.seq; ddbjgss69.seq; ddbjgss7.seq; ddbjgss70.seq; ddbjgss71.seq; ddbjgss72.seq; ddbjgss7...3.seq; ddbjgss74.seq; ddbjgss75.seq; ddbjgss76.seq; ddbjgss77.seq; ddbjgss78.seq; ddbjgss79.seq;

Dicty_cDB: Contig-U05674-1 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available jgss68.seq; ddbjgss69.seq; ddbjgss7.seq; ddbjgss70.seq; ddbjgss71.seq; ddbjgss72.seq; ddbjgss73.seq; ddbjgss74.seq; ddbjgss7...5.seq; ddbjgss76.seq; ddbjgss77.seq; ddbjgss78.seq; ddbjgss79.seq; ddbjgss8.seq; ddbjgss80.s

Dicty_cDB: Contig-U12930-1 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available .seq; ddbjgss68.seq; ddbjgss69.seq; ddbjgss7.seq; ddbjgss70.seq; ddbjgss71.seq; ddbjgss72.seq; ddbjgss73.seq; ddbjgss74.seq; ddbjgss7...5.seq; ddbjgss76.seq; ddbjgss77.seq; ddbjgss78.seq; ddbjgss79.seq; ddbjgss8.seq; dd

Dicty_cDB: Contig-U14125-1 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available gss67.seq; ddbjgss68.seq; ddbjgss69.seq; ddbjgss7.seq; ddbjgss70.seq; ddbjgss71.seq; ddbjgss72.seq; ddbjgss73.seq; ddbjgss7...4.seq; ddbjgss75.seq; ddbjgss76.seq; ddbjgss77.seq; ddbjgss78.seq; ddbjgss79.seq; ddbjgss8.se

Dicty_cDB: Contig-U14671-1 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available ss66.seq; ddbjgss67.seq; ddbjgss68.seq; ddbjgss69.seq; ddbjgss7.seq; ddbjgss70.seq; ddbjgss71.seq; ddbjgss72.seq; ddbjgss7...3.seq; ddbjgss74.seq; ddbjgss75.seq; ddbjgss76.seq; ddbjgss77.seq; ddbjgss78.seq; ddbjgss7

Dicty_cDB: Contig-U15380-1 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available s66.seq; ddbjgss67.seq; ddbjgss68.seq; ddbjgss69.seq; ddbjgss7.seq; ddbjgss70.seq; ddbjgss71.seq; ddbjgss72.seq; ddbjgss7...3.seq; ddbjgss74.seq; ddbjgss75.seq; ddbjgss76.seq; ddbjgss77.seq; ddbjgss78.seq; ddbjgss7

Dicty_cDB: Contig-U13294-1 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available dbjgss66.seq; ddbjgss67.seq; ddbjgss68.seq; ddbjgss69.seq; ddbjgss7.seq; ddbjgss70.seq; ddbjgss71.seq; ddbjgss72.seq; ddbjgss7...3.seq; ddbjgss74.seq; ddbjgss75.seq; ddbjgss76.seq; ddbjgss77.seq; ddbjgss78.seq; ddbjgss7

Kinematics of Rotation in Joints of the Lower Limbs and Pelvis during Gait: Early Results—SB ACLR Approach versus DB ACLR Approach

Directory of Open Access Journals (Sweden)

Andrzej Czamara

2015-01-01

Full Text Available It is difficult to find publications comparing rotation kinematics in large joints of the lower limbs and pelvis during gait in patients after single-bundle (SB reconstruction of the anterior cruciate ligament (ACLR with double-bundle (DB ACLR of the knee. The aim of this study was to compare rotation kinematics in ankle, knee, and hip joints and the pelvis during gait in the 14th week after SB and DB ACLR. The subjects were males after SB (n=10 and DB (n=13 ACLR and a control group (n=15. The values of kinematic parameters were recorded during internal (IR and external (ER rotation in the joints during gait using the BTS SMART. The SB ACLR group obtained significantly higher values of ER in the involved knee comparing to DB ACLR and controls and excessive IR in the hip comparing to controls. In the DB ACLR group, excessive ER was noted in the involved leg's foot. Comparing with the DB ACLR and control groups, SB ACLR subjects had more substantial disorders of rotation kinematics in the lower limb joints. However, in both ACLR groups, 14 weeks of postoperative physiotherapy were not enough to fully restore rotation kinematics in joints of the lower limbs during gait.

Disease - MicrobeDB.jp | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...File name: disease.tar.gz File URL: ftp://ftp.biosciencedbc.jp/archive/microbedb/...iption Download License Update History of This Database Site Policy | Contact Us Disease - MicrobeDB.jp | LSDB Archive ...

Dicty_cDB: Contig-U14612-1 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available gss65.seq; ddbjgss66.seq; ddbjgss67.seq; ddbjgss68.seq; ddbjgss69.seq; ddbjgss7.seq; ddbjgss70.seq; ddbjgss71.seq; ddbjgss7...2.seq; ddbjgss73.seq; ddbjgss74.seq; ddbjgss75.seq; ddbjgss76.seq; ddbjgss77.seq; ddbjgss78.seq; ddbjgss7

Dicty_cDB: Contig-U15192-1 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available 145 6e-59 AB241251_1( AB241251 |pid:none) Symbiotic protist of Reticuliterme... 154 1e-58 AC155898_18( AC15...6368 |pid:none) Entamoeba histolytica EhRAB7G gene... 75 5e-26 AB241241_1( AB241241 |pid:none) Symbiotic pro

DB4US: A Decision Support System for Laboratory Information Management.

Science.gov (United States)

Carmona-Cejudo, José M; Hortas, Maria Luisa; Baena-García, Manuel; Lana-Linati, Jorge; González, Carlos; Redondo, Maximino; Morales-Bueno, Rafael

2012-11-14

Until recently, laboratory automation has focused primarily on improving hardware. Future advances are concentrated on intelligent software since laboratories performing clinical diagnostic testing require improved information systems to address their data processing needs. In this paper, we propose DB4US, an application that automates information related to laboratory quality indicators information. Currently, there is a lack of ready-to-use management quality measures. This application addresses this deficiency through the extraction, consolidation, statistical analysis, and visualization of data related to the use of demographics, reagents, and turn-around times. The design and implementation issues, as well as the technologies used for the implementation of this system, are discussed in this paper. To develop a general methodology that integrates the computation of ready-to-use management quality measures and a dashboard to easily analyze the overall performance of a laboratory, as well as automatically detect anomalies or errors. The novelty of our approach lies in the application of integrated web-based dashboards as an information management system in hospital laboratories. We propose a new methodology for laboratory information management based on the extraction, consolidation, statistical analysis, and visualization of data related to demographics, reagents, and turn-around times, offering a dashboard-like user web interface to the laboratory manager. The methodology comprises a unified data warehouse that stores and consolidates multidimensional data from different data sources. The methodology is illustrated through the implementation and validation of DB4US, a novel web application based on this methodology that constructs an interface to obtain ready-to-use indicators, and offers the possibility to drill down from high-level metrics to more detailed summaries. The offered indicators are calculated beforehand so that they are ready to use when the user

AmbientDB: relational query processing in a P2P network

NARCIS (Netherlands)

P.A. Boncz (Peter); C. Treijtel

2003-01-01

textabstractA new generation of applications running on a network of nodes, that share data on an ad-hoc basis, will benefit from data management services including powerful querying facilities. In this paper, we introduce the goals, assumptions and architecture of AmbientDB, a new peer-to-peer

AmbientDB : relational query processing in a P2P network

NARCIS (Netherlands)

P.A. Boncz (Peter); C. Treijtel

2003-01-01

textabstractA new generation of applications running on a network of nodes, that share data on an ad-hoc basis, will benefit from data management services including powerful querying facilities. In this paper, we introduce the goals, assumptions and architecture of AmbientDB, a new peer-to-peer

The acoustic properties of Salpa thompsoni

KAUST Repository

Wiebe, Peter H.; Chu, Dezhang; Kaartvedt, Stein; Hundt, Anna; Melle, Webjø rn; Ona, Egil; Batta-Lona, Paola G.

2009-01-01

distributions peaked between-75 and - 76 dB at 38 kHz, with a secondary peak at approximately - 65 dB. TS ranged between-85 and - 65 dB at 120 and 200 kHz and peaked around-74 dB. The measured in situ TS of salps reasonably matched the theoretical scattering

Database Description - PGDBj - Ortholog DB | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available e relevant data in the databases. By submitting queries to the PGDBj Ortholog DB with keywords or amino acid sequences, users... taxa including both model plants and crop plants. Following the links obtained, users can retrieve the actu

Assessment of the sedative effects of buprenorphine administered with 10 μg/kg detomidine in horses.

Science.gov (United States)

Love, E J; Taylor, P M; Murrell, J; Whay, H R; Waterman-Pearson, A E

2011-04-09

The aim of this randomised, observer-blinded, crossover study was to compare the effects of six treatments, administered intravenously to six horses: saline and saline (S/S); detomidine and saline (D/S); detomidine and 5 µg/kg buprenorphine (D/B5); detomidine and 7.5 µg/kg buprenorphine (D/B7.5); detomidine and 10 µg/kg buprenorphine (D/B10); and detomidine and 25 µg/kg butorphanol (D/BUT). The detomidine dose was 10 µg/kg for all treatments in which it was included. Sedation was subjectively assessed and recorded on a visual analogue scale. Peak sedation, duration of sedation and the area under the curve (AUC) for sedation scores were investigated using a univariate general linear model with post-hoc Tukey tests (P<0.05). Peak sedation and duration of sedation were statistically significantly different between treatments (P<0.001). No sedation was apparent after administration of S/S. The AUC was significantly different between treatments (P=0.010), with S/S being significantly different from D/S, D/BUT, D/B5 and D/B7.5, but not D/B10 (P=0.051).

Results on (UNPublished Wet Runs on Pulsating DB White Dwarfs

Directory of Open Access Journals (Sweden)

Handler G.

2003-03-01

Full Text Available I have collected all the WET archival data on the pulsating DB white dwarf stars (DBVs and re-reduced them. In addition, the WET has recently observed three DBVs. Preliminary results on PG 1115+158, PG 1351+489, KUV 05134+2605, PG 1654+160 and PG 1456+103 are presented, and the future use of the data is outlined.

SciDB versus Spark: A Preliminary Comparison Based on an Earth Science Use Case

Science.gov (United States)

Clune, T.; Kuo, K. S.; Doan, K.; Oloso, A.

2015-12-01

We compare two Big Data technologies, SciDB and Spark, for performance, usability, and extensibility, when applied to a representative Earth science use case. SciDB is a new-generation parallel distributed database management system (DBMS) based on the array data model that is capable of handling multidimensional arrays efficiently but requires lengthy data ingest prior to analysis, whereas Spark is a fast and general engine for large scale data processing that can immediately process raw data files and thereby avoid the ingest process. Once data have been ingested, SciDB is very efficient in database operations such as subsetting. Spark, on the other hand, provides greater flexibility by supporting a wide variety of high-level tools including DBMS's. For the performance aspect of this preliminary comparison, we configure Spark to operate directly on text or binary data files and thereby limit the need for additional tools. Arguably, a more appropriate comparison would involve exploring other configurations of Spark which exploit supported high-level tools, but that is beyond our current resources. To make the comparison as "fair" as possible, we export the arrays produced by SciDB into text files (or converting them to binary files) for the intake by Spark and thereby avoid any additional file processing penalties. The Earth science use case selected for this comparison is the identification and tracking of snowstorms in the NASA Modern Era Retrospective-analysis for Research and Applications (MERRA) reanalysis data. The identification portion of the use case is to flag all grid cells of the MERRA high-resolution hourly data that satisfies our criteria for snowstorm, whereas the tracking portion connects flagged cells adjacent in time and space to form a snowstorm episode. We will report the results of our comparisons at this presentation.

Anti-Diabetic Effects of Dung Beetle Glycosaminoglycan on db Mice and Gene Expression Profiling.

Science.gov (United States)

Ahn, Mi Young; Kim, Ban Ji; Yoon, Hyung Joo; Hwang, Jae Sam; Park, Kun-Koo

2018-04-01

Anti-diabetes activity of Catharsius molossus (Ca, a type of dung beetle) glycosaminoglycan (G) was evaluated to reduce glucose, creatinine kinase, triglyceride and free fatty acid levels in db mice. Diabetic mice in six groups were administrated intraperitoneally: Db heterozygous (Normal), Db homozygous (CON), Heuchys sanguinea glycosaminoglycan (HEG, 5 mg/kg), dung beetle glycosaminoglycan (CaG, 5 mg/kg), bumblebee ( Bombus ignitus ) queen glycosaminoglycan (IQG, 5 mg/kg) and metformin (10 mg/kg), for 1 month. Biochemical analyses in the serum were evaluated to determine their anti-diabetic and anti-inflammatory actions in db mice after 1 month treatment with HEG, CaG or IQG treatments. Blood glucose level was decreased by treatment with CaG. CaG produced significant anti-diabetic actions by inhiting creatinine kinase and alkaline phosphatase levels. As diabetic parameters, serum glucose level, total cholesterol and triglyceride were significantly decreased in CaG5-treated group compared to the controls. Dung beetle glycosaminoglycan, compared to the control, could be a potential therapeutic agent with anti-diabetic activity in diabetic mice. CaG5-treated group, compared to the control, showed the up-regulation of 48 genes including mitochondrial yen coded tRNA lysine (mt-TK), cytochrome P450, family 8/2, subfamily b, polypeptide 1 (Cyp8b1), and down-regulation of 79 genes including S100 calcium binding protein A9 (S100a9) and immunoglobulin kappa chain complex (Igk), and 3-hydroxy-3-methylglutaryl-CoenzymeAsynthase1 (Hmgcs1). Moreover, mitochondrial thymidine kinase (mt-TK), was up-regulated, and calgranulin A (S100a9) were down-regulated by CaG5 treatment, indicating a potential therapeutic use for anti-diabetic agent.

Dicty_cDB: SHJ574 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available t in 5'HPRT insertion targeting and chromosome engineering clone MHPN46d24. 44 3.6 1 CR250482 |CR250482.1 Re...verse strand read from insert in 5'HPRT insertion targeting and chromosome engineering...rgeting and chromosome engineering clone MHPN111m08. 44 3.6 1 DU965366 |DU965366.1 312103 Tomato MboI BAC Li... clone MHPN408l04. 44 3.6 1 CR115379 |CR115379.1 Reverse strand read from insert in 5'HPRT insertion ta

Low-resolution Airborne Radar Air/ground Moving Target Classification and Recognition

Directory of Open Access Journals (Sweden)

Wang Fu-you

2014-10-01

Full Text Available Radar Target Recognition (RTR is one of the most important needs of modern and future airborne surveillance radars, and it is still one of the key technologies of radar. The majority of present algorithms are based on wide-band radar signal, which not only needs high performance radar system and high target Signal-to-Noise Ratio (SNR, but also is sensitive to angle between radar and target. Low-Resolution Airborne Surveillance Radar (LRASR in downward-looking mode, slow flying aircraft and ground moving truck have similar Doppler velocity and Radar Cross Section (RCS, leading to the problem that LRASR air/ground moving targets can not be distinguished, which also disturbs detection, tracking, and classification of low altitude slow flying aircraft to solve these issues, an algorithm based on narrowband fractal feature and phase modulation feature is presented for LRASR air/ground moving targets classification. Real measured data is applied to verify the algorithm, the classification results validate the proposed method, helicopters and truck can be well classified, the average discrimination rate is more than 89% when SNR ≥ 15 dB.

Dicty_cDB: Contig-U11980-1 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available one) Debaryomyces hansenii chromosome... 75 1e-11 AY155346_1( AY155346 |pid:none) Bactrocera cucurbita... |pid:none) Bactrocera tryoni scarlet gene, co... 52 2e-04 AY055816_1( AY055816 |pid:none) Bactrocera cucu...rbitae ABC membrane... 52 2e-04 CP000497_149( CP000497 |pid:none) Pichia stipitis C

Dicty_cDB: Contig-U16063-1 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available osis and Prognosis of Breast Cancer Patients. 56 0.005 1 ( DD187155 ) Novel targets for obesity from subcuta...neous fat. 56 0.005 1 ( DD187154 ) Novel targets for obesity from subcutaneous fa

Database Description - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available List Contact us PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods ... QTL list, Plant DB link & Genome analysis methods Alternative name - DOI 10.18908/lsdba.nbdc01194-01-000 Cr...ers and QTLs are curated manually from the published literature. The marker information includes marker sequences, genotyping methods... Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ...

DB2: a probabilistic approach for accurate detection of tandem duplication breakpoints using paired-end reads.

Science.gov (United States)

Yavaş, Gökhan; Koyutürk, Mehmet; Gould, Meetha P; McMahon, Sarah; LaFramboise, Thomas

2014-03-05

With the advent of paired-end high throughput sequencing, it is now possible to identify various types of structural variation on a genome-wide scale. Although many methods have been proposed for structural variation detection, most do not provide precise boundaries for identified variants. In this paper, we propose a new method, Distribution Based detection of Duplication Boundaries (DB2), for accurate detection of tandem duplication breakpoints, an important class of structural variation, with high precision and recall. Our computational experiments on simulated data show that DB2 outperforms state-of-the-art methods in terms of finding breakpoints of tandem duplications, with a higher positive predictive value (precision) in calling the duplications' presence. In particular, DB2's prediction of tandem duplications is correct 99% of the time even for very noisy data, while narrowing down the space of possible breakpoints within a margin of 15 to 20 bps on the average. Most of the existing methods provide boundaries in ranges that extend to hundreds of bases with lower precision values. Our method is also highly robust to varying properties of the sequencing library and to the sizes of the tandem duplications, as shown by its stable precision, recall and mean boundary mismatch performance. We demonstrate our method's efficacy using both simulated paired-end reads, and those generated from a melanoma sample and two ovarian cancer samples. Newly discovered tandem duplications are validated using PCR and Sanger sequencing. Our method, DB2, uses discordantly aligned reads, taking into account the distribution of fragment length to predict tandem duplications along with their breakpoints on a donor genome. The proposed method fine tunes the breakpoint calls by applying a novel probabilistic framework that incorporates the empirical fragment length distribution to score each feasible breakpoint. DB2 is implemented in Java programming language and is freely available

Resource implications of a national health target

DEFF Research Database (Denmark)

Jones, Peter; Sopina, Liza Elizaveta; Ashton, Toni

2014-01-01

Background The Shorter Stays in Emergency Departments health target was introduced in New Zealand in 2009. District Health Boards (DHBs) are expected to meet the target with no additional funding or incentives. The costs of implementing such targets have not previously been studied. Method A survey.......03), whereas expenditure in the hospital was not (r = 0.08, P = 0.75). Conclusion The fact that estimated expenditure on the target was over $50 million without additional funding suggests that DHBs were able to make savings through improved efficiencies and/or that funds were reallocated from other services...

Altered metabolic incorporation of fucose and leucine into PNS myelin of 25-week-old diabetic (C57BL/Ks [db/db]) mice: effects of untreated diabetes on nerve metabolism

International Nuclear Information System (INIS)

Chez, M.G.; Peterson, R.G.

1983-01-01

Sciatic nerves of 25-week-old genetically diabetic (C57BL/Ks [db/db]) mice and their litter-mate controls were removed, and their metabolic incorporation of [ 3 H]fucose and [ 14 C]leucine into myelin was studied in vitro. Untreated diabetic animals showed significant increases (p less than 0.05) in the fucose/leucine incorporation into myelin when compared to values found for their litter-mates. These results correlated well with previous experiments performed on alloxan or streptozotocin-diabetic rats and thus show the in vitro incubation procedure to be a good indicator of altered metabolic conditions in peripheral nerves due to diabetes mellitus. The resulting ratio increases seen in diabetic animals is at variance with the decrease in ratios found in animals undergoing typical Wallerian degeneration. These results suggest that different metabolic processes operate in untreated diabetics than in normals or in those undergoing other degenerative nerve processes

Apparatus for producing laser targets

International Nuclear Information System (INIS)

Jarboe, T.R.; Baker, W.R.

1975-01-01

This patent relates to an apparatus and method for producing deuterium targets or pellets of 25u to 75u diameter. The pellets are sliced from a continuously spun solid deuterium thread at a rate of up to 10 pellets/second. The pellets after being sliced from the continuous thread of deuterium are collimated and directed to a point of use, such as a laser activated combustion or explosion chamber wherein the pellets are imploded by laser energy or laser produced target plasmas for neutral beam injection

Dicty_cDB: Contig-U05306-1 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available ( FG300482 ) 1108793371534 New World Screwworm Larvae 9387 EST... 44 5.1 1 ( FG300022 ) 1108793358663 New World... Screwworm Larvae 9387 EST... 44 5.1 1 ( FG298906 ) 1108793323573 New World Screwworm Larvae 9387 EST...... 44 5.1 1 ( FG295524 ) 1108770734276 New World Screwworm Larvae 9387 EST... 44 5.1 1 ( FD524352 ) RUS75C05w

Getting the most out of parasitic helminth transcriptomes using HelmDB: implications for biology and biotechnology.

Science.gov (United States)

Mangiola, Stefano; Young, Neil D; Korhonen, Pasi; Mondal, Alinda; Scheerlinck, Jean-Pierre; Sternberg, Paul W; Cantacessi, Cinzia; Hall, Ross S; Jex, Aaron R; Gasser, Robin B

2013-12-01

Compounded by a massive global food shortage, many parasitic diseases have a devastating, long-term impact on animal and human health and welfare worldwide. Parasitic helminths (worms) affect the health of billions of animals. Unlocking the systems biology of these neglected pathogens will underpin the design of new and improved interventions against them. Currently, the functional annotation of genomic and transcriptomic sequence data for socio-economically important parasitic worms relies almost exclusively on comparative bioinformatic analyses using model organism- and other databases. However, many genes and gene products of parasitic helminths (often >50%) cannot be annotated using this approach, because they are specific to parasites and/or do not have identifiable homologs in other organisms for which sequence data are available. This inability to fully annotate transcriptomes and predicted proteomes is a major challenge and constrains our understanding of the biology of parasites, interactions with their hosts and of parasitism and the pathogenesis of disease on a molecular level. In the present article, we compiled transcriptomic data sets of key, socioeconomically important parasitic helminths, and constructed and validated a curated database, called HelmDB (www.helmdb.org). We demonstrate how this database can be used effectively for the improvement of functional annotation by employing data integration and clustering. Importantly, HelmDB provides a practical and user-friendly toolkit for sequence browsing and comparative analyses among divergent helminth groups (including nematodes and trematodes), and should be readily adaptable and applicable to a wide range of other organisms. This web-based, integrative database should assist 'systems biology' studies of parasitic helminths, and the discovery and prioritization of novel drug and vaccine targets. This focus provides a pathway toward developing new and improved approaches for the treatment and control

MicroRNA-214 suppresses gluconeogenesis by targeting activating transcriptional factor 4.

Science.gov (United States)

Li, Kai; Zhang, Jin; Yu, Junjie; Liu, Bin; Guo, Yajie; Deng, Jiali; Chen, Shanghai; Wang, Chunxia; Guo, Feifan

2015-03-27

Although the gluconeogenesis pathway is already a target for the treatment of type 2 diabetes, the potential role of microRNAs (miRNAs) in gluconeogenesis remains unclear. Here, we investigated the physiological functions of miR-214 in gluconeogenesis. The expression of miR-214 was suppressed by glucagon via protein kinase A signaling in primary hepatocytes, and miR-214 was down-regulated in the livers of fasted, high fat diet-induced diabetic and leptin receptor-mutated (db/db) mice. The overexpression of miR-214 in primary hepatocytes suppressed glucose production, and silencing miR-214 reversed this effect. Gluconeogenesis was suppressed in the livers of mice injected with an adenovirus expressing miR-214 (Ad-miR-214). Additionally, Ad-miR-214 alleviated high fat diet-induced elevation of gluconeogenesis and hyperglycemia. Furthermore, we found that activating transcription factor 4 (ATF4), a reported target of miR-214, can reverse the suppressive effect of miR-214 on gluconeogenesis in primary hepatocytes, and this suppressive effect was blocked in liver-specific ATF4 knock-out mice. ATF4 regulated gluconeogenesis via affecting forkhead box protein O1 (FOXO1) transcriptional activity. Finally, liver-specific miR-214 transgenic mice exhibited suppressed gluconeogenesis and reduced expression of ATF4, phosphoenolpyruvate carboxykinase, and glucose-6-phosphatase in liver. Taken together, our results suggest that the miR-214-ATF4 axis is a novel pathway for the regulation of hepatic gluconeogenesis. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Fully-etched apodized fiber-to-chip grating coupler on the SOI platform with -0.78 dB coupling efficiency using photonic crystals and bonded Al mirror

DEFF Research Database (Denmark)

Ding, Yunhong; Ou, Haiyan; Peucheret, Christophe

2014-01-01

We design and fabricate an ultra-high coupling efficiency fully-etched apodized grating coupler on the SOI platform using photonic crystals and bonded aluminum mirror. Ultra-high coupling efficiency of -0.78 dB with a 3 dB bandwidth of 74 nm are demonstrated.......We design and fabricate an ultra-high coupling efficiency fully-etched apodized grating coupler on the SOI platform using photonic crystals and bonded aluminum mirror. Ultra-high coupling efficiency of -0.78 dB with a 3 dB bandwidth of 74 nm are demonstrated....

MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource based on the first complete plant genome

Science.gov (United States)

Schoof, Heiko; Zaccaria, Paolo; Gundlach, Heidrun; Lemcke, Kai; Rudd, Stephen; Kolesov, Grigory; Arnold, Roland; Mewes, H. W.; Mayer, Klaus F. X.

2002-01-01

Arabidopsis thaliana is the first plant for which the complete genome has been sequenced and published. Annotation of complex eukaryotic genomes requires more than the assignment of genetic elements to the sequence. Besides completing the list of genes, we need to discover their cellular roles, their regulation and their interactions in order to understand the workings of the whole plant. The MIPS Arabidopsis thaliana Database (MAtDB; http://mips.gsf.de/proj/thal/db) started out as a repository for genome sequence data in the European Scientists Sequencing Arabidopsis (ESSA) project and the Arabidopsis Genome Initiative. Our aim is to transform MAtDB into an integrated biological knowledge resource by integrating diverse data, tools, query and visualization capabilities and by creating a comprehensive resource for Arabidopsis as a reference model for other species, including crop plants. PMID:11752263

MycoDB, a global database of plant response to mycorrhizal fungi

Science.gov (United States)

Chaudhary, V. Bala; Rúa, Megan A.; Antoninka, Anita; Bever, James D.; Cannon, Jeffery; Craig, Ashley; Duchicela, Jessica; Frame, Alicia; Gardes, Monique; Gehring, Catherine; Ha, Michelle; Hart, Miranda; Hopkins, Jacob; Ji, Baoming; Johnson, Nancy Collins; Kaonongbua, Wittaya; Karst, Justine; Koide, Roger T.; Lamit, Louis J.; Meadow, James; Milligan, Brook G.; Moore, John C.; Pendergast, Thomas H., IV; Piculell, Bridget; Ramsby, Blake; Simard, Suzanne; Shrestha, Shubha; Umbanhowar, James; Viechtbauer, Wolfgang; Walters, Lawrence; Wilson, Gail W. T.; Zee, Peter C.; Hoeksema, Jason D.

2016-05-01

Plants form belowground associations with mycorrhizal fungi in one of the most common symbioses on Earth. However, few large-scale generalizations exist for the structure and function of mycorrhizal symbioses, as the nature of this relationship varies from mutualistic to parasitic and is largely context-dependent. We announce the public release of MycoDB, a database of 4,010 studies (from 438 unique publications) to aid in multi-factor meta-analyses elucidating the ecological and evolutionary context in which mycorrhizal fungi alter plant productivity. Over 10 years with nearly 80 collaborators, we compiled data on the response of plant biomass to mycorrhizal fungal inoculation, including meta-analysis metrics and 24 additional explanatory variables that describe the biotic and abiotic context of each study. We also include phylogenetic trees for all plants and fungi in the database. To our knowledge, MycoDB is the largest ecological meta-analysis database. We aim to share these data to highlight significant gaps in mycorrhizal research and encourage synthesis to explore the ecological and evolutionary generalities that govern mycorrhizal functioning in ecosystems.

Decommissioning Facility Characterization DB System

International Nuclear Information System (INIS)

Park, S. K.; Ji, Y. H.; Park, J. H.; Chung, U. S.

2010-01-01

Basically, when a decommissioning is planed for a nuclear facility, an investigation into the characterization of the nuclear facility is first required. The results of such an investigation are used for calculating the quantities of dismantled waste and estimating the cost of the decommissioning project. In this paper, it is presented a computer system for the characterization of nuclear facilities, called DEFACS (DEcommissioning FAcility Characterization DB System). This system consists of four main parts: a management coding system for grouping items, a data input system, a data processing system and a data output system. All data is processed in a simplified and formatted manner in order to provide useful information to the decommissioning planner. For the hardware, PC grade computers running Oracle software on Microsoft Windows OS were selected. The characterization data results for the nuclear facility under decommissioning will be utilized for the work-unit productivity calculation system and decommissioning engineering system as basic sources of information

Decommissioning Facility Characterization DB System

Energy Technology Data Exchange (ETDEWEB)

Park, S. K.; Ji, Y. H.; Park, J. H.; Chung, U. S. [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

2010-10-15

Basically, when a decommissioning is planed for a nuclear facility, an investigation into the characterization of the nuclear facility is first required. The results of such an investigation are used for calculating the quantities of dismantled waste and estimating the cost of the decommissioning project. In this paper, it is presented a computer system for the characterization of nuclear facilities, called DEFACS (DEcommissioning FAcility Characterization DB System). This system consists of four main parts: a management coding system for grouping items, a data input system, a data processing system and a data output system. All data is processed in a simplified and formatted manner in order to provide useful information to the decommissioning planner. For the hardware, PC grade computers running Oracle software on Microsoft Windows OS were selected. The characterization data results for the nuclear facility under decommissioning will be utilized for the work-unit productivity calculation system and decommissioning engineering system as basic sources of information

TcruziDB, an Integrated Database, and the WWW Information Server for the Trypanosoma cruzi Genome Project

Directory of Open Access Journals (Sweden)

Degrave Wim

1997-01-01

Full Text Available Data analysis, presentation and distribution is of utmost importance to a genome project. A public domain software, ACeDB, has been chosen as the common basis for parasite genome databases, and a first release of TcruziDB, the Trypanosoma cruzi genome database, is available by ftp from ftp://iris.dbbm.fiocruz.br/pub/genomedb/TcruziDB as well as versions of the software for different operating systems (ftp://iris.dbbm.fiocruz.br/pub/unixsoft/. Moreover, data originated from the project are available from the WWW server at http://www.dbbm.fiocruz.br. It contains biological and parasitological data on CL Brener, its karyotype, all available T. cruzi sequences from Genbank, data on the EST-sequencing project and on available libraries, a T. cruzi codon table and a listing of activities and participating groups in the genome project, as well as meeting reports. T. cruzi discussion lists (tcruzi-l@iris.dbbm.fiocruz.br and tcgenics@iris.dbbm.fiocruz.br are being maintained for communication and to promote collaboration in the genome project

SensorDB: a virtual laboratory for the integration, visualization and analysis of varied biological sensor data.

Science.gov (United States)

Salehi, Ali; Jimenez-Berni, Jose; Deery, David M; Palmer, Doug; Holland, Edward; Rozas-Larraondo, Pablo; Chapman, Scott C; Georgakopoulos, Dimitrios; Furbank, Robert T

2015-01-01

To our knowledge, there is no software or database solution that supports large volumes of biological time series sensor data efficiently and enables data visualization and analysis in real time. Existing solutions for managing data typically use unstructured file systems or relational databases. These systems are not designed to provide instantaneous response to user queries. Furthermore, they do not support rapid data analysis and visualization to enable interactive experiments. In large scale experiments, this behaviour slows research discovery, discourages the widespread sharing and reuse of data that could otherwise inform critical decisions in a timely manner and encourage effective collaboration between groups. In this paper we present SensorDB, a web based virtual laboratory that can manage large volumes of biological time series sensor data while supporting rapid data queries and real-time user interaction. SensorDB is sensor agnostic and uses web-based, state-of-the-art cloud and storage technologies to efficiently gather, analyse and visualize data. Collaboration and data sharing between different agencies and groups is thereby facilitated. SensorDB is available online at http://sensordb.csiro.au.

Rice DB: an Oryza Information Portal linking annotation, subcellular location, function, expression, regulation, and evolutionary information for rice and Arabidopsis.

Science.gov (United States)

Narsai, Reena; Devenish, James; Castleden, Ian; Narsai, Kabir; Xu, Lin; Shou, Huixia; Whelan, James

2013-12-01

Omics research in Oryza sativa (rice) relies on the use of multiple databases to obtain different types of information to define gene function. We present Rice DB, an Oryza information portal that is a functional genomics database, linking gene loci to comprehensive annotations, expression data and the subcellular location of encoded proteins. Rice DB has been designed to integrate the direct comparison of rice with Arabidopsis (Arabidopsis thaliana), based on orthology or 'expressology', thus using and combining available information from two pre-eminent plant models. To establish Rice DB, gene identifiers (more than 40 types) and annotations from a variety of sources were compiled, functional information based on large-scale and individual studies was manually collated, hundreds of microarrays were analysed to generate expression annotations, and the occurrences of potential functional regulatory motifs in promoter regions were calculated. A range of computational subcellular localization predictions were also run for all putative proteins encoded in the rice genome, and experimentally confirmed protein localizations have been collated, curated and linked to functional studies in rice. A single search box allows anything from gene identifiers (for rice and/or Arabidopsis), motif sequences, subcellular location, to keyword searches to be entered, with the capability of Boolean searches (such as AND/OR). To demonstrate the utility of Rice DB, several examples are presented including a rice mitochondrial proteome, which draws on a variety of sources for subcellular location data within Rice DB. Comparisons of subcellular location, functional annotations, as well as transcript expression in parallel with Arabidopsis reveals examples of conservation between rice and Arabidopsis, using Rice DB (http://ricedb.plantenergy.uwa.edu.au). © 2013 The Authors The Plant Journal © 2013 John Wiley & Sons Ltd.

A 75 GHz silicon metal-semiconductor-metal Schottky photodiode

International Nuclear Information System (INIS)

Alexandrou, S.; Wang, C.; Hsiang, T.Y.; Liu, M.Y.; Chou, S.Y.

1993-01-01

The ultrafast characteristics of crystalline-silicon metal-semiconductor-metal (MSM) photodiodes with 300 nm finger width and spacing were measured with a subpicosecond electro-optic sampling system. Electrical responses with full width at half maximum as short as 5.5 and 11 ps, at corresponding 3 dB bandwidths of 75 and 38 GHz, were generated by violet and red photons, respectively. The difference is attributed to the photon penetration depth which is much larger than the diode finger spacing at red, but smaller at violet. Light-intensity dependence was also examined at different wavelengths, indicating a linear relation and a higher sensitivity in the violet. These results not only demonstrated the fastest silicon photodetector reported to date, but also pinpointed the dominant speed-limiting factor of silicon MSM photodiodes. A configuration is suggested to improve the speed of these detectors at long wavelengths

Design of Miniaturized 10dB Wideband Branch Line Coupler Using Dual and T-Shape Transmission Lines

Directory of Open Access Journals (Sweden)

M. Kumar

2018-04-01

Full Text Available This paper presents a design mechanism of miniaturized wideband branch line coupler (BLC with loose coupling of 10 dB. Dual transmission lines are used as a feed network which provides a size reduction of 32% with a fractional bandwidth (FBW of 60% for 10±0.5 dB coupling but return loss performance is found to be poor in the operating band. For further improvement of return loss performance as well as for size reduction of the BLC, a T- shape transmission lines are used instead of series quarter wavelength transmission lines, and hence the overall size reduction of around 44% with FBW of 50.4% is achieved. The return loss and isolation performance is found to be les than 15 dB in the entire operating band (2.5–4.1 GHz with respect to design frequency 3G Hz. The proposed BLC is analyzed, fabricated and tested.

ImmuneDB: a system for the analysis and exploration of high-throughput adaptive immune receptor sequencing data.

Science.gov (United States)

Rosenfeld, Aaron M; Meng, Wenzhao; Luning Prak, Eline T; Hershberg, Uri

2017-01-15

As high-throughput sequencing of B cells becomes more common, the need for tools to analyze the large quantity of data also increases. This article introduces ImmuneDB, a system for analyzing vast amounts of heavy chain variable region sequences and exploring the resulting data. It can take as input raw FASTA/FASTQ data, identify genes, determine clones, construct lineages, as well as provide information such as selection pressure and mutation analysis. It uses an industry leading database, MySQL, to provide fast analysis and avoid the complexities of using error prone flat-files. ImmuneDB is freely available at http://immunedb.comA demo of the ImmuneDB web interface is available at: http://immunedb.com/demo CONTACT: Uh25@drexel.eduSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

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Dicty_cDB: Contig-U12687-1 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available s64.seq; ddbjgss65.seq; ddbjgss66.seq; ddbjgss67.seq; ddbjgss68.seq; ddbjgss69.seq; ddbjgss7.seq; ddbjgss70.seq; ddbjgss7...1.seq; ddbjgss72.seq; ddbjgss73.seq; ddbjgss74.seq; ddbjgss75.seq; ddbjgss76.seq; ddbjgss7...7.seq; ddbjgss78.seq; ddbjgss79.seq; ddbjgss8.seq; ddbjgss80.seq; ddbjgss81.seq; ddbjg

Dicty_cDB: Contig-U14661-1 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available eq; ddbjgss69.seq; ddbjgss7.seq; ddbjgss70.seq; ddbjgss71.seq; ddbjgss72.seq; ddbjgss73.seq; ddbjgss7...4.seq; ddbjgss75.seq; ddbjgss76.seq; ddbjgss77.seq; ddbjgss78.seq; ddbjgss79.seq; ddbjgs...1.seq; ddbjgss62.seq; ddbjgss63.seq; ddbjgss64.seq; ddbjgss65.seq; ddbjgss66.seq; ddbjgss67.seq; ddbjgss68.s

Dicty_cDB: Contig-U03915-1 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available q; ddbjgss62.seq; ddbjgss63.seq; ddbjgss64.seq; ddbjgss65.seq; ddbjgss66.seq; ddbjgss67.seq; ddbjgss68.seq; ddbjgss69.seq; ddbjgss7....seq; ddbjgss70.seq; ddbjgss71.seq; ddbjgss72.seq; ddbjgss73.seq; ddbjgss74.seq; ddbjgss75.seq; ddbjgss7...6.seq; ddbjgss77.seq; ddbjgss78.seq; ddbjgss79.seq; ddbjgss8.s

Dicty_cDB: Contig-U15350-1 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available all GTP-binding protein mRNA, ... 90 1e-16 AB241248_1( AB241248 |pid:none) Symbiotic.... 87 1e-15 AB241247_1( AB241247 |pid:none) Symbiotic protist of Reticuliterme... 87 1e-15 ( P51159 ) RecName...rabidopsis thaliana mRNA for AtRa... 75 3e-12 AB241251_1( AB241251 |pid:none) Symbiotic protist of Reticulit

An undersampling 14-bit cyclic ADC with over 100-dB SFDR

Energy Technology Data Exchange (ETDEWEB)

Li Weitao; Li Fule; Guo Dandan; Zhang Chun; Wang Zhihua, E-mail: liwt07@mails.tsinghua.edu.c [Institute of Microelectronics, Tsinghua University, Beijing 100084 (China)

2010-02-15

A high linearity, undersampling 14-bit 357 kSps cyclic analog-to-digital convert (ADC) is designed for a radio frequency identification transceiver system. The passive capacitor error-average (PCEA) technique is adopted for high accuracy. An improved PCEA sampling network, capable of eliminating the crosstalk path of two pipelined stages, is employed. Opamp sharing and the removal of the front-end sample and hold amplifier are utilized for low power dissipation and small chip area. An additional digital calibration block is added to compensate for the error due to defective layout design. The presented ADC is fabricated in a 180 nm CMOS process, occupying 0.65 x 1.6 mm{sup 2}. The input of the undersampling ADC achieves 15.5 MHz with more than 90 dB spurious free dynamic range (SFDR), and the peak SFDR is as high as 106.4 dB with 2.431 MHz input. (semiconductor integrated circuits)

BRC - MicrobeDB.jp | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...table). Data file File name: brc.tar.gz File URL: ftp://ftp.biosciencedbc.jp/archive/microbedb/LATEST/brc.ta...rains in JCM. About This Database Database Description Download License Update History of This Database Site Policy | Contact Us BRC - MicrobeDB.jp | LSDB Archive ...

SRA - MicrobeDB.jp | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...e following table). Data file File name: sra.tar.gz File URL: ftp://ftp.biosciencedbc.jp/archive/microbedb/L...t This Database Database Description Download License Update History of This Database Site Policy | Contact Us SRA - MicrobeDB.jp | LSDB Archive ...

Dynamics of Db isotopes formed in reactions induced by 238U, 248Cm, and 249Bk across the Coulomb barrier

Science.gov (United States)

Kaur, Gurjit; Sandhu, Kirandeep; Kaur, Amandeep; Sharma, Manoj K.

2018-05-01

The dynamical cluster decay model is employed to investigate the decay of *265Db and *267Db nuclei, formed in the 27Al+238U , 18O+249Bk , and 19F+248Cm hot fusion reactions at energies around the Coulomb barrier. First, the fission dynamics of the 27Al+238U reaction is explored by investigating the fragmentation and preformation yield of the reaction. The symmetric mass distribution of the fission fragments is observed for *265Db nucleus, when static β2 i deformations are used within hot optimum orientation approach. However, the mass split gets broaden for the use of β2 i-dynamical hot configuration of the fragments and becomes clearly asymmetric for the cold-static-deformed approach. Within the application of cold orientations of fragments, a new fission channel is observed at mass asymmetry η =0.29 . In addition to 238U-induced reaction, the work is carried out to address the fission and neutron evaporation cross sections of *267Db nucleus formed via 19F+248Cm and 18O+249Bk reactions, besides a comprehensive analysis of fusion and capture processes. Higher fusion cross sections and compound nucleus formation probabilities (PCN) are obtained for the 18O+249Bk reaction, as larger mass asymmetry in the entrance channel leads to reduced Coulomb factor. Finally, the role of sticking (IS) and nonsticking (INS) moments of inertia is analyzed for the 4 n and 5 n channels of *267Db nuclear system.

MonetDB/SQL Meets SkyServer: the Challenges of a Scientific Database.

NARCIS (Netherlands)

M.G. Ivanova (Milena); N.J. Nes (Niels); R.A. Goncalves (Romulo); M.L. Kersten (Martin)

2007-01-01

textabstractThis paper presents our experiences in porting the Sloan Digital Sky Survey(SDSS)/ SkyServer to the state-of-the-art open source database system MonetDB/SQL. SDSS acts as a well-documented benchmark for scientific database management. We have achieved a fully functional prototype for the

Dicty_cDB: Contig-U14383-1 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available jgss64.seq; ddbjgss65.seq; ddbjgss66.seq; ddbjgss67.seq; ddbjgss68.seq; ddbjgss69.seq; ddbjgss7.seq; ddbjgss70.seq; ddbjgss7...1.seq; ddbjgss72.seq; ddbjgss73.seq; ddbjgss74.seq; ddbjgss75.seq; ddbjgss76.seq; ddbjgss77.seq; ddbjgss7...8.seq; ddbjgss79.seq; ddbjgss8.seq; ddbjgss80.seq; ddbjgss81.seq; ddbjgss82.seq; ddbjgss83.seq;

Dicty_cDB: Contig-U08565-1 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available 3.seq; ddbjgss64.seq; ddbjgss65.seq; ddbjgss66.seq; ddbjgss67.seq; ddbjgss68.seq; ddbjgss69.seq; ddbjgss7.seq; ddbjgss7...0.seq; ddbjgss71.seq; ddbjgss72.seq; ddbjgss73.seq; ddbjgss74.seq; ddbjgss75.seq; ddbjgss76.seq; ddbjgss77.seq; ddbjgss7...8.seq; ddbjgss79.seq; ddbjgss8.seq; ddbjgss80.seq; ddbjgss81.seq; ddbjgss82.seq; ddbj

Dicty_cDB: Contig-U14112-1 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available Oryza sativa Japonica Group genom... 77 8e-14 FJ787374_1( FJ787374 |pid:none) Nicotiana repanda protein kin..._1( FJ787369 |pid:none) Nicotiana repanda protein kinase-c... 79 1e-13 AC004260_13( AC004260 |pid:none) Arab...8... 72 2e-12 FJ787371_1( FJ787371 |pid:none) Nicotiana repanda protein kinase-c... 75 2e-12 FB875947_1( FB8

Dicty_cDB: Contig-U11323-1 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available AF134321 |pid:none) Dissostichus mawsoni clone Dm7m ch... 84 3e-14 AM747721_702( ...S101... 81 2e-13 U58944_1( U58944 |pid:none) Dissostichus mawsoni AFGP antifreeze g... 81 2e-13 AM182501_1( ...017194_2467( AE017194 |pid:none) Bacillus cereus ATCC 10987, com... 75 1e-11 U43149_1( U43149 |pid:none) Dissostichus mawson

Exome sequencing generates high quality data in non-target regions

Directory of Open Access Journals (Sweden)

Guo Yan

2012-05-01

Full Text Available Abstract Background Exome sequencing using next-generation sequencing technologies is a cost efficient approach to selectively sequencing coding regions of human genome for detection of disease variants. A significant amount of DNA fragments from the capture process fall outside target regions, and sequence data for positions outside target regions have been mostly ignored after alignment. Result We performed whole exome sequencing on 22 subjects using Agilent SureSelect capture reagent and 6 subjects using Illumina TrueSeq capture reagent. We also downloaded sequencing data for 6 subjects from the 1000 Genomes Project Pilot 3 study. Using these data, we examined the quality of SNPs detected outside target regions by computing consistency rate with genotypes obtained from SNP chips or the Hapmap database, transition-transversion (Ti/Tv ratio, and percentage of SNPs inside dbSNP. For all three platforms, we obtained high-quality SNPs outside target regions, and some far from target regions. In our Agilent SureSelect data, we obtained 84,049 high-quality SNPs outside target regions compared to 65,231 SNPs inside target regions (a 129% increase. For our Illumina TrueSeq data, we obtained 222,171 high-quality SNPs outside target regions compared to 95,818 SNPs inside target regions (a 232% increase. For the data from the 1000 Genomes Project, we obtained 7,139 high-quality SNPs outside target regions compared to 1,548 SNPs inside target regions (a 461% increase. Conclusions These results demonstrate that a significant amount of high quality genotypes outside target regions can be obtained from exome sequencing data. These data should not be ignored in genetic epidemiology studies.

Short-term exercise worsens cardiac oxidative stress and fibrosis in 8-month-old db/db mice by depleting cardiac glutathione.

Science.gov (United States)

Laher, Ismail; Beam, Julianne; Botta, Amy; Barendregt, Rebekah; Sulistyoningrum, Dian; Devlin, Angela; Rheault, Mark; Ghosh, Sanjoy

2013-01-01

Moderate exercise improves cardiac antioxidant status in young humans and animals with Type-2 diabetes (T2D). Given that both diabetes and advancing age synergistically decrease antioxidant expression in most tissues, it is unclear whether exercise can upregulate cardiac antioxidants in chronic animal models of T2D. To this end, 8-month-old T2D and normoglycemic mice were exercised for 3 weeks, and cardiac redox status was evaluated. As expected, moderate exercise increased cardiac antioxidants and attenuated oxidative damage in normoglycemic mice. In contrast, similar exercise protocol in 8-month-old db/db mice worsened cardiac oxidative damage, which was associated with a specific dysregulation of glutathione (GSH) homeostasis. Expression of enzymes for GSH biosynthesis [γ-glutamylcysteine synthase, glutathione reductase] as well as for GSH-mediated detoxification (glutathione peroxidase, glutathione-S-transferase) was lower, while toxic metabolites dependent on GSH for clearance (4-hydroxynonenal) were increased in exercised diabetic mice hearts. To validate GSH loss as an important factor for such aggravated damage, daily administration of GSH restored cardiac GSH levels in exercised diabetic mice. Such supplementation attenuated both oxidative damage and fibrotic changes in the myocardium. Expression of transforming growth factor beta (TGF-β) and its regulated genes which are responsible for such profibrotic changes were also attenuated with GSH supplementation. These novel findings in a long-term T2D animal model demonstrate that short-term exercise by itself can deplete cardiac GSH and aggravate cardiac oxidative stress. As GSH administration conferred protection in 8-month-old diabetic mice undergoing exercise, supplementation with GSH-enhancing agents may be beneficial in elderly diabetic patients undergoing exercise.

footprintDB: a database of transcription factors with annotated cis elements and binding interfaces.

Science.gov (United States)

Sebastian, Alvaro; Contreras-Moreira, Bruno

2014-01-15

Traditional and high-throughput techniques for determining transcription factor (TF) binding specificities are generating large volumes of data of uneven quality, which are scattered across individual databases. FootprintDB integrates some of the most comprehensive freely available libraries of curated DNA binding sites and systematically annotates the binding interfaces of the corresponding TFs. The first release contains 2422 unique TF sequences, 10 112 DNA binding sites and 3662 DNA motifs. A survey of the included data sources, organisms and TF families was performed together with proprietary database TRANSFAC, finding that footprintDB has a similar coverage of multicellular organisms, while also containing bacterial regulatory data. A search engine has been designed that drives the prediction of DNA motifs for input TFs, or conversely of TF sequences that might recognize input regulatory sequences, by comparison with database entries. Such predictions can also be extended to a single proteome chosen by the user, and results are ranked in terms of interface similarity. Benchmark experiments with bacterial, plant and human data were performed to measure the predictive power of footprintDB searches, which were able to correctly recover 10, 55 and 90% of the tested sequences, respectively. Correctly predicted TFs had a higher interface similarity than the average, confirming its diagnostic value. Web site implemented in PHP,Perl, MySQL and Apache. Freely available from http://floresta.eead.csic.es/footprintdb.

The Opportunistic Pathogen Serratia marcescens Utilizes Type VI Secretion To Target Bacterial Competitors ▿†

Science.gov (United States)

Murdoch, Sarah L.; Trunk, Katharina; English, Grant; Fritsch, Maximilian J.; Pourkarimi, Ehsan; Coulthurst, Sarah J.

2011-01-01

The type VI secretion system (T6SS) is the most recently described and least understood of the protein secretion systems of Gram-negative bacteria. It is widely distributed and has been implicated in the virulence of various pathogens, but its mechanism and exact mode of action remain to be defined. Additionally there have been several very recent reports that some T6SSs can target bacteria rather than eukaryotic cells. Serratia marcescens is an opportunistic enteric pathogen, a class of bacteria responsible for a significant proportion of hospital-acquired infections. We describe the identification of a functional T6SS in S. marcescens strain Db10, the first report of type VI secretion by an opportunist enteric bacterium. The T6SS of S. marcescens Db10 is active, with secretion of Hcp to the culture medium readily detected, and is expressed constitutively under normal growth conditions from a large transcriptional unit. Expression of the T6SS genes did not appear to be dependent on the integrity of the T6SS. The S. marcescens Db10 T6SS is not required for virulence in three nonmammalian virulence models. It does, however, exhibit dramatic antibacterial killing activity against several other bacterial species and is required for S. marcescens to persist in a mixed culture with another opportunist pathogen, Enterobacter cloacae. Importantly, this antibacterial killing activity is highly strain specific, with the S. marcescens Db10 T6SS being highly effective against another strain of S. marcescens with a very similar and active T6SS. We conclude that type VI secretion plays a crucial role in the competitiveness, and thus indirectly the virulence, of S. marcescens and other opportunistic bacterial pathogens. PMID:21890705

75 FR 26939 - Target Corporation: Provisional Acceptance of a Settlement Agreement and Order

Science.gov (United States)

2010-05-13

... CONSUMER PRODUCT SAFETY COMMISSION [CPSC Docket No. 09-C0037] Target Corporation: Provisional...(e). Published below is a provisionally-accepted Settlement Agreement with Target Corporation..., Target Corporation (``Target '') and the staff (``Staff '') of the United States Consumer Product Safety...

Diabetic db/db mice do not develop heart failure upon pressure overload: a longitudinal in vivo PET, MRI, and MRS study on cardiac metabolic, structural, and functional adaptations.

Science.gov (United States)

Abdurrachim, Desiree; Nabben, Miranda; Hoerr, Verena; Kuhlmann, Michael T; Bovenkamp, Philipp; Ciapaite, Jolita; Geraets, Ilvy M E; Coumans, Will; Luiken, Joost J F P; Glatz, Jan F C; Schäfers, Michael; Nicolay, Klaas; Faber, Cornelius; Hermann, Sven; Prompers, Jeanine J

2017-08-01

Heart failure is associated with altered myocardial substrate metabolism and impaired cardiac energetics. Comorbidities like diabetes may influence the metabolic adaptations during heart failure development. We quantified to what extent changes in substrate preference, lipid accumulation, and energy status predict the longitudinal development of hypertrophy and failure in the non-diabetic and the diabetic heart. Transverse aortic constriction (TAC) was performed in non-diabetic (db/+) and diabetic (db/db) mice to induce pressure overload. Magnetic resonance imaging, 31P magnetic resonance spectroscopy (MRS), 1H MRS, and 18F-fluorodeoxyglucose-positron emission tomography (PET) were applied to measure cardiac function, energy status, lipid content, and glucose uptake, respectively. In vivo measurements were complemented with ex vivo techniques of high-resolution respirometry, proteomics, and western blotting to elucidate the underlying molecular pathways. In non-diabetic mice, TAC induced progressive cardiac hypertrophy and dysfunction, which correlated with increased protein kinase D-1 (PKD1) phosphorylation and increased glucose uptake. These changes in glucose utilization preceded a reduction in cardiac energy status. At baseline, compared with non-diabetic mice, diabetic mice showed normal cardiac function, higher lipid content and mitochondrial capacity for fatty acid oxidation, and lower PKD1 phosphorylation, glucose uptake, and energetics. Interestingly, TAC affected cardiac function only mildly in diabetic mice, which was accompanied by normalization of phosphorylated PKD1, glucose uptake, and cardiac energy status. The cardiac metabolic adaptations in diabetic mice seem to prevent the heart from failing upon pressure overload, suggesting that restoring the balance between glucose and fatty acid utilization is beneficial for cardiac function. Published on behalf of the European Society of Cardiology. All rights reserved. © The Author 2017. For permissions

Radiological safety research of food irradiation with 7.5 MeV X-rays

International Nuclear Information System (INIS)

Yang Bin; Tang Weidong; Zhang Yue; Xu Tao; Jin Jianqiao; Ye Mingyang

2012-01-01

China and America both have 7.5 MeV high energy X-ray accelerator. The radiological safety of food irradiated with 7.5 MeV X-rays (bremsstrahlung) has been investigated. Samples of meat and meat ash were located in a large volume of fresh meat at the position of the highest photoneutron fluence and irradiated to an X-ray dose of 15 kGy, twice the maximum dose allowed by the US FDA for meat irradiation. An evaluation of the corresponding radiation exposure from ingestion of the irradiated product has been compared to natural background radiation. The paper concludes that the risk to individuals from intake of food irradiated with X-rays from 7.5 MeV electrons, even with a broad energy spectrum, would be trivial. The common target materials are Au, Ta and W. The U.S, requires only Au and Ta can be used as food irradiation target materials and China has not yet relevant provisions. The first 7.5 MeV accelerator for food irradiation in China is under built, and will do the explore research for the choice of target material. (authors)

QTL list - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available List Contact us PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods ...Policy | Contact Us QTL list - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ...

Nucleotide Sequence and Analysis of an orotate transporter-containing plasmid isolated from the Lactococcus lactis ssp. lactis biovar diacetylactis strain DB0410

DEFF Research Database (Denmark)

Defoor, Els Marie Celine; Martinussen, Jan

A new lactococcal plasmid, pDBORO, was isolated from the Lactococcus lactis ssp. lactis biovar diacetylactis strain DB0410 responsible for the sensitivity of DB0410 towards the pyrimidine-analog 5´-fluoroorotate. The plasmid pDBORO amounts to 16404 bp and its complete nucleotide sequence has been...

Establishment and Evaluation of Decommissioning Plant Inventory DB and Waste Quantity

International Nuclear Information System (INIS)

Oh, Jae Yong; Moon, Sang-Rae; Yun, Taesik; Kim, Hee-Geun; Sung, Nak-Hoon; Jung, Seung Hyuk

2016-01-01

Korea Hydro and Nuclear Power (KHNP) made a decision for permanent shutdown of Kori-1 and has progressed the strategy determination and R and D for the decommissioning of Kori-1. Decommissioning waste, Structure, System and Components (SSCs) is one of the most important elements. Decommissioning waste quantity is calculated based on Plant Inventory Database (PI DB) with activation and contamination data. Due to the largest portion of waste management and disposal in decommissioning, it is necessary to exactly evaluate waste quantity (applying the regulation, guideline and site-specific characterization) for economic feasibility. In this paper, construction of PI DB and evaluation of waste quantity for Optimized Pressurized Reactor (OPR-1000) are mainly described. Decommissioning waste quantities evaluated are going to be applied to calculation of the project cost. In fact, Ministry of Trade, Industry and Energy (MOTIE) in Korea expected the decommissioning waste quantity in a range of 14,500-18,850 drums, and predicted appropriate liability for decommissioning fund by using waste quantity. The result of this study is also computed by the range of 14,500-18,850 drums. Since there is no site-specific data for the NPP site, this evaluation is the preliminary analysis

SerpentinaDB: a database of plant-derived molecules of Rauvolfia serpentina.

Science.gov (United States)

Pathania, Shivalika; Ramakrishnan, Sai Mukund; Randhawa, Vinay; Bagler, Ganesh

2015-08-04

Plant-derived molecules (PDMs) are known to be a rich source of diverse scaffolds that could serve as a basis for rational drug design. Structured compilation of phytochemicals from traditional medicinal plants can facilitate prospection for novel PDMs and their analogs as therapeutic agents. Rauvolfia serpentina is an important medicinal plant, endemic to Himalayan mountain ranges of Indian subcontinent, reported to be of immense therapeutic value against various diseases. We present SerpentinaDB, a structured compilation of 147 R. serpentina PDMs, inclusive of their plant part source, chemical classification, IUPAC, SMILES, physicochemical properties, and 3D chemical structures with associated references. It also provides refined search option for identification of analogs of natural molecules against ZINC database at user-defined cut-off. SerpentinaDB is an exhaustive resource of R. serpentina molecules facilitating prospection for therapeutic molecules from a medicinally important source of natural products. It also provides refined search option to explore the neighborhood of chemical space against ZINC database to identify analogs of natural molecules obtained as leads. In a previous study, we have demonstrated the utility of this resource by identifying novel aldose reductase inhibitors towards intervention of complications of diabetes.